def create_input_multislice():
"""
Create the input multislice parameters
"""
# Initialise the input and system configuration
input_multislice = multem.Input()
# Set simulation experiment
input_multislice.simulation_type = "EWRS"
# Electron-Specimen interaction model
input_multislice.interaction_model = "Multislice"
# input_multislice.potential_type = "Lobato_0_12"
input_multislice.potential_type = "Peng_0_12"
# Potential slicing
input_multislice.potential_slicing = "dz_Proj"
# Electron-Phonon interaction model
input_multislice.pn_model = "Still_Atom"
# Specimen thickness
input_multislice.thick_type = "Whole_Spec"
# Illumination model
input_multislice.illumination_model = "Partial_Coherent"
input_multislice.temporal_spatial_incoh = "Temporal_Spatial"
# Set the energy
input_multislice.E_0 = 300
return input_multislice
def create_input_multislice(n_phonons, single_phonon_conf=False):
# Initialise the input and system configuration
input_multislice = multem.Input()
# Set simulation experiment
input_multislice.simulation_type = "EWRS"
# Electron-Specimen interaction model
input_multislice.interaction_model = "Multislice"
input_multislice.potential_type = "Lobato_0_12"
# Potential slicing
input_multislice.potential_slicing = "dz_Proj"
# Electron-Phonon interaction model
input_multislice.pn_model = "Still_Atom"
input_multislice.pn_coh_contrib = 0
input_multislice.pn_single_conf = False
input_multislice.pn_nconf = 10
input_multislice.pn_dim = 110
input_multislice.pn_seed = 300_183
# Specimen thickness
input_multislice.thick_type = "Whole_Spec"
# Illumination model
input_multislice.illumination_model = "Partial_Coherent"
input_multislice.temporal_spatial_incoh = "Temporal_Spatial"
input_multislice.nx = 1024
input_multislice.ny = 1024
input_multislice.obj_lens_m = 0
input_multislice.obj_lens_c_10 = 15.836
input_multislice.obj_lens_c_30 = 1e-03
input_multislice.obj_lens_c_50 = 0.00
input_multislice.obj_lens_c_12 = 0.0
input_multislice.obj_lens_phi_12 = 0.0
input_multislice.obj_lens_c_23 = 0.0
input_multislice.obj_lens_phi_23 = 0.0
input_multislice.obj_lens_inner_aper_ang = 0.0
input_multislice.obj_lens_outer_aper_ang = 24.0
input_multislice.obj_lens_zero_defocus_type = "Last"
input_multislice.obj_lens_zero_defocus_plane = 0
return input_multislice
import multem import numpy import pickle from cu001_crystal import cu001_crystal input_multislice = multem.Input() system_conf = multem.SystemConfiguration() system_conf.precision = "float" system_conf.device = "host" # Set simulation experiment input_multislice.simulation_type = "HRTEM" # Electron-Specimen interaction model input_multislice.interaction_model = "Multislice" # Potential slicing input_multislice.potential_slicing = "Planes" # Electron-Phonon interaction model input_multislice.pn_model = "Frozen_Phonon" input_multislice.pn_coh_contrib = 0 input_multislice.pn_single_conf = False input_multislice.pn_nconf = 10 input_multislice.pn_dim = 110 input_multislice.pn_seed = 300183 # Specimen information na = 16 nb = 16
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()
def create_input_multislice(
microscope, slice_thickness, margin, simulation_type, centre=None
):
"""
Create the input multislice object
Args:
microscope (object): The microscope object
slice_thickness (float): The slice thickness
margin (int): The pixel margin
Returns:
object: The input multislice object
"""
# Initialise the input and system configuration
input_multislice = multem.Input()
# Set simulation experiment
input_multislice.simulation_type = simulation_type
# Electron-Specimen interaction model
input_multislice.interaction_model = "Multislice"
input_multislice.potential_type = "Lobato_0_12"
# Potential slicing
# XXX If this is set to "Planes" then for the ribosome example I found that
# the simulation would not work well (e.g. The image may have nothing or a
# single point of intensity and nothing else). Best to keep this set to
# dz_Proj.
input_multislice.potential_slicing = "dz_Proj"
# Electron-Phonon interaction model
input_multislice.pn_model = "Still_Atom" # "Frozen_Phonon"
# input_multislice.pn_model = "Frozen_Phonon"
input_multislice.pn_coh_contrib = 0
input_multislice.pn_single_conf = False
input_multislice.pn_nconf = 50
input_multislice.pn_dim = 110
input_multislice.pn_seed = 300_183
# Set the slice thickness
input_multislice.spec_dz = slice_thickness
# Specimen thickness
input_multislice.thick_type = "Whole_Spec"
# x-y sampling
input_multislice.nx = microscope.detector.nx + margin * 2
input_multislice.ny = microscope.detector.ny + margin * 2
input_multislice.bwl = False
# Microscope parameters
input_multislice.E_0 = microscope.beam.energy
input_multislice.theta = 0.0
input_multislice.phi = 0.0
# Illumination model
input_multislice.illumination_model = "Partial_Coherent"
input_multislice.temporal_spatial_incoh = "Temporal_Spatial"
# Condenser lens
# source spread function
ssf_sigma = multem.mrad_to_sigma(
input_multislice.E_0, microscope.beam.source_spread
)
input_multislice.cond_lens_ssf_sigma = ssf_sigma
# Objective lens
input_multislice.obj_lens_m = microscope.lens.m
input_multislice.obj_lens_c_10 = microscope.lens.c_10
input_multislice.obj_lens_c_12 = microscope.lens.c_12
input_multislice.obj_lens_phi_12 = microscope.lens.phi_12
input_multislice.obj_lens_c_21 = microscope.lens.c_21
input_multislice.obj_lens_phi_21 = microscope.lens.phi_21
input_multislice.obj_lens_c_23 = microscope.lens.c_23
input_multislice.obj_lens_phi_23 = microscope.lens.phi_23
input_multislice.obj_lens_c_30 = microscope.lens.c_30
input_multislice.obj_lens_c_32 = microscope.lens.c_32
input_multislice.obj_lens_phi_32 = microscope.lens.phi_32
input_multislice.obj_lens_c_34 = microscope.lens.c_34
input_multislice.obj_lens_phi_34 = microscope.lens.phi_34
input_multislice.obj_lens_c_41 = microscope.lens.c_41
input_multislice.obj_lens_phi_41 = microscope.lens.phi_41
input_multislice.obj_lens_c_43 = microscope.lens.c_43
input_multislice.obj_lens_phi_43 = microscope.lens.phi_43
input_multislice.obj_lens_c_45 = microscope.lens.c_45
input_multislice.obj_lens_phi_45 = microscope.lens.phi_45
input_multislice.obj_lens_c_50 = microscope.lens.c_50
input_multislice.obj_lens_c_52 = microscope.lens.c_52
input_multislice.obj_lens_phi_52 = microscope.lens.phi_52
input_multislice.obj_lens_c_54 = microscope.lens.c_54
input_multislice.obj_lens_phi_54 = microscope.lens.phi_54
input_multislice.obj_lens_c_56 = microscope.lens.c_56
input_multislice.obj_lens_phi_56 = microscope.lens.phi_56
input_multislice.obj_lens_inner_aper_ang = microscope.lens.inner_aper_ang
input_multislice.obj_lens_outer_aper_ang = microscope.lens.outer_aper_ang
# Do we have a phase plate
if microscope.phase_plate:
input_multislice.phase_shift = pi / 2.0
# defocus spread function
input_multislice.obj_lens_dsf_sigma = multem.iehwgd_to_sigma(
defocus_spread(
microscope.lens.c_c * 1e-3 / 1e-10, # Convert from mm to A
microscope.beam.energy_spread,
microscope.lens.current_spread,
microscope.beam.acceleration_voltage_spread,
)
)
# zero defocus reference
if centre is not None:
input_multislice.cond_lens_zero_defocus_type = "User_Define"
input_multislice.obj_lens_zero_defocus_type = "User_Define"
input_multislice.cond_lens_zero_defocus_plane = centre
input_multislice.obj_lens_zero_defocus_plane = centre
else:
input_multislice.cond_lens_zero_defocus_type = "Last"
input_multislice.obj_lens_zero_defocus_type = "Last"
# Return the input multislice object
return input_multislice