def setUp(self):
self.dir_name = 'temp_dir_for_testing'
os.chdir(originalPath)
os.mkdir(self.dir_name)
os.chdir(self.dir_name)
self.databaseDirectory = settings['database.directory']
self.thermoDir = os.path.join(self.databaseDirectory,'thermo','libraries','testSeed.py')
self.kineticsDir = os.path.join(self.databaseDirectory,'kinetics','libraries','testSeed')
inputFile = """
database(
thermoLibraries = ['primaryThermoLibrary'],
reactionLibraries = [],
seedMechanisms = [],
kineticsDepositories = ['training'],
kineticsFamilies = ['R_Recombination'],
kineticsEstimator = 'rate rules',
)
species(
label='ethane',
reactive=True,
structure=SMILES("CC"),
)
simpleReactor(
temperature=(1350,'K'),
pressure=(1.0,'bar'),
initialMoleFractions={
"ethane": 1.0,
},
terminationConversion={
'ethane': 0.000000000001,
},
terminationTime=(1e6,'s'),
)
model(
toleranceKeepInEdge=0.0,
toleranceMoveToCore=0.2,
toleranceInterruptSimulation=0.2,
)
options(
name='testSeed',
units='si',
generateSeedEachIteration=True,
saveSeedToDatabase=True,
saveRestartPeriod=None,
generateOutputHTML=False,
generatePlots=False,
saveEdgeSpecies=False,
saveSimulationProfiles=False,
)
"""
f = open('input.py','w')
f.write(inputFile)
f.close()
self.rmg = RMG(inputFile=os.path.join(os.getcwd(), 'input.py'), outputDirectory=os.getcwd())
def setUpClass(cls):
"""A function that is run ONCE before all unit tests in this class."""
cls.testDir = os.path.join(originalPath, 'rmg', 'test_data', 'mainTest')
cls.outputDir = 'output'
cls.databaseDirectory = settings['database.directory']
cls.seedKinetics = os.path.join(cls.databaseDirectory, 'kinetics', 'libraries', 'testSeed')
cls.seedKineticsEdge = os.path.join(cls.databaseDirectory, 'kinetics', 'libraries', 'testSeed_edge')
os.mkdir(os.path.join(cls.testDir, cls.outputDir))
cls.rmg = RMG(inputFile=os.path.join(cls.testDir, 'input.py'),
outputDirectory=os.path.join(cls.testDir, cls.outputDir))
cls.rmg.execute()
def setUp(self):
self.chemkin_files={"""ELEMENTS
H
D /2.014/
T /3.016/
C
CI /13.003/
O
OI /18.000/
N
END
SPECIES
ethane(1)
CH3(4)
END
THERM ALL
300.000 1000.000 5000.000
ethane(1) H 6 C 2 G100.000 5000.000 954.52 1
4.58987205E+00 1.41507042E-02-4.75958084E-06 8.60284590E-10-6.21708569E-14 2
-1.27217823E+04-3.61762003E+00 3.78032308E+00-3.24248354E-03 5.52375224E-05 3
-6.38573917E-08 2.28633835E-11-1.16203404E+04 5.21037799E+00 4
CH3(4) H 3 C 1 G100.000 5000.000 1337.62 1
3.54144859E+00 4.76788187E-03-1.82149144E-06 3.28878182E-10-2.22546856E-14 2
1.62239622E+04 1.66040083E+00 3.91546822E+00 1.84153688E-03 3.48743616E-06 3
-3.32749553E-09 8.49963443E-13 1.62856393E+04 3.51739246E-01 4
END
REACTIONS KCAL/MOLE MOLES
CH3(4)+CH3(4)=ethane(1) 8.260e+17 -1.400 1.000
END
""": True,
"""ELEMENTS
CI /13.003/
O
OI /18.000/
N
END
SPECIES
ethane(1)
CH3(4)
END
THERM ALL
300.000 1000.000 5000.000
ethane(1) H 6 C 2 G100.000 5000.000 954.52 1
4.58987205E+00 1.41507042E-02-4.75958084E-06 8.60284590E-10-6.21708569E-14 2
-1.27217823E+04-3.61762003E+00 3.78032308E+00-3.24248354E-03 5.52375224E-05 3
-6.38573917E-08 2.28633835E-11-1.16203404E+04 5.21037799E+00 4
CH3(4) H 3 C 1 G100.000 5000.000 1337.62 1
3.54144859E+00 4.76788187E-03-1.82149144E-06 3.28878182E-10-2.22546856E-14 2
1.62239622E+04 1.66040083E+00 3.91546822E+00 1.84153688E-03 3.48743616E-06 3
-3.32749553E-09 8.49963443E-13 1.62856393E+04 3.51739246E-01 4
END
REACTIONS KCAL/MOLE MOLES
CH3(4)+CH3(4)=ethane(1) 8.260e+17 -1.400 1.000
END
""": False,
"""ELEMENTS
H
D /2.014/
T /3.016/
C
CI /13.003/
O
OI /18.000/
N
END
SPECIES
ethane(1)
CH3(4)
END
THERM ALL
300.000 1000.000 5000.000
ethane(1) H 6 C 2 G100.000 5000.000 954.52 1
4.58987205E+00 1.41507042E-02-4.75958084E-06 8.60284590E-10-6.21708569E-14 2
-1.27217823E+04-3.61762003E+00 3.78032308E+00-3.24248354E-03 5.52375224E-05 3
-6.38573917E-08 2.28633835E-11-1.16203404E+04 5.21037799E+00 4
END
REACTIONS KCAL/MOLE MOLES
CH3(4)+CH3(4)=ethane(1) 8.260e+17 -1.400 1.000
END
""": False,
}
self.rmg = RMG()
self.dir_name = 'temp_dir_for_testing'
self.rmg.outputDirectory = os.path.join(originalPath, self.dir_name)
self.tran_dat = '''