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")),
],
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.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.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.configuration = Configuration(self.nC4H8, self.H2O)
def generate_statmech(self):
"""
Generate molecular degree of freedom data for the species. You must
have already provided a thermodynamics model using e.g.
:meth:`generate_thermo_data()`.
"""
logging.debug("Generating statmech for species {}".format(self.label))
from rmgpy.data.rmg import get_db
try:
statmech_db = get_db('statmech')
if not statmech_db: raise Exception
except Exception:
logging.debug(
'Could not obtain the stat. mech database. Not generating stat. mech...'
)
raise
molecule = self.molecule[0]
conformer = statmech_db.get_statmech_data(molecule,
self.get_thermo_data())
if self.conformer is None:
self.conformer = Conformer()
if self.conformer.E0 is None:
self.set_e0_with_thermo()
self.conformer.modes = conformer.modes
self.conformer.spin_multiplicity = conformer.spin_multiplicity
if self.conformer.E0 is None or not self.has_statmech():
logging.error('The conformer in question is {}'.format(
self.conformer))
raise StatmechError(
'Species {0} does not have stat mech after generate_statmech called'
.format(self.label))
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 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 read_scan(self):
"""
Read quantum optimization job files at self.calc_path to determine
vectors of angles self.phis, xyz coordinates (self.xyzs)
energies (self.Es) and atom numbers (self.atnums) for each point
"""
from arkane.util import determine_qm_software
if os.path.isdir(self.calc_path):
massdict = {
el.number: el.mass
for el in element_list if el.isotope == -1
}
N = len(self.pivots)
phis = []
xyzs = []
Es = []
atnums = []
for f in os.listdir(self.calc_path):
name, identifier = '.'.join(
f.split('.')[:-1]), f.split('.')[-1]
if identifier != 'out':
continue
outs = name.split('_')
phivals = [float(x) for x in outs[-N:]]
phivals = fill360s(phivals)
fpath = os.path.join(self.calc_path, f)
lg = determine_qm_software(fpath)
E = lg.load_energy()
xyz, atnum, _ = lg.load_geometry()
for phival in phivals:
phis.append(np.array(phival))
Es.append(lg.load_energy())
xyzs.append(xyz)
if not self.atnums:
atnums.append(atnum)
if atnums:
self.atnums = atnums
q = len(phis)
for i in range(
N): # add the negative values to improve fit near 0.0
for j in range(q):
phi = phis[j]
if np.isclose(phi[i], 360.0):
continue
nvec = deepcopy(phi)
nvec[i] -= 360.0
if any([np.array_equal(nvec, x) for x in phis]):
continue
phis.append(nvec)
Es.append(Es[j])
xyzs.append(xyzs[j])
atnums.append(atnums[j])
self.xyzs = np.array(xyzs)
self.Es = np.array(Es)
self.E0 = self.Es.min()
self.Es -= self.E0
self.phis = np.array(phis)
self.phis *= np.pi / 180.0
inds = None
if len(self.phis[0]) == 1:
self.phis = np.array([phi[0] for phi in self.phis])
inds = np.argsort(self.phis)
self.confs = [
Conformer(number=self.atnums,
coordinates=(self.xyzs[k], "angstrom"),
mass=(np.array([massdict[x]
for x in self.atnums]), "amu"))
for k in range(len(self.xyzs))
]
self.rootDs = np.array([
np.prod([
conf.get_internal_reduced_moment_of_inertia(self.pivots[k],
self.tops[k],
option=3)
for k in range(len(self.pivots))
])**0.5 for conf in self.confs
])
if inds is not None:
self.rootDs = self.rootDs[inds]
self.phis = self.phis[inds]
self.Es = self.Es[inds]
self.xyzs = self.xyzs[inds]
elif os.path.isfile(
self.calc_path
): # reading a 1-D scan file, assume internal reduced moment of inertia is constant
N = len(self.pivots)
lg = determine_qm_software(self.calc_path)
self.Es, self.phis = lg.load_scan_energies()
self.atnums = self.conformer.number
rootD = self.conformer.get_internal_reduced_moment_of_inertia(
self.pivots[0], self.tops[0])**0.5
self.rootDs = [rootD for i in range(len(self.Es))]
phis = self.phis.tolist()
for j, phi in enumerate(
self.phis
): # add the negative values to improve fit near 0.0
if phi != 2.0 * np.pi:
phis.append(phi - 2.0 * np.pi)
phis = np.array(phis)
inds = np.argsort(phis)
self.phis = phis[inds]
Es = self.Es.tolist()
Es.extend(Es[1:])
self.Es = np.array(Es)[inds]
self.rootDs.extend(self.rootDs[1:])
self.rootDs = np.array(self.rootDs)[inds].tolist()
else:
raise IOError("path {} is not a file or a directory".format(
self.calc_path))
def species(label, *args, **kwargs):
"""Load a species from an input file"""
global species_dict, job_list
if label in species_dict:
raise ValueError(
'Multiple occurrences of species with label {0!r}.'.format(label))
logging.info('Loading species {0}...'.format(label))
spec = Species(label=label)
species_dict[label] = spec
path = None
if len(args) == 1:
# The argument is a path to a conformer input file
path = args[0]
job = StatMechJob(species=spec, path=path)
logging.debug('Added species {0} to a stat mech job.'.format(label))
job_list.append(job)
elif len(args) > 1:
raise InputError('species {0} can only have two non-keyword argument '
'which should be the species label and the '
'path to a quantum file.'.format(spec.label))
if len(kwargs) > 0:
# The species parameters are given explicitly
structure = None
E0 = None
modes = []
spin_multiplicity = 0
optical_isomers = 1
molecular_weight = None
collision_model = None
energy_transfer_model = None
thermo = None
reactive = True
for key, value in kwargs.items():
if key == 'structure':
structure = value
elif key == 'E0':
E0 = value
elif key == 'modes':
modes = value
elif key == 'spinMultiplicity':
spin_multiplicity = value
elif key == 'opticalIsomers':
optical_isomers = value
elif key == 'molecularWeight':
molecular_weight = value
elif key == 'collisionModel':
collision_model = value
elif key == 'energyTransferModel':
energy_transfer_model = value
elif key == 'thermo':
thermo = value
elif key == 'reactive':
reactive = value
else:
raise TypeError(
'species() got an unexpected keyword argument {0!r}.'.
format(key))
if structure:
spec.molecule = [structure]
spec.conformer = Conformer(E0=E0,
modes=modes,
spin_multiplicity=spin_multiplicity,
optical_isomers=optical_isomers)
if molecular_weight is not None:
spec.molecular_weight = molecular_weight
elif spec.molecular_weight is None and is_pdep(job_list):
# If a structure was given, simply calling spec.molecular_weight will calculate the molecular weight
# If one of the jobs is pdep and no molecular weight is given or calculated, raise an error
raise ValueError(
"No molecularWeight was entered for species {0}. Since a structure wasn't given"
" as well, the molecularWeight, which is important for pressure dependent jobs,"
" cannot be reconstructed.".format(spec.label))
spec.transport_data = collision_model
spec.energy_transfer_model = energy_transfer_model
spec.thermo = thermo
spec.reactive = reactive
if spec.reactive and path is None and spec.thermo is None and spec.conformer.E0 is None:
if not spec.molecule:
raise InputError(
'Neither thermo, E0, species file path, nor structure specified, cannot estimate'
' thermo properties of species {0}'.format(spec.label))
try:
db = get_db('thermo')
if db is None:
raise DatabaseError('Thermo database is None.')
except DatabaseError:
logging.warning(
"The database isn't loaded, cannot estimate thermo for {0}. "
"If it is a bath gas, set reactive = False to avoid generating "
"thermo.".format(spec.label))
else:
logging.info(
'No E0 or thermo found, estimating thermo and E0 of species {0} using'
' RMG-Database...'.format(spec.label))
spec.thermo = db.get_thermo_data(spec)
if spec.thermo.E0 is None:
th = spec.thermo.to_wilhoit()
spec.conformer.E0 = th.E0
spec.thermo.E0 = th.E0
else:
spec.conformer.E0 = spec.thermo.E0
if spec.reactive and spec.thermo and not spec.has_statmech(
) and structure is not None:
# generate stat mech info if it wasn't provided before
spec.generate_statmech()
if not energy_transfer_model:
# default to RMG's method of generating energy_transfer_model
spec.generate_energy_transfer_model()
return spec
def species(label, *args, **kwargs):
global speciesDict, jobList
if label in speciesDict:
raise ValueError(
'Multiple occurrences of species with label {0!r}.'.format(label))
logging.info('Loading species {0}...'.format(label))
spec = Species(label=label)
speciesDict[label] = spec
if len(args) == 1:
# The argument is a path to a conformer input file
path = args[0]
job = StatMechJob(species=spec, path=path)
jobList.append(job)
if len(kwargs) > 0:
# The species parameters are given explicitly
structure = None
E0 = None
modes = []
spinMultiplicity = 1
opticalIsomers = 1
molecularWeight = None
collisionModel = None
energyTransferModel = None
thermo = None
for key, value in kwargs.items():
if key == 'structure':
structure = value
elif key == 'E0':
E0 = value
elif key == 'modes':
modes = value
elif key == 'spinMultiplicity':
spinMultiplicity = value
elif key == 'opticalIsomers':
opticalIsomers = value
elif key == 'molecularWeight':
molecularWeight = value
elif key == 'collisionModel':
collisionModel = value
elif key == 'energyTransferModel':
energyTransferModel = value
elif key == 'thermo':
thermo = value
else:
raise TypeError(
'species() got an unexpected keyword argument {0!r}.'.
format(key))
if structure: spec.molecule = [structure]
spec.conformer = Conformer(E0=E0,
modes=modes,
spinMultiplicity=spinMultiplicity,
opticalIsomers=opticalIsomers)
spec.molecularWeight = molecularWeight
spec.transportData = collisionModel
spec.energyTransferModel = energyTransferModel
spec.thermo = thermo
return spec
def transitionState(label, *args, **kwargs):
"""Load a transition state from an input file"""
global transition_state_dict, job_list, directory
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:
# The argument is a path to a conformer input file
path = os.path.join(directory, args[0])
ts.path = path
job = SamplingJob(label=label,
input_file=path,
output_directory=output_directory,
is_ts=True)
Log = QChemLog(path)
ts.conformer, unscaled_frequencies = Log.load_conformer()
ts.frequency = (Log.load_negative_frequency(), "cm^-1")
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.'
)
if len(kwargs) > 0:
# The species parameters are given explicitly
protocol = 'UMVT'
E0 = None
rotors = None
for key, value in kwargs.items():
if key == 'protocol':
protocol = value.upper()
elif key == 'E0':
E0 = value
elif key == 'rotors':
rotors = value
else:
raise TypeError(
'species() got an unexpected keyword argument {0!r}.'.
format(key))
if protocol == 'UMVT' and rotors is None:
raise InputError(
'If the transition state is sampled by using UMVT algorithm, the rotors are needed to be specified.'
)
job.protocol = protocol
ts.conformer.E0 = E0
job.rotors = rotors
return ts
elif number[i] == 7:
mass[i] = 14.0030740048
elif number[i] == 8:
mass[i] = 15.99491461956
elif number[i] == 15:
mass[i] = 30.97376163
elif number[i] == 16:
mass[i] = 31.97207100
elif number[i] == 17:
mass[i] = 35.4527
else:
print 'Atomic number {0:d} not yet supported in loadGeometry().'.format(
number[i])
conformer = Conformer(number=number,
mass=(mass, "amu"),
coordinates=(coord, "angstroms"))
"""
Define rotors
"""
pivots = [2, 3]
top = [2, 4, 7, 9]
symmetry = 1
linear = False
TS = False
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'),
),
)
