{"action":"created","issue":{"url":"https://api.github.com/repos/ReactionMechanismGenerator/RMG-Py/issues/831","repository_url":"https://api.github.com/repos/ReactionMechanismGenerator/RMG-Py","labels_url":"https://api.github.com/repos/ReactionMechanismGenerator/RMG-Py/issues/831/labels{/name}","comments_url":"https://api.github.com/repos/ReactionMechanismGenerator/RMG-Py/issues/831/comments","events_url":"https://api.github.com/repos/ReactionMechanismGenerator/RMG-Py/issues/831/events","html_url":"https://github.com/ReactionMechanismGenerator/RMG-Py/issues/831","id":193033201,"number":831,"title":"Redundant Species in a Reaction Mechanism","user":{"login":"rgillis8","id":17207564,"avatar_url":"https://avatars.githubusercontent.com/u/17207564?v=3","gravatar_id":"","url":"https://api.github.com/users/rgillis8","html_url":"https://github.com/rgillis8","followers_url":"https://api.github.com/users/rgillis8/followers","following_url":"https://api.github.com/users/rgillis8/following{/other_user}","gists_url":"https://api.github.com/users/rgillis8/gists{/gist_id}","starred_url":"https://api.github.com/users/rgillis8/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rgillis8/subscriptions","organizations_url":"https://api.github.com/users/rgillis8/orgs","repos_url":"https://api.github.com/users/rgillis8/repos","events_url":"https://api.github.com/users/rgillis8/events{/privacy}","received_events_url":"https://api.github.com/users/rgillis8/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":5,"created_at":"2016-12-02T04:42:21Z","updated_at":"2016-12-02T17:26:48Z","closed_at":null,"body":"I have encountered a strange error where the core contains multiple copies of the same species. The species are all polycyclic aromatic radicals and the error seems to only occur when the saturated version of these species are included in a thermodynamic library (adding the saturated species to a thermo library seemed to trigger the problem).\r\n\r\nConsider these consecutive \"enlarge\" steps recorded in the RMG.log file.\r\n\r\nSummary of Secondary Model Edge Enlargement\r\n---------------------------------\r\nAdded 0 new core species\r\nCreated 8 new edge species\r\n    [CH] (Cc1ccccc1)c1ccccc1(11694)\r\n    [c]1ccccc1CCc1ccccc1(11695)\r\n    [c]1ccc(cc1)CCc1ccccc1(11696)\r\n    [c]1cccc(c1)CCc1ccccc1(11697)\r\n    [CH] (SCc1ccccc1)c1ccccc1(11698)\r\n    [c]1ccccc1CSCc1ccccc1(11699)\r\n    [c]1cccc(c1)CSCc1ccccc1(11700)\r\n    [c]1ccc(cc1)CSCc1ccccc1(11701)\r\nAdded 0 new core reactions\r\nCreated 8 new edge reactions\r\n    [CH] (Cc1ccccc1)c1ccccc1(11694) + c1ccc(cc1)CSCc1ccccc1(34) <=> [CH]1C=CC=CC1=CSCc1ccccc1(271) + c1ccc(cc1)CCc1ccccc1(76)\r\n    [c]1ccccc1CCc1ccccc1(11695) + c1ccc(cc1)CSCc1ccccc1(34) <=> [CH]1C=CC=CC1=CSCc1ccccc1(271) + c1ccc(cc1)CCc1ccccc1(76)\r\n    [c]1ccc(cc1)CCc1ccccc1(11696) + c1ccc(cc1)CSCc1ccccc1(34) <=> [CH]1C=CC=CC1=CSCc1ccccc1(271) + c1ccc(cc1)CCc1ccccc1(76)\r\n    [c]1cccc(c1)CCc1ccccc1(11697) + c1ccc(cc1)CSCc1ccccc1(34) <=> [CH]1C=CC=CC1=CSCc1ccccc1(271) + c1ccc(cc1)CCc1ccccc1(76)\r\n    [CH]1C=CC=CC1=CSCc1ccccc1(271) + c1ccc(cc1)CSCc1ccccc1(34) <=> [CH](SCc1ccccc1)c1ccccc1(11698) + c1ccc(cc1)CSCc1ccccc1(34)\r\n    [c]1ccccc1CSCc1ccccc1(11699) + c1ccc(cc1)CSCc1ccccc1(34) <=> [CH]1C=CC=CC1=CSCc1ccccc1(271) + c1ccc(cc1)CSCc1ccccc1(34)\r\n    [c]1cccc(c1)CSCc1ccccc1(11700) + c1ccc(cc1)CSCc1ccccc1(34) <=> [CH]1C=CC=CC1=CSCc1ccccc1(271) + c1ccc(cc1)CSCc1ccccc1(34)\r\n    [c]1ccc(cc1)CSCc1ccccc1(11701) + c1ccc(cc1)CSCc1ccccc1(34) <=> [CH]1C=CC=CC1=CSCc1ccccc1(271) + c1ccc(cc1)CSCc1ccccc1(34)\r\n\r\nAfter model enlargement:\r\n    The model core has 398 species and 6766 reactions\r\n    The model edge has 11307 species and 43274 reactions\r\n\r\n\r\nSaving current model core to Chemkin file...\r\nChemkin file contains 6766 reactions.\r\nSaving current model to verbose Chemkin file...\r\nChemkin file contains 6766 reactions.\r\nUpdating RMG execution statistics...\r\n    Execution time (DD:HH:MM:SS): 01:20:07:34\r\n    Memory used: 1658.88 MB\r\n\r\nConducting simulation of reaction system 1...\r\nAt time 1.0000e-01 s, species [CH] (SCc1ccccc1)c1ccccc1(11562) exceeded the minimum rate for moving to model core\r\n    Characteristic rate: 8.0216e+03 mol/m^3*s\r\n    [CH](SCc1ccccc1)c1ccccc1(11562) rate: 8.1141e+02 mol/m^3*s (0.1012)\r\n    DBDS(1) conversion: 0.5313\r\nAt time 1.0000e-01 s, species [CH] (SCc1ccccc1)c1ccccc1(11562) exceeded the minimum rate for simulation interruption\r\n    Characteristic rate: 8.0216e+03 mol/m^3*s\r\n    [CH] (SCc1ccccc1)c1ccccc1(11562) rate: 8.1141e+02 mol/m^3*s (0.1012)\r\n    DBDS(1) conversion: 0.5313\r\n\r\n\r\nAdding species [CH] (SCc1ccccc1)c1ccccc1(11562) to model core\r\nGenerating kinetics for new reactions...\r\n\r\nSummary of Model Enlargement\r\n---------------------------------\r\nAdded 1 new core species\r\n    [CH] (SCc1ccccc1)c1ccccc1(11562)\r\nCreated 0 new edge species\r\nMoved 1 reactions from edge to core\r\n    [CH]1C=CC=CC1=CSCc1ccccc1(271) + c1ccc(cc1)CSCc1ccccc1(34) <=> [CH] (SCc1ccccc1)c1ccccc1(11562) + c1ccc(cc1)CSCc1ccccc1(34)\r\nAdded 0 new core reactions\r\nCreated 0 new edge reactions\r\n\r\nAfter model enlargement:\r\n    The model core has 399 species and 6767 reactions\r\n    The model edge has 11306 species and 43273 reactions\r\n\r\n\r\nAt time 1.0646e+00 s, reached target termination conversion: 0.800000 of DBDS(1)\r\n    DBDS(1) conversion: 0.8\r\n\r\nGenerating kinetics for new reactions...\r\n\r\nSummary of Secondary Model Edge Enlargement\r\n---------------------------------\r\nAdded 0 new core species\r\nCreated 8 new edge species\r\n    [CH](Cc1ccccc1)c1ccccc1(11702)\r\n    [c]1ccccc1CCc1ccccc1(11703)\r\n    [c]1ccc(cc1)CCc1ccccc1(11704)\r\n    [c]1cccc(c1)CCc1ccccc1(11705)\r\n    [CH](SCc1ccccc1)c1ccccc1(11706)\r\n    [c]1ccccc1CSCc1ccccc1(11707)\r\n    [c]1cccc(c1)CSCc1ccccc1(11708)\r\n    [c]1ccc(cc1)CSCc1ccccc1(11709)\r\nAdded 0 new core reactions\r\nCreated 8 new edge reactions\r\n    [CH](Cc1ccccc1)c1ccccc1(11702) + c1ccc(cc1)CSCc1ccccc1(34) <=> [CH]1C=CC=CC1=CSCc1ccccc1(271) + c1ccc(cc1)CCc1ccccc1(76)\r\n    [c]1ccccc1CCc1ccccc1(11703) + c1ccc(cc1)CSCc1ccccc1(34) <=> [CH]1C=CC=CC1=CSCc1ccccc1(271) + c1ccc(cc1)CCc1ccccc1(76)\r\n    [c]1ccc(cc1)CCc1ccccc1(11704) + c1ccc(cc1)CSCc1ccccc1(34) <=> [CH]1C=CC=CC1=CSCc1ccccc1(271) + c1ccc(cc1)CCc1ccccc1(76)\r\n    [c]1cccc(c1)CCc1ccccc1(11705) + c1ccc(cc1)CSCc1ccccc1(34) <=> [CH]1C=CC=CC1=CSCc1ccccc1(271) + c1ccc(cc1)CCc1ccccc1(76)\r\n    [CH]1C=CC=CC1=CSCc1ccccc1(271) + c1ccc(cc1)CSCc1ccccc1(34) <=> [CH](SCc1ccccc1)c1ccccc1(11706) + c1ccc(cc1)CSCc1ccccc1(34)\r\n    [c]1ccccc1CSCc1ccccc1(11707) + c1ccc(cc1)CSCc1ccccc1(34) <=> [CH]1C=CC=CC1=CSCc1ccccc1(271) + c1ccc(cc1)CSCc1ccccc1(34)\r\n    [c]1cccc(c1)CSCc1ccccc1(11708) + c1ccc(cc1)CSCc1ccccc1(34) <=> [CH]1C=CC=CC1=CSCc1ccccc1(271) + c1ccc(cc1)CSCc1ccccc1(34)\r\n    [c]1ccc(cc1)CSCc1ccccc1(11709) + c1ccc(cc1)CSCc1ccccc1(34) <=> [CH]1C=CC=CC1=CSCc1ccccc1(271) + c1ccc(cc1)CSCc1ccccc1(34)\r\n\r\nAfter model enlargement:\r\n    The model core has 399 species and 6767 reactions\r\n    The model edge has 11314 species and 43281 reactions\r\n\r\n\r\nSaving current model core to Chemkin file...\r\nChemkin file contains 6767 reactions.\r\nSaving current model to verbose Chemkin file...\r\nChemkin file contains 6767 reactions.\r\nUpdating RMG execution statistics...\r\n    Execution time (DD:HH:MM:SS): 01:20:19:56\r\n    Memory used: 1657.63 MB\r\n\r\nConducting simulation of reaction system 1...\r\nAt time 1.0000e-01 s, species [CH](SCc1ccccc1)c1ccccc1(11570) exceeded the minimum rate for moving to model core\r\n    Characteristic rate: 7.9141e+03 mol/m^3*s\r\n    [CH] (SCc1ccccc1)c1ccccc1(11570) rate: 8.1752e+02 mol/m^3*s (0.1033)\r\n    DBDS(1) conversion: 0.5313\r\nAt time 1.0000e-01 s, species [CH](SCc1ccccc1)c1ccccc1(11570) exceeded the minimum rate for simulation interruption\r\n    Characteristic rate: 7.9141e+03 mol/m^3*s\r\n    [CH](SCc1ccccc1)c1ccccc1(11570) rate: 8.1752e+02 mol/m^3*s (0.1033)\r\n    DBDS(1) conversion: 0.5313\r\n\r\n\r\nAdding species [CH] (SCc1ccccc1)c1ccccc1(11570) to model core\r\nGenerating kinetics for new reactions...\r\n\r\nSummary of Model Enlargement\r\n---------------------------------\r\nAdded 1 new core species\r\n[CH] (SCc1ccccc1)c1ccccc1(11570)\r\nCreated 0 new edge species\r\nMoved 1 reactions from edge to core\r\n[CH]1C=CC=CC1=CSCc1ccccc1(271) + c1ccc(cc1)CSCc1ccccc1(34) <=> [CH] (SCc1ccccc1)c1ccccc1(11570) + c1ccc(cc1)CSCc1ccccc1(34)\r\nAdded 0 new core reactions\r\nCreated 0 new edge reactions\r\n\r\nAfter model enlargement:\r\n    The model core has 400 species and 6768 reactions\r\n    The model edge has 11313 species and 43280 reactions\r\n\r\n\r\nAt time 1.0662e+00 s, reached target termination conversion: 0.800000 of DBDS(1)\r\n    DBDS(1) conversion: 0.8001\r\n\r\nThe Summary of Model Enlargement for these two steps shows that the exact same species is added twice in a row (in this model the species had been added many many times before this as well). In fact, looking at the Summary of Secondary Model Edge Enlargement shows that the exact same reactions are considered twice in a row.\r\n\r\nI believe the issue has to do with the ability of the resonance isomers to be recognized. Since the species in the core is not recognized to be the same as the newly generated edge species, the edge species and the associated identical reactions are added to the core in fault.\r\n\r\nI am not sure how adding the species to a thermo library would affect the resonance isomer generation/recognition... it seems like it shouldn't. If anyone has any ideas I would be grateful! Or perhaps in the short term if you know a sneaky way to attach a thermo value to a species without sticking it in a library (maybe a very very specific branch in a thermo tree?)\r\n\r\nThanks!"},"comment":{"url":"https://api.github.com/repos/ReactionMechanismGenerator/RMG-Py/issues/comments/264511017","html_url":"https://github.com/ReactionMechanismGenerator/RMG-Py/issues/831#issuecomment-264511017","issue_url":"https://api.github.com/repos/ReactionMechanismGenerator/RMG-Py/issues/831","id":264511017,"user":{"login":"rgillis8","id":17207564,"avatar_url":"https://avatars.githubusercontent.com/u/17207564?v=3","gravatar_id":"","url":"https://api.github.com/users/rgillis8","html_url":"https://github.com/rgillis8","followers_url":"https://api.github.com/users/rgillis8/followers","following_url":"https://api.github.com/users/rgillis8/following{/other_user}","gists_url":"https://api.github.com/users/rgillis8/gists{/gist_id}","starred_url":"https://api.github.com/users/rgillis8/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rgillis8/subscriptions","organizations_url":"https://api.github.com/users/rgillis8/orgs","repos_url":"https://api.github.com/users/rgillis8/repos","events_url":"https://api.github.com/users/rgillis8/events{/privacy}","received_events_url":"https://api.github.com/users/rgillis8/received_events","type":"User","site_admin":false},"created_at":"2016-12-02T17:26:48Z","updated_at":"2016-12-02T17:26:48Z","body":"Another update. When I relabeled the bonds in the relevant species in the thermo library with B labels rather than alternating S and D labels the redundant species error disappeared. I'll keep looking into why this would make a difference."}}
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