def test_input_gen():
xtb = XTB()
calc = Calculation(name='tmp',
molecule=test_mol,
method=xtb,
keywords=xtb.keywords.sp)
Config.keep_input_files = True
calc.generate_input()
assert os.path.exists('tmp_xtb.xyz')
calc.clean_up()
# Clean-up should do nothing if keep_input_files = True
assert os.path.exists('tmp_xtb.xyz')
# but should be able to be forced
calc.clean_up(force=True)
assert not os.path.exists('tmp_xtb.xyz')
# Test the keywords parsing
unsupported_func = Functional('PBE', orca='PBE')
calc_kwds = Calculation(name='tmp',
molecule=test_mol,
method=xtb,
keywords=SinglePointKeywords([unsupported_func]))
with pytest.raises(ex.UnsuppportedCalculationInput):
calc_kwds.generate_input()
def test_xtb_calculation():
test_mol = Molecule(name='test_mol',
smiles='O=C(C=C1)[C@@](C2NC3C=C2)([H])[C@@]3([H])C1=O')
calc = Calculation(name='opt', molecule=test_mol, method=method,
keywords=Config.XTB.keywords.opt)
calc.run()
assert os.path.exists('opt_xtb.xyz') is True
assert os.path.exists('opt_xtb.out') is True
assert len(calc.get_final_atoms()) == 22
assert calc.get_energy() == -36.990267613593
assert calc.output.exists()
assert calc.output.file_lines is not None
assert calc.input.filename == 'opt_xtb.xyz'
assert calc.output.filename == 'opt_xtb.out'
with pytest.raises(NotImplementedError):
calc.optimisation_nearly_converged()
with pytest.raises(NotImplementedError):
calc.get_imaginary_freqs()
with pytest.raises(NotImplementedError):
calc.get_normal_mode_displacements(4)
charges = calc.get_atomic_charges()
assert len(charges) == 22
assert all(-1.0 < c < 1.0 for c in charges)
const_opt = Calculation(name='const_opt', molecule=test_mol,
method=method,
distance_constraints={(0, 1): 1.2539792},
cartesian_constraints=[0],
keywords=Config.XTB.keywords.opt)
const_opt.generate_input()
assert os.path.exists('const_opt_xtb.xyz')
assert os.path.exists('xcontrol_const_opt_xtb')
const_opt.clean_up(force=True)
assert not os.path.exists('xcontrol_const_opt_xtb')
# Write an empty output file
open('tmp.out', 'w').close()
const_opt.output.filename = 'tmp.out'
const_opt.output.set_lines()
# cannot get atoms from an empty file
with pytest.raises(AtomsNotFound):
_ = const_opt.get_final_atoms()
