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Add units check for kinetics depositories to database test
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Make checkLibraryRateUnits more generic
Add test definition for kinetics depositories
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@mliu49
mliu49 committed Jan 29, 2019
1 parent c9ec8e5 commit cce2a3c
Showing 1 changed file with 31 additions and 25 deletions.
56 changes: 31 additions & 25 deletions testing/databaseTest.py
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Original file line number Diff line number Diff line change
Expand Up @@ -103,7 +103,13 @@ def test_kinetics(self):
for depository in family.depositories:

test = lambda x: self.kinetics_checkAdjlistsNonidentical(depository)
test_name = "Kinetics {1} Depository: check adjacency lists are nonidentical?".format(family_name, depository.label)
test_name = "Kinetics depository {0}: check adjacency lists are nonidentical?".format(depository.label)
test.description = test_name
self.compat_func_name = test_name
yield test, depository.label

test = lambda x: self.kinetics_checkRateUnitsAreCorrect(depository, tag='depository')
test_name = "Kinetics depository {0}: check rates have correct units?".format(depository.label)
test.description = test_name
self.compat_func_name = test_name
yield test, depository.label
Expand All @@ -116,8 +122,8 @@ def test_kinetics(self):
self.compat_func_name = test_name
yield test, library_name

test = lambda x: self.kinetics_checkLibraryRateUnits(library)
test_name = "Kinetics library {0}: check rates have OK units?".format(library_name)
test = lambda x: self.kinetics_checkRateUnitsAreCorrect(library)
test_name = "Kinetics library {0}: check rates have correct units?".format(library_name)
test.description = test_name
self.compat_func_name = test_name
yield test, library_name
Expand Down Expand Up @@ -433,9 +439,9 @@ def kinetics_checkAdjlistsNonidentical(self, database):

nose.tools.assert_false(speciesList[i].molecule[0].isIsomorphic(speciesList[j].molecule[0], initialMap), "Species {0} and species {1} in {2} database were found to be identical.".format(speciesList[i].label,speciesList[j].label,database.label))

def kinetics_checkLibraryRateUnits(self, library):
def kinetics_checkRateUnitsAreCorrect(self, database, tag='library'):
"""
This test ensures that every library reaction has acceptable units on the A factor.
This test ensures that every reaction has acceptable units on the A factor.
"""
boo = False

Expand All @@ -445,7 +451,7 @@ def kinetics_checkLibraryRateUnits(self, library):
3: ((pq.m**6) / (pq.mole**2) / pq.s).dimensionality,
}

for entry in library.entries.values():
for entry in database.entries.values():
k = entry.data
rxn = entry.item
molecularity = len(rxn.reactants)
Expand All @@ -454,31 +460,31 @@ def kinetics_checkLibraryRateUnits(self, library):
A = k.A
if pq.Quantity(1.0, A.units).simplified.dimensionality != dimensionalities[molecularity]:
boo = True
logging.error('library reaction {0} from library {1}, has invalid units {2}'.format(rxn, library.label, A.units))
logging.error('Reaction {0} from {1} {2}, has invalid units {3}'.format(rxn, tag, database.label, A.units))
elif isinstance(k, (rmgpy.kinetics.Lindemann, rmgpy.kinetics.Troe )):
A = k.arrheniusHigh.A
if pq.Quantity(1.0, A.units).simplified.dimensionality != dimensionalities[molecularity]:
boo = True
logging.error('library reaction {0} from library {1}, has invalid high-pressure limit units {2}'.format(rxn, library.label, A.units))
logging.error('Reaction {0} from {1} {2}, has invalid high-pressure limit units {3}'.format(rxn, tag, database.label, A.units))
elif isinstance(k, (rmgpy.kinetics.Lindemann, rmgpy.kinetics.Troe, rmgpy.kinetics.ThirdBody)):
A = k.arrheniusLow.A
if pq.Quantity(1.0, A.units).simplified.dimensionality != dimensionalities[molecularity+1]:
boo = True
logging.error('library reaction {0} from library {1}, has invalid low-pressure limit units {2}'.format(rxn, library.label, A.units))
logging.error('Reaction {0} from {1} {2}, has invalid low-pressure limit units {3}'.format(rxn, tag, database.label, A.units))
elif hasattr(k, 'highPlimit') and k.highPlimit is not None:
A = k.highPlimit.A
if pq.Quantity(1.0, A.units).simplified.dimensionality != dimensionalities[molecularity-1]:
boo = True
logging.error(
'library reaction {0} from library {1}, has invalid high-pressure limit units {2}'.format(rxn, library.label, A.units))
'Reaction {0} from {1} {2}, has invalid high-pressure limit units {3}'.format(rxn, tag, database.label, A.units))
elif isinstance(k, rmgpy.kinetics.MultiArrhenius):
for num, arrhenius in enumerate(k.arrhenius):
A = arrhenius.A
if pq.Quantity(1.0, A.units).simplified.dimensionality != dimensionalities[molecularity]:
boo = True
logging.error(
'library reaction {0} from library {1}, has invalid units {2} on rate expression {3}'.format(
rxn, library.label, A.units, num+1)
'Reaction {0} from {1} {2}, has invalid units {3} on rate expression {4}'.format(
rxn, tag, database.label, A.units, num + 1)
)

elif isinstance(k, rmgpy.kinetics.PDepArrhenius):
Expand All @@ -494,16 +500,16 @@ def kinetics_checkLibraryRateUnits(self, library):
if pq.Quantity(1.0, A.units).simplified.dimensionality != dimensionalities[molecularity]:
boo = True
logging.error(
'library reaction {0} from library {1}, has invalid units {2} on {2!r} rate expression {3}'.format(
rxn, library.label, P, A.units, num + 1)
'Reaction {0} from {1} {2}, has invalid units {3} on {4!r} rate expression {5}'.format(
rxn, tag, database.label, A.units, P, num + 1)
)
else:
A = arrhenius.A
if pq.Quantity(1.0, A.units).simplified.dimensionality != dimensionalities[molecularity]:
boo = True
logging.error(
'library reaction {0} from library {1}, has invalid {2!r} units {3}'.format(
rxn, library.label, P, A.units)
'Reaction {0} from {1} {2}, has invalid {3!r} units {4}'.format(
rxn, tag, database.label, P, A.units)
)

elif isinstance(k, rmgpy.kinetics.MultiPDepArrhenius):
Expand All @@ -519,35 +525,35 @@ def kinetics_checkLibraryRateUnits(self, library):
molecularity]:
boo = True
logging.error(
'library reaction {0} from library {1}, has invalid units {2} on {3!r} rate expression {4!r}'.format(
rxn, library.label, A.units, P, arrhenius2)
'Reaction {0} from {1} {2}, has invalid units {3} on {4!r} rate expression {5!r}'.format(
rxn, tag, database.label, A.units, P, arrhenius2)
)
else:
A = arrhenius.A
if pq.Quantity(1.0, A.units).simplified.dimensionality != dimensionalities[
molecularity]:
boo = True
logging.error(
'library reaction {0} from library {1}, has invalid {2!r} units {3} in rate expression {4}'.format(
rxn, library.label, P, A.units, num)
'Reaction {0} from {1} {2}, has invalid {3!r} units {4} in rate expression {5}'.format(
rxn, tag, database.label, P, A.units, num)
)


elif isinstance(k, rmgpy.kinetics.Chebyshev):
if pq.Quantity(1.0, k.kunits).simplified.dimensionality != dimensionalities[molecularity]:
boo = True
logging.error(
'library reaction {0} from library {1}, has invalid units {2}'.format(
rxn, library.label, k.kunits)
'Reaction {0} from {1} {2}, has invalid units {3}'.format(
rxn, tag, database.label, k.kunits)
)

else:
logging.warning('library reaction {0} from library {1}, did not have units checked.'.format(rxn, library.label))
logging.warning('Reaction {0} from {1} {2}, did not have units checked.'.format(rxn, tag, database.label))
except:
logging.error("Error when checking units on reaction {0} from library {1} with rate expression {2!r}.".format(rxn, library.label, k))
logging.error("Error when checking units on reaction {0} from {1} {2} with rate expression {3!r}.".format(rxn, tag, database.label, k))
raise
if boo:
raise ValueError('library {0} has some incorrect units'.format(library.label))
raise ValueError('{0} {1} has some incorrect units'.format(tag.capitalize(), database.label))

def kinetics_checkLibraryRatesAreReasonable(self, library):
"""
Expand Down

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