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 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