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_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] == 0
assert 19 < energies[1] < 21
assert -21 < energies[2] < -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] == 0
assert -0.1 < energies[3] < 0.1
assert -41 < energies[4] < -39
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_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_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_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_optts_no_reactants_products():
da_ts_guess = TSguess(atoms=xyz_file_to_atoms('da_TS_guess.xyz'))
da_ts = TransitionState(da_ts_guess)
da_ts.optimise()
assert len(da_ts.imaginary_frequencies) == 1
imag_freq = da_ts.imaginary_frequencies[0]
assert -500 < imag_freq < -300 # cm-1
# Should raise exceptions for TSs not initialised with reactants and
# products
with pytest.raises(ValueError):
_ = da_ts.could_have_correct_imag_mode()
with pytest.raises(ValueError):
_ = da_ts.has_correct_imag_mode()
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)
tsguess = TSguess(reactant=reac_complex,
product=product_complex,
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)
])
tsguess.bond_rearrangement = BondRearrangement(breaking_bonds=[(2, 1)],
forming_bonds=[(0, 2)])
ts = TransitionState(ts_guess=tsguess)
@testutils.work_in_zipped_dir(os.path.join(here, 'data', 'ts.zip'))
def test_ts_guess_class():
# Force ORCA to appear available
def test_no_graph():
ts_no_graph = TSguess(atoms=None)
assert ts_no_graph.graph is None