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faribas wants to merge 172 commits into from
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New Ring opening/closing reaction classes #40

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fc0e4e9
Extending thermochemistry library thermo_DFT_CCSDTF12_BAC
bbuesser Dec 11, 2013
1003743
Extending thermochemistry library thermo_DFT_CCSDTF12_BAC
bbuesser Dec 13, 2013
643f9f5
Extending thermochemistry library thermo_DFT_CCSDTF12_BAC
bbuesser Dec 15, 2013
d6f57b4
Update thermochemistry library primaryThermoLibrary
bbuesser Dec 15, 2013
d84cecc
Update thermochemistry library primaryThermoLibrary
bbuesser Dec 16, 2013
5942f0b
New Entry: R_Recombination/training/
bbuesser Dec 18, 2013
4d16be7
New Entry: R_Recombination/training/
bbuesser Dec 18, 2013
81cdb83
New Entry: R_Recombination/training/
bbuesser Dec 18, 2013
51237e4
Extending thermochemistry library thermo_DFT_CCSDTF12_BAC
bbuesser Dec 18, 2013
35f3155
update tree of intra_NO2_ONO_conversion
bbuesser Dec 18, 2013
b344e64
Extending thermochemistry library thermo_DFT_CCSDTF12_BAC
bbuesser Dec 19, 2013
11d94c6
Extending thermochemistry library thermo_DFT_CCSDTF12_BAC
bbuesser Dec 19, 2013
23f1300
Extending thermochemistry library thermo_DFT_CCSDTF12_BAC
bbuesser Dec 19, 2013
5b5fe0f
1,2_Insertion; add nitrogen to top node
bbuesser Dec 19, 2013
0ad5368
1,3_Insertion_CO2; add nitrogen to top node
bbuesser Dec 19, 2013
247983a
1,3_Insertion_ROR; add nitrogen to top node
bbuesser Dec 19, 2013
6ba8838
1+2_Cycloaddition; add nitrogen groups
bbuesser Dec 19, 2013
440f506
Birad_recombination; add nitrogen to top nodes
bbuesser Dec 19, 2013
f9113d7
Cyclic_Ether_Formation; add nitrogen to top nodes
bbuesser Dec 19, 2013
134215c
HO2_Elimination_From_PeroxyRadical; add nitrogen to top node
bbuesser Dec 19, 2013
1b888cb
intra_OH_migration; add nitrogen to top nodes
bbuesser Dec 19, 2013
9cb521a
Intra_R_Add_Endocyclic; add nitrogen to top nodes
bbuesser Dec 19, 2013
063088d
Intra_R_Add_Exocyclic; add nitrogen to top nodes
bbuesser Dec 19, 2013
53dd69d
update Intra_R_Add_Endocyclic reverse
bbuesser Dec 19, 2013
bee01be
update Intra_R_Add_Exocyclic reverse
bbuesser Dec 19, 2013
442e1e8
update intra_OH_migration
bbuesser Dec 19, 2013
798b01b
update kinetics library Nitrogen_Dean_and_Bozzelli.py
bbuesser Dec 20, 2013
0e85a37
New Entry: R_Recombination/training/
bbuesser Dec 20, 2013
94a6e52
New Entry: R_Recombination/training/
bbuesser Dec 20, 2013
3fb6f01
Add tri-radical top-node to statmech groups
bbuesser Feb 4, 2014
eec6dd8
Changing ä to a in Aäron Vandeputte's name due to encoding problems.
connie Feb 6, 2014
3d1bdb7
Removing duplicates from Dean and Bozelli library
shamelmerchant Feb 7, 2014
07f2461
Updated output folder to RMG-Java at commit bb21002
connie Feb 6, 2014
86952ba
Updated kinetic libraries with adjlists containing paired electrons (…
connie Feb 6, 2014
12d28da
Updating thermo libraries with new adjlists.
connie Feb 6, 2014
7894310
Fixes to adjlists in DFT_QCI_Thermo. Commented out cis-butene.
connie Feb 11, 2014
a78f14a
Commented out GRI-Mech3.0 version of OH in primaryThermoLibrary. Use …
connie Feb 11, 2014
75abafd
Delete Nitrogen_Dean_and_Bozzelli.py
bbuesser Feb 11, 2014
aa34eb4
Rename Nitrogen_Dean_and_Bozelli.py to Nitrogen_Dean_and_Bozzelli.py
bbuesser Feb 11, 2014
61bd7c4
Remove duplicate from thermo libraries
bbuesser Feb 11, 2014
3033d7f
Adding Thermo for alpha radical from ethylamine
shamelmerchant Feb 12, 2014
e30619a
Adding HBI for Carbon centered radical with neighboring N atom.
shamelmerchant Feb 12, 2014
65c3ce0
Correcting typos in previous commits!
shamelmerchant Feb 12, 2014
940b386
More fixes to the last commit
shamelmerchant Feb 13, 2014
bb55a40
Adding thermo for more radicals formed from ethylamine
shamelmerchant Feb 13, 2014
39b45c0
Accomodate both 2T and 2S in Ybirad for SubstitutionO group.
connie Feb 13, 2014
936dd26
Manual merge of RMG-Java 8ce558. New Family 1,4_Cyclic_birad_scissio…
connie Feb 17, 2014
cbac951
Manual merge of RMG-Java 8ce558. New Family 1,4_Linear_birad_scissio…
connie Feb 17, 2014
0760775
Manual merge of RMG-Java 8ce558. New Family Intra_Diels_alder added.
connie Feb 17, 2014
a45dad4
Manual merge of RMG-Java 8ce558. New Family ketoenol added.
connie Feb 17, 2014
acc3d68
Manual merge of RMG-Java 8ce558. 'Ring' thermo groups updated.
connie Feb 17, 2014
eb65d46
Manual merge of RMG-Java 8ce558. 'Radical' thermo groups updated with…
connie Feb 17, 2014
5bf063b
Manual merge of RMG-Java 8ce558. 'Polycyclic' thermo groups updated.
connie Feb 17, 2014
d231b97
Manual merge of RMG-Java 8ce558. 'Group' thermo groups updated.
connie Feb 17, 2014
4d86473
Manual merge of RMG-Java 8ce558. Cyclic_Ether_Formation family updated.
connie Feb 17, 2014
b40c05e
Manual merge of RMG-Java 8ce558. 1,2_Insertion updated.
connie Feb 17, 2014
b9f6d77
Manual merge of RMG-Java 8ce558. HO2_Elimination_from_PeroxyRadical f…
connie Feb 17, 2014
e55fed5
Manual merge of RMG-Java 8ce558. 1,3_Insertion_CO2 family updated.
connie Feb 17, 2014
d6177bb
Manual merge of RMG-Java 8ce558. 1,3_Insertion_RSR family updated.
connie Feb 17, 2014
00c100c
Manual merge of RMG-Java 8ce558. 1,3_Insertion_ROR family updated.
connie Feb 17, 2014
c13995a
Manual merge of RMG-Java 8ce558. 1+2_Cycloaddition family updated.
connie Feb 17, 2014
52619d8
Manual merge of RMG-Java 8ce558. SubstitutionS family updated.
connie Feb 17, 2014
64abf63
Manual merge of RMG-Java 8ce558. Intra_Disproportionation family upda…
connie Feb 17, 2014
1f8db03
Manual merge of RMG-Java 8ce558. Intra_R_Add_Exocyclic family updated.
connie Feb 17, 2014
5b54d7e
Manual merge of RMG-Java 8ce558. Intra_R_Add_Endocyclic family updated.
connie Feb 17, 2014
74b2b58
Manual merge of RMG-Java 8ce558. R_Recombination family updated.
connie Feb 17, 2014
10fe88e
Manual merge of RMG-Java 8ce558. Diels_alder_addition family updated.
connie Feb 17, 2014
3be2b39
Manual merge of RMG-Java 8ce558. intra_H_migration family updated.
connie Feb 17, 2014
c98e9b5
Manual merge of RMG-Java 8ce558. H_Abstraction family updated.
connie Feb 17, 2014
e997da9
Manual merge of RMG-Java 8ce558. R_Addition_MultipleBond family updated.
connie Feb 17, 2014
3757db1
Change Ns group to N3s,N5s in R_Addition_MultipleBond family.
connie Feb 17, 2014
235c4b1
Fix indentations in tree for R_Addition_MultipleBond family.
connie Feb 17, 2014
c94e311
Add missing nitrogen groups Nt_R and N5d_R to the R_Addition_Multiple…
connie Feb 17, 2014
8f691d5
Kicked out N5d_R and N5J from R_Addition_MultipleBond groups.
connie Feb 17, 2014
c6c6e84
Fix Y_1centerbirad group in H_Abstraction family.
connie Feb 17, 2014
2e711b5
Forbid carbene triplet form in 1+2_Cycloaddition family.
connie Feb 17, 2014
f8196d5
Change all carbon atoms to 4T triplet state.
connie Feb 17, 2014
dacf420
Add CO,CS, and N to H_Abstraction family Y_1centerbirad group.
connie Feb 17, 2014
ce42015
Updating Dean and Bozzelli librray with PLOGs
shamelmerchant Feb 18, 2014
0d13efb
Add EvaluateKinetics.py
nyee Feb 18, 2014
5cdcfa0
Remove duplicate from Thermo SulfurLibrary
nyee Feb 18, 2014
b921c97
Convert some thermo libraries to 4 column adjlist
nyee Feb 21, 2014
bda8760
Reordering the intra H migration tree. Update to RMG-Java commit 2d57f8
connie Feb 21, 2014
5f673e5
Added reverse to Intra_Diels_alder family. Mirror of RMG-Java f599b3…
connie Feb 23, 2014
10f8b24
Removal of duplicate group in intra_H_migration family. Mirror of RMG…
connie Feb 23, 2014
69169af
Database clean up
nyee Feb 24, 2014
f8c76fa
Fixed more history on groups and libraries
nyee Feb 25, 2014
395eb73
Convert kinetic libraries to give 4-column adjlist
nyee Feb 25, 2014
936b265
Update adjacency lists to 4 column format
bbuesser Feb 26, 2014
42a699f
Update adjacency lists to 4 column format in PrimaryTransportLibrary
bbuesser Feb 26, 2014
74ac9ec
Update adjacency list in GRI-Mech transport library
bbuesser Feb 26, 2014
0e2c92b
Cyclic_Ether_Formation: Update adjacency list with explicit lone pairs
bbuesser Feb 27, 2014
51507ec
H_abstraction: Update adjacency list with explicit lone pairs
bbuesser Feb 27, 2014
d3f90ba
HO2_Elimination_from_PeroxyRadical: Update adjacency list with explicit
bbuesser Feb 27, 2014
2db9412
intra_H_migration: Update adjacency list with explicit lone pairs
bbuesser Feb 27, 2014
95dbf83
R_Addition_MultipleBond: Update adjacency list with explicit lone pairs
bbuesser Feb 27, 2014
189d665
R_Recombination: Update adjacency list with explicit lone pairs
bbuesser Feb 27, 2014
e48e9c3
Cyclic_Ether_Formation: C#O and update adjacency list with explicit lone
bbuesser Feb 27, 2014
6badab7
combuction_core version2: Update carbon monoxide to C#O
bbuesser Feb 27, 2014
08cf87f
combuction_core version3: Update carbon monoxide to C#O
bbuesser Feb 27, 2014
15786ea
combuction_core version4: Update carbon monoxide to C#O
bbuesser Feb 27, 2014
83e7dbe
combuction_core version5: Update carbon monoxide to C#O
bbuesser Feb 27, 2014
72bd1aa
Dooley C1: Update carbon monoxide to C#O
bbuesser Feb 27, 2014
0d9641a
methylformate_2: Update carbon monoxide to C#O
bbuesser Feb 27, 2014
d454fa5
Dooley methylformate_all_ARHEbathgas: Update carbon monoxide to C#O
bbuesser Feb 27, 2014
0593222
Dooley methylformate_all_N2bathgas: Update carbon monoxide to C#O
bbuesser Feb 27, 2014
dea37f0
methylformate: Update carbon monoxide to C#O
bbuesser Feb 27, 2014
59218ff
Glarborg C1: Update carbon monoxide to C#O
bbuesser Feb 27, 2014
bb9cc46
Glarborg C2: Update carbon monoxide to C#O
bbuesser Feb 27, 2014
8c9b122
Glarborg C2: Update carbon monoxide to C#O
bbuesser Feb 27, 2014
1dc2750
Glarborg highP: Update carbon monoxide to C#O
bbuesser Feb 27, 2014
4739902
Hexanethial: Update carbon monoxide to C#O
bbuesser Feb 27, 2014
1df2049
ERC-FoundationFuelv0.9: Update carbon monoxide to C#O
bbuesser Feb 27, 2014
f2acb51
GRI-HCO: Update carbon monoxide to C#O
bbuesser Feb 27, 2014
11a0ea1
GRI-Mech3.0: Update carbon monoxide to C#O
bbuesser Feb 27, 2014
9287222
GRI-Mech3.0-N: Update carbon monoxide to C#O
bbuesser Feb 27, 2014
2fbb3c8
Methylformate: Update carbon monoxide to C#O
bbuesser Feb 27, 2014
7d42035
Nitrogen_Dean_and_Bozzelli: Update carbon monoxide to C#O
bbuesser Feb 27, 2014
42b877e
Nitrogen_Glarborg_Gimenez_et_al: Update carbon monoxide to C#O
bbuesser Feb 27, 2014
daaf163
Nitrogen_Glarborg_Lucassen_et_al: Update carbon monoxide to C#O
bbuesser Feb 27, 2014
26a65a8
Nitrogen_Glarborg_Zhang_et_al: Update carbon monoxide to C#O
bbuesser Feb 27, 2014
f7906c9
Replace standard brackets () with curly brackets {} in adjacency lists
bbuesser Feb 27, 2014
1035fa3
DFT_QCI_thermo: Update carbon monoxide to C#O
bbuesser Feb 27, 2014
b2e8ee7
GRI-Mech3.0: Update carbon monoxide to C#O
bbuesser Feb 27, 2014
451eec7
GRI-Mech3.0-N: Update carbon monoxide to C#O
bbuesser Feb 27, 2014
fb42360
KlippensteinH2O2: Update carbon monoxide to C#O
bbuesser Feb 27, 2014
0e28d9d
thermo_DFT_CCSDTF12_BAC: Update carbon monoxide to C#O
bbuesser Feb 27, 2014
16a532c
USC-Mech_ii: Update carbon monoxide to C#O
bbuesser Feb 27, 2014
d9aa2a3
GRI-Mech transport: Update carbon monoxide to C#O
bbuesser Feb 27, 2014
d179aa1
PrimaryTransportLibrary: Update carbon monoxide to C#O
bbuesser Feb 27, 2014
e03b421
Add Od_rad to forbiddenStructures
bbuesser Feb 27, 2014
694003d
Correct adjacency list of He in primaryThermoLibrary
bbuesser Feb 27, 2014
e5611b0
Add the structure Ods to forbiddenStructures.py
bbuesser Feb 27, 2014
1a5efe6
Rename the functional element N2d to N1d
bbuesser Feb 27, 2014
53142cb
Fixed typo in combustion core kinetic library
nyee Feb 27, 2014
ff80bd4
Fix misnamed groups in rules
nyee Mar 5, 2014
b8cb73a
Add wrapper for testing database
nyee Mar 17, 2014
777c75e
Add output for checking for unique groups
nyee Mar 28, 2014
1e9f96f
fix AdjList in rules of Intra_R_Add_Exocyclic
nyee Mar 28, 2014
1139e59
Fix child relationships in R_Addition_Csm
nyee Mar 28, 2014
c399546
Fix errors in Disproportionation family
nyee Mar 30, 2014
cc48eba
Remove history fields permanently and clean up empty reference and re…
connie Apr 1, 2014
5907ac1
Remove `recommended` field in databases since they have no functional…
connie Apr 1, 2014
3f16046
Remove rogue git conflict lines in R_Recombination/NIST.py
connie Apr 1, 2014
f8664bf
Add a list of recommended families for setting the 'default' option i…
connie Apr 3, 2014
e3b6d93
Minor fixes to intra_H_migration family
nyee Apr 1, 2014
8ec7b6b
Fix bug with Leave one out test
nyee Apr 1, 2014
c5933ff
Minor corrections to in 1,2 Insertion family
nyee Apr 1, 2014
7116adf
Added suggested solutions to name errors in checkWellFormed
nyee Apr 9, 2014
d3b9a33
Fixes to R_Addition_MultipleBond family
nyee Apr 9, 2014
7c06bad
Fixes to EvaluateKinetics.py database testing script.
rwest Apr 9, 2014
e4fd6b7
More fixes to R_Addition Multiple Bond
nyee Apr 11, 2014
a6f2a44
Removed biradical singlets from R_MultipleBond Addition
nyee Apr 11, 2014
37a1659
Fixes to rule adj lists in Intra_R_Add_Endocyclic
nyee Apr 11, 2014
78f0737
Fixes to group definitions in Intra_R_Add_Endocylic
nyee Apr 14, 2014
c4f87aa
Fixes to Disproportionation family
nyee Apr 14, 2014
9f2b6b4
Fixes to adjLists of 1,3_Insertion_RSR
nyee Apr 14, 2014
edaad23
Fixes to R_Addition_CSm using checkWellFormed
nyee May 9, 2014
c07e367
Fix errors in 1,2_Insertion found with databaseTester
nyee May 9, 2014
9be284f
Fixes to H-Abstraction family: Part 1
nyee May 12, 2014
d1a85bb
Fixes to H-Abstraction: Part 2
nyee May 12, 2014
3825fc1
Fixes to Intra_substitutionCS_cyclization family
connie May 23, 2014
3a59507
Fixes to intra_substitutionS_cyclization family
connie May 23, 2014
dd06b43
Fixes to intra_substitutionCS_isomerization family
connie May 23, 2014
39e6b61
Fixes to Intra_substitutionS_isomerization family
connie May 23, 2014
74ad2b0
Fixes to R_Addition_COm family
connie May 26, 2014
b0340d8
Fixes to Birad_recombination family
connie May 26, 2014
68f0c79
Fixes to lone_electron_pair_bond
connie May 26, 2014
7418f80
Fixes to HO2_Elimination_from_PeroxyRadical family
connie May 26, 2014
9adc87f
Change Disproportionation training rxn to Arrhenius rather than Arrhe…
connie May 27, 2014
783549a
Updated RMG-database with three new reaction families for ring openin…
faribas Jun 13, 2014
5118859
Deleting some history comments!
faribas Jun 13, 2014
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511 changes: 511 additions & 0 deletions EvaluateKinetics.py
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84 changes: 29 additions & 55 deletions input/forbiddenStructures.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,35 @@
longDesc = u"""

"""
recommended = False

entry(
label = "Ods",
group =
"""
1 O {0,1,2,3,4} {2,D} {3,S}
2 R {0,1,2,3,4} {1,D}
3 R {0,1,2,3,4} {1,S}
""",
shortDesc = u"""""",
longDesc =
u"""

""",
)

entry(
label = "Od_rad",
group =
"""
1 O 1 {2,D}
2 R {0,1,2,3,4} {1,D}
""",
shortDesc = u"""""",
longDesc =
u"""

""",
)

entry(
label = "N_birad_RsRsRs",
Expand All @@ -22,9 +50,6 @@
u"""

""",
history = [
("Mon Nov 18 12:27:50 2013","Beat Buesser <[email protected]>","action","""Beat Buesser <[email protected]> created this entry."""),
],
)

entry(
Expand All @@ -40,9 +65,6 @@
u"""

""",
history = [
("Mon Nov 18 12:27:50 2013","Beat Buesser <[email protected]>","action","""Beat Buesser <[email protected]> created this entry."""),
],
)

entry(
Expand All @@ -56,9 +78,6 @@
u"""

""",
history = [
("Mon Nov 18 12:27:50 2013","Beat Buesser <[email protected]>","action","""Beat Buesser <[email protected]> created this entry."""),
],
)

entry(
Expand All @@ -73,9 +92,6 @@
u"""

""",
history = [
("Mon Nov 18 12:27:50 2013","Beat Buesser <[email protected]>","action","""Beat Buesser <[email protected]> created this entry."""),
],
)

entry(
Expand Down Expand Up @@ -106,9 +122,6 @@
u"""

""",
history = [
("Thu Nov 15 12:27:50 2012","Josh Allen <[email protected]>","action","""Josh Allen <[email protected]> imported this entry from the old RMG database."""),
],
)

entry(
Expand Down Expand Up @@ -139,9 +152,6 @@
u"""

""",
history = [
("Thu Nov 15 12:27:50 2012","Josh Allen <[email protected]>","action","""Josh Allen <[email protected]> imported this entry from the old RMG database."""),
],
)

entry(
Expand All @@ -156,9 +166,6 @@
u"""

""",
history = [
("Thu Nov 15 12:27:50 2012","Josh Allen <[email protected]>","action","""Josh Allen <[email protected]> imported this entry from the old RMG database."""),
],
)

entry(
Expand All @@ -173,9 +180,6 @@
u"""

""",
history = [
("Thu Nov 15 12:27:50 2012","Josh Allen <[email protected]>","action","""Josh Allen <[email protected]> imported this entry from the old RMG database."""),
],
)

entry(
Expand All @@ -191,9 +195,6 @@
u"""

""",
history = [
("Thu Nov 15 12:27:50 2012","Josh Allen <[email protected]>","action","""Josh Allen <[email protected]> imported this entry from the old RMG database."""),
],
)

entry(
Expand All @@ -209,9 +210,6 @@
u"""

""",
history = [
("Thu Nov 15 12:27:50 2012","Josh Allen <[email protected]>","action","""Josh Allen <[email protected]> imported this entry from the old RMG database."""),
],
)

entry(
Expand All @@ -227,9 +225,6 @@
u"""

""",
history = [
("Thu Nov 15 12:27:50 2012","Josh Allen <[email protected]>","action","""Josh Allen <[email protected]> imported this entry from the old RMG database."""),
],
)

entry(
Expand All @@ -246,9 +241,6 @@
u"""

""",
history = [
("Thu Nov 15 12:27:50 2012","Josh Allen <[email protected]>","action","""Josh Allen <[email protected]> imported this entry from the old RMG database."""),
],
)

entry(
Expand All @@ -265,9 +257,6 @@
u"""

""",
history = [
("Thu Nov 15 12:27:50 2012","Josh Allen <[email protected]>","action","""Josh Allen <[email protected]> imported this entry from the old RMG database."""),
],
)

entry(
Expand All @@ -284,9 +273,6 @@
u"""

""",
history = [
("Thu Nov 15 12:27:50 2012","Josh Allen <[email protected]>","action","""Josh Allen <[email protected]> imported this entry from the old RMG database."""),
],
)

entry(
Expand All @@ -302,9 +288,6 @@
u"""

""",
history = [
("Thu Nov 15 12:27:50 2012","Josh Allen <[email protected]>","action","""Josh Allen <[email protected]> imported this entry from the old RMG database."""),
],
)

entry(
Expand All @@ -320,9 +303,6 @@
u"""

""",
history = [
("Thu Nov 15 12:27:50 2012","Josh Allen <[email protected]>","action","""Josh Allen <[email protected]> imported this entry from the old RMG database."""),
],
)

entry(
Expand All @@ -339,9 +319,6 @@
u"""

""",
history = [
("Thu Nov 15 12:27:50 2012","Josh Allen <[email protected]>","action","""Josh Allen <[email protected]> imported this entry from the old RMG database."""),
],
)

entry(
Expand All @@ -359,8 +336,5 @@
u"""

""",
history = [
("Thu Nov 15 12:27:50 2012","Josh Allen <[email protected]>","action","""Josh Allen <[email protected]> imported this entry from the old RMG database."""),
],
)

2 changes: 0 additions & 2 deletions input/kinetics/families/1+2_Cycloaddition/NIST.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,5 +6,3 @@
longDesc = u"""

"""
recommended = False

2 changes: 0 additions & 2 deletions input/kinetics/families/1+2_Cycloaddition/depository.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,5 +6,3 @@
longDesc = u"""

"""
recommended = False

Loading