Dr. Probe - Graphical User Interface

 

The main purpose of the Dr. Probe graphical user interface (GUI) program is a straightforward STEM image simulation including direct visualization of results and intermediate steps. By this way you may quickly setup a simulation for a preliminary test of a more comprehensive simulation task or to approximate the success of a specific experimental setup. The GUI version supports multithreaded calculations with multi-core CPUs for 64-bit Windows operating systems.

 

Screenshot of the Dr. Probe GUI showing the main dailog, an aberration phase-plate, object data, and the result of a single beam-position multislice calculation.

[Screenshot of the Dr. Probe GUI, showing the main dialog, the sum of all phase gratings up to the selected object thickness for SrTiO3, and the calculated power of an exit-plane wave for a specific probe position]

 

Input data

Required input data for an image simulation with Dr. Probe are the atomic structure parameters for a crystal super cell. The atomic structure data is supplied by a structure definition file either in the CEL file format or as Crystallographic Information File (CIF) . A structure file contains general super-cell parameters, atom symbols, relative atom coordinates, atom site occupancies, and thermal atomic displacement parameters such as the Biso values used for the calculation of Debye-Waller factors.

 

User interface

The general purpose of the user interface is to provide an intuitive way of setting up the simulation parameters, for managing intermediate results and simulation data. It also provides functions to visualize and save the final results of a simulation. The interface is kept in dialog form with controls for parameter setup. The results are visualized in additional windows, which automatically attach to the main dialog when the main dialog is repositioned on the desktop.

The user interface keeps track of the main user actions in a log file, which can be accessed by clicking the Dr. Probe icon in the upper left corner and choosing the respective item of the system menu. Error messages and messages concerning important program actions are displayed in the message log area of the main dialog. The most recent messages appear on top of the list and earlier messages are at the bottom.

When starting calculations or when exiting the program, the current parameter settings are stored to a default setup file which will be loaded again after a program restart. Specific parameter settings can be saved to (loaded from) alternative setup files using the [Save] and [Load] buttons in the lower right corner of the main dialog.

Main dialog of the Dr. Probe GUI.

[Main dialog of the Dr. Probe GUI.]

The main dialog as shown in the above figure is separated in three sections concerning simulation related operations: a section for the setup of microscope parameters, a section for the setup of multislice calculation parameters, and a section for handling calculation results. The controls contained in each of the three sections are described in detail below.

Microscope Parameters

Section of the Dr. Probe main dialog for microscope parameter setup.

[Section of the Dr. Probe main dialog for microscope parameter setup.]

The microscope parameter section of the main dialog contains a box showing a summary of the most important microscope parameters with their current values. By pressing the button [Microscope Setup ... ], another dialog will open up, which allows you to change all microscope parameters. Quick access to some important microscope parameters is provided by a dropdown list where you can select a parameter and enter a value directly from the main dialog window.

Multislice Calculation

Section of the Dr. Probe main dialog for controlling the multislice calculation.

[Section of the Dr. Probe main dialog for controlling the multislice calculation.]

Multislice calculations are done based on a set of object phase gratings, which describe the elastic interaction between the incoming electron wave and the atoms. The current set of phase gratings can be visualized in an extra window by activating the respective check box [Show Object Data]. The dropdown list control to the right of the check box allows you to select the type of data, which will be displayed. You may choose between the a display of the projected object structure, of the selected slice structure, of the sum of all phase gratings, of individual phase gratings, and of the amplitude of individual phase gratings.

Pressing the button [Multislice Setup ... ], will open an additional dialog for the setup and management of parameters and phase grating data for the multislice calculations.
The object thickness slider allows you to select an object thickness between zero and the maximum object thickness, which corresponds to the size of the object slice stack. The object slice stacking is also set up in the multislice setup dialog. Multislice calculations will be performed only up to the object thickness, which is selected by the object thickness slider.

Before starting a multislice calculation you should select the calculation type from the dropdown list just left to the button labeled [Start Calculation ... ]. Two calculation types are supported currently: Scan image and Wave propagation.

Scan image calculations involve a multitude of multislice calculations for a set of probe positions distributed equidistantly over a rectangular scan frame. Scan images can be calculated simultaneously for a periodic sequence of object thicknesses up to the selected maximum thickness, showing the integrated detector signal for each detector defined by the microscope parameters. The calculations are done on a user defined number of CPU cores in parallel, which may significantly reduce the calculation time if many cores are available.

Calculations of the wave propagation are done for a fix probe position and show the real-space and Fourier-space wave power distribution in the calculation frame. The current probe position is denoted by a white cross in the object data display window and can be changed by mouse click and moving.
Wave power distributions are calculated for a periodic sequence of object thicknesses up to the selected maximum thickness. By setting the multislice parameters appropriately, the wave propagation through the object can be calculated by explicitly averaging over thermal atom vibrations (Einstein model), a geometric source distribution, and a defocus distribution in a Monte-Carlo approach.

Progress information window for the currently running image calculation.

[Progress information window for the currently running image calculation. In the present example, STEM images (55 x 78 pixels) are calculated for a set of detectors and object thicknesses in steps of approximately 1 nm up to 18 nm using phase gratings for 132 object slices sampled by 864 x 960 pixels. The calculation is done on a conventional PC using four calculation threads in parallel. A different (random) frozen lattice variant of the object structure is applied for the calculation of each scan pixel.]

When a calculation has been started, a dialog opens up informing you about the calculation progress and the estimated time until the calculation is finished. Based on the calculations already finished within a longer computational sequence, the approximate remaining time to finish the whole calculation is estimated. After finishing a calculation, a backup of the result is saved to disk in the application folder. The backup is saved to the public application data folder ("C:\ProgramData\Dr. Probe") in order to prevent data loss in the case of an unforeseen computer crash. Backup files are named "ScanDump*" and "WaveDump*" distinguishing the two calculation types. Text files with similar naming are added for storing important image sampling information.

Calculation Results

Section of the Dr. Probe main dialog dealing with calculation results.

[Section of the Dr. Probe main dialog dealing with calculation results.]

Calculation results are accessible using the controls of the calculation results section. The resulting images are displayed in an extra window. Depending on the selection made with the dropdown list, either scan images or wave power distributions are displayed. Results can be present for each calculation type separately and remain in memory until a new calculation is started for the same calculation type. The object thickness slider allows you to display the results depending on the object thickness.

Scan images can be convoluted by the effective geometric source distribution, which is set up currently in the microscope parameters. This convolution can account for the partial spatial coherence of the microscope if the scan image has been calculated with a scan step size, which is significantly smaller than the effective source diameter. You may change the source distribution settings after the scan image calculation and apply the convolution with different source functions as often as you want by pressing the [Apply Source Profile] button. The convolution is applied to all scan images (all thicknesses and all detectors). Images calculated for a certain detector are displayed in the calculation results window when choosing the respective detector from the dropdown list in the lower left part.

Wave power images can be displayed in real-space and Fourier-space representation by selecting the respective result type from the dropdown list. The source profile convolution is deactivated in this case. However, the simulation can account for the effects of partial spatial coherence, partial temporal coherence, and thermal diffuse scattering by using a sufficiently large number of variations in the multislice calculation (see multislice processing parameter setup).

The selected result can be saved to files on your hard disk via an additional dialog, which opens up after pressing the [Save Results to File ... ] button. Multiple formats of saving the data are supported.

 

Data display windows

The Dr. Probe graphical user interface displays data in separate windows. On the level of the main dialog there are two data display windows, which attach to the left border and to the right border of the main dialog when the main dialog is moved by mouse over the desktop area. The left window displays object data represented by the currently loaded phase gratings. The right window displays the currently selected calculation results. A third display window opens up on the level of the dialog for microscope parameter setup and is attached to the right border of this dialog.

All data display windows adjust their size automatically to the size of the displayed data. If the data is larger than a certain fraction of the screen, the window size will not be increased further, instead scroll bars are added allowing you to move the view port to each part of the data.

The data display windows contain an [Options] button, which opens a dialog to adjust the display parameters. The [Save] button allows you to save the current display content as an image or the underlying raw data to a file. The [Refresh] button forces an update of the display area. General data information is presented in the status bar at the lower window border. The three numbers represent (from left to right) the physical data dimension, the minimum data value and the maximum data value. Values from individual data points can be seen by a tool tip, which is displayed when the mouse is moved over the image area.

 


Last update: August 1, 2017

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