Powder3D 1.2 A short tutorial
Contents
1. Powder 3D File Edit Display Tools Plat Window Help tal si Film plot 7 BE Data set range 040 am i D Brightness D O WE Contrast 200 M Display square root M Invert display Interpolate 150 101 Set No 51 1 1 90 13 34 24 80 36 23 47 67 20 DOF 21 lherations 2 Chie 0 043625579 Figure 40 2D film plot 3D line waterfall plot Orientation Lights File Edit Display Tools Plot Window Help El Rotation La RH Anis 10 RER Axis Top Slant Surface Ce Line i i 181 Pr EE m CG Set NO DOF 1 Iterations 2 Chie 0043625579 Figure 41 3D line plot By clicking the 3D plot button the default 3D line plot is displayed Figure 41 The data range can be set as with the 2D film plot Rotation around X and Y axes can be controlled via slides Two preset views are stored and can be accessed via the buttons Top and Slant Mouse rotation is enabled by default pressing the appropriate radio buttons activates translation and scaling modes Finally the line plot can be immediately changed to a rendered surface plot by selecting the Surface radio button 3D surface plot The surface plot Figure 42 is identical to the line plot in handling As rendering the surface can be a slow process dependant on the amount data displayed the2. File Edit Display Tools Plot Window Help tal 8 x 10 6 x 10 4 x 10 Intensity Counts 2x 10 5000 5000 10 20 30 40 26 r Select fitting range by dragging mouse over peak Figure 33 Le Bail refinement Peak analysis A new tool has been designed to assist in the sequential refinement of peak profiles To call it you should select the menu Tool gt Peak analysis SS tts play Tools Plot Window Help Le Bail Peak Analysis Export cell data Figure 34 Peak analysis menu The window in Figure 35 shall appear The pattern ranges that have been set in the main program interface are the initial ranges displayed by the peak progression tool It is therefore very useful to select the interesting range using the film plot display and the zoom function before starting the tool The rendering of a couple of hundred patterns might be slow on older hardware so it is in your own interest to reduce the amount of information The aim was to create a module which does sequential peak profile refinement in a robust manner The tools that you can select on the left are 1 a zoom tool works in very much the same manner as the normal zoom tool 2 select ranges Drag this tool across a peak to select it and have the peaks displayed or found should none have been determined 3 a peak editor Add remove peaks using this tool Once you have selected a range with the range tool y
3. Although every effort has been made to ensure that the software in the Powder 3D program operates correctly and in accordance with its documentation Powder 3D is distributed strictly as is Responsibility for interpreting its output lies exclusively with the user and no liability direct or indirect shall be incurred by Notes The Powder 3D program may be copied and distributed to other academic and non profit users provided that the entire program is transferred as embodied in its distribution file apart from authourised updates and any minor modifications that may be needed for it to run in a particular computing environment Users are asked to send details of any suggested corrections and or enhancements to R Dinnebier fkf mpg de so that all users may Figure 1 Welcome screen The sample data set The data set that is the basis for the graphics displayed in the manual is available for download from http www fkf mpg de xray The data stems from an experiment carried out at the X7B beamline of the NSLS Dinnebier et al 2005 The wavelength was 0 9224 A The initial substance was d Rb C 0 Seven phases can be identified and are tabulated below Table 1 Phases identified in the sample data set Rb C204 Pbam 11129 169 D 6S3K B Rb C204 Pnma 1816 1658 og gt 661K a Rb C204 Pomme 6 47 86 gt 723K _a Rby CO Poxmme 139 an B Rb2 CO Dom 768 1589 IOM 830K 5 87 The temperature
4. Further set the transparency to 40 Sy Untitled lol x File Edit Insert Operations Window Help visualization E 100 v x ols El Al al ol Glo Legend Golorbar Click to select items click and drag to select multiple items u 72 446 Figure 47 Insert visualization S Insert Yisualization x GES Data Manager Image d Image Parameters IMAGEPIXELS MN PALETTE PALETTE z Z ma RE Sc Surface parameters PALETTE 010 X om Y x Ebe Plot Profile IK Gr af Import Variable Import File Type IDLPALETTE Description BYTE 3 256 ok Cancel Figure 48 Define the type and variables for the visualization Sj IDL iTool Visualization Browser OI xi EM Window BO View_1 7 GEN Visualization Layer Ei Data Space Tia SC ZE mage palette Edit color table S mg en Interpolation Nearest Neighbor i mik AxisO 85000 SR oe 0 023913 m Lights 1 im Annotation Layer mage transparency Poworder Bottomtotop zauri TT Figure 49 Correcting the height of the image Now our image is complete All that remains to be done is to improve the lighting and export a high resolution image You might have become aware of the Lights branch on the left in the Visualization Browser Figure 49 Open this branch and select the directional light You should observe something like Figure 50 Figure 50 Lighting in iT
5. S Set increments and phase ranges 10 x Increments Phase ranges Phase Phase2 32 278 000 DI aj 33 282 000 wus 34 286 000 xyz El 35 290 000 xyz zyx 36 294 000 zyx TT gt Phase2 DI DEER SS From set no 35 To set no 73 Figure 19 Define phase ranges Ka stripping Should you have collected laboratory data using Ka and Kay rays these can be separated using the menu Edit gt K alpha stripping Select which wavelength you wish to keep Figure 20 Sl Powder 3D loj x File Edit Display Tools Plot Window Help tal 2 00000 8 x 10 alphaz stripping Keep K alphal 6 x 10 Keep alphaz Cancel a 4x 10 2x 10 Raw Data 10 20 30 40 50 K alphal K alpha Drag mouse to zoom into region Figure 20 Koo stripping The following dialog Figure 21 enables you to select the sets which should be stripped The raw data is overwritten and therefore this action cannot be undone 1 Apply K alpha stripping je EX Fram zet no fi Tosetno 200 Select phase Phasel Apply Cancel Figure 21 Batch stripping Smoothing An advanced full width at half maximum FWHM optimised smoothing Figure 22 algorithm described by Dinnebier Dinnebier 2003 is implemented Edit gt Smoothing The variation of the FWHM of the peaks is generally described by the Caglioti Caglioti et al 1958 formula FWHM VU
6. Search between 4 76 and 20 14 8 x 10 6 x 10 Een 5 Sp a ZT heiss Intensity 4x 10 Overwite Append Crystire Search Save Done 2x 10 Lr JL oade 10 20 30 40 l l l 10 l l l l l l l l l l l l l l 26 peaks found Click to add shitt click to remove peak Figure 26 Peak searching The peak positions and intensities can be saved to a Crysfire Shirley 2002 format file via the button Save on the Peak search tab Peaks can be added and removed manually by selecting the edit button as with the background points Single peak fitting Once the peaks have been found their position can be Figure 27 using a pseudo Voigt function corrected for axial divergence Finger et al 1994 All refined values are stored for later use You can select the peak by dragging over it A light blue box fills the border of the selection Pressing enter starts the refinement with the default values The fit is overlaid in blue for visual inspection Please note The FWHM estimated using the Caglioti function has a profound effect on the convergence of the fit Should the procedure fail ensure the FWHM distribution is set to a realistic value Peak markers can be added and removed manually by returning to the peak search window Figure 25 the modus operandi is identical to the addition and removal of background points Data exp
7. interpolates the background giving it the same number of data points as the diffraction pattern Then a linear function fitted using the least absolute deviation method is added to correct the background Should the background be higher than the powder pattern at any point it is lowered The Calculate background method utilises a robust algorithm based on an low pass filter as proposed by Sonneveld and Visser Sonneveld amp Visser 1975 Select the number of iterations curvature value and number of background points to attain an optimal background Please note that every iteration costs computing power for large data sets many iterations can make the automatic background reduction time consuming The apply button greets you with the following dialog Figure 24 SY Apply background red From zet no fi Tosetno 200 Select phase Phase Apply Cancel Figure 24 Batch background reduction To edit background points manually select the edit tool Figure 25 This can become necessary if the background varies strongly from pattern to pattern You can now remove background points with a shift click left click while pressing the shift button and add background points with a click Figure 25 The edit tool You can cycle through the patterns in the usual fashion either by selecting the next and previous buttons in the context menu or by pressing the arrow buttons on the Main tab If a ba
8. length 0 05 i Minor tick length 0 5 il Tick interval 0 F Axis plus labels Grouping r Tick direction Right Above Order Use logarithmic axis False Export to IDL Text show True i Text nnsitinn Below left xl Axis Parameters Figure 46 Deleting an element We also alter X axis properties to Titel 2Q Font Symbol And the Y axis to Titel Scan number Font Times These changes give us a 2 on the X axis and a similar font for the Y axis Now we create that semi transparent 2D visualization hovering over the surface Select the menu item Insert gt Visualization Figure 47 You shall then be prompted for the type and variables defining the item We chose an Image type top right box opened the Surface branch on the left that is where the data is and assigned the Z value to the pixels Y values to the Y axis and X values to the X axis To do the assigning mark the data value on the left and click on the small right arrow in front of the fields you wish to be associated with the data Leave palette empty and press OK So that is done but where is the image Find your way back to the Visualization Browser or properties window as described above It shall have a new entry for the image Highlight the image and alter the Z value to well above the maximum intensity in your data array In our case it is 85000 Figure 49
9. ramp was set to 298 gt 838 gt 298 K The sample was heated at a rate of 2 8 Kmin and cooled at a rate of 4 8 Kmin Considering the exposure and development time this leads to a heating rate of 4 2 Kframe and a cooling rate of 7 62 Kframe I J t l e N Rb C 0 280 l l l l E l i I Rb CO T l l l N 2 3 D I l il i l l Li l N l i 2 Li l N l l tt N gt ii i i II l l l Li l N l l V1 l N l l 1 l i l f l N l D l i l l l I l ii I l l t 2 l i KAS l 1 I i i gt i l T I i l u l I t L l l I l 2 l D lal d a E EE Mel RR SE E ees OR GE ia l i l S a c V3 H d l t I l i Es I I t N I l e IN a 2 DO l belt ad 8 ees Ce sees OE OOK Py L PA i me Pnma i l 14 l 300 400 500 600 700 80077 X800 700 600 500 400 300 Temperature K Figure 2 Powder diffraction patterns lattice parameters and cell volumes of Rb2 C204 and Rb2 CO3 as a function of temperature in the range from 298 to 838 K 2 4 K min and back down to 298 K 4 8 K min Taken from Dinnebier et al 2005 Import One of the first things you shall want to do is to import data To do that press the import button Figure 3 or select File gt Import ei Powder 3D File Edit Display Tools Plot Wind der 3D Vers inrichsen B Copyrig The Powder 3D program is freely availat its parts is assert
10. surface mode requires more patience while adjusting the view All images can be exported either by copying to the clipboard Edit gt Copy exporting to an image file File gt Export gt Image or printing File gt Print For the latter two operations the image is rendered from scratch and dependant on the resolution of the image file or printer can take a considerable amount of time Lights The 2nd tab on the 3D display control board is Lights Figure 42 Four light sources can be controlled One ambient and three positional light sources can be manipulated Al Powder 3D File Edit Display Tools Plot Window Help EE ES Orientation Lights El Ambient Positional Ce Positional i Pasitional3 0 000000 ll Position 0 500000 Al J D Y Positon 1 00000 Al Jr amp Position asco E I g Intensity DOF 21 Iterations 2 Chie 0 043625579 Figure 42 3D surface plot showing the lights control panel iTools presentation graphics Version 2 0 For the very ambitious there is the extremely powerful data visualisation and manipulation software iTools that is called by pressing the button Presentation Graphics Figure 43 iTools has been developed by RSI Inc and is a completely independent of Powder3D Powder3D passes on the data to iTools and is free for user interaction again Dk ardt marve O zonen pr on on Zoom F
11. the left and displays the pattern in a 20 region shifted 10 higher Clicking in the other borders works in analogous fashion A single click in the plot window resizes it to the maximum view Selecting multiple patterns from the list displays them up to 6 colour coded overlaid patterns Figure 15 BER File Edit Display Tools Plot Window Help zel 8x 10 6 x 10 4 x 10 Intensity 2x 10 Drag mouse to zoom into region Figure 15 Multiple pattern display An interesting feature is the ability to export an AVI film of the single patterns cycling through the selected sets and the zoomed range To do this press Export gt AVI in the context menu To make this export as versatile as possible it creates a film only of the currently selected data range 20 intensity and selected data sets You will have to select an appropriate compression algorithm for the video In our experience DiV X4 high motion gives the best results This feature is only available on the Windows operating system Please note the installation of the library for this function are described above see Installation Normalizing Patterns Data collected using image plates generally lacks a beam decay correction This can be partially alleviated by normalization Two or more patterns can be corrected using this function Menu Edit gt Normalize patterns Select the patterns via the list or select patterns belonging to a phase by choosin
12. Display Tools Plot Window Help Open Close Save cH Export gt XY Print AYE GDA UXD Figure amp Adding a single pattern Figure 9 Pattern selection tool Sj Powder 3D sia Figure 10 The first powder pattern Data reduction Cropping tool The limits of the powder patterns can often be reduced This is conveniently done by means of the cropping tool A click on the crop button Figure 11 draws two vertical lines which you can drag to define the desired range Figure 12 Figure 11 Crop button DIE File Edit Display Tools Plot Window Help tal 8 x 10 6 x 10 Aw 10 Intensity 2x 10 10 20 30 40 50 Select outer ranges of data and press enter to crop Figure 12 Cropping bars On pressing the enter button the entire array is cropped to the new range Please note It is a good idea to save the data regularly to avoid possible data loss File gt Save Single pattern visualization Figure 13 Zoom button DIE File Edit Display Tools Plot Window Help tal 8 x 10 6x 10 Aw 10 Intensity 2x 10 Drag mouse to zoom into region Figure 14 Zoom tool The default tool in the 2D plot window is the zoom box Figure 14 Pull it over a region you wish to enlarge Once the enlarged window is displayed click in the borders around the plot to navigate A click to the right of the X axis moves the pattern s to
13. Max cycles per ZOE Refinement progress Refine Cancel Plat Export Done Figure 37 Peak analysis window range selected and peaks marked Bi Analyze peak progression ol x Select pattern range and peak position C Zoom Multipattem Single Pattern 2000 deg f Select ranges C Edit peaks 1300 LU 1700 L600 1500 LO L 10 2 10 3 LO 4 10 5 LO 6 Function Peak Ge FC Remove Eta 0 0476025 Intensity 559 107 r Plat Hero f Pseudo Yoiat E Pearson WI SL 0 00200000 Position 10 3567 m F Normalize HA 0 00200000 Fw Hbi 0 186643 ke C Export Refinement run Refinement progress 115 Max cycles per ZER Cancel Plat Export Done Figure 38 Peak analysis window peak refinement in progress Select function bor ft Fb Peak Progression Figure 39 Peak analysis a rudimentary initial plot of peak development Graphics 2D film plot This module simulates a Guinier film Figure 40 Two sliding bars enable you set the brightness and contrast of the plot Colour inversion and square root scaling can be set A tick box Interpolate allows you to do a bicubic interpolation between your patterns This smoothes plots of small data sets Of course the data range displayed can be set via the Ze and Data range fields Needless to say background corrected data has a far higher contrast The zoom and pan tools are available for this display
14. Powder3D 1 2 A short tutorial Bernd Hinrichsen Robert E Dinnebier and Martin Jansen Max Planck Institute for Solid State Research Heisenbergstra e 1 Stuttgart Germany Introduction Powder3D is a program for data reduction and publication quality visualisation aimed specifically at large data sets collected in time resolved powder diffraction experiments The program is in ongoing development so there shall be regular updates and extensions to the present functionality For comments or suggestions please contact r dinnebier fkf mpg de Getting Started Installation The latest version of Powder3D can be downloaded from http www fkf mpg de xray As Powder3D is written in the programming language IDL you will need to install the IDL virtual machine IDL VM 5 before being able to run Powder3D Virtual machines for various platforms can be downloaded from the RSI website http www rsinc com idlvm free of charge When you have installed IDL VM unpack Powder3D into a directory of your choice and double click on the file Powder3D sav After dismissing the IDL VM current version 6 3 only splash screen the following window Figure 1 should welcome you Please note the libraries necessary for the AVI export and peak refinement namely IDLtoAVI dll IDLtoAVI dlm p3d dlm and p3d dll should be in the same directory as Powder3D The functions only work on the Windows operating system Other o
15. actor 1 P Figure 43 iTools The iTools do represent an excellent set of programmes and contain complex architecture For this reason I shall extend the tutorial to cover the creation of an image like that in Figure 26 First we shall have to subtract the background from all the data sets so that we rid ourselves of the undulations of background intensity visible in Figure 26 A value of 1 smoothing box and 3 iterations worked well for this data set It is convenient to decide on with part of the pattern array you wish to use by previewing it in the 3D surface mode in Powder3D Once you are happy with your selection a click on Presentation graphics copies the data over to the iSurface programme It is always possible to further reduce the displayed data in the iTools programme suite should you find it necessary A right click on the data opens a context menu which lets you select the properties of the view Figure 45 File Cdt inset Operations Window es peaa afer hes fw ael alslalslelel Figure 44 The primary iTools display Open the properties window to the full extent by pressing an unobtrusive left arrow in the top left corner of the window Figure 45 left ei IDL iTool Visualization Browser Si IDL iTool Visualization Browser Surface El Window Surface Name Surface a GI Vi
16. ckground has been calculated for the pattern it will be displayed Should phases have been defined it is possible to select the data sets associated to the phase by choosing the appropriate phase The Fullprof Rodriguez Carvajal 2001 format is a simple XY ASCII file containing 20 values in the first column and intensities in the second The GSAS Larson amp Von Dreele 1994 format contains four columns the first contains a single 1 the second contains 2 values the third the intensities and the fourth the standard errors Peak hunting By selecting the menu Edit gt Peak search and clicking the search button you shall see the following window Figure 26 Changing the mouse to edit mode enables you to remove peaks with a right click and add peaks with the left click You can drag the borders of the peak search to encompass all important areas of the powder pattern by selecting the range tool in the context menu right click on the image Peaks are searched by a multiple pass variable FWHM second derivative method The convolution range is set via the Caglioti diagram the threshold and minimum distance between peaks can be set via the sliding bar The radio buttons under the Caglioti diagram determine if a new peak list is written with every run or the current peak list appended with the newly found peaks lol x File Edit Display Tools Plot Window Help Threshold 0 10 Ta Bi Minimum peak distance
17. ed by and reserved by t Figure 3 Import menu Six different formats are available although XY and Chi formats are identical You shall be prompted to select a file Figure 4 Standard versions of GSAS GDA Fullprof DAT Bruker UXD and DASH XYE data files are imported Select files to load ix My Recent Documents Desktop o My Documents Mu Computer KA KH MyNewok Fic rome Places Files of type chi X Cancel E Figure 4 Select import files Select all files you wish to import This is different to the previous version in which you only had to select a single file for the entire directory to be imported The files are sorted by the operating system so please ensure they are displayed in the correctly Should your files have a different suffix type lt your suffix here gt lt Enter gt in the File name field to display them Upon pressing enter the file names in the directory are read then the first file is loaded and the theta range read The next window prompts you for the wavelength and the two theta range and increment The increment entered cannot be altered later The range can only be cropped Should the range of your files differ from the set values the intensities are interpolated using the selected function linear recommended quadratic or spline The entries correspond to the values of the sample data provided Si Imported files Xl Radiation monochromatic white Wa
18. efine If the refinement is successful some statistics of the refinement are displayed at the bottom of the window The button Reset sets the phase information back to zero The button Remove HKL removes all HKL files for this pattern and forces Fullprof to recalculate them Please note The assistant expects sequentially numbered Fullprof compatible data sets Please make sure that you export your patterns immediately before attempting a Le Bail fit All the data is written to that directory Si LeBail refinement Ioj x Phase information Selected phase ranges from zet number to 0 Current zet for refinement Pattern Zero offset Fou DEEL reine Import Fullprof Reset Remove HEL Cell profile Spacegroup P b am refine cell a 11 2244 alpha 30 0000 b 6 25995 beta 30 0000 c 3 602498 gamme 30 0000 por Refinement information Cancel Refine e Figure 31 Le Bail refinement cell parameters Once the refinements for all the data sets have been completed close the window by pressing cancel The cell dimensions can be exported to a text file by selecting the menu Refine gt Export cell data Sl LeBail refinement Phasel Phase Phase 0 002750 7 Ber ne nen 0075172 sue woo em v fosses 0 001730 Ir 0 001400 TI 0017 ts L L Load profile Cancel Fine Auto Figure 32 Le Bail refinement profile parameters B Powder 3D oj x
19. ew 1 Surface Description Surface a m Visualization Layer Surface Show True E Data Space Tue Color CEA NY Sul CEA Use surface color for bottom True amp Use surface color for bottom True Image palette Edit Sill enen Image palette Bottom color _ 255 255 255 Bottom colo Minimum value 0 Minimum value Maximum value 840493 4 Maximum value 34043 4 Surface style Filled Surface style Filled Fill shading Flat Draw method Quads Line style Line thickness Remove hidden lines False Show skirt False x Surface Figure 45 The iTools property window folded and unfolded In the left side of Visualisation Browser Figure 45 You see the various elements that make up the image Once an element is highlighted its properties are displayed in the right part of the window We shall change the surface values to the following Color 145 145 145 Fill shading Gouraud Draw method Triangles The last two changes make the rendering slower but the picture better We open up the Axes branch and delete the Z axis by a right click and delete Figure 46 S IDL iTool Visualization Browser loj x EM Window GI View 1 a m Visualization Layer El E Data Space HAG Surface G Axes E Axis 0 E Anis 1 Axis 2 gt Name Axis 2 Description Axis i Show True Color dd alte o d Lights cut Annotation Layer Copy Major tick
20. g Phases and ranges The increments between the patterns can be entered into a table Figure 18 which is called by Edit gt Increments and phase ranges For unvarying increments the fields on the right of the window can be used to insert values into the table Once two of the first three fields are filled the other is calculated and filled automatically Should all fields contain values no updating takes place Pressing the Insert button fills the table with the calculated values These values are used for labelling purposes only Sj Set increments and phase ranges j iol x Increments Phase ranges Set increment values 154 000 K IB PE 2 00000 158 000 E Increment K 3 00000 162 000 i 4150 4 00000 166 000 First vue K 5 00000 170 000 1466 6 00000 174 000 Last value 466 000 K 7 00000 178 000 2 e 8 00000 182 000 rom set no 900000 186 000 fs 130 000 Ge gt Insert Done Cancel Figure 18 Insert increments Adding phase ranges can either be done manually by editing the fields of the range table Figure 19 Please note while editing you have to leave the cell you are editing for the values to be read properly by the Insert command The assistant for entering the values at the bottom of the window works in the same fashion as the one used in the increment window These values are necessary for the Le Bail assistant of which a first version is included
21. g the appropriate phase Next ensure the method of normalization is correct All patterns that have been selected are superimposed over one another It is possible to zoom by dragging open a zoom box with a left click Select the region you wish to normalize the patterns with by dragging over a range with a right click The range selected in this manner is used to normalize the data By pressing Test you can preview the results of the normalization Press Cancel to discard or OK to accept the normalization B Normalize Patterns O x Data sets to normalize Phase 1 Please select scaling method Scale to maximum Ce Scale to minimum Scale to difffmas min C Scale to average Subtract minimum Left click to zoom right to mark region UK Test Cancel Figure 16 Normalization function Wavelength The wavelength dialog accessible via the menu Edit Wavelength allows you to alter the radiation wavelength Figure 17 Should you wish to recalculate the pattern select the radio button recalculate patterns The wavelengths for some standard anode elements have integrated in the top list Bil Change Wavelength x Operation Ge corect value recalculate patterns wavelength Theta E Dispersive C S Er Lambda 1 0 322400 Co Hi Lambda A 0 000000 Cu 7 K alpha singlet Lambda ratio 0 000000 C K alpha doublet Polarization 0 000000 Figure 17 Wavelength dialo
22. o Powder3D in the following manner Hinrichsen B Dinnebier R E and Jansen M 2004 Powder3D An easy to use program for data reduction and graphical presentation of large numbers of powder diffraction patterns Z Krist 23 231 236 Caglioti G Paoletti A amp Ricci F P 1958 Nucl Instr 3 223 228 Dinnebier R 2003 Powder Diffraction 18 199 204 Dinnebier R E Vensky S Jansen M amp Hanson J C 2005 Chemistry A European Journal 11 1119 1129 Finger L W Cox D E amp Jephcoat A P 1994 Journal of Applied Crystallography 27 892 900 Larson A C amp Von Dreele R B 1994 Los Alamos National Laboratory Report 86 748 Le Bail A Duroy H amp Fourquet J L 1988 Mat Res Bull 23 447 452 Rodriguez Carvajal J 2001 Commission on Powder Diffraction Newsletter 26 12 19 Shirley R 2002 The Crysfire 2002 System for Automatic Powder Indexing User s Manual Sonneveld E J amp Visser J W 1975 Journal of Applied Crystallography 8 1 7 IDL IDL VM and 1Tools are trademarks of Research Systems Inc Boulder CO USA Windows is a registered trademark of Microsoft Corporation Redmond WA USA Written by B Hinrichsen 06 10 2004 Last updated by B Hinrichsen 12 02 2007
23. ools Now you can manipulate the geometric coordinates with the mouse and alter the intensity in the properties window This you can do three different light types ambient positional and directional Add further lighting via Insert gt Light The mouse has two modes while manipulating lights positional and rotational Change between the two by selecting the pointer or the circled arrow Figure 51 aj be fw alai IE ji AlNlalc Figure 51 Mouse modus buttons This should be the last fine tuning the image needs When complete export the image via File gt Export Select To a file in the following dialog When questioned whether Window View or Data are to be exported either Window or View shall suffice Next specify your export file name and type and resolution Recipe This section will give you a run down on how to reduce your data sets effectively using the sample data 1 The data format is CHI the wavelength is roughly 0 9184 Angstroms These values should be used to import the data successfully The temperature ramp of the experiment was 298 gt 838 gt 298 K These values can be entered into Increments and phase ranges dialog available via the menu Edit gt Increments and phase ranges 2 A first step in the data reduction would be to crop the data to a sensible range 3 4 46 7 20 3 Next we define the background As the background lacks g
24. ort By pressing the export button you are able to export the peak data of the pattern in a variety of methods The positions and heights can be exported to Crysfire format file cdt The refined values can be exported to text file Should you have refined more than six peaks an instrument resolution file in Fullprof format irf can be exported EAN Lx 0x10 Figure 27 Peak refinement Peak Indexing Powder3D has no own indexing capabilities but does provide a simple interface to the powerful indexing suite Crysfire http www ccp14 ac uk ccp web mirrors crys r shirley Shirley 2002 Two very similar methods can be chosen for interaction 1 Save the peak file in the Crysfire format and start Crysfire manually 2 Should Crysfire be installed only Windows operating systems according to the installation instructions in the Crysfire manual it can be called by pressing the Crysfire button The file is exported to the current working directory and Crysfire is started in there A message is displayed with the name of the file that has been exported a 4 H Zb 35 af ET het f Ovenwite Append Crysfir Done Figure 28 Crysfire button Le Bail refinement assistant Selecting Refine gt Le Bail via the menu opens the following window Figure 31 Here you can set up the starting values for a Le Bail refinement Le Bail et al 1988 using Fullprof Should a single pattern fo
25. ou can start refining those peaks The refinement will start with the strongest peak and work its way down to the smallest peak fixing the peak position automatically once the peak intensity drops below a threshold of 361 A maximum of two ranges can be refined together This is equivalent to refining them separately should there be no overlap Should you wish to plot the peak development first select the peaks with the Select peaks Figure 36 tool Now press the plot button The main program window is brought forward and a rudimentary plot of the refined parameters is displayed Bi Analyze peak progression ol x Select pattern range and peak position Zoom Multipattern Single Patter C Select ranges C Edit peaks Function Peak Ge FC Eta 0 500 tu D 000 Plot D Pseudo Yoiat EE D Hr C Pearson VI S L 0 002 a Position 0 000 TT Normalize HIL 0 002 a FwHM 0 010 CT Export Refinement rum Refinement progress Max cycles per ZER Refine Cancel Plot Export Done Figure 36 Peak analysis window initial display Bi Analyze peak progression SS ol x Select pattern range and peak position C Zoom f Select ranges C Edit peaks Function Peak FC Eta 0 500000 f Pseudo Voigt u Pearson WII SL 0 00200000 Position 10 3451 E F Normalize L Intensity 2551 58 Plot HL 0 00200000 FHM ja S075 04 a Export Refinement run
26. perating systems are not supported UNC unmapped network paths will cause the program to fail Sj Powder 3D File Edit Display Tools Plot Window Help kal 10 x Powder 3D Version 1 2 25th June 2006 B Hinrichsen R Dinnebier M Jansen Copyright The Powder 3D program is freely available for non profit use but it is not public domain Copyright in all its parts is asserted by and reserved by the authors Licence for Academic and other Non Profit Use of Powder 3D The Powder 3D program is licensed free of charge for all academic and other non profit use This software may only be distributed on the same terms that it was received which is freely for non profit use Neither the original versions nor any derived or modified versions may be sold or incorporated in any commercially distributed system without the express permission in writing of the relevant copyright holders These terms shall be binding on all subsequent recipients If use of Powder 3D makes possible a published paper then Powder 3D should be cited in the references section of the paper Hinrichsen D Dinnebier A E Jansen M 2004 Powder 3D program for evaluation and presentation of multiple powder patterns in dependence of an independant variable in preparation Commercial Licensing Commercial licences for Powder 3D are also available For further details and for current rates please contact he authours at R Dinnebier fkf mpg de General Limitations
27. reat relief high values for the smoothing box smoothing box 0 9 iterations 4 resulting n a flatter underground do the job well For the data sets from 80 to 140 slightly lower values were chosen due to the higher background at around 18 smoothing box 0 7 iterations 4 4 For the next step it is recommended to have the indexing package Crysfire installed Select the first pattern and do a peak search Save the found peaks to your working directory and then start Crysfire preferably by pressing the Crysfire button Using the peak refinement the profile can be refined and the position of the peaks determined more precisely 5 Should you have indexed your phase s using Crysfire you can import them back into Powder3D in the Le Bail fit dialog For this step to be successful Fullprof gt Version 3 3 has to be installed Bij LeBail refinement Ioj x Phase information Selected phase ranges from zet number U to 0 Current zet for refinement Pattern Zero offset O 015760 refine Import Fullprot Reset Remove HEL Cell Profile Spacegroup bam PF refine cell ER 11 2244 alpha 90 0000 b 6 25995 beta 30 0000 C 3 60249 gamma 30 0000 Import Refinement information Cancel Refine Auto Figure 52 Cell data for Le Bail fit On the phase tab press import and choose a Crysfire summary file then select the appropriate cell from the table and the values shall be in
28. rmat PCR file exist you can load it by pressing the button Import Fullprof All the values displayed in the window are then imported rn Tools Plot Help Peak Analysis Export cell data Figure 29 Le Bail menu The cell dimensions can alternatively be imported from a Crysfire summary file Pressing Import in the cell frame does this You can select a SUM file and the cell dimensions are displayed in a table Select the desired cell by marking the entry Figure 30 The lengths and angles are imported on clicking OK B Select the values you wish to import alpha beta gamma 27 17 0000 11 6400 35 221 0 780000 11 2755 11 2857 6 38560 90 0000 100 305 90 0000 SEH 20 17 0000 11 6200 585 678 050000 11 3758 12 5650 4 13970 90 0000 94 4550 90 0000 i 29 17 0000 11 4500 55 463 0 740000 10 5946 11 2801 6 63480 90 0000 107 679 90 0000 20 17 0000 H 00000 591 003 0 870000 8 89660 2 89660 11 2574 90 0000 90 0000 90 0000 32 16 0000 16 4500 1025 51 1 00000 11 2997 12 5672 d AU 30 0000 30 0000 30 0000 3 Cancel OK Figure 30 Crysfire import The peak shape descriptors can also be imported if a peak refinement has been done for the pattern Otherwise enter your desired starting values Figure 32 The background correction is integrated into the refinement if a background was defined using the background function The space group should be entered and then you can start the refinement by pressing R
29. serted into the cell fields B Select the values you wish to import K x alpha beta gamma Ek 140100 1047 08 100000 119383 127550 7 83830 106 569 846490 113 695 0000 13 6600 1196 53 1 13000 11 7274 125680 864290 103657 101 374 75 7330 11 9600 282010 0270000 641640 11 2638 4 01120 94 2100 102733 99 0730 11 9200 924399 O880000 341710 11 3398 874800 95 3920 326370 94 3920 10 8400 913302 0870000 109171 123414 7453970 103088 921970 109762 10 7100 753911 0720000 100773 11 2517 686730 91 0250 104252 921500 u k A onu 74471 4m d OO 174 OF 47 44494 rd ATA AA Ad s ZE an dad CO Selected phase ranges from zet number to 0 Current zet for refinement Pattern Zero offset O 015760 refine Import Fullprot Reset Remove HEL Cell Profile DAHM constant variable U 1 133923 Wi 0 05645 W 0 031660 D refine E 0 001 00 r 0 026704 M refine Asummetrp S L 0 000370 refine DL 0 001750 refine x Refinement information Cancel Refine Auto Should you have refined profiles you can load these to the profile mask by pressing the import button on the profile tab Data from an existing Fullprof file pcr can be loaded using the Import Fullprof button On pressing Refine a Fullprof file is written and should Fullprof be installed on the system a LeBail refinement is started The refined data are read back to the fields References When publishing please give reference t
30. tan 0 V tan 0 W This can be graphically set with aid of the function window on the left Here the function can be dragged to the desired shape with the aid of three red boxes lol xl File Edit Display Tools Plot Window Help tal 1 smoothing Jas Order of polynomial ua vu Ms Mo of iterations 8x10 DAHM factor 07 6x10 z u F r S oO 4x10 T OD E Test Apply Done Chi 2446 67 2x10 0 1000 0 1000 10 20 AU 40 50 25 Drag mouse to zoom into region Figure 22 Smoothing window The correct selection of the function shape has great effect on the smoothing efficacy Background File Edit Display Tools Plot Window Help zel Sonneveld RE ER ER 1 Iterations ECS a Secondary iterations en ER I g Curvature 5 00 A Ex 10 i 6x 10 all D anchor points M Reduce anchor number Y Keep anchors under data Intensity 4x 10 MF Magnetize anchors Generate Export Import Done 2x 10 ee A K LL d M A JA kd GE E 10 20 30 40 Select outer ranges of data and press enter to crop Figure 23 Background reduction Background determination Edit gt Background can be done in two modes Either a pattern can be loaded XY format as for import or it can be calculated Figure 23 Should a pattern be loaded it is displayed as is the calculated background The normalize button then
31. velength Theta E Dispersive Lambda 1 1 54060 Lambda 2 0 000000 K alpha singlet Lambda ratio 0 000000 K alpha doublet Polarisation 0 300000 Cancel Figure 5 Import settings After the files have been read a message displays a few details on the current database Figure 6 There is no set limit to the number of files that can be read the only limitation is the available memory Database information x Ten d The database now contains 200 datasets Each patterns is comprised of 2299 datapoints Theta range 0 011956500 to 54 964087 degrees Intensity range 0 0967653 to 66 706 1 counts Figure 6 Import report As soon as you acknowledge the message you are displayed the first of your powder patterns Figure 10 Later pattern loading and deletion Should you wish to load a single pattern only or wish to compare a pattern to already loaded data this can be done by using the function File gt Import Figure 7 The pattern is added to the end of the pattern array Should the pattern differ with regard to the step width or position the intensities are interpolated to match the range and step width of the data already loaded A dialog requiring you to enter the wavelength for this pattern is displayed If one or more patterns need to be deleted select them in the Main controls window and press Delete pattern in the Edit menu ei Powder 3D File Edit
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