New Ring opening/closing reaction classes#40

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Extending thermochemistry library thermo_DFT_CCSDTF12_BAC

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Extending thermochemistry library thermo_DFT_CCSDTF12_BAC

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Extending thermochemistry library thermo_DFT_CCSDTF12_BAC

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Update thermochemistry library primaryThermoLibrary

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Update thermochemistry library primaryThermoLibrary

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New Entry: R_Recombination/training/

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New Entry: R_Recombination/training/

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New Entry: R_Recombination/training/

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Extending thermochemistry library thermo_DFT_CCSDTF12_BAC

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update tree of intra_NO2_ONO_conversion

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Extending thermochemistry library thermo_DFT_CCSDTF12_BAC

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Extending thermochemistry library thermo_DFT_CCSDTF12_BAC

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Extending thermochemistry library thermo_DFT_CCSDTF12_BAC

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1,2_Insertion; add nitrogen to top node

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1,3_Insertion_CO2; add nitrogen to top node

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1,3_Insertion_ROR; add nitrogen to top node

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1+2_Cycloaddition; add nitrogen groups

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Birad_recombination; add nitrogen to top nodes

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Cyclic_Ether_Formation; add nitrogen to top nodes

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HO2_Elimination_From_PeroxyRadical; add nitrogen to top node

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intra_OH_migration; add nitrogen to top nodes

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Intra_R_Add_Endocyclic; add nitrogen to top nodes

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Intra_R_Add_Exocyclic; add nitrogen to top nodes

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update Intra_R_Add_Endocyclic reverse

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update Intra_R_Add_Exocyclic reverse

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update intra_OH_migration

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update kinetics library Nitrogen_Dean_and_Bozzelli.py

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New Entry: R_Recombination/training/

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New Entry: R_Recombination/training/

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Add tri-radical top-node to statmech groups

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Changing ä to a in Aäron Vandeputte's name due to encoding problems.

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Removing duplicates from Dean and Bozelli library

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Updated output folder to RMG-Java at commit bb21002

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Updated kinetic libraries with adjlists containing paired electrons (new Py format).

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Updating thermo libraries with new adjlists.

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Fixes to adjlists in DFT_QCI_Thermo. Commented out cis-butene.

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Commented out GRI-Mech3.0 version of OH in primaryThermoLibrary. Use AcTc instead.

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Delete Nitrogen_Dean_and_Bozzelli.py

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Rename Nitrogen_Dean_and_Bozelli.py to Nitrogen_Dean_and_Bozzelli.py

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Remove duplicate from thermo libraries

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Adding Thermo for alpha radical from ethylamine

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Adding HBI for Carbon centered radical with neighboring N atom.

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Correcting typos in previous commits!

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More fixes to the last commit

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Adding thermo for more radicals formed from ethylamine

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Accomodate both 2T and 2S in Ybirad for SubstitutionO group.

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Manual merge of RMG-Java 8ce558. New Family 1,4_Cyclic_birad_scission added.

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Manual merge of RMG-Java 8ce558. New Family 1,4_Linear_birad_scission added.

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Manual merge of RMG-Java 8ce558. New Family Intra_Diels_alder added.

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Manual merge of RMG-Java 8ce558. New Family ketoenol added.

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Manual merge of RMG-Java 8ce558. 'Ring' thermo groups updated.

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Manual merge of RMG-Java 8ce558. 'Radical' thermo groups updated with phenoxy change.

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Manual merge of RMG-Java 8ce558. 'Polycyclic' thermo groups updated.

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Manual merge of RMG-Java 8ce558. 'Group' thermo groups updated.

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Manual merge of RMG-Java 8ce558. Cyclic_Ether_Formation family updated.

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Manual merge of RMG-Java 8ce558. 1,2_Insertion updated.

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Manual merge of RMG-Java 8ce558. HO2_Elimination_from_PeroxyRadical family updated.

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Manual merge of RMG-Java 8ce558. 1,3_Insertion_CO2 family updated.

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Manual merge of RMG-Java 8ce558. 1,3_Insertion_RSR family updated.

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Manual merge of RMG-Java 8ce558. 1,3_Insertion_ROR family updated.

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Manual merge of RMG-Java 8ce558. 1+2_Cycloaddition family updated.

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Manual merge of RMG-Java 8ce558. SubstitutionS family updated.

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Manual merge of RMG-Java 8ce558. Intra_Disproportionation family updated.

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Manual merge of RMG-Java 8ce558. Intra_R_Add_Exocyclic family updated.

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Manual merge of RMG-Java 8ce558. Intra_R_Add_Endocyclic family updated.

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Manual merge of RMG-Java 8ce558. R_Recombination family updated.

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Manual merge of RMG-Java 8ce558. Diels_alder_addition family updated.

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Manual merge of RMG-Java 8ce558. intra_H_migration family updated.

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Manual merge of RMG-Java 8ce558. H_Abstraction family updated.

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Manual merge of RMG-Java 8ce558. R_Addition_MultipleBond family updated.

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Change Ns group to N3s,N5s in R_Addition_MultipleBond family.

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Fix indentations in tree for R_Addition_MultipleBond family.

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Add missing nitrogen groups Nt_R and N5d_R to the R_Addition_MultipleBond groups.

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Kicked out N5d_R and N5J from R_Addition_MultipleBond groups.

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Fix Y_1centerbirad group in H_Abstraction family.

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Forbid carbene triplet form in 1+2_Cycloaddition family.

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Change all carbon atoms to 4T triplet state.

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Add CO,CS, and N to H_Abstraction family Y_1centerbirad group.

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Updating Dean and Bozzelli librray with PLOGs

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Add EvaluateKinetics.py

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Remove duplicate from Thermo SulfurLibrary

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Convert some thermo libraries to 4 column adjlist

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Reordering the intra H migration tree. Update to RMG-Java commit 2d57f8

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Added reverse to Intra_Diels_alder family. Mirror of RMG-Java f599b33 commit.

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Removal of duplicate group in intra_H_migration family. Mirror of RMG-Java d47a8d9

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Database clean up

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Fixed more history on groups and libraries

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Convert kinetic libraries to give 4-column adjlist

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Update adjacency lists to 4 column format

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Update adjacency lists to 4 column format in PrimaryTransportLibrary

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Update adjacency list in GRI-Mech transport library

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Cyclic_Ether_Formation: Update adjacency list with explicit lone pairs

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H_abstraction: Update adjacency list with explicit lone pairs

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HO2_Elimination_from_PeroxyRadical: Update adjacency list with explicit

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intra_H_migration: Update adjacency list with explicit lone pairs

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R_Addition_MultipleBond: Update adjacency list with explicit lone pairs

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R_Recombination: Update adjacency list with explicit lone pairs

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Cyclic_Ether_Formation: C#O and update adjacency list with explicit lone

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combuction_core version2: Update carbon monoxide to C#O

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combuction_core version3: Update carbon monoxide to C#O

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combuction_core version4: Update carbon monoxide to C#O

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combuction_core version5: Update carbon monoxide to C#O

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Dooley C1: Update carbon monoxide to C#O

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methylformate_2: Update carbon monoxide to C#O

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Dooley methylformate_all_ARHEbathgas: Update carbon monoxide to C#O

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Dooley methylformate_all_N2bathgas: Update carbon monoxide to C#O

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methylformate: Update carbon monoxide to C#O

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Glarborg C1: Update carbon monoxide to C#O

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Glarborg C2: Update carbon monoxide to C#O

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Glarborg C2: Update carbon monoxide to C#O

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Glarborg highP: Update carbon monoxide to C#O

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Hexanethial: Update carbon monoxide to C#O

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ERC-FoundationFuelv0.9: Update carbon monoxide to C#O

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GRI-HCO: Update carbon monoxide to C#O

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GRI-Mech3.0: Update carbon monoxide to C#O

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GRI-Mech3.0-N: Update carbon monoxide to C#O

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Methylformate: Update carbon monoxide to C#O

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Nitrogen_Dean_and_Bozzelli: Update carbon monoxide to C#O

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Nitrogen_Glarborg_Gimenez_et_al: Update carbon monoxide to C#O

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Nitrogen_Glarborg_Lucassen_et_al: Update carbon monoxide to C#O

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Nitrogen_Glarborg_Zhang_et_al: Update carbon monoxide to C#O

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Replace standard brackets () with curly brackets {} in adjacency lists

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DFT_QCI_thermo: Update carbon monoxide to C#O

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GRI-Mech3.0: Update carbon monoxide to C#O

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GRI-Mech3.0-N: Update carbon monoxide to C#O

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KlippensteinH2O2: Update carbon monoxide to C#O

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thermo_DFT_CCSDTF12_BAC: Update carbon monoxide to C#O

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USC-Mech_ii: Update carbon monoxide to C#O

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GRI-Mech transport: Update carbon monoxide to C#O

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PrimaryTransportLibrary: Update carbon monoxide to C#O

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Add Od_rad to forbiddenStructures

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Correct adjacency list of He in primaryThermoLibrary

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Add the structure Ods to forbiddenStructures.py

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Rename the functional element N2d to N1d

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Fixed typo in combustion core kinetic library

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Fix misnamed groups in rules

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Add wrapper for testing database

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Add output for checking for unique groups

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fix AdjList in rules of Intra_R_Add_Exocyclic

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Fix child relationships in R_Addition_Csm

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Fix errors in Disproportionation family

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Remove history fields permanently and clean up empty reference and referenceType fields.

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Remove `recommended` field in databases since they have no functionality.

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Remove rogue git conflict lines in R_Recombination/NIST.py

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Add a list of recommended families for setting the 'default' option in RMG.

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Minor fixes to intra_H_migration family

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Fix bug with Leave one out test

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Minor corrections to in 1,2 Insertion family

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Added suggested solutions to name errors in checkWellFormed

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Fixes to R_Addition_MultipleBond family

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Fixes to EvaluateKinetics.py database testing script.

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More fixes to R_Addition Multiple Bond

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Removed biradical singlets from R_MultipleBond Addition

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Fixes to rule adj lists in Intra_R_Add_Endocyclic

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Fixes to group definitions in Intra_R_Add_Endocylic

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Fixes to Disproportionation family

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Fixes to adjLists of 1,3_Insertion_RSR

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Fixes to R_Addition_CSm using checkWellFormed

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Fix errors in 1,2_Insertion found with databaseTester

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Fixes to H-Abstraction family: Part 1

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Fixes to H-Abstraction: Part 2

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Fixes to Intra_substitutionCS_cyclization family

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Fixes to intra_substitutionS_cyclization family

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Fixes to intra_substitutionCS_isomerization family

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Fixes to Intra_substitutionS_isomerization family

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Fixes to R_Addition_COm family

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Fixes to Birad_recombination family

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Fixes to lone_electron_pair_bond

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Fixes to HO2_Elimination_from_PeroxyRadical family

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Change Disproportionation training rxn to Arrhenius rather than ArrheniusEP

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Updated RMG-database with three new reaction families for ring opening/closing reactions.
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Deleting some history comments!
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