def test_graph_no_other_bonds():
reac = Reactant(name='r',
atoms=xyz_file_to_atoms('h_shift_correct_ts_mode.xyz'))
br = BondRearrangement(breaking_bonds=[(1, 10)],
forming_bonds=[(5, 10)])
calc = Calculation(name='h_shift',
molecule=reac,
method=orca,
keywords=orca.keywords.opt_ts,
n_cores=1)
calc.output.filename = 'h_shift_correct_ts_mode.out'
calc.output.file_lines = open('h_shift_correct_ts_mode.out', 'r').readlines()
f_ts = Species(name='f_displaced', charge=0, mult=1,
atoms=get_displaced_atoms_along_mode(calc,
mode_number=6,
disp_magnitude=1.0))
b_ts = Species(name='b_displaced', charge=0, mult=1,
atoms=get_displaced_atoms_along_mode(calc,
mode_number=6,
disp_magnitude=-1.0))
assert not imag_mode_generates_other_bonds(ts=reac,
f_species=f_ts,
b_species=b_ts,
bond_rearrangement=br)
def print_imag_vector(self, mode_number=6, name=None):
"""Print a .xyz file with multiple structures visualising the largest
magnitude imaginary mode
Keyword Arguments:
mode_number (int): Number of the normal mode to visualise,
6 (default) is the lowest frequency vibration
i.e. largest magnitude imaginary, if present
name (str):
"""
assert self.optts_calc is not None
name = self.name if name is None else name
disp = -0.5
for i in range(40):
atoms = get_displaced_atoms_along_mode(
calc=self.optts_calc,
mode_number=int(mode_number),
disp_magnitude=disp,
atoms=self.atoms)
atoms_to_xyz_file(atoms=atoms, filename=f'{name}.xyz', append=True)
# Add displacement so the final set of atoms are +0.5 Å displaced
# along the mode, then displaced back again
sign = 1 if i < 20 else -1
disp += sign * 1.0 / 20.0
return None
def test_correct_imag_mode():
os.chdir(os.path.join(here, 'data'))
bond_rearrangement = BondRearrangement(breaking_bonds=[(4, 1), (4, 18)],
forming_bonds=[(1, 18)])
g09 = G09()
g09.available = True
calc = Calculation(name='tmp',
molecule=ReactantComplex(
Reactant(smiles='CC(C)(C)C1C=CC=C1')),
method=g09,
keywords=Config.G09.keywords.opt_ts)
calc.output.filename = 'correct_ts_mode_g09.log'
calc.output.set_lines()
f_displaced_atoms = get_displaced_atoms_along_mode(calc,
mode_number=6,
disp_magnitude=1.0)
f_species = Species(name='f_displaced',
atoms=f_displaced_atoms,
charge=0,
mult=1) # Charge & mult are placeholders
b_displaced_atoms = get_displaced_atoms_along_mode(calc,
mode_number=6,
disp_magnitude=-1.0)
b_species = Species(name='b_displaced',
atoms=b_displaced_atoms,
charge=0,
mult=1)
# With the correct mode no other bonds are made
assert not imag_mode_generates_other_bonds(
ts=calc.molecule,
f_species=f_species,
b_species=b_species,
bond_rearrangement=bond_rearrangement)
calc.output.filename = 'incorrect_ts_mode_g09.log'
calc.output.set_lines()
assert not imag_mode_has_correct_displacement(calc, bond_rearrangement)
os.chdir(here)
def optimise(self, name_ext='optts'):
"""Optimise this TS to a true TS """
logger.info(f'Optimising {self.name} to a transition state')
self._run_opt_ts_calc(method=get_hmethod(), name_ext=name_ext)
# A transition state is a first order saddle point i.e. has a single
# imaginary frequency
if len(self.imaginary_frequencies) == 1:
logger.info('Found a TS with a single imaginary frequency')
return
if len(self.imaginary_frequencies) == 0:
logger.error('Transition state optimisation did not return any '
'imaginary frequencies')
return
if all([freq > -50 for freq in self.imaginary_frequencies[1:]]):
logger.warning('Had small imaginary modes - not displacing along')
return
# There is more than one imaginary frequency. Will assume that the most
# negative is the correct mode..
for disp_magnitude in [1, -1]:
logger.info('Displacing along second imaginary mode to try and '
'remove')
dis_name_ext = name_ext + '_dis' if disp_magnitude == 1 else name_ext + '_dis2'
atoms, energy, calc = deepcopy(self.atoms), deepcopy(
self.energy), deepcopy(self.optts_calc)
self.atoms = get_displaced_atoms_along_mode(
self.optts_calc, mode_number=7, disp_magnitude=disp_magnitude)
self._run_opt_ts_calc(method=get_hmethod(), name_ext=dis_name_ext)
if len(self.imaginary_frequencies) == 1:
logger.info('Displacement along second imaginary mode '
'successful. Now have 1 imaginary mode')
break
self.optts_calc = calc
self.atoms = atoms
self.energy = energy
self.imaginary_frequencies = self.optts_calc.get_imaginary_freqs()
return None
