def transitionState(label, *args, **kwargs):
"""Load a transition state from an input file"""
global transition_state_dict
if label in transition_state_dict:
raise ValueError(
'Multiple occurrences of transition state with label {0!r}.'.
format(label))
logging.info('Loading transition state {0}...'.format(label))
ts = TransitionState(label=label)
transition_state_dict[label] = ts
if len(args) == 1 and len(kwargs) == 0:
# The argument is a path to a conformer input file
path = args[0]
job = StatMechJob(species=ts, path=path)
job_list.append(job)
elif len(args) == 0:
# The species parameters are given explicitly
E0 = None
modes = []
spin_multiplicity = 1
optical_isomers = 1
frequency = None
for key, value in kwargs.items():
if key == 'E0':
E0 = value
elif key == 'modes':
modes = value
elif key == 'spinMultiplicity':
spin_multiplicity = value
elif key == 'opticalIsomers':
optical_isomers = value
elif key == 'frequency':
frequency = value
else:
raise TypeError(
'transition_state() got an unexpected keyword argument {0!r}.'
.format(key))
ts.conformer = Conformer(E0=E0,
modes=modes,
spin_multiplicity=spin_multiplicity,
optical_isomers=optical_isomers)
ts.frequency = frequency
else:
if len(args) == 0 and len(kwargs) == 0:
raise InputError(
'The transition_state needs to reference a quantum job file or contain kinetic information.'
)
raise InputError(
'The transition_state can only link a quantum job or directly input information, not both.'
)
return ts
def transitionState(label, *args, **kwargs):
global transitionStateDict
if label in transitionStateDict:
raise ValueError(
'Multiple occurrences of transition state with label {0!r}.'.
format(label))
logging.info('Loading transition state {0}...'.format(label))
ts = TransitionState(label=label)
transitionStateDict[label] = ts
if len(args) == 1 and len(kwargs) == 0:
# The argument is a path to a conformer input file
path = args[0]
job = StatMechJob(species=ts, path=path)
jobList.append(job)
elif len(args) == 0 and len(kwargs) > 0:
# The species parameters are given explicitly
E0 = None
modes = []
spinMultiplicity = 1
opticalIsomers = 1
frequency = None
for key, value in kwargs.items():
if key == 'E0':
E0 = value
elif key == 'modes':
modes = value
elif key == 'spinMultiplicity':
spinMultiplicity = value
elif key == 'opticalIsomers':
opticalIsomers = value
elif key == 'frequency':
frequency = value
else:
raise TypeError(
'transitionState() got an unexpected keyword argument {0!r}.'
.format(key))
ts.conformer = Conformer(E0=E0,
modes=modes,
spinMultiplicity=spinMultiplicity,
opticalIsomers=opticalIsomers)
ts.frequency = frequency
return ts
def test_give_tlist_for_kineticsjob(self):
"""
Ensures that the proper temperature ranges are set when Tlist is specified
"""
rxn = Reaction(transition_state=TransitionState())
t_list = [50.7, 100, 300, 800, 1255]
kjob = KineticsJob(rxn, Tlist=(t_list, 'K'))
self.assertEqual(min(t_list), kjob.Tmin.value_si)
self.assertEqual(max(t_list), kjob.Tmax.value_si)
self.assertEqual(len(t_list), kjob.Tcount)
def transitionState(label, *args, **kwargs):
global transitionStateDict
if label in transitionStateDict:
raise ValueError('Multiple occurrences of transition state with label {0!r}.'.format(label))
logging.info('Loading transition state {0}...'.format(label))
ts = TransitionState(label=label)
transitionStateDict[label] = ts
if len(args) == 1 and len(kwargs) == 0:
# The argument is a path to a conformer input file
path = args[0]
job = StatMechJob(species=ts, path=path)
jobList.append(job)
elif len(args) == 0:
# The species parameters are given explicitly
E0 = None
modes = []
spinMultiplicity = 1
opticalIsomers = 1
frequency = None
for key, value in kwargs.items():
if key == 'E0':
E0 = value
elif key == 'modes':
modes = value
elif key == 'spinMultiplicity':
spinMultiplicity = value
elif key == 'opticalIsomers':
opticalIsomers = value
elif key == 'frequency':
frequency = value
else:
raise TypeError('transitionState() got an unexpected keyword argument {0!r}.'.format(key))
ts.conformer = Conformer(E0=E0, modes=modes, spinMultiplicity=spinMultiplicity, opticalIsomers=opticalIsomers)
ts.frequency = frequency
else:
if len(args) == 0 and len(kwargs) == 0:
raise InputError('The transitionState needs to reference a quantum job file or contain kinetic information.')
raise InputError('The transitionState can only link a quantum job or directly input information, not both.')
return ts
def test_give_temperature_range_for_kineticsjob(self):
"""
Ensures that Tlist is set when a range of temperatures is specified
"""
rxn = Reaction(transition_state=TransitionState())
kjob = KineticsJob(rxn, Tmin=(50, 'K'), Tmax=(4000, 'K'), Tcount=5)
self.assertEqual(5, len(kjob.Tlist.value_si))
self.assertEqual(50, min(kjob.Tlist.value_si))
self.assertAlmostEqual(4000, max(kjob.Tlist.value_si))
inverse_tlist = 1 / kjob.Tlist.value_si
self.assertAlmostEqual(inverse_tlist[1] - inverse_tlist[0],
inverse_tlist[-1] - inverse_tlist[-2],
msg='The points for fitting do not appear 1/T spaced. '
'Obtained values of {0} and {1}'.format(inverse_tlist[1] - inverse_tlist[0],
inverse_tlist[-1] - inverse_tlist[-2]))
def test_get_tlist_for_kineticsjob(self):
"""
Ensures that Tlist is set when no range is specified
"""
rxn = Reaction(transition_state=TransitionState())
kjob = KineticsJob(rxn)
self.assertAlmostEqual(298, kjob.Tmin.value_si)
self.assertAlmostEqual(2500, kjob.Tmax.value_si)
self.assertEqual(50, kjob.Tcount)
self.assertEqual(50, len(kjob.Tlist.value_si))
self.assertAlmostEqual(298, min(kjob.Tlist.value_si))
self.assertAlmostEqual(2500, max(kjob.Tlist.value_si))
inverse_tlist = 1 / kjob.Tlist.value_si
self.assertAlmostEqual(inverse_tlist[1] - inverse_tlist[0],
inverse_tlist[-1] - inverse_tlist[-2],
msg='The points for fitting do not appear 1/T spaced. '
'Obtained values of {0} and {1}'.format(inverse_tlist[1] - inverse_tlist[0],
inverse_tlist[-1] - inverse_tlist[-2]))
def loadFAMEInput(path, moleculeDict=None):
"""
Load the contents of a FAME input file into the MEASURE object. FAME
is an early version of MEASURE written in Fortran and used by RMG-Java.
This script enables importing FAME input files into MEASURE so we can
use the additional functionality that MEASURE provides. Note that it
is mostly designed to load the FAME input files generated automatically
by RMG-Java, and may not load hand-crafted FAME input files. If you
specify a `moleculeDict`, then this script will use it to associate
the species with their structures.
"""
def readMeaningfulLine(f):
line = f.readline()
while line != '':
line = line.strip()
if len(line) > 0 and line[0] != '#':
return line
else:
line = f.readline()
return ''
moleculeDict = moleculeDict or {}
logging.info('Loading file "{0}"...'.format(path))
f = open(path)
job = PressureDependenceJob(network=None)
# Read method
method = readMeaningfulLine(f).lower()
if method == 'modifiedstrongcollision':
job.method = 'modified strong collision'
elif method == 'reservoirstate':
job.method = 'reservoir state'
# Read temperatures
Tcount, Tunits, Tmin, Tmax = readMeaningfulLine(f).split()
job.Tmin = Quantity(float(Tmin), Tunits)
job.Tmax = Quantity(float(Tmax), Tunits)
job.Tcount = int(Tcount)
Tlist = []
for i in range(int(Tcount)):
Tlist.append(float(readMeaningfulLine(f)))
job.Tlist = Quantity(Tlist, Tunits)
# Read pressures
Pcount, Punits, Pmin, Pmax = readMeaningfulLine(f).split()
job.Pmin = Quantity(float(Pmin), Punits)
job.Pmax = Quantity(float(Pmax), Punits)
job.Pcount = int(Pcount)
Plist = []
for i in range(int(Pcount)):
Plist.append(float(readMeaningfulLine(f)))
job.Plist = Quantity(Plist, Punits)
# Read interpolation model
model = readMeaningfulLine(f).split()
if model[0].lower() == 'chebyshev':
job.interpolationModel = ('chebyshev', int(model[1]), int(model[2]))
elif model[0].lower() == 'pdeparrhenius':
job.interpolationModel = ('pdeparrhenius',)
# Read grain size or number of grains
job.minimumGrainCount = 0
job.maximumGrainSize = None
for i in range(2):
data = readMeaningfulLine(f).split()
if data[0].lower() == 'numgrains':
job.minimumGrainCount = int(data[1])
elif data[0].lower() == 'grainsize':
job.maximumGrainSize = (float(data[2]), data[1])
# A FAME file is almost certainly created during an RMG job, so use RMG mode
job.rmgmode = True
# Create the Network
job.network = Network()
# Read collision model
data = readMeaningfulLine(f)
assert data.lower() == 'singleexpdown'
alpha0units, alpha0 = readMeaningfulLine(f).split()
T0units, T0 = readMeaningfulLine(f).split()
n = readMeaningfulLine(f)
energyTransferModel = SingleExponentialDown(
alpha0 = Quantity(float(alpha0), alpha0units),
T0 = Quantity(float(T0), T0units),
n = float(n),
)
speciesDict = {}
# Read bath gas parameters
bathGas = Species(label='bath_gas', energyTransferModel=energyTransferModel)
molWtunits, molWt = readMeaningfulLine(f).split()
if molWtunits == 'u': molWtunits = 'amu'
bathGas.molecularWeight = Quantity(float(molWt), molWtunits)
sigmaLJunits, sigmaLJ = readMeaningfulLine(f).split()
epsilonLJunits, epsilonLJ = readMeaningfulLine(f).split()
assert epsilonLJunits == 'J'
bathGas.transportData = TransportData(
sigma = Quantity(float(sigmaLJ), sigmaLJunits),
epsilon = Quantity(float(epsilonLJ) / constants.kB, 'K'),
)
job.network.bathGas = {bathGas: 1.0}
# Read species data
Nspec = int(readMeaningfulLine(f))
for i in range(Nspec):
species = Species()
species.conformer = Conformer()
species.energyTransferModel = energyTransferModel
# Read species label
species.label = readMeaningfulLine(f)
speciesDict[species.label] = species
if species.label in moleculeDict:
species.molecule = [moleculeDict[species.label]]
# Read species E0
E0units, E0 = readMeaningfulLine(f).split()
species.conformer.E0 = Quantity(float(E0), E0units)
species.conformer.E0.units = 'kJ/mol'
# Read species thermo data
H298units, H298 = readMeaningfulLine(f).split()
S298units, S298 = readMeaningfulLine(f).split()
Cpcount, Cpunits = readMeaningfulLine(f).split()
Cpdata = []
for i in range(int(Cpcount)):
Cpdata.append(float(readMeaningfulLine(f)))
if S298units == 'J/mol*K': S298units = 'J/(mol*K)'
if Cpunits == 'J/mol*K': Cpunits = 'J/(mol*K)'
species.thermo = ThermoData(
H298 = Quantity(float(H298), H298units),
S298 = Quantity(float(S298), S298units),
Tdata = Quantity([300,400,500,600,800,1000,1500], "K"),
Cpdata = Quantity(Cpdata, Cpunits),
Cp0 = (Cpdata[0], Cpunits),
CpInf = (Cpdata[-1], Cpunits),
)
# Read species collision parameters
molWtunits, molWt = readMeaningfulLine(f).split()
if molWtunits == 'u': molWtunits = 'amu'
species.molecularWeight = Quantity(float(molWt), molWtunits)
sigmaLJunits, sigmaLJ = readMeaningfulLine(f).split()
epsilonLJunits, epsilonLJ = readMeaningfulLine(f).split()
assert epsilonLJunits == 'J'
species.transportData = TransportData(
sigma = Quantity(float(sigmaLJ), sigmaLJunits),
epsilon = Quantity(float(epsilonLJ) / constants.kB, 'K'),
)
# Read species vibrational frequencies
freqCount, freqUnits = readMeaningfulLine(f).split()
frequencies = []
for j in range(int(freqCount)):
frequencies.append(float(readMeaningfulLine(f)))
species.conformer.modes.append(HarmonicOscillator(
frequencies = Quantity(frequencies, freqUnits),
))
# Read species external rotors
rotCount, rotUnits = readMeaningfulLine(f).split()
if int(rotCount) > 0:
raise NotImplementedError('Cannot handle external rotational modes in FAME input.')
# Read species internal rotors
freqCount, freqUnits = readMeaningfulLine(f).split()
frequencies = []
for j in range(int(freqCount)):
frequencies.append(float(readMeaningfulLine(f)))
barrCount, barrUnits = readMeaningfulLine(f).split()
barriers = []
for j in range(int(barrCount)):
barriers.append(float(readMeaningfulLine(f)))
if barrUnits == 'cm^-1':
barrUnits = 'J/mol'
barriers = [barr * constants.h * constants.c * constants.Na * 100. for barr in barriers]
elif barrUnits in ['Hz', 's^-1']:
barrUnits = 'J/mol'
barriers = [barr * constants.h * constants.Na for barr in barriers]
elif barrUnits != 'J/mol':
raise Exception('Unexpected units "{0}" for hindered rotor barrier height.'.format(barrUnits))
inertia = [V0 / 2.0 / (nu * constants.c * 100.)**2 / constants.Na for nu, V0 in zip(frequencies, barriers)]
for I, V0 in zip(inertia, barriers):
species.conformer.modes.append(HinderedRotor(
inertia = Quantity(I,"kg*m^2"),
barrier = Quantity(V0,barrUnits),
symmetry = 1,
semiclassical = False,
))
# Read overall symmetry number
species.conformer.spinMultiplicity = int(readMeaningfulLine(f))
# Read isomer, reactant channel, and product channel data
Nisom = int(readMeaningfulLine(f))
Nreac = int(readMeaningfulLine(f))
Nprod = int(readMeaningfulLine(f))
for i in range(Nisom):
data = readMeaningfulLine(f).split()
assert data[0] == '1'
job.network.isomers.append(speciesDict[data[1]])
for i in range(Nreac):
data = readMeaningfulLine(f).split()
assert data[0] == '2'
job.network.reactants.append([speciesDict[data[1]], speciesDict[data[2]]])
for i in range(Nprod):
data = readMeaningfulLine(f).split()
if data[0] == '1':
job.network.products.append([speciesDict[data[1]]])
elif data[0] == '2':
job.network.products.append([speciesDict[data[1]], speciesDict[data[2]]])
# Read path reactions
Nrxn = int(readMeaningfulLine(f))
for i in range(Nrxn):
# Read and ignore reaction equation
equation = readMeaningfulLine(f)
reaction = Reaction(transitionState=TransitionState(), reversible=True)
job.network.pathReactions.append(reaction)
reaction.transitionState.conformer = Conformer()
# Read reactant and product indices
data = readMeaningfulLine(f).split()
reac = int(data[0]) - 1
prod = int(data[1]) - 1
if reac < Nisom:
reaction.reactants = [job.network.isomers[reac]]
elif reac < Nisom+Nreac:
reaction.reactants = job.network.reactants[reac-Nisom]
else:
reaction.reactants = job.network.products[reac-Nisom-Nreac]
if prod < Nisom:
reaction.products = [job.network.isomers[prod]]
elif prod < Nisom+Nreac:
reaction.products = job.network.reactants[prod-Nisom]
else:
reaction.products = job.network.products[prod-Nisom-Nreac]
# Read reaction E0
E0units, E0 = readMeaningfulLine(f).split()
reaction.transitionState.conformer.E0 = Quantity(float(E0), E0units)
reaction.transitionState.conformer.E0.units = 'kJ/mol'
# Read high-pressure limit kinetics
data = readMeaningfulLine(f)
assert data.lower() == 'arrhenius'
Aunits, A = readMeaningfulLine(f).split()
if '/' in Aunits:
index = Aunits.find('/')
Aunits = '{0}/({1})'.format(Aunits[0:index], Aunits[index+1:])
Eaunits, Ea = readMeaningfulLine(f).split()
n = readMeaningfulLine(f)
reaction.kinetics = Arrhenius(
A = Quantity(float(A), Aunits),
Ea = Quantity(float(Ea), Eaunits),
n = Quantity(float(n)),
)
reaction.kinetics.Ea.units = 'kJ/mol'
f.close()
job.network.isomers = [Configuration(isomer) for isomer in job.network.isomers]
job.network.reactants = [Configuration(*reactants) for reactants in job.network.reactants]
job.network.products = [Configuration(*products) for products in job.network.products]
return job
def setUp(self):
"""
A function 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")),
],
spin_multiplicity=1,
optical_isomers=1,
),
molecular_weight=(74.07, "g/mol"),
transport_data=TransportData(sigma=(5.94, 'angstrom'),
epsilon=(559, 'K')),
energy_transfer_model=SingleExponentialDown(
alpha0=(447.5 * 0.011962, "kJ/mol"), T0=(300, "K"), n=0.85),
)
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")),
],
spin_multiplicity=1,
optical_isomers=1,
),
)
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")),
],
spin_multiplicity=1,
optical_isomers=1,
),
)
self.N2 = Species(
label='N2',
molecular_weight=(28.04, "g/mol"),
transport_data=TransportData(sigma=(3.41, "angstrom"),
epsilon=(124, "K")),
energy_transfer_model=None,
)
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")),
],
spin_multiplicity=1,
optical_isomers=1,
),
frequency=(-2038.34, 'cm^-1'),
)
self.reaction = Reaction(
label='dehydration',
reactants=[self.nC4H10O],
products=[self.nC4H8, self.H2O],
transition_state=self.TS,
)
self.network = Network(
label='n-butanol',
isomers=[Configuration(self.nC4H10O)],
reactants=[],
products=[Configuration(self.nC4H8, self.H2O)],
path_reactions=[self.reaction],
bath_gas={self.N2: 1.0},
)
def setUp(self):
"""
A method that is called prior to each unit test in this class.
"""
ethylene = Species(
label = 'C2H4',
conformer = Conformer(
E0 = (44.7127, 'kJ/mol'),
modes = [
IdealGasTranslation(
mass = (28.0313, 'amu'),
),
NonlinearRotor(
inertia = (
[3.41526, 16.6498, 20.065],
'amu*angstrom^2',
),
symmetry = 4,
),
HarmonicOscillator(
frequencies = (
[828.397, 970.652, 977.223, 1052.93, 1233.55, 1367.56, 1465.09, 1672.25, 3098.46, 3111.7, 3165.79, 3193.54],
'cm^-1',
),
),
],
spinMultiplicity = 1,
opticalIsomers = 1,
),
)
hydrogen = Species(
label = 'H',
conformer = Conformer(
E0 = (211.794, 'kJ/mol'),
modes = [
IdealGasTranslation(
mass = (1.00783, 'amu'),
),
],
spinMultiplicity = 2,
opticalIsomers = 1,
),
)
ethyl = Species(
label = 'C2H5',
conformer = Conformer(
E0 = (111.603, 'kJ/mol'),
modes = [
IdealGasTranslation(
mass = (29.0391, 'amu'),
),
NonlinearRotor(
inertia = (
[4.8709, 22.2353, 23.9925],
'amu*angstrom^2',
),
symmetry = 1,
),
HarmonicOscillator(
frequencies = (
[482.224, 791.876, 974.355, 1051.48, 1183.21, 1361.36, 1448.65, 1455.07, 1465.48, 2688.22, 2954.51, 3033.39, 3101.54, 3204.73],
'cm^-1',
),
),
HinderedRotor(
inertia = (1.11481, 'amu*angstrom^2'),
symmetry = 6,
barrier = (0.244029, 'kJ/mol'),
semiclassical = None,
),
],
spinMultiplicity = 2,
opticalIsomers = 1,
),
)
TS = TransitionState(
label = 'TS',
conformer = Conformer(
E0 = (266.694, 'kJ/mol'),
modes = [
IdealGasTranslation(
mass = (29.0391, 'amu'),
),
NonlinearRotor(
inertia = (
[6.78512, 22.1437, 22.2114],
'amu*angstrom^2',
),
symmetry = 1,
),
HarmonicOscillator(
frequencies = (
[412.75, 415.206, 821.495, 924.44, 982.714, 1024.16, 1224.21, 1326.36, 1455.06, 1600.35, 3101.46, 3110.55, 3175.34, 3201.88],
'cm^-1',
),
),
],
spinMultiplicity = 2,
opticalIsomers = 1,
),
frequency = (-750.232, 'cm^-1'),
)
self.reaction = Reaction(
reactants = [hydrogen, ethylene],
products = [ethyl],
kinetics = Arrhenius(
A = (501366000.0, 'cm^3/(mol*s)'),
n = 1.637,
Ea = (4.32508, 'kJ/mol'),
T0 = (1, 'K'),
Tmin = (300, 'K'),
Tmax = (2500, 'K'),
),
transitionState = TS,
)
# CC(=O)O[O]
acetylperoxy = Species(
label='acetylperoxy',
thermo=Wilhoit(Cp0=(4.0*constants.R,"J/(mol*K)"), CpInf=(21.0*constants.R,"J/(mol*K)"), a0=-3.95, a1=9.26, a2=-15.6, a3=8.55, B=(500.0,"K"), H0=(-6.151e+04,"J/mol"), S0=(-790.2,"J/(mol*K)")),
)
# C[C]=O
acetyl = Species(
label='acetyl',
thermo=Wilhoit(Cp0=(4.0*constants.R,"J/(mol*K)"), CpInf=(15.5*constants.R,"J/(mol*K)"), a0=0.2541, a1=-0.4712, a2=-4.434, a3=2.25, B=(500.0,"K"), H0=(-1.439e+05,"J/mol"), S0=(-524.6,"J/(mol*K)")),
)
# [O][O]
oxygen = Species(
label='oxygen',
thermo=Wilhoit(Cp0=(3.5*constants.R,"J/(mol*K)"), CpInf=(4.5*constants.R,"J/(mol*K)"), a0=-0.9324, a1=26.18, a2=-70.47, a3=44.12, B=(500.0,"K"), H0=(1.453e+04,"J/mol"), S0=(-12.19,"J/(mol*K)")),
)
self.reaction2 = Reaction(
reactants=[acetyl, oxygen],
products=[acetylperoxy],
kinetics = Arrhenius(
A = (2.65e12, 'cm^3/(mol*s)'),
n = 0.0,
Ea = (0.0, 'kJ/mol'),
T0 = (1, 'K'),
Tmin = (300, 'K'),
Tmax = (2000, 'K'),
),
)