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Tree fitting for several rxn families #485

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Tree fitting for several rxn families #485

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@yunsiechung yunsiechung commented Jun 7, 2021 •
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The trees for the following reaction families are fitted using Matt's code:

  • HO2_Elimination_from_PeroxyRadical
  • 1+2_Cycloaddition
  • 1,2-Birad_to_alkene
  • 1,2_Insertion_CO
  • 1,2_Insertion_carbene (this family will be affected by Halogen Kinetics, so only groups.py and rules.py files have been added)
  • 1,2_shiftC

@yunsiechung yunsiechung force-pushed the tree_fitting_yunsie branch 2 times, most recently from 116587a to 083cbfe Compare June 21, 2021 16:40
@yunsiechung yunsiechung changed the title Tree fitting for 3 rxn families Tree fitting for several rxn families Jul 19, 2021
@davidfarinajr
added F_Abstraction family with autogen tree
31241b6
@davidfarinajr
added Cl_Abstraction family with autogen tree
94df9e7
@davidfarinajr
added Br_Abstraction family with autogen tree
22dde3c
@davidfarinajr
added XY_Addition_MulitpleBond with autogen tree
b8a7b7d
@davidfarinajr
added 1,2_XY_interchange family
425c063
@davidfarinajr
added Disproportionation-Y family with autogen tree
30c6df2
@davidfarinajr
added halogen kinetic libraries
67428b3
@davidfarinajr
added halogen families to halogens folder in recommended.py
fd31c46
@davidfarinajr
added chemdraw templates for new halogen families
53f7678
@davidfarinajr
added Surface_Adsorption_Dissociative_Double template png
2549e74
@davidfarinajr
added halogen families to rmg_reaction_families.pdf
447d0ac
@davidfarinajr
added key halogen species to halogens thermo library
5eea095
@davidfarinajr
added halocarbene_recombination reaction family
7ef0958
@davidfarinajr
added halocarbene_recombination_double reaction family
37d132d
@davidfarinajr
added halocarbene_recombination and `halocarbene_recombination_doub…
ffc85d0 
…le` to halogens folder in recommended families
@davidfarinajr
added chemdraw templates for halocarbene families
d0bf35d
@davidfarinajr
added CF2BrCl kinetics library
39872a9
@davidfarinajr
added CH3Cl kinetics library
c327a2e
@davidfarinajr
commented out reactions with more than 3 products in CH3Cl kinetics l…
4bd1dfc 
…ibrary
@davidfarinajr
renamed identical species in CF2BrCl kinetics library
43e89ad
@davidfarinajr
commented out excited CH* and OH* reactions in CF2BrCl kinetics library
f33e3bd
@davidfarinajr
allowed some max rate violators in CF2BrCl kinetics library
8a06514
@davidfarinajr
added F_Abstraction training reactions calculated with autotst
d106c2d
@davidfarinajr
regenerated F Absraction tree with autotst data
6b32435 
regenerated F Abstraction groups and rules with autotst training data
@davidfarinajr
retrained Cl_Abstraction family tree with autotst kinetics
914e7db 
removed imported reactions from literature mechanisms, and added training data from autotst calculations, then regenerated the tree and rules
xiaoruiDong and others added 29 commits March 28, 2022 16:33
@xiaoruiDong
Merge pull request #530 from ReactionMechanismGenerator/tree_training…
344e5cd 
…_co_disproportionation

Tree training co disproportionation
@kspieks
Add species to thermo library
8161f0c
@kspieks
Update adj list for p004006
787c73f
@kspieks
Add more ketoenol training reactions
b4b31c1
@kspieks
Refit ketoenol rate rules
9695c97
@kspieks
Add 1D rotor scans to thermo library
7bfdc86
@kspieks
Update values for training reactions
81cfbad
@kspieks
Refit rate rules
638e91a
@kspieks
Refit 1,3 sigmatropic rearrangement rate rules
74ffecd
@xiaoruiDong
Merge pull request #571 from ReactionMechanismGenerator/more_ketoenol…
3c823db 
…_rxns

More ketoenol rxns
@xiaoruiDong
Merge pull request #574 from ReactionMechanismGenerator/retroene_roto…
23299aa 
…r_scans

Retroene rotor scans
@xiaoruiDong
Merge pull request #575 from ReactionMechanismGenerator/refit_1,3_sig…
c9bf474 
…matropic

Refit 1,3 sigmatropic
@kspieks
Add thermo library
8cc2265 
This library contains species participating in reactions relevant to heavy oil pyrolysis mechanisms
@kspieks
Intra_R_Add_Endocyclic: update value of training reaction
ad50b2a 
This value was previously estimated using group additivity. Now it is calculated with TST after doing conformer search and 1D rotor scans
@kspieks
Intra_R_Add_Endocyclic: refit rate rules
e6453dd
@kspieks
Intra_R_Add_Exocyclic: add training reaction
dee9321
@kspieks
Intra_R_Add_Exocyclic: refit rate rules
02a58d5
@xiaoruiDong
Merge pull request #570 from ReactionMechanismGenerator/eni_1dhr
89564b6 
Refit Intra R Add Endo/Exocyclic Rate Rules
@xiaoruiDong
Add the missing reactant and product number in the intra_R families
7083943
@xiaoruiDong
Remove extra labels in the dictionary.py of Intra_R_Add families
986b751
@xiaoruiDong
Merge pull request #576 from ReactionMechanismGenerator/fix_intra_R
52cc322 
Add the missing reactant and product number in the intra_R_Add families
@yunsiechung
HO2_Elimination_from_PeroxyRadical tree fitted
b826d71
@yunsiechung
1+2_Cycloaddition tree fitting
0bcfbc9
@yunsiechung
1,2-Birad_to_alkene tree fitting
27f8e89
@yunsiechung
Set autoGenerated=True in the groups.py
274c76a
@yunsiechung
1,2_Insertion_CO tree fitting
1b93982
@yunsiechung
1,2_Insertion_carbene tree fitting (affected by Halogen Kinetics)
1cb2109 
This family will be affected by Halogen Kinetics, so only groups.py and
rules.py files have been added.
@yunsiechung
1,2_shiftC tree fitting
8d5dd13
@yunsiechung
1,3_Insertion_CO2 tree fitting
27a1213
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@mjohnson541 mjohnson541 Awaiting requested review from mjohnson541

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