TST and Collision limit violations

So I just ran positivity, TST and collision limit tests as a part of https://github.com/ReactionMechanismGenerator/RMG-Py/pull/1341 and we have a lot of failures in existing libraries:

======================================================================
ERROR: Kinetics library Sulfur/DMDS: check rates can be evaluated?

Traceback (most recent call last):
File "/usr/local/Cellar/numpy/1.12.0/libexec/nose/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/Users/mattjohnson/RMGCODE/RMG-Py/testing/databaseTest.py", line 116, in
test = lambda x: self.kinetics_checkLibraryRatesCanBeEvaluated(library)
File "/Users/mattjohnson/RMGCODE/RMG-Py/testing/databaseTest.py", line 448, in kinetics_checkLibraryRatesCanBeEvaluated
raise ValueError('library reaction {0} from library {1}, exceeds the collision limit at 1000 K, 1 bar'.format(rxn,library.label))
ValueError: library reaction Sa + Sa <=> S2 from library Sulfur/DMDS, exceeds the collision limit at 1000 K, 1 bar

======================================================================
ERROR: Kinetics library Sulfur/GlarborgH2S: check rates can be evaluated?

Traceback (most recent call last):
File "/usr/local/Cellar/numpy/1.12.0/libexec/nose/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/Users/mattjohnson/RMGCODE/RMG-Py/testing/databaseTest.py", line 116, in
test = lambda x: self.kinetics_checkLibraryRatesCanBeEvaluated(library)
File "/Users/mattjohnson/RMGCODE/RMG-Py/testing/databaseTest.py", line 448, in kinetics_checkLibraryRatesCanBeEvaluated
raise ValueError('library reaction {0} from library {1}, exceeds the collision limit at 1000 K, 1 bar'.format(rxn,library.label))
ValueError: library reaction HSS + H <=> SH + SH from library Sulfur/GlarborgH2S, exceeds the collision limit at 1000 K, 1 bar

======================================================================
ERROR: Kinetics library Sulfur/GlarborgBozzelli: check rates can be evaluated?

Traceback (most recent call last):
File "/usr/local/Cellar/numpy/1.12.0/libexec/nose/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/Users/mattjohnson/RMGCODE/RMG-Py/testing/databaseTest.py", line 116, in
test = lambda x: self.kinetics_checkLibraryRatesCanBeEvaluated(library)
File "/Users/mattjohnson/RMGCODE/RMG-Py/testing/databaseTest.py", line 448, in kinetics_checkLibraryRatesCanBeEvaluated
raise ValueError('library reaction {0} from library {1}, exceeds the collision limit at 1000 K, 1 bar'.format(rxn,library.label))
ValueError: library reaction SO + H <=> HSO from library Sulfur/GlarborgBozzelli, exceeds the collision limit at 1000 K, 1 bar

======================================================================
ERROR: Kinetics library Dooley/methylformate_all_N2bathgas: check rates can be evaluated?

Traceback (most recent call last):
File "/usr/local/Cellar/numpy/1.12.0/libexec/nose/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/Users/mattjohnson/RMGCODE/RMG-Py/testing/databaseTest.py", line 116, in
test = lambda x: self.kinetics_checkLibraryRatesCanBeEvaluated(library)
File "/Users/mattjohnson/RMGCODE/RMG-Py/testing/databaseTest.py", line 445, in kinetics_checkLibraryRatesCanBeEvaluated
raise ValueError('library reaction {0} from library {1}, exceeds the TST limit at 1000 K, 1 bar'.format(rxn,library.label))
ValueError: library reaction C3H6OOH2-2 <=> CH3COCH3 + OH from library Dooley/methylformate_all_N2bathgas, exceeds the TST limit at 1000 K, 1 bar

======================================================================
ERROR: Kinetics library Sulfur/GlarborgNS: check rates can be evaluated?

Traceback (most recent call last):
File "/usr/local/Cellar/numpy/1.12.0/libexec/nose/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/Users/mattjohnson/RMGCODE/RMG-Py/testing/databaseTest.py", line 116, in
test = lambda x: self.kinetics_checkLibraryRatesCanBeEvaluated(library)
File "/Users/mattjohnson/RMGCODE/RMG-Py/testing/databaseTest.py", line 448, in kinetics_checkLibraryRatesCanBeEvaluated
raise ValueError('library reaction {0} from library {1}, exceeds the collision limit at 1000 K, 1 bar'.format(rxn,library.label))
ValueError: library reaction S + NO <=> SNO from library Sulfur/GlarborgNS, exceeds the collision limit at 1000 K, 1 bar

======================================================================
ERROR: Kinetics library Sulfur/DTBS: check rates can be evaluated?

Traceback (most recent call last):
File "/usr/local/Cellar/numpy/1.12.0/libexec/nose/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/Users/mattjohnson/RMGCODE/RMG-Py/testing/databaseTest.py", line 116, in
test = lambda x: self.kinetics_checkLibraryRatesCanBeEvaluated(library)
File "/Users/mattjohnson/RMGCODE/RMG-Py/testing/databaseTest.py", line 445, in kinetics_checkLibraryRatesCanBeEvaluated
raise ValueError('library reaction {0} from library {1}, exceeds the TST limit at 1000 K, 1 bar'.format(rxn,library.label))
ValueError: library reaction S2 <=> S2JJ from library Sulfur/DTBS, exceeds the TST limit at 1000 K, 1 bar

======================================================================
ERROR: Kinetics library Chernov: check rates can be evaluated?

Traceback (most recent call last):
File "/usr/local/Cellar/numpy/1.12.0/libexec/nose/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/Users/mattjohnson/RMGCODE/RMG-Py/testing/databaseTest.py", line 116, in
test = lambda x: self.kinetics_checkLibraryRatesCanBeEvaluated(library)
File "/Users/mattjohnson/RMGCODE/RMG-Py/testing/databaseTest.py", line 448, in kinetics_checkLibraryRatesCanBeEvaluated
raise ValueError('library reaction {0} from library {1}, exceeds the collision limit at 1000 K, 1 bar'.format(rxn,library.label))
ValueError: library reaction H2CCCH + C2H2 <=> C5H5 from library Chernov, exceeds the collision limit at 1000 K, 1 bar

======================================================================
ERROR: Kinetics library CurranPentane: check rates can be evaluated?

Traceback (most recent call last):
File "/usr/local/Cellar/numpy/1.12.0/libexec/nose/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/Users/mattjohnson/RMGCODE/RMG-Py/testing/databaseTest.py", line 116, in
test = lambda x: self.kinetics_checkLibraryRatesCanBeEvaluated(library)
File "/Users/mattjohnson/RMGCODE/RMG-Py/testing/databaseTest.py", line 445, in kinetics_checkLibraryRatesCanBeEvaluated
raise ValueError('library reaction {0} from library {1}, exceeds the TST limit at 1000 K, 1 bar'.format(rxn,library.label))
ValueError: library reaction C4H71-1,2OOH <=> NC4KET12 + OH from library CurranPentane, exceeds the TST limit at 1000 K, 1 bar

======================================================================
ERROR: Kinetics library Nitrogen_Glarborg_Zhang_et_al: check rates can be evaluated?

Traceback (most recent call last):
File "/usr/local/Cellar/numpy/1.12.0/libexec/nose/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/Users/mattjohnson/RMGCODE/RMG-Py/testing/databaseTest.py", line 116, in
test = lambda x: self.kinetics_checkLibraryRatesCanBeEvaluated(library)
File "/Users/mattjohnson/RMGCODE/RMG-Py/testing/databaseTest.py", line 445, in kinetics_checkLibraryRatesCanBeEvaluated
raise ValueError('library reaction {0} from library {1}, exceeds the TST limit at 1000 K, 1 bar'.format(rxn,library.label))
ValueError: library reaction CHCHNO <=> C2H2 + NO from library Nitrogen_Glarborg_Zhang_et_al, exceeds the TST limit at 1000 K, 1 bar

======================================================================
ERROR: Kinetics library Dooley/methylformate_all_ARHEbathgas: check rates can be evaluated?

Traceback (most recent call last):
File "/usr/local/Cellar/numpy/1.12.0/libexec/nose/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/Users/mattjohnson/RMGCODE/RMG-Py/testing/databaseTest.py", line 116, in
test = lambda x: self.kinetics_checkLibraryRatesCanBeEvaluated(library)
File "/Users/mattjohnson/RMGCODE/RMG-Py/testing/databaseTest.py", line 445, in kinetics_checkLibraryRatesCanBeEvaluated
raise ValueError('library reaction {0} from library {1}, exceeds the TST limit at 1000 K, 1 bar'.format(rxn,library.label))
ValueError: library reaction C3H6OOH2-2 <=> CH3COCH3 + OH from library Dooley/methylformate_all_ARHEbathgas, exceeds the TST limit at 1000 K, 1 bar

======================================================================
ERROR: Kinetics library primaryNitrogenLibrary: check rates can be evaluated?

Traceback (most recent call last):
File "/usr/local/Cellar/numpy/1.12.0/libexec/nose/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/Users/mattjohnson/RMGCODE/RMG-Py/testing/databaseTest.py", line 116, in
test = lambda x: self.kinetics_checkLibraryRatesCanBeEvaluated(library)
File "/Users/mattjohnson/RMGCODE/RMG-Py/testing/databaseTest.py", line 448, in kinetics_checkLibraryRatesCanBeEvaluated
raise ValueError('library reaction {0} from library {1}, exceeds the collision limit at 1000 K, 1 bar'.format(rxn,library.label))
ValueError: library reaction NCN + CN <=> NCNCN from library primaryNitrogenLibrary, exceeds the collision limit at 1000 K, 1 bar

======================================================================
ERROR: Kinetics library NOx2018: check rates can be evaluated?

Traceback (most recent call last):
File "/usr/local/Cellar/numpy/1.12.0/libexec/nose/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/Users/mattjohnson/RMGCODE/RMG-Py/testing/databaseTest.py", line 116, in
test = lambda x: self.kinetics_checkLibraryRatesCanBeEvaluated(library)
File "/Users/mattjohnson/RMGCODE/RMG-Py/testing/databaseTest.py", line 445, in kinetics_checkLibraryRatesCanBeEvaluated
raise ValueError('library reaction {0} from library {1}, exceeds the TST limit at 1000 K, 1 bar'.format(rxn,library.label))
ValueError: library reaction CHCHNO <=> C2H2 + NO from library NOx2018, exceeds the TST limit at 1000 K, 1 bar

Ran 842 tests in 210.412s

There are likely more of them than the above as it only returns the first reaction that errors in each library. This can be checked by running database tests on https://github.com/ReactionMechanismGenerator/RMG-Py/pull/1341.

Start by running the database tests against PR #1341 and inspect testing/databaseTest.py, especially the checks at lines 445 and 448. Trace each reported reaction to its kinetics-library entry and determine the required data correction; done means the TST and collision-limit checks pass for all affected libraries, not only the first failure.