def test_get_bond_rearrangs():
if os.path.exists('test_bond_rearrangs.txt'):
os.remove('test_bond_rearrangs.txt')
# ethane --> Ch3 + Ch3
reac = Molecule(smiles='CC')
prod = Molecule(atoms=[Atom('C', -8.3, 1.4, 0.0),
Atom('C', 12, 1.7, -0.0),
Atom('H', -8.6, 0.5, -0.5),
Atom('H', -8.6, 2.3, -0.4),
Atom('H', -8.6, 1.3, 1),
Atom('H', 12.3, 1.7, -1.0),
Atom('H', 12.4, 0.8, 0.4),
Atom('H', 12.3, 2.5, 0.5)])
assert br.get_bond_rearrangs(ReactantComplex(reac), ProductComplex(prod), name='test') == [br.BondRearrangement(breaking_bonds=[(0, 1)])]
# Rerunning the get function should read test_bond_rearrangs.txt, so modify it, swapping 0 and 1 in the breaking
# bond then reopen
with open('test_bond_rearrangs.txt', 'w') as rearr_file:
print('fbond\n'
'bbonds\n'
'1 0\n'
'end', file=rearr_file)
rearr = br.get_bond_rearrangs(ReactantComplex(reac), ProductComplex(prod), name='test')[0]
assert rearr == BondRearrangement(breaking_bonds=[(1, 0)])
assert br.get_bond_rearrangs(ReactantComplex(prod), ProductComplex(reac), name='test2') is None
# If reactants and products are identical then the rearrangement is undetermined
assert br.get_bond_rearrangs(ReactantComplex(reac), ProductComplex(reac), name='test3') is None
os.remove('test_bond_rearrangs.txt')
def test_calc_delta_e():
r1 = reaction.Reactant(name='h', atoms=[Atom('H', 0.0, 0.0, 0.0)])
r1.energy = -0.5
r2 = reaction.Reactant(name='h', atoms=[Atom('H', 0.0, 0.0, 0.0)])
r2.energy = -0.5
tsguess = TSguess(atoms=None,
reactant=ReactantComplex(r1),
product=ProductComplex(r2))
tsguess.bond_rearrangement = BondRearrangement()
ts = TransitionState(tsguess)
ts.energy = -0.8
p = reaction.Product(
name='hh', atoms=[Atom('H', 0.0, 0.0, 0.0),
Atom('H', 1.0, 0.0, 0.0)])
p.energy = -1.0
reac = reaction.Reaction(r1, r2, p)
reac.ts = ts
assert -1E-6 < reac.calc_delta_e() < 1E-6
assert 0.2 - 1E-6 < reac.calc_delta_e_ddagger() < 0.2 + 1E-6
def test_sum_mep():
reactant = ReactantComplex(Molecule(smiles='C', charge=0, mult=1))
product = ProductComplex(Molecule(smiles='C', charge=0, mult=1))
product.graph.remove_edge(0, 1)
product.graph.remove_edge(0, 2)
# Fictitious PES
pes = PES2d(reactant,
product,
r1s=np.linspace(1, 2, 3),
r1_idxs=(0, 1),
r2s=np.linspace(1, 2, 3),
r2_idxs=(0, 2))
# Energies are all 0 apart from at the 'saddle point' (1, 1)
for i in range(3):
for j in range(3):
pes.species[i, j] = deepcopy(reactant)
pes.species[i, j].energy = 0
if i == j == 2:
pes.species[i, j].graph = product.graph
pes.species[1, 1].energy = 1
mep_sum = mep.get_sum_energy_mep(saddle_point_r1r2=(1.5, 1.5), pes_2d=pes)
# Energy over the saddle point is 1 both sides -> 2 Ha
assert mep_sum == 2
def test_constrained_opt():
os.chdir(os.path.join(here, 'data'))
mol = Molecule(name='h3',
mult=2,
charge=0,
atoms=[
Atom('H', 0.0, 0.0, 0.0),
Atom('H', 0.7, 0.0, 0.0),
Atom('H', 1.7, 0.0, 0.0)
])
Config.XTB.path = here # A path that exists
ts_guess = get_ts_guess_constrained_opt(
reactant=ReactantComplex(mol),
distance_consts={(0, 1): 1.0},
method=orca,
keywords=Config.ORCA.keywords.low_opt,
name='template_ts_guess',
product=ProductComplex(mol))
assert ts_guess.n_atoms == 3
os.remove('xcontrol_template_ts_guess_constrained_opt_ll_xtb')
os.remove('template_ts_guess_constrained_opt_ll_xtb.xyz')
os.remove('template_ts_guess_constrained_opt_orca.inp')
os.chdir(here)
def test_reaction_warnings():
test_reac = Reactant(name='test', smiles='C')
test_reac.energy = -1
test_prod = Product(name='test', smiles='C')
test_prod.energy = -1.03187251
tsguess = TSguess(atoms=test_reac.atoms,
reactant=ReactantComplex(test_reac),
product=ProductComplex())
tsguess.bond_rearrangement = BondRearrangement()
ts = TransitionState(tsguess)
ts.energy = -0.98
ts.imaginary_frequencies = [-100]
reaction = Reaction(test_reac, test_prod)
reaction.ts = None
# Should be some warning with no TS
assert len(
plotting.get_reaction_profile_warnings(reactions=[reaction])) > 10
# Should be no warnings with a TS that exists and has an energy and one
# imaginary freq
reaction.ts = ts
warnings = plotting.get_reaction_profile_warnings(reactions=[reaction])
assert 'None' in warnings
def test_plot_reaction_profile():
r = Reactant(name='reactant', smiles='C')
p = Product(name='product', smiles='C')
tsguess = TSguess(atoms=r.atoms,
reactant=ReactantComplex(r),
product=ProductComplex(p))
tsguess.bond_rearrangement = BondRearrangement()
ts = TransitionState(tsguess)
reaction = Reaction(r, p)
reaction.ts = ts
plotting.plot_reaction_profile(reactions=[reaction],
units=KjMol,
name='test')
assert os.path.exists('test_reaction_profile.png')
os.remove('test_reaction_profile.png')
with pytest.raises(AssertionError):
plotting.plot_reaction_profile(reactions=[reaction],
units=KjMol,
name='test',
free_energy=True,
enthalpy=True)
return None
def test_3b():
reac = Molecule(atoms=[Atom('H', 0, 0, 0), Atom('H', 0.6, 0, 0), Atom('H', 1.2, 0, 0), Atom('H', 1.8, 0, 0)])
make_graph(reac, allow_invalid_valancies=True)
prod = Molecule(atoms=[Atom('H', 0, 0, 0), Atom('H', 10, 0, 0), Atom('H', 20, 0, 0), Atom('H', 30, 0, 0)])
# Reactants to products must break three bonds but this is not yet supported in any form
assert br.get_bond_rearrangs(ReactantComplex(reac), ProductComplex(prod), name='3b_test') is None
def test_ts_conformer(tmpdir):
os.chdir(tmpdir)
ch3cl = Reactant(charge=0,
mult=1,
atoms=[
Atom('Cl', 1.63664, 0.02010, -0.05829),
Atom('C', -0.14524, -0.00136, 0.00498),
Atom('H', -0.52169, -0.54637, -0.86809),
Atom('H', -0.45804, -0.50420, 0.92747),
Atom('H', -0.51166, 1.03181, -0.00597)
])
f = Reactant(charge=-1, mult=1, atoms=[Atom('F', 4.0, 0.0, 0.0)])
ch3f = Product(charge=0,
mult=1,
atoms=[
Atom('C', -0.05250, 0.00047, -0.00636),
Atom('F', 1.31229, -0.01702, 0.16350),
Atom('H', -0.54993, -0.04452, 0.97526),
Atom('H', -0.34815, 0.92748, -0.52199),
Atom('H', -0.36172, -0.86651, -0.61030)
])
cl = Reactant(charge=-1, mult=1, atoms=[Atom('Cl', 4.0, 0.0, 0.0)])
f_ch3cl_tsguess = TSguess(reactant=ReactantComplex(f, ch3cl),
product=ProductComplex(ch3f, cl),
atoms=[
Atom('F', -2.66092, -0.01426, 0.09700),
Atom('Cl', 1.46795, 0.05788, -0.06166),
Atom('C', -0.66317, -0.01826, 0.02488),
Atom('H', -0.78315, -0.58679, -0.88975),
Atom('H', -0.70611, -0.54149, 0.97313),
Atom('H', -0.80305, 1.05409, 0.00503)
])
f_ch3cl_tsguess.bond_rearrangement = BondRearrangement(breaking_bonds=[
(2, 1)
],
forming_bonds=[(0,
2)])
f_ch3cl_ts = TransitionState(ts_guess=f_ch3cl_tsguess)
atoms = conf_gen.get_simanl_atoms(
species=f_ch3cl_ts, dist_consts=get_distance_constraints(f_ch3cl_ts))
regen = Molecule(name='regenerated_ts', charge=-1, mult=1, atoms=atoms)
# regen.print_xyz_file()
# Ensure the making/breaking bonds retain their length
regen_coords = regen.get_coordinates()
assert are_coords_reasonable(regen_coords) is True
assert 1.9 < np.linalg.norm(regen_coords[0] - regen_coords[2]) < 2.1
assert 2.0 < np.linalg.norm(regen_coords[1] - regen_coords[2]) < 2.2
os.chdir(here)
def test_2b():
reac = Molecule(atoms=[Atom('H', 0, 0, 0), Atom('H', 0.6, 0, 0), Atom('H', 1.2, 0, 0)])
make_graph(reac, allow_invalid_valancies=True)
prod = Molecule(atoms=[Atom('H', 0, 0, 0), Atom('H', 10, 0, 0), Atom('H', 20, 0, 0)])
# Reactants to products must break two bonds
assert len(br.get_bond_rearrangs(ReactantComplex(reac), ProductComplex(prod), name='2b_test')) == 1
os.remove('2b_test_bond_rearrangs.txt')
assert br.get_fbonds_bbonds_2b(reac, prod, [], [[(0, 1), (1, 2)]], [], [], [(0, 2)], []) == [br.BondRearrangement(breaking_bonds=[(0, 1), (1, 2)])]
def test_two_possibles():
ch2ch3f = Molecule(name='radical', charge=0, mult=2,
smiles='FC[C]([H])[H]')
ch3ch2f = Molecule(name='radical', charge=0, mult=2,
smiles='C[C]([H])F')
rearrs = br.get_bond_rearrangs(ReactantComplex(ch2ch3f), ProductComplex(ch3ch2f),
name='H_migration')
# There are two possibilities for H migration by they should be considered the same
assert len(rearrs) == 1
os.remove('H_migration_bond_rearrangs.txt')
def test_multiple_possibilities():
r1 = Molecule(name='h_dot', smiles='[H]')
r2 = Molecule(name='methane', smiles='C')
p1 = Molecule(name='h2', smiles='[HH]')
p2 = Molecule(name='ch3_dot', smiles='[CH3]')
reac = ReactantComplex(r1, r2)
reac.print_xyz_file()
rearrs = br.get_bond_rearrangs(reac, ProductComplex(p1, p2),
name='H_subst')
os.remove('H_subst_bond_rearrangs.txt')
# All H abstractions are the same
assert len(rearrs) == 1
def test_plot_reaction_profile():
r = Reactant(name='reactant', smiles='C')
p = Product(name='product', smiles='C')
tsguess = TSguess(atoms=r.atoms,
reactant=ReactantComplex(r),
product=ProductComplex(p))
tsguess.bond_rearrangement = BondRearrangement()
ts = TransitionState(tsguess)
reaction = Reaction(r, p)
reaction.ts = ts
plotting.plot_reaction_profile(reactions=[reaction],
units=KjMol,
name='test_reaction')
assert os.path.exists('test_reaction_reaction_profile.png')
os.remove('test_reaction_reaction_profile.png')
def test_plot_reaction_profile():
# only tests the file is created with the right name
os.chdir(os.path.join(here, 'data'))
r = Reactant(name='reactant', smiles='C')
p = Product(name='product', smiles='C')
tsguess = TSguess(atoms=r.atoms, reactant=ReactantComplex(r), product=ProductComplex(p))
tsguess.bond_rearrangement = BondRearrangement()
ts = TransitionState(tsguess)
reaction = Reaction(r, p)
reaction.ts = ts
plotting.plot_reaction_profile(reactions=[reaction], units=KjMol, name='test_reaction')
assert os.path.exists('test_reaction_reaction_profile.png')
os.remove('test_reaction_reaction_profile.png')
os.chdir(here)
def test_constrained_opt():
mol = Molecule(name='h3',
mult=2,
charge=0,
atoms=[
Atom('H', 0.0, 0.0, 0.0),
Atom('H', 0.7, 0.0, 0.0),
Atom('H', 1.7, 0.0, 0.0)
])
# Spoof an XTB install
Config.XTB.path = here
ts_guess = get_ts_guess_constrained_opt(
reactant=ReactantComplex(mol),
distance_consts={(0, 1): 1.0},
method=XTB(),
keywords=Config.XTB.keywords.low_opt,
name='template_ts_guess',
product=ProductComplex(mol))
assert ts_guess.n_atoms == 3
def test_fb_rp_isomorphic():
reac = ReactantComplex(f, ch3cl)
prod = ProductComplex(ch3f, cl)
assert f_b_isomorphic_to_r_p(forwards=prod,
backwards=reac,
reactant=reac,
product=prod)
assert f_b_isomorphic_to_r_p(forwards=reac,
backwards=prod,
reactant=reac,
product=prod)
assert not f_b_isomorphic_to_r_p(
forwards=reac, backwards=reac, reactant=reac, product=prod)
# Check for e.g. failed optimisation of the forwards displaced complex
mol_no_atoms = Product()
assert not f_b_isomorphic_to_r_p(
forwards=mol_no_atoms, backwards=reac, reactant=reac, product=prod)
def test_calculate_reaction_profile_energies():
test_reac = Reactant(name='test', smiles='C')
test_reac.energy = -1
test_prod = Product(name='test', smiles='C')
test_prod.energy = -1.03187251
tsguess = TSguess(atoms=test_reac.atoms,
reactant=ReactantComplex(test_reac),
product=ProductComplex())
tsguess.bond_rearrangement = BondRearrangement()
ts = TransitionState(tsguess)
ts.energy = -0.96812749
reaction = Reaction(test_reac, test_prod)
reaction.ts = ts
energies = plotting.calculate_reaction_profile_energies(
reactions=[reaction], units=KcalMol)
# Energies have been set to ∆E = -20 and ∆E‡ = 20 kcal mol-1 respectively
assert energies[0].item() == 0
assert 19 < energies[1].item() < 21
assert -21 < energies[2].item() < -19
# Copying the reaction should give relative energies [0, 20, -20, 0, -40]
energies = plotting.calculate_reaction_profile_energies(
reactions=[reaction, deepcopy(reaction)], units=KcalMol)
# Energies have been set to ∆E = -20 and ∆E‡ = 20 kcal mol-1 respectively
assert energies[0].item() == 0
assert -0.1 < energies[3].item() < 0.1
assert -41 < energies[4].item() < -39
Atom('H', -0.51166, 1.03181, -0.00597)
])
f = Reactant(charge=-1, mult=1, atoms=[Atom('F', 4.0, 0.0, 0.0)])
reac_complex = ReactantComplex(f, ch3cl)
ch3f = Product(charge=0,
mult=1,
atoms=[
Atom('C', -0.05250, 0.00047, -0.00636),
Atom('F', 1.31229, -0.01702, 0.16350),
Atom('H', -0.54993, -0.04452, 0.97526),
Atom('H', -0.34815, 0.92748, -0.52199),
Atom('H', -0.36172, -0.86651, -0.61030)
])
cl = Product(charge=-1, mult=1, atoms=[Atom('Cl', 4.0, 0.0, 0.0)])
product_complex = ProductComplex(ch3f, cl)
@testutils.work_in_zipped_dir(os.path.join(here, 'data', 'ts_guess.zip'))
def test_ts_template_save():
ts_graph = reac_complex.graph.copy()
# Add the F-C bond as active
ts_graph.add_edge(0, 2, active=True)
# Remove then re-add the C-Cl bond as active
ts_graph.remove_edge(1, 2)
ts_graph.add_edge(1, 2, active=True)
truncated_graph = get_truncated_active_mol_graph(ts_graph)
from autode.pes.pes import get_closest_species
from autode.species.complex import ReactantComplex, ProductComplex
from autode.atoms import Atom
from autode.species.species import Species
from autode.mol_graphs import make_graph
from autode.exceptions import NoClosestSpecies
from autode.pes.pes import FormingBond, BreakingBond
from autode.reactions.reaction import Reaction
from autode.species.molecule import Reactant, Product
import pytest
import numpy as np
mol = Species(name='H2', charge=0, mult=1, atoms=[Atom('H'), Atom('H', z=1.0)])
make_graph(mol)
reactant = ReactantComplex(mol, mol)
product = ProductComplex(mol, mol)
pes = PES2d(reactant=reactant,
product=reactant,
r1s=np.linspace(1, 3, 3),
r1_idxs=(0, 1),
r2s=np.linspace(1, 0, 2),
r2_idxs=(2, 3))
def test_2d_pes_class():
assert reactant.n_atoms == 4
assert pes.rs.shape == (3, 2)
assert pes.species.shape == (3, 2)
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
# Override the availability of
orca.available = True
xtb.available = True
# Set the reactant and product complexes
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 = Molecule(name='H2', atoms=[h1, h2], charge=0, mult=1)
h = Molecule(name='H', atoms=[h3], charge=0, mult=2)
reac = ReactantComplex(hydrogen, h)
prod = ProductComplex(h, hydrogen)
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)