def test_orca_optts_calculation():
methane = SolvatedMolecule(name='methane', smiles='C')
methane.qm_solvent_atoms = []
calc = Calculation(name='test_ts_reopt_optts',
molecule=methane,
method=method,
bond_ids_to_add=[(0, 1)],
keywords=opt_keywords,
other_input_block='%geom\n'
'Calc_Hess true\n'
'Recalc_Hess 40\n'
'Trust 0.2\n'
'MaxIter 100\nend')
calc.run()
assert os.path.exists('test_ts_reopt_optts_orca.inp')
assert calc.get_normal_mode_displacements(mode_number=6) is not None
assert calc.terminated_normally()
assert calc.optimisation_converged()
assert calc.optimisation_nearly_converged() is False
assert len(calc.get_imaginary_freqs()) == 1
# Gradients should be an n_atom x 3 array
gradients = calc.get_gradients()
assert len(gradients) == 5
assert len(gradients[0]) == 3
assert -599.437 < calc.get_enthalpy() < -599.436
assert -599.469 < calc.get_free_energy() < -599.468
def test_gauss_optts_calc():
os.chdir(os.path.join(here, 'data'))
calc = Calculation(name='test_ts_reopt_optts',
molecule=test_mol,
method=method,
keywords=optts_keywords,
bond_ids_to_add=[(0, 1)])
calc.run()
print(calc.input.added_internals)
assert os.path.exists('test_ts_reopt_optts_g09.com')
bond_added = False
for line in open('test_ts_reopt_optts_g09.com', 'r'):
if 'B' in line and len(line.split()) == 3:
bond_added = True
assert line.split()[0] == 'B'
assert line.split()[1] == '1'
assert line.split()[2] == '2'
assert bond_added
assert calc.get_normal_mode_displacements(mode_number=6) is not None
assert calc.terminated_normally()
assert calc.optimisation_converged()
assert calc.optimisation_nearly_converged() is False
assert len(calc.get_imaginary_freqs()) == 1
assert -40.324 < calc.get_free_energy() < -40.322
assert -40.301 < calc.get_enthalpy() < -40.299
os.remove('test_ts_reopt_optts_g09.com')
os.chdir(here)
def test_calc_class():
xtb = XTB()
calc = Calculation(name='-tmp',
molecule=test_mol,
method=xtb,
keywords=xtb.keywords.sp)
# Should prepend a dash to appease some EST methods
assert not calc.name.startswith('-')
assert calc.molecule is not None
assert calc.method.name == 'xtb'
assert calc.get_energy() is None
assert calc.get_enthalpy() is None
assert calc.get_free_energy() is None
assert not calc.optimisation_converged()
assert not calc.optimisation_nearly_converged()
with pytest.raises(ex.AtomsNotFound):
_ = calc.get_final_atoms()
with pytest.raises(ex.CouldNotGetProperty):
_ = calc.get_gradients()
with pytest.raises(ex.CouldNotGetProperty):
_ = calc.get_atomic_charges()
# Calculation that has not been run shouldn't have an opt converged
assert not calc.optimisation_converged()
assert not calc.optimisation_nearly_converged()
# With a filename that doesn't exist a NoOutput exception should be raised
calc.output.filename = '/a/path/that/does/not/exist/tmp'
with pytest.raises(ex.NoCalculationOutput):
calc.output.set_lines()
# With no output should not be able to get properties
calc.output.filename = 'tmp'
calc.output.file_lines = []
with pytest.raises(ex.CouldNotGetProperty):
_ = calc.get_atomic_charges()
# or final atoms
with pytest.raises(ex.AtomsNotFound):
_ = calc.get_final_atoms()
# Should default to a single core
assert calc.n_cores == 1
calc_str = str(calc)
new_calc = Calculation(name='tmp2',
molecule=test_mol,
method=xtb,
keywords=xtb.keywords.sp)
new_calc_str = str(new_calc)
# Calculation strings need to be unique
assert new_calc_str != calc_str
new_calc = Calculation(name='tmp2',
molecule=test_mol,
method=xtb,
keywords=xtb.keywords.sp,
temp=5000)
assert str(new_calc) != new_calc_str
mol_no_atoms = Molecule()
with pytest.raises(ex.NoInputError):
_ = Calculation(name='tmp2',
molecule=mol_no_atoms,
method=xtb,
keywords=xtb.keywords.sp)
