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Tree fitting for several rxn families #485

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31241b6
added F_Abstraction family with autogen tree
davidfarinajr Jul 13, 2021
94df9e7
added Cl_Abstraction family with autogen tree
davidfarinajr Jul 13, 2021
22dde3c
added Br_Abstraction family with autogen tree
davidfarinajr Jul 13, 2021
b8a7b7d
added XY_Addition_MulitpleBond with autogen tree
davidfarinajr Jul 13, 2021
425c063
added 1,2_XY_interchange family
davidfarinajr Jul 13, 2021
30c6df2
added Disproportionation-Y family with autogen tree
davidfarinajr Jul 13, 2021
67428b3
added halogen kinetic libraries
davidfarinajr Jul 16, 2021
fd31c46
added halogen families to `halogens` folder in recommended.py
davidfarinajr Jul 16, 2021
53f7678
added chemdraw templates for new halogen families
davidfarinajr Jul 28, 2021
2549e74
added `Surface_Adsorption_Dissociative_Double` template png
davidfarinajr Jul 28, 2021
447d0ac
added halogen families to `rmg_reaction_families.pdf`
davidfarinajr Jul 28, 2021
5eea095
added key halogen species to `halogens` thermo library
davidfarinajr Aug 2, 2021
7ef0958
added halocarbene_recombination reaction family
davidfarinajr Aug 2, 2021
37d132d
added `halocarbene_recombination_double` reaction family
davidfarinajr Aug 2, 2021
ffc85d0
added `halocarbene_recombination` and `halocarbene_recombination_doub…
davidfarinajr Aug 2, 2021
d0bf35d
added chemdraw templates for halocarbene families
davidfarinajr Aug 2, 2021
39872a9
added CF2BrCl kinetics library
davidfarinajr Aug 7, 2021
c327a2e
added CH3Cl kinetics library
davidfarinajr Aug 7, 2021
4bd1dfc
commented out reactions with more than 3 products in CH3Cl kinetics l…
davidfarinajr Aug 9, 2021
43e89ad
renamed identical species in CF2BrCl kinetics library
davidfarinajr Aug 9, 2021
f33e3bd
commented out excited CH* and OH* reactions in CF2BrCl kinetics library
davidfarinajr Aug 9, 2021
8a06514
allowed some max rate violators in CF2BrCl kinetics library
davidfarinajr Aug 9, 2021
d106c2d
added F_Abstraction training reactions calculated with autotst
davidfarinajr Sep 23, 2021
6b32435
regenerated F Absraction tree with autotst data
davidfarinajr Oct 7, 2021
914e7db
retrained Cl_Abstraction family tree with autotst kinetics
davidfarinajr Oct 7, 2021
c7d6c0a
retrained Br_Abstraction family tree with autotst kinetics
davidfarinajr Oct 12, 2021
f1a84af
Merge pull request #514 from ReactionMechanismGenerator/only_halogens…
mazeau Oct 14, 2021
2ea4f29
Add training reactions for keto-enol heavy atom transfers
kspieks Oct 5, 2021
0b3184b
Refit keto-enol rate rules
kspieks Oct 5, 2021
aafe755
Merge pull request #534 from ReactionMechanismGenerator/refit_ketoeno…
amarkpayne Oct 18, 2021
cc94168
change top node from logic node to group node
hwpang Jun 21, 2021
4c480d5
tree gen for cyclopentadiene scission
hwpang Oct 18, 2021
aaccd98
Add reactant/productNum and autoGenerated tag
hwpang Jun 21, 2021
17a08f0
Merge pull request #498 from ReactionMechanismGenerator/tree_gen_cycl…
amarkpayne Oct 18, 2021
a10364c
Run GitHub actions using the main branch
amarkpayne Oct 18, 2021
ab5cd1b
Database Label Fix: Disproportionation, CH3
oscarwumit Apr 25, 2019
5848a17
fix issue with use of CH3 vs CH3_r1 in species dictionary for disprop…
mjohnson541 May 27, 2019
5a286a0
change logic root node to group node and add react/prod num
hwpang Jun 14, 2021
ac50fff
Tree generation and change autoGenerated tag to True
hwpang Jun 21, 2021
8ee83a0
Merge pull request #493 from ReactionMechanismGenerator/tree_gen_Disp…
amarkpayne Oct 18, 2021
7ecf9fd
Generalize ketoenol reaction template 1,3-sigmatropic rearrangement
kspieks Oct 18, 2021
3e6e90c
Add training reactions for 1,3 sigmatropic rearrangement
kspieks Oct 10, 2021
a1c4e44
Minor: update long description reference to the reaction index
kspieks Oct 10, 2021
74a175c
Add training reactions from Zhu et al. 2003
kspieks Oct 19, 2021
48b586e
Refit 1,3 sigmatropic rearrangement rate rules
kspieks Oct 19, 2021
5661573
Minor: update .gitignore to ignore MacOS files
kspieks Oct 10, 2021
9b44970
Merge pull request #532 from ReactionMechanismGenerator/rename_ketoen…
xiaoruiDong Oct 19, 2021
0ce495f
Removed duplicate training reactions in XY_Addition_MulitpleBond
davidfarinajr Oct 18, 2021
2dcb4cd
regenerated new XY_AdditionMultipleBond groups and rules
davidfarinajr Oct 19, 2021
8d3025b
Merge pull request #536 from ReactionMechanismGenerator/xy_add_training
xiaoruiDong Oct 20, 2021
b5065de
Modify Peroxyl_disprop to be ready for tree generation
xiaoruiDong Oct 20, 2021
afd823b
Auto Tree generation for the Peroxyl_Disprop family
xiaoruiDong Oct 20, 2021
32b1d20
Merge pull request #537 from ReactionMechanismGenerator/peroxyl_dispr…
amarkpayne Oct 21, 2021
facec1c
added F/Cl/Br-benzene to halogens thermo lib
davidfarinajr Oct 22, 2021
a64b2fc
fitted Cb-Cl gav using C6H5Cl in halogens thermo lib
davidfarinajr Oct 22, 2021
c6ffb9a
derived`Cb-F` and `Cb-Br` thermo groups
davidfarinajr Oct 22, 2021
b659258
Merge pull request #539 from ReactionMechanismGenerator/Cb_hal_gav
davidfarinajr Oct 22, 2021
ce85727
added "C2_triplebond" to forbidden structures
davidfarinajr Mar 16, 2021
51fa1f5
Merge pull request #503 from ReactionMechanismGenerator/ctc
davidfarinajr Oct 22, 2021
6e13a33
Adding missing commas to coverage dependent parameters
mazeau Oct 15, 2021
45d2d60
Merge pull request #533 from ReactionMechanismGenerator/vlachos_fix
davidfarinajr Oct 22, 2021
0667535
Update reaction family images to reflect the merged 2+2_cycloaddition
kspieks Oct 26, 2021
82e848d
Update rmg_reaction_families.pdf
kspieks Oct 27, 2021
9ac14fb
Merge pull request #543 from ReactionMechanismGenerator/2+2_cycloaddi…
xiaoruiDong Oct 28, 2021
f45ab6f
added `ODCBr` to `CHOBr_G4` thermolib
davidfarinajr Oct 23, 2021
fe4a200
added data for `COBrHO` thermo group
davidfarinajr Oct 23, 2021
1fd9527
added HO-C(-OH)(-OH)-Y to CHOY_G4 thermo libs (Y=F,Cl,Br)
davidfarinajr Oct 24, 2021
a2da542
added thermo data for CsYOOO (Y=F,Cl,Br) thermo groups
davidfarinajr Oct 24, 2021
7e70273
added pointer for `CsC2sBrBrBr` thermo group
davidfarinajr Oct 24, 2021
d881489
Merge pull request #540 from ReactionMechanismGenerator/OCBrH_thermo
davidfarinajr Nov 1, 2021
9a7a2ed
Added `xy_elim_hydroxyl` family
davidfarinajr Oct 26, 2021
a8cbd47
added autotree groups and rules for `XY_elim_hydroxyl`
davidfarinajr Oct 26, 2021
0afbfd1
fixed node in xy_elim_hydroxyl tree
davidfarinajr Oct 30, 2021
610858f
added chemdraw template for `xy_elim_hydroxyl` family
davidfarinajr Nov 1, 2021
0e49f29
added `XY_elimination_hydroxyl` to rmg reaction families pdf
davidfarinajr Nov 1, 2021
486800b
Merge pull request #542 from ReactionMechanismGenerator/XY_elim_carboxyl
davidfarinajr Nov 1, 2021
41e23fa
Prepare Bimolec_Hydroperoxide_Decomposition for tree generation
hwpang Nov 4, 2021
6577348
Tree generation for Bimolec_Hydroperoxide_Decomposition
hwpang Nov 4, 2021
0e44d41
Merge pull request #545 from ReactionMechanismGenerator/Bimolec_Hydro…
xiaoruiDong Nov 5, 2021
230d3e6
added `intra_halogen_migration` familiy
davidfarinajr Nov 7, 2021
c080ecf
added `intra_halogen_migration` tranining reactions
davidfarinajr Nov 7, 2021
f552b30
added `intra_halogen_migration` semi-auto tree
davidfarinajr Nov 7, 2021
8e58995
removed labels>3 in intra_hal_migration forbidden structs
davidfarinajr Nov 7, 2021
90ed06a
added `intra_hal_migration` image to families pdf
davidfarinajr Nov 7, 2021
74ddf9d
added `intra_halogen_migration` to `halogens` recommended families fo…
davidfarinajr Nov 7, 2021
1268e4b
Merge pull request #546 from ReactionMechanismGenerator/intra_halogen…
davidfarinajr Nov 15, 2021
bc74451
Generated trees for 1,3_NH3_elimination
sevyharris Nov 30, 2021
686713a
Merge pull request #529 from ReactionMechanismGenerator/tree_gen_1_3_…
davidfarinajr Nov 30, 2021
62599ed
Adding new surface abstraction families
bjkreitz Aug 26, 2021
2880205
Merge pull request #521 from ReactionMechanismGenerator/new_abstracti…
davidfarinajr Dec 1, 2021
3144483
Adding thermo for Pt111
bjkreitz Jul 26, 2021
aa0fa02
Merge pull request #513 from ReactionMechanismGenerator/add_thermo_Pt111
davidfarinajr Dec 1, 2021
3e8ea4f
added "heavy halogen interaction" long distance correction
davidfarinajr Oct 24, 2021
3d52e19
averaged data for long distance halogen interaction parents
davidfarinajr Nov 15, 2021
4823559
added cis C(hal3)-C=C-C(hal3) long distance thermo groups
davidfarinajr Nov 15, 2021
5ffec73
added handful of spcs from PFOA model to CHOF_G4 thermolib
davidfarinajr Nov 15, 2021
d2bb634
added ChalX-CdOs long distance thermo grooups
davidfarinajr Nov 16, 2021
9fc77df
Merge pull request #541 from ReactionMechanismGenerator/long_range_th…
davidfarinajr Dec 3, 2021
d237d99
Add thermo values for ketoenol and 1,3 sigmatropic rearrangement
kspieks Nov 27, 2021
15a992a
Create reaction family for ketoenol tautomerization
kspieks Nov 26, 2021
717b6c0
Ketoenol: add training reactions and refit rate tree
kspieks Dec 9, 2021
8fcb504
Update reaction family pdf with ketoenol image
kspieks Nov 26, 2021
00df5ea
Update reaction family for 1,3 sigmatropic rearrangement
kspieks Nov 27, 2021
d3a74ee
1,3 sigmatropic rearrangement: add training reactions + refit rate tree
kspieks Dec 9, 2021
694a7dc
Minor: remove .DS_Store file
kspieks Nov 26, 2021
c47c48b
add `Ketoenol` family to recommended families
davidfarinajr Dec 9, 2021
b6cfa54
Merge pull request #550 from ReactionMechanismGenerator/separate_1_3_…
davidfarinajr Dec 9, 2021
ab9e1ea
added `halogens_G4` statmech library
davidfarinajr Aug 31, 2021
6fff2e1
added halogens to statmech groups
davidfarinajr Aug 31, 2021
525d820
Merge pull request #522 from ReactionMechanismGenerator/halogens_pdep
davidfarinajr Dec 14, 2021
f9cfd17
Rates from Hou et al
hwpang Jan 8, 2022
92280f2
Merge pull request #328 from ReactionMechanismGenerator/Aromatic_H_Ab…
xiaoruiDong Jan 10, 2022
362ab2c
Add fitThermoGroupsFromThermoLibrary notebook
hwpang Jan 11, 2022
c4a64d3
Automated fitted new groups using thermo libraries
hwpang Jan 11, 2022
c563c99
Merge pull request #451 from ReactionMechanismGenerator/new_gavs_from…
xiaoruiDong Jan 12, 2022
f7d7aa5
Add O2d-Cdd and Cdd-CdO2d to special list
hwpang Jan 12, 2022
9126383
Use the updated notebook to refit all the groups added in PR #451
hwpang Jan 12, 2022
755853b
Merge pull request #559 from ReactionMechanismGenerator/remove_O2d-Cd…
xiaoruiDong Jan 12, 2022
53188e3
Commented out the entry with index 57 (C-*RCR2) in adsorptionPt111.py.
kblondal Jan 9, 2022
d975a84
Merge pull request #556 from ReactionMechanismGenerator/vinyl_adsorpt…
rwest Jan 13, 2022
e28d96c
Fix labels, structures, and reactions for C:3 H:2 species in CurranPe…
mefuller Dec 6, 2021
3c87de2
fix master to main in trigger script
mefuller Dec 19, 2021
726ecea
Merge pull request #552 from ReactionMechanismGenerator/CurranPentane…
alongd Jan 18, 2022
bbffc12
Added freq factor for b2plypd3/def2tzvp
alongd Jan 16, 2022
bbd3f21
Merge pull request #561 from ReactionMechanismGenerator/b2plypd3
xiaoruiDong Jan 19, 2022
6216356
Add notebook for AEC fitting
kspieks Feb 23, 2022
ee608c9
Add notebook for BAC fitting
kspieks Feb 23, 2022
c2c3848
Merge pull request #501 from ReactionMechanismGenerator/AEC_BAC_noteb…
xiaoruiDong Feb 24, 2022
00be953
Update reference database for b97-d3/def2-msvp
kspieks Jan 31, 2022
f71c322
Update BACs for b97-d3/def2-msvp
kspieks Jan 31, 2022
861f958
Update reference database with wb97xd3/def2-tzvp
kspieks Jan 31, 2022
7c2c98e
Update BACs for wb97xd3/def2-tzvp
kspieks Jan 31, 2022
9e8da17
Update ref database with CCSD(T)-F12/cc-pVDZ-F12//ωB97X-D3/def2-TZVP
kspieks Feb 1, 2022
1d8c8a9
Update BACs for CCSD(T)-F12/cc-pVDZ-F12//ωB97X-D3/def2-TZVP
kspieks Feb 1, 2022
348e763
Update ref database with CCSD(T)-F12/cc-pVTZ-F12//ωB97X-D3/def2-TZVP
kspieks Feb 1, 2022
b060b5a
Update BACs for CCSD(T)-F12/cc-pVTZ-F12//ωB97X-D3/def2-TZVP
kspieks Feb 1, 2022
1106d86
Merge pull request #563 from ReactionMechanismGenerator/update_BAC
xiaoruiDong Feb 25, 2022
3c979b5
Added Matt's tree fitting notebook, as provided in Slack
mjohnson541 Jun 7, 2021
ce28e40
Fitting notebook: removed Matt's hard-coded paths.
rwest Jun 10, 2021
f57bfb0
Tree fitting: change settings per Matt's recommendation in Developer …
rwest Jun 14, 2021
5b2e48a
Minor: remove unused imports
kspieks Jun 21, 2021
e04c324
Merge pull request #490 from ReactionMechanismGenerator/treegennotebook
mjohnson541 Feb 28, 2022
7b6f8c8
Add Nitrogen groups to transport
yunsiechung Feb 28, 2022
3a87fc3
tree generation for Birad_recombination
mjohnson541 Jan 22, 2021
a26c6c3
remove data_mean that master doesn't have yet
mjohnson541 Jan 22, 2021
b28593a
fix keywords
mjohnson541 Jan 22, 2021
03ff129
Merge pull request #452 from ReactionMechanismGenerator/Birad_recombi…
mjohnson541 Mar 2, 2022
70470ac
Add 1D rotor scans to thermo library
kspieks Mar 9, 2022
1dff3d2
Refit ketoenol rate rules
kspieks Mar 9, 2022
e118363
Refit 1,3 sigmatropic rearrangement rate rules
kspieks Mar 9, 2022
eaf7c1a
Merge pull request #565 from ReactionMechanismGenerator/rotor_scans
xiaoruiDong Mar 9, 2022
8f0d574
Add species to thermo library
kspieks Mar 18, 2022
e51f10a
Add ketoenol training reactions
kspieks Mar 18, 2022
ea365c7
Refit ketoenol rate rules
kspieks Mar 18, 2022
6471dcb
Merge pull request #568 from ReactionMechanismGenerator/ketoenol_trai…
xiaoruiDong Mar 23, 2022
e2ee69f
change units from mole to mol
sevyharris Nov 9, 2021
9bafbd6
Merge pull request #547 from ReactionMechanismGenerator/fix_units_typ…
xiaoruiDong Mar 28, 2022
09d6ea6
tree generation for CO_Disproportionation
sevyharris Nov 30, 2021
9f17b5b
refitted family tree
sevyharris Mar 28, 2022
344e5cd
Merge pull request #530 from ReactionMechanismGenerator/tree_training…
xiaoruiDong Mar 28, 2022
8161f0c
Add species to thermo library
kspieks Mar 28, 2022
787c73f
Update adj list for p004006
kspieks Mar 28, 2022
b4b31c1
Add more ketoenol training reactions
kspieks Mar 28, 2022
9695c97
Refit ketoenol rate rules
kspieks Mar 28, 2022
7bfdc86
Add 1D rotor scans to thermo library
kspieks Mar 28, 2022
81cfbad
Update values for training reactions
kspieks Mar 28, 2022
638e91a
Refit rate rules
kspieks Mar 28, 2022
74ffecd
Refit 1,3 sigmatropic rearrangement rate rules
kspieks Mar 28, 2022
3c823db
Merge pull request #571 from ReactionMechanismGenerator/more_ketoenol…
xiaoruiDong Mar 30, 2022
23299aa
Merge pull request #574 from ReactionMechanismGenerator/retroene_roto…
xiaoruiDong Mar 30, 2022
c9bf474
Merge pull request #575 from ReactionMechanismGenerator/refit_1,3_sig…
xiaoruiDong Mar 30, 2022
8cc2265
Add thermo library
kspieks Apr 4, 2022
ad50b2a
Intra_R_Add_Endocyclic: update value of training reaction
kspieks Mar 21, 2022
e6453dd
Intra_R_Add_Endocyclic: refit rate rules
kspieks Mar 30, 2022
dee9321
Intra_R_Add_Exocyclic: add training reaction
kspieks Mar 21, 2022
02a58d5
Intra_R_Add_Exocyclic: refit rate rules
kspieks Mar 30, 2022
89564b6
Merge pull request #570 from ReactionMechanismGenerator/eni_1dhr
xiaoruiDong Apr 5, 2022
7083943
Add the missing reactant and product number in the intra_R families
xiaoruiDong Apr 12, 2022
986b751
Remove extra labels in the dictionary.py of Intra_R_Add families
xiaoruiDong Apr 13, 2022
52cc322
Merge pull request #576 from ReactionMechanismGenerator/fix_intra_R
xiaoruiDong Apr 13, 2022
b826d71
HO2_Elimination_from_PeroxyRadical tree fitted
yunsiechung Jun 7, 2021
0bcfbc9
1+2_Cycloaddition tree fitting
yunsiechung Jun 7, 2021
27f8e89
1,2-Birad_to_alkene tree fitting
yunsiechung Jun 7, 2021
274c76a
Set autoGenerated=True in the groups.py
yunsiechung Jun 21, 2021
1b93982
1,2_Insertion_CO tree fitting
yunsiechung Jun 21, 2021
1cb2109
1,2_Insertion_carbene tree fitting (affected by Halogen Kinetics)
yunsiechung Jun 21, 2021
8d5dd13
1,2_shiftC tree fitting
yunsiechung Jun 21, 2021
27a1213
1,3_Insertion_CO2 tree fitting
yunsiechung Jul 19, 2021
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added Cl_Abstraction family with autogen tree
davidfarinajr committed Oct 7, 2021
commit 94df9e794b41c824d87bf4aa49600e52cae388ce
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