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_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_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_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)