{"shas":[["925a9be4f59d8c8c0c97e5e81a8f94de8c35bd2b","9bd490a4f453b93cf9fd9834a38e01d2badc8a91@mit.edu","Added 'java' job to kineticsGroups.py to run PrIMe or test data through RMG-java.\n\nYou need to have the RMG-java PopulateReactionsServer running at the time.\nThis will try to create \"PrIMe-RMG-java.py\" files for each reaction family.\nAt the moment it crashes half way through Disproportionation, but it saves\nwhat it's done so far.","Richard West"],["a760f1ff257a5f4bd6e192026b78d18494df53b9","9bd490a4f453b93cf9fd9834a38e01d2badc8a91@mit.edu","Ran \"kineticsGroups.py java\" on H_Abstraction to run PrIMe reactions through RMG-Java.\n\nThe new PrIMe-RMG-Java.py file contains the results of running each\nof the PrIMe reactions through RMG-Java to see how it would have estimated the kinetics.\n\nNB>> some reactions the kinetics may be in the reverse direction\n - the only way to check is to read the longDesc comments.","Richard West"],["7d3d15e027b30aa9ce8fe00ce599927fdf29206a","9bd490a4f453b93cf9fd9834a38e01d2badc8a91@mit.edu","Renamed from PrIMe-RMG-Java.py to PrIMe_RMG_Java.py\n\nThe hyphens mean PrIMe-RMG-Java can't be used as an attribute name\nin RMG-Py structures, which is a problem the way things are \ncurrently implemented. Underscores are OK.","Richard West"],["7d5b17a2ea76fddf0350123f9b044aab02ba4ac3","9bd490a4f453b93cf9fd9834a38e01d2badc8a91@mit.edu","kineticsGroups.py java now runs all reaction families.\n\nIf the input depository doesn't exist it doesn't create an (empty)\noutput depository.\nWith the current versions of the database, website, and RMGpy repositories, I get:\n\nCOMPLETED making RMG-Java kinetics for:\n  2+2_cycloaddition_CCO\n  H_Abstraction\n  1,3_Insertion_ROR\n  Cyclic_Ether_Formation\n  HO2_Elimination_from_PeroxyRadical\n(plus a bunch of families that don't actually have any PrIMe reactions)\nFAILED while making RMG-Java kinetics for:\n  Disproportionation\n  R_Addition_MultipleBond\n  R_Recombination\n  Intra_R_Add_Endocyclic\n  1,3_Insertion_CO2\n  intra_H_migration\n  Diels_alder_addition\n  2+2_cycloaddition_Cd","Richard West"],["4919ed4b344a9b5df3973be6d728610ba8e12c3b","9bd490a4f453b93cf9fd9834a38e01d2badc8a91@mit.edu","The kineticsGroups.py java fitting reverses the reaction if necessary to match kinetics.\n\nRather than try to get the kinetics in the opposite direction,\nwe reverse the direction of the reaction. This will make comparison \nbetween PrIMe and PrIMe_RMG_Java harder, but between PrIMe_RMG_Java\nand RMG-Py easier.","Richard West"],["f220fc16e5ffa858d5ce25c41ce6dc73208de03b","9bd490a4f453b93cf9fd9834a38e01d2badc8a91@mit.edu","\"kineticsGroups.py evaluate [family]\" can (and does) read PrIMe_RMG_Java set.\n\nThis should plot the RMG-Java generated rates (x axis) against the\nRMG-Py generated rates (y axis) for all the PrIMe reactions that \nwere generated by \"kineticsGroups.py java\".","Richard West"],["8885906a581177dc586a7d225fe1f477a80f75be","9bd490a4f453b93cf9fd9834a38e01d2badc8a91@mit.edu","Applied the new RMG-Java lookup to H_Abstraction family\n\nSome reactions are omitted (because the isomorphism check failed - probably\nresonance isomers were found) and many more reactions were reversed so\nthat the kinetics actually match the description.\n\n(I actually applied it to all families, but only H_Abstraction is currently\nin the git repo)","Richard West"],["4f279b4d4bc6cdd7047d7a6872a4bc1c3ca47260","d2efaa4c3e5af267960de800d4d586f2bce0207f@mit.edu","Significant rewrite of kineticsGroups script.\n\nThe motivation for this rewrite was to enable the script to be much more\nflexible in terms of what it can do, and what options it has. To that end,\nthe command-line interface is noticeably different (and more complex).\n\nThe other big change is that the generate and evaluate operations are now\ncompletely separate. Before the group additivity values would be generated\neven during the evaluate operation, which is silly to be doing over and\nover again. To enable this, the generate operation now also saves the\ngroup values if they have changed, in either KineticsData or Arrhenius\nformat depending on how the group values are fitted.\n\nThe separation of generation and evaluation also means that we don't need\na test set during the generation step, nor do we need a training set during\nthe evaluation step. This makes things simpler.\n\nThe java operation is (hopefully) unchanged from before.","Josh Allen"],["876717a9d28b34e8ff630f7715fb0a12ed2d8a76","d2efaa4c3e5af267960de800d4d586f2bce0207f@mit.edu","Added convertKineticsToPerSiteBasis() to kineticsGroups.py.\n\nThe evaluation is always done on a per-site basis to eliminate\nconsideration of reaction-path degeneracies. This helper function improves\nreadability and should be useful in other places in the script in the\nfuture.","Josh Allen"],["72800d18b251e94a427b43b6d4d216df2624a973","d2efaa4c3e5af267960de800d4d586f2bce0207f@mit.edu","Added preliminary plotting of parity plots using RMG-Java as model.\n\nThe goal is to be able to evaluate the kinetics estimation accuracy of\nboth the rate rules approach of RMG-Java and the group additivity approach\nof RMG-Py, to see which is \"better\". The implementation assumes the\npresence of *_RMG_Java.py files in the kinetics libraries that contain\nthe RMG-Java estimated kinetics for the same reactions as in the\ncorresponding depository. (The java operation of kineticsGroups.py can\nbe used to generate such files.)","Josh Allen"],["cf32a0347feade07b2427325f14aa0c5911cac3a","d2efaa4c3e5af267960de800d4d586f2bce0207f@mit.edu","Merge branch 'java'","Josh Allen"],["7010d5c96d9a71fa99b6ec2db6580934719b186c","d2efaa4c3e5af267960de800d4d586f2bce0207f@mit.edu","Merge remote-tracking branch 'connie/master'","Josh Allen"],["97bc389f3d09026f4b698170de1c2f100d2f0e14","9bd490a4f453b93cf9fd9834a38e01d2badc8a91@mit.edu","kineticsGroups java script has more filtering.\n\nIt now filters out reactions in the wrong direction,\nand by editing the code (read the comments) you can \nreplace rates with those from rmg-py (so that you can\nplot parity plots). It also skips over rates that \nthe java does not need to use an \"Average of\" for,\nso that you can tell which are which (edit the code to\ninclude *only* these rates instead of excluding them).\n\nVarious versions of this script were used to generate the \nparity plots for the poster presented at the 7th International\nConference on Chemical Kinetics.","Richard West"],["f6bc3d0d79c4f3ae62265a60f13fe5e5a5e08990","9bd490a4f453b93cf9fd9834a38e01d2badc8a91@mit.edu","Debugging aids in kineticsGroups.py\n\nIf you want the script to stop when there's an exception\n(so that you can catch it in the pyd debugger and deal \nwith it) then only catch the VerySpecificException and\nnot the Exception, on line 812.","Richard West"],["a2f67c5e8a574ad2322e846e1e3192ead754bb86","9bd490a4f453b93cf9fd9834a38e01d2badc8a91@mit.edu","Merge branch 'java'","Richard West"]],"ref":"refs/heads/master","size":15,"head":"a2f67c5e8a574ad2322e846e1e3192ead754bb86","push_id":36673711}