def species(label='', E0=None, states=None, lennardJones=None, molecularWeight=0.0):
global speciesDict
if E0 is not None: E0 = processQuantity(E0)[0]
else: E0 = 0.0
spec = Species(label=label, states=states, E0=E0, lennardJones=lennardJones)
spec.molecularWeight = processQuantity(molecularWeight)[0]
speciesDict[label] = spec
logging.debug('Found species "%s"' % spec)
def testThermoGeneration(self):
# The test cases represent 1,3-hexadiene and all of its possible
# unimolecular bond fission products (i.e. products resulting from the
# breaking of any single bond in 1,3-hexadiene)
testCases = [
# SMILES symm H298 S298 Cp300 Cp400 Cp500 Cp600 Cp800 Cp1000 Cp1500
['C=CC=CCC', 3, 13.45, 86.3671, 29.49, 37.67, 44.54, 50.12, 58.66, 64.95, 74.71],
['[CH]=CC=CCC', 3, 72.55, 87.7571, 29.3 , 36.92, 43.18, 48.20, 55.84, 61.46, 70.18],
['C=[C]C=CCC', 3, 61.15, 87.0771, 29.68, 36.91, 43.03, 48.11, 55.96, 61.78, 71.54],
['C=C[C]=CCC', 3, 61.15, 87.0771, 29.68, 36.91, 43.03, 48.11, 55.96, 61.78, 71.54],
['C=CC=[C]CC', 3, 70.35, 88.1771, 29.15, 36.46, 42.6 , 47.60, 55.32, 61.04, 69.95],
['C=CC=C[CH]C', 6, 38.24, 84.4098, 27.79, 35.46, 41.94, 47.43, 55.74, 61.92, 71.86],
['C=CC=CC[CH2]', 2, 62.45, 89.7827, 28.72, 36.31, 42.63, 47.72, 55.5 , 61.21, 70.05],
#['[H]', 1, 49.00, 2.61 , -0.77, -1.36, -1.91, -2.4 , -3.16, -3.74, -4.66],
['[CH3]', 6, 34.81, 46.3698, 9.14, 10.18, 10.81, 11.34, 12.57, 13.71, 15.2 ],
['C=CC=C[CH2]', 2, 46.11, 75.8227, 22.54, 28.95, 34.24, 38.64, 45.14, 49.97, 57.85],
['[CH2]C', 6, 28.60, 59.8698, 11.73, 14.46, 17.05, 19.34, 23.02, 25.91, 31.53],
['C=CC=[CH]', 1, 85.18, 69.37 , 18.93, 23.55, 27.16, 29.92, 34.02, 37.03, 41.81],
['C=[CH]', 1, 71.62, 56.61 , 10.01, 11.97, 13.66, 15.08, 17.32, 19.05, 21.85],
['[CH]=CCC', 3, 58.99, 74.9971, 20.38, 25.34, 29.68, 33.36, 39.14, 43.48, 50.22],
]
thermoDatabase = loadThermoDatabase('output/RMG_Database/thermo_groups', group=True, old=True)
failMessage = '\n'
for smiles, symm, H298, S298, Cp300, Cp400, Cp500, Cp600, Cp800, Cp1000, Cp1500 in testCases:
species = Species(molecule=[Molecule(SMILES=smiles)])
species.generateResonanceIsomers()
thermoData = generateThermoData(species.molecule[0])
molecule = species.molecule[0]
for mol in species.molecule[1:]:
thermoData0 = generateThermoData(mol)
if thermoData0.getEnthalpy(298) < thermoData.getEnthalpy(298):
thermoData = thermoData0
molecule = mol
if molecule.calculateSymmetryNumber() != symm:
failMessage += "For %s, expected symmetry number of %g, got %g\n" % (smiles, symm, molecule.calculateSymmetryNumber())
if abs(1 - thermoData.getEnthalpy(298) / 4184 / H298) > 0.001:
failMessage += "For %s, expected H298 of %g kcal/mol, got %g kcal/mol\n" % (smiles, H298, thermoData.getEnthalpy(298) / 4184)
if abs(1 - thermoData.getEntropy(298) / 4.184 / S298) > 0.001:
failMessage += "For %s, expected S298 of %g cal/mol*K, got %g cal/mol*K\n" % (smiles, S298, thermoData.getEntropy(298) / 4.184)
for T, Cp in zip([300, 400, 500, 600, 800, 1000, 1500], [Cp300, Cp400, Cp500, Cp600, Cp800, Cp1000, Cp1500]):
if abs(1 - thermoData.getHeatCapacity(T) / 4.184 / Cp) > 0.001:
failMessage += "For %s, expected Cp at %g K of %g cal/mol*K, got %g cal/mol*K\n" % (smiles, T, Cp, thermoData.getHeatCapacity(T) / 4.184)
self.assertEqual(failMessage, '\n', failMessage)
def species(label='', E0=None, states=None, thermo=None, lennardJones=None, molecularWeight=0.0, SMILES='', InChI=''):
global speciesDict
if label == '': raise InputError('Missing "label" attribute in species() block.')
if E0 is not None: E0 = processQuantity(E0)[0]
else: E0 = 0.0
spec = Species(label=label, states=states, thermo=thermo, E0=E0, lennardJones=lennardJones)
if InChI != '':
spec.molecule = [Molecule(InChI=InChI)]
elif SMILES != '':
spec.molecule = [Molecule(SMILES=SMILES)]
spec.molecularWeight = processQuantity(molecularWeight)[0]
speciesDict[label] = spec
logging.debug('Found species "%s"' % spec)
# If the molecular weight was not specified but the structure was, then
# get the molecular weight from the structure
if spec.molecularWeight == 0.0 and spec.molecule is not None and len(spec.molecule) > 0:
spec.molecularWeight = spec.molecule[0].getMolecularWeight()
grainSize = 0.0
elif data[0].lower() == 'grainsize':
assert data[2] == 'J/mol'
Ngrains = 0
grainSize = float(data[2])
network = Network()
# Read collision model
data = readMeaningfulLine(f).split()
assert data[0].lower() == 'singleexpdown'
assert data[1] == 'J/mol'
network.collisionModel = SingleExponentialDownModel(alpha0=float(data[2]), T0=298, n=0.0)
# Read bath gas parameters
bathGas = Species()
bathGas.molecularWeight = float(readMeaningfulLine(f).split()[1]) / 1000.0
bathGas.lennardJones = LennardJones(sigma=float(readMeaningfulLine(f).split()[1]), epsilon=float(readMeaningfulLine(f).split()[1]))
# Read species data
Nspec = int(readMeaningfulLine(f))
speciesDict = {}
for i in range(Nspec):
spec = Species()
# Read species label
spec.label = readMeaningfulLine(f)
speciesDict[spec.label] = spec
if spec.label in moleculeDict:
spec.molecule = [moleculeDict[spec.label]]
# Read species E0
data = readMeaningfulLine(f).split()
