def test_frozen_phonons():
atoms = Atoms('CO', positions=[(2.5, 2.5, 2), (2.5, 2.5, 3)], cell=(5, 5, 4))
fp1 = FrozenPhonons(atoms, 10, sigmas={'C': .1, 'O': .1})
fp2 = FrozenPhonons(atoms, 10, sigmas=.1)
fp3 = FrozenPhonons(atoms, 10, sigmas=[.1, .1])
assert np.all(fp1._sigmas == fp2._sigmas) & np.all(fp2._sigmas == fp3._sigmas)
def test_probe_waves_line_scan():
atoms = Atoms('CO',
positions=[(2.5, 2.5, 2), (2.5, 2.5, 3)],
cell=(5, 5, 4))
frozen_phonons = FrozenPhonons(atoms, 2, sigmas={'C': 0, 'O': 0.})
potential = Potential(atoms, sampling=.05)
tds_potential = Potential(frozen_phonons, sampling=.05)
linescan = LineScan(start=[0, 0], end=[2.5, 2.5], gpts=10)
detector = AnnularDetector(inner=80, outer=200)
probe = Probe(semiangle_cutoff=30, energy=80e3, gpts=500)
measurements = probe.scan(linescan, [detector],
potential,
max_batch=50,
pbar=False)
tds_measurements = probe.scan(linescan, [detector],
tds_potential,
max_batch=50,
pbar=False)
assert np.allclose(measurements[detector].array,
tds_measurements[detector].array,
atol=1e-6)
frozen_phonons = FrozenPhonons(atoms, 2, sigmas={'C': 0, 'O': 0.1})
tds_potential = Potential(frozen_phonons, sampling=.05)
tds_measurements = probe.scan(linescan, [detector],
tds_potential,
max_batch=50,
pbar=False)
assert not np.allclose(measurements[detector].array,
tds_measurements[detector].array,
atol=1e-6)
def test_frozen_phonons_raise():
atoms = Atoms('CO', positions=[(2.5, 2.5, 2), (2.5, 2.5, 3)], cell=(5, 5, 4))
with pytest.raises(RuntimeError) as e:
FrozenPhonons(atoms, 10, sigmas={'C': .1})
assert str(e.value) == 'Displacement standard deviation must be provided for all atomic species.'
with pytest.raises(RuntimeError) as e:
FrozenPhonons(atoms, 10, sigmas=[.1])
assert str(e.value) == 'Displacement standard deviation must be provided for all atoms.'