{"shas":[["b60ea8c6e4eee12af1a563edb9511c05cc318396","b1063c6ecf4e141d62862c7361346d12e74c651f@mit.edu","Storing comments related to estimating thermo properties\n\nAfter finding nodes in any of the thermo_groups tree (Group, Radical, Ring,\nGauche, 15, Other), store this information in a string instance in the\nChemGraph class.\n\nFurthermore, when running the ThermoDataEstimator class, report this\ninformation.","Michael Harper"],["bc31ebb54dfd341f8c603f4f8363d1fd9493a69d","b1063c6ecf4e141d62862c7361346d12e74c651f@mit.edu","ThermoDataEstimator: Make user specify name for each chemgraph\n\nInstead of listing only chemgraphs in the input file for the\nThermoDataEstimator class, force the user to also list a name with each\nchemgraph.  This is consistent with all other RMG (and related class)\ninput files.\n\nExample: A user has a list of InChIs.  Passing this list to InChI2AdjList\nproduces a list of names+chemgraphs.  If the user then wanted to know\nthe thermo or transport of each of these species, they can use the generated\nfile (with minor updates, e.g. adding PrimaryThermoLibrary field).  Before,\nthe user would need to remove every species name.","Michael Harper"],["2a55f35cd21175976a6e4ab714fa9d679c980593","9bd490a4f453b93cf9fd9834a38e01d2badc8a91@mit.edu","Correct bug in ArrheniusKinetics.equals()\n\nIt used to return TRUE for the following pair of rates:\n  (1e10, 0, 123)\n  (1e10, 3, 123)\nalso for\n  (1e10, 3, 0)\n  (1e10, 3, 123)\nor even\n  (1e10, 0, 0)\n  (1e10, 3, 123)\nbecause if the E or n values of the first set were zer, then they weren't used in the comparison.","Richard West"],["1deba306d4e47f60837b8c600caae48d7ecfb4a2","9bd490a4f453b93cf9fd9834a38e01d2badc8a91@mit.edu","Correct uncertainty propagation in UncertainDouble.multiply(double)\n\nIt used to multiply the uncertainty even for \"Multilpy\" type uncertainties.","Richard West"],["e2e3772e4b43d5779b360f731c925dc8604d8342","9bd490a4f453b93cf9fd9834a38e01d2badc8a91@mit.edu","Correct uncertainty bug in averaging of ArrheniusKinetics\n\nThe 'min' value of A was initiated to zero, so a lower one was never found.\nThis would then lead to an estimated uncertainty of infinity (new average / zero)\nwhich would persist throughout the simulation. i.e all avegared rate coefficients\nhad infinite uncertainty in the A factor.","Richard West"],["beea4df86f74770393679b8c2393a1f09117d6ac","9bd490a4f453b93cf9fd9834a38e01d2badc8a91@mit.edu","Multiplicative uncertainties should not be less than one.\n\n(X *|/ d)  means the largest X is X*d and the the smallest is X/d.\nThis implies d>=1","Richard West"],["74d378ce446b0e59c63fa3a6f5306a6ac8085969","9bd490a4f453b93cf9fd9834a38e01d2badc8a91@mit.edu","Bug fix in UncertainDouble.getAddingUncertainty()\n\nThis function converts whatever form the uncertainty is in, into an additive one.\nThe trouble is, if your mulciplicative uncertainty is greater than (or equal to) 2,\nthen the additive uncertainty will be greater than (or equal to) the value, and\nyour lower bound will be negative. This is usually best avoided.\nBut with this fix, at least it does what it claims!","Richard West"],["7033aa5d2991a78f4194578ad56b25ad641d65d2","9bd490a4f453b93cf9fd9834a38e01d2badc8a91@mit.edu","Improved means of adding with UncertainDouble.plus\n\nInstead of forcing all the uncertainties to be additive (which has problems with\nnegative lower bounds), if both uncertainties were already multiplicative,\nit leaves them as so, and uses the highest (or only if they're equal) uncertainty.\nThis makes the new add-redundant-A-factors-together code work much better, as\nyou can avoid having negative lower bounds on your A factors.","Richard West"],["33faabaa53f2802b0ded9871d8e43a28a12c05cf","9bd490a4f453b93cf9fd9834a38e01d2badc8a91@mit.edu","Instead of increasing redundancy, add A factors when you find multiple kinetics the same.\n\nPreviously, whenever kinetics were added to a reaction but the same kinetics were already\nthere (eg. you had already found an equivalent pathway with differently labeled atoms)\nthe redundancy *of the reaction structure* was increased. THis redundancy, however, applies\nto all the pathways of that reaction. If there are two pathways, each is found several times,\nthe redendancy is incremented a lot, then multiplied by each pathway.\n\nFor the 1,3_Insertion_CO2 reaction: CO2 + H2 --> CH2O2\nthis would lead to final rates that were 16 times higher than the group values (instead of ~4?)\n\nNow, if we find kinetics with the same N and E and Source (matched nodes) then we\nadd the A values.\n\nI believe this closes #156.","Richard West"],["7f608ee645cd98fd502231a170ff86b218c8ee71","9bd490a4f453b93cf9fd9834a38e01d2badc8a91@mit.edu","Remove the blank line from after DUP duplicate reactions in chemkin file.\n\nMinor change, but it was bugging me!","Richard West"],["7d8f30acfd8d0a28210b79af2e3fa26f59f35db4","9bd490a4f453b93cf9fd9834a38e01d2badc8a91@mit.edu","Use Logger.error() instead of System.err.println() n JDAS etc.\n\nI wonder if in some of these cases we should follow the\n    Logger.logStackTrace(e);\nwith a\n    throw new RuntimeExcetption(e);\nso the errors are not ignored.\n\nRecommended reading:\nhttp://onjava.com/pub/a/onjava/2003/11/19/exceptions.html","Richard West"],["cee3aa56d9df1ccacfa0dc1c4a4c1449d7c9e3a1","9bd490a4f453b93cf9fd9834a38e01d2badc8a91@mit.edu","Improvements to Logger module.\n\n1) If something is wrong with the log file, we throw a RuntimeException,\n   which will be uncaught and will cause the java to exit with a stack trace.\n   This is probably better than ignoring the problem.\n\n2) logStackTrace(e) now uses ERROR level instead of INFO\n\n3) I've made a new method Logger.flush() which will flush the log file.\n   This can be called when you want to make sure the log file is up to date,\n   eg. you're about to do something time-consuming, or you've just reported\n   an error. This is called automatically after ERRORs and CRITICALs.","Richard West"],["affbe2fc2c62b8d139e015d37aca5c4e338017cc","9bd490a4f453b93cf9fd9834a38e01d2badc8a91@mit.edu","Flush the log file once per iteration, after reporting progress.\n\nThis seems like a resonable place to ensure the log file is up to date.","Richard West"],["75cae43d44ccc8b737ac961ffb8b28b2cd1e4a12","b1063c6ecf4e141d62862c7361346d12e74c651f@mit.edu","Additions to the FrequencyEstimator class\n\n1) Make appropriate working directories\n\tRunning the frankie.exe requires the \"GATPFit\" (because a species is\n\tmade, and thus its thermochemistry must be estimated) and \"frankie\"\n\tfolders be present in the working folder\n2) Allow user to define RMG_database\n\tThe user's desired database may not be the default \"RMG_database\"\n\tfolder.\n3) Force the user to define a name with each ChemGraph\n\tThe species is created with the user-supplied name, instead of a\n\tblank string.","Michael Harper"],["f4e34295471b274eacf640944a51248b921c5f57","3b479e37c4f92713801a640a9812614d3444f064@mit.edu","removed timeout for embedding process, which seems to have been associated with an older version of RDKit\n\ncf. Issue #161","Gregory Magoon"],["a6488c62699ff736ca2d15046eb61f67bb39e0ab","b1063c6ecf4e141d62862c7361346d12e74c651f@mit.edu","Store information regarding which frequency groups were matched\n\nRMG determines how many of each frequency functional groups were found for\neach molecule, however this information is not stored anywhere.  This commit\nstores the information to a String in the ChemGraph class.\n\nPresently, the only RMG class that asks for this information is the\nFrequencyEstimator class.","Michael Harper"],["8aa25c644ed5d78def51f0ba893680f452071c67","b1063c6ecf4e141d62862c7361346d12e74c651f@mit.edu","Force \"dup\" tag to be used in kinetic_libraries reactions.txt files\n\nWhen a user supplies a kinetic library, reaction library, or seed mechanism:\nRMG reads in the reactions.txt file.  If it finds more than one instance of\na reaction string (e.g. A+B=C), it used to assume that the user\nwanted this duplicate instance and would add the kinetics of the\nduplicate instance to the array of kinetics of the original instance\nof the reaction.\n\nNow, I am enforcing the user to specify \"DUP\" or \"DUPLICATE\" after each\nduplicate reaction.  This should lead to fewer possible errors when\nsupplying a kinetics_library folder to RMG.\n\nAfter reading in all reactions in the reactions.txt file, RMG now iterates over\nall reactions.  If the reaction is marked as a duplicate, but has only one\nset of ArrheniusKinetics, RMG will print an error message (with the offending\nreaction) and terminate the simulation.","Michael Harper"],["e3c5daec719fdc130d5814731650df017bfacb95","b1063c6ecf4e141d62862c7361346d12e74c651f@mit.edu","Updating combustion_core/version2 and /version3 folders\n\nNeither folder's reactions.txt nor pdepreactions.txt files had the three\nuncertainty values.  Obviously no one has used these in a while, but in case\nsomeone does in the future, RMG will read these properly.\n\nUpdating current reaction_libraries directories: Duplicate tags\n\nThese libraries are now consistent with the new method of RMG reading in\nreactions from reaction_libraries folders, namely, that a dupliate tag must\nbe added to dupliate reaction entries.","Michael Harper"],["ca8188d04b14abd668079f9e4c7249406b4928a1","b1063c6ecf4e141d62862c7361346d12e74c651f@mit.edu","Check for chemgraph redundancy when reading in kinetics_library\n\nWhen reading in the species.txt file from any kinetics_library folder,\nRMG now checks if the species (i.e. chemgraph) was already read-in.  If\nso, RMG prints the two species' names (as defined by the user) and\nterminates immediately.\n\nBefore, RMG would not make a new Species, but would add a new entry\nto the localSpecies LinkedHashSet.  The entry would then have the same\nspecies twice, with different names.","Michael Harper"],["1e9ecef664f78ac81bde6aabe8de21758f501213","9bd490a4f453b93cf9fd9834a38e01d2badc8a91@mit.edu","Fix negative Ea from Evans-Polyani when Eo<=0.\n\nThe 'correction' to activation energies estimated via Evans-Polyani\nexpressions was only applied when the intrinsic barrier height Eo\nwas greater than zero. Now it is also applied when Eo==0. Furthermore,\nwhen Eo<0, the resulting Ea is not allowed to be more negative than Eo.\n\nThis should correct some crazy rates that were appearing such as\nlog10(kf) = 46.82 at T = 300K for C2(36)+HCCOH(45)=C2H(3)+HCCO(49)                     1.000e+11 \t  0.00 \t -49.17 \t!H_Abstraction estimate: (Average of: (Average of: (O/H/NonDeC O2b)))  [ C2b , O/H/OneDe ] Ea computed using Evans-Polanyi dHrxn(298K)=-49.2 kcal/mol and alpha=1.00.","Richard West"]],"repo":"jwallen/RMG-Java","actor":"jwallen","ref":"refs/heads/master","size":27,"head":"c3fd2efb71474b20abe25a18e16caacc540d63a0","actor_gravatar":"df2d93b7ed5cb40868128c0c086870db","push_id":29473078}