STEM Image Simulation
Contents
1. choosing Execute STEM from the File menu of the MultiGUI A window showing the progress of the calculation appears When an execution terminates normally you will get the message Execution completed Congratulation TIPS Calculation of a STEM image by scanning many points will take a long time Thus you can stop calculation and continue it layer In order to resume calculation choose Append from MultiGUI gt Multislice Calculation When you stop calculation a calculation will resume from the following scan point on which a full propagation has been completed You can save the result window by choosing Save As from the File menu of the result window STEM 11 Gray scale STEM Images Display STEM for xHREM Gray scale STEM images will be generated by using the STEMimage utility The STEM data has been output to a SD file To display a gray scale STEM image do this 1 Launch STEMimage 2 Select a SD file with your sample name in the file selection dialog Windows When you can not find your SD file confirm that the file type specification is SD Data SD The following window will be appeared E GaAs011s_0 3 SD xStemImage 2 File Edit Window Help Title GaAs 011 Unit Cell a 4000 Ane 6 5650 Ane angle 0 00 Scan Control Whole Unit a 0 000 lt gt 0500 Z 5 points b 0 000 lt gt 0500 points Display Control Display Mo2. multislice technique developed at Arizona State University USA see References This is one of the most reliable and efficient HREM image simulation programs High Quality Image Output Numerical data such as projected potential wave function propagating the specimen simulated image intensities could printed as high quality gray scale maps Bitmap by using Output Graphic Utilities Numerical value of each pixel of the gray scale can be exported for further analysis with other software Concept of STEM Extension 1 User Friendly Graphical Interface STEM Extension employs user friendly Data Generation Utilities based on the Graphical User Interface for Windows or Mac OS STEM 3 STEM for xHREM Reliable and Efficient Algorithm Thermal Diffuse Scattering TDS is believed to be the main source of signal for STEM HAADF image STEM Extension will efficiently treat TDS using absorption potentials Please consult the following paper for a detailed description K Ishizuka A practical approach for STEM image simulation based on the FFT multislice method Ultramicroscopy 90 2001 71 83 Efficient Computation Multi CPU Support STEM image simulation is number crunching since scattering calculation is necessary at each scanning point Therefore STEM Extension supports multi CPU Core to accelerate computation Note From the version v3 7 the two STEM Extensions will be released STEM Extension 32bit Cluster and S
3. specified for this mode Whole Unit The whole unit area will be calculated assuming an applicable symmetry Thus the two dimensional symmetry group and an approximate scanning step interval will be specified Integral number of scanning points will be calculated internally according to the approximate sampling interval Scan Control Scan Mode Whole Unit v Symmetry pl v Calculation step 0 2 Anestrom Data Output Cycle STEM image intensity output interval in terms of the slices List Output the list output showing a scan progress When a computing time for each slice is very quick the scan list output may control the overall turnaround time In this case a simpler lit output is effective to shorten the turnaround time STEM 8 STEM for xHREM i STEM Parameters l jes 1 gt Optional Optical Parameters 41 012 0 nm 0 deg Coma C21 0 nm D deg A2 C23 0 nm 0 deg G32 0 um 0 deg A3 C34 0 um D deg C41 0 mm D deg C43 0 mm D deg Ad O45 0 mm D deg C52 0 mm 0 deg c54 0 mm 0 deg A5 C56 0 mm D deg Wave aberration Gnm n 1 ee 3 Use STEM Extension 32 bit version Use STEM Extension Pro 64 bit version 5 Use STEM Extension Cluster Cluster Setup Use STEM Extension Pro Cluster Cancel High Order Aberration Coefficients High order geometrical aberration coefficients up to 5th order can be specified here Although vari
4. HAADF TDS absorption potentials TIPS For STEM image calculation the super cell less than Standard is not recommended in order to evaluate scattering profile STEM simulation will use a large number of the sampling points Therefore you will get a huge amount of the list output when you try to print out the whole area of the potential distribution or the scattering distribution STEM 10 STEM for xHREM Dynamical Scattering Calculation 1 Create the general scattering calculation controls in the main WORKSHEET TIPS To calculate elastic scattering to high angle a calculation range of s 1 5 2 0 A d 3 0 4 0 A or higher will be set by Preferences gt Dynamical calculation gt Range However Doyle Turner cannot be used above s 2 0 A You have to select Weikenmeier Kohl foa a calculation over s 2 0 A TIPS Choose Weikenmeier Kohl Scattering Factor from Preferences Atomic Scattering factor and check Including TDS Absorption box However when you want to ignore TDS absorption and obtain a STEM image using only elastic scattering you don t need to check this box Please note that including TDS absorption requires a thermal factor Debye Waller factor of each atom Set up the optional data for STEM simulation Save the new data using Save or Save As from the File menu of the MultiGUI Before saving the data you can t select the Execute command Launch STEM program by
5. STEM for xHREM WinHREM MacHREM Scanning Transmission Electron Microscope Image Simulation Program User s Guide STEM for xHREM Scanning Transmission Electron Microscope Image Simulation Program User s Guide Contents m Introduction m Installation m Let s Start Tutorials Data Preparation Dynamical Scattering Calculation Gray scale STEM Images Display m Topics TDS Absorption Required RAM Size STEM 2 STEM for xHREM m Introduction This is a program to simulate a scanning transmission electron microscope STEM image This program is designed as an optional function of XHREM WinHREM MacHREM a program suite simulating a high resolution electron microscope image for Windows Mac OS xHREM has the following features Concept of xHREM 1 User Friendly Graphical Interface xHREM employs user friendly Data Generation Utilities based on the Graphical User Interface for Windows or Mac OS xHREM is general purpose software that can be used to simulate all the images expected from any crystal systems defect structures and interfaces Although data generation for such general purpose software normally becomes complex a novice user can easily generate his her data by using the graphical Data Generation Utilities with minimum requirements for the special knowledge Reliable and Efficient Algorithm xHREM emerges from the HREM image simulation programs based on FFT
6. TEM Extension 64bit Cluster STEM 4 STEM for xHREM m Installation STEM program 32bit version and some sample data should be already installed into your hard disk when you have installed x HREM Simulation Suite In the case of STEM program 64bit version please copy it manually to Programs folder of XHREM STEMxx exe is not an installer When you purchase STEM program as an additional order you have to update your user key This update can be done by using Remote Update System RUS When you send current key information then we will send back information to update your key STEM 5 STEM for xHREM m Let s Start Tutorials Data Preparation Most of the data for scattering calculation control will be prepared by using MultiGUI A set of data specific to the STEM simulation will be specified in the optional windows Please consult xHREM User s Manual about the general scattering calculation controls A sample data for SnO2 will be provided with the program In order to set up the optional data specific to the STEM simulation click STEM from the Options at the bottom of the MulttiGUI WORKSHEET Options DIFFUSE GBED STEM Model View Then the following window will open STEM 6 STEM for xHREM E T STEM Parameters l i Option Optical Parameters 1 gt Aperture radius 11 9 mrad Third order Gs 1 mm Defocus Genter Defocus 500 Angstrom Defocus Step 0 Angstrom of ove
7. ansform gives smoother image Thus a wider step scan distance can be used in calculation and a computation time may be substantially decreased TIPS Partial coherency due to a probe size as well as a defocus spread can be estimated Here Gaussian distributions are assumed for both the probe size and the defocus spread and a full width at 1 e value is specified NOTE In order to estimate partial coherency due to a defocus spread the STEM images at multiple defocuses in a sufficient range should be calculated TIPS Each pixel value of a gray scale map produced by STEMimage can be output using Save As command as you can do by using ImageBMP The original data used to produce the gray scale map can also be output using Save As command Please consult Numerical Data Output Using ImageBMP in the xHREM manual for more details STEM 13 STEM for xHREM E Topics In this section some useful functions as well as advanced topics will be introduced It is not necessary to read through all the topics at the first time You may want to study each topic when you need to use it Including TDS Absorption You can include absorption of elastically scattered wave due to thermal diffuse scattering TDS in your dynamical calculation In this case however thermal displacement parameter temperature factor Debye Waller factor for each atom in your atomic model is required When you don t know a corresponding param
8. de STEM Image x 24 Pixels Angstrom Display Range slice a 00 lt gt 2 193 pixels b 0 0 lt gt 2 272 pixels Image Mode Bright Field Dark Field VITOS Coherent BF Aperture 0 474 DF Aperture 2 233 lt gt 5 000 Interpolation Fourier Transform x Display Limit Partial Coherency Full Width at 1 e Low Minimum 4 Probe Size 0 Ane High Maximum V Defocus Spread 0 Ane Generate Reverse Contrast 3 Select Display Mode Select a display mode from STEM Image Thickness Map and STEM 12 STEM for xHREM Point Selectable display mode is depending on the Scan Mode As in this case of a two dimensional scan image you have to select the specimen thickness slice number a display area and a resolution Pixels length When multiple defocus data is available you can select a defocus value or a center defocus value of Defocus Spread When the Scan Mode is Whole Unit you can extend the display area more than one unit cell 4 From Image Mode you can select the image type from Bright Field or Dark Field In the case of the dark field image you cal also select the image signal s from TDS inelastic signal and or coherent elastic signal 5 Click Generate to display a gray scale image TIPS You can select one of the two interpolation methods Fourier Transform Bi linear Interpolation to estimate intensity between the calculated points Usually an interpolation using Fourier tr
9. eter an approximate value may be specified To include TDS absorption in your dynamical calculation 1 Launch MultiGUI 2 Choose Preferences from Edit menu 3 Select Weikenmeier Kohl Scattering Factor in Atomic Scattering Factor section of the Preferences dialog and check Include TDS absorption Atomic Scattering Factor Mott Formula with Doyle Turner X ray Scattering Factor Weikenmeier Kohl Scattering Factor Including TDS Absorption STEM 14 STEM for xHREM Required RAM Size For STEM image simulation scattering calculation is necessary at each scanning point Then we have to use all the phase gratings for each scan point A cotemporary operating system OS allows us to use many phase gratings by using a virtual memory management However when a main memoty is short to store only a single phase grating all the phase gratings should be read from an external memory as a result of roll in roll out If an external memory is a hard disk a significant time is required to read the phase gratings into the main memory Therefore all the phase gratings should be stored in the main memory for an efficient computation Typically each program can use a roughly 2GB using a 32 bit OS If the total phase gratings is bigger than this size you have to use STEM Extension Pro that supports a 64 bit OS TIPS In the case of a Standard model with 512x612 pixels each phase grating requires the followi
10. ng memory 512x512 x 8 complex x 2 4MB A larger model uses more phase gratings of larger size so the total phase gratings will become more than 2GB STEM 15
11. ous definitions of the coefficients appear in the literatures we simply define them in terms of wave aberration as any a cos m P Pan Super cell Size Super cell size used in computation will be selected from the following pull down list Normally Standard can be selected here STEM 9 NOTE STEM for xHREM standard Large Huge Ultimate The super cell size in computation should be larger than the input structure model If the structure mode is smaller than the super cell size the input model is repeated to fill the super cell Thus the model size in computation is a multiple of the input model 32bit 64bit Selector If the 64bit module and or Cluster module is not installed to Programs folder you cannot select it Super cell size and sampling Model Model size Sampling FT space interval 2 Approximate Approximate a E o trina so aos oos The number of the sampling points is estimated for a rectangular unit cell assuming the calculation Range of 5 0 A in d An approximate number of the sampling points is 2xRange sampling interval TIPS The calculation limit in Fourier space is specified by Range at Preferences Dynamical calculation The numbers of the sampling point will increase proportionally with the Range For an oblique system the required number of pixels becomes larger than the number shown here TIPS Normally the Range of 5 0 A is enough for calculation using
12. r under foci 0 Defocus Range 500 To 500 Angstrom Fifth order Cs 0 mm 2 gt Detector Parameters Bright Field 0 1 mrad Dark Field Inner 0 5 mrad Outer 1 mrad 3 5 Scan Control Scan Mode Area X x 0 lt gt 1 f 11 Points 0 lt gt 1 f 11 Paints Data Output Every 1 Slices List Output Y XSLICE x Cancel Optical Parameters Input an aperture radius aberration coefficients The aperture radius may be given in mrad You have to select mrad in the Preferences before open this window You can perform calculations at multiple defocuses Here the center defocus defocus step and a number of defocuses at over and under focus sides Detector Parameters Detector radiuses of the bright field imaging and the dark field imaging will be specified here These radii may be given in mrad You have to select mrad in the Preferences before open this window STEM 7 STEM for xHREM Scan Control Scan Mode Scanning scheme will be selected from the list shown below Position Scanning position s will be specified here The scanning positions will be specified in different ways according to the scanning mode Area The ranges of the scanning area and numbers of scanning points along x and y will be specified for this mode Line The starting position and the ending position as well as the number of scanning points will be specified for this mode Point A single position will be
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