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_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_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)