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Unimol kinetics #164

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4e48fa3
Add labels to backbone atoms of intra_OH_migration groups
nyee Jan 3, 2017
795d3cf
Made all backbone end subgraphs isomorphic to general end group Y_rad…
nyee Jan 6, 2017
991ce66
Add labels for backbone between end groups in Intra_Disproportionation
nyee Jan 6, 2017
6ed75e7
Add backbones labels and standardized end groups for Birad_recombinat…
nyee Jan 6, 2017
2cae572
Standardized use of rad_add_intra in backbones of Intra_RH_Add_Endocy…
nyee Jan 9, 2017
053a96e
Add backbone labels for Cyclic_Ether_Formation
nyee Jan 10, 2017
ba29122
Added tree to Cyclic_Ether_Formation so that it follows backbone;end;…
nyee Jan 10, 2017
08c6e0d
Removed extra labels from Y_rad_intra end group of Cyclic_Ether_Forma…
nyee Jan 10, 2017
d38a39e
Standardized end groups on backbones to be general for Cyclic_Ether_F…
nyee Jan 10, 2017
9bd566b
Removed a top level OR end group and replaced it with its only child
nyee Jan 10, 2017
856ff2a
intra_H_migration database reorganization, too specific backbone grou…
mjohnson541 Feb 7, 2017
5cf298f
improve atomtyping and labeling in intrasubstitutionCS_cyclization
mjohnson541 Feb 7, 2017
7896c7c
intra_substitutionCS_isomerization fixing, removed extraneous labels,…
mjohnson541 Feb 7, 2017
8a28b29
reorganization of intra_substitutionCS_cyclization removal of redunda…
mjohnson541 Feb 14, 2017
455754b
reorganization of intra_substitutionCS_isomerization removal of redun…
mjohnson541 Feb 14, 2017
f3b80cb
intra_substitutionS_cyclization, removed extraneous labels, changed *…
mjohnson541 Feb 7, 2017
86b12ce
intra_substitutionS_isomerization fixes, removed extraneous labels, r…
mjohnson541 Feb 7, 2017
78df3ea
reorganization of intra_substitutionS_isomerization removal of redund…
mjohnson541 Feb 14, 2017
8eb80d1
Change top level node S-RR to use *2R!H in intra_substitutionS_cycliz…
mjohnson541 Feb 7, 2017
ca6e614
Added in Nitrogen to the *2 and *3 options in the backbone, eliminate…
mjohnson541 Feb 9, 2017
39a8723
Intra_R_Add_ExoTetCyclic fixes, removed Cs/O entries related tot eh *…
mjohnson541 Feb 9, 2017
4a5ee14
Inra_R_Add_Endocyclic fixes, Generalized the doublebond_intra *2 and …
mjohnson541 Feb 9, 2017
560356d
Intra_RH_Add_Exocyclic fixes, removed extraneous labels, removed all …
mjohnson541 Feb 10, 2017
b5d3234
Reorganization of the Ketoenol group
mjohnson541 Feb 10, 2017
76407af
Add 'boundaryAtom' attribute to all unimolecular families
nyee Feb 19, 2017
df78915
addition of a database test for unimolecular groups having multiple t…
mjohnson541 Feb 13, 2017
f1f42ee
reorganization of the intra_substitutionS_cyclization group to meet t…
mjohnson541 Feb 14, 2017
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214 changes: 104 additions & 110 deletions input/kinetics/families/1,2_shiftS/groups.py
Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,8 @@
['LOSE_RADICAL', '*3', '1'],
])

boundaryAtoms = ["*1", "*3"]

entry(
index = 1,
label = "XSYJ",
Expand All @@ -40,13 +42,6 @@
kinetics = None,
)

entry(
index = 3,
label = "X-Ss",
group = "OR{C-Ss}",
kinetics = None,
)

entry(
index = 4,
label = "CJ-Ss",
Expand Down Expand Up @@ -1572,109 +1567,108 @@
L5: CsJ-SsOneDeSs
L6: CsJ-SsCdSs
L2: SJ-Ss
L1: X-Ss
L2: C-Ss
L3: Cb-Ss
L3: Ct-Ss
L3: Cds-Ss
L4: Cds-SsH
L4: Cds-SsCs
L4: Cds-SsCt
L4: Cds-SsCb
L4: Cds-SsCO
L4: Cds-SsOs
L4: Cds-SsSs
L4: Cds-SsCd
L4: Cds-SsC=S
L3: C=S-Ss
L4: C=S-SsH
L4: C=S-SsCs
L4: C=S-SsCt
L4: C=S-SsCb
L4: C=S-SsCO
L4: C=S-SsOs
L4: C=S-SsSs
L4: C=S-SsCd
L4: C=S-SsC=S
L3: Cs-Ss
L4: Cs-SsHHH
L4: Cs-SsCsHH
L4: Cs-SsCsCsH
L4: Cs-SsCsCsCs
L4: Cs-SsOsHH
L4: Cs-SsOsCsH
L4: Cs-SsOsCsCs
L4: Cs-SsOsOsH
L4: Cs-SsOsOsCs
L4: Cs-SsOsOsOs
L4: Cs-SsSsHH
L4: Cs-SsSsCsH
L4: Cs-SsSsCsCs
L4: Cs-SsSsSsH
L4: Cs-SsSsSsCs
L4: Cs-SsSsSsSs
L4: Cs-SsOneDe
L5: Cs-SsOneDeHH
L6: Cs-SsCtHH
L6: Cs-SsCbHH
L6: Cs-SsCOHH
L6: Cs-SsCdHH
L6: Cs-SsC=SHH
L5: Cs-SsOneDeCsH
L6: Cs-SsCtCsH
L6: Cs-SsCbCsH
L6: Cs-SsCOCsH
L6: Cs-SsCdCsH
L6: Cs-SsC=SCsH
L5: Cs-SsOneDeOsH
L5: Cs-SsOneDeSsH
L5: Cs-SsOneDeCsCs
L6: Cs-SsCtCsCs
L6: Cs-SsCbCsCs
L6: Cs-SsCOCsCs
L6: Cs-SsCdCsCs
L6: Cs-SsC=SCsCs
L5: Cs-SsOneDeOsCs
L5: Cs-SsOneDeSsCs
L5: Cs-SsOneDeOsOs
L5: Cs-SsOneDeOsSs
L5: Cs-SsOneDeSsSs
L4: Cs-SsTwoDe
L5: Cs-SsTwoDeH
L6: Cs-SsCtCtH
L6: Cs-SsCtCbH
L6: Cs-SsCtCOH
L6: Cs-SsCbCbH
L6: Cs-SsCbCOH
L6: Cs-SsCOCOH
L6: Cs-SsCdCtH
L6: Cs-SsCdCbH
L6: Cs-SsCdCOH
L6: Cs-SsCtC=SH
L6: Cs-SsCbC=SH
L6: Cs-SsCOC=SH
L6: Cs-SsCdCdH
L6: Cs-SsCdC=SH
L6: Cs-SsC=SC=SH
L5: Cs-SsTwoDeCs
L6: Cs-SsCtCtCs
L6: Cs-SsCtCbCs
L6: Cs-SsCtCOCs
L6: Cs-SsCbCbCs
L6: Cs-SsCbCOCs
L6: Cs-SsCOCOCs
L6: Cs-SsCdCtCs
L6: Cs-SsCdCbCs
L6: Cs-SsCdCOCs
L6: Cs-SsCtC=SCs
L6: Cs-SsCbC=SCs
L6: Cs-SsCOC=SCs
L6: Cs-SsCdCdCs
L6: Cs-SsCdC=SCs
L6: Cs-SsC=SC=SCs
L5: Cs-SsTwoDeOs
L5: Cs-SsTwoDeSs
L4: Cs-SsThreeDe
L1: C-Ss
L2: Cb-Ss
L2: Ct-Ss
L2: Cds-Ss
L3: Cds-SsH
L3: Cds-SsCs
L3: Cds-SsCt
L3: Cds-SsCb
L3: Cds-SsCO
L3: Cds-SsOs
L3: Cds-SsSs
L3: Cds-SsCd
L3: Cds-SsC=S
L2: C=S-Ss
L3: C=S-SsH
L3: C=S-SsCs
L3: C=S-SsCt
L3: C=S-SsCb
L3: C=S-SsCO
L3: C=S-SsOs
L3: C=S-SsSs
L3: C=S-SsCd
L3: C=S-SsC=S
L2: Cs-Ss
L3: Cs-SsHHH
L3: Cs-SsCsHH
L3: Cs-SsCsCsH
L3: Cs-SsCsCsCs
L3: Cs-SsOsHH
L3: Cs-SsOsCsH
L3: Cs-SsOsCsCs
L3: Cs-SsOsOsH
L3: Cs-SsOsOsCs
L3: Cs-SsOsOsOs
L3: Cs-SsSsHH
L3: Cs-SsSsCsH
L3: Cs-SsSsCsCs
L3: Cs-SsSsSsH
L3: Cs-SsSsSsCs
L3: Cs-SsSsSsSs
L3: Cs-SsOneDe
L4: Cs-SsOneDeHH
L5: Cs-SsCtHH
L5: Cs-SsCbHH
L5: Cs-SsCOHH
L5: Cs-SsCdHH
L5: Cs-SsC=SHH
L4: Cs-SsOneDeCsH
L5: Cs-SsCtCsH
L5: Cs-SsCbCsH
L5: Cs-SsCOCsH
L5: Cs-SsCdCsH
L5: Cs-SsC=SCsH
L4: Cs-SsOneDeOsH
L4: Cs-SsOneDeSsH
L4: Cs-SsOneDeCsCs
L5: Cs-SsCtCsCs
L5: Cs-SsCbCsCs
L5: Cs-SsCOCsCs
L5: Cs-SsCdCsCs
L5: Cs-SsC=SCsCs
L4: Cs-SsOneDeOsCs
L4: Cs-SsOneDeSsCs
L4: Cs-SsOneDeOsOs
L4: Cs-SsOneDeOsSs
L4: Cs-SsOneDeSsSs
L3: Cs-SsTwoDe
L4: Cs-SsTwoDeH
L5: Cs-SsCtCtH
L5: Cs-SsCtCbH
L5: Cs-SsCtCOH
L5: Cs-SsCbCbH
L5: Cs-SsCbCOH
L5: Cs-SsCOCOH
L5: Cs-SsCdCtH
L5: Cs-SsCdCbH
L5: Cs-SsCdCOH
L5: Cs-SsCtC=SH
L5: Cs-SsCbC=SH
L5: Cs-SsCOC=SH
L5: Cs-SsCdCdH
L5: Cs-SsCdC=SH
L5: Cs-SsC=SC=SH
L4: Cs-SsTwoDeCs
L5: Cs-SsCtCtCs
L5: Cs-SsCtCbCs
L5: Cs-SsCtCOCs
L5: Cs-SsCbCbCs
L5: Cs-SsCbCOCs
L5: Cs-SsCOCOCs
L5: Cs-SsCdCtCs
L5: Cs-SsCdCbCs
L5: Cs-SsCdCOCs
L5: Cs-SsCtC=SCs
L5: Cs-SsCbC=SCs
L5: Cs-SsCOC=SCs
L5: Cs-SsCdCdCs
L5: Cs-SsCdC=SCs
L5: Cs-SsC=SC=SCs
L4: Cs-SsTwoDeOs
L4: Cs-SsTwoDeSs
L3: Cs-SsThreeDe
"""
)

2 changes: 1 addition & 1 deletion input/kinetics/families/1,2_shiftS/rules.py
Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@
"""
entry(
index = 1,
label = "XSYJ;YJ-Ss;X-Ss",
label = "XSYJ;YJ-Ss;C-Ss",
kinetics = ArrheniusEP(
A = (1e+08, 's^-1'),
n = 2,
Expand Down
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