def setUp(self):
"""
A function run before each unit test in this class.
"""
self.ethylene = Conformer(
E0=(0.0, "kJ/mol"),
modes=[
IdealGasTranslation(mass=(28.03, "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")),
],
spin_multiplicity=1,
optical_isomers=1,
)
self.oxygen = Conformer(
E0=(0.0, "kJ/mol"),
modes=[
IdealGasTranslation(mass=(31.99, "amu")),
LinearRotor(inertia=(11.6056, "amu*angstrom^2"), symmetry=2),
HarmonicOscillator(frequencies=([1621.54], "cm^-1")),
],
spin_multiplicity=3,
optical_isomers=1,
)
# The following data is for ethane at the CBS-QB3 level
self.coordinates = np.array([
[0.0000, 0.0000, 0.0000],
[-0.0000, -0.0000, 1.0936],
[1.0430, -0.0000, -0.3288],
[-0.4484, 0.9417, -0.3288],
[-0.7609, -1.2051, -0.5580],
[-0.7609, -1.2051, -1.6516],
[-0.3125, -2.1468, -0.2292],
[-1.8039, -1.2051, -0.2293],
])
self.number = np.array([6, 1, 1, 1, 6, 1, 1, 1])
self.mass = np.array([12, 1.007825, 1.007825, 1.007825, 12, 1.007825, 1.007825, 1.007825])
self.E0 = -93.5097
self.conformer = Conformer(
E0=(self.E0, "kJ/mol"),
modes=[
IdealGasTranslation(mass=(30.0469, "amu")),
NonlinearRotor(inertia=([6.27071, 25.3832, 25.3833], "amu*angstrom^2"), symmetry=6),
HarmonicOscillator(frequencies=([818.917, 819.479, 987.099, 1206.76, 1207.05, 1396, 1411.35, 1489.73,
1489.95, 1492.49, 1492.66, 2995.36, 2996.06, 3040.77, 3041, 3065.86,
3066.02], "cm^-1")),
HinderedRotor(inertia=(1.56768, "amu*angstrom^2"), symmetry=3,
barrier=(2.69401, "kcal/mol"), quantum=False, semiclassical=False),
],
spin_multiplicity=1,
optical_isomers=1,
coordinates=(self.coordinates, "angstrom"),
number=self.number,
mass=(self.mass, "amu"),
)
def setUp(self):
"""
A method that is run before each unit test in this class.
"""
self.species = Species(
index=1,
label='C2H4',
thermo=ThermoData(
Tdata=([300.0,400.0,500.0,600.0,800.0,1000.0,1500.0],'K'),
Cpdata=([3.0,4.0,5.0,6.0,8.0,10.0,15.0],'cal/(mol*K)'),
H298=(-20.0,'kcal/mol'),
S298=(50.0,'cal/(mol*K)'),
Tmin=(300.0,'K'),
Tmax=(2000.0,'K'),
),
conformer=Conformer(
E0=(0.0,'kJ/mol'),
modes=[
IdealGasTranslation(mass=(28.03,'amu')),
NonlinearRotor(inertia=([5.6952e-47, 2.7758e-46, 3.3454e-46],'kg*m^2'), symmetry=1),
HarmonicOscillator(frequencies=([834.50, 973.31, 975.37, 1067.1, 1238.5, 1379.5, 1472.3, 1691.3, 3121.6, 3136.7, 3192.5, 3221.0],'cm^-1')),
],
spinMultiplicity=1,
opticalIsomers=1,
),
molecule=[Molecule().fromSMILES('C=C')],
transportData=TransportData(sigma=(1, 'angstrom'), epsilon=(100, 'K')),
molecularWeight=(28.03,'amu'),
reactive=True,
)
def setUp(self):
"""
A method that is run before each unit test in this class.
"""
self.species = Species(
index=1,
label='C2H4',
thermo=ThermoData(
Tdata=([300.0, 400.0, 500.0, 600.0, 800.0, 1000.0,
1500.0], 'K'),
Cpdata=([3.0, 4.0, 5.0, 6.0, 8.0, 10.0, 15.0], 'cal/(mol*K)'),
H298=(-20.0, 'kcal/mol'),
S298=(50.0, 'cal/(mol*K)'),
Tmin=(300.0, 'K'),
Tmax=(2000.0, 'K'),
),
conformer=Conformer(
E0=(0.0, 'kJ/mol'),
modes=[
IdealGasTranslation(mass=(28.03, 'amu')),
NonlinearRotor(
inertia=([5.6952e-47, 2.7758e-46,
3.3454e-46], 'kg*m^2'),
symmetry=1),
HarmonicOscillator(frequencies=([
834.50, 973.31, 975.37, 1067.1, 1238.5, 1379.5, 1472.3,
1691.3, 3121.6, 3136.7, 3192.5, 3221.0
], 'cm^-1')),
],
spin_multiplicity=1,
optical_isomers=1,
),
molecule=[Molecule().from_smiles('C=C')],
transport_data=TransportData(sigma=(1, 'angstrom'),
epsilon=(100, 'K')),
molecular_weight=(28.03, 'amu'),
reactive=True,
)
self.species2 = Species().from_adjacency_list("""
1 C u0 p0 c0 {2,D} {6,S} {7,S}
2 C u0 p0 c0 {1,D} {3,S} {8,S}
3 C u0 p0 c0 {2,S} {4,D} {9,S}
4 C u0 p0 c0 {3,D} {5,S} {10,S}
5 C u0 p0 c0 {4,S} {6,D} {11,S}
6 C u0 p0 c0 {1,S} {5,D} {12,S}
7 H u0 p0 c0 {1,S}
8 H u0 p0 c0 {2,S}
9 H u0 p0 c0 {3,S}
10 H u0 p0 c0 {4,S}
11 H u0 p0 c0 {5,S}
12 H u0 p0 c0 {6,S}
""")
def load_conformer(self, symmetry=None, spin_multiplicity=0, optical_isomers=None, label=''):
"""
Load the molecular degree of freedom data from a log file created as
the result of a Gaussian "Freq" quantum chemistry calculation. As
Gaussian's guess of the external symmetry number is not always correct,
you can use the `symmetry` parameter to substitute your own value; if
not provided, the value in the Gaussian log file will be adopted. In a
log file with multiple Thermochemistry sections, only the last one will
be kept.
"""
modes = []
unscaled_frequencies = []
e0 = 0.0
if optical_isomers is None or symmetry is None:
_optical_isomers, _symmetry, _ = self.get_symmetry_properties()
if optical_isomers is None:
optical_isomers = _optical_isomers
if symmetry is None:
symmetry = _symmetry
with open(self.path, 'r') as f:
line = f.readline()
while line != '':
# Read the spin multiplicity if not explicitly given
if spin_multiplicity == 0 and 'Multiplicity =' in line:
spin_multiplicity = int(line.split()[-1])
logging.debug('Conformer {0} is assigned a spin multiplicity of {1}'
.format(label, spin_multiplicity))
# The data we want is in the Thermochemistry section of the output
if '- Thermochemistry -' in line:
modes = []
in_partition_functions = False
line = f.readline()
while line != '':
# This marks the end of the thermochemistry section
if '-------------------------------------------------------------------' in line:
break
# Read molecular mass for external translational modes
elif 'Molecular mass:' in line:
mass = float(line.split()[2])
translation = IdealGasTranslation(mass=(mass, "amu"))
modes.append(translation)
# Read moments of inertia for external rotational modes
elif 'Rotational constants (GHZ):' in line:
inertia = [float(d) for d in line.split()[-3:]]
for i in range(3):
inertia[i] = constants.h / (8 * constants.pi * constants.pi * inertia[i] * 1e9) \
* constants.Na * 1e23
rotation = NonlinearRotor(inertia=(inertia, "amu*angstrom^2"), symmetry=symmetry)
modes.append(rotation)
elif 'Rotational constant (GHZ):' in line:
inertia = [float(line.split()[3])]
inertia[0] = constants.h / (8 * constants.pi * constants.pi * inertia[0] * 1e9) \
* constants.Na * 1e23
rotation = LinearRotor(inertia=(inertia[0], "amu*angstrom^2"), symmetry=symmetry)
modes.append(rotation)
# Read vibrational modes
elif 'Vibrational temperatures:' in line:
frequencies = []
frequencies.extend([float(d) for d in line.split()[2:]])
line = f.readline()
frequencies.extend([float(d) for d in line.split()[1:]])
line = f.readline()
while line.strip() != '':
frequencies.extend([float(d) for d in line.split()])
line = f.readline()
# Convert from K to cm^-1
if len(frequencies) > 0:
frequencies = [freq * 0.695039 for freq in frequencies] # kB = 0.695039 cm^-1/K
unscaled_frequencies = frequencies
vibration = HarmonicOscillator(frequencies=(frequencies, "cm^-1"))
modes.append(vibration)
# Read ground-state energy
elif 'Sum of electronic and zero-point Energies=' in line:
e0 = float(line.split()[6]) * 4.35974394e-18 * constants.Na
# Read spin multiplicity if above method was unsuccessful
elif 'Electronic' in line and in_partition_functions and spin_multiplicity == 0:
spin_multiplicity = int(float(line.split()[1].replace('D', 'E')))
elif 'Log10(Q)' in line:
in_partition_functions = True
# Read the next line in the file
line = f.readline()
if 'Error termination' in line:
raise LogError(f'The Gaussian job in {self.path} did not converge.')
# Read the next line in the file
line = f.readline()
return Conformer(E0=(e0 * 0.001, "kJ/mol"), modes=modes, spin_multiplicity=spin_multiplicity,
optical_isomers=optical_isomers), unscaled_frequencies
def load_conformer(self,
symmetry=None,
spin_multiplicity=0,
optical_isomers=None,
label=''):
"""
Load the molecular degree of freedom data from a log file created as
the result of a MolPro "Freq" quantum chemistry calculation with the thermo printed.
"""
modes = []
unscaled_frequencies = []
e0 = 0.0
if optical_isomers is None or symmetry is None:
_optical_isomers, _symmetry, _ = self.get_symmetry_properties()
if optical_isomers is None:
optical_isomers = _optical_isomers
if symmetry is None:
symmetry = _symmetry
with open(self.path, 'r') as f:
line = f.readline()
while line != '':
# Read the spin multiplicity if not explicitly given
if spin_multiplicity == 0 and 'spin' in line:
splits = line.replace('=', ' ').replace(',',
' ').split(' ')
for i, s in enumerate(splits):
if 'spin' in s:
spin_multiplicity = int(splits[i + 1]) + 1
logging.debug(
'Conformer {0} is assigned a spin multiplicity of {1}'
.format(label, spin_multiplicity))
break
if spin_multiplicity == 0 and 'SPIN SYMMETRY' in line:
spin_symmetry = line.split()[-1]
if spin_symmetry == 'Singlet':
spin_multiplicity = 1
elif spin_symmetry == 'Doublet':
spin_multiplicity = 2
elif spin_symmetry == 'Triplet':
spin_multiplicity = 3
elif spin_symmetry == 'Quartet':
spin_multiplicity = 4
elif spin_symmetry == 'Quintet':
spin_multiplicity = 5
elif spin_symmetry == 'Sextet':
spin_multiplicity = 6
if spin_multiplicity:
logging.debug(
'Conformer {0} is assigned a spin multiplicity of {1}'
.format(label, spin_multiplicity))
break
# The data we want is in the Thermochemistry section of the output
if 'THERMODYNAMICAL' in line:
modes = []
line = f.readline()
while line != '':
# This marks the end of the thermochemistry section
if '*************************************************' in line:
break
# Read molecular mass for external translational modes
elif 'Molecular Mass:' in line:
mass = float(line.split()[2])
translation = IdealGasTranslation(mass=(mass,
"amu"))
modes.append(translation)
# Read moments of inertia for external rotational modes
elif 'Rotational Constants' in line and line.split(
)[-1] == '[GHz]':
inertia = [float(d) for d in line.split()[-4:-1]]
for i in range(3):
inertia[i] = constants.h / (8 * constants.pi * constants.pi * inertia[i] * 1e9) \
* constants.Na * 1e23
rotation = NonlinearRotor(
inertia=(inertia, "amu*angstrom^2"),
symmetry=symmetry)
modes.append(rotation)
elif 'Rotational Constant' in line and line.split(
)[3] == '[GHz]':
inertia = float(line.split()[2])
inertia = constants.h / (8 * constants.pi * constants.pi * inertia * 1e9) \
* constants.Na * 1e23
rotation = LinearRotor(inertia=(inertia,
"amu*angstrom^2"),
symmetry=symmetry)
modes.append(rotation)
# Read vibrational modes
elif 'Vibrational Temperatures' in line:
frequencies = []
frequencies.extend(
[float(d) for d in line.split()[3:]])
line = f.readline()
while line.strip() != '':
frequencies.extend(
[float(d) for d in line.split()])
line = f.readline()
# Convert from K to cm^-1
if len(frequencies) > 0:
frequencies = [
freq * 0.695039 for freq in frequencies
] # kB = 0.695039 cm^-1/K
unscaled_frequencies = frequencies
vibration = HarmonicOscillator(
frequencies=(frequencies, "cm^-1"))
modes.append(vibration)
# Read the next line in the file
line = f.readline()
# Read the next line in the file
line = f.readline()
return Conformer(E0=(e0 * 0.001, "kJ/mol"),
modes=modes,
spin_multiplicity=spin_multiplicity,
optical_isomers=optical_isomers), unscaled_frequencies
def loadConformer(self, symmetry=None, spinMultiplicity=0, opticalIsomers=None, label=''):
"""
Load the molecular degree of freedom data from an output file created as the result of a
QChem "Freq" calculation. As QChem's guess of the external symmetry number is not always correct,
you can use the `symmetry` parameter to substitute your own value;
if not provided, the value in the QChem output file will be adopted.
"""
modes = []; freq = []; mmass = []; rot = []; inertia = []
unscaled_frequencies = []
E0 = 0.0
if opticalIsomers is None or symmetry is None:
_opticalIsomers, _symmetry = self.get_optical_isomers_and_symmetry_number()
if opticalIsomers is None:
opticalIsomers = _opticalIsomers
if symmetry is None:
symmetry = _symmetry
f = open(self.path, 'r')
line = f.readline()
while line != '':
# Read spin multiplicity if not explicitly given
if '$molecule' in line and spinMultiplicity == 0:
line = f.readline()
if len(line.split()) == 2:
spinMultiplicity = int(float(line.split()[1]))
logging.debug('Conformer {0} is assigned a spin multiplicity of {1}'.format(label,spinMultiplicity))
# The rest of the data we want is in the Thermochemistry section of the output
elif 'VIBRATIONAL ANALYSIS' in line:
modes = []
line = f.readline()
while line != '':
# This marks the end of the thermochemistry section
if 'Thank you very much for using Q-Chem.' in line:
break
# Read vibrational modes
elif 'VIBRATIONAL FREQUENCIES (CM**-1)' in line:
frequencies = []
while 'STANDARD THERMODYNAMIC QUANTITIES AT' not in line:
if ' Frequency:' in line:
if len(line.split()) == 4:
frequencies.extend([float(d) for d in line.split()[-3:]])
elif len(line.split()) == 3:
frequencies.extend([float(d) for d in line.split()[-2:]])
elif len(line.split()) == 2:
frequencies.extend([float(d) for d in line.split()[-1:]])
line = f.readline()
line = f.readline()
# If there is an imaginary frequency, remove it
if frequencies[0] < 0.0:
frequencies = frequencies[1:]
unscaled_frequencies = frequencies
vibration = HarmonicOscillator(frequencies=(frequencies,"cm^-1"))
# modes.append(vibration)
freq.append(vibration)
# Read molecular mass for external translational modes
elif 'Molecular Mass:' in line:
mass = float(line.split()[2])
translation = IdealGasTranslation(mass=(mass,"amu"))
# modes.append(translation)
mmass.append(translation)
# Read moments of inertia for external rotational modes, given in atomic units
elif 'Eigenvalues --' in line:
inertia = [float(d) for d in line.split()[-3:]]
# Read the next line in the file
line = f.readline()
# Read the next line in the file
line = f.readline()
if len(inertia):
if inertia[0] == 0.0:
# If the first eigenvalue is 0, the rotor is linear
inertia.remove(0.0)
logging.debug('inertia is {}'.format(str(inertia)))
for i in range(2):
inertia[i] *= (constants.a0 / 1e-10) ** 2
inertia = numpy.sqrt(inertia[0] * inertia[1])
rotation = LinearRotor(inertia=(inertia, "amu*angstrom^2"), symmetry=symmetry)
rot.append(rotation)
else:
for i in range(3):
inertia[i] *= (constants.a0 / 1e-10) ** 2
rotation = NonlinearRotor(inertia=(inertia, "amu*angstrom^2"), symmetry=symmetry)
# modes.append(rotation)
rot.append(rotation)
inertia = []
# Close file when finished
f.close()
modes = mmass + rot + freq
return Conformer(E0=(E0*0.001,"kJ/mol"), modes=modes, spinMultiplicity=spinMultiplicity,
opticalIsomers=opticalIsomers), unscaled_frequencies
def loadConformer(self, symmetry=None, spinMultiplicity=None, opticalIsomers=1):
"""
Load the molecular degree of freedom data from a log file created as
the result of a Gaussian "Freq" quantum chemistry calculation. As
Gaussian's guess of the external symmetry number is not always correct,
you can use the `symmetry` parameter to substitute your own value; if
not provided, the value in the Gaussian log file will be adopted. In a
log file with multiple Thermochemistry sections, only the last one will
be kept.
"""
modes = []
E0 = 0.0
f = open(self.path, 'r')
line = f.readline()
while line != '':
# The data we want is in the Thermochemistry section of the output
if '- Thermochemistry -' in line:
modes = []
inPartitionFunctions = False
line = f.readline()
while line != '':
# This marks the end of the thermochemistry section
if '-------------------------------------------------------------------' in line:
break
# Read molecular mass for external translational modes
elif 'Molecular mass:' in line:
mass = float(line.split()[2])
translation = IdealGasTranslation(mass=(mass,"amu"))
modes.append(translation)
# Read Gaussian's estimate of the external symmetry number
elif 'Rotational symmetry number' in line and symmetry is None:
symmetry = int(float(line.split()[3]))
# Read moments of inertia for external rotational modes
elif 'Rotational constants (GHZ):' in line:
inertia = [float(d) for d in line.split()[-3:]]
for i in range(3):
inertia[i] = constants.h / (8 * constants.pi * constants.pi * inertia[i] * 1e9) *constants.Na*1e23
rotation = NonlinearRotor(inertia=(inertia,"amu*angstrom^2"), symmetry=symmetry)
modes.append(rotation)
elif 'Rotational constant (GHZ):' in line:
inertia = [float(line.split()[3])]
inertia[0] = constants.h / (8 * constants.pi * constants.pi * inertia[0] * 1e9) *constants.Na*1e23
rotation = LinearRotor(inertia=(inertia[0],"amu*angstrom^2"), symmetry=symmetry)
modes.append(rotation)
# Read vibrational modes
elif 'Vibrational temperatures:' in line:
frequencies = []
frequencies.extend([float(d) for d in line.split()[2:]])
line = f.readline()
frequencies.extend([float(d) for d in line.split()[1:]])
line = f.readline()
while line.strip() != '':
frequencies.extend([float(d) for d in line.split()])
line = f.readline()
# Convert from K to cm^-1
if len(frequencies) > 0:
frequencies = [freq * 0.695039 for freq in frequencies] # kB = 0.695039 cm^-1/K
vibration = HarmonicOscillator(frequencies=(frequencies,"cm^-1"))
modes.append(vibration)
# Read ground-state energy
elif 'Sum of electronic and zero-point Energies=' in line:
E0 = float(line.split()[6]) * 4.35974394e-18 * constants.Na
# Read spin multiplicity if not explicitly given
elif 'Electronic' in line and inPartitionFunctions and spinMultiplicity is None:
spinMultiplicity = int(float(line.split()[1].replace('D', 'E')))
elif 'Log10(Q)' in line:
inPartitionFunctions = True
# Read the next line in the file
line = f.readline()
# Read the next line in the file
line = f.readline()
# Close file when finished
f.close()
return Conformer(E0=(E0*0.001,"kJ/mol"), modes=modes, spinMultiplicity=spinMultiplicity, opticalIsomers=opticalIsomers)
def get_enthalpy_of_formation(self,
freq_scale_factor=1.0,
apply_bond_corrections=True):
"""
Calculate the enthalpy of formation at 298.15 K.
Apply bond energy corrections if desired and if
model chemistry is compatible.
"""
temperature = 298.15
mol = pybel.readstring('smi',
self.smiles) # Use OBMol to extract bond types
# Use RMG molecule to determine if it's linear
# Assume it's not linear if we can't parse SMILES with RMG
rmg_mol = None
try:
rmg_mol = Molecule().fromSMILES(self.smiles)
except AtomTypeError:
try:
rmg_mol = Molecule().fromSMILES(self.smiles2)
except AtomTypeError:
try:
rmg_mol = Molecule().fromInChI(self.inchi)
except AtomTypeError:
warnings.warn(
'Could not determine linearity from RMG molecule in {}'
.format(self.file_name))
if rmg_mol is not None:
is_linear = rmg_mol.isLinear()
else:
is_linear = False
# Translation
translation = IdealGasTranslation()
# Rotation
if is_linear:
rotation = LinearRotor()
else:
rotation = NonlinearRotor(
rotationalConstant=(self.rotational_consts, 'GHz'))
# Vibration
freqs = [f * freq_scale_factor
for f in self.freqs] # Apply scale factor
vibration = HarmonicOscillator(frequencies=(freqs, 'cm^-1'))
# Group modes
modes = [translation, rotation, vibration]
conformer = Conformer(modes=modes)
# Energy
e0 = self.e0 * constants.E_h * constants.Na
zpe = self.zpe * constants.E_h * constants.Na * freq_scale_factor
# Bring energy to gas phase reference state at 298.15K
atom_energies = energy_data.atom_energies[self.model_chemistry]
for element in self.elements:
e0 -= atom_energies[element] * constants.E_h * constants.Na
e0 += self.enthalpy_corrections[element] * 4184.0
if apply_bond_corrections:
bond_energies = energy_data.bond_energy_corrections[
self.model_chemistry]
for bond in pybel.ob.OBMolBondIter(mol.OBMol):
bond_symbol_split = [
self.atomic_num_dict[bond.GetBeginAtom().GetAtomicNum()],
self.bond_symbols[bond.GetBondOrder()],
self.atomic_num_dict[bond.GetEndAtom().GetAtomicNum()]
]
try:
bond_energy = bond_energies[''.join(bond_symbol_split)]
except KeyError:
bond_energy = bond_energies[''.join(
bond_symbol_split[::-1])] # Try reverse order
e0 += bond_energy * 4184.0
conformer.E0 = (e0 + zpe, 'J/mol')
self.hf298 = conformer.getEnthalpy(temperature) + conformer.E0.value_si
return self.hf298
def loadConformer(self,
symmetry=None,
spinMultiplicity=None,
opticalIsomers=1):
"""
Load the molecular degree of freedom data from a log file created as
the result of a Qchem "Freq" calculation. As
Qchem's guess of the external symmetry number is not always correct,
you can use the `symmetry` parameter to substitute your own value; if
not provided, the value in the Qchem output file will be adopted.
"""
modes = []
freq = []
mmass = []
rot = []
E0 = 0.0
f = open(self.path, 'r')
line = f.readline()
while line != '':
# The data we want is in the Thermochemistry section of the output
if 'VIBRATIONAL ANALYSIS' in line:
modes = []
inPartitionFunctions = False
line = f.readline()
while line != '':
# This marks the end of the thermochemistry section
if 'Thank you very much for using Q-Chem.' in line:
break
# Read vibrational modes
elif 'VIBRATIONAL FREQUENCIES (CM**-1)' in line:
frequencies = []
while 'STANDARD THERMODYNAMIC QUANTITIES AT' not in line:
if ' Frequency:' in line:
frequencies.extend(
[float(d) for d in line.split()[-3:]])
line = f.readline()
line = f.readline()
# If there is an imaginary frequency, remove it
if frequencies[0] < 0.0:
frequencies = frequencies[1:]
vibration = HarmonicOscillator(
frequencies=(frequencies, "cm^-1"))
#modes.append(vibration)
freq.append(vibration)
# Read molecular mass for external translational modes
elif 'Molecular Mass:' in line:
mass = float(line.split()[2])
translation = IdealGasTranslation(mass=(mass, "amu"))
#modes.append(translation)
mmass.append(translation)
# Read moments of inertia for external rotational modes, given in atomic units
elif 'Eigenvalues --' in line:
inertia = [float(d) for d in line.split()[-3:]]
# If the first eigenvalue is 0, the rotor is linear
if inertia[0] == 0.0:
inertia.remove(0.0)
for i in range(2):
inertia[i] *= (constants.a0 / 1e-10)**2
rotation = LinearRotor(
inertia=(inertia, "amu*angstrom^2"),
symmetry=symmetry)
#modes.append(rotation)
rot.append(rotation)
else:
for i in range(3):
inertia[i] *= (constants.a0 / 1e-10)**2
rotation = NonlinearRotor(
inertia=(inertia, "amu*angstrom^2"),
symmetry=symmetry)
#modes.append(rotation)
rot.append(rotation)
# Read Qchem's estimate of the external rotational symmetry number, which may very well be incorrect
elif 'Rotational Symmetry Number is' in line and symmetry is None:
symmetry = int(float(line.split()[4]))
elif 'Final energy is' in line:
E0 = float(
line.split()[3]) * constants.E_h * constants.Na
print 'energy is' + str(E0)
# Read ZPE and add to ground-state energy
# NEED TO MULTIPLY ZPE BY scaling factor!
elif 'Zero point vibrational energy:' in line:
ZPE = float(line.split()[4]) * 4184
E0 = E0 + ZPE
# Read spin multiplicity if not explicitly given
# elif 'Electronic' in line and inPartitionFunctions and spinMultiplicity is None:
# spinMultiplicity = int(float(line.split()[1].replace('D', 'E')))
# elif 'Log10(Q)' in line:
# inPartitionFunctions = True
# Read the next line in the file
line = f.readline()
# Read the next line in the file
line = f.readline()
# Close file when finished
f.close()
modes = mmass + rot + freq
#modes.append(mmass), modes.append(rot), modes.append(freq)
return Conformer(E0=(E0 * 0.001, "kJ/mol"),
modes=modes,
spinMultiplicity=spinMultiplicity,
opticalIsomers=opticalIsomers)
def get_thermo(optfreq_log, optfreq_level, energy_level, energy_log=None,
mol=None, bacs=None, soc=False,
infer_symmetry=False, infer_chirality=False, unique_id='0', scr_dir='SCRATCH'):
q = QChem(logfile=optfreq_log)
symbols, coords = q.get_geometry()
inertia = q.get_moments_of_inertia()
freqs = q.get_frequencies()
zpe = q.get_zpe()
if energy_log is None:
e0 = q.get_energy()
multiplicity = q.get_multiplicity()
else:
m = Molpro(logfile=energy_log)
e0 = m.get_energy()
multiplicity = m.get_multiplicity()
# Infer connections only if not given explicitly
if mol is None:
mol = geo_to_rmg_mol((symbols, coords)) # Does not contain bond orders
# Try to infer point group to calculate symmetry number and chirality
symmetry = optical_isomers = 1
point_group = None
if infer_symmetry or infer_chirality:
qmdata = QMData(
groundStateDegeneracy=multiplicity, # Only needed to check if valid QMData
numberOfAtoms=len(symbols),
atomicNumbers=[atomic_symbol_dict[sym] for sym in symbols],
atomCoords=(coords, 'angstrom'),
energy=(e0 * 627.5095, 'kcal/mol') # Only needed to avoid error
)
settings = type("", (), dict(symmetryPath='symmetry', scratchDirectory=scr_dir))() # Creates anonymous class
pgc = PointGroupCalculator(settings, unique_id, qmdata)
point_group = pgc.calculate()
if point_group is not None:
if infer_symmetry:
symmetry = point_group.symmetryNumber
if infer_chirality and point_group.chiral:
optical_isomers = 2
# Translational mode
mass = mol.getMolecularWeight()
translation = IdealGasTranslation(mass=(mass, 'kg/mol'))
# Rotational mode
if isinstance(inertia, list): # Nonlinear
rotation = NonlinearRotor(inertia=(inertia, 'amu*angstrom^2'), symmetry=symmetry)
else:
rotation = LinearRotor(inertia=(inertia, 'amu*angstrom^2'), symmetry=symmetry)
# Vibrational mode
freq_scale_factor = freq_scale_factors.get(optfreq_level, 1.0)
freqs = [f * freq_scale_factor for f in freqs]
vibration = HarmonicOscillator(frequencies=(freqs, 'cm^-1'))
# Bring energy to gas phase reference state
e0 *= constants.E_h * constants.Na
zpe *= constants.E_h * constants.Na * freq_scale_factor
for sym in symbols:
if soc:
e0 -= (atom_energies[energy_level][sym] - atom_socs[sym]) * constants.E_h * constants.Na
else:
e0 -= atom_energies[energy_level][sym] * constants.E_h * constants.Na
e0 += (h0expt[sym] - h298corr[sym]) * 4184.0
if bacs is not None:
e0 -= get_bac_correction(mol, **bacs) * 4184.0
# Group modes into Conformer object
modes = [translation, rotation, vibration]
conformer = Conformer(modes=modes, spinMultiplicity=multiplicity, opticalIsomers=optical_isomers)
# Calculate heat of formation, entropy of formation, and heat capacities
conformer.E0 = (e0 + zpe, 'J/mol')
hf298 = conformer.getEnthalpy(298.0) + conformer.E0.value_si
s298 = conformer.getEntropy(298.0)
Tlist = [300.0, 400.0, 500.0, 600.0, 800.0, 1000.0, 1500.0]
cp = np.zeros(len(Tlist))
for i, T in enumerate(Tlist):
cp[i] = conformer.getHeatCapacity(T)
# Return in kcal/mol and cal/mol/K
return hf298/4184.0, s298/4.184, cp/4.184
