def test_plane_waves_raises():
plane_waves = PlaneWave(energy=60e3)
with pytest.raises(RuntimeError) as e:
plane_waves.multislice(DummyPotential(extent=5), pbar=False)
assert str(e.value) == 'Grid gpts cannot be inferred'
def test_propagator_cache():
wave = PlaneWave(extent=10, gpts=100, energy=60e3).build()
propagator = FresnelPropagator()
propagator.propagate(wave, .5)
propagator.propagate(wave, .5)
assert propagator.cache._hits == 1
assert propagator.cache._misses == 1
def test_fig_5_12():
atoms = Atoms('CSiCuAuU',
positions=[(x, 25, 4) for x in np.linspace(5, 45, 5)],
cell=(50, 50, 8))
potential = Potential(atoms=atoms,
gpts=512,
parametrization='kirkland',
cutoff_tolerance=1e-4)
waves = PlaneWave(energy=200e3)
waves = waves.multislice(potential, pbar=False)
waves = waves.apply_ctf(defocus=700, Cs=1.3e7, semiangle_cutoff=.01037)
intensity = np.abs(waves.array)**2
assert np.round(intensity.min(), 2) == np.float32(.72)
assert np.round(intensity.max(), 2) == np.float32(1.03)
def test_plane_waves_multislice():
plane_waves = PlaneWave(gpts=50, energy=60e3)
plane_waves.multislice(DummyPotential(extent=5))
plane_waves = PlaneWave(sampling=.1, energy=60e3)
plane_waves.multislice(DummyPotential(extent=5))
def test_create_plane_waves():
plane_wave = PlaneWave(extent=2, gpts=10, energy=60e3)
waves = plane_wave.build()
assert np.all(waves.array == np.ones((10, 10), dtype=np.complex64))
orientation='vertical')
#plt.colorbar(sc, cax=cax, orientation='vertical',ticks=[-5,-2.5,0,2.5,5],label='$\epsilon_p$ [\%]')
#plt.tight_layout()
plt.show()
for i, model in enumerate(models_list):
# # # Building the potential
potential = Potential(model,
gpts=L,
slice_thickness=1,
parametrization='kirkland',
projection='infinite')
wave = PlaneWave(energy=300e3 # acceleration voltage in eV
)
exit_wave = wave.multislice(potential)
np.savez('{0}/points/points_{1:04d}.npz'.format(dir_name,
first_number + i),
sites=sites_list[i],
classes=classes_list[i])
exit_wave.write('{0}/wave/wave_{1:04d}.hdf5'.format(
dir_name, first_number + i))
write('{0}/model/model_{1:04d}.cfg'.format(dir_name, first_number + i),
model)
print('TEM images finnished: ' + str(100 * (i + 1) // num_examples) + '%')