ANAELU USER`S MANUAL
Contents
1. Naturally different preferred orientations may be tested in the search for the optimum qualitative fit Patterns modelled by the Programmed Rotations procedure fit well with experimental patterns from sharp axial textures 2D diffraction modelling via Inverse Pole Figure The PF amp IPF window contains a generator of inverse pole figures IPF The user defines the IPF resolution and proposes the number and characteristics of the texture components For each component its width and relative intensity must be entered IPF modelling In the PF amp IPF window the user first clicks Restart IPF To run the demo the user may preserve the default 111 orientation with 3 width and click Pref Pole The program will model and display two different representations of the IPF including symmetry generated multiplicity See Figure 10 wl PF amp IPF Cryst Syst Cubic lt Inverse Pole Figure Resolution 280 Restart IPF fi fi f __ Pref Pole Peak Width 5 Peak Max fi AnglPos 87 64001 Figure 10 Modelling IPF and PFs To become familiar with the IPF generator restart the IPF and try other Pref Pole and Peak Width combinations With a chosen IPF the user can click in Selected PF and see the pole figure PF of a selected family of planes Otherwise the user can click on All PF and XRD to ask the program to calculate all PF and the 2D pattern The2. Y For cubic crystals the 111 direction represents a 3 fold symmetry axis so a rotation interval of 120 120 cycles x 1 cycle will be representative Insert the mouse pointer into the box below the Num of Cycles label the default value of 120 is suggested Re type 120 Insert the mouse pointer into the box below the Num of Sub Cycles label the default value of 3 is suggested Re type 3 As the angular step is 1 the boxes Total Angle and Total Sub Angle will show respectively 120 and 3 Click on Run and wait while Anaelu works For the simulation to work the windows Hybrid Cell and Reciprocal Lattice must be activated Anaelu will generate the 2D pattern of a textured sample This modelling has two stages The user should be patient for both of them Explanation of Stage 1 Rotating the crystal according to user instructions The user has chosen the primary rotation axis step and rotation interval He She has also chosen how much will the crystal depart by secondary rotations or sub cycles from the orientations determined by the primary rotations The program now will rotate around the primary axis and on every step it will execute secondary rotations In every rotation no matter if primary or secondary the program will calculate the positions and intensities of every generated diffraction peak corresponding to the considered crysta
3. 200 sep Coke Ss Color Style E pots 290 step Coke Ss Color Style 7 pots 200 sep Coke Sy Color Style E powts 200 step Physical Rainbow Oe ees con no an OMe ee Color Style J ponts 200 stepfz ICokeSs Color Style ig Hpowts 399 step fg ICoke Sy 4 Color Style 72 pots 200 steps Color S5 a eee Color Style 13 8 ponts 200 ponts 200 stepf Color Ss fig pons 299 step Color S5 Color Style ig Hports a9g stepfz Color Ss Figure 1 Scales and color conventions for plotting 2D diffraction patterns Determination of the diffraction pattern center Several alternatives are possible Mouse pointer selection Hybrid window Click on Beam Centr Click on Click Manual Click on the beam center location The coordinates of the checked point are entered into the Configuration Window and applied to Anaelu Selection of Debye ring points Figure 2 Hybrid window Click on Beam Centr Click on Debye Ring Point and then in a Debye ring representative point Do this several 3 to 30 times Finish the process by clicking Calc Beam Center The coordinates of the calculated beam center are entered into the Configuration Window and applied to Anaelu Keyboard Center coordinates can also be keyed in directly into the Configuration Window After entering the center coordinates click on Ap
4. Powder Pattern button By clicking this button the user asks the program to calculate and display in the ShowCut window a pattern that may be used for comparing model and experiment Peak broadening is calculated as a function of crystal size which can be entered at the low left corner of the Reciprocal Lattice window The program first calculates the pattern as obtained with a conventional diffractometer Then it asks the user if a 2D pattern is needed For the demo to favour time economy it is recommended to answer no to the 2D Detector Model option Check peaks coincidence between experimental and calculated 1D patterns The Hybrid window with the experimental 2D pattern and the ShowCut one with the calculated 1D powder pattern should be activated The rest of the windows may be minimised it is not recommended to close child windows By using the RadCut or the Integrate command from the Hybrid window experimental 1D red diffraction patterns will appear superposed to the calculated blue one See Figure 7 6000000 5000000 4000000 3000000 2000000 1000000 Figure 7 Observed red and calculated blue 1D diffraction patterns Manual rotation of the unit cell and modelling single crystal 2D diffraction spots Crystal orientation is controlled under the View Rotate Cell tab of the Cell window The user may chose to rotate the unit cell in one of th
5. and displays all the atoms in the unit cell The so created cell represents a crystal For the demo it is recommended to preserve the default Pt structure This will lead to fitting results when modelling the experimental pattern Platinum_2D_XRD asc Figure 6 shows a Pt unit cell and its stereographic projection as plotted by Anaelu My Anaelu 1 0 File Config Experiment 5 Cell babaka Edit Cell Rotate Cell Cycle View Rotate Cell Angle 1 Z 359 2568 Angle 2 Y 3501343 zap HKL scan Fom olee M HKL Angle 3 daleer Tob bp iS 353 3265 Reset Calculate Calculate XRD ir HKL tensities Powder patern Rotate To YZ Angles i 010 Reset ngles a b c Trace WAF y 121 411 122 011 i 111 1228 211 peo 211 Oyo 112 012 112 549 201 401 402 ooi 1027101 201 LTTE TTL Fay 112 oS ale 214 switch to s HKL Scan AT a 2a oe 221 Figure 6 Anaelu Cell and Reciprocal Lattice windows Pt crystal Crystal rotations are controlled by the user via keyboard given rotation angles or by dragging the mouse The crystal cell and its stereographic projection rotate synchronically Modelling a powder 1D diffraction pattern With the unit cell in memory the program can now calculate the J 20 diffraction pattern of a non textured powder In the Reciprocal Lattice window near to the upper border there is the Calculate XRD
6. user programs and Anaelu runs a scan of orientations The program calculates the positions and intensities of all the generated reflections The modelled diffraction spots are superposed to the experimental diagram b By using statistical descriptors of a proposed texture Inverse Pole Figure and corresponding Pole Figures Anaelu calculates the theoretical 2D pattern Next different methods for using the software are described The functions of all the windows in Anaelu are presented STEPS TO FOLLOW Unzip the installation file The following files must be located in the same folder P_Anaelu10 exe f d_atm dat TABCTL32 0cx atomic_radi dat mass_atm dat 230 sym files Platinum _2D_ XRD asc an example of experimental data file for training Run the program by double clicking on the executable file When the program starts up it normally takes some seconds activating and minimising all the interior windows It is strongly recommended to work with the operational windows activated opened and all the other windows minimised but not closed The program constantly transfers information among internal windows and if one of them is closed it will pop up and disorient the user Check or edit the correct configuration The first window that must be checked is the Configuration one In this window different constants that describe the experiment are editable These are resolution detector diameter sample detecto
7. ANAELU USER S MANUAL L Fuentes Montero M E Montero Cabrera L Fuentes Cobas Diffraction Group Institute Laue Langevin ILL Grenoble France Centro de Investigaci n en Materiales Avanzados CIMAV Chihuahua Mexico fuentes montero ill fr Anaelu is Software for analysing diffraction patterns obtained with area detectors This Users s Guide complements the article devoted to the presentation of the program The software represents crystalline structures including their stereographic projections and textures with axial symmetry It represents the texture by means of the Inverse Pole Figure of the sample symmetry axis The information that the user must give is a Crystal Space group lattice parameters and asymmetric unit b Texture Miller indexes of the preferred orientation s widths and relative intensities of maxima in the distribution of orientations To characterise the diffraction pattern the software comprises different tools namely displaying radial and azimuthal profiles azimuthal integration zooming on the image and providing information related to the position of the pointer in the pattern Anaelu models diffraction patterns from single crystals and from textured polycrystals For single crystals the user virtually explores orientations and the software generates in real time the positions of the diffraction peaks Laue or monochromatic beam For polycrystals there are two possible paths a The
8. calculation of the pattern may last from a few seconds to a few hours depending on the IPF resolution the 2D pattern resolution and the number of Debye rings For each pixel Anaelu calculates how much contributes each Debye ring and how intense is the ring in the corresponding azimuthal angle Click on All Pf and XRD and wait until the calculated pattern appears in the Model XRD window Analysis of calculated pattern and comparison with the experiment The 2D pattern calculated from IPF can be studied and compared just like it was done with the pattern obtained from a cycle of rotations The user can move the mouse and compare the positions and intensity distributions of peaks can observe cuts and can also ask the program to recalculate with different parameters See Figures 11 and 12 Figure 11 Pt observed 2D XRD pattern and ArcCut 3 eu umha o Boe Bms gt a uw Pz a P len leo ho h h h h o Figure 12 Pt calculated 2D XRD pattern and ArcCut Sample rotation Consideration of samples where the symmetry axis is inclined with respect to the vertical Y axis is possible In the PF amp IPF window entering a certain angle in degrees will rotate the modelled 2D XRD pattern by that amount in clockwise direction The authors of Anaelu are active on expanding and optimizing the program We appreciate possible suggestions and bugs detection from the use
9. e following ways a By dragging the unit cell Dragging with the left button will rotate the crystal in the direction of the mouse movement around an axis perpendicular to the said movement but parallel to the screen Dragging with the right button will rotate the crystal around an axis normal to the computer display b By dragging the mouse pointer over the stereographic projection c By typing the orientation angles that are shown in the Cell window d By clicking the rotation buttons that surround the unit cell No matter how the user rotates the cell the program calculates the corresponding positions of diffracted spots in an area detector in real time The user should imagine that the X rays hit the computer display perpendicularly the user itself is the X ray source and the crystal is oriented just like the shown unit cell in the cell window The positions of diffraction maxima are shown red points in the upper left corner of the Reciprocal Lattice window see Figure 8 o Anaelu 1 0 BCEA k f P gt Reciprocal Lattice Lataa ARD Model AD HKL scan S Froml_s 6 switch to W Laue Tole E HKL list ofe e e Trace Reset Calculate Calculate XRD tensties Powder patern Figure 8 A Pt crystal stereographic projection and its calculated Laue pattern Diffraction maxima also appear as blue spots over the experimental pattern in the Hybrid window See Figure 9 b
10. elow To visualize the diffraction spots it is necessary to have activated the tree involved windows Cell Reciprocal Lattice and Hybrid Programmed rotation of a crystal and simulation of diffraction by a sharp axial texture Crystal initial orientation Simulation of the 2D diffraction pattern from a highly textured sample can now be prepared As a first step the analysed crystal must be put on the appropriate initial orientation For example put the Pt crystal with its 111 direction perpendicular to the sample surface This means that the 111 pole must be located in the upper border of the stereographic projection This exercise may be performed by dragging the mouse pointer over the unit cell or over the stereographic projection View Rotate Cell tab left and right mouse buttons The angular step for crystal orientation control step 1 by default is also applied on the Rotate Cell Cycle tab Edit cycles and sub cycles for simulating a sharp axial texture Consider that the adequate initial orientation has being established In the considered example the crystal direction 111 is parallel to the virtual experiment vertical Y axis For programming the simulation of a sharp axial texture the tab Rotate Cell Cycle must be activated This tab is the second one from left to right on the Cell window As can be seen in the Rotate Cell Cycle window the default rotation axis is
11. l orientation Anaelu displays the positions of all the generated diffraction spots in the Hybrid window see Figure 9 Cole Style g Epona step 5 Coke Site Loganithen Hast Figure 9 Simulated 2D XRD pattern Pt polycrystal sharp 1 I 1 axial texture Rotating crystal model After completing the scan Anaelu will ask the user if he she wants to continue with calculations The user should check if the calculated blue spots coincide with the experimental red and yellow maxima In this demo they will coincide so the user can choose yes to ask for more results Stage 2 With the permission of the user the program will calculate the 2D pattern Anaelu will calculate the intensity of every pixel taking into account all the positions and intensities calculated in the previous stage Then it will show the calculated 2D pattern in the Model XRD window The user should wait until the program activates the Model XRD window with the image of the calculated pattern Experiment model comparison With Model XRD and Hybrid windows activated the user can move the mouse pointer in one of them and the program will show a sign in exactly the same position of the other window The user can put the mouse pointer over a diffraction spot of a window and check if it coincides with the corresponding spot in the other window The window Model XRD also has the commands ArcCut and RadCut
12. ply Config To check the correctness of the Beam Center location displaying Arc Cuts is highly demonstrative Once confirmed that the Beam Center selection is correct saving the Configuration is strongly recommended To save enter the Config menu in the Main window Figure 2 Determination of the incident beam position by selection of points belonging to a Debye ring Integration of the Debye rings Hybrid window click on Integrate Anaelu opens the Show Cut window and displays on it the integrated 2 0 pattern The result is analogous to a Bragg Brentano experiment with texture effect averaged out Figure 3 Dake Spe neat tool Head eb rota nt Lie Angh aiden Poston ea F Show Model Figure 3 Integration along Debye rings Zoom of a selected area Hybrid window Clicking the left button of the mouse select a pattern area See Figure 4 toep foi i RF er ee ivi tis Figure 4 Zoom of selected area in a diffraction pattern Pattern analysis with the ArcCut and RadCut tools Figure 5 RadCut If the RadCut button in the window Hybrid is clicked and the mouse pointer over the pattern is moved then Anaelu will display in the ShowCut window the intensity distribution along a straight line that goes from the direct beam position to the mouse pointer location ArcCut In the Hybrid
13. r distance position where the direct beam hits the 2D detector Beam Center and path to the file with the experimental pattern For training with the default demo it is recommended to preserve the preloaded configuration The files with configuration parameters generally have the extension cfn and may be saved or loaded from the Config pull down menu in the Main window of the program Load the experimental pattern To show the dialog box that helps finding the experimental pattern use the command Browse 2D XRD Pattern There are two equivalent ways to call this command from the Experiment menu in the upper part of the Main window or in the Configuration child window To run the demo it is recommended to load the file Platinum _2D_XRD asc To load this file click the Apply Load ASC command in the same windows where Browse 2D XRD Pattern may be found The program Anaelu is capable of loading XRD Patterns in binary unsigned integer two bytes per pixel or ASCII format To convert among different formats pertinent programs for example fit2d may be used 2D patterns are displayed with different scales and color conventions see Figure 1 Tue 5 Hybrid ot bodo lEH 5 Hybrid folos S Color Style fi points 300 sepf z Cole Sy Color Style Ro points 200 step m Colce Ss Em Say as pee E Hybrid ty Hybrid foto B Hybrid Color Style 5 points
14. rs Enjoy modelling
15. window click the ArcCut button and move the mouse pointer over the pattern image Anaelu will activate the ShowCut window In this new window the intensity distribution along the arc that contains the mouse pointer will be shown If the user puts the mouse pointer over a Debye ring then Anaelu will show the intensity distribution along the ring Angee a Mouse Postion F szg F Shor Model Figure 5 Radial and arc cuts Movement of the mouse over the Hybrid window When the mouse pointer is in the Hybrid window Anaelu shows information about the pixel behind the pointer in one of the fields of the Hybrid window This information is azimuthal angle 20 dispersion angle inter planar distance colour palette scale and intensity at the considered point Loading and editing the unit cell Crystal structure information may be loaded and edited via the Main window of Anaelu Click the pull down Menu File and select the desired option The files that contain crystal structures data normally have the extension cel In the Cell Window the first tab Edit Cell allows the user to introduce crystal structure data After typing the space group the asymmetric unit and lattice parameters by clicking the Ok button the user commands Anaelu to generate the complete unit cell Anaelu automatically activates a third tab View Rotate Cell
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