def testAllEntriesAccessibleInSearchTargetIndex(self):
butene1 = Species()
butene1.fromSMILES('C=CCC')
butene1.label = 'C4H8'
butene2 = Species()
butene2.fromSMILES('CC=CC')
butene2.label = 'C4H8'
species_list = [butene1, butene2]
# make sure different species with same label
assert not species_list[0].isIsomorphic(species_list[1])
assert species_list[0].label == species_list[1].label
# make fake reactionModel object to fit in with the unittest
reaction_model = CoreEdgeReactionModel()
reaction_model.core.species = species_list
# ensure second species index is returned when it's label is used
# in `searchTargetIndex`.
input_index = 1
output_index = searchTargetIndex(species_list[input_index].label,
reaction_model)
self.assertEqual(
input_index, output_index,
'searchTargetIndex will not return the second occurance of species with the same label.'
)
def testAllEntriesAccessibleInSearchTargetIndex(self):
butene1 = Species()
butene1.fromSMILES('C=CCC')
butene1.label = 'C4H8'
butene2 = Species()
butene2.fromSMILES('CC=CC')
butene2.label = 'C4H8'
species_list =[butene1,butene2]
# make sure different species with same label
assert not species_list[0].isIsomorphic(species_list[1])
assert species_list[0].label == species_list[1].label
# make fake reactionModel object to fit in with the unittest
reaction_model = CoreEdgeReactionModel()
reaction_model.core.species = species_list
# ensure second species index is returned when it's label is used
# in `searchTargetIndex`.
input_index = 1
output_index = searchTargetIndex(species_list[input_index].label,reaction_model)
self.assertEqual(input_index,output_index,'searchTargetIndex will not return the second occurance of species with the same label.')
class TestPdep(unittest.TestCase):
def setUp(self):
"""
A method that is run before each unit test in this class.
"""
self.nC4H10O = Species(
label = 'n-C4H10O',
conformer = Conformer(
E0 = (-317.807,'kJ/mol'),
modes = [
IdealGasTranslation(mass=(74.07,"g/mol")),
NonlinearRotor(inertia=([41.5091,215.751,233.258],"amu*angstrom^2"), symmetry=1),
HarmonicOscillator(frequencies=([240.915,341.933,500.066,728.41,809.987,833.93,926.308,948.571,1009.3,1031.46,1076,1118.4,1184.66,1251.36,1314.36,1321.42,1381.17,1396.5,1400.54,1448.08,1480.18,1485.34,1492.24,1494.99,1586.16,2949.01,2963.03,2986.19,2988.1,2995.27,3026.03,3049.05,3053.47,3054.83,3778.88],"cm^-1")),
HinderedRotor(inertia=(0.854054,"amu*angstrom^2"), symmetry=1, fourier=([[0.25183,-1.37378,-2.8379,0.0305112,0.0028088], [0.458307,0.542121,-0.599366,-0.00283925,0.0398529]],"kJ/mol")),
HinderedRotor(inertia=(8.79408,"amu*angstrom^2"), symmetry=1, fourier=([[0.26871,-0.59533,-8.15002,-0.294325,-0.145357], [1.1884,0.99479,-0.940416,-0.186538,0.0309834]],"kJ/mol")),
HinderedRotor(inertia=(7.88153,"amu*angstrom^2"), symmetry=1, fourier=([[-4.67373,2.03735,-6.25993,-0.27325,-0.048748], [-0.982845,1.76637,-1.57619,0.474364,-0.000681718]],"kJ/mol")),
HinderedRotor(inertia=(2.81525,"amu*angstrom^2"), symmetry=3, barrier=(2.96807,"kcal/mol")),
],
spinMultiplicity = 1,
opticalIsomers = 1,
),
molecularWeight = (74.07,"g/mol"),
transportData=TransportData(sigma=(5.94, 'angstrom'), epsilon=(559, 'K')),
energyTransferModel = SingleExponentialDown(alpha0=(447.5*0.011962,"kJ/mol"), T0=(300,"K"), n=0.85),
)
self.nC4H10O.fromSMILES('CCCCO')
self.nC4H8 = Species(
label = 'n-C4H8',
conformer = Conformer(
E0 = (-17.8832,'kJ/mol'),
modes = [
IdealGasTranslation(mass=(56.06,"g/mol")),
NonlinearRotor(inertia=([22.2748,122.4,125.198],"amu*angstrom^2"), symmetry=1),
HarmonicOscillator(frequencies=([308.537,418.67,636.246,788.665,848.906,936.762,979.97,1009.48,1024.22,1082.96,1186.38,1277.55,1307.65,1332.87,1396.67,1439.09,1469.71,1484.45,1493.19,1691.49,2972.12,2994.31,3018.48,3056.87,3062.76,3079.38,3093.54,3174.52],"cm^-1")),
HinderedRotor(inertia=(5.28338,"amu*angstrom^2"), symmetry=1, fourier=([[-0.579364,-0.28241,-4.46469,0.143368,0.126756], [1.01804,-0.494628,-0.00318651,-0.245289,0.193728]],"kJ/mol")),
HinderedRotor(inertia=(2.60818,"amu*angstrom^2"), symmetry=3, fourier=([[0.0400372,0.0301986,-6.4787,-0.0248675,-0.0324753], [0.0312541,0.0538,-0.493785,0.0965968,0.125292]],"kJ/mol")),
],
spinMultiplicity = 1,
opticalIsomers = 1,
),
)
self.nC4H8.fromSMILES('CCC=C')
self.H2O = Species(
label = 'H2O',
conformer = Conformer(
E0 = (-269.598,'kJ/mol'),
modes = [
IdealGasTranslation(mass=(18.01,"g/mol")),
NonlinearRotor(inertia=([0.630578,1.15529,1.78586],"amu*angstrom^2"), symmetry=2),
HarmonicOscillator(frequencies=([1622.09,3771.85,3867.85],"cm^-1")),
],
spinMultiplicity = 1,
opticalIsomers = 1,
),
)
self.H2O.fromSMILES('O')
self.N2 = Species(
label = 'N2',
molecularWeight = (28.04,"g/mol"),
transportData=TransportData(sigma=(3.41, "angstrom"), epsilon=(124, "K")),
energyTransferModel = None,
)
self.N2.fromSMILES('N#N')
logging.error('to TS')
self.TS = TransitionState(
label = 'TS',
conformer = Conformer(
E0 = (-42.4373,"kJ/mol"),
modes = [
IdealGasTranslation(mass=(74.07,"g/mol")),
NonlinearRotor(inertia=([40.518,232.666,246.092],"u*angstrom**2"), symmetry=1, quantum=False),
HarmonicOscillator(frequencies=([134.289,302.326,351.792,407.986,443.419,583.988,699.001,766.1,777.969,829.671,949.753,994.731,1013.59,1073.98,1103.79,1171.89,1225.91,1280.67,1335.08,1373.9,1392.32,1417.43,1469.51,1481.61,1490.16,1503.73,1573.16,2972.85,2984.3,3003.67,3045.78,3051.77,3082.37,3090.44,3190.73,3708.52],"kayser")),
HinderedRotor(inertia=(2.68206,"amu*angstrom^2"), symmetry=3, barrier=(3.35244,"kcal/mol")),
HinderedRotor(inertia=(9.77669,"amu*angstrom^2"), symmetry=1, fourier=([[0.208938,-1.55291,-4.05398,-0.105798,-0.104752], [2.00518,-0.020767,-0.333595,0.137791,-0.274578]],"kJ/mol")),
],
spinMultiplicity = 1,
opticalIsomers = 1,
),
frequency=(-2038.34,'cm^-1'),
)
self.reaction = Reaction(
label = 'dehydration',
reactants = [self.nC4H10O],
products = [self.nC4H8, self.H2O],
transitionState = self.TS,
kinetics = Arrhenius(A=(0.0387, 'm^3/(mol*s)'), n=2.7, Ea=(2.6192e4, 'J/mol'), T0=(1, 'K'))
)
self.network = Network(
label = 'n-butanol',
isomers = [Configuration(self.nC4H10O)],
reactants = [],
products = [Configuration(self.nC4H8, self.H2O)],
pathReactions = [self.reaction],
bathGas = {self.N2: 1.0},
)
self.pdepnetwork = deepcopy(self.network)
self.pdepnetwork.__class__ = PDepNetwork
self.pdepnetwork.source = [self.pdepnetwork.isomers[0].species[0]]
self.pdepnetwork.index = 1
self.pdepnetwork.explored = []
def test_SS_solver(self):
c = self.pdepnetwork.solve_SS_network(1000.0,100000.0)
self.assertAlmostEquals(c[0],4.791463e-06,2)
def test_energy_filter(self):
rxns = self.pdepnetwork.get_energy_filtered_reactions(1000.0,0.0)
self.assertEquals(len(rxns),1)
self.assertEquals(rxns[0],self.pdepnetwork.pathReactions[0])
def test_flux_filter(self):
rxns = self.pdepnetwork.get_rate_filtered_reactions(1000.0,100000.0,1.0)
self.assertEquals(len(rxns),0)
class TestPdep(unittest.TestCase):
def setUp(self):
"""
A method that is run before each unit test in this class.
"""
self.nC4H10O = Species(
label='n-C4H10O',
conformer=Conformer(
E0=(-317.807, 'kJ/mol'),
modes=[
IdealGasTranslation(mass=(74.07, "g/mol")),
NonlinearRotor(inertia=([41.5091, 215.751,
233.258], "amu*angstrom^2"),
symmetry=1),
HarmonicOscillator(frequencies=([
240.915, 341.933, 500.066, 728.41, 809.987, 833.93,
926.308, 948.571, 1009.3, 1031.46, 1076, 1118.4,
1184.66, 1251.36, 1314.36, 1321.42, 1381.17, 1396.5,
1400.54, 1448.08, 1480.18, 1485.34, 1492.24, 1494.99,
1586.16, 2949.01, 2963.03, 2986.19, 2988.1, 2995.27,
3026.03, 3049.05, 3053.47, 3054.83, 3778.88
], "cm^-1")),
HinderedRotor(inertia=(0.854054, "amu*angstrom^2"),
symmetry=1,
fourier=([[
0.25183, -1.37378, -2.8379, 0.0305112,
0.0028088
],
[
0.458307, 0.542121, -0.599366,
-0.00283925, 0.0398529
]], "kJ/mol")),
HinderedRotor(
inertia=(8.79408, "amu*angstrom^2"),
symmetry=1,
fourier=([[
0.26871, -0.59533, -8.15002, -0.294325, -0.145357
], [1.1884, 0.99479, -0.940416, -0.186538,
0.0309834]], "kJ/mol")),
HinderedRotor(inertia=(7.88153, "amu*angstrom^2"),
symmetry=1,
fourier=([[
-4.67373, 2.03735, -6.25993, -0.27325,
-0.048748
],
[
-0.982845, 1.76637, -1.57619,
0.474364, -0.000681718
]], "kJ/mol")),
HinderedRotor(inertia=(2.81525, "amu*angstrom^2"),
symmetry=3,
barrier=(2.96807, "kcal/mol")),
],
spinMultiplicity=1,
opticalIsomers=1,
),
molecularWeight=(74.07, "g/mol"),
transportData=TransportData(sigma=(5.94, 'angstrom'),
epsilon=(559, 'K')),
energyTransferModel=SingleExponentialDown(alpha0=(447.5 * 0.011962,
"kJ/mol"),
T0=(300, "K"),
n=0.85),
)
self.nC4H10O.fromSMILES('CCCCO')
self.nC4H8 = Species(
label='n-C4H8',
conformer=Conformer(
E0=(-17.8832, 'kJ/mol'),
modes=[
IdealGasTranslation(mass=(56.06, "g/mol")),
NonlinearRotor(inertia=([22.2748, 122.4,
125.198], "amu*angstrom^2"),
symmetry=1),
HarmonicOscillator(frequencies=([
308.537, 418.67, 636.246, 788.665, 848.906, 936.762,
979.97, 1009.48, 1024.22, 1082.96, 1186.38, 1277.55,
1307.65, 1332.87, 1396.67, 1439.09, 1469.71, 1484.45,
1493.19, 1691.49, 2972.12, 2994.31, 3018.48, 3056.87,
3062.76, 3079.38, 3093.54, 3174.52
], "cm^-1")),
HinderedRotor(inertia=(5.28338, "amu*angstrom^2"),
symmetry=1,
fourier=([[
-0.579364, -0.28241, -4.46469, 0.143368,
0.126756
],
[
1.01804, -0.494628,
-0.00318651, -0.245289,
0.193728
]], "kJ/mol")),
HinderedRotor(
inertia=(2.60818, "amu*angstrom^2"),
symmetry=3,
fourier=([[
0.0400372, 0.0301986, -6.4787, -0.0248675,
-0.0324753
], [0.0312541, 0.0538, -0.493785, 0.0965968,
0.125292]], "kJ/mol")),
],
spinMultiplicity=1,
opticalIsomers=1,
),
)
self.nC4H8.fromSMILES('CCC=C')
self.H2O = Species(
label='H2O',
conformer=Conformer(
E0=(-269.598, 'kJ/mol'),
modes=[
IdealGasTranslation(mass=(18.01, "g/mol")),
NonlinearRotor(inertia=([0.630578, 1.15529,
1.78586], "amu*angstrom^2"),
symmetry=2),
HarmonicOscillator(
frequencies=([1622.09, 3771.85, 3867.85], "cm^-1")),
],
spinMultiplicity=1,
opticalIsomers=1,
),
)
self.H2O.fromSMILES('O')
self.N2 = Species(
label='N2',
molecularWeight=(28.04, "g/mol"),
transportData=TransportData(sigma=(3.41, "angstrom"),
epsilon=(124, "K")),
energyTransferModel=None,
)
self.N2.fromSMILES('N#N')
logging.error('to TS')
self.TS = TransitionState(
label='TS',
conformer=Conformer(
E0=(-42.4373, "kJ/mol"),
modes=[
IdealGasTranslation(mass=(74.07, "g/mol")),
NonlinearRotor(inertia=([40.518, 232.666,
246.092], "u*angstrom**2"),
symmetry=1,
quantum=False),
HarmonicOscillator(frequencies=([
134.289, 302.326, 351.792, 407.986, 443.419, 583.988,
699.001, 766.1, 777.969, 829.671, 949.753, 994.731,
1013.59, 1073.98, 1103.79, 1171.89, 1225.91, 1280.67,
1335.08, 1373.9, 1392.32, 1417.43, 1469.51, 1481.61,
1490.16, 1503.73, 1573.16, 2972.85, 2984.3, 3003.67,
3045.78, 3051.77, 3082.37, 3090.44, 3190.73, 3708.52
], "kayser")),
HinderedRotor(inertia=(2.68206, "amu*angstrom^2"),
symmetry=3,
barrier=(3.35244, "kcal/mol")),
HinderedRotor(inertia=(9.77669, "amu*angstrom^2"),
symmetry=1,
fourier=([[
0.208938, -1.55291, -4.05398, -0.105798,
-0.104752
],
[
2.00518, -0.020767, -0.333595,
0.137791, -0.274578
]], "kJ/mol")),
],
spinMultiplicity=1,
opticalIsomers=1,
),
frequency=(-2038.34, 'cm^-1'),
)
self.reaction = Reaction(label='dehydration',
reactants=[self.nC4H10O],
products=[self.nC4H8, self.H2O],
transitionState=self.TS,
kinetics=Arrhenius(A=(0.0387, 'm^3/(mol*s)'),
n=2.7,
Ea=(2.6192e4, 'J/mol'),
T0=(1, 'K')))
self.network = Network(
label='n-butanol',
isomers=[Configuration(self.nC4H10O)],
reactants=[],
products=[Configuration(self.nC4H8, self.H2O)],
pathReactions=[self.reaction],
bathGas={self.N2: 1.0},
)
self.pdepnetwork = deepcopy(self.network)
self.pdepnetwork.__class__ = PDepNetwork
self.pdepnetwork.source = [self.pdepnetwork.isomers[0].species[0]]
self.pdepnetwork.index = 1
self.pdepnetwork.explored = []
def test_SS_solver(self):
c = self.pdepnetwork.solve_SS_network(1000.0, 100000.0)
self.assertAlmostEquals(c[0], 4.791463e-06, 2)
def test_energy_filter(self):
rxns = self.pdepnetwork.get_energy_filtered_reactions(1000.0, 0.0)
self.assertEquals(len(rxns), 1)
self.assertEquals(rxns[0], self.pdepnetwork.pathReactions[0])
def test_flux_filter(self):
rxns = self.pdepnetwork.get_rate_filtered_reactions(
1000.0, 100000.0, 1.0)
self.assertEquals(len(rxns), 0)
