Fix multi pdep arrhenius calculation #1341

mjohnson541 · 2018-04-06T17:37:10Z

This removes the requirement that PdepArrhenius objects in a MultiPdepArrhenius must have the same pressure lists by changing the getRateCoefficient function to evaluate each PdepArrhenius object independently. Also adds a database test that checks that all library reactions can be evaluated.

mliu49 · 2018-04-06T17:58:20Z

Are these two calculation approaches actually the same? I was looking through git history yesterday to understand why we have MultiArrhenius and MultiPDepArrhenius, and discovered that for a brief period, we actually had a MultiKinetics class:

5821ad3 (7/25/11): MultiArrhenius was replaced by MultiKinetics, which simply sums together rates in the list, allowing any type of kinetics to be used.
d5803cc (9/3/12): MultiArrhenius and MultiPDepArrhenius classes were added, with MultiPDepArrhenius having the fancier calculation method.
d386cb2 (9/3/12): The old classes were removed.

Based on those commits, I don't think that this is an appropriate fix for this issue. At the very least, I think we need to look deeper into the difference between the calculation methods.

mjohnson541 · 2018-04-06T18:03:32Z

Suppose they were different, the point of having a MultiPdepArrhenius is to combine multiple PdepArrhenius rates together so they can be the kinetics for a single reaction object. Why should the rate of a MultiPdepArrhenius object be different from the sum of the rates of the PdepArrhenius objects it contains?

I should also clarify that we have a test that checks that a particular MultiPdepArrhenius evaluates to particular values and both versions pass that test.

codecov · 2018-04-06T18:04:45Z

Codecov Report

Merging #1341 into master will decrease coverage by <.01%.
The diff coverage is 0%.

@@            Coverage Diff            @@
##           master   #1341      +/-   ##
=========================================
- Coverage   41.31%   41.3%   -0.01%     
=========================================
  Files         178     178              
  Lines       30348   30351       +3     
  Branches     6140    6141       +1     
=========================================
  Hits        12537   12537              
- Misses      16948   16950       +2     
- Partials      863     864       +1

Impacted Files	Coverage Δ
rmgpy/data/kinetics/library.py	`43.45% <ø> (ø)`	⬆️
rmgpy/reaction.py	`0% <0%> (ø)`	⬆️
rmgpy/data/kinetics/common.py	`72.76% <0%> (-0.6%)`	⬇️

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mliu49 · 2018-04-06T19:19:55Z

After looking at it some more, I'm now convinced that the previous method wasn't doing anything special. The only difference should be the check to ensure identical plists.

I think this PR can be merged to address ReactionMechanismGenerator/RMG-website#165. Following this change, there is effectively no difference between MultiArrhenius and MultiPDepArrhenius except for the additional toArrhenius method in MultiArrhenius. I propose that we recombine these two classes into MultiKinetics in the near future.

@rwest, I know this is from a long time ago, but do you remember any details regarding the reasoning for the current implementation of MultiArrhenius/MultiPDepArrhenius?

alongd

The technical changes look good, I agree this should be the solution. Thanks @mjohnson541. If everything else is accepted on everyone, this could be merged.

rwest · 2018-04-07T19:48:38Z

I don't recall exactly, @mliu49, but I had enough of a deja-vu to make me search, leading me to this discussion which may be informative:
#147
#329

cgrambow · 2018-04-07T21:07:53Z

testing/databaseTest.py

+        This test ensures that every library reaction has evaluable kinetics
+        """
+        for entry in library.entries.values():
+            entry.data.getRateCoefficient(1000.0,1.0)


Should we also add some additional checks here? For example, check that the rate is non-negative and within a reasonable range?

mjohnson541 · 2018-05-08T15:00:41Z

Do we want to proceed with this solution?

mliu49 · 2018-05-08T15:06:56Z

Yes, I think we can proceed with this. Do you want to add additional checks like @cgrambow suggested?

mjohnson541 · 2018-05-08T15:17:18Z

Yes, we can check that it's nonnegative pretty easily, @cgrambow were you thinking of checking the diffusion and TST limits?

cgrambow · 2018-05-08T15:19:37Z

Yeah, that probably makes the most sense.

mjohnson541 · 2018-05-29T16:30:37Z

So I just pushed positivity, TST and collision limit tests 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 <lambda>
    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 <lambda>
    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 <lambda>
    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 <lambda>
    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 <lambda>
    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 <lambda>
    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 <lambda>
    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 <lambda>
    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 <lambda>
    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 <lambda>
    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 <lambda>
    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 <lambda>
    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

mjohnson541 · 2018-05-29T16:31:19Z

I tested the rates at 1000 K 1 bar, the collision and TST limit calculations should be in the commit log.

alongd · 2018-06-01T13:04:40Z

One of the reactions this reports is:
root: ERROR: library reaction ONONO2 <=> NO2 + NO2 from library primaryNitrogenLibrary, exceeds the TST limit at 1000 K, 1 bar
This is barrierless scission of:

I double-checked with the source by M.C. Lin to make sure there are no typos.
Does it make sense that a high-P limit unimolecular decomposition reaction has a TST limit as the error suggests?

alongd · 2018-06-11T18:59:40Z

testing/databaseTest.py

@@ -443,14 +443,14 @@ def kinetics_checkLibraryRatesAreReasonable(self, library):
            if k < 0:
                boo = True
                logging.error('library reaction {0} from library {1}, had a negative rate at 1000 K, 1 bar'.format(rxn,library.label))
-            if len(rxn.reactants) == 1:
+            if len(rxn.reactants) == 1 and rxn.allow_max_rate_violation==False:


The test fails with AttributeError: 'rmgpy.reaction.Reaction' object has no attribute 'allow_max_rate_violation', I think you should first check hasattr

Sorry, I forgot to actually set the attribute Reaction.init

alongd · 2018-06-12T01:13:27Z

@mjohnson541, I still get an error:
TypeError: loadEntry() got an unexpected keyword argument 'allow_max_rate_violation'
ReactionMechanismGenerator/RMG-database#279 fails when I run the tests locally on this -Py branch

mliu49 · 2018-06-22T15:29:03Z

Any chance we could separate this from the collision limit check? It would be nice to fix the rate evaluation.

mjohnson541 · 2018-06-22T15:31:00Z

The collision limit check stuff is almost fixed I think we're just waiting for @jimchu10 to look at the aromatic ones.

…f the PdepArrhenius objects within it before there was a requirement that the pressure lists of each PdepArrhenius objects had to be the same

checks that a 1000 K 1 bar all rates are positive and less than the TST/collision limit

…ax rate requirements

mliu49 · 2018-07-04T15:49:29Z

I went ahead and rebased this. Any final considerations before merging?

mjohnson541 · 2018-07-04T16:42:37Z

Together with the database maxviol branch there shouldn’t be any issues, might be some issues merging them individually. You could merge the unit test separately and merge the rest of the RMG-Py branch first then the database branch and then the unit test. I think that would avoid unit tests failing. Best, Matt

…

On Wed, Jul 4, 2018 at 11:49 AM Max Liu ***@***.***> wrote: I went ahead and rebased this. Any final considerations before merging? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#1341 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AHacLCDMAAEAX7cSY2AONhhtFDtC42dEks5uDOQKgaJpZM4TKb3h> .

mjohnson541 requested review from alongd and cgrambow April 6, 2018 17:37

mliu49 added the Status: Blocked This PR should not be merged label Apr 6, 2018

mliu49 removed the Status: Blocked This PR should not be merged label Apr 6, 2018

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mjohnson541 mentioned this pull request May 29, 2018

Some updates to recently added libraries ReactionMechanismGenerator/RMG-database#274

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mjohnson541 dismissed alongd’s stale review via b11138a May 29, 2018 16:29

mjohnson541 force-pushed the fixMultiPdepArrhenius branch from 6372753 to b11138a Compare May 29, 2018 16:29

mjohnson541 mentioned this pull request May 29, 2018

TST and Collision limit violations ReactionMechanismGenerator/RMG-database#275

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mjohnson541 force-pushed the fixMultiPdepArrhenius branch from b11138a to eb3210b Compare May 29, 2018 19:57

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mjohnson541 force-pushed the fixMultiPdepArrhenius branch 2 times, most recently from 2b44210 to ab2430a Compare June 11, 2018 19:35

mjohnson541 force-pushed the fixMultiPdepArrhenius branch 2 times, most recently from 5515206 to 9568307 Compare June 12, 2018 17:15

mjohnson541 force-pushed the fixMultiPdepArrhenius branch 2 times, most recently from cf4acda to 27b0e3e Compare June 13, 2018 19:15

mjohnson541 force-pushed the fixMultiPdepArrhenius branch from 27b0e3e to 99ec8a6 Compare June 28, 2018 21:00

mjohnson541 and others added 4 commits July 3, 2018 18:30

changes MultiPdepArrhenius getRateCoefficient to calculate as a sum o…

a0cb5fd

…f the PdepArrhenius objects within it before there was a requirement that the pressure lists of each PdepArrhenius objects had to be the same

Add unit test for MultiPDepArrhenius with different plists

8df7d80

adds a database test to check reasonability for every library reaction

bb50e9f

checks that a 1000 K 1 bar all rates are positive and less than the TST/collision limit

add allow_max_rate_violation attribute to exempt reactions from the m…

d01dc79

…ax rate requirements

mliu49 force-pushed the fixMultiPdepArrhenius branch from 99ec8a6 to cbc7d4a Compare July 3, 2018 22:30

mliu49 force-pushed the fixMultiPdepArrhenius branch from cbc7d4a to d01dc79 Compare July 5, 2018 19:25

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mliu49 merged commit d4da791 into master Jul 5, 2018

mliu49 deleted the fixMultiPdepArrhenius branch July 5, 2018 19:27

mliu49 mentioned this pull request Jul 9, 2018

MultiPDepArrhenius with different pressure lists ReactionMechanismGenerator/RMG-database#212

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mliu49 mentioned this pull request Feb 27, 2019

Library duplicate reactions not of Arrhenius and PDepArrhenius type ReactionMechanismGenerator/RMG-database#315

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rwest mentioned this pull request Oct 6, 2022

RMG not handling pressure dependent - multiple Arrhenius type reactions correctly ReactionMechanismGenerator/RMG-website#245

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Fix multi pdep arrhenius calculation #1341

Fix multi pdep arrhenius calculation #1341

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Fix multi pdep arrhenius calculation #1341

Fix multi pdep arrhenius calculation #1341

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