def test_partition_measurement():
atoms = read(
os.path.join(os.path.dirname(os.path.abspath(__file__)),
'data/amorphous_carbon.cif'))
potential = Potential(atoms,
gpts=512,
slice_thickness=1,
projection='infinite',
parametrization='kirkland').build(pbar=False)
detector = AnnularDetector(inner=70, outer=100)
gridscan = GridScan(start=[0, 0], end=potential.extent, gpts=16)
S = SMatrix(expansion_cutoff=15, interpolation=1, energy=300e3)
S = S.multislice(potential, pbar=False)
measurements = S.scan(gridscan, [detector], pbar=False)
scans = gridscan.partition_scan((2, 2))
partitioned_measurements = {
detector: detector.allocate_measurement(S.collapse((0, 0)), gridscan)
}
for scan in scans:
partitioned_measurements = S.scan(scan, measurements, pbar=False)
assert np.allclose(partitioned_measurements[detector].array,
measurements[detector].array)
def test_detector_consistency():
atoms = read('data/srtio3_100.cif')
atoms *= (4, 4, 1)
potential = Potential(
atoms,
gpts=256,
projection='infinite',
slice_thickness=.5,
parametrization='kirkland',
).build(pbar=False)
probe = Probe(energy=300e3, semiangle_cutoff=9.4, rolloff=0.05)
flexible_detector = FlexibleAnnularDetector()
annular_detector = AnnularDetector(inner=20, outer=40)
pixelated_detector = PixelatedDetector()
end = (potential.extent[0] / 4, potential.extent[1] / 4)
gridscan = GridScan(start=[0, 0], end=end, sampling=.5)
measurements = probe.scan(
gridscan, [flexible_detector, pixelated_detector, annular_detector],
potential,
pbar=False)
assert np.allclose(measurements[0].integrate(20, 40).array,
measurements[2].array)
assert np.allclose(
annular_detector.integrate(measurements[1]).array,
measurements[2].array)
def test_partition_measurement():
atoms = read(
os.path.join(os.path.dirname(os.path.abspath(__file__)),
'data/amorphous_carbon.cif'))
potential = Potential(atoms,
gpts=256,
slice_thickness=1,
projection='infinite',
parametrization='kirkland').build(pbar=False)
detector = AnnularDetector(inner=70, outer=100)
gridscan = GridScan(start=[0, 0], end=potential.extent, gpts=4)
probe = Probe(semiangle_cutoff=15, energy=300e3)
measurements = probe.scan(gridscan, detector, potential, pbar=False)
scans = gridscan.partition_scan((2, 2))
partitioned_measurements = detector.allocate_measurement(probe, gridscan)
for scan in scans:
probe.scan(scan,
detector,
potential,
measurements=partitioned_measurements,
pbar=False)
assert np.allclose(partitioned_measurements.array, measurements.array)
def test_fig():
atoms = Atoms('CSiCuAuU',
positions=[(x, 25, 4) for x in np.linspace(5, 45, 5)],
cell=(50, 50, 8))
gpts = 2048
potential = Potential(atoms=atoms,
gpts=gpts,
parametrization='kirkland',
slice_thickness=8)
probe = Probe(energy=200e3, defocus=700, Cs=1.3e7, semiangle_cutoff=10.37)
probe.grid.match(potential)
scan = LineScan(start=[5, 25], end=[45, 25], gpts=5)
detector = AnnularDetector(inner=40, outer=200)
measurements = probe.scan(scan, [detector], potential, pbar=False)
#assert np.allclose(measurements[detector].array, [0.00010976, 0.00054356, 0.00198158, 0.00997221, 0.01098883])
assert np.allclose(
measurements[detector].array,
[0.0001168, 0.00059303, 0.00214667, 0.00977803, 0.01167613],
atol=1e-5)
def test_interpolation_scan():
atoms = Atoms('C', positions=[(2.5, 2.5, 2)], cell=(5, 5, 4))
potential = Potential(atoms)
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=250)
measurements = probe.scan(linescan, [detector],
potential,
max_batch=50,
pbar=False)
S_builder = SMatrix(semiangle_cutoff=30.,
energy=80e3,
interpolation=2,
gpts=500)
atoms = Atoms('C', positions=[(2.5, 2.5, 2)], cell=(5, 5, 4))
atoms *= (2, 2, 1)
potential = Potential(atoms)
S = S_builder.multislice(potential, pbar=False)
prism_measurements = S.scan(linescan,
detector,
max_batch_probes=10,
pbar=False)
assert np.allclose(measurements.array, prism_measurements.array, atol=1e-6)
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_cropped_scan():
atoms = read(
os.path.join(os.path.dirname(os.path.abspath(__file__)),
'data/amorphous_carbon.cif'))
potential = Potential(atoms,
gpts=512,
slice_thickness=1,
device='gpu',
projection='infinite',
parametrization='kirkland',
storage='gpu').build(pbar=True)
detector = AnnularDetector(inner=40, outer=60)
gridscan = GridScan(start=[0, 0], end=potential.extent, gpts=16)
S = SMatrix(expansion_cutoff=20,
interpolation=4,
energy=300e3,
device='gpu',
storage='cpu') # .build()
S = S.multislice(potential, pbar=True)
S = S.downsample('limit')
measurements = S.scan(gridscan, [detector], max_batch_probes=64)
scans = gridscan.partition_scan((2, 2))
cropped_measurements = {
detector: detector.allocate_measurement(S.collapse((0, 0)), gridscan)
}
for scan in scans:
cropped = S.crop_to_scan(scan)
cropped = cropped.transfer('gpu')
cropped_measurements = cropped.scan(scan,
cropped_measurements,
pbar=False)
assert np.allclose(cropped_measurements[detector].array,
measurements[detector].array)
def test_preallocated_measurement():
atoms = read(
os.path.join(os.path.dirname(os.path.abspath(__file__)),
'data/amorphous_carbon.cif'))
potential = Potential(atoms,
gpts=256,
slice_thickness=1,
projection='infinite',
parametrization='kirkland').build(pbar=False)
scan = GridScan(start=[0, 0], end=potential.extent, gpts=4)
detector1 = AnnularDetector(inner=70, outer=100)
probe = Probe(semiangle_cutoff=15,
energy=300e3,
extent=potential.extent,
gpts=512)
measurement = detector1.allocate_measurement(probe, scan)
probe.scan(scan, detector1, potential, measurement, pbar=False)
assert np.any(measurement.array > 0)
detector2 = PixelatedDetector()
measurement1 = detector1.allocate_measurement(probe, scan)
measurement2 = detector2.allocate_measurement(probe, scan)
with pytest.raises(ValueError) as e:
probe.scan(scan, [detector1, detector2],
potential,
measurement1,
pbar=False)
probe.scan(scan, [detector1, detector2],
potential, {
detector1: measurement1,
detector2: measurement2
},
pbar=False)
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_probe_waves_line_scan():
potential = Potential(Atoms('C', positions=[(2.5, 2.5, 2)],
cell=(5, 5, 4)))
linescan = LineScan(start=[0, 0], end=[2.5, 2.5], gpts=10)
detector = AnnularDetector(inner=80, outer=200)
S = SMatrix(30, 80e3, 1, gpts=500).multislice(potential, pbar=False)
probe = Probe(semiangle_cutoff=30, energy=80e3, gpts=500)
prism_measurement = S.scan(linescan,
detector,
max_batch_probes=10,
pbar=False)
measurement = probe.scan(linescan,
detector,
potential,
max_batch=50,
pbar=False)
assert np.allclose(measurement.array, prism_measurement.array, atol=1e-6)
def test_fig_5_22():
atoms = Atoms('CSiCuAuU',
positions=[(x, 25, 4) for x in np.linspace(5, 45, 5)],
cell=(50, 50, 8))
gpts = 2048
potential = Potential(atoms=atoms,
gpts=gpts,
parametrization='kirkland',
slice_thickness=8)
#probe = Probe(energy=200e3, defocus=700, Cs=1.3e7, semiangle_cutoff=10.37, rolloff=.1)
probe = Probe(energy=200e3, defocus=700, Cs=1.3e7, semiangle_cutoff=10.37)
probe.grid.match(potential)
scan = LineScan(start=[5, 25], end=[45, 25], gpts=5)
detector = AnnularDetector(inner=40, outer=200)
measurement = probe.scan(scan, detector, potential, pbar=False)
#correct_values = np.array([0.0001168, 0.00059303, 0.00214667, 0.00977803, 0.01167613])
correct_values = np.array(
[0.00010675, 0.00055145, 0.00199743, 0.00911063, 0.01087296])
assert np.allclose(measurement.array, correct_values, atol=1e-5)