Simulator User`s Manual
Contents
1. mayenite ICSD 62787 hkl Reciprocal space viewer mayenite ICSD 627867 cif Dynamical simulation Ca Si 0 0 34 hkl Reciprocal space viewer Brownmillerite hkl Reciprocal space viewer hydroxyapatite hkl Reciprocal space viewer Ferrisicklerite hkl Reciprocal space viewer hydroxyapatite cif Dynamical simulation Brownmillerite cif Dynamical simulation Densit otential ma o Peak search F Structure factors p Reciprocal space viewer D HKI calculator i Dynamical simulation PM 5D viewer 2 1 What can we do using Simulator Simulator provides you with a great possibility of calculating and displaying different types of information needed in the area of Transmission Electron Microscopy TEM The following set demonstrates some of the features that Simulator offers e Projected potential e Exit wave function e Electron Diffraction ED patterns e High Resolution Electron Microscopy HREM images 2 1 2 2 Contrast Transfer Function view 2 2 Loading the structural information The most commonly used file formats are available to you in the Simulator You can open PDB CIF INS and XYZ formatted files plus an XML formatted file used by Simulator to store the structural information as well as calculation settings 9 Structures Nano Co0 NaCltype cif YBCO CIF 2b0353 cif 3 delts Al203 ins yeco ins i AI203 alpha CIF h ydroxyapatite cif Al203 delta CIF may2. Simulator User s Manual Version 2 0 Copyright 2003 2008 Analitex Visit our web page at www analitex com June 2008 1 2 Contents Contents SO 1 1 2a OFS AA AS ee ee ere ee ee 2 1 2 1 What can we do using Simulator ss 2 1 2 2 Loading the structural information 2 2 2 WO OMD 1 RE RS 2 3 2 4 Multislice toolbar buttons description 2 4 2 5 Working with the image toolbar ss 2 5 20 AVC COLOR ne S 2 6 DOCS DAS rey eore tener 3 7 Dies Microscope dockins DAME a a EE EE ec ous 3 7 3 2 Contrast Transfer Function CTF docking pane ccccccssssesseeceeeeeeeeeeeeees 3 8 33 Dilirachon COCK ING AIC eo 3 9 4 Contrast Transfer Function view seen 4 10 Je VETER Se Ns a as de a eo 5 11 Dale ORC ARIS SO ee nem eens emer eee eee 5 11 I TUN Ieee tates 5 13 Del MI CMOCUS te ee de ce ne 5 13 SA AP U a ene ene Penne enn nee 5 13 Dc MMC A peas tec oases tens E E E E 5 14 5 2 4 Non linear imaging for partially coherent and incoherent illuminations 5 14 Die DISC LCM SSD a ee 5 15 3A CMOS OSM OG res poh sss 1c atecotge sions aaceidesnel E RE 5 15 CONSO CaO OS ectemneduneesacesauenaccusqenacecueneaueeeane 6 16 C AON ae ceSeettes snc E E E E E E 6 16 7 Reviewing the calculation results 2 0 eccccccccccccceesssseeececceecseeeeeseecceeeesssaeeeseeeeeees 7 1 Tle PG ACCME COINS do eos 7 1 7 2 Exploring projected potential ss 7 2 J3 Exploring theexit wave DAC ae te 7 3 JA Explonns HREM Mates at oi c
3. successfuly HREM image for t 103 0 and def 450 0 saved to Au gold 7 1030 450 hrem successfuly H 4 gt Output lt j Ready HREM image for defocus 700 8 1 8 2 Working with non crystalline objects aag eMap Au gold 7 xyz 8X Diffraction Zone Axis 00 1 Convergence Reflection Thickness A angle mrad threshold HREM image for t 103 0 and def 650 0 A saved to Au gold 7 1030 650 hrem successfuly HREM image for t 103 0 and def 600 0 A saved to Au gold 7 1030 600 hrem successfuly HREM image for t 103 0 and def 550 0 saved to Au gold 7 1030 550 hrem successfuly HREM image for t 103 0 and def 500 0 A saved to Au gold 7 1030 500 hrem successfuly HREM image for t 103 0 and def 450 0 A saved to Au gold 7 1030 450 hrem successfuly H 4 gt pt Output ld 5 iul L Ready CAP NUM SCRL 14 00 12 7 shells Au nanoparticle electron diffraction pattern Default settings in the Diffraction docking pane 8 2 8 3 Working with non crystalline objects aag eMap Au gold 7 xyz 80X Diffraction Zone Axis 00 1 Convergence angle mrad threshold 0 010 0 0025 103 0 HREM image for t 103 0 and def 650 0 A saved to Au gold 7 1030 650 hrem successfuly HREM image for t 103 0 and def 600 0 A saved to Au gold 7 1030 600 hrem successfuly HREM image for t 103 0 and def 550 0 saved to Au gold 7 1030 550 hrem su
4. in order to observe the HOLZ lines in the 000 disk the following three rules should be satisfied 1 The Ewald sphere should be switched ON 1 e with the frame around it 2 The calculated diffraction pattern should contain enough spots enough resolution so that the Ewald sphere can reach the upper reciprocal layers 3 The value in the Max HOLZ index should be greater than or equal to O default is 0 Checking unchecking the HOLZ shift will switch ON OFF the dynamical correction in the calculations of the HOLZ lines positions within the 000 disk which leads to the so called HOLZ lines shift E Hwag ayenite ICSD 6287 hkl 4b x k ZONE 0 0 1 is L 0 HKO 3659 7319 1830 3659 Wu Li J e 915 1830 Sg AL ee Pass Ba as e 457 915 e 229 457 114 229 57 114 0 57 2 4 0 d 2 6808 Fhkl 73 92 Pha 0 Intensity 5464 17 9 8 9 9 Simulator Reciprocal space viewer 9 3 3 The Precession dialog pane Precession angle Bf Diffraction FRB Kikuchi ii The Precession dialog pane The Precession dialog pane allows the user to control the precession angle in Precession and Precession animation modes The min and max values of the precession angles can be changed by the user Here 0 and 3 degrees are used Animate precession allows you to follow how an electron precession pattern is built up namely by the succe
5. sample is tilted back and forth in that direction It is fixed to the range l to 1 with 30 Steps Precession mode and Precession animation Can be controlled using the Precession pane see 9 3 3 allows you to scale the simulated diffraction pattern exactly 9 5 Preferences Window Help Set scale D vie KikuchifHOLZ lines Rotation Rotation animation Precession Animate precession 9 6 Simulator Reciprocal space viewer 9 3 Working side pane dialog bars The Reciprocal space viewer offers 3 pane dialog bars on the right side default of the main view These bars can be re attached to any side of the current view or the main window left or right sides are preferable due to the vertical nature of the dialog bar items placement Any dialog pane can be closed or hidden any time by using the 2 buttons in the right top corner of the bar 9 3 1 The Diffraction dialog pane The Diffraction dialog pane allows the user to Diffracuon control the current zone axis indices the Stereographic projection view show hide the Akl Miller indices for all reflections show hide the annotation text change some parameters of the diffraction pattern such as the beam convergence angle the voltage electron diffraction and the thickness electron diffraction fone Axis When you move around over the stereographic projection the index at the bottom left gives the nearest Miller indices Left clic
6. www fos su se svenh index html Peter Oleynikov Exploring reciprocal space Electron diffraction texture and precession Ph D thesis at Stockholm University Department of Structural Chemistry 2006 90 pages 7 papers Free copies may be obtained from the author or via Calidris Jean Paul Morniroli A Redjaimia and Stavros Nicolopoulos Contribution of electron precession to the identification of the space group from microdiffraction patterns Ultramicroscopy 107 2007 514 522 Jean Paul Morniroli and John W Steeds Microdiffraction as a tool for crystal structure identification and determination Ultramicroscopy 45 1992 219 239 The whole of Ultramicroscopy Vol 107 2007 issues 6 7 is devoted to the electron precession technique A large number of references on electron precession can be found at the NanoMEGAS home page http www nanomegas com bibliography2 php 10 1
7. 20 100 C Save potential C Save exit wave Fr k Laue circle 0 U C Save diffraction The number of slices to split the unit cell along the projection direction Simulator calculates the translation vector along the projection direction and suggests the number of slices per unit cell so that the slice thickness is 1 A The user can modify this number However some factors should be considered when choosing other values see section 6 16 for more details The Thickness range start and end values and the step between the bounding values Beam tilt off from the specified zone axis can be set through the Laue circle position by changing the h and k values can be real numbers along corresponding 2D axes in reciprocal space The configuration without any beam tilt corresponds to 00 for h and k 5 11 5 12 Multislice calculations The calculations results will be saved for future use only if the specified check boxes for example Save potential will be marked The files with calculation results will be deleted after closing Simulator Only images and diffraction patterns for specified thickness values can be shown after the calculations are done In case with Thickness start 20 A step 20 A and end 100A only 5 exit wave functions 5 electron diffraction patterns and at least 5 rows of HREM images number of those within each row depends on the number of the specified defocus values will be stored for reviewing The cor
8. should fit the zone axis equation hu kv lw 0 e Defining 2D plane indices in the local axes h k The transition between indices is possible using lt and gt buttons Indices can be Added Removed and Updated using corresponding buttons The data can be viewed using Excell The format is thickness Amplitude Phase and further pairs of Amplitude Phase if more than one beam has been selected Can be viewed using Excel Multislice settings AONE axis Beams pendellosung j Imaging Objective lens hk 2 Fo Fo nk 2 EX Beams pendellosung 5 15 6 16 Multislice calculations 6 Multislice calculations CL The multislice calculations will start after pressing the Run button see section 2 4 The following progress dialog will be shown Operation progress projected pt hdine of 512 If you are working with the same structure file and are trying to repeat the same calculations or calculations with modified settings then Simulator will ask if you would like to clean up e g by removing files generated by previous Run In this case Simulator will come up with the following question h Delete previous result o cme In case of pressing the Cancel button the calculations will be terminated Simulator will try to use the data left from any available previous calculations 6 1 Cautions The major error source in the multislice calculations is the slice thickness 1 and
9. simulations Microscope CTF Diffraction 3 8 3 9 Contrast Transfer Function view 3 3 Diffraction docking pane This pane is designed to work with the parameters of the simulated electron diffraction D itfr achion pattern The user can e Draw hide the hkl imdices and text m Zone Axis annotations on the diffraction pattern mon view by marking unmarking the corresponding check boxes e Change the convergence angle the spot size in mrad e Change the threshold values of reflections to be shown on the C Draw hklindices C Draw annotations diffraction pattern view Convergence Reflection Thickness A e Change the thickness of the diffraction angle mrad threshold pattern to be shown Only diffraction patterns at specified thickness are available see Thickness in the Zone Axis property page section 5 11 Manually edit the convergence angle reflection threshold and thickness values by typing into the corresponding edit boxes under the sliders In order to apply D changes the user must do a mouse click outside the edit box In case the manually modified Thickness value doesn t correspond to any specified thickness values the diffraction pattern at closest calculated thickness will be shown Microscope CTF Diffraction 4 10 Contrast Transfer Function view 4 Contrast Transfer Function view The user can observe the Contrast Transfer Function CTF and modify the
10. sliders into their initial positions Provides the possibility to modify the color palette NOTE not available in the current release of the Simulator 2 6 Contrast Transfer Function view 2 6 Palette control There is a special palette control available in any of the image view modes This control helps in modifying the brightness and contrast values of all images in the current view Visible in Projected potential Chapter 7 2 Exit wave function Chapter 7 3 and HREM image views Chapter 7 4 The following 3 screenshots show the way of changing the brightness and contrast by dragging one of 3 sliders on the left side of the control The slider in the middle remains equidistant from the upper and lower sliders when dragging one of these two sliders During dragging the middle slider the program tries to keep distances to upper and lower sliders equal except in the cases when upper slider reaches the upper bound and then remains at the same position or when the lower slider reaches the bottom bound and then remains at the same position Neutral positions of palette Dragging the upper slider Dragging the bottom slider sliders down up 3 7 Contrast Transfer Function view 3 Docking panes This chapter describes the available Docking panes MEENE GES COUT Que DORE They can be used when simulating HRTEM images and electron diffraction patterns as described in Chapter 4 3 1 Microscope docking pane This pane is d
11. the user can E specify the radii of the visible resolution Red i A Switches ON OFF the coloring of reflections If the button is ON then all reflections will be colored according their crystallographic phases Red color corresponds to close to 0 blue close to 180 1 close to 270 and green close to 90 Default is OFF Centrosymmetric projections will only show red and blue reflections Note Coloring is available for solid spot and disk mode only 1 e not the middle one of the three opion l Switches ON OFF taking the Ewald sphere into account If the Ewald sphere is in the OFF mode the High Order Laue Zone HOLZ reflections cannot be observed but on the other hand all reflections as far out as they have been calculated are seen for the zero order Laue zone ZOLZ Green i Blue 2 9 4 9 5 Simulator Reciprocal space viewer 9 2 The Preferences menu In addition to the functions of the Reciprocal Space Viewer toolbar described above several other diffraction type visualization modes are available through the Preferences of the main menu These modes are Set scale D VIEW Regular 2D diffraction mode default Can be controlled using the Diffraction pane see 9 3 1 Kikuchi lines Can be controlled using the Kikuchi pane see 9 3 2 Rotation mode and Rotation animation In rotation mode the electron beam 1s rocked back and forth in one direction or equivalently the
12. 2 The upper limit of the slice thickness can be estimated as Az lt 2Ar A where Ar is the distance within which the potential doesn t change appreciably In case of 300 kV electrons and Ar 0 1 A we have Az lt 1 An acceptable accuracy is typically achieved when the slice thickness 1s chosen as the radius of an atom 1 e 1 2 Artificial HOLZ reflections may appear in case the slice thickness is too big or if the resolution is too high 6 16 6 17 Multislice calculations sesssssssss 44 4 444 a v rit ttt e o ss i ss s 3338 _cee eeo essessesessesss 7 8 titi tit thd amp MgO 001 simulated electron diffraction pattern The contrast of the diffraction pattern to the right is enhanced with respect to the left pattern The HOLZ rings can be clearly observed The slice thickness was too big and the selected resolution was too high This led to the leak of some intensity from ZOLZ into HOLZ which is incorrect in this case 6 17 7 1 Reviewing the calculation results 7 Reviewing the calculation results This chapter explains how to inspect the results of calculations na different SO Et Ing viewing options They are activated using any of the options 7 1 Adjacent cells The user can create a view with several cells adjacent one to the other Default value is 1x1 single cell In order to modify the number of adjacent cells the user should click on the Adjacent cells button o
13. 3 Toolbars The following two toolbars are available when Simulator starts Multislice toolbar and Image properties toolbar If you observing an electron diffraction pattern then the third toolbar becomes visible Reciprocal space viewer see Reciprocal space viewer Chapter 9 for details If no previously calculated data is available then the Multislice toolbar will have the following appearance Some of the buttons are disabled Some buttons become available only after some calculations have been done These buttons are also available when you save your calculation data on the disk In this case Simulator checks these files during start and loads the corresponding data from disk Run CIF Proj Wait ing is Most of the buttons are enabled 2 3 2 4 Contrast Transfer Function view 2 4 Multislice toolbar buttons description Calculation button Run Performs the multislice calculation with given settings see chapter 6 Change settings button Modify most of the multislice settings here see chapter 5 Contrast Transfer Function CTF view Modify some settings of CTF and observe the CTF curve in real time for the selected microscope see chapter 4 Projected potential view Observe the calculated projected potential see section 7 2 Exit wave function view Observe the calculated exit wave functions for selected thickness values see section 7 3 High resolution electron microscopy HREM im
14. Microscope E Hitachi E JEOL Philips H Topcon Voltage kV Cs mm 200 i i CAP NUM SCRL 08 53 18 7 5 Reviewing the calculation results 7 5 Montage mode Simulator provides the montage mode to help the user to observe more than one simulated image at the same time You can use the Magnifying glass to Zoom in and out in order to see more simulated images see section 2 5 for details on Magnifying glass Microscope Hitachi H JEOL Philips l Topcon Thickness Voltage kV 200 CAP NUM SCRL 08 53 18 7 5 7 6 Reviewing the calculation results 7 6 Exploring diffraction The Electron diffraction patterns mode can be selected from the Multislice toolbar see section 2 4 Use the thickness slider on the Diffraction pane in order to select the calculated electron diffraction pattern at the required thickness Shown one by one eMap mayenite ICSD 6287 laj x File Edit View Preferences Window Help 8X Dees 2p an KH OF ty Ne CE d EI 3 51 Qi Oo GEF Low 1 ag 4px X Diffraction ax Start page mayenite ICSD 6287 Zone Axis 001 O Draw hkl indices C Draw annotations Convergence Reflection Thickness angle mrad threshol Microscope CTF Diffraction Mayenite electron diffraction patterns Thickness 20 above and 100
15. O on Precession precession pattern at 0 precession 1s Animate precession eMap Mayenite hkl 4 lel xj File Edit View Preferences Window Help A x DaS4 B eoGe F S LCORL A z Start page EE Mayenite hkl Diffraction aX ann AO ASS AG ef cel Mel asd On wel Selle Te eme Saone ES vx Increasing the precession angle will lead to an expansion of the central ZOLZ and even more marked broadening of the FOLZ circle Already at 0 2 precession angle the ZOLZ and FOLZ start to merge eMap Mayenite hkl E la x HH File Edit View Preferences Window Help ale J x Daca e Rle ceGgur LOM s Aa re Start page Mayenite hkl recession Precession angl 0 deg T 0 2 deg 3 deg es Bf Diffraction BH Precession ern swf HO Sera gel Sel Bel sf On wel se Te s Me SAMOA LC ES wm 9 11 9 12 Simulator Reciprocal space viewer 9 5 Symmetry determination from precession patterns The combined information from ZOLZ and FOLZ is very useful for symmetry determination Notice in the case of mayenite above space group 43d a 11 98 A that there are twice as many diffraction spots per unit area in the FOLZ ring than in the central ZOLZ are Notice also that the diffraction spots in the FOLZ are shifted relative those of the ZOLZ This information can be used to determine the space group as described in detail by 7 Experimentally the symmetry can be d
16. XXX exe Both eMap and Simulator require MSXML Microsoft XML engine The redistributable of MSXML is available from the installation CD file msxml msi or from www microsoft com If you have an old version of eMap Simulator you must deinstall that first before installing a new version FF Install the program by clicking on Setup exe setup located in the directory eMap on the CD The program will ask you to choose destination location the default is C Program Files AnaliTEX eMap Use Browse if you want to put the program in another directory or on another drive When the directory and drive are as required click Next Then you will be asked to select program folders under which eMap is run from the Start menu Select the program folder default eMap and click on Finish Copy the manual Multislice simulator 1 0 manual pdf from the directory eMap on the CD into the directory to where eMap exe is located 1 1 2 1 Contrast Transfer Function view 2 User interface The Multislice Simulator as any other processing module can be started from the Start page by clicking on the Dynamical simulation link NOTE This page will only appear if the MS Internet Explorer is installed In case eMap will fail to locate the Internet Explorer then the simplified Installed components dialog will appear eMap Start page File Edit View Preferences Window Help Dla i AnaliteX Crystallographic computing Recent files Module
17. age Observe the calculated HREM images for selected thickness and defocus values see section 7 4 Electron diffraction pattern Observe the calculated electron diffraction patterns based on the calculated Exit wave functions for selected thickness values see section 7 6 Crystal structure view for current zone axis only See the structure from the present direction zone axis Microscopes docking pane Specify the electron microscope to be used in the simulation see section 3 1 Adjacent cells dialog Select the required number of adjacent unit cells see section 7 1 2 5 Contrast Transfer Function view 2 5 The second available toolbar in Simulator allows working with calculated images Working with the image toolbar See Chapter 7 for full details Standard arrow pointer Magnifying glass zooming in and out Zooming in is done using the Magnifying glass on the toolbar and then clicking anywhere within the image NOTE the cursor will change from standard to the magnifying glass with a symbol inside Zooming out can be done using the same toolbar button and holding the CTRL keyboard button while pressing the left mouse button within the view NOTE the cursor will change from standard to the magnifying glass with a symbol inside Grayscale palette Sets the colors of the current image view into grayscale Color palette Sets the color palette of the current image view Resets the palette
18. ated HREM images The exit wave functions will be displayed only for specified thickness values A set of images will be shown if you have specified a range of focus values so called Montage mode see Chapter 7 5 A re arr F air dase E eMap mayenite ICSD ar 6287 cif k gt e Ci RSS aD ene TRUE gt File E Vie File Edit View Prefer ps sis Run I CIE An amp Xx Hitachi JEOL E Philips E Topcon Thickness 20 Voltage KW Cs mm 200 i CAP NUM SCRL 08 52 34 7 3 7 4 Reviewing the calculation results 7 4 Exploring HREM images The HREM images mode can be selected by Img from the Multislice toolbar see section 2 4 The thickness dependence of the HREM images is represented vertically starting from the smallest calculated thickness top and finishing with the highest thickness bottom The defocus dependence of the HREM images is represented horizontally starting from the smallest calculated defocus left and finishing with the highest defocus value right The user can demagnify by holding down CTRL while left clicking the mouse or use the scroll bars on the sides of the window in order to see all the simulated HREM images The HREM images for the specified thickness and defocus values will be displayed in montage mode see 7 5 3 eMap mayenite ICSD 62 FRERE SES Poe FRERES Eile Edit View
19. below eMap mayenite ICSD 6287 E 4 la xi File Edit View Preferences Window Help a T D eh Sap fn CF fs a mE HIT 38 S RIHO o GEF s Low lowang p 4b xX X Diffraction aX Start page mayenite ICSD 6287 Zone Axis 001 O Draw hkl indices C Draw annotations Convergence Reflection Thickness angle mrad threshold LT 0 010 fo 100 0 i 4 Microscope Z CTF ZE Diffraction m shart step end 20 2U 100 If you specified 5 thickness values in Mo see Chapter 5 1 then there will be 5 thickness values available here 7 6 8 1 Working with non crystalline objects 8 Working with non crystalline objects Simulator is capable to simulate HREM images and electron diffraction patterns for non crystalline objects and nano materials This chapter presents an example of simulations of 7 shell gold nanoparticle eMap Au gold 7 xyz D if a Vi v c lt H Voltage k 5 ooo Cc mm n Convergence mrad Company es Unknown Energy spread e Model Output pane i Unknown HREM image for t 103 0 and def 650 0 A saved to Au gold 7 1030 650 hrem successfuly a HREM image for t 103 0 and def 600 0 A saved to Au gold 7 1030 600 hrem successfuly HREM image for t 103 0 and def 550 0 A saved to Au gold 7 1030 550 hrem successfuly HREM image for t 103 0 and def 500 0 A saved to Au gold 7 1030 S00 hrem
20. ccessfuly HREM image for t 103 0 and def 500 0 A saved to Au gold 7 1030 500 hrem successfuly HREM image for t 103 0 and def 450 0 A saved to Au gold 7 1030 450 hrem successfuly H 4 gt bt Output lA 5 iul L Ready CAP NUM SCRL 14 03 48 7 shells Au nanoparticle electron diffraction pattern The Reflections threshold was manually changed to 0 0025 8 3 Simulator Reciprocal Space Viewer Simulator Reciprocal Space Viewer 9 1 Simulator Reciprocal space viewer 9 Simulator Reciprocal space viewer The reciprocal space viewer module is designed for the visualization of reciprocal space If you have just been running multi slice simulations it is best to close down and restart eMap else the Diffraction panes seen to the right of the figure below will not be displayed Click on the 2 E start page icon and then open a file by i for example C Program files Analitex eMap Examples mayenite hkl eMap Mayenite hkl Oo 13 x f Fie Edit View Preferences Window Help amp x DES amp R cs e ZEL s Lols L Ee Start page EH Mayenite hkl Diffraction ax ZONE 0 0 1 L 0 HKO 4046 8093 2023 4046 1012 2023 506 1012 253 506 e 126 253 63 126 0 63 aued saipadosd 4 2 0 d 2 6766 ee Fhkl 69 83 Pha 45 C Draw hkl indices brew annatatic LAVRA Voltage kv Thickne Intensity 4876 23 ang
21. diffraction pattern around the z axis which always points into the screen Useful when comparing with an experimental diffraction pattern ZONE 1 0 0 In plane rotation of the H 0 0KL 0 8 0 d 1 4963 Rotation about vertical and horizontal axes 9 2 9 3 Simulator Reciprocal space viewer i Mouse zooming Clicking and holding the left mouse button on any point on the main view Will fix the Starting reference point for the zooming The left mouse button should be pressed and held down during the whole zooming procedure Releasing the left mouse button will stop the zooming Moving the mouse towards the centre of the diffraction pattern from the Starting point will zoom down the diffraction pattern while moving away from the centre will zoom up Spot amplitudes mode Can be F structure factor amplitudes or default F squared structure factor amplitudes Switches ON OFF the displaying of the in plane axes Switches ON OFF the displaying of the resolution circles Spot visualization mode Clicking on the arrow will bring up an extra small toolbar where the user can choose the corresponding mode 3 different visualization modes are available 1 solid spot mode 2 Gaussian shape grayscale mode and 3 disk mode 9 3 9 4 Simulator Reciprocal space viewer gt Ewald sphere OFF only ZOLZ is seen Specifies the current zone axis indices Shows the dialog box where
22. e to the energy spread of the electron source or instabilities of the objective lens current In this case the spatial extent of the electron source is large and the image can be considered as incoherent when formed with different defocus and with electrons emitted from different positions on the electron source The resulting image 1s given by the average of the set of images formed for all angles of incidence and defocus values NOTE The non linear imaging will be used when TCC is selected in the Imaging property page 5 15 Multislice calculations 5 3 Objective lens setup NOTE Both 2 fold and 3 fold astigmatisms and coma are available only for the Linear imaging in the current version of Simulator After click on Objective lens Multislice settings Zone anis Objective lens Imaging Objective lens Astigmatism 2 fold 3 fold Coma Beams pendellosung Ampi 3l A 0 A 0 A Direction 0 deg 0 deg 0 deg 5 4 Pendellosung plots The user can specify the beam s the amplitudes and phases of which should be kept during the multislice calculations for every calculated slice In this case the information will be stored in the file Pendellosung XXXX dat in the same folder as the loaded structure file After click on Beams pendellosung The reflections can be defined in two different ways e Defining 3D Miller indices of the reflections by filling in the left 3 boxes with h k and l indices In this case the 3D indices
23. enite ICSD 6287 cif Aluminium cif MgO CIF Au gold 15 xyz MoO3 cif FE Boron pdb NbSe2 1T P 3m1_164 CIF Brownmillerite cif NbSe2 1T P 3m1_164 XYZ Ca3C0206 cif A NbSe2 2H X Z c diamond ins si ins 3cas ins Si XYZ La Co304 icsd_69371 cf Silicon ins coesite ins SiO2 xyz A Coesite XYZ 505 ins coesite rect ins 7102 CIF t ii gt File name Files of type All supported files xml xyz pdb ins cf at AT files at CIF files cif INS files ins PDE files pdb ATZ files xyz AML files xml All tiles Simulator will start with an empty page if you click on the Dynamical simulations link on the Start page In this case you should open your file with structural information If you can find the file you previously opened on the Start page then you can open it directly in Simulator by clicking on the file name in the Recent files column of the Start page In this case Simulator will load and display the crystal structure read from your file 2 2 2 3 Contrast Transfer Function view Open the file Mayenite ICSD 6287 cif and you will see this r Z eMap mayenite ICSD 6287 cif l LA i File Edit View Preferences Window Help Run zx CTF Proj Ex Img a cope eN ET Microscope ff Hitachi JEOL Philips Topcon Voltage kV Cs mm 200 fi Ce mm 1 Microsc a F Diffracti CAP NUM SCRL 08 43 38 2
24. esigned to work with microscopes The user can e Browse microscopes in the Tree control Edit selected microscope parameters e Create a new microscope with specified haa A F parameters W Hitachi J e Save the existing updates JEOL os 2000Ex 201 0 HR 201 0 HT z 2010 UHR 2010F HR 201 0F HT 2010F UHR SO0 F UHR 3010 HT z Voltage ki Ls mm 200 i Microscope m Convergence mad Company 0 5 Unknown Energy spread Model i U nknown cu CTF Diffracti 3 7 3 8 Contrast Transfer Function view 3 2 Contrast Transfer Function CTF docking pane This pane is designed to work with the Defocus Convergence o El El Chromatic Envelope Spatial Envelope parameters of the Contrast Transfer Function CTF The user can Change the defocus value by dragging the Defocus slider Manually edit the defocus value by typing in the edit box under the Defocus slider In order to apply changes the user must do a mouse click outside the edit box The defocus values are in nm Change the convergence angle value by dragging the Convergence slider Show hide the Chromatic and Spatial Envelopes by marking unmarking the corresponding check boxes Set the defocus value to the Scherzer defocus by pressing the Scherzer button All changes will be applied to the CTF plot in run time see section 4 However they will not affect the image
25. etermined from such precession patterns by the program Space Group Determinator from Calidris Sollentuna Sweden An example is shown below 9 6 Precession electron diffraction pattern of Mayenite along 111 Mayenite_111 tif 746H721H6 1 2 Suggestions from intensities Trigonal m 3m 0001 ubic m 3m 111 11 22 Partial space group symbol from extinctions ALZ0L2 0 94 h k l 3n RIHOLZ 1 54 ken Trigonal 0001 hA Cubic 111 1 Here the symmetry is 6mm in the ZOLZ but only 3m in the FOLZ This excludes tetragonal and hexagonal space groups but allows trigonal and cubic space groups The systematic absences analysed in the bottom window are only compatible with rhomohedral in hexagonal setting 001 and I centered cubic along 1 1 1 9 12 10 1 References 10 References Z L Wang Elastic and Inelastic Scattering in Electron Diffraction and Imaging Springer 1995 476 pp E J Kirkland Advanced Computing in Electron Microscopy Springer 1998 250 pp Roger Vincent and Paul Midgley Double conical beam rocking system for measurement of integrated electron diffraction intensities Ultramicroscopy 55 1994 271 282 Peter Oleynikov Sven Hovmoller and Xiaodong Zou Precession electron diffraction observed and calculated intensities Ultramicroscopy 107 2007 523 533 A PDF file may be downloaded from the home page of Sven Hovmoller http
26. ette ne 7 4 T Montage TMOG asic ccsiace errn an E EEEE R E E A EEE Tn i 7 5 DO ESPORA a A O a ant aces keenest erase eneaetes 7 6 8 Working with non crystalline objects 8 1 9 Simulator Reciprocal space VIC WT na ss esoteitaie na senedesse tante asc setett iena side 9 1 9 1 The Reciprocal space viewer toolbar ccccccccssssessecceceeeeeaeeeseeeeeeeeeeaaeeesees 9 2 D Wie P e RC eee ee 9 5 Des VOIRIE SIGE Pane CHAOS Dii uenen A 9 6 HS MM Tne TOMIEACMOn dialog WANG en os 9 6 9 3 2 The Kikuchi dialog pane cc cccccccsssesssecccceeeeeeeeseesecceeeeeeaeeseeeeeeeeeeaaas 9 8 Oa Tne Precession dialog pane cesses EE 9 9 9 4 Simulating Precession Patterns 8 8 his 9 11 9 5 Symmetry determination from precession patterns 9 12 9 6 Precession electron diffraction pattern of Mayenite along 1111 9 12 l O RM CS E E eye te ages E E T E E A E E 10 1 1 1 Installation Simulator is part of the eMap amp Simulator suite of programs for advanced calculations in electron crystallography 1 Installation Simulator runs under Windows 2000 XP and Vista About 65MB of hard disk space 1s needed for the whole package eMap and Simulator programs NOTE Windows 2000 users may need to install Windows Installer 3 1 available on the CD The latest redistributable version of Windows Installer is available from the www microsoft com web site or from the installation CD file WindowsInstaller XXX
27. k and the stereographic projection will be reoriented with that zone axis given at upper left at its center pn wa a TITI te ma iyah De a 4 mines K x an C Draw hkl indices Draw annotations Convergence Voltage kY Thickness 4 angle mrad Press and Simulator will display the j l electron diffraction pattern along that zone axis 0 010 200 00 33 00 EH Diffraction BH Kikuchi lines EH Precession The Diffraction dialog pane 9 6 9 7 Simulator Reciprocal space viewer Draw hkl indices does just that Draw annotations toggles on off all the descriptive text on the screen 4046 8093 3 13 0 d 0 8972 2023 4046 Fhkl 1 26 Pha 90 1012 2023 Intensity 1 5876 etc hho 9 8 Simulator Reciprocal space viewer 9 3 2 The Kikuchi dialog pane Kikuchi HOL lines 1 x fy A Kikuchi li Hiie d ti il TAIR Convergence Kikuchi line angle mrad Le rey L show disk circles LI HOL lines HOL shift Max HOLZ index RE Above Kikuchi dialog pane Below Central beam highly magnified using k Kikuchi lines are useful for crystals with small unit cells 1 e lt 8 A or so Preferences KikuchifHOLe lines The Kikuchi dialog pane allows the user to control the disk size convergence angle the threshold for Kikuchi lines and HOLZ lines visualization mode Checking the HOLZ lines will show the central disk O00 spot enlarged NOTE
28. le mrad Output pane ax map initialization succeeded ile C Program Files Analittex eMap iMayenite hkl has been loaded Tir H 4 gt M Output JEI Ta CE com L EH Kikuch E Ready CAP NUM SCRL 18 43 44 start Desktop GLORE F Erec EJ Eudora SjeMap m emap an 2J Search R Elema cS anodi 8 33 14 9 1 9 2 Simulator Reciprocal space viewer 9 1 The Reciprocal space viewer toolbar These icons give direct access to many of the functions available under Preferences SG Blip oeoo H F Lloje La The normal mouse pointer for picking reflections on the diffraction pattern Placing the mouse pointer over any reflection high lighted in yellow on the main view will display the corresponding reflection information in the right bottom corner of the view This information includes the Akl Miller indices of the reflections the d value in Angstroms the Fyul amplitude of the reflection the crystal structure phase and the kinematical Intensity usually projection view see section 9 3 1 for details and then pressing display the corresponding direction zone axis Free rotation tool around x y axes for navigation in reciprocal space Directly related to the rotation of the crystal in an X ray diffractometer or an electron microscope In order to get the correct results the Ewald sphere toolbar button should be switched ON see below page 9 4 Sea rotation 1 82
29. main parameters of the CTF in real time for the selected microscope using CTF See section 3 2 for the details on the properties of the CTF docking pane eMap Au gold xyz UT 0 tl 1 L 0 0 1 0 2 0 3 0 4 0 5 0 map initialization succeeded Diffraction pattern for t 103 A loaded from Au gold 7 1030 diff successfuly 1A 2 M A ctr Diffraction H 4 M Output 2 CT CAP NUM SCRL 13 55 31 Ready 4 10 5 11 Multislice calculations 5 Multislice settings This chapter explains the basic settings which the user can change in order to achieve the required results using the multislice method implemented in the Multislice Simulator The dialog with all available settings can be opened using the Settings default when entering the Multislice settings 5 1 Zone Axis settings This property page can be used for modifying the basic settings of the multislice calculator related to the crystal direction Among them are The Zone Axis can be changed using 3 indices u v and w The reciprocal resolution g max limits the total number of beams to be used in the calculations in reciprocal Angstr ms g max 2 corresponds to a maximal resolution of 0 5 A Multislice settings X o gt AONE anis maging Objective lens LI y W Beams pendellasung mere Eg po EE ee Eu Act Multislice settings Split cell by 12 slices C use absorption shart step end Thickness 20
30. n the Multislice toolbar see section 2 4 The following dialog will appear Using the mouse one can choose the required number of cells in both x and y directions by holding the left mouse button and moving it across the dialog box In this case the number of adjacent cells changes dynamically and will be accepted when the user releases the left mouse button The other way of choosing the number of adjacent cells is by clicking within the corresponding square in the Adjacent cells dialog box Adjacent cells The Adjacent cells dialog with 3x3 cells selected 7 1 7 2 Reviewing the calculation results 2 Exploring projected potential The Projected potential mode can be selected by Pros from the Multislice toolbar see section 2 4 A single image will always be shown Microsco BX FT ape Microscope E Hitachi JEOL Philips Topcon Voltage KW Cs mm 200 1 Cc mm L Microsc CTF 2 Diffracti CAP NUM SCRL 08 51 25 7 2 7 3 Reviewing the calculation results 7 3 Exploring the exit wave function The Exit wave function mode can be selected by Kat from the Multislice toolbar see section 2 4 The thickness dependence of the exit wave function is represented vertically starting from the smallest calculated thickness top and finishing with the highest thickness bottom The user can lower the magnification or use the scroll bars on the sides of the window in order to see all the simul
31. onding files for later use 5 2 2 Aperture The aperture radius value is in reciprocal Angstrom A It is possible to specify the centre of the aperture by changing the centre h and k values NOTE These values can be real The 00 setting corresponds to the aligned aperture position Multislice settings Zone ati Imaging Objective lens Defocus Beams pendellosung step end meh 50 450 Save HREM Aperture radius 1 Imaging amp Linear Envelopes lf Chromatic aberration i Spatial coherence Cancel Help 5 13 5 14 Multislice calculations 5 2 3 Linear imaging Finite energy spread envelope function Ee chromatic aberration envelope E u exp s n where is the defocus spread Finite size of the electron source E spatial coherence envelope E u Af expt mAy u af C Ru Py where Af is the defocus value so is the convergence angle C 1s the spherical aberration Perfectly coherent illumination transfer function T u Af A u exp iz u Af JIE u Af JE u Scherzer defocus AF scherzer aal 2 V CA Lichte defocus AF tiche 0 75C u A max where Umax 1S the maximum transmitted spatial frequency 5 2 4 Non linear imaging for partially coherent and incoherent illuminations Takes place in case when we need to take into account the effects associated with the finite size of the electron source beam divergence effects and fluctuations of defocus spread du
32. responding 5 thickness values are 20 A 40 A 60 A 80 A and 100 A The diffraction patterns can only be shown one by one see Chapter 7 6 while the others can all be seen in Montage mode see Chapter 7 5 1 e all at the same time NOTE The use of absorption during the structure factors calculation is not available in the current version of Simulator The slicing scheme used in the current version of Simulator assumes that if the cell extension in the projection direction is larger than 20A the user should consider using the 3D potential In this case a WARNING will appear as this WARNING C parameter of the projected cell is 177 54 A Sub slicing is probably needed NOTE the 3D potential calculations are not available in the current version of Simulator 5 12 5 13 Multislice calculations 5 2 Imaging The Imaging property page allows the user to control the settings for the HREM images during the multislice calculations Click on settings and then Imaging 5 2 1 Defocus The defocus range can be assigned by selecting the starting point start the finish end and the step between start and end If only one defocus value should be calculated then the start value must be equal to the end value If the step is set to O and the start is different from the end then only 2 defocus values will be calculated The Save HREM check box sets the flag that indicates if the calculated HREM images should be saved in the corresp
33. ssive summation of a large number of different electron diffraction patterns In order to see the same thing in the electron microscope the precession must be slowed down to about 1 Hz For more information about the precession technique see the home pages of NanoMEGAS at http www nanomegas com 9 9 9 10 Simulator Reciprocal space viewer The pink circle is centered on a small red cross at the distance corresponding to the respective tilt in degrees It is shown only when the Spot visualization mode is set to the right e 1 At 0 precession right the electron diffraction pattern is just the normal selected area electron diffraction SAED pattern 2 As the precession angle is increased middle the momentary electron diffraction pattern looks more and more misaligned Notice also that the highest resolution reflections are further out with Precession ON 3 When the precession angle is even larger left the FOLZ reflections marked red here start to appear at high resolution 9 10 9 11 Simulator Reciprocal space viewer 9 4 Simulating Precession Patterns When simulating electron precession patterns the most Preferences Window clear patterns are obtained when choosing Data type 2 S Fhkl a LF and Rendering Greyscale Ok For the mineral mayenite along the 011 zone axis the D view Kikuchi lines Rotation Rotation animation
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