def test_get_ts_guess_neb():
reactant = Reactant(name='inital',
charge=-1,
mult=0,
solvent_name='water',
atoms=xyz_file_to_atoms(init_xyz))
product = Reactant(name='final',
charge=-1,
mult=0,
solvent_name='water',
atoms=xyz_file_to_atoms(final_xyz))
xtb = XTB()
# Don't run the NEB without a working XTB install
if shutil.which('xtb') is None or not shutil.which('xtb').endswith('xtb'):
return
xtb.path = shutil.which('xtb')
ts_guess = neb.get_ts_guess_neb(reactant, product, method=xtb, n=10)
assert ts_guess is not None
# Approximate distances at the TS guess
assert 1.8 < ts_guess.get_distance(0, 2) < 2.2 # C-F
assert 1.9 < ts_guess.get_distance(2, 1) < 2.3 # C-Cl
if os.path.exists('NEB'):
shutil.rmtree('NEB')
if os.path.exists('neb.xyz'):
os.remove('neb.xyz')
def test_full_calc_with_xtb():
sn2_neb = neb.NEB(
initial_species=Species(name='inital',
charge=-1,
mult=0,
atoms=xyz_file_to_atoms('sn2_init.xyz')),
final_species=Species(name='final',
charge=-1,
mult=0,
atoms=xyz_file_to_atoms('sn2_final.xyz')),
num=14)
sn2_neb.interpolate_geometries()
xtb = XTB()
# Don't run the NEB without a working XTB install
if shutil.which('xtb') is None or not shutil.which('xtb').endswith('xtb'):
return
xtb.path = shutil.which('xtb')
sn2_neb.calculate(method=xtb, n_cores=2)
# There should be a peak in this surface
assert len(list(sn2_neb.get_species_saddle_point())) > 0
assert all(image.energy is not None for image in sn2_neb.images)
energies = [image.energy for image in sn2_neb.images]
path_energy = sum(energy - min(energies) for energy in energies)
assert 0.35 < path_energy < 0.45
def test_get_ts_guess_neb():
reactant = Reactant(name='inital',
charge=-1,
mult=0,
solvent_name='water',
atoms=xyz_file_to_atoms('sn2_init.xyz'))
product = Reactant(name='final',
charge=-1,
mult=0,
solvent_name='water',
atoms=xyz_file_to_atoms('sn2_final.xyz'))
xtb = XTB()
# Don't run the NEB without a working XTB install
if shutil.which('xtb') is None or not shutil.which('xtb').endswith('xtb'):
return
xtb.path = shutil.which('xtb')
ts_guess = get_ts_guess_neb(reactant, product, method=xtb, n=10)
assert ts_guess is not None
# Approximate distances at the TS guess
assert 1.8 < ts_guess.distance(0, 2) < 2.3 # C-F
assert 1.9 < ts_guess.distance(2, 1) < 2.5 # C-Cl
if os.path.exists('NEB'):
shutil.rmtree('NEB')
if os.path.exists('neb.xyz'):
os.remove('neb.xyz')
# Trying to get a TS guess with an unavailable method should return None
# as a TS guess
orca = ORCA()
orca.path = None
orca_ts_guess = get_ts_guess_neb(reactant, product, method=orca, n=10)
assert orca_ts_guess is None