sim_config.yaml

  molecular_model:
    voxel_size_nm: 0.1         # [nm]
    particle_name: 'toto'      # Name of the particle.
    particle_mrcout: None      # volume map of sample is written.

  specimen_grid_params:
    hole_diameter_nm: 1200         # [nm]
    hole_thickness_center_nm: 100  # [nm]
    hole_thickness_edge_nm: 100    # [nm]
    particle_slice_pad: 5          #

  beam_parameters:
    voltage_kv: 300                  # [kV]
    energy_spread_v: 1.3             # [V]
    electron_dose_e_per_nm2: 100     # [e/nm**2] dose per image
    electron_dose_std_e_per_nm2: 0   # standard deviation of dose per image

  optics_parameters:
    magnification: 81000             #
    spherical_aberration_mm: 2.7     # [mm]
    chromatic_aberration_mm: 2.7     # [mm]
    aperture_diameter_um: 50         # [um] in back focal plane
    focal_length_mm: 3.5             # [mm]
    aperture_angle_mrad: 0.1         # [mrad] of the condenser lens
    defocus_um: 1.0                  # [um]
    defocus_syst_error_um: 0.0       # [um]
    defocus_nonsyst_error_um: 0.0    # [um]
    optics_defocusout: None          # file to write defocus values

  detector_parameters:
    detector_nx_px: 5760               # [px] number of pixels along X axis
    detector_ny_px: 4092               # [px] number of pixels along Y axis
    detector_pixel_size_um: 5          # [um]
    average_gain_count_per_electron: 2 # average number of counts per electron
    noise: 'no'                 # whether quantized electron waves result in noise
    detector_q_efficiency: 0.5  # detector quantum efficiency
    mtf_params: [0,0,1,0,0]     # to be described. [0,0,1,0,0] is perfect detector.

  geometry_parameters:
    n_samples: 4                       # number of samples to be generated

  ctf_parameters:
   distribution_type: 'uniform'        # type of distribution, either 'gaussian' or 'uniform'
   distribution_parameters: [0, 1]     # distribution parameters, uniform: (low, high), gaussian: (loc, scale)

   noise_parameters:
    signal_to_noise: 0.67       # signal-to-noise-ratio for added white noise.

   miscellaneous:
    seed : 1234                 # seed for simulator.