def test_prism_raises():
with pytest.raises(ValueError) as e:
SMatrix(.01, 80e3, .5)
assert str(e.value) == 'Interpolation factor must be int'
with pytest.raises(RuntimeError) as e:
prism = SMatrix(10, 80e3, 1)
prism.build()
assert str(e.value) == 'Grid extent is not defined'
def test_downsample_smatrix():
S = SMatrix(expansion_cutoff=10,
interpolation=2,
energy=300e3,
extent=10,
sampling=.05)
S = S.build().downsample()
S2 = SMatrix(expansion_cutoff=10,
interpolation=2,
energy=300e3,
extent=10,
gpts=S.gpts)
S2 = S2.build()
assert np.allclose(S.array - S2.array, 0., atol=5e-6)
def test_unequal_interpolation():
from ase.build import nanotube
def make_atoms(l):
atoms = nanotube(6, 0, length=l)
atoms.rotate(-90, 'x', rotate_cell=True)
atoms.center(vacuum=5, axis=(0, 1))
cell = atoms.cell.copy()
cell[1] = np.abs(atoms.cell[2])
cell[2] = np.abs(atoms.cell[1])
atoms.set_cell(cell)
return atoms
detector = AnnularDetector(50, 150)
atoms1 = make_atoms(8)
S1 = SMatrix(energy=80e3,
expansion_cutoff=10,
semiangle_cutoff=10,
interpolation=(2, 4),
device='cpu',
gpts=(256, 512))
S1.extent = np.diag(atoms1.cell)[:2]
scan = GridScan((0, 0), (atoms1.cell[0, 0], atoms1.cell[1, 1] / 2),
sampling=S1.ctf.nyquist_sampling * .9)
measurement1 = S1.scan(scan, detector, atoms1, pbar=False)
atoms2 = make_atoms(4)
S2 = SMatrix(energy=80e3,
expansion_cutoff=10,
semiangle_cutoff=10,
interpolation=(2, 2),
device='cpu',
gpts=(256, 256))
S2.extent = np.diag(atoms2.cell)[:2]
scan = GridScan((0, 0), (atoms2.cell[0, 0], atoms2.cell[1, 1]),
sampling=S2.ctf.nyquist_sampling * .9)
measurement2 = S2.scan(scan, detector, atoms2, pbar=False)
assert len(S1) == len(S2)
assert np.allclose((S1.build().collapse().intensity() -
S2.build().collapse().intensity()).array, 0)
assert np.allclose((measurement2 - measurement1).array, 0, atol=1e-5)
def test_prism_translate():
S = SMatrix(30, 60e3, 1, extent=5, gpts=50)
probe = Probe(extent=5,
gpts=50,
energy=60e3,
semiangle_cutoff=30,
rolloff=0)
assert np.allclose(probe.build(np.array([(2.5, 2.5)])).array,
S.build().collapse([(2.5, 2.5)]).array,
atol=1e-5)
def test_prism_match_probe():
S = SMatrix(30., 60e3, 1, extent=5, gpts=50)
probe = Probe(extent=5,
gpts=50,
energy=60e3,
semiangle_cutoff=30.,
rolloff=0.)
assert np.allclose(probe.build([(0., 0.)]).array,
S.build().collapse([(0., 0.)]).array,
atol=2e-5)
def test_prism_interpolation():
S_builder = SMatrix(30, 60e3, 2, extent=10, gpts=100)
probe = Probe(extent=5,
gpts=50,
energy=60e3,
semiangle_cutoff=30,
rolloff=0)
assert np.allclose(probe.build(np.array([(2.5, 2.5)])).array,
S_builder.build().collapse([(2.5, 2.5)]).array,
atol=1e-5)
def test_prism_tilt():
S = SMatrix(semiangle_cutoff=30.,
energy=60e3,
interpolation=1,
extent=5,
gpts=50,
tilt=(1, 2))
S_array = S.build()
wave = S_array.collapse()
assert S_array.tilt == S.tilt == wave.tilt
def test_prism_interpolation():
S = SMatrix(semiangle_cutoff=30.,
energy=60e3,
interpolation=2,
extent=10,
gpts=100,
rolloff=0.)
probe = Probe(extent=5,
gpts=50,
energy=60e3,
semiangle_cutoff=30,
rolloff=0)
probe_array = probe.build(np.array([(2.5, 2.5)])).array
S_array = S.build().collapse([(2.5, 2.5)]).array
assert np.allclose(probe_array, S_array, atol=1e-5)
def test_prism_tilt():
S = SMatrix(30., 60e3, 1, extent=5, gpts=50, tilt=(1, 2))
S_array = S.build()
wave = S_array.collapse()
assert S_array.tilt == S.tilt == wave.tilt
