def get_sim_params(sp_cell,
slab_t=100,
sampling=np.array([512, 512]),
d_cutoff=4,
grid_steps=np.array([32, 32]),
cell_dim=100,
energy=100e3,
orientation_num=3,
beam_overlap=1):
"""
return a dict object to set params of simulation and write to h5.
"""
sim_params = dict()
# scattering params
hkls, dhkls = get_kinematic_reflection(sp_cell.structure, top=3)
if hkls[0].size > 3: # hexagonal systems
hkls = np.array([[itm[0], itm[1], itm[-1]] for itm in hkls])
cutoff = np.logical_and(
dhkls < 5., dhkls > 1.) # not considering less than 5 ang. d-spacing
if dhkls[cutoff].size > 2:
hkls = hkls[cutoff]
dhkls = dhkls[cutoff]
if dhkls.size > orientation_num:
dhkls = dhkls[:orientation_num]
hkls = hkls[:orientation_num]
y_dirs = np.array([get_cell_orientation(z_dir) for z_dir in hkls])
semi_angles, _, _ = overlap_params(0.5, dhkls, voltage2Lambda(energy))
sim_params['y_dirs'] = y_dirs
sim_params['z_dirs'] = hkls
sim_params['semi_angles'] = semi_angles * 1e-3 # mrad
sim_params['d_hkl'] = dhkls
sim_params['cell_dim'] = cell_dim # ang.
sim_params['energy'] = energy * 1e-3 # keV
sim_params['sampling'] = sampling
sim_params['slab_t'] = slab_t # ang.
sim_params['grid_steps'] = grid_steps
# optics params
sim_params['probe_params'] = {
'smooth_apert': True,
'scherzer': False,
'apert_smooth': 30,
'aberration_dict': {
'C1': 0.,
'C3': 0,
'C5': 0.
},
'spherical_phase': True
}
return sim_params
def get_slice_thickness(sp_cell, direc=np.array([0, 0, 1])):
hkls, dhkls = get_kinematic_reflection(sp_cell.structure, top=10)
if hkls[0].size > 3: # hexagonal systems
hkls = np.array([[itm[0], itm[1], itm[-1]] for itm in hkls])
idx = np.argmin(np.abs(np.cross(hkls, direc).sum(1)))
return dhkls[idx]