01

<string>

File name of the input wave function
Example: 'wav\exit-wave.dat'

02

<number>, <number>

Number of columns and rows (samples) of the input wave function [pixels]
Example: 192, 256

03

<float>, <float>

Physical row and column sampling rate of the input wave function [nm/pixel]
Example: 0.003878, 0.003727

04

<float>

Primary electron energy [keV]
Example: 300.0

05

<number>

Switch option for the type of output:

• 0 = TEM image
• 1 = wave function
• 2 = w.f. amplitude
• 3 = w.f. phase
• 4 = w.f. real part
• 5 = w.f. imaginary part
• 6 = TEM image map from a 2D parameter variation

Example: 0

06

<string>

File name of the output image or wave function data
Example: 'img\TEM-image.dat'

07

<number>, <number>

Number of columns and rows (samples) of the output image [pixels]
Example: 64, 72

08

<number>, <float>, <float>, <float>

Image output data type, image vacuum mean intensity [counts], conversion rate [counts/e-], readout noise rms amplitude [counts]
Image data types: 0 = 32-bit float, 1 = 32-bit integer, 2 = 16-bit integer
Example (default simulation): 0, 1.0, 1.0, 0.0
Example (simulation with noise): 1, 3451.2, 5.1, 3.0

09

<number>

Switch S_F for extracting a specific image frame
S_F = 0: OFF, S_F = 1: ON
The parameters defined in lines 10 - 12 are ignored when S_F = 0.
Example: 1

10

<float>

Image sampling rate [nm/pixel]
Applies only if S_F = 1
Example: 0.008973

11

<float>, <float>

Image frame offset in pixels of the input wave functions
Applies only if S_F = 1
e.g. 13.4, 16.2

12

<float>

Image frame rotation with respect to the input wave horizontal axis [deg]
Applies only if S_F = 1
Example: 0.0

13

<number>

Switch option for selecting the model for the simulation of partial coherence in the image formation. Numbers from 1 to 6, see table of supported coherence models below.

Example: 1

14

<number>, <float>

Partial temporal coherence switch and focus-spread (1/e-half width) [nm]
Set the switch = 0 to deactivate and = 1 to activate the simulation of partial temporal coherence
Example: 1, 3.8

15

<number>, <float>

Partial spatial coherence switch and semi-convergence angle (1/e-half width) [mrad]
Set the switch = 0 to deactivate and = 1 to activate the simulation of partial spatial coherence
Example: 1, 0.4

16

<number>, <float>, <string>

Switch, k-space scaling, and file name for the simulation of a frequency modulated detector transfer function (MTF)
Set the switch = 0 to deactivate and = 1 to activate the MTF simulation.
The k-space scaling should be equal to the ratio of sampling rates of experiment and simulation (s_exp/s_sim).
Example: 1, 1.0, 'C:\data\CCD-MTF-300kV.dat'

17

<number>, <float>, <float>, <float>

Switch and rms amplitudes [nm, nm, deg] of the effective image spread.
Set the switch = 0 to deactivate or = 1 or = 2 to activate the simulation of an image spread envelope.
Switch = 1 assumes an isotropic image spread defined by one rms amplitude.
Switch = 2 assumes an anisotropic image spread defined by two perpendicular major rms amplitudes and an azimuth orientation angle. The orientation determines the direction of the first major vibration axis with respect to the horizontal image axis.
Example: 1, 0.016

18

<number>

Number N_abr of image aberrations set below
You have to provide exactly this number of aberration definitions in the following lines.
Example: 2

18+

<number>, <float>, <float>

Aberration definition by an index number and two coefficient values given in [nm] (details)
N_abr aberration definitions are expected following line 11. By default aberration coefficient values are all zero. You may set N_abr = 0 and leave out all aberration definitions.

Note that depending on the number of aberration definitions N_abr, the following content is moved further lines down in the parameter file.

19+ N_abr

<float>

Objective aperture radius [mrad]
Example: 250.0

20+ N_abr

<float>, <float>

Center of the objective aperture with respect to the zero beam [mrad, mrad]
Example: 0.0, 0.0

21+ N_abr

<number>

Number of parameter loops N_lp defined below.
At least N_lp loop definitions have to follow this line. Since each loop definition itself requires 5 lines, we restrict the description here to 1 loop definition. When more than one loop is defined, the first loop definition in the parameter file will be the innermost loop of a nested loop calculation.
As the parameter file ends after the loop definitions, you may simply switch off all parameter loops by setting N_lp = 0.
Example: 1

22+ N_abr

<number>

Loop parameter class L_c.

• 1 = coherent aberration
• 2 = incoherent aberration
• 3 = input wave function file

Example: 1

23+ N_abr

<number>

Loop parameter index L_p
Example (defocus): 1

24+ N_abr

<number>

Loop variation form L_f

• 1 = linear ramp
• 2 = cosine oscillation
• 3 = list directed aberration parameters

Example: 1

25+ N_abr

<float>, <float>, <number>

Loop range (L_r0, L_r1, L_rn)

• case L_f = 1: L_r0 = min., L_r1 = max., L_rn = number of samples
• case L_f = 2: L_r0 = amplitude, L_r1 = frequency, L_rn = number of samples
• case L_f = 3: ignored, parameter values are taken from file

Example: 0.0, 10.0, 21

26+ N_abr

<string>

Loop string identifier L_s

This string is used very flexible depending on the loop class and form:

• L_c = 3: The string L_s specifies the exact substring preceding the index in a loop over input wave function file names.
  For example set L_s = '_sl' to address the wave function files of a thickness series obtained with MSA, such as 'wave_sl001.dat', 'wave_sl002.dat', 'wave_sl003.dat', etc.
• L_f = 3: The string L_s specifies the exact file name describing a list directed parameter variation.

Example: '_sl'

1

Non-linear image calculation including partial temporal coherence (focus spread) by explicit averaging. Partial spatial coherence is treated by a quasi-coherent approach with a dampening envelope applied to the wave function. This model is good for HRTEM with Cs-corrected microscopes, where the partial spatial coherence can be largely ignored but the partial temporal coherence limits the resolution as a compromise for faster calculation.

2

Non-linear image calculation by explicit averaging of coherent sub-images with focal variation and angular variation. With sufficient numbe rof focal and angular samples, this is a fully accurate calculation of partial coherence including all cross-terms and non-linearities. It is valid for all kinds of TEMs but quite time consuming.

3

Linear image calculation considering partial coherence by linear envelopes applied to the linear interference terms. This approximation remains valid for weak-phase objects. Non-linear image components are ignored.

4

Fourier-space synthesis with partially coherent transmission cross-coefficient (TCC). This is a fully non-linear imaging model with dampening including a first-order derivative solution of the TCC. It can be applied to moderate coherence cases. The calculation is very time consuming and only implemented for reference. Mode 2 should be preferred over mode 4.

5

Non-linear image calculation including frozen-lattice variations with explicit averaging of focal and angular distributions for partial coherence. The averaging is over random samples of the distribution functions.

6

Non-linear image calculation in a quasi-coherent approximation of partial coherence. A dampened wave function in the image plane is calculated by multiplying linear dampening envelopes in Fourier space and then calculating the absolute square in real space. This approximation applies a too strong dampening to some of the non-linear interference terms. It is of limited use and valid only for very thin samples or microscopes where the resolution is not limited by partial coherence effects.