TEMScripts Real-time Crystallography Manual. TEMScripts LLC. Last updated: 11/4/2016

Transcription

1 TEMScripts Real-time Crystallography Manual TEMScripts LLC. Last updated: 11/4/2016

2 Close Digital Micrograph Installation Copy following files to \\Gatan\DigitalMicrograph\PlugIns (normally under C:\Program Files (x86)\ or C:\Program Files\) TEMScriptLicense.dll TEMScripts Crystallography.gtk HREMMouse.bmp (freeware from HREMReserch Inc.) HREMMouse.gtk (freeware from HREMReserch Inc.) Restart Digital Micrograph Select TS Crystgraphy under menu Windows Floating Windows TS Crystgraphy palette should be visible.

3 TS Crystallography modules Conf Configuration of paths to save the crystallography files. Cell Unit cell generation d_hkl Calculation of interplanar spacing Ang Calculation of interplanar angles Poly Simulation of poly-crystal diffraction pattern SADP Simulation of single crystal diffraction pattern Calcu A convenient tool for generic crystallography calculation XRD Pseudo XRD pattern with peak intensity given by electron diffraction

4 1. Conf (to configure file directory) Configuration of directory to save basis, unit cell, and d-hkl files. Basis file: the input file from ICSD or manual input. This file will be used to generate unit cell file. Unit cell file: a complete list of atomic positions. This file is either generated by program through crystallography symmetry operation, or manually set up by user. This file will be used to generate d-hkl file. d-hkl file: a complete list of hkl, d-spacing, and structure factors (electron beam). This file will be used for the crystallography calculation and simulation, similar to PDF files for XRD analysis.

5 1. Conf (to configure file directory) Format of basis file: the input file from ICSD or manual input. This file will be used to generate unit cell file. Example of file modified from Si ICSD file () Si a Unit cell parameters: a, b, c,,, Space group number: 227 A list of basis atom positions Example of manually input file () Unit cell parameters: a, b, c,,, 227 Space group number: 227 Si A list of basis atom positions

6 1. Conf (to configure file directory) Format of unit cell file: a complete list of atomic positions. This file is either generated by program through crystallography symmetry operation, or manually set up by user. This file will be used to generate d-hkl file. Here shows an example of Silicon (Si cell.xyz) Unit cell parameters: a, b, c,,, Space group number: 227 A list of atomic positions Atomic number x y z -1 in the unit cell indicates an empty space.

7 1. Conf (to configure file directory) Format of d-hkl file: a complete list of hkl, d-spacing, and structure factors (electron beam). This file will be used for the crystallography calculation and simulation, similar to PDF files for XRD analysis. Below shows an example of Silicon (Si hkl.csv) Unit cell parameters: a, b, c,,, Space group number: 227 A list of d_hkl and intensity d h k l SF2

8 2. Cell (to generate unit cell) There are three approaches to generate unit cell. Unit cell from ICSD basis file 1) Click From ICSD File and select the file (1) 2) Click Apply Symmetry (2) 3) Save the result through Save unit cell (3) Unit cell from manually input basis file 1) Click From CSV file and select the file (4) 2) Click Apply Symmetry (2) 3) Save the result through Save unit cell (3) Manually set up unit cell 1) Set up the phase name, lattice parameters, and space group number if you would like to generate the unit cell through space group symmetry operation (5) 2) Input positions of each atom (6) 3) Add the atom position to the list (7) 4) You can also remove the atom from the list (8) or modify the element or position (9). 5) Save the result through Save unit cell (3)

9 3. d_hkl (to calculate interplanar spacing) To generate d_hkl file for phase analysis Load unit cell file (1) Generate d_hkl file for analysis (2) Save the file (3) To make a longer or shorter d_hkl file Load unit cell file (1) Set the up limit of h, k, and l and Create List (4) Calculate d spacing and Intensity (5) Save the file (3) To see the d_spacing of family planes Load unit cell file (1) Set up h, k, and l and click { } (6) Calculate d spacing and Intensity (5) Save the file (3) if needed To see the d_spacing of a specific plane Load unit cell file (1) Set up h, k, and l and click ( ) (7) Calculate d spacing and Intensity (5) Save the file (3) if needed

10 4. Ang (to calculate angle list between plans) Procedures to calculate angle list Load unit cell file (1). Create the hkl list through Create List (3), family planes { } -> (4), or specific plane ( )-> (5). Calculate the angle list between any two planes in the hkl list by click Calculate (5)

11 5. Poly (to simulate poly crystal diffractions) Procedures to simulate poly crystal diffractions Load d_hkl file (1), not unit cell file. Set the unit scale in the unit of 1/nm(2). It is recommended to set the unit scale same with that of the actual diffraction pattern for comparison. Set the image size in pixel. Again it is recommended to set this value to the pixel of the camera (3). Show the simulated diffraction pattern (4)

12 6. SADP (to simulate single crystal diffractions) Procedures to simulate single crystal diffraction Load d_hkl file (1), not unit cell file. Set the unit scale in the unit of 1/nm(2). It is recommended to set the unit scale same with that of the actual diffraction pattern for comparison. Set the image size in pixel. Again it is recommended to set this value to the pixel of the camera (3). Set the zone axis (4) Show the simulated diffraction pattern (5)

13 7. Calcu (a generic calculator) Between two planes Load unit cell file (1) Input two planes: h1, k1, l1 and h2, k2, l2 (2) Calculate (3) D-spacing, angle between two planes, and zone axis will be given. Between two directions Load unit cell file (1) Input two directions: u1, v1, w1, and u2, v2, w2 (4) Calculate (5) Angle between two directions and the common plane will be given. Goniometer angle Input ( 1, 1) and ( 2, 2) (6) Calculate (7) The angle difference between them will be given

14 8. XRD (to simulate XRD pattern) Procedures to simulate poly crystal diffractions 1 Load d_hkl file (1), not unit cell file. Set the Low limit and upper limit of the 2 theta angle range (2). Show the simulated XRD pattern (3). hkl, d-spacing, and 2 theta will be shown near each peak. 2 3