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_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_calibration_coordinates():
for endpoint in (True, False):
gridscan = GridScan(sampling=.7,
start=(0, 0),
end=(4, 4),
endpoint=endpoint)
calibration_coordinates = gridscan.calibrations[0].coordinates(
gridscan.gpts[0])
assert np.all(calibration_coordinates == gridscan.get_positions()
[::gridscan.gpts[0], 0])
def test_crop():
S = SMatrix(expansion_cutoff=30,
interpolation=3,
energy=300e3,
extent=10,
sampling=.02).build()
gridscan = GridScan(start=[0, 0], end=S.extent, gpts=64)
scans = gridscan.partition_scan((2, 2))
cropped = S.crop_to_scan(scans[0])
assert cropped.gpts != S.gpts
position = (4.9, 0.)
assert np.allclose(
S.collapse(position).array - cropped.collapse(position).array, 0.)
def test_downsample_detect():
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)
detector = FlexibleAnnularDetector()
end = (potential.extent[0] / 4, potential.extent[1] / 4)
gridscan = GridScan(start=[0, 0], end=end, sampling=.2)
S = SMatrix(energy=300e3,
semiangle_cutoff=9.4,
rolloff=0.05,
expansion_cutoff=10)
S_exit = S.multislice(potential, pbar=False)
measurement = S_exit.scan(gridscan, detector, pbar=False)
S_downsampled = S_exit.downsample()
downsampled_measurement = S_downsampled.scan(gridscan,
detector,
pbar=False)
assert S_downsampled.array.shape != S_exit.array.shape
assert not np.all(measurement.array == downsampled_measurement.array)
assert np.allclose(measurement.array, downsampled_measurement.array)
def test_gridscan_to_file(tmp_path):
d = tmp_path / 'sub'
d.mkdir()
path = d / 'measurement2.hdf5'
atoms = read(_set_path('orthogonal_graphene.cif'))
potential = Potential(atoms=atoms, sampling=.05)
probe = Probe(energy=200e3, semiangle_cutoff=30)
probe.grid.match(potential)
scan = GridScan(start=[0, 0], end=[0, potential.extent[1]], gpts=(10, 9))
detector = PixelatedDetector()
export_detector = PixelatedDetector(save_file=path)
measurements = probe.scan(scan, [detector, export_detector],
potential,
pbar=False)
measurement = measurements[0]
imported_measurement = Measurement.read(measurements[1])
assert np.allclose(measurement.array, imported_measurement.array)
assert measurement.calibrations[0] == imported_measurement.calibrations[0]
assert measurement.calibrations[1] == imported_measurement.calibrations[1]
def test_flexible_annular_detector():
atoms = read('data/srtio3_100.cif')
atoms *= (4, 4, 1)
potential = Potential(
atoms,
gpts=512,
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=30, outer=80)
end = (potential.extent[0] / 4, potential.extent[1] / 4)
gridscan = GridScan(start=[0, 0], end=end, sampling=.2)
measurements = probe.scan(gridscan, [flexible_detector, annular_detector],
potential,
pbar=False)
assert np.allclose(measurements[flexible_detector].integrate(30, 80).array,
measurements[annular_detector].array)
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_grid_scan():
probe = Probe(energy=60e3)
detector = DummyDetector()
potential = DummyPotential(extent=5, sampling=.1)
scan = GridScan((0, 0), (1, 1), gpts=10)
measurement = probe.scan(scan, detector, potential, max_batch=1, pbar=False)
assert detector._detect_count == 100
assert np.all(measurement.array == 1.)
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_partition():
gridscan = GridScan(start=(0, 0), end=(2, 2), sampling=.5, endpoint=False)
scans = gridscan.partition_scan((2, 2))
positions = []
for scan in scans:
positions.append(scan.get_positions())
assert np.allclose(((np.vstack(positions)[None] -
gridscan.get_positions()[:, None])**2).min(0), 0)
assert np.allclose(((np.vstack(positions)[None] -
gridscan.get_positions()[:, None])**2).min(1), 0)
gridscan = GridScan(start=(0, 0), end=(2, 2), sampling=.5, endpoint=True)
scans = gridscan.partition_scan((2, 2))
positions = []
for scan in scans:
positions.append(scan.get_positions())
assert np.allclose(((np.vstack(positions)[None] -
gridscan.get_positions()[:, None])**2).min(0), 0)
assert np.allclose(((np.vstack(positions)[None] -
gridscan.get_positions()[:, None])**2).min(1), 0)
def test_grid_scan():
start = (0, 0)
end = (1, 2)
scan = GridScan(start, end, gpts=5, endpoint=True)
positions = scan.get_positions()
assert np.all(positions[0] == start)
assert np.all(positions[-1] == end)
assert np.allclose(positions[4], [start[1], end[1]])
assert np.allclose(np.linalg.norm(np.diff(positions[:4], axis=0), axis=1), scan.sampling[1])
scan = GridScan(start, end, gpts=5, endpoint=False)
positions = scan.get_positions()
assert np.all(positions[0] == start)
assert np.allclose(positions[-1], (end[0] - (end[0] - start[0]) / 5, end[1] - (end[1] - start[1]) / 5))
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_gridscan_raises():
with pytest.raises(ValueError) as e:
GridScan(start=0, end=1)
assert str(e.value) == 'Scan start/end has incorrect shape'