def calculate_symmetry_number(self):
from rmgpy.qm.symmetry import PointGroupCalculator
from rmgpy.qm.qmdata import QMData
atom_numbers = self.ase_molecule.get_atomic_numbers()
coordinates = self.ase_molecule.get_positions()
qmdata = QMData(
groundStateDegeneracy=1, # Only needed to check if valid QMData
numberOfAtoms=len(atom_numbers),
atomicNumbers=atom_numbers,
atomCoords=(coordinates, str('angstrom')),
energy=(0.0, str('kcal/mol')) # Only needed to avoid error
)
settings = type(str(''), (), dict(symmetryPath=str(
'symmetry'), scratchDirectory="."))() # Creates anonymous class
pgc = PointGroupCalculator(settings, self.smiles, qmdata)
pg = pgc.calculate()
#os.remove("{}.symm".format(self.smiles))
if pg is not None:
symmetry_number = pg.symmetryNumber
else:
symmetry_number = 1
return symmetry_number
def get_symmetry_properties(self):
"""
This method uses the symmetry package from RMG's QM module
and returns a tuple where the first element is the number
of optical isomers, the second element is the symmetry number,
and the third element is the point group identified.
"""
coordinates, atom_numbers, _ = self.load_geometry()
unique_id = '0' # Just some name that the SYMMETRY code gives to one of its jobs
# Scratch directory that the SYMMETRY code writes its files in:
scr_dir = os.path.join(os.path.abspath('.'), str('scratch'))
if not os.path.exists(scr_dir):
os.makedirs(scr_dir)
try:
qmdata = QMData(
groundStateDegeneracy=1, # Only needed to check if valid QMData
numberOfAtoms=len(atom_numbers),
atomicNumbers=atom_numbers,
atomCoords=(coordinates, str('angstrom')),
energy=(0.0, str('kcal/mol')) # Only needed to avoid error
)
# Dynamically create custom class to store the settings needed for the point group calculation
# Normally, it expects an rmgpy.qm.main.QMSettings object, but we don't need all of those settings
settings = type(
str(''), (),
dict(symmetryPath=str('symmetry'), scratchDirectory=scr_dir))()
pgc = PointGroupCalculator(settings, unique_id, qmdata)
pg = pgc.calculate()
if pg is not None:
optical_isomers = 2 if pg.chiral else 1
symmetry = pg.symmetry_number
logging.debug(
"Symmetry algorithm found {0} optical isomers and a symmetry number of {1}"
.format(optical_isomers, symmetry))
else:
logging.error(
'Symmetry algorithm errored when computing point group\nfor log file located at{0}.\n'
'Manually provide values in Arkane input.'.format(
self.path))
return optical_isomers, symmetry, pg.point_group
finally:
shutil.rmtree(scr_dir)
def determine_symmetry(coords, symbols):
"""
Determine external symmetry and chirality (optical isomers) of the species.
Args:
coords (list): The 3D coordinates of a molecule in array-format.
symbols (list): Entries are atomic symbols correcponding to coords.
Returns:
int: The external symmetry number.
Returns:
int: 1 if no chiral centers are present, 2 if chiral centers are present.
"""
atom_numbers = list() # List of atomic numbers
for symbol in symbols:
atom_numbers.append(getElement(str(symbol)).number)
coords = np.array(coords,
np.float64) # N x 3 numpy.ndarray of atomic coordinates
# in the same order as `atom_numbers`
unique_id = '0' # Just some name that the SYMMETRY code gives to one of its jobs
scr_dir = os.path.join(
arc_path, str('scratch')
) # Scratch directory that the SYMMETRY code writes its files in
if not os.path.exists(scr_dir):
os.makedirs(scr_dir)
symmetry = optical_isomers = 1
qmdata = QMData(
groundStateDegeneracy=1, # Only needed to check if valid QMData
numberOfAtoms=len(atom_numbers),
atomicNumbers=atom_numbers,
atomCoords=(coords, str('angstrom')),
energy=(0.0, str('kcal/mol')) # Only needed to avoid error
)
settings = type(
str(''), (),
dict(symmetryPath=str('symmetry'), scratchDirectory=scr_dir))()
pgc = PointGroupCalculator(settings, unique_id, qmdata)
pg = pgc.calculate()
if pg is not None:
symmetry = pg.symmetryNumber
optical_isomers = 2 if pg.chiral else optical_isomers
return symmetry, optical_isomers
def get_optical_isomers_and_symmetry_number(self):
"""
This method uses the symmetry package from RMG's QM module
and returns a tuple where the first element is the number
of optical isomers and the second element is the symmetry number.
"""
coordinates, atom_numbers, _ = self.loadGeometry()
unique_id = '0' # Just some name that the SYMMETRY code gives to one of its jobs
scr_dir = os.path.join(
os.path.abspath('.'), str('scratch')
) # Scratch directory that the SYMMETRY code writes its files in
if not os.path.exists(scr_dir):
os.makedirs(scr_dir)
try:
qmdata = QMData(
groundStateDegeneracy=1, # Only needed to check if valid QMData
numberOfAtoms=len(atom_numbers),
atomicNumbers=atom_numbers,
atomCoords=(coordinates, str('angstrom')),
energy=(0.0, str('kcal/mol')) # Only needed to avoid error
)
settings = type(
str(''), (),
dict(symmetryPath=str('symmetry'),
scratchDirectory=scr_dir))() # Creates anonymous class
pgc = PointGroupCalculator(settings, unique_id, qmdata)
pg = pgc.calculate()
if pg is not None:
optical_isomers = 2 if pg.chiral else 1
symmetry = pg.symmetryNumber
logging.debug(
"Symmetry algorithm found {0} optical isomers and a symmetry number of {1}"
.format(optical_isomers, symmetry))
else:
logging.error(
"Symmetry algorithm errored when computing point group\nfor log file located at{0}.\nManually provide values in Arkane input."
.format(self.path))
return optical_isomers, symmetry
finally:
shutil.rmtree(scr_dir)
def determine_symmetry(xyz: dict) -> Tuple[int, int]:
"""
Determine external symmetry and chirality (optical isomers) of the species.
Args:
xyz (dict): The 3D coordinates.
Returns: Tuple[int, int]
- The external symmetry number.
- ``1`` if no chiral centers are present, ``2`` if chiral centers are present.
"""
atom_numbers = list() # List of atomic numbers
for symbol in xyz['symbols']:
atom_numbers.append(get_element(symbol).number)
# coords is an N x 3 numpy.ndarray of atomic coordinates in the same order as `atom_numbers`
coords = np.array(xyz['coords'], np.float64)
unique_id = '0' # Just some name that the SYMMETRY code gives to one of its jobs
scr_dir = os.path.join(
arc_path, 'scratch'
) # Scratch directory that the SYMMETRY code writes its files in
if not os.path.exists(scr_dir):
os.makedirs(scr_dir)
symmetry = optical_isomers = 1
qmdata = QMData(
groundStateDegeneracy=1, # Only needed to check if valid QMData
numberOfAtoms=len(atom_numbers),
atomicNumbers=atom_numbers,
atomCoords=(coords, 'angstrom'),
energy=(0.0, 'kcal/mol') # Only needed to avoid error
)
symmetry_settings = type(
'', (), dict(symmetryPath='symmetry', scratchDirectory=scr_dir))()
pgc = PointGroupCalculator(symmetry_settings, unique_id, qmdata)
pg = pgc.calculate()
if pg is not None:
symmetry = pg.symmetry_number
optical_isomers = 2 if pg.chiral else optical_isomers
return symmetry, optical_isomers
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