def test_has_correct_mode_no_calc():
bond_rearr = BondRearrangement(breaking_bonds=[(2, 1)],
forming_bonds=[(0, 2)])
calc = Calculation(molecule=ts,
method=method,
keywords=method.keywords.opt_ts,
name='tmp')
# Calculation has no output so should not have the correct mode
assert not imag_mode_has_correct_displacement(
calc, bond_rearrangement=bond_rearr)
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 has_correct_mode(name, fbonds, bbonds):
reac = Reactant(name='r', atoms=xyz_file_to_atoms(f'{name}.xyz'))
calc = Calculation(name=name,
molecule=reac,
method=orca,
keywords=orca.keywords.opt_ts,
n_cores=1)
calc.output.filename = f'{name}.out'
calc.output.file_lines = open(f'{name}.out', 'r').readlines()
bond_rearr = BondRearrangement(breaking_bonds=bbonds,
forming_bonds=fbonds)
# Don't require all bonds to be breaking/making in a 'could be ts' function
return imag_mode_has_correct_displacement(calc, bond_rearr,
delta_threshold=0.05,
req_all=False)