def test_get_ts_guess_1dscan():
os.chdir(os.path.join(here, 'data'))
fbond = FormingBond(atom_indexes=(1, 2), species=reac)
fbond.final_dist = 0.7
ts_guess = get_ts_guess_1d(name='H+H2_H2+H',
reactant=reac,
product=prod,
bond=fbond,
method=orca,
keywords=opt_keywords,
dr=0.06)
assert ts_guess.n_atoms == 3
# Peak in the PES is at r = 0.85 Å
assert 0.84 < ts_guess.get_distance(1, 2) < 0.86
assert os.path.exists('H+H2_H2+H.png')
for filename in os.listdir(os.getcwd()):
if filename.endswith(('.inp', '.png')):
os.remove(filename)
os.chdir(here)
def test_get_ts_guess_1dscan():
fbond = FormingBond(atom_indexes=(1, 2), species=reac)
fbond.final_dist = 0.7
ts_guess = get_ts_guess_1d(name='H+H2_H2+H',
reactant=reac,
product=prod,
bond=fbond,
method=orca,
keywords=opt_keywords,
dr=0.06)
assert ts_guess.n_atoms == 3
# Peak in the PES is at r = 0.85 Å
assert 0.84 < ts_guess.get_distance(1, 2) < 0.86
assert os.path.exists('H+H2_H2+H.png')
os.remove('H+H2_H2+H.png')
def test_removing_active_bonds():
filepath = os.path.join(here, 'data', 'neb', 'co_complex.xyz')
mol = Molecule(name='co_complex', atoms=xyz_file_to_atoms(filepath))
bbond = BreakingBond(atom_indexes=(1, 2), species=mol)
fbond = FormingBond(atom_indexes=(3, 1), species=mol)
bonds = neb.active_bonds_no_rings(mol, fbonds=[fbond], bbonds=[bbond])
# Should remove the breaking bond as it forms a ring with an already
# present atom pair
assert len(bonds) == 1
assert isinstance(bonds[0], FormingBond)
# Also check that the number of images to generate are somewhat reasonable
n_images = neb.calc_n_images(fbonds=[fbond],
bbonds=[bbond],
average_spacing=0.1)
assert 0 < n_images < 20
def test_bonds():
h1 = Atom(atomic_symbol='H', x=0.0, y=0.0, z=0.0)
h2 = Atom(atomic_symbol='H', x=0.0, y=0.0, z=0.7)
h3 = Atom(atomic_symbol='H', x=0.0, y=0.0, z=1.7)
hydrogen = Reactant(name='H2', atoms=[h1, h2], charge=0, mult=1)
h = Reactant(name='H', atoms=[h3], charge=0, mult=2)
reac = ReactantComplex(hydrogen, h)
prod_h2 = Product(name='H2', atoms=[h1, h2], charge=0, mult=1)
prod_h = Product(name='H', atoms=[h3], charge=0, mult=2)
fbond = FormingBond(atom_indexes=(1, 2), species=reac)
bbond = BreakingBond(atom_indexes=(0, 1), species=reac, reaction=Reaction(hydrogen, h, prod_h2, prod_h))
assert fbond.curr_dist == 1.0
assert 0.6 < fbond.final_dist < 0.8
assert 2.0 < bbond.final_dist < 2.5
assert bbond.curr_dist == 0.7
def test_get_ts_guess_2dscan():
ch3cl_f = Reactant(name='CH3Cl_F-',
charge=-1,
mult=1,
atoms=[
Atom('F', -4.14292, -0.24015, 0.07872),
Atom('Cl', 1.63463, 0.09787, -0.02490),
Atom('C', -0.14523, -0.00817, 0.00208),
Atom('H', -0.47498, -0.59594, -0.86199),
Atom('H', -0.45432, -0.49900, 0.93234),
Atom('H', -0.56010, 1.00533, -0.04754)
])
ch3f_cl = Product(name='CH3Cl_F-',
charge=-1,
mult=1,
atoms=[
Atom('F', 1.63463, 0.09787, -0.02490),
Atom('Cl', -4.14292, -0.24015, 0.07872),
Atom('C', -0.14523, -0.00817, 0.00208),
Atom('H', -0.47498, -0.59594, -0.86199),
Atom('H', -0.45432, -0.49900, 0.93234),
Atom('H', -0.56010, 1.00533, -0.04754)
])
# H H
# F- C--Cl -> F--C Cl-
# H H H H
pes = pes_2d.PES2d(reactant=ReactantComplex(ch3cl_f),
product=ProductComplex(ch3f_cl),
r1s=np.linspace(4.0, 1.5, 9),
r1_idxs=(0, 2),
r2s=np.linspace(1.78, 4.0, 8),
r2_idxs=(1, 2))
pes.calculate(name='SN2_PES', method=xtb, keywords=xtb.keywords.low_opt)
assert pes.species[0, 1] is not None
assert -13.13 < pes.species[0, 1].energy < -13.11
assert pes.species.shape == (9, 8)
assert pes.rs.shape == (9, 8)
assert type(pes.rs[0, 1]) == tuple
assert pes.rs[1, 1] == (np.linspace(4.0, 1.5,
9)[1], np.linspace(1.78, 4.0, 8)[1])
# Fitting the surface with a 2D polynomial up to order 3 in r1 and r2 i.e.
# r1^3r2^3
pes.fit(polynomial_order=3)
assert pes.coeff_mat is not None
assert pes.coeff_mat.shape == (4, 4) # Includes r1^0 etc.
pes.print_plot(name='pes_plot')
assert os.path.exists('pes_plot.png')
os.remove('pes_plot.png')
# Products should be made on this surface
assert pes.products_made()
# Get the TS guess from this surface calling all the above functions
reactant = ReactantComplex(ch3cl_f)
fbond = FormingBond(atom_indexes=(0, 2), species=reactant)
fbond.final_dist = 1.5
bbond = BreakingBond(atom_indexes=(1, 2),
species=reactant,
reaction=Reaction(ch3cl_f, ch3f_cl))
bbond.final_dist = 4.0
ts_guess = pes_2d.get_ts_guess_2d(reactant=reactant,
product=ProductComplex(ch3f_cl),
bond1=fbond,
bond2=bbond,
polynomial_order=3,
name='SN2_PES',
method=xtb,
keywords=xtb.keywords.low_opt,
dr=0.3)
assert ts_guess is not None
assert ts_guess.n_atoms == 6
assert ts_guess.energy is None
assert 1.9 < ts_guess.get_distance(0, 2) < 2.1
assert 1.9 < ts_guess.get_distance(1, 2) < 2.0
def get_ts_guess_function_and_params(reaction, bond_rearr):
"""Get the functions (1dscan or 2dscan) and parameters required for the
function for a TS scan
Arguments:
reaction (autode.reaction.Reaction):
bond_rearr (autode.bond_rearrangement.BondRearrangement):
Returns:
(list): updated funcs and params list
"""
name = str(reaction)
scan_name = name
r, p = reaction.reactant, reaction.product
lmethod, hmethod = get_lmethod(), get_hmethod()
# Bonds with initial and final distances
bbonds = [BreakingBond(pair, r, reaction) for pair in bond_rearr.bbonds]
scan_name += "_".join(str(bb) for bb in bbonds)
fbonds = [FormingBond(pair, r) for pair in bond_rearr.fbonds]
scan_name += "_".join(str(fb) for fb in fbonds)
# Ideally use a transition state template, then only a single constrained
# optimisation needs to be run...
yield get_template_ts_guess, (r, p, bond_rearr,
f'{name}_template_{bond_rearr}', hmethod)
# Otherwise try a nudged elastic band calculation, don't use the low level
# method if there are any metals..
if not any(atom.label in metals for atom in r.atoms):
yield get_ts_guess_neb, (r, p, lmethod, fbonds, bbonds,
f'{name}_ll_neb_{bond_rearr}')
# Always attempt a high-level NEB
yield get_ts_guess_neb, (r, p, hmethod, fbonds, bbonds,
f'{name}_hl_neb_{bond_rearr}')
# Otherwise run 1D or 2D potential energy surface scans to generate a
# transition state guess cheap -> most expensive
if len(bbonds) == 1 and len(fbonds) == 1 and reaction.type in (Substitution, Elimination):
yield get_ts_guess_2d, (r, p, fbonds[0], bbonds[0], f'{scan_name}_ll2d',
lmethod, lmethod.keywords.low_opt)
yield get_ts_guess_1d, (r, p, bbonds[0], f'{scan_name}_hl1d_bbond',
hmethod, hmethod.keywords.low_opt)
yield get_ts_guess_1d, (r, p, bbonds[0], f'{scan_name}_hl1d_alt_bbond',
hmethod, hmethod.keywords.opt)
if len(bbonds) > 0 and len(fbonds) == 1:
yield get_ts_guess_1d, (r, p, fbonds[0], f'{scan_name}_hl1d_fbond',
hmethod, hmethod.keywords.low_opt)
yield get_ts_guess_1d, (r, p, fbonds[0], f'{scan_name}_hl1d_alt_fbond',
hmethod, hmethod.keywords.opt)
if len(bbonds) >= 1 and len(fbonds) >= 1:
for fbond in fbonds:
for bbond in bbonds:
yield get_ts_guess_2d, (r, p, fbond, bbond,
f'{scan_name}_ll2d', lmethod,
lmethod.keywords.low_opt)
yield get_ts_guess_2d, (r, p, fbond, bbond,
f'{scan_name}_hl2d', hmethod,
hmethod.keywords.low_opt)
if len(bbonds) == 1 and len(fbonds) == 0:
yield get_ts_guess_1d, (r, p, bbonds[0], f'{scan_name}_hl1d', hmethod,
hmethod.keywords.low_opt)
yield get_ts_guess_1d, (r, p, bbonds[0], f'{scan_name}_hl1d_alt',
hmethod, hmethod.keywords.opt)
if len(fbonds) == 2:
yield get_ts_guess_2d, (r, p, fbonds[0], fbonds[1],
f'{scan_name}_ll2d_fbonds', lmethod,
lmethod.keywords.low_opt)
yield get_ts_guess_2d, (r, p, fbonds[0], fbonds[1],
f'{scan_name}_hl2d_fbonds', hmethod,
hmethod.keywords.low_opt)
if len(bbonds) == 2:
yield get_ts_guess_2d, (r, p, bbonds[0], bbonds[1],
f'{scan_name}_ll2d_bbonds', lmethod,
lmethod.keywords.low_opt)
yield get_ts_guess_2d, (r, p, bbonds[0], bbonds[1],
f'{scan_name}_hl2d_bbonds', hmethod,
hmethod.keywords.low_opt)
return None