eMap user`s Manual
Contents
1. First select one or several atoms as shown below 1 0 1 0 J 0 1 0 1 0 1 0 1 0 1 0 4 32 User s Manual eSlice v 1 0 Then mark the Free var check box against the atomic parameters that should be assigned Uiso in our example Uso Refine C B Oren Please note that after the Free var has been checked the combo box on the left side from the check box became enabled Click on the combo box This will bring down the list of available global variables Select Nb_Uiso from the drop down list list gt mo Jone Uso ee Pre mm Frevar mm ieem NOTE the check box Refine will be hidden by the program for Uiso value because now it cannot be refined since it is referred to the global variable Nb_Uiso Please note that all Uiso values in the corresponding column for all Nb atoms in the table have changed their values to 0 12 which is the value of the global variable Nb_Uiso 4 33 User s Manual eSlice v 1 0 1 0 1 0 1 0 al 0 1 0 1 0 1 0 JL 0 NOTE All original Uiso values for all selected Nb atoms will be overwritten by the value of Nb_Uiso 0 12 in this example In order to restore the original values the user must reload the project 4 5 6 The Refinement tab The Refinement tab displays all information during the refinement 4 34 User s Manual eSlice v 1 0 Thickness A Visualize check box The Visualize c2. Crystal data Space Group P4 mbm 127 Tetragonal a 275A a 90 b 27 5 B 90 Unit Cell c 3 94 y 90 V 2979 625 Atoms data Formula K7 68 Nb56 8 0146 K0 96 Nb7 1 018 25 Z8 The information on the Crystal Structure tab is general and thus is not editable 4 22 User s Manual eSlice v 1 0 4 5 2 The Zone Axis tab The Zone Axis tab displays all information about the selected zone axis Crystal Structure Zone Axis General Variables Atoms Refine Zone axis d spacing Preview Wilson Plot Progress a axis Min d value Max d value m1 Jefo Jefo oss6a7 A 275 A b axis Omit reflections tlo Jef Jeo h 0 k 0 t o Sna Add _ Remove u 0 v 0 w 1 z0 1 Plane Cell 1 0 0 0 1 0 20 275 0 10 b 25 11 0 SS 1 1 0 y 90 j 1 1 0 1 1 0 Other parameters h tilt 0 M Refine 24 3 0 0 2 0 k tilt 0 M Refine thickness 425 52 Refine FF Max thickness 500 Try This dialog is the most complicated and the most important in the program Since eSlice accepts only 2D electron diffraction intensities data it is crucial to set the correct hkl indices for a and b reciprocal axes and the place unit cell parameters a b and y The correctness of these parameters can be controlled on the right side in the Preview panel 4 23 User s Manual eSlice v 1 0 The Z
3. eSlice Dynamical Refinement User s Manual v 1 0 Copyright 2003 2011 AnaliteX AnaliteX Crystallography Software November 201 1 Visit our web page at www analitex com User s Manual eSlice v 1 0 Table of Contents ME PRIOR E A E ee 2 4 1 1 General introduction 2 4 1 2 Support offerings 2 4 1 3 Reporting problems 2 4 2 istallat on te i oa ces eet ese a a a 2 6 2 1 Installation 2 6 2 2 Numbers format in eSlice 2 6 22 1 Widlows XP nn ue 2 7 2 2 2 Windows Vist siiin din 2 9 2 2 3 CANIN ST 2 nu 2 10 Supported file formats a ennuis 2 10 3 1 Native format XESLICE 2 10 3 2 Crystallographic file types 2 11 3 3 Experimental intensities files 2 11 THE SP fc SP ee nT eee 4 13 4 1 The program start 4 13 2 2 User s Manual eSlice v 1 0 4 2 4 3 4 4 4 5 Creating a new project Loading existing project The toolbar The main window 4 5 1 The Crystal Structure Mb menidene 4 5 2 The Zone Axis tab 4 5 3 The General tab sise 4 54 The Variables tab iii ASS The Atoms tabescere ennie ae a 4 5 6 The Refinement tab sise 5 RAMDIOS dd E E Suggested SATS non nant 4 15 4 17 4 19 4 20 4 21 4 23 4 25 4 27 4 28 4 34 5 40 5 42 2 3 User s Manual eSlice v 1 0 1 Preface This preface provides information about the The eSlice Software User s Manual and links to AnaliteX technica
4. Location To help services provide you with local information such as news and weather select your present location Click Customize button This brings up the Customize Regional Options another multi tabbed dialog box 2 8 User s Manual eSlice v 1 0 Positive 123 456 789 00 Decimal symbol No of digits after decimal Digit grouping symbol Digit grouping Negative sign symbol Negative number format Display leading zeros List separator Measurement system Negative 123 456 789 00 2 v 123 456 789 0 7 Change the comma to the dot if not already and press OK button 2 2 2 Windows Vista Similar to Windows XP except that the Customize button becomes Customize this format button 2 9 User s Manual eSlice v 1 0 2 2 3 Windows 7 Similar to Windows XP except that the Customize button becomes Additional settings button 3 Supported file formats The Software supports several file types as input data 3 1 Native format XESLICE The native format for eSlice is the XML file format with custom file extension xeslice The Software will produce files in this format automatically on exit from the Simulator asking for the user s permission to save XESLICE XML files contain all the Software project settings Any XESLICE file keeps crystallographic information about the loaded crystal st
5. 5 The main window After successful loading or project creating the main window of eSlice will look as shown below Zone axes Variables Atoms Parameters Zone axes files iv a 1 0 0 b 0 1 0 saed_O0Lhke The panel on the left contains the general information about the loaded crystal structure and all loaded experimental intensity files zone axes files 4 20 User s Manual eSlice v 1 0 Zone axes Variables Atoms Parameters Zone axes files 1 0 0 b 0 1 0 seed COL hike General information Loaded zone axes The right panel is designed in the form of a tab panel that allows an easy access to all refinement setting The detailed information about the selected zone axis in the Zone axes files list can be reviewed in the Zone Axis tab 4 5 1 The Crystal Structure tab The Crystal Structure tab displays all general information about the loaded crystal structure e The full file path on the disk e The file name 4 21 User s Manual eSlice v 1 0 e The symmetry the space group the space group number and the symmetry e The unit cell e The unit cell volume e The chemical composition full and single unit e The number of units per unit cell Z Crystal Structure Zone Axis General Variables Atoms Refine Crystal structure info General File D Work eSlice KNbO icsd 8005 K cif Title icsd 8005 K cif
6. following steps describe how to add a new global variable into the list e Click inside the first cell in the Name column in the first row of the table with a text Click here to add a new row e Enter a name of the new variable for example Nb_Uiso 427 User s Manual eSlice v 1 0 e Click in the next column Value of the same row and enter the value 0 12 in our case Next section will describe how to assign the created global variables to the selected atom s in the Atoms tab 4 5 5 The Atoms tab The Atoms tab displays all information about the atoms in the loaded crystal structure model file Hee er re ee et ee tee 19 9 9 9 9 9 9 o o in o in ooo ww uw Hee ee re te ee ee andi Dandi andi Lai ian 4 28 User s Manual eSlice v 1 0 The global variables become important if for example we want to fix the Uiso to the same value for all K atoms we can create a global variable and assign it to all K atoms In this case the program will use the value of this variable during the refinement and ignore the loaded Uiso for K atoms Enable All button will mark all atomic parameters that can be used in the refinement as refined variables Disable All button will remove marks from all atomic parameters so that none of atomic parameters will be used during the refinement NOTE In ca
7. 7 5 and y 90 Adjust these parameters if needed Set the Maximum thickness to 500 A and evaluate the optimal thickness by clicking the Try button 5 40 User s Manual eSlice v 1 0 Mark the h tilt and k tilt check boxes Go to the Atoms tab Mark the atomic parameters which you wish to be refined or alternatively click Enable All button Go to the Refine tab mark the Visualize check box and click the Refine button The program will start the refinement which can take some time depending on the CPU and the total number of parameters to be refined NOTE the refinement time may take from 30 min up to 2 hours depending on the complexity of the structure the number of zone axes and the total number of parameters 5 41 User s Manual eSlice v 1 0 Suggested literature 1 Z L Wang Elastic and Inelastic Scattering in Electron Diffraction and Imaging Springer 1995 476 pp 2 E J Kirkland Advanced Computing in Electron Microscopy Springer 1998 250 pp 3 Marc De Graef Introduction to Conventional Transmission Electron Microscopy Cambridge University Press 2003 718 pp 4 L M Peng S L Dudarev M J Whelan High Energy Electron Diffraction and Microscopy Oxford University Press 2004 536 pp 5 P Oleynikov eMap and eSlice a software package for crystallographic computing Crystal Research and Technology 46 2011 569 579 5 42
8. cial position 0 0 5 0 then it would not be possible to edit the corresponding coordinates 4 30 User s Manual eSlice v 1 0 4 5 5 2 Selecting and editing a group of atoms Any number of rows can be selected in the atoms table by clicking on the corresponding rows The program will show all atomic parameters available for editing on the right side Selected atoms 8 rows Editable parameters of the selected atoms Only common values are displayed NOTE only same values will be displayed in this case in the edit boxes For example in the figure above all selected Nb atoms have different values for their x and y coordinates but the equal zero value for the z coordinate and 1 for occupancies Thus the x a and y b edit boxes on the right side are empty while the z c edit box shows 0 and Occupancy shows 1 In order to select adjacent rows 4 31 User s Manual eSlice v 1 0 1 Click on the first row to be selected 2 Scroll if needed to the last row 3 Hold the SHIFT keyboard button and click on the last row In order to select separate rows 1 Click on the first row to be selected 2 Hold the CTRL keyboard button and click on other needed TOWS In order to deselect a row hold the CTRL keyboard button and click on row that must be deselected 4 5 5 3 Assigning global variables to atoms The following sequence of actions shows how to assign a global variable to some atomic parameter
9. eneral tab displays all information about 4 25 User s Manual eSlice v 1 0 e The refinement type multislice in the current version of eSlice e The voltage of the microscope in Kv e The maximum number of iterations during refinement General Settings Method Voltage w Max interations The maximum number of iterations is used by the application in order to terminate the refinement in case when the total number of multislice calculations will exceed this maximum limit The default value is set to 2000 The program performs S steps during the refinement Each step requires N 1 multislice calculations where N is the number of variables used in the refinement Thus the total number of iterations is S N 1 If the program will reach the maximum number of iterations specified by the user it will terminate the refinement The number of steps S is not known in advance due to the iterative algorithm of the refinement 4 26 User s Manual eSlice v 1 0 4 5 4 The Variables tab The Variable tab displays all information about the global variables that can be used in the refinement The global variables become important if for example we want to fix the Uiso to the same value for all Nb atoms we can create a global variable and assign it to all Nb atoms In this case the program will use the value of this variable during the refinement and ignore the loaded Uiso for Nb atoms The
10. heck box switches on the visualization of the refinement progress if checked This will update the progress plot and the current calculated diffraction pattern in run time NOTE When switched on the visualization can slow down the overall refinement process due to an extra CPU time needed to present the calculated data to the user This is relevant for the case when the total number of refined parameters is quite small 1 10 and the unit cell is relatively small 5 10 A 4 35 User s Manual eSlice v 1 0 4 5 6 1 Progress tab This tab has a chart that represents the current progress step There are three curves which represent R F as R1 R F as R2 and Ry F as RwF 200 Thickness A The least squares calculation of partial derivatives doesn t updated the chart 4 5 6 2 Diffraction tab The diffraction tab represents the experimental left and calculated right electron diffraction patterns 4 36 User s Manual eSlice v 1 0 Experimental Calculated It is possible to visually compare the calculation progress using these two graphical representations of the observed and calculated data during the refinement 4 5 6 3 Results tab This tab displays the final results of the refinement The first line shows the location of the file where these results are stored on the disk Copy to Clipboard This button will copy the final results into the Windo
11. l support 1 1 General introduction The eSlice Dynamical Refinement Program which we will refer as the Software or simply eSlice further on is a program which allows you to refine atomic and other parameters for a given crystal structure model against experimentally measured selected area or nano beam electron diffraction amplitudes using dynamical calculation methods multislice 1 2 Support offerings You can always contact AnaliteX by email support analitex com 1 3 Reporting problems If you can have problems running The Software or any component please report them to the AnaliteX support team by email support analitex com User s Manual eSlice v 1 0 2 5 User s Manual eSlice v 1 0 2 Installation The Software runs under Windows XP Vista and Win7 and usually included as an optional component in the eMap software package 2 1 Installation Install the program by clicking on Setup exe located in the directory eSlice on the CD The program will ask you to choose destination location the default is C Program Files AnaliteX eSlice Use Browse if you want to put the program in another directory or on another drive Click Next when the program folder and drive are as required Then you will be asked to select program folders under which eSlice is run from the Start menu Select the program folder default eSlice and click on Finish 2 2 Numbers format in eSlice The Decimal symb
12. ol used by Microsoft Windows XP and other versions is determined by settings in the Regional Settings dialog of gt the Control Panel It can be a dot or a comma eSlice 2 6 User s Manual eSlice v 1 0 recognized all numbers with the dot as the decimal separator valid number is 1 2 and is not 1 2 If Windows setting is comma then it must be changed in order to run eSlice correctly In order to check and change this settings do the following 2 2 1 Windows XP Click the Windows XP Start button and then click the Control Panel as shown below Cr contrat Panel Set Program Access and Defaults Help and Support Search IF Run All Programs D Logoff O Turn Off Computer In the Control panel find a link to Date Time Language and Regional Options or Regional and Language Settings 2 7 User s Manual eSlice v 1 0 depending on simple or advanced mode of the Control panel and click on it This will open the following dialog Regional Options Languages Advanced Standards and formats This option affects how some programs format numbers currencies dates and time Select an item to match its preferences or click Customize to choose your own formats Samples Number 1 23 456 789 00 Currency 123 456 789 00 Time 12 30 59 PM Short date 11 Apr 11 Long date Monday April 11 2011
13. one axis indices will be calculated automatically by the program from the provided hkl indices of a and b reciprocal axes If the program will fail to validate the parameters for example if the user will specify the same a and b an error icon will appear 4 5 2 1 Omit reflections It is possible to specify reflections that the program should exclude from the refinement The user can add these reflections by specifying their 2D indices in the Omit reflections area and pressing the Add button Any reflection can be removed from the list by selecting it in the list box and pressing the Remove button Each omitted reflections will be show as a red circle in the Preview tab 4 5 2 2 Other parameters It is possible to refine the beam tilt from the exact zone axis orientation by marking the check boxes next to h tilt and k tilt edit boxes 4 5 2 3 Optimal thickness evaluation Each zone axis must be pre evaluated in order to estimate the best thickness for the refinement It can be done by specifying the maximum thickness Max thickness edit box for the zone axis and pressing the Try 4 24 User s Manual eSlice v 1 0 button This will start the dynamical calculations and will activate the Progress tab After the calculations will be finished the program will evaluate the best R factor and set the thickness edit box to the corresponding value 4 5 3 The General tab The G
14. ructure data needed for the refinement This crystallographic data includes e the reference to the crystal structure model file with the space group the unit cell parameters and the list of all atoms e the reference s to files with experimental two dimensional selected area or nano beam electron diffraction intensities 2 10 User s Manual eSlice v 1 0 e other information related to the refinement the list of free variables TEM voltage and etc 3 2 Crystallographic file types The Software can load files which contain crystallographic information such as symmetry unit cell and atomic positions The file types are CIF XYZ AT and PDB 3 3 Experimental intensities files The Software can load files which contain experimental two dimensional selected area or nano beam electron diffraction intensities information The file extension is HKE and can be described as follows Any line starting with is considered as a comment line and is not considered for parsing during loading The header should have at least 2 lines one with the plane 2D unit cell must start with the comment symbol and contain a b and gamma plane real space unit cell parameters and the other with the data format description as show in the figure below User s Manual eSlice v 1 0 File D Working KNbO SAED dm3 a 27 5A b 27 5A gamma 90 lt Plane 2D unit cell Format hksa lt Da
15. se if only one zone axis used in the refinement the atomic coordinates x y and z enabled for the refinement must be chosen carefully in the current version of the program The reason is that the single zone axis provides only 2D information about the crystal structure For example if the zone axis used in the refinement is 001 then only x and y coordinates can be refined while z coordinate must be remain fixed Such case with a single zone axis 001 in this example must be examined manually because Enable All will mark all coordinates including z coordinate for the refinement 4 29 User s Manual eSlice v 1 0 4 5 5 1 Selecting and editing single atom Any atom can be selected in the atoms table by clicking on the corresponding row The program will show all atomic parameters available for editing on the right side Editable parameters of the selected atom Selected atom row CS Nea 4 0 and Nb3 Nb0e i 1 0 Not Nite fi 1 0 jo No5 NbO Si 1 0 N5 NBO gt amp 1 0 Nb Nb0e amp 1 0 sh NES Nb0e amp 1 0 oi e 2 1 0 os OS 02360 mm 02 O0 dh 1 01976 06976 05 02439 o3 o 1 0228 09377 OS 0 1916 ot o 1 03653 09601 OS 01916 os e 2 0052 0721 OS 02360 06 gt fi 2 01975 08273 OS 02044 Some parameters will not be available for editing For example if the atomic coordinates are restricted by the symmetry as shown in the above figure Nb1 atom is in the spe
16. ser s Manual eSlice v 1 0 4 3 Loading existing project If the Open Existing Project button has been pressed then the following standard Open File dialog Windows 7 will appear nl 4 ppna v 4 s kim 5 p Ordna Ny mapp a m my Hamtade a TERT Bibliotek Work De Mapp IM 5 Bibliotek z Bilder Namn Senast ndrad Typ Storlek Dokumen L im 5 xeslice 2011 12 2311 50 XESLICE fil H Filmer d Musik 8 My docur ia Structures a TODO list 6 Visual Stu 13 Work ERI m Filnamn eSlice project files xeslice Ca ar The dialog by default will only show files with the standard eSlice project file extension XESLICE During the project loading eSlice will block the user interface by a special overlay as shown below User s Manual eSlice v 1 0 aE esie m5 Anm Please Wait Cancel The loading operation can be terminated by pressing the Cancel button 4 18 User s Manual eSlice v 1 0 4 4 The toolbar There is only one toolbar in eSlice The following table describes each button in the toolbar Description Toolbar button New project Launches the Create New D Project dialog Open project Shows the Open existing project dialog Save project Saves the current project data Close project Closes the existing project E User s Manual eSlice v 1 0 4
17. ta format line 5h k lobs zs 0 al 1000 1000 0 2 2000 2000 L J L J L J L J j T Y Y h k lobs lest h and k are is for h and k 2D Miller indices s and a are for the observed and estimated intensities Each data line should contain single reflection information The content of each data column is explicitly described by the Data format line 2 12 User s Manual eSlice v 1 0 4 The user interface The Software has several ways for data handling and calculations The following paragraphs will explain every command available in more details 4 1 The program start At the program start the following splash screen appears pm a eSlice version 1 0 ti Analite Crystallography Software After the program initialization is completed the Startup Dialog will be shown by the program 4 13 User s Manual eSlice v 1 0 KNbO Last accessed 12 20 2011 11 31 31 AM Double mouse click to load Recent files list Here the user can create a new or open an existing project or exit the program The buttons on this dialog are self explanatory and don t need to be introduced The left side of the dialog contains the recent files list After a new project has been created or an existing project has been loaded the program will add them into the recent files list for faster access next time the program will start Any project in this list can be loaded immediately by do
18. uble clicking on the corresponding item in the list User s Manual eSlice v 1 0 4 2 Creating a new project If the Create New Project button has been pressed then the following dialog will appear Browse buttons No Folder No Structure model file No Title The tooltip Empty title is not allowed The dialog by default has all fields empty The Folder and the Structure model fields cannot be entered using the keyboard however they can be changed using the corresponding Browse buttons LJ The Title field must be changed manually from the keyboard It will represent the file name of the project to be stored on the disk in the folder specified by the Folder field The Description field is not obligatory and represents some comments related to the project User s Manual eSlice v 1 0 NOTE the Title cannot contain special symbols that Windows uses in the file system for example V and etc would be forbidden The program will show the error icon in case of any error NOTE The dialog will not accept the OK button click until all fields Folder Structure model and Title are correctly set An example of the valid dialog fields is shown below Here the folder selected to keep the project files is E Work KNbO and the project title is KNbO When the user will press the OK button a new project file will be created and stored as E Work KNbO KNbO xeslice U
19. ws clipboard so that this text can be inserted elsewhere 4 37 User s Manual eSlice v 1 0 The results file The total refinement time The list of refined parameters The list of used zone axes The list of used global variables The list of refined atomic parameters 4 5 6 4 Least Squares Refinement The program provides the following R factors which can be used as reliability parameters EJIE EI ROSE 4 38 User s Manual eSlice v 1 0 EIRE F2 Ry SRL FA SIR F2 SUR All these factors can be plotted by the program as their dependency on the thickness 4 39 User s Manual eSlice v 1 0 5 Examples This section will describe step by step example of the refinement of the Koo6Nb70 825 structure The eSlice samples folder contains both files needed for the calculations Create a new folder using the Windows Explorer for example C Work KNbO and copy both files KNbO cif and KNbO hkKe from the eSlice samples folder into the newly created folder Start eSlice software and press Create New Project button on the start up dialog Browse for the created folder C Work KNbO Browse for structure model C Work KNbO KNbO cif Type the title as KNbO Type the description KNbO test project Press OK button Go to the Zone Axis tab Check that a axis is 100 b axis is 010 plane unit cell parameters are a 27 5 b 2
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