Code

Automatic Tree Generation Part 4#1486

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mliu49 merged 64 commits intomasterReactionMechanismGenerator/RMG-Py:masterfrom atg4ReactionMechanismGenerator/RMG-Py:atg4Copy head branch name to clipboardAug 7, 2019

+1,172-400

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Commits on Aug 5, 2019

• Enable estimation of bond dissociation energies

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• simplify w0 calculations for parallelization

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• add '' as a key for uncertainties

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• parallelize BM rule creation using multiprocessing

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• parallelize treeGeneration process

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• add a leave-one-out option for the cross-validation functions

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• fix bug with checkTree

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• add uncertainty attribute to kinetics models

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• avoid entries with index = -1 when searching for root node during tree generation

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• Allow use of ArrheniusBM in tree rules

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• add reactantNum and productNum as groups.py file variables

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• generalize template matching algorithm

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• add clearRegDims function

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• ensure ArrheniusBM kinetics are properly converted into Arrhenius kinetics

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• make BM curve fitting robust to optimization errors

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• add bond regularization dimension debugging to extendNode

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• fix bond regularization dimension tracking

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• enable processing of families with labels that don't correspond to the mapping

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Commits on Aug 6, 2019

• add RateUncertainty class and cythonize

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• fix import in arrhenius now that uncertainties is properly spelled

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• add test for RateUncertainty

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• manage uncertainties within arrhenius rate expressions

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• assign uncertainties to node kinetics when fitting rules

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Commits on Aug 7, 2019

• make getAllDescendants a bound method of Entry

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• import ArrheniusBM directly from kinetics

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• remove extra spaces between functions

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• use recipe instead of family to determine w0

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• allow generateTree to be directly fed a list of reactions to use

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• allow crossValidate to be fed a set of indicies for the reactions that should be tested against (for entirely independent testing)

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• include associated uncertainties in crossValidate output

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• remove alpha and add rank to the input for rule creation

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• enable generateTree to be passed options controlling how it tree generation is parallelized

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• convert isomorphic_species_lists to new same_species_lists

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• enable parsing of RateUncertainty in database

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• add script for generating new decision tree estimators

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• add a sudo BDE entry for a 2.5 order CC bond, as C#C - CbC + CsC

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• implement label fixing for families that aren't their own reverse

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• make it possiible to call getLabeledAtom on a molecule where a label occurs twice

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• make it possible to run isomorphism checks when duplicate atom labels are present

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• add an option in mergeGroups to keep any identical labels

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• update molecule and group tests to handle getLabeledAtom -> list

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• fix bugs with subgraph isomorphism involving duplicate labels

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• fix bug related to the merging a graph with itself

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• add repr method for LibraryReaction

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• adapt isEntryMatch to deal with duplicate labels

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• adapt family test to getLabeledAtom changes

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• modify testing families to work with new recombination and repr methods

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• adapt recipe application to handle duplicate labels

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• adapt tree cleaning to handle duplicate labels

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• add a resonance option to isEntryMatch

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• remove hardcoding of R_Recombination

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• adapt database tests to new trees

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• ensure generated tree comments appended during loading

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• improve generated tree rule comments

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• don't add rules from training for generated trees

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• solve the symmetry issue with node expansion

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• adds function for breaking up a set of reactions into batches for tree generation

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• add pruneTree function for removing nodes with low number of reactions from the tree before reoptimizing with an additional batch

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• Implements the Cascade algorithm in generateTree

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• skip node generation if the root node is empty

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• randomize rule generation order

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• fix Cascade algorithm regularization

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• use consistent list of reactions in familyTest

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• privatize appropriate tree generation methods

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