def cu001_crystal(na, nb, nc, ncu, rms3d):
params = multem.CrystalParameters()
params.na = na
params.nb = nb
params.nc = nc
params.a = 3.6150
params.b = 3.6150
params.c = 3.6150
occ = 1
region = 0
charge = 0
# Cu = 29
# Z charge x y z rms3d occupancy region charge
params.layers = [
multem.AtomList([
(29, 0.0, 0.0, 0.0, rms3d, occ, region, charge),
(29, 0.5, 0.5, 0.0, rms3d, occ, region, charge),
]),
multem.AtomList([
(29, 0.0, 0.5, 0.5, rms3d, occ, region, charge),
(29, 0.5, 0.0, 0.5, rms3d, occ, region, charge),
]),
]
atoms = multem.crystal_by_layers(params)
dz = params.c / ncu
lx = na * params.a
ly = nb * params.b
lz = nc * params.c
return atoms, lx, ly, lz, params.a, params.b, params.c, dz
def test_crystal_parameters():
crystal_parameters = multem.CrystalParameters()
crystal_parameters.na = 10
crystal_parameters.nb = 20
crystal_parameters.nc = 30
crystal_parameters.a = 40
crystal_parameters.b = 50
crystal_parameters.c = 60
crystal_parameters.layers = [
multem.AtomList([(1, 2, 3, 4, 5, 6, 7, 8),
(9, 10, 11, 12, 13, 14, 15, 16)]),
multem.AtomList([(1, 2, 3, 4, 5, 6, 7, 8),
(9, 10, 11, 12, 13, 14, 15, 16)]),
]
assert crystal_parameters.na == 10
assert crystal_parameters.nb == 20
assert crystal_parameters.nc == 30
assert crystal_parameters.a == 40
assert crystal_parameters.b == 50
assert crystal_parameters.c == 60
assert list(crystal_parameters.layers[0]) == [
(1, 2, 3, 4, 5, 6, 7, 8),
(9, 10, 11, 12, 13, 14, 15, 16),
]
assert list(crystal_parameters.layers[0]) == [
(1, 2, 3, 4, 5, 6, 7, 8),
(9, 10, 11, 12, 13, 14, 15, 16),
]
def compute_exit_wave(atom_data, pixel_size):
"""
Compute the exit wave
"""
# Get the dimensions
x_min = atom_data.data["x"].min()
x_max = atom_data.data["x"].max()
y_min = atom_data.data["y"].min()
y_max = atom_data.data["y"].max()
z_min = atom_data.data["z"].min()
z_max = atom_data.data["z"].max()
x_size = x_max - x_min
y_size = y_max - y_min
select = ((atom_data.data["x"] > x_min + x_size / 6)
& (atom_data.data["x"] < x_max - x_size / 6)
& (atom_data.data["y"] > y_min + y_size / 6)
& (atom_data.data["y"] < y_max - y_size / 6))
atom_data = parakeet.sample.AtomData(data=atom_data.data[select])
x_min = atom_data.data["x"].min()
x_max = atom_data.data["x"].max()
y_min = atom_data.data["y"].min()
y_max = atom_data.data["y"].max()
z_min = atom_data.data["z"].min()
z_max = atom_data.data["z"].max()
x_size = x_max - x_min
y_size = y_max - y_min
z_size = z_max - z_min
# Translate to centre
x_box_size = x_size
y_box_size = y_size
z_box_size = z_size
# Create the system configuration
system_conf = multem.SystemConfiguration()
system_conf.precision = "float"
system_conf.device = "device"
# Create the input multislice configuration
input_multislice = create_input_multislice()
# Compute the number of pixels
nx = next_power_2(int(x_box_size / pixel_size))
ny = next_power_2(int(y_box_size / pixel_size))
assert nx <= 4096
assert ny <= 4096
x_box_size = nx * pixel_size
y_box_size = ny * pixel_size
x_trans = (x_box_size - x_size) / 2.0 - x_min
y_trans = (y_box_size - y_size) / 2.0 - y_min
z_trans = (z_box_size - z_size) / 2.0 - z_min
atom_data.translate((x_trans, y_trans, z_trans))
# Create the specimen size
input_multislice.nx = nx
input_multislice.ny = ny
input_multislice.spec_lx = x_box_size
input_multislice.spec_ly = y_box_size
input_multislice.spec_lz = z_box_size
input_multislice.spec_dz = 5
# Set the specimen atoms
input_multislice.spec_atoms = atom_data.to_multem()
# Run the simulation
output_multislice = multem.simulate(system_conf, input_multislice)
# Get the image
physical_image = numpy.array(output_multislice.data[0].psi_coh).T
# Create the masker
masker = multem.Masker(input_multislice.nx, input_multislice.ny,
pixel_size)
# Create the size of the cuboid
masker.set_cuboid(
(
x_box_size / 2 - x_size / 2,
y_box_size / 2 - y_size / 2,
z_box_size / 2 - z_size / 2,
),
(x_size, y_size, z_size),
)
# Run the simulation
input_multislice.spec_atoms = multem.AtomList()
output_multislice = multem.simulate(system_conf, input_multislice, masker)
# Get the image
random_image = numpy.array(output_multislice.data[0].psi_coh).T
# Return the images
x0 = numpy.array(
(x_box_size / 2 - x_size / 2, y_box_size / 2 - y_size / 2))
x1 = numpy.array(
(x_box_size / 2 + x_size / 2, y_box_size / 2 + y_size / 2))
return physical_image, random_image, x0, x1
def compute_observed_mean(size, pixel_size):
"""
Compute the observed mean
"""
# Create the system configuration
system_conf = multem.SystemConfiguration()
system_conf.precision = "float"
system_conf.device = "device"
# Create the input multislice configuration
input_multislice = create_input_multislice()
# Compute the number of pixels
nx = int(ceil(size / pixel_size))
ny = int(ceil(size / pixel_size))
size = nx * pixel_size
# Create the specimen atoms
input_multislice.nx = nx
input_multislice.ny = ny
input_multislice.spec_lx = nx * pixel_size
input_multislice.spec_ly = ny * pixel_size
input_multislice.spec_lz = nx * pixel_size
input_multislice.spec_dz = 1
# For N random placements compute the mean intensity
means = []
for j in range(10):
# Compute the position
x0 = numpy.random.uniform(0, 1) + nx // 2
y0 = numpy.random.uniform(0, 1) + ny // 2
x0 = pixel_size * x0
y0 = pixel_size * y0
# Set the atom list
input_multislice.spec_atoms = multem.AtomList([
(1, x0, y0, size / 2.0, 0, 1, 0, 0),
(1, x0, y0, size / 2.0, 0, 1, 0, 0),
(8, x0, y0, size / 2.0, 0, 1, 0, 0),
])
thickness = []
potential = []
def callback(z0, z1, V):
V = numpy.array(V)
thickness.append(z1 - z0)
potential.append(V)
# Run the simulation
multem.compute_projected_potential(system_conf, input_multislice,
callback)
# Compute the mean potential
V = numpy.sum(potential, axis=0)
means.append(numpy.mean(V))
# Return the size and mean potential
return size, numpy.mean(means)
def test_input():
stem_detector = multem.STEMDetector()
stem_detector.type = "Test"
stem_detector.cir = [(0, 1), (2, 3)]
stem_detector.radial = [(0, [1, 2, 3, 4]), (2, [5, 6, 8, 9])]
stem_detector.matrix = [(3, [1, 2, 3, 4]), (4, [5, 6, 7, 8])]
input = multem.Input()
input.interaction_model = "Interaction Model"
input.potential_type = "Potential Type"
input.operation_mode = "Operation Mode"
input.memory_size = 10
input.reverse_multislice = False
input.pn_model = "Phonon Interaction Model"
input.pn_coh_contrib = True
input.pn_single_conf = False
input.pn_nconf = 20
input.pn_dim = 30
input.pn_seed = 40
input.spec_atoms = multem.AtomList([(1, 2, 3, 4, 5, 6, 7, 8),
(2, 3, 4, 5, 6, 7, 8, 9)])
input.spec_dz = 50.1
input.spec_lx = 60.1
input.spec_ly = 70.1
input.spec_lz = 80.1
input.spec_cryst_na = 90
input.spec_cryst_nb = 100
input.spec_cryst_nc = 110
input.spec_cryst_a = 120.1
input.spec_cryst_b = 130.1
input.spec_cryst_c = 140.1
input.spec_cryst_x0 = 150.1
input.spec_cryst_y0 = 160.1
input.spec_amorp = [(0.1, 0.2, 0.3), (0.4, 0.5, 0.6)]
input.spec_rot_theta = 0
input.spec_rot_u0 = (1, 2, 3)
input.spec_rot_center_type = "Spec Rot Center Type"
input.spec_rot_center_p = (4, 5, 6)
input.thick_type = "Thick Type"
input.thick = [1.1, 2.2, 3.3, 4.4]
input.potential_slicing = "Potential Slicing"
input.nx = 1
input.ny = 2
input.bwl = True
input.simulation_type = "Simulation Type"
input.iw_type = "IW Type"
input.iw_psi = [1 + 1j, 2 + 2j, 3 + 3j, 4 + 4j]
input.iw_x = [1.1, 2.2, 3.3, 4.4, 5.5]
input.iw_y = [6.6, 7.7, 8.8, 9.9, 0.0]
input.E_0 = 3.1
input.theta = 4.1
input.phi = 5.9
input.illumination_model = "Illumination Model"
input.temporal_spatial_incoh = "Temporal Spatial Incoherence"
input.cond_lens_m = 1
input.cond_lens_c_10 = 0.1
input.cond_lens_c_12 = 0.2
input.cond_lens_phi_12 = 0.3
input.cond_lens_c_21 = 0.4
input.cond_lens_phi_21 = 0.5
input.cond_lens_c_23 = 0.6
input.cond_lens_phi_23 = 0.7
input.cond_lens_c_30 = 0.8
input.cond_lens_c_32 = 0.9
input.cond_lens_phi_32 = 1.0
input.cond_lens_c_34 = 1.1
input.cond_lens_phi_34 = 1.2
input.cond_lens_c_41 = 1.3
input.cond_lens_phi_41 = 1.4
input.cond_lens_c_43 = 1.5
input.cond_lens_phi_43 = 1.6
input.cond_lens_c_45 = 1.7
input.cond_lens_phi_45 = 1.8
input.cond_lens_c_50 = 1.9
input.cond_lens_c_52 = 2.0
input.cond_lens_phi_52 = 2.1
input.cond_lens_c_54 = 2.2
input.cond_lens_phi_54 = 2.3
input.cond_lens_c_56 = 2.4
input.cond_lens_phi_56 = 2.5
input.cond_lens_inner_aper_ang = 2.6
input.cond_lens_outer_aper_ang = 2.7
input.cond_lens_ssf_sigma = 0.1
input.cond_lens_ssf_npoints = 2
input.cond_lens_dsf_sigma = 0.3
input.cond_lens_dsf_npoints = 4
input.cond_lens_zero_defocus_type = "Cond Lens Zero Defocus Type"
input.cond_lens_zero_defocus_plane = 0.123
input.obj_lens_m = 12
input.obj_lens_c_10 = 0.1
input.obj_lens_c_12 = 0.2
input.obj_lens_phi_12 = 0.3
input.obj_lens_c_21 = 0.4
input.obj_lens_phi_21 = 0.5
input.obj_lens_c_23 = 0.6
input.obj_lens_phi_23 = 0.7
input.obj_lens_c_30 = 0.8
input.obj_lens_c_32 = 0.9
input.obj_lens_phi_32 = 0.10
input.obj_lens_c_34 = 0.11
input.obj_lens_phi_34 = 0.12
input.obj_lens_c_41 = 0.13
input.obj_lens_phi_41 = 0.14
input.obj_lens_c_43 = 0.15
input.obj_lens_phi_43 = 0.16
input.obj_lens_c_45 = 0.17
input.obj_lens_phi_45 = 0.18
input.obj_lens_c_50 = 0.19
input.obj_lens_c_52 = 0.20
input.obj_lens_phi_52 = 0.21
input.obj_lens_c_54 = 0.22
input.obj_lens_phi_54 = 0.23
input.obj_lens_c_56 = 0.24
input.obj_lens_phi_56 = 0.25
input.obj_lens_inner_aper_ang = 0.26
input.obj_lens_outer_aper_ang = 0.27
input.obj_lens_dsf_sigma = 0.1
input.obj_lens_dsf_npoints = 20
input.obj_lens_zero_defocus_type = "Obj Lens Zero Defocus Type"
input.obj_lens_zero_defocus_plane = 1.1
input.detector = stem_detector
input.scanning_type = "Scanning Type"
input.scanning_periodic = True
input.scanning_ns = 20
input.scanning_x0 = 0.1
input.scanning_y0 = 0.2
input.scanning_xe = 0.3
input.scanning_ye = 0.4
input.ped_nrot = 0.5
input.ped_theta = 0.6
input.hci_nrot = 0.7
input.hci_theta = 0.8
input.eels_Z = 20
input.eels_E_loss = 0.9
input.eels_collection_angle = 10.1
input.eels_m_selection = 30
input.eels_channelling_type = "EELS Channelling Type"
input.eftem_Z = 50
input.eftem_E_loss = 0.1
input.eftem_collection_angle = 0.2
input.eftem_m_selection = 60
input.eftem_channelling_type = "EFTEM Channelling Type"
input.output_area_ix_0 = 10
input.output_area_iy_0 = 20
input.output_area_ix_e = 30
input.output_area_iy_e = 40
def check():
assert input.interaction_model == "Interaction Model"
assert input.potential_type == "Potential Type"
assert input.operation_mode == "Operation Mode"
assert input.memory_size == 10
assert input.reverse_multislice == False
assert input.pn_model == "Phonon Interaction Model"
assert input.pn_coh_contrib == True
assert input.pn_single_conf == False
assert input.pn_nconf == 20
assert input.pn_dim == 30
assert input.pn_seed == 40
assert input.spec_atoms == pytest.approx(
numpy.array([(1, 2, 3, 4, 5, 6, 7, 8), (2, 3, 4, 5, 6, 7, 8, 9)]))
assert input.spec_dz == 50.1
assert input.spec_lx == 60.1
assert input.spec_ly == 70.1
assert input.spec_lz == 80.1
assert input.spec_cryst_na == 90
assert input.spec_cryst_nb == 100
assert input.spec_cryst_nc == 110
assert input.spec_cryst_a == 120.1
assert input.spec_cryst_b == 130.1
assert input.spec_cryst_c == 140.1
assert input.spec_cryst_x0 == 150.1
assert input.spec_cryst_y0 == 160.1
assert input.spec_amorp == pytest.approx(
numpy.array([(0.1, 0.2, 0.3), (0.4, 0.5, 0.6)]))
assert input.spec_rot_theta == 0
assert input.spec_rot_u0 == pytest.approx((1, 2, 3))
assert input.spec_rot_center_type == "Spec Rot Center Type"
assert input.spec_rot_center_p == pytest.approx((4, 5, 6))
assert input.thick_type == "Thick Type"
assert tuple(input.thick) == pytest.approx([1.1, 2.2, 3.3, 4.4])
assert input.potential_slicing == "Potential Slicing"
assert input.nx == 1
assert input.ny == 2
assert input.bwl == True
assert input.simulation_type == "Simulation Type"
assert input.iw_type == "IW Type"
assert input.iw_psi == [1 + 1j, 2 + 2j, 3 + 3j, 4 + 4j]
assert input.iw_x == [1.1, 2.2, 3.3, 4.4, 5.5]
assert input.iw_y == [6.6, 7.7, 8.8, 9.9, 0.0]
assert input.E_0 == 3.1
assert input.theta == 4.1
assert input.phi == 5.9
assert input.illumination_model == "Illumination Model"
assert input.temporal_spatial_incoh == "Temporal Spatial Incoherence"
assert input.cond_lens_m == 1
assert input.cond_lens_c_10 == 0.1
assert input.cond_lens_c_12 == 0.2
assert input.cond_lens_phi_12 == 0.3
assert input.cond_lens_c_21 == 0.4
assert input.cond_lens_phi_21 == 0.5
assert input.cond_lens_c_23 == 0.6
assert input.cond_lens_phi_23 == 0.7
assert input.cond_lens_c_30 == 0.8
assert input.cond_lens_c_32 == 0.9
assert input.cond_lens_phi_32 == 1.0
assert input.cond_lens_c_34 == 1.1
assert input.cond_lens_phi_34 == 1.2
assert input.cond_lens_c_41 == 1.3
assert input.cond_lens_phi_41 == 1.4
assert input.cond_lens_c_43 == 1.5
assert input.cond_lens_phi_43 == 1.6
assert input.cond_lens_c_45 == 1.7
assert input.cond_lens_phi_45 == 1.8
assert input.cond_lens_c_50 == 1.9
assert input.cond_lens_c_52 == 2.0
assert input.cond_lens_phi_52 == 2.1
assert input.cond_lens_c_54 == 2.2
assert input.cond_lens_phi_54 == 2.3
assert input.cond_lens_c_56 == 2.4
assert input.cond_lens_phi_56 == 2.5
assert input.cond_lens_inner_aper_ang == 2.6
assert input.cond_lens_outer_aper_ang == 2.7
assert input.cond_lens_ssf_sigma == 0.1
assert input.cond_lens_ssf_npoints == 2
assert input.cond_lens_dsf_sigma == 0.3
assert input.cond_lens_dsf_npoints == 4
assert input.cond_lens_zero_defocus_type == "Cond Lens Zero Defocus Type"
assert input.cond_lens_zero_defocus_plane == 0.123
assert input.obj_lens_m == 12
assert input.obj_lens_c_10 == 0.1
assert input.obj_lens_c_12 == 0.2
assert input.obj_lens_phi_12 == 0.3
assert input.obj_lens_c_21 == 0.4
assert input.obj_lens_phi_21 == 0.5
assert input.obj_lens_c_23 == 0.6
assert input.obj_lens_phi_23 == 0.7
assert input.obj_lens_c_30 == 0.8
assert input.obj_lens_c_32 == 0.9
assert input.obj_lens_phi_32 == 0.10
assert input.obj_lens_c_34 == 0.11
assert input.obj_lens_phi_34 == 0.12
assert input.obj_lens_c_41 == 0.13
assert input.obj_lens_phi_41 == 0.14
assert input.obj_lens_c_43 == 0.15
assert input.obj_lens_phi_43 == 0.16
assert input.obj_lens_c_45 == 0.17
assert input.obj_lens_phi_45 == 0.18
assert input.obj_lens_c_50 == 0.19
assert input.obj_lens_c_52 == 0.20
assert input.obj_lens_phi_52 == 0.21
assert input.obj_lens_c_54 == 0.22
assert input.obj_lens_phi_54 == 0.23
assert input.obj_lens_c_56 == 0.24
assert input.obj_lens_phi_56 == 0.25
assert input.obj_lens_inner_aper_ang == 0.26
assert input.obj_lens_outer_aper_ang == 0.27
assert input.obj_lens_dsf_sigma == 0.1
assert input.obj_lens_dsf_npoints == 20
assert input.obj_lens_zero_defocus_type == "Obj Lens Zero Defocus Type"
assert input.obj_lens_zero_defocus_plane == 1.1
assert input.detector.type == "Test"
assert input.detector.cir == [(0, 1), (2, 3)]
assert input.detector.radial == [(0, [1, 2, 3, 4]), (2, [5, 6, 8, 9])]
assert input.detector.matrix == [(3, [1, 2, 3, 4]), (4, [5, 6, 7, 8])]
assert input.scanning_type == "Scanning Type"
assert input.scanning_periodic == True
assert input.scanning_ns == 20
assert input.scanning_x0 == 0.1
assert input.scanning_y0 == 0.2
assert input.scanning_xe == 0.3
assert input.scanning_ye == 0.4
assert input.ped_nrot == 0.5
assert input.ped_theta == 0.6
assert input.hci_nrot == 0.7
assert input.hci_theta == 0.8
assert input.eels_Z == 20
assert input.eels_E_loss == 0.9
assert input.eels_collection_angle == 10.1
assert input.eels_m_selection == 30
assert input.eels_channelling_type == "EELS Channelling Type"
assert input.eftem_Z == 50
assert input.eftem_E_loss == 0.1
assert input.eftem_collection_angle == 0.2
assert input.eftem_m_selection == 60
assert input.eftem_channelling_type == "EFTEM Channelling Type"
assert input.output_area_ix_0 == 10
assert input.output_area_iy_0 == 20
assert input.output_area_ix_e == 30
assert input.output_area_iy_e == 40
check()
input = pickle.loads(pickle.dumps(input))
check()