{"shas":[["6766b9da207ad9facd6b9d20aac05c62c0a55219","b1063c6ecf4e141d62862c7361346d12e74c651f@mit.edu","Fixing comment in H_Abstraction rateLibrary.txt file\n\nThere appears to be an entire rate coefficient node (#486) in the comments\nof node #313.  MRH is removing this from the database.","Michael Harper"],["09d8023080bada0b8de85061a670793de8e19c54","b1063c6ecf4e141d62862c7361346d12e74c651f@mit.edu","Adding new rate coefficient in H_Abstraction rxn family\n\nThe new rate coefficient is for the reaction CH3CH2CH=CH2 + OOCH3 = HOOCH3 +\nCH3CHCH=CH2.  It was calculated using the CBS-QB3 method, with hindered rotor\ncorrections.\n\nThis calculation is in reasonable agreement with similar reactions in the\nliterature (e.g. Tsang recommendation for propene + OOCH3 = HOOCH3 + allyl).","Michael Harper"],["552f64cba06ee5efb228e3c59a6569dcefa30a58","9bd490a4f453b93cf9fd9834a38e01d2badc8a91@mit.edu","Tidying up confusing code.\n\nThis commit should have no effect on how the program runs (except perhaps\nbing a teeeny bit faster). The aim is to make the code clearer to read.","Richard West"],["c609844d2d05b4d0783a0284072cafa454e02f06","9bd490a4f453b93cf9fd9834a38e01d2badc8a91@mit.edu","Change where \"Created new __ reaction\" message appears and added direction.\n\nThis is to help clarify eg. when a reverse intra_H_abstraction reaction is made,\nthe forwards direction is immediately made and both are reported to the console.\nThe new message says which direction each reaction is being made in.\nSee https://github.com/GreenGroup/RMG-Java/issues/185#issuecomment-1245662","Richard West"],["dd001ea444e1efaf13e8635fc51a3821423938d7","0760f249c4b90093adf9bfc76fa1f335d126611f@mit.edu","Updating H_abstraction rate rule","Mary Schnoor"],["ddd1628017e577c6811e5472bcee11bc7deffd7e","b1063c6ecf4e141d62862c7361346d12e74c651f@mit.edu","Fixing node definition in H_Abstraction rxn family\n\nThe node definition for InChI=1/C3H5/c1-3-2/h3H,1-2H2 was causing the\nerror message: \"ERROR: InChI=1/C3H5/c1-3-2/h3H,1-2H2 is not actually a\nchild of C_rad/H2/Cd\".\n\nThe *3 label was added to Carbon 1 of the node definition and the 2\nhydrogen atoms bonded to Carbon 1 are now explicitly stated (in line with\nthe definitio of C_rad/H2/Cd).","Michael Harper"],["28d7a00f256f95833be704debd7dd9c4a174f92f","d2efaa4c3e5af267960de800d4d586f2bce0207f@mit.edu","Fixed a formatting issue in the H_Abstraction comments.txt.\n\nOne of the rate rule comments sections did not use the correct section\nformatting style. This is important because my script to import the\nRMG-Java database to the new format assumes that the comments.txt file\nis well-formed.","Josh Allen"],["bef039ab7355bb171b2bdda2cc276bbc291f2a7a","d2efaa4c3e5af267960de800d4d586f2bce0207f@mit.edu","Some fixes to the Dooley methylformate kinetics libraries.\n\nThe reaction H + CO2 = OCHO was listed in both the pressure-independent\nand pressure-dependent sections with the same kinetics, despite their\nhaving vastly different meanings (and units!) in both places. After\nconsulting the reference we made a best guess as to which is correct\n(the pressure-dependent one) and deleted the other.\n\nAlso changed the A-factor of CH2O + HCO = CH2OCHO to match what was in\nthe same reference; it was off by an order of magnitude. The reference\nsuggests that they had to fit this value to their data, which implies\nthat this reaction is rather important (and that it is very important\nfor these significant reactions that you check their kinetic parameters\nvery closely!) Note that we got the original value from their Chemkin\nfile in the Supporting Materials. If this commit makes models worse we\nshould follow up with Dooley et al.","Josh Allen"],["7cba24b92bfd777668fe9e76319a4531528a48e9","d2efaa4c3e5af267960de800d4d586f2bce0207f@mit.edu","Fixed a few malformed adjacency lists in the Dooley kinetics libraries.\n\nIt's a bit disconcerting that RMG-Java will just carry on when this is\nencountered. I'm not sure if it just dropped the species, or tried to\nguess which is correct, or exactly what the outcome was. RMG-Py will\nfail loudly in this situation, which is how I found the bug in the\nfirst place.","Josh Allen"],["ebc7c755ae801ecea86e889903b55a84f60ddffe","d2efaa4c3e5af267960de800d4d586f2bce0207f@mit.edu","Added DUPLICATE tags to reactions in several kinetics libraries.\n\nIt is likely that these libraries simply haven't been used since the\nDUPLICATE tag requirement was added. This commit should reduce the risk\nof surprises in case someone tries to use them in the far future.","Josh Allen"],["da4a567a0400903ea34dbc74bb6d05e993849c66","d2efaa4c3e5af267960de800d4d586f2bce0207f@mit.edu","Removed a few unexpected duplicate reactions from Glarborg C3 library.\n\nThe reactions H2CCCH2 + H = CH3CHCH, H2CCCH2 + H = CH3CCH2, and\nH2CCCH2 + H = CH2CHCH2 have entries in both the pressure-independent and\npressure-dependent sections of the Glarborg C3 mechanism. (This was only\ndiscovered when trying to import to the new database format, for which\nmy script checks for duplicates between these sections, while Chemkin\ndoes not.) Checking the reference, it seems the values given in the\npressure-independent section are for 0.1 bar only, and the reference\nalso has Arrhenius parameters at several other pressures.\n\nSince we already have Troe expressions for these reactions in the\npressure-dependent sections, and since the low-P Arrhenius expression\nin the Troe form matches those from the pressure-independent section,\nwe decided to keep the Troe forms and comment out the 0.1 bar Arrhenius\nparameters.","Josh Allen"],["6fbb3dcd61253f70f4c5d594e1a44032d7043398","d2efaa4c3e5af267960de800d4d586f2bce0207f@mit.edu","Merge branch 'database'","Josh Allen"],["ebb389f7b3ee7ed6ea5e95f7156da92de4810a21","b1063c6ecf4e141d62862c7361346d12e74c651f@mit.edu","Moved references to end of comments.rst file\n\nNo changes to text.","Michael Harper"],["2954148fe922162af88240068d238d962a7bfadf","b1063c6ecf4e141d62862c7361346d12e74c651f@mit.edu","Adding 4 rate rules to R_Addition_COm reaction template library\n\nMRH computed the rate coefficients for the following 4 reactions using the\nCBS-QB3 method + TST w/1d hindered rotor corrections + asymmetric Eckart\ntunneling:\n\tCO + CH3 = CH3CO\n\tCO + C2H5 = CH3CH2CO\n\tCO + n-C3H7 = CH3CH2CH2CO\n\tCO + iso-C3H7 = CH3CH(CH3)CO\nThe CBS-QB3 calculations are faster than RMG's previous (Average of Average)\nestimates by as much as an order of magnitude at temperatures > 1000 K.  At\nlower temperatures, the new calculations are usually within a factor of three\nof the old RMG estimates.\n\nThe butanol mechanism was sensitive to these types of reactions (in particular,\nthe CO + n-C3H7 = CH3CH2CH2CO reaction) at the low temperature, high pressure\nconditions of the RCM.","Michael Harper"],["29c96524782e7e6bb2a204382508d4145ab5bf59","b1063c6ecf4e141d62862c7361346d12e74c651f@mit.edu","Adding new rate coefficient for HO2_Elimination_from_PeroxyRadical family\n\nThe top level node for the HO2_Elimination_from_PeroxyRadical rxn family was\nR2OO, whose definition appears below:\n\n\t1 *1 C 0 {2,S} {5,S}\n\t2 *2 C 0 {1,S} {3,S}\n\t3 *3 O 0 {2,S} {4,S}\n\t4 *4 O 1 {3,S}\n\t5 *5 H 0 {1,S}\n\nNote that the atom bonded to the H atom is forced to be a carbon atom.  Thus,\nif the species CH3-CH(OO)-OH was run against the rxn family template, only the\nproducts HO2 + CH2=CH-OH would be found (and not HO2 + CH3CHO).\n\nMRH has modified the R2OO definition to include \"O\" as a possible atom for the\n*1 site.  I have also added two nodes beneath the R2OO node: a child, called\nOCOO (which simply distinguishes between an O and C *1 node), and a grandchild,\ncalled HOCH[OO]CH3.\n\nI calculated the rate coefficient for the grandchild node, HOCH[OO]CH3 => HO2 +\nCH3CHO, using the CBS-QB3 method with 1-d hindered rotor corrections.  Note: I\ndid not apply a tunneling correction (see my notes in the comments.rst file).\n\nFurthermore, I assigned this rate coefficient expression to the more general\nnode OCOO.\n\nThis type of reaction should be important in low-temperature chemistry of\nalcohol oxidation.","Michael Harper"],["0cd0c9a82f1ff011a7aa26b806d966f9017043ac","414eca01d6882c6a077ae8b858b5205a9eef0524@gmail.com","Merge remote-tracking branch 'upstream/master'","Nick Vandewiele"]],"ref":"refs/heads/master","size":16,"head":"0cd0c9a82f1ff011a7aa26b806d966f9017043ac","push_id":33657928}