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Profex User Manual

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1. Bi nn 0 01 8 0 707 Uequiv 50 X O Import CIF File em o x Files STR File CIF File XML File Calcite cif PHASE Calcite Reference amcsd_0009873 Formula Ca C 03 SpacegroupNo 167 Setting 1 HermannMauguin R 32 c Lattice Trigonal UniqueAxis c PARAM A 0 499100_0 49410970 504091 PARAM C 1 706200_1 689138 1 723262 RP 3 k1 0 PARAM k2 0_070 0001 B1 ANISO 0 01 GEWICHT SPHARG GOAL GrainSize 1 1 1 GOAL Calcite2 GEWICHT E Wyckoff x 0 00000000 y 0 00000000 z 0 00000000 TDS 0 00796938 E Wyckoff x 0 00000000 y 0 00000000 z 0 25000000 TDS 0 00757986 E Wyckoff x 0 25730000 y 0 00000000 z 0 25000000 TDS 0 01400168 Warning No Wyckoff information found in atom Ca Check manually for standard setting Warning No Wyckoff information found in atom C Check manually for standard setting Warning No Wyckoff information found in atom 0 Check manually for standard setting v Add Files Save STR Close Figure 15 After importing a CIF file and adding all space group information the STR file is dis played It may still be incomplete Check the warnings at the bottom of the dialog and fix the STR file text manually The CIF file is also shown in the second tab for compar isong The XML file in the third tab is only used internally by Profex X w Space Group Settings Spacegroup Number Hermann Mauguin Wyckoff Symmetry 157 EPI 00 1 4 158 R32 C 0 0 3 4 159 16
2. A M ALVA a ll J 6000 F 3000 5000 m 4000 7 H 4 2000 3000 7 m Intensity counts Intensity counts 2000 F 1000 7 F a 0 0 z 10 00 20 00 30 00 40 00 50 00 60 01 10 00 20 00 30 00 40 00 50 00 60 01 Angle 2Theta Angle 2Theta a Regular offset b Adaptive offset Figure 9 When starting with no offset calling View Increase vertical displacement will apply an even offset of the maximum intensity of the strongest scan a Calling View Decrease vertical displacement will apply an adaptive offset each scan will be placed at the maximum intensity of the scan below b gaps above scans with low maximum intensity however it can also be confusing with scans of very low intensity e g amorphous samples or the background curve In the latter case applying a regular stacking interval by calling View Increase vertical displacement may be preferred 5 4 Text Editors Text editors can show any kind of text files including control files list files structure files or any generic text file For control files and list files they will show syntax highlighting for better visual orientation Besides the standard actions for text editors such as copy paste undo redo and selection the context menu shown by clicking with the right mouse button has some special features for control and structure files 23 5 4 1 Control Files Open File When placin
3. Hovering the mouse pointer on a hkl index line at the top of the plot will show a tool tip displaying the phase name hkl Miller indices and the texture factor Zooming Use the left mouse button and drag the mouse to zoom into the plot Alternatively use the mouse scroll wheel to zoom horizontally to the location of the mouse cursor or hold the Ctrl key and use the scroll wheel to zoom vertically to the location of the mouse cursor Hold the Ctrl key and left mouse button to move the zoomed scan Unzooming Click with the right mouse button to view the entire scan range Cross hair cursor Press the c key on the keyboard to activate a cross hair cursor Fig P Press C again to disable it Counting noise cursor Press the n key on the keyboard to show or hide a cursor indicating a range of V Intensity counts This range represents the statistical counting noise and allows to evaluate mismatches be tween Iyps and Ica c for example at the tips of peaks Fig 7 When moving to the difference curve the noise cursor will show the counting noise at the intensity of the first scan e g p at the same 20 position Spectral line cursor Press the s key to show or hide a cursor showing lines at the position of Kay Kaz and Kp The Ka line will be drawn at the position of the mouse cursor Fig 17 Positions for Ka and Kf lines will be calculated from the d value at the cursor position If no wavelength is av
4. If checked the box appearing when pointing the mouse cursor on hkl index tick marks on the plot also shows the texture factor 31 Y axis unit Shows the y axis unit either in counts or in counts per second cps Counts per second may not be available depending on the file format of the loaded scan If the time per step is not available Profex will fall back to the unit Counts and assume a counting time of 1 second per step Only the display of scans will be affected by the choice of the unit Internally all calcula tions and file format conversions will be performed in Counts As a consequence when converting a format supporting Counts per second such as XRDML to a format not sup porting it such as ASCII XY the displayed unit may change from cps to counts Show major grid lines Show or hide vertical and horizontal grid lines at the positions of major tick marks Major grid lines will be drawn as medium dashed lines Show minor grid lines Show or hide vertical and horizontal grid lines at the positions of minor tick marks Minor grid lines will be drawn as light dotted lines 6 2 2 Fonts Font Title Select the font of the file name at the top right of the graph Font Axis Labels Select the font of the graph axis labels Font Tick Marks Select the font of the graph tick marks Font Legend Select the font of the graph legend 6 2 3 Scan Styles Color Customize the list of colors to be used to draw scans by
5. as refined local parameters in the summary dockable windows These values are read from the LST output file Local parameters can be customized in the preferences as described in section 44 File Sample Parameter Goal Value ESD path scanl lst scanl alphaTCP sum 0 0311 0 0023 path scan2 lst scan2 alphaTCP sum 0 0161 0 0022 path scan3 lst scan3 alphaTCP sum 0 0147 0 0024 path scanl lst scanl hap sum 0 9689 0 0023 path scan2 lst scan2 hap sum 0 9839 0 0022 path scan3 lst scan3 hap sum 0 9853 0 0024 Table 1 Global parameters and GOALS exported from Profex and sorted by the Paramter Goal column Sorted like this mean values and standard deviations can easily be calculated Profex allows to easily export the global and local refined parameters of all open projects into spreadsheet files Project Export Global Paramters and GOALS will write the global parameters and goals of all open projects to a CSV file Project Export Local Paramters will write the local parameters of all open projects to a CSV file Project Export Chemistry will export the chemical composition see section to a CSV file The exported files are text files containing semicolon separated fields Open the file in a spread sheet program and specify the semicolon character as a field separator Since the exported files also contain the source file name using the spreadsheet program s sorting function allows
6. gt lt device gt Devices myInstrument geq lt device gt lt template gt Devices myTemplate tpl lt template gt lt structures gt lt structure gt Structures myPhaseA str lt structure gt lt structure gt Structures myPhaseB str lt structure gt lt structure gt Structures myPhaseC str lt structure gt lt structures gt lt other gt lt textfile gt description txt lt textfile gt lt textfile gt some other text file txt lt textfile gt binaryfile some other binary file jpg binaryfile lt other gt lt preset gt Exactly one lt device gt and lt template gt node must be present If one of them is missing applying the preset will be refused If more than one of these nodes is present all but the first will be ignored An arbitrary number of lt structure gt and other file nodes may be present All paths can either be absolute or relative to the location of the preset file Device and template files do not need to have the same file name It is possible to use different template files with the same device file Files specified in 38 Projects sharing structure files working directory scan 1 sav Scan l sav STRUC 1 structure_l str scan_2 sav STRUC 2 structure_2 str structure l str structure_2 str scan_2 sav STRUC 1 structure 1 str STRUC 2 structure_2 str Projects in s
7. 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 Zi BGMN Device Configuration File for Panalytical CubiX Created by Nicola Doebelin RMS Foundation Switzerland small window Radiation CuKa Graphite monochromated KARAAAARAAAARARAAAA AAA AAA AAA AAA AAA AAA AAA AAA AAA AAA ARA AAA III II 14 Calculations v Raytrace GEOMET y Interpolate MakeGEQ Calculate Profile GERTEST e Figure 17 Instrument gt Edit Configuration configuration v Create Template for Refinenement Control File Tube Emission Profile cu Y e Kbeta Filter Energy Dispersive Detector No Filtering Sl save As kisave OrRun Bclose 4 26 60 theta Monochromator Crystal pid opens a dialog to edit an existing instrument 54 13 Scan File Handling In contrast to the BGMN Rietveld backend which only supports a limited number of scan file for mats natively Profex reads a wide and growing range of file formats When running a refinement on a scan file format not supported by BGMN Profex will by default automatically convert the file in the background and modify the control file accordingly This section describes the conversion process and the settings allowing the user to control the conversion Automatic scan file conversion can be switched on and o
8. Global Parameters and GOALs Ctrl E see section 5 6 1 18 Profex 3 2 0 alpha140407 File Edit View Run Instrument Window Help b lt di ld i AL re 009 scan xrdml home doebelinn Documents scan xrdml T T T T T Context Help y E 5 o 2 2 E c g i L 8 I 20 00 30 00 Projects Plot Options Angle 2Theta Refinement Protocol lobal Parameters and GOALs 3 1 Global Parameters and GOALs Local Parameters Wavelength 1 5406 Angle 16 327 Intensity 178 262 cts d Spacing 5 425 Figure 6 Many elements of the user interface can be re arranged by grabbing the title bar and dragging the window to a different place 1 stacked 2 detached from the main window 3 closed Green rectangles show the title bars that can be grabbed with the mouse to rearrange the windows 5 2 5 Local Parameters At the end of the refinement this window shows a summary of refined local phase related pa rameters This function depends on the Rietveld refinement backend and is not available for all backends In case of BGMN is is available and can be configured in the preferences as described in section 6 3 4 Values summarized here can also be exported to a CSV table using the function File Export Local Parameters see section D 6 1 5 2 6 Chemistry The Chemistry dock window shows the refined chemical composition of the sample This infor mation is only available for BGMN
9. PNG uses lossless compression therefore relatively small files free of compression artifacts will be created 42 If the line width or font size is too small it will have to be changed prior to the export in the graph preferences see section e 2 Use display line width to change the export line width All elements visible on screen will be exported including hkl lines and the legend Visibility of the scans will be considered invisible scans will also be invisible on the exported file The export will create a high resolution image of the on screen graph Pixel images can be edited in any photo editing software such as Adobe Photoshop GIMP Paintshop Pro Corel PhotoPaint and others 8 1 3 Gnuplot GPL Gnuplot is a powerful cross platform graphing utility able to create quality graphs in various formats Scans exported as Gnuplot files are saved as Gnuplot scripts with inline data The graphs are a fairly accurate but not perfectly identical representation of the plot as displayed in Profex It includes hkl indices a legend all selected scans and it preserves scan colors and symbol styles The output file may be edited to optimize the appearance of the Gnuplot graph or to change the output terminal Gnuplot code created by Profex version 3 5 0 was optimized for Gnuplot version 4 6 On a system with a working Gnuplot installation the following command entered in a terminal emulator will output the graph scan gpl to the defau
10. This is the same as double clicking at the strongest peak just after loading the scan file Note that only indexed reference structures will be considered Automatically index new structure files If checked Profex will scan the structure file directory for new structure files each time Profex is started and the first project is loaded If not checked new structures will be indexed the first time they are selected in the Reference Structures box Structures will not be available for double click phase identification as long as they have not been indexed Clear Buffer Clears the buffer file with structure file hkl indices Profex must be restarted for this to take effect All structure files will be re indexed either automatically or when selected from the Reference Structures box 30 Calculate hkl positions in range Specifies the lower and upper 20 angle for hkl indices to be cal culated Larger ranges will require more time to index The range may be smaller or larger than scan file ranges 6 2 Graphs 6 2 1 General Appearance Use AntiAliasing for Graphs slow Uses anti aliasing to draw the plots If checked lines look smoother but also wider Drawing will be slower if checked Update Graph after each Cycle If checked the plots will be updated continuously during the re finement If not checked they will remain static and only be updated at the end of the refinement Updating the graph takes some time For very long refine
11. backend These databases are directories containing template files Official Profex BGMN bundles usually contain default template files for structures and devices The location of these directories can be chosen freely For example installations on several computers can access structures device files and presets stored on a network share and maintained centrally In that case new structure files device configurations or presets will immediately become available to all users using the same database directories Write access is not required for normal use only for maintenance Configuration automatic or manual is explained in section 3 4 1 Structure Template Files Template files for crystal structures are normal BGMN structure files str stored at a central place in the Structures database directory When appending a structure file from the database to 10 a refinement using Profex s Add Phase dialog the file will be copied to the location of the XRD scan The original file will never be modified The following information is relevant when creating new structure files e Use the file extension str other files will be ignored by Profex e Profex will display the name given after the keyword PHASE in the Add Phase dialog e It is recommended to add further information e g an original database code PDF AMCSD COD after a comment sign trailing the PHASE keyword see following example This text
12. be configured in the program s preferences dialog 11 Local Parameters and GOALs shows a summary table of refined local parameters The pa rameters shown here can be customized in the program s preferences dialog 12 Context help shows the context help text when pressing F1 on a keyword in a control file 16 X Profex 3 3 0 beta140727 File Edit Vie 1 n Instrument Window Help BBE P9 la Projects Name Status srm676 idle aw em 3 040 NL 5 srm676a 1 dia Q srm676a 1 sav srm676a 1 lst home nic srm676a 1 dia Context Help ag VERZERR defines the file ger T T T T T T T T T T T T T T T which should be interpolated into i 5000 l observed 4 the geq format Defaults from I calculated L GEQ Background 7 4000 Corundum AI203 3000 F 8 Plot Options e gt Show Scan a 2000 12 Y observed 2 v I calculated y 1000 Y Background Y Corundum AI203 0 8 1 L 1 l 1 1 1 li L L L 1 1 1 1 40 00 Angle 28 Global Parameters and GOALs home nic srm676a 1 1st Refinement Protocol Local Parameters home nic srm676a 1 1st Chemistry Je Quantity Goal AI203 wt Rup 9 17 Rexp 8 16 X 1 1238 Rup 9 17 Rexp 8 16 Xx 1 123 Corundum AI203 100 00 r3 9 Parameter Value ESD Phase A Total 13 100 00 corundum sum il 0 Corundum T 0 4760354 0 OK gt 4 Wavelength 1 54098 A Angle 14 4 Intensity 2250 477
13. cts d Spacing 1 825 _ Line 0 Column 0 Figure 5 The Profex main window Elements 1 14 are described in section 5 1 13 Chemical composition shows the bulk chemical composition of all crystalline phases calcu lated from refined crystal structures and phase quantities 14 Status bar shows various information such as mouse cursor coordinates on the graph and the wavelength used to transform 20 angles to d values 5 2 Dockable windows All windows arranged around the central plot and editor area no 7 13 in Fig 5 can be rear ranged or closed to match the user s preferences They are called dockable windows because they can be docked to different areas of the main window Some examples are shown in Fig fjand explained below Moving Grab the dockable window at it s title bar e g the bar green rectangles on Fig le and drag it to a different location If the window can be docked the area will be highlighted Stacking Drag the dockable window onto another dockable window The dragged window will be stacked on top Tab buttons will automatically appear to give access to both windows Unlimited numbers of windows can be stacked Detaching Drag a window outside of the main window and release it when no dockable area is highlighted The window is now detached from the main window and floating freely on the screen Use this configuration to place windows on a second screen Detached windows can also be stacked Drag the de
14. ees ee ee Oe a oed B L5 Fityk Session A 8 2 Pontang t PDH usu icm oe bI SES EOS br 8 3 Refinement results 2 3 2444 624 4 434 2 cy QUE A Ru RES 9 Chemical composition 10 Scan batch conversion 30 30 30 30 30 31 31 32 32 32 32 33 34 34 35 35 36 36 36 37 38 40 42 42 42 42 43 43 45 48 11 CIF and ICDD XML import 11 1 Automatic conversion of thermal displacement parameters 12 Instrument configurations 13 Scan File Handling A Bundle File Structure AJ Windows ee 22 0 2 be ee a RR ee A2 MacOS Xie 38 e semel Some seat wae ana a Bd ace aay eas 49 49 53 55 62 62 62 63 65 1 Introduction Profex is a graphical user interface for Rietveld refinement of powder X ray diffraction data It supports two different Rietveld backends BGMN 1 and FullProf 2k 2 Profex does not perform any refinement calculations but it simplifies the use of the Rietveld backends in many ways e It displays diffraction patterns e It converts pattern files to formats supported by the backends e It simplifies setting up control files with databases for crystal structures and instrument configurations e It handles file names e It summarizes the results and supports export to CSV file format e It supports batch processing and parallel processing of several datasets at a time Profex runs on Windows Linux and Mac OS X operating systems and is available as free so
15. lt structure gt phaseB str lt structure gt lt structure gt phaseC str lt structure gt lt structures gt lt preset gt The preset is now ready for use The following files should be present Presets tsoxyz ISOxyz pfp xpert ads 10mm geq xpert ads 10mm tpl phaseA str phaseB str phaseC str It can be applied as follows 1 Load your raw data using File gt Open Graph File 2 Select Project Refinement Presets ISOxyz or use the button in the project toolbar to create the control file 3 Click Run Run Refinement 41 8 Exporting data 8 1 Graphs Scans shown in the plot area can be exported to various formats Depending on the export format some information may get lost if it is not supported by the output format Scans can be exported as follows 1 Make sure the graph to be exported is shown by selecting the project and showing the Graph tab 2 Select File Save File As 3 Select the format for the export in the file format dropdown menu 4 Specify the file name and save the file Profex exports some generic file formats and some formats specific for other applications The generic formats are useful for most users interested in further data processing or creation of fig ures They will be discussed in further detail in the following paragraphs 8 1 1 ASCII free format XY A generic text format writing t
16. ome lt user gt BGMN Templates Structures home user BGMN Templates Devices home user BGMN Templates Presets 3 opt Structures opt Devices opt Presets 4 opt BGMN Templat opt BGMN Templa tes Structures tes Devices opt BGMN Templa 3 1 3 Mac OS X tes Presets On Mac OS X the BGMN installation and Structures and Devices directories will be scanned rela tive to the path of the Profex application bundle Profex expects to find the following files starting at the position of the Profex application bundle e location of pro e location of pro e location of pro e location of pro 3 2 Manual setup fex app gt BGMN Temp fex app gt BGMN Temp fex app gt BGMN Temp fex app gt BGMNwin bgmn lates Structures lates Devices lates Presets The following sections describe how to configure Profex to find the BGMN backend as well as the structure device and preset database directories manually There are some scenarios when automatic setup will fail and the backend and database directories are not found or when the automatic configuration is not desired e if only Profex was downloaded instead of a Profex BGMN bundle e if the Profex and BGMN folders from the bundle were not copied to the same location on the harddisk e if Profex is supposed to use existing BGMN and structure device databases rather than the on
17. the main window e g to be placed on another screen or closed 5 1 User Interface Elements The following list explains the elements of the user interface shown in Fig Blin more detail 1 Menu bar gives access to most features as well as the program s preferences All menu items are discussed in section 2 Main tool bar gives access to file operating features such as opening saving etc 3 Project tool bar gives access to project related functions such as opening closing structure files exporting results adding removing phases etc 4 Refinement tool bar gives access to starting stopping refinements or batch refinements 5 Reference structure tool bar allows to select reference structures to display hkl indices as well as to start scanning and indexing new structure files See section 5 5 for more information 6 Plot area displays raw or refined scans and opens text editors for control files results files structure files or generic text files 7 Projects window lists all open projects and the refinement status Selecting a project from this list will show it in the central plot area 8 Plot options lists all scans loaded in the plot area The Show checkbox can be used to show hide certain scans to customize the appearance of the plot 9 Refinement protocol shows output generated by the refinement backend 10 Global Parameters and GOALs shows a summary table of refined global parameters Listing EPS parameters can
18. 0 161 162 163 164 165 166 17 Trigonal show all am SpacegroupNo 167 HermannMauguin R 32 c Setting 1 Lattice Trigonal UniqueAxis c Close Figure 16 Help BGMN SPACEGRP DAT opens a dialog to browse all space group numbers settings and atomic positions 51 CIF File _che nical_name_mineral _che _che dat che sym _spa _sym mical name common mical name systematic abase code a z mical formula a z metry Int Tables number ce group IT number metry space group name H M Space group name H M alt celllengtha b c cell angle alpha beta gamma atom site label atom site type symbol atom site Wyckoff symbol atom site occupancy atom site fract x y _2 atom site B iso or equiv atom site U iso or equiv _atom_site_aniso_U_ 1 3 atom 1 Site aniso B 1 3 STR File PHASE name PHASE name PHASE name Reference name Formula name SpacegroupNo number SpacegroupNo number HermannMauguin symbol HermannMauguin symbol A B C value ALPHA BETA GAMMA value E M n value E M n value Wyckoff symbol E Mtn value x y z value TDS value TDS value TDS value TDS value Table 2 Assignment of CIF parameter tags to BGMN STR variables 12 Instrument configurations Raytraced geometric peak profiles must be cal
19. 27 Reset 27 Right Vertical Dockable Window 16 16 17 19 18 Double Click EPS Export Chemistry Global Parameters Graphs Local Parameters Results Extension First Steps 15 Fityk Fix parameter 4 Font Axis Labels 32 hkl Indices Legend Title Fullprof GEOMET EXE 10 B3 53 GERTEST EXE 10 53 GEWICHT Gnuplot GOAL 16 18 19 28 29 B4 Graph File Open Remove Save Save As 25 GraphFile Open hkl Indices Font Range ICDD Import 26 Import CIF File 49 ICDD XML 49 Insert Scans Installation 6 Bundle 6 Compiling 7 Linux 6 Mac OS X Windows 6 Instrument Instrument Configuration Isotropic k1 34 k2 34 rena Font Line a Line Width Display Printing List Coordinates Main Window MAKEGEO EXE Menu Menu Bar 16 Micro Absorption Multi Scan Files NTHREADS Open file 24 OUTPUT EXE 10 B3 Parameters Chemistry 66 Global Local PDF Performance Phase Add Remove Phase Pattern Pixel Image Plot Plot Area Plot Options PNG Preferences Appearance Editor Fonts General Graph Reference Structure Scan esc E Preset Database 8H10 Presets Presets Database B3 Print profex exe 8 Musics Close Close AIL 26 Organization Projects Quit Recent Graph WE Text Files Redo 6 Referen
20. E HERE RER ped 20 00 25 00 30 00 35 00 40 00 45 00 50 00 55 00 Angle 28 AAA q oy 50000 F KB Kaa 3 E az J 40000 E j 4 L i i 4 m Ht J 30000 H B E 1 1 7 B tr 1 E F i i 7 S 20000 i H m o i H 1 o 5 n M al i Hl gt Hn 4 3 F if 2 10000 i d 4 5 dE 5 F i di a i E J H bg L E i it i it i tt i it F i HE 7 i pa N bs i id o Lara ra aaa ara ra ra Dara aaa ra aa ra ra ra ar aa ra ra ra rc aa arra ra ra aia a a ara ra Da rada a rar Dra 30 00 31 00 32 00 33 00 34 00 35 00 36 00 37 00 Angle 2Theta c Figure 7 Different cursors of the plot area a counting noise cursor b cross hair cursor c spectral lines cursor 22 q AA A ATT A 900 55 u 14022810 1402281 0 M 1402282 0 800 14022820 7 en hund Me ant 14022840 3 700 h ee ll Re sd F 7 300 j i N M J rn O EM LA Mi SNS E i E ac da MNT UNE HAN SAM i Ni a 14022840 4 1402285 0 14022860 o EE Intensity counts Intensity counts gt S T 10 00 20 00 30 00 40 00 50 00 60 01 10 00 20 00 30 00 40 00 50 00 60 00 Angle 2Theta Angle 2Theta a b Figure 8 Vertically a and both vertically and horizontally stacked scans fb SSS SS SA SS Se 8000 F 13041110 f 13041110 F 13051430 13051430 7000 4 4000 f 7 di 1920310 1304031 0
21. File Export Local Parameters and GOALs or press Shift Ctrl E or the corresponding button in the project tool bar to export the local results to a CSV file The exported CSV files can be opened in a spreadsheet program such as Microsoft Excel Li breOffice Calc or Softmaker PlanMaker Specify the semicolon as field separator and use the spreadsheet program s sort feature to sort the parameters as needed 1Profex supports a large number of raw data formats If a format is not supported or support is broken other software such as PowDLL is required to convert the scan to a format supported by Profex 15 5 Main Window The program s main window features a menu bar and several tool bars to access all functions and settings Fig b The central area of the main window is occupied by the plot area and optionally one or several text editors which are accessible by tabs at the top of the plot area The plot area cannot be closed but text editors can be closed by clicking the close button on their tab The central area is surrounded by several dockable windows showing additional information and giving access to more features These dockable windows can be closed and opened from the Window menu They can also be re arranged Fig le by clicking on the title bar showing the window s name and dragging it to another location Dockable windows can be stacked on top of each other to hide less frequently used windows or detached from
22. Profex User Manual Version 3 5 0 BGMN Backend Nicola D belin May 6 2015 Contents 1 Introduction 21 WindOWS e o a ne EX a eo X tute a RUE CX oe Rzk a 2 1 1 Profex BGMN bundle 2 222222 cA A RR 2 2 1 Getting the source ove 8 3 8 88 ONES BEES SS A AA 222 Compiling from source code 2444 4 h4 2d 54 eb ee rose da 23 MacOS Xl uu posce eomm a n sh i we aap bee uo e woe en de woe 3 1 Automaliesetip Ao 4 22 44 eat BILL Windows storas wa wo eom a Er ee xA ee ne N ee ee tee ee ge gee A STEIF Mac OD Al ee ee TT 8 2 Manual set p 224 Sa 32 die 4 ran EROR E E Ba qi E a a EN a ds do och aes er Tee A E n A E oe Gace eons 5427 STR File Handli g es e 24 e EKER REOR a REOR OS 343 Device Configuration Files x 8024 Er c3 RR 54 4 82 es 3 4 4 Refinement Preset Files en 4 First steps 5 Main Window 5 1 User Interface Elements ss 5 2 Dockable windows pablo Projects sase IEA RAR UA AAA 5 2 3 Refinement protocol i s se secs a ee nu 5 24 Global Parameters and GOALS 5 2 5 Local Parameters 2 22 22 CC a ee 52 6 Ch mistty 2 2 05 Yuan 2 nes a DES AREA 5 27 Context Helpi uox cx ai eR ee ea ee a E aanib gai A ee at eve a re re eae ee Ben 5 3 1 Stacking Scans As Text Editors y mss aos dex 8 200 4 Roe RUE a Xo NES Ae a ee 541 Control Files oi 8644446 6 2222 22 23 Oe as Rs SSR SoG Bee 54 2 Structure Files 4 2 een doe nn aa aa B
23. ailable the default wavelength specified in the preferences dialog will be used see section For monochromatic synchrotron radiation this feature is meaningless Use the cross hair cursor instead 20 Additionally peaks from characteristic Tungsten radiation WLa and WLp can be shown by activating the option Show characteristic Tungsten lines with spectral line cursor in the preferences dialog section This allows to inspect the diffraction pattern for Tungsten contamination lines caused by aging X ray tubes The relative intensities of Tungsten lines are WLa 100 WLB4 49 4 WLB 20 2 WLB is not shown Load reference structure Double click with left mouse button will load the reference structure with it s strongest peak closest to the double click position This is a very simplistic way for phase identification however it can be very efficient and useful in some situations Note that only indexed structure files are considered Refer to section 5 5 for more information on indexing of references structure files Also note that the strongest peak of the reference structure indices depends on the instrument configuration used for indexing fix or variable divergence slit and may therefore not be at the location of the currently processed scan Scale reference lines Hold the middle mouse button and move the mouse vertically to scale the intensity of reference lines Dragging the lines below the line of zero counts allows
24. and the setting of Edit Preferences gt BGMN Convert raw scans to XY format If a format natively supported by BGMN is detected the file will be used without conversion If the format is not supported the behavior will depend on the setting Convert raw scans to XY format If active the file will be converted to xy format and the VAL n file entry will be adapted accordingly If inactive no conversion will be done and it is in the user s responsibility to guarantee correct file names and formats See Fig 18 for more explanations However the processes described above represent relatively simple scenarios when the raw scan file is opened and the format and file name are known In many situations it gets a lot trickier to determine the correct file name The following situation represents a worst case A DIA file is opened conversion to xy is inactive and the control file is created from another project using the Copy control file feature Normally when a DIA file exists a control file should also exist with a valid VAL n entry However when sharing or moving DIA files or when the base name of the DIA and control file do not match it may still occur that a DIA file is present but the corresponding control file cannot be located Trying to find the correct raw scan file used to create die DIA file is difficult in such a situation 1 The control file copied over from another project contains input and output
25. assing the dialog mentioned above Element Oxide and Molecular Weight table This table holds the oxide formula and oxide molec ular weight for each element Edit the values by double clicking a cell Double clicking an element cell will open a dialog to determine oxides and their molecular weight Double clicking any other cell allows direct input of oxide formulas and values Reset Resets the table to the internal default values All customizations will be lost 35 7 Adding and Removing Structure Files 7 1 Add Phase Dialog One of Profex central components is the Add Phase dialog Fig 10 It is accessed by clicking Project Add Phase or pressing F8 or the corresponding button on the project tool bar This dialog is used to easily create or modify the refinement control file It will automatically add a STRUC n reference and related GOALs for phase quantification to the control file and copy the selected STR files from the structure file database to the working directory Fig 4 The individual elements of this dialog are described in detail below Generate default control file If this option is checked Profex will generate a default control file for the selected instrument configuration If a template file is found section B 4 it will be used to create the control file Else Profex will present a dialog asking for basic information about the instrument configuration If the option is active an existing cont
26. ate a control file from a template file 58 Start Copy control file Temporarily store file name of previous VAL n entry if available m Apply new con trol file content Previous VAL n empty VAL n previous VAL file yes Convert to xy VAL n dis played scan file p Disp scan file native BGMN format VAL n dis played scan file Search natively supported file with the same base name at the same location as the displayed scan file Alternative scan file found VAL n alter native scan file Leave VAL n empty display warning Proceed to VAL file verification Figure 20 VAL file name handling when using the Copy control file function 59 Start VAL file verification VAL n dis played scan file Convert to xy Change basename of VAL n file to project base name keep extension and format of previous entry VAL n native BGMN format VAL n file exists VAL n dis played scan file Displayed scan format native VAL n pro Proceed to Cre jectBasename xy ate VAL file Figure 21 Automatic verification of a VAL n file entry in the SAV control file This function is called at
27. but not for other Rietveld refinement backends See sections 9 for more information 5 2 7 Context Help This window shows the context help which can be accessed by placing the mouse cursor on a keyword in a control file and pressing F1 Context help is available for BGMN but may not be available for other Rietveld refinement backends see section 5 6 8 19 5 3 The Plot area The plot area is the central area of the main window It shows the loaded scans Some appearance options can be configured in the preferences dialog as described in section 6 2 Visibilities of the legend hkl indices and phase patterns can globally be switched on or off in the menu View Plot as described in section b 6 The plot area interacts with the following mouse and key operations A summary of mouse and keyboard commands can be displayed by pressing the Shift key or selecting Help Mouse and keyboard commands Moving the mouse cursor The cursor position will be displayed in the status bar at the bottom of the main window The horizontal and vertical position will be shown in degrees 20 and counts or counts per second depending on the unit of the y axis see section 6 Addition ally the horizontal position will also be shown as d value in A The wavelength is used to calculate d values If no wavelength information is found in the scan file Profex will use the default wavelength specified in the preferences see section 6
28. ce Structure Automatic Indexing 30 Clear Buffer B0 hkl Range B1 Index 25 Reset 25 Refine parameter 24 Refinement Abort 28 Run 15 8 TDS 49 Run Batch 28 Template 11 Refinement Protocol 16 18 29 Template File Remove Phase 28 36 Text AME Remove Scan Text File Reset File 26 an Restore open projects 30 Save RP Save As 25 Run Texture Thermal Displacement Parameters 49 Scalable vector graphics 43 48 Thumbnail 31 Scalin 8 z Title Scan Font 2 Insert 25 Tool Bar 16 24 Remove Layout Scan oc Main Tool Bar Color Project Tool Bar 16 Point Style B2 Reference Structure Setup 8 Reference Structure Tool Bar 16 Automatic B Refinement Tool Bar 16 Linux B Tungsten 21 Mac OS X 9 Manual 9 Un Zoom 20 Windows 8 Undo 26 SPACEGRPDAT Update Graph Spectral line cursor 20 User A Stacking Let bm View 27 Reset 27 Visibility 18 Right Wavelength Vertical Wind indow 29 Status Bar 17 WINE STR File Handling 11 3 Structure XML Fil Structure Database Import Structure File 37 Close All Zoom Open dea Zoom Range P7 Structure file Summary Table B4 SVG Switch to Control File Graph 27 Output File 27 Symbol Size 67
29. cess has completed BGMN has created two new files ger and geq which are required for refinements If they were created outside of the Device database directory they should be moved there in order to appear in the Add Phase dialog It is also recommended to manually create a template file for the new configuration as described in section 3 4 3 Running GERTEST will also create a file with the extension xy which contains a simulated pattern with peaks at regular positions This is convenient for comparing the peak profile shape of different instruments graphically similar to Tools gt Show Device Function in BGMNwin but otherwise it is of not much use Using Instrument New Configuration will allow to read some hardware information from Bruker RAW V4 Bruker BRML V5 and PANalytical XRDML files to create a BGMN instru ment configuration file from scratch Other raw data formats are not supported Usually several variable required by BGMN will still not be available from the raw data files and will thus have to be entered manually n 53 X Instrument Configuration op BGMN Templates Devices cubix ads 10mm sav y Q9 June 04 2012 Device Configuration Detector PW3011 Point Detector Soller Slits 0 04 rad Divergence Slit variable 10 mm Goniometer Radius 200 mm SR a a a BF a ak a L af ak af af af af Output files for Geomet and MakeGeq 4 GA He 2 2 2 2 2 2 2 2 2 2 2 2
30. comparing peaks in the difference curve List of coordinates Hold the Ctrl key and double click with the left mouse button to copy the co ordinates of the mouse cursor to the refinement output console From there the coordinates can be copied and pasted to another program for further processing Scans from different graph files can be added to the plot area by the function File Insert Graph File Several files can be selected at a time To remove a specific scan select it in the dock window Plot Options and click File Remove scan When starting a refinement the project s main graph file will automatically be reloaded and all added or removed scans will be reset to the main graph file s content 5 3 1 Stacking Scans All scans in the plot area originating from a single graph file or combined from several graph files using File Insert Graph File can be stacked vertically and or horizontally Offsets can be adjusted by View Increase vertical displacement View Decrease vertical displacement View Displace left and View Displace right All displacements can be reset by View Reset Displacement An initial offset will be applied which can be reduced incrementally by calling the function moving the scans in the opposite direction The following commands were used to create the graphs shown in Fig 1 View Increase vertical displacement to stack the scans vertical
31. convenience function for easy showing or hiding all phase patterns but the same result can be obtained by manually checking or unchecking all phase patterns of all open projects hkl tick marks are considered as part of phase patterns Showing hiding a phase pattern will also show or hide the phase s hkl lines By using the functions in View Plot see section b 6 3 drawing of hkl lines and phase patterns can be controlled separately This allows to draw either no phase information hkl lines only phase patterns only or both Scans can be added or removed to the project by the functions File Insert Graph File and File Remove Scan However as soon as the main graph file is reloaded for example automatically during a refinement and added or removed scans will be reset and only the content of the reloaded file will be shown 5 2 3 Refinement protocol This windows shows the output of the Rietveld refinement backend 5 2 4 Global Parameters and GOALs At the end of the refinement this window shows a summary of the refinement results The dis played parameters depend on the Rietveld refinement backend For BGMN the table shows all global goals and parameters including estimated standard deviations ESD as calculated by BGMN Some configuration options are available in the preferences as described in section 6 3 4 Values summarized here can also be exported to a CSV table using the function File Export
32. culated by BGMN prior to refinement The instru ment configuration is described in a control file and the two programs GEOMET and MAKEGEQ which are part of the BGMN software distribution are used to calculate and interpolate the peak profile in a specific 20 range For more information please refer to the BGMN documentation 1 Profex allows editing instrument control files in a simple text editor and runs GEOMET and MAKEGEQ to generate the output files A common workflow to modify an existing device configu ration is shown below 1 Run Profex and click Instrument Edit Configuration Profex will open a file dialog in the Device database directory Select the instrument control file sav you intend to modify 2 The instrument dialog shown in Fig 17 will be shown Edit the file as intended 3 Save the file under a new name using the dialog s Save As button Be sure to save it ina directory with write access 4 Check the options Raytrace GEOMET and Interpolate MakeGEQ The option Cal culate Profile GERTEST is optional 5 Check the option Create Template for Refinement Control File and select your tube s target material and the type of monochromator you use 6 Click the Run button and wait until the progress dialog has completed Depending on hardware simulated angular range and device configuration this process may take several minutes to complete Once the pro
33. double clicking on the color cell If more scans are loaded than colors are available from the list a random color will be created and added to the list It can be changed manually later Line widths can be changed on the Graph s General Appearance page Point Style Select the style to draw scans Solid draws the scan as a solid line Points draws a dot at the measured position Cross draws a cross at the measured position Symbol sizes of crosses and points can be changed on the Graph s General Appearance page Add another color to the color list Remove the currently selected color from the list 6 3 BGMN 6 3 1 Configuration BGMN Backend BGMN Executable Select the BGMN executable file This file is part of the BGMN installation It is called BGMN EXE on Windows and bgmn on Mac OS X and Linux 32 MakeGEQ Executable Select the MakeGEQ executable file This file is part of the BGMN installa tion It is called MakeGEQ EXE on Windows and makegeq on Mac OS X and Linux Geomet Executable Select the Geomet executable file This file is part of the BGMN installation It is called GEOMET EXE on Windows and geomet on Mac OS X and Linux Output Executable Select the Output executable file This file is part of the BGMN installation It is called OUTPUT EXE on Windows and output on Mac OS X and Linux Run in WINE This box is only available on Linux and Mac OS X It allows to use the Window
34. e mouse cursor to be fixed i e not refined Refine Isotropically This will release the parameter under the mouse cursor for isotropic refine ment Reasonable lower and upper limits will be applied by default Refine Anisotropically This will release the parameter under the mouse cursor for anisotropic refinement A reasonable upper limit will be applied by default Note that if the parameter cannot be refined anisotropically e g unit cell parameters fractional coordinates etc this option will not be available 5 5 Tool bars All functions shown in the main toolbar project toolbar and refinement toolbar are also accessible in the menu bar and are described in detail in section 5 6 Toolbars can be re arranged by dragging the left end to another position or shown hiden by right clicking on a toolbar and checking or unchecking the toolbar in the context menu Elements of the reference structure toolbar are only visible if at least one project is loaded They are not accessible through a menu only by the toolbar buttons Reference structures A menu allowing to select a reference structure from all STR files found in the structure database directory If selected the STR file s hkl lines will be shown in the graph This is a generic way of phase identification When using the Add Phase dialog 24 while a reference structure is displayed this structure file will be pre selected in the Add Phase dialog If STR file
35. easy sorting and statistical evaluation of the results The following example shows how the exported CSV file with global parameters and goals looks like if opened in a text editor Table shows how the same data looks after importing and sorting in a spreadsheet program File Sample Parameter Goal Value ESD lt path gt scanl 1lst scanl alphaTCP sum 0 0311 0 0023 lt path gt scanl 1lst scanl hap sum 0 9689 0 0023 Xpath scan2 1st scan2 alphaTCP sum 0 0161 0 0022 lt path gt scan2 1st scan2 hap sum 0 9839 0 0022 lt path gt scan3 1st scan3 alphaTCP sum 0 0147 0 0024 lt path gt scan3 1st scan3 hap sum 0 9853 0 0024 9 Chemical composition After the refinement Profex will calculate the bulk chemical composition of the sample from the structural information and refined site occupancies reported in the list file 1st The elemen tal composition expressed in wt of the oxide is shown in the Chemistry dockable widget Fig 12 In a first step Profex will calculate the chemical composition of each phase and nor malize it to 100 Fig 12a In order to calculate the bulk composition of the entire sample Profex 45 Chemistry 599 Quantity Goal Al203 wt CaO wt F wt 96 Li2O wt Corundum 100 00 0 00 0 00 0 00 Fluorite 0 00 59 61 40 39 0 00 LiF 0 00 0 00 38 87 61 13 Total a Chemistry ON Quantity Goal Al203 wt CaO wt F wt 96 Li2O wt Corundum corund
36. erences 1 http www bgmn de 2 https www ill eu sites fullprof 3 http profex doebelin org 4 http qt project org 5 http www zlib net 6 http quazip sourceforge net 7 http support apple com kb ht3696 8 Andrew VJ The Relative Intensities of the Las B1 B and Y Lines in Tantalum Tungsten Iridium and Platinum Phys Rev 42 5 591 1932 9 http www iucr org resources cif spec version1 1 cifsyntax 10 http users uoi gr nkourkou powdll 11 http fityk nieto pl 12 Fischer R X Tillmanns E The equivalent isotropic displacement factor Acta Cryst C44 1988 775 776 64 Index Bij Biso Ueuiv ui Abort 28 About Profex 9 Add Phase 15 27 B6 Anisotropic AntiAliasing ASCII free format 42 Axis Font Labels 32 y axis Scaling 31 B1 Backend 5 6 Batch Conversion Batch Refinement BGMN Configuration BGMN Variables BGMN EXE B 10 22 BGMNwin Brindley Chemical Composition Chemical pa Chemistry 19 35 45 CIF File 34 Limi B Limits 3 Color ee 29 Context Help 16 19 29 Context menu 23 Control file 24 Coordinates 1 Copy Control s Counting Noise CPU Cores Cross Hair 20 Cursor Custom Profile Function B3 65 Default Control File 15 B6 Default Project Type Device Configuration Device Database 8 Displacement Left
37. erts the current project s control file to the state before the last refinement This function is only used for the Fullprof 2k backend but not for BGMN because BGMN usually does not modify STR and SAV files Preferences Opens the program s preferences dialog All preference options are discussed in detail in section 6 26 5 6 3 View Switch to Graphs Ctrl 1 Raises the Graph page of all projects Switch to Control Files Ctrl 2 Raises page 2 usually the control file of all projects Switch to Output Files Ctrl 3 Raises page 3 usually the results file of all projects Set Zoom Range Opens a dialog to zoom the graph to precise upper and lower limits for angle and intensity Show Hide Phase Patterns Ctrl 0 Activates or deactivates visibility of all phases This option applies to all open projects It only checks or unchecks the visibility boxes of all phase pat terns in the Plot Options list for convenient displaying or hiding of all phases Individual phases can be shown or hidden by selecting or un selecting the show option in the Plot Options list More information is given in section 5 2 2 Plot Configure the visibility of the following elements on the plot Phase Patterns Shows or hides patterns of phases Legend Shows or hides the plot legend hkl Indices Shows or hides the hkl index tick marks at the top of the plots Increase Vertical Displacement Ctrl Up Applies a regular vertical offset to all scans The
38. es downloaded with the bundle e on Linux no bundles are available In these cases manual configuration is necessary Follow these instructions to set up Profex manually 1 Run Profex and go to Edit Preferences 2 On the page General set the Default Project Type to BGMN Fig 2 3 Go to page BGMN On the tab Configuration check the configuration of BGMN Back end If auto detection was successful the lines for executable files and files directories are not empty Fig 4 If the lines are empty click the button on the right of each line and navigate to the corre sponding executable file The file names depend on the operating system On Windows the files are called BGMN EXE MAKEG EQ EX E G EOM ET EX E and OUTPUT EXI Mac OS X these files are called bgmn makegeq geomet and output E On Linux and A Preferences gc amp General Graphs Configuration STR File Handling CIF File Handling Summary lt gt Fullprof BGMN Backend Chemistry BGMN Executable lopt bgmnwin bgmn MakeGEQ Executable opt bgmnwin makegeg Geomet Executable Jopt bgmnwin geomet Output Executable Jopt bgmnwin output GERTEST Executable opt bgmnwin gertest Run in WINE Structure Files Directory pt BGMN Templates Structures X Preferences Yy s x Device Files Directory op BGMN Templates Devices Editor Presets Directory opt BGMN Templa
39. eset file for a standard refinement according to ISOxyz to quantify impurities of phaseB and phaseC in a sample of phaseA Since only traces of impurities are expected no texture or peak broadening shall be refined in phaseB and phaseC Additionally the angular range of the file measured from 5 60 20 shall be restricted to 10 60 20 Instrument configuration xpert ads 10mm geq will be used to measure the data and a control file tem plate xpert ads 10mm tpl has already been created along with the instrument configuration files 1 Create a new directory ISOxyz in the Presets directory 2 Copy the structure files phaseA str phaseB str and phaseC str from the Struc tures to the Presets ISOxyz directory 3 Modify the phase str files to your needs i e refine texture and peak broadening in phaseA str but fix them in phaseB str and phaseC str 4 Copy the instrument and template files xpert ads 10mm geqand xpert ads 10mm tpl from the Devices to the Presets ISOxyz directory 40 5 Edit the template file xpert ads 10mm tpl to your needs by adding WMIN 10 6 Create a new preset file in the Presets ISOxyz directory with the following content lt xml version 1 0 encoding UTF 8 gt preset name ISOxyz gt lt device gt xpert ads 10mm geq lt device gt lt template gt xpert ads 10mm tpl lt template gt lt structures gt lt structure gt phaseA str lt structure gt
40. ets the font of the text editor and refinement protocol window 6 1 2 Appearance and Behaviour Default Project Type For files not specific for either BGMN or Fullprof 2k this option determines which type of project will be created when such a file is opened The file type is identified by the file extension File extensions can also be associated with either of the two backends by adding the exten sion either to the list of File Extensions associated with BGMN or File Extensions asso ciated with Fullprof on the corresponding backend configuration pages of the preferences dialog Toolbar Layout Select how icons and text in Profex toolbars are shown Multi Scan Files Select whether multi range files will be shown as individual scans as the sum of all ranges or as the average of all ranges Default Wavelength This wavelength given in is used for scan files not containing any infor mation about the wavelength Always use default Wavelength If checked Profex will ignore the wavelength read from the scan file and always use the default wavelength to calculate d values from diffraction angles Restore open projects If checked Profex will load all previously open graph files upon program start 6 1 3 Reference Structures Automatically select best matching reference phase When opening a graph file automatically search and select the reference phase with it s strongest peak at the position of the scan s highest intensity
41. ff in the preferences dialog by checking or unchecking the option Edit Preferences BGMN Convert raw scans to XY format Scan file handling by Profex will be different depending on this setting Unless conversion is not desired for specific reasons users are strongly advised to activate this option It is a surprisingly complex task to determine the correct file name of a project s raw scan VAL n keyword in the control file The possible scenarios to be considered are manifold Profex has sophisticated routines to determine the best guess for a VAL file name under all circumstances These routines are illustrated in Figures 19 22 In principle when creating a new project a raw scan file as obtained from the instrument is opened and a new control file is created either by using the Add a new phase dialog or the Copy control file function see section A Either way the loaded raw scan file determines the location and the base name of the project and all input and output file names in the control file will automatically be set to this scan s file base name More information on file name handling is givenin section 3 4 3 The scan file name to be read by the BGMN Rietveld backend is specified with the VAL n ScanFile xxx line in the control file The scan file name is given by the project name as described above but the file format and extension is determined by Profex automatically depending on the raw scan format
42. file names VAL DIAGRAMM OUTPUT etc of the source project All file names must be changed to the destination project The VAL file name found in this control file must not be used 2 The displayed scan is a DIA file which cannot be used as input file 55 3 Converting the DIA file to xy is not allowed 4 There is no reference to the raw scan in any of the available files 5 In that case Profex will scan the directory of the DIA file for a raw scan file in a format natively supported by BGMN But there is no guarantee that such a file is found This is one of many scenarios when finding the correct VAL file name is not trivial However the complex processes illustrated in Figures cover most situations and if no solution can be found a warning will be issued 56 If the raw scan format here xrdml is not natively supported by BGMN Profex will change the VAL n file name to xy and convert the file automatically 2 working directory scan_l sav Input files VAL 1 scan_1 xy OUTP DIAGRAMM scan_l dia scan_1 xrdml VERZERR instrument geq structure l str LAMBDA CU instrument sav STRUC 1 structure_l str i instrument geq Output files instrument ger LIST scan_1 1lst UT scan_l par If conversion to xy is deactivated VAL n will be the raw scan file If it is not supported natively by BGMN e g xrdml refinement will not start e workin
43. ft ware licensed under the GNU General Public License GPL version 2 or any later version The latest version can be downloaded from 3 2 Installation 2 1 Windows 2 1 1 Profex BGMN bundle Since Profex requires a Rietveld refinement backend a bundle containing both Profex and BGMN is offered for download on the Profex website Using the bundle is the preferred way of installa tion if no previous installation is present on the computer The directory and file structure of the bundle is shown in appendix The software does not need installation The downloaded archive can be extracted to any location on the computer Automatic configuration of Profex will be able to locate the BGMN installation if the relative paths of the BGMNwin and Profex 3 5 0 folders are maintained Therefore it is recommended to copy the entire bundle to the same location on the hard disk as shown in Fig 1 Follow these instructions to install BGMN and Profex 1 Download Profex BGMN Bundle 3 5 0 zip from 2 Extract the bundle to your harddisk e g C Program Files 3 Run Profex by executing the file profex exe e g CA Program Files Profex 3 5 01 profex exe The file and directory structure of the bundle is explained in appendix A Profex is also avail able for download without BGMN This is the preferred way of installation if BGMN is already installed on the computer or if previous versions of Profex are to be upgraded The Profex binary archive does n
44. g directory 2 scan_l sav Input files VAL 1 scan_1 xrdml OUTP DIAGRAMM scan_l dia scan_l xrdml VERZERR instrument geq structure l str LAMBDA CU instrument sav STRUC 1 structure_l str i instrument geq Output files instrument ger LIST scan_1 1lst UT scan l par Natively supported file formats here Seifert val do not require conversion to xy Profex will use the raw scan file name for the VAL n entry regardless of the state of the Convert raw scans to XY setting o working directory Input files i Scan l sav VAL 1 2scan 1 val scan_l val VERZERR instrument geq structure l str LAMBDA CU instrument sav STRUC 1 structure_l str instrument geq Output files L instrument ger LrSTsscan list OUTP DIAGRAMM scan_l dia UT scan_l par Figure 18 Some examples for working and failing VAL n file scenarios 57 Start Generate de fault control file in Add Phase dialog y Temporarily store pre vious VAL n file name if available Apply control file con tent from template Previous VAL file name available VAL n previous VAL file p VAL n remains empty Proceed to Verify VAL file Figure 19 VAL file handling when calling the Add Phase dialog and activating the option Gen erate default control file to cre
45. g the cursor on a file name and clicking with the right mouse button the context menu will show the action Open File at the bottom Depending on the file type the file will be opened as a scan file VAL n DIAGRAMM or as a text file GTRUC n STRUCOUTIn SimpleSTRUCOUT n RESOUT n PDBOUT n FCFOUTIn Note that if the file name contains spaces or underscores the file name must be selected before right clicking Else the file name will not be recognized correctly Add lt output gt file When placing the cursor on aSTRUC n file line and clicking the right mouse button the context menu will offer to add various structure output files The refined crystal structure will be written to these files at the end of the refinement They may be useful for import into other programs e g for structure visualization or publication in databases or papers The output file names will be set to lt phaseName gt lt projectBasename gt ext so as to create unique file names and prevent accidential overwriting of output files from other projects in the same directory The formats offered are STRUCOUT n SimpleSTRUCOUT n RESOUT n PDBOUT n and FCFOUT n Please refer to the BGMN documentation for more information on the file formats 5 4 2 Structure Files When placing the cursor on a parameter and clicking with the right mouse button the context menu will offer the following actions Fix Parameter This will set the parameter under th
46. ge the structure files E g create a copy of structure l str and name it structure_la str Then change the STRUC 1 structure_l str line in the corre sponding control file to STRUC 1 structure la str e Manually manage structure files by creating sub directories for structure files only E g create a copy of structure l str in strFiles 1 structure 1 str Then change the STRUC 1 structure_1 str line in the corresponding control file to STRUC 1 estrFiles l structure l str The project directory remains unchanged but it will access the structure files in a specific sub directory which can be managed manually for each project 7 4 Refinement Preset For routine analyses or refinements of series of measurements it is often recommended to use exactly the same structure files and refinement strategy Instead of using the Add Phase dialog each time to select the device configuration and structure files this information can also be loaded from a refinement preset file A preset thus automates the choice of device configuration and structure files and reduces the user input to a single mouse click Preset files store their data in XML format Their storage location can be configured in Edit Preferences gt BGMN Configuration Presets directory as described in section 3 4 When opened in a text editor the file must have the following structure lt xml version 1 0 encoding UTF 8 gt lt preset name anyName
47. gt tags will be copied to the project directory These tags can be used for arbitrary files such as descriptions background scans raw data report files etc It is important to specify whether the file is stored in text or binary format For text format files Profex will convert the line endings to the target platform to maintain platform independence Binary files will be copied without modification Note that custom profile functions Edit Preferences gt BGMN STR File Handling will not be applied when using presets as it would undermine the purpose of reproducing pre cisely defined refinement scenarios 7 4 1 Creating and using presets Presets can be created from an existing refinement or manually To create a preset from an existing refinement set up an example refinement Add all phases GOALs custom calculations etc and modify the structure files as desired Then select Project Save as Refinement Preset and save the file in the Preset directory specified in the Preferences dialog section 5 The preset is now ready to use Note that write access to the Presets directory is required Manually creating a Refinement Preset The following example for manual preset creation as sumes that the Devices Structures and Presets directories are stored at the same place for example inside a Profex BGMN application bundle as described in section A The goal of this hypothetical example is to create a pr
48. he data in columns starting with the angle followed by columns with intensities for each scan These files can be imported in spreadsheet or plotting software for further processing Spreadsheet software includes Microsoft Excel LibreOffice Calc SoftMaker PlanMaker and others Plotting software includes OriginLab Origin GNUplot and others hkl lines will not be exported Scan colors line styles and the legend will also get lost during the export Visibilities of scans will be ignored all scans will be exported A white space character is used for field separation The following example shows an exported ASCII free format file with all scans written into one file The first column contains the x values 20 angle the following columns contain y values l ps Icaler laiff Ivackground and two phase patterns Note that the phase patterns include the background intensity 4 007500 22 000000 21 070000 0 930000 21 050000 21 050000 21 070000 4 022500 19 000000 20 910000 1 910000 20 890000 20 890000 20 910000 4 037500 20 000000 20 760000 0 760000 20 740000 20 740000 20 760000 4 052500 22 000000 20 610000 1 390000 20 590000 20 590000 20 610000 4 067500 24 000000 20 470000 3 530000 20 450000 20 450000 20 470000 4 082500 13 000000 20 330000 7 330000 20 310000 20 310000 20 330000 8 1 2 Pixel image PNG Pixel image export will write the file to a Portable Network Graphics PNG image A dialog will open to ask for the output size in pixels
49. ib Tool b fsl satu sau aa a Re ee OR Rn Be aes doug eae Gs ee ee ee 5 61 Eles gi Ste eee ee oe a eet Ds bo hea teu es a tae es Ghee eke rrr M 5606 Instrument uu uos onum Sohn D RC ROB QUEUE REOR UR edo deg dun de ode ds d MI A IIA 6 Preferences 6 1 General i uses esos o mex Rex a Pda mo don E SEE bor V XU RANA 6 11 Editor A ee TTC CPP dis 6 1 3 Reference Structures 22 22 22 Cm nommen IS OR Gan AA a ge ls Br 6 2 2 ROMS vs 0 ta va uw A US aute ddr CE d enr ad Lm DTE Ae Ds o A ee aa aa da a 6 3 1 Configuration s s s sam asas ria AAA AAA ARA 5 92 SIR Fil H ndli g sweex sa ARA EA AAA os UN ene 6 238 CIF File Handling scs TT BA EullDrllo E rad ESAS E AAA EA RE a qx EY 6 5 Chemisty ee ee SORORE Reb BE ie ae RA REY e E Red 7 Adding and Removing Structure Files 7 1 Add Phase Dialog ic esac ra XX 4 X9 e A dnd a X wea Be 7 2 Remove Phase Dialog lt lt recia Dr RO Np Kae EORR nn A esce Elk Rok er Ax ee er EC Gace Sak Be Oe u ig 7 4 Refinement Preset nme 74 1 Creating and USE presel PT 8 Exporting data 8 1 ah srs e si e s an a ae ee ee ee ne rede 8 1 1 ASCII free format XY 3 i 444 oy errar OY X OR RO RR 8 1 2 Pixel image PNG ce eom See arar ria a Be Re Pos 813 Gnuplot GPL reas cia AAA rob ok Vo dE Erb n 8 1 4 Scalable vector graphics SVG xod
50. initial offset will correspond to the maximum intensity of the strongest scan When called again this function will increase the previous offset by a constant value Decrease Vertical Displacement Ctrl Down Reduces the vertical offset of all scans by a constant value If no vertical offset exists an initial adaptive offset will be applied with a vertical displacement of each scan corresponding to the maximum intensity of the scan below Displace left Ctrl Left If no horizontal offset exists it will apply a horizontal offset to the left to all scans If an offset to the left exists the offset will be increased by a constant value If an offset to the right exists the offset will be reduced by a constant value Displace right Ctrl Right If no horizontal offset exists it will apply a horizontal offset to the right to all scans If an offset to the right exists the offset will be increased by a constant value If an offset to the left exists the offset will be reduced by a constant value Reset Displacement Ctrl Space Resets all horizontal and vertical offsets 5 6 4 Project Add Phase F8 Opens a dialog to create a control file by selecting an instrument configuration and phases crystal structure files If a phase is activated in the Reference Phase box it will be preselected in the Add Phase dialog The option to create a default control file is automatically activated or deactivated depend ing on whether or not a cont
51. is running a message will ask for confirmation before aborting the refinement Close All Projects Closes all open projects If one or more refinements are in progress a warning will be displayed and no project will be closed Import CIF Opensa dialog to convert CIF files cif to BGMN structure files str See section 11 for more information Import ICDD XML Opens a dialog to import a structure file exported in XML format from the ICDD PDF 4 graphical user interface using Save PDF card as See section 11 for more information Scan Batch Conversion Opens a dialog for batch conversion of graph files All currently opened project scans will be added to the batch list by default More files can be added or deleted in the dialog See section 10 for more information Quit Ctrl Q Quits the application 5 6 2 Edit Undo Reverts the last change in the currently shown text file Redo Restores the last undone change in the currently shown text file Copy Control File Copies the current project s control file to other projects and adapts all input and output file names to match the projects base names A dialog will allow to select which projects control file shall be modified Existing control files will be overwritten Note that this function does not check whether referenced structure files are actually present in all project directories It only manages control files but not structure files Reset File Rev
52. lt terminal gnuplot p scan gpl 8 1 4 Scalable vector graphics SVG Scalable vector graphics SVG is a resolution independent vector graphics format ideal for post processing of graphs All elements scans axes hkl lines text are exported as editable paths or text elements allowing to change fonts sizes places colors line widths or add annotations easily in the exported file It is the most powerful and flexible of all export formats to create high quality figures However it is necessary to use vector drawing software and convert the format before importing into a word processor as most programs including Microsoft Word LibreOffice Writer SoftMaker TextMaker and I4TEX do not import SVG files directly All modern webbrowsers are capable of viewing SVG files natively SVG files can therefore be viewed and printed easily on all operating systems without requiring any additional software In order to edit the files a vector drawing program such as Adobe Illustrator Inkscape Corel DRAW or others is necessary Note that not all vector drawing programs interpret SVG files correctly Wrong SVG drawing may need manual optimization The recommended workflow to add a scan to a manuscript in high quality is the following 1 Exort the scan to SVG as described above 2 Open or import the SVG file in a vector drawing program of your choice 3 Make sure the SVG file looks as expected Modify if necessary 4 Select the entire plo
53. ly at regular intervals of the maximum intensity of the strongest scan Fig Ba 2 View Decrease vertical displacement was called several times to reduce not reset the vertical offset followed by View Displace right to stack the scans to the right Fig Bb A special vertical offset will be applied when calling View Decrease vertical displacement first In that case positive vertical stacking will be applied but instead of regular intervals each scan will be displaced to the maximum intensity of the previous scan Fig 9 This will avoid large 21 q AA AA 99 55 5 7 5 5 55 55551 1000 L I observed I calculated Background 7 800 Corundum A1203 7 F Fluorite 7 F LiF 4 L J 2 c 600 2 o H 4 o 2 L al gt L a 5 oh c 5 L 4 2 E al H 4 J i 4 so a ce EN RE Ey TONNES Ce TIUS ae ET EN ER DEE LER N TEN TR FOREN NET A ny Wem Ser E WERE NEBEN 20 00 25 00 30 00 35 00 40 00 45 00 50 00 55 00 Angle 28 a qqA AA gt 5 a gt U 5 7551 1000 l d f I observed J It i I calculated i u Background 7 800 Corundum A1203 7 F Fluorite 1 H LiF 4 o F 1 4 H 1 E 1 2 o o 2 gt ben mn o a c H A Eg apap c os pep ge A A N HERE E TE BEN R
54. m online or commercial databases are usually supplied in the CIF format 9 or in an XML file format if exported from the ICDD PDF 4 database Before they can be used with BGMN the structure information needs to be converted the the BGMN STR file format Profex provides support to facilitate the conversion process for both CIF and XML formats PDF 4 XML files are usually complete and require very little user input CIF files on the other hand often lack important information and require manual revision The import and conversion process in Profex is identical to both CIF and XML formats The following instructions show how to convert a CIF file to a BGMN STR file using Profex CIF import feature 1 Retrieve a CIF file from an external resource online or local database 2 Start Profex and choose File Import CIF to open the CIF file 3 If no space group number was found in the CIF file Profex will display a dialog to select the number Fig 14a Select the space group number of your structure It has to be known or determined from an external source The field Supported Settings shows all Hermann Mauguin symbols of the selected space group number The correct number must contain a symbol remotely similar to the symbol read from the CIF file Due to the lack of standard ization CIF and BGMN Hermann Mauguin symbols often look similar but not identical 4 If more than one space group setting is available select the correct one f
55. matic setup When starting Profex for the first time the program will try to locate the BGMN installation di rectory and structure and device database directories automatically Automatic configuration will also be executed later if the configured paths are invalid It is therefore possible to force automatic setup later by deleting the paths to BGMN and the database directories in the preferences dialog Automatic setup is platform specific The locations scanned automatically are listed below 3 1 1 Windows Three directories named Structures Devices and Presets are expected to be located in the directory of profex exe BGMN EXE is expected to be found in a directory called BGMNwin stored next to the parent directory of profex exe In other words automatic setup on Windows will work if BGMN and Profex directories are organized as shown in Figure 1 3 1 2 Linux On Linux a list of directories is scanned for the executable file bgmn Scanning will stop at the first match The directories are scanned in the following order 1 home lt user gt BGMN 2 home lt user gt BGMNwin je opt bgmnwin TN opt bgmn 5 opt BGMNwin 6 usr bin 7 usr local bin Directories named Structures Devices and Presets will be searched in the following order at home user Structures ome user Devices xo J home lt user gt Presets N IS y
56. me using the File Scan batch conversion feature However due to limitations given by the formats SVG and pixel images PNG are not available for batch conversion When opening the batch conversion dialog by clicking File Scan batch conversion the file queue will contain all currently opened scan files by default More files can be added by clicking the Add File button and selecting one or more files and selected files can be removed from the queue by clicking the Remove File button Some output format support multiple scans stored in a single file The option Write scans to one file will instruct Profex to store all scans found in a source file into one single file In that case all scans lobs Icale aig fr Ibackgrouna and all sub phase patterns found in a DIA file will be stored in a single output file Use Write scans to individual files to write these patterns into single output files instead Note that storing multiple scans in one file must be supported by the output format as well as by Profex output filter which is currently only the case for ASCII and Gnuplot files Click Convert to start the conversion process or Close to close the dialog without conver sion Output files will be stored at the location of their source files using the same base file name Existing output files will be overwritten without warning 48 11 CIF and ICDD XML import Crystal structure files retrieved fro
57. ments or batch refinements deacti vating this option may save some time For normal operation it is recommended to activate this option Show characteristic Tungsten lines with spectral line cursor When using the spectral line cursor 5 3 additional lines will be shown for characteristig Tungsten radiation WLa and WLB1 This allows to inspect the diffraction pattern for Tungsten contamination lines caused by aging X ray tubes Display Line Width Width in pixels of all lines plots axes tick marks of the graph on computer screens Printing Line Width Width in points of all lines plots axes tick marks of the graph on printouts This value should usually be greater than the display line width Symbol Size Size of the measured data points when not using solid lines e g dots or crosses in pixels Y axis Scaling Scaling of the y axis Options are linear logarithmic with a base of 10 log10 or square root sqrt Color of Reference hkl Lines Color of the hkl lines when selecting a reference structure from the Reference Structures box Create Thumbnail If checked a thumbnail picture of the refined plot will be created at the end of the refinement This file is stored in the project directory with the name project basename tn png lt allows easy browsing of refined projects The width of the picture can be specified in pixels The height is calculated from the displayed aspect ratio Show Texture of hkl Lines if available
58. nd GOALs List EPS values If checked refined EPSn will be shown in the summary table for global parame ters and GOAL s Else EPS7 parameters will be skipped Output Local Parameters Text Editor Enter the parameters to be read from the local parameters and goals section in the BGMN List file 1st and shown in the summary table for local parameters and goals Enter one parameter per line The parameters must be written exactly as in the list file including case sensitivity Reset Pressing this button erases the text field with parameters and inserts a default set of pa rameters 34 6 4 Fullprof FullProf 2k options are described in the user manual for Profex using the Fullprof backend 6 5 Chemistry The chemistry page allows to edit the oxide forms and their molecular weights used to calculate the elemental composition of the sample Elements with empty molecular weight or with molec ular weight of 0 0 g mol will be ignored It is recommended to leave the oxide and molecular weight cells of oxygen element No 8 empty to suppress display of oxygen as a separate element in the chemistry results table A dialog to easily select the oxide form and automatically calculate the corresponding molecular weight can be opened by double clicking on the element symbol left column Double clicking an oxide cell middle column or molecular weight cell right column allows to enter oxide names and molecular weights directly by byp
59. ntrol and or results file with the same base name is found Profex will open it too Insert Scans Ctrl I Inserts scans from one or more graph files into an existing project The additional scans will only be displayed in the project s graph view Other files such as the control file will not be modified If no project is available a new one will be created based on the name of the first selected graph file Inserted scans will be discarded when the project s graph file is reloaded e g during a refinement Remove Scan Removes the scan selected in the Plot Options window from the graph view No other files will be modified Removed scans will be restored when the project s graph file is reloaded e g during a refinement Save Ctrl S Saves the current file under the same file name This function only works for text files Save file as Shift Ctrl S Saves the current file under a new file name A file dialog is shown to ask for the file name location and file format 25 Recent Graph Files Shows a list of recently opened graph files Recent Text Files Shows a list of recently opened text files For scan files different output formats can be selected Scans can be saved as raw data for further processing or images Print Ctrl P Prints the currently shown text or graph file Printing options may differ depending on the platform and device driver Close Project Ctrl W Closes the current project If a refinement
60. oal has been selected for a phase the element composition will be normalized to the phase s quantity The total chemical composition will be calculated only when all phases were assigned a valid Quantity Goal Fig 12b 46 XG ihid Chemistry o ES Element 23 V 24 Cr 25 Mn 26 Fe 27 Ni Reset Figure 13 Oxides and molecular weights can be customized in the preferences dialog a Double click on a Element cell in the oxide table to open a dialog for calculation of oxide Preferences Oxide TiO2 V205 Cr203 MnO Fe203 NiO lolecular Weigt 79 8658 A 181 88 151 9904 70 9374 159 6882 74 6928 OK Cancel a molecular weights b The oxides and their molecular weights used to calculate the composition can be accessed and customized in the preferences by calling Edit Preferences gt Chemistry Fig 13a Ele ments without molecular weight value or with a value of 0 0 will be ignored for the calculation It is recommended to leave the molecular weight of oxygen element No 8 empty or at 0 0 to avoid listing oxygen as a separate element in the chemistry output table See section 6 5 for more information on customizing the oxide parameters Select Project Export Chemistry to export the data to a csv file 47 Oxide Molecu 2 Fez04 231 532600 g mol OK b Cancel 10 Scan batch conversion Several scan files can be converted to other data formats at a ti
61. ojects accessing the same structure files will be affected too The Add Phase dialog will not allow to add the same phase more than once to a control file If a selected file is already referenced in the control file it will just be skipped by the dialog If multiple entries of the same structure file are requested the control file will have to be modified by hand 7 2 Remove Phase Dialog The Remove Phase dialog accessed via Project Remove Phase is used to remove STRUC n entries from the control file and update all related GOALs accordingly If Delete 36 KE Append Phase JUE x v Generate default control file xpert xcel ads 10mm geq X Structures File Name Phase Comme Al str Al 04 012 AI203 theta str AI203 theta 01 086 alpha Ft str alpha Ft alphaCPP str alphaCPP 04 009 alphaTCP str alphaTCP 04 010 anatase str Anatase 04 007 Aragonite str Aragonite 01 071 Arcanite str Arcanite 04 006 Archerite str Archerite KH2PO4 04 006 4 Li Expand Collapse Overwrite existing files OK Cancel Figure 10 The Add Phase dialog showing all instrument configuration files and structure files found in the database directories STR Files is selected the local copies of the selected structure files will be deleted from the hard disk Note that this can affect other projects accessing the same copies of the structure files If the control file contains multiple references to the same structure file only
62. onfiguration To be processed with GEOMET ger Containing the raytraced profile shape To be processed with MAKEGEO geq Containing the interpolated profile tpl A sample sav control file for the refinement not containing any file names or phases 11 X Preferences Y O Q9 General Graphs Configuration STR File Handling CIF File Handling Summary T BGMN i Fullprof Custom Profile Function v Use custom profile function Profile Function RP 4 Scaling GEWICHT Isotropic X Lorenzian Size Broadening B1 0 0 0 01 v refined Gaussian Size Broadening k1 0 0 1 v refined Micro Strain k2 0 refined GOALs v Add Default Goals GOAL GrainSize 1 1 1 Micro Absorption Correction Add Correction for Micro Absorption e Default Function GEWICHT ifthenelse ifdef d exp my d 3 4 1 O Custom Function 0K conca Figure 3 Profex allows to modify structure files automatically to apply custom profile functions and goals 12 The tpl file is specific to Profex all other files will be required by BGMN The tpl file can be any existing refinement control file but all output file names LIST OUTPUT DIAGRAMM all scan file names VAL n and all structure file names STRUC n should be empty tpl files allow to add goals calculations numbers of threads and similar customizations which
63. ot need installation Extracting the archive to the local hard drive is sufficient If a previous version is installed on the same computer using a new version will not interfere with the existing installation Old and new versions can be used at the same time they will share the configuration options 2 2 Linux A binary archive of BGMN for Linux 1686 is available for download on the Profex website 3 Profex however must be compiled from source It requires a C compiler environment and the Qt toolkit version 5 to be installed 4 including header files Ot version 5 4 or later is required The following Ot 5 modules and header files must be installed widgets xml printsupport sql svg Support for Bruker BRML raw data files requires the 3rd party libraries zlib 5 and QuaZip 6 Both libraries are included in the Profex source code archive and linked statically into the binary in order to avoid version conflicts with system wide installed libraries linked against Ot version 4 2 2 1 Getting the source Download the source code archive profex 3 5 0 tar gz from the Profex website 3 extract it to your harddisk and navigate into the source code directory tar xzvf profex 3 5 0 tar gz cd profex 3 5 0 Profex BGMN Bundle 3 5 0 zip C Program Files Profex BGMN BGMNwin BGMNwin BGMN EXE BGMN EXE Profex 3 5 0 Profex 3 5 0 profex exe profex exe Structures Structures st
64. r L_x str Devices Devices geq ger L geq x ger x sav x tpl L Sav x tpl Presets Presets pfp i pfp a Structure of the bundle archive b Structure on the hard disk Figure 1 When extracting the Profex BGMN Bundle to the hard disk automatic setup will only be successful if the BGMNwin and Profex 3 5 0 directories are copied to the same location 2 2 2 Compiling from source code Run the following commands from the source code directory qmake profex pro make j 4 src profex Make sure qmake of Qt version 5 is used If unsure run qmake with the full path e g usr 1ib64 qt5 bin qmake profex pro If error messages occur and the program does not start after typing src profex read the error messages carefully and try to solve all depen dency and version problems with your distribution s software repository 2 3 Mac OS X A disk image containing Profex and BGMN for Mac OS X 10 6 8 or newer is provided for down load on the Profex website 3 The binary requires a 64bit CPU Visit 7 to find out whether a specific Apple computer uses a 64bit or a 32bit CPU Mount the disk image and drag the folder Profex BGMN to the Applications folder The file and directory structure of the bundle is explained in appendix A Then run the application Profex BGMN profex The automatic setup routine section B will find the BGMN installation and the structure and device directories 3 Setup 3 1 Auto
65. res It is useful for standard refinement always using the same device configuration and structure files as it allows to set up the control file with a single mouse click The format and application of preset files is described in detail in section 7 4 13 Devices database Instrument1 tpl Instrumentl sav Instrumentl ger Instrumentl geq Instrument2 tpl Instrument2 sav Project directory Instrument2 ger Instrument2 geq Instrument3 tpl myscan xrdml mE myscan sav Copies files from database directories Instrument1 sav Structures database to project directory Instrumentl ger Instrumentl geq Albite str Modifies str files Barite str if requested Calcite str Dolomite str Converts instrument Ettringite str template tpl file to Fluorite str control file sav Gypsum str Hematite str Illite str Jade str Kaolinite str Lime str Magnesite str Nahpoite str Figure 4 The Add Phase dialog will copy structure files and device files from the database di rectories to the project directory If selected in the preferences the structure files will be modified according to the preferences in STR File Handling Files already existing in the project directory will not be overwritten unless the option is checked manually in the Add Phase dialog 14 4 First steps When Profex and BGMN have been installed and configured correctly as described in sections and 3 and at least one de
66. rol file already exists 27 If a default control file is created despite an existing control file the existing one will be overwritten any previously added modifications or phases will be lost Selected structure files and instrument configuration files will be copied from the structure and device database directory to the project directory Files already existing in the destina tion directory will be skipped If the option overwrite existing files is checked existing structure files will be overwritten with the file copied from the structure file database See section 7 1 for more information Remove Phase F7 Removes a phase from the control file Optionally the structure file will be deleted Deleting structure files may cause problems with other projects stored in the same directory and accessing the same structure files Open all project STR files Ctrl F8 Opens all BGMN structure files str referenced in the cur rent project s control file sav in new pages Close all project STR files Ctrl F7 Closes all BGMN structure files str shown in the current project Export Global Parameters and GOALs Ctrl E Exports the global parameters and goals e g phase quantities to a semicolon separated spread sheet csv See section 8 3 for more information Export Local Parameters and GOALs Shift Ctrl E Exports the local parameters and goals e g structural parameters to a semicolon separated spread sheet c
67. rol file will be overwritten The default state of this option depends on the presence of a previous control file e If a control file was found this function will be unchecked Manually activating the option will overwrite the existing control file with a newly created default file e If no control file was found this function will be active Instrument configurations This dropdown menu lists all instrument configurations found in the device database directory section B 4 Structures This list shows all structure files found in the structure file database directory section 5 4 Clicking on the header of the table File Name Phase or Comment will sort the table in ascending or descending order of the clicked column Structures which are selected in the first column will be added to the control file If a reference structure is shown on the main graph it will be pre selected in this dialog Expand Collapse If structure files are organized in sub directories in the structure database di rectory they will be organized in a tree structure in this dialog Clicking Expand Collapse will expand or collapse all items in the tree structure for easy navigation Overwrite existing files If a selected structure file is already present in the project directory it will normally not be overwritten This preserves customized files Checking this option will force overwriting of existing files Use this option with care as other pr
68. rom the dialog shown in Fig Again the available Hermann Mauguin symbol often looks similar but not identical to the one read from the CIF file 5 The STR file will be created and shown in an editor Fig 15 Most likely the STR file is in complete due to information missing in the CIF file Some warnings are issued in the dialog Check manually for complete information Typically Wyckoff sequences and element types are often missing The dialog also shows the original CIF file on a second tab It may be useful to verify the STR file or to retrieve more information if it was not extracted automatically The XML file shown on the third tab is the intermediate format used by Profex It is only shown for debugging purposes 6 Once the STR file is complete choose Save STR to save the file in the structure file database directory Sometimes it is helpful to browse the space group numbers and symbols in the form supported by BGMN Open Help BGMN SPACEGRP DAT to open a dialog which shows all space group numbers settings and Wyckoff sequences in the nomenclature used by BGMN Fig 16 The assignment CIF file tags to STR parameters is described in Table 2 11 1 Automatic conversion of thermal displacement parameters During the conversion from CIF to STR format Profex automatically transforms the thermal dis placement parameters to the format supported by BGMN Depending on the source format the following conversions are calc
69. s version of BGMN to be run in WINE Check this option if the executable files specified above belong to the Windows version of BGMN Structure Files Directory Specify the location where BGMN structure files str are stored Device Files Directory Specify the location where BGMN instrument files sav ger geq tpl are stored Presets Directory Specify the location where refinement preset files pfp are stored See section 4 for more information on presets File Extensions File Extensions associated with BGMN These file types will always be opened as BGMN projects regardless of the default project type Convert raw scans to XY format If checked raw scan files will be converted to ASCII XY free format xy prior to starting the refinement This option must only be disabled if the raw file format is directly supported by the BGMN backend e g val rd Performance Number of CPU cores used by BGMN Specifies how many CPU cores will be used by BGMN by adding NTHREADS n to the control file Automatic will use all available cores 6 3 2 STR File Handling Custom Profile Function Use custom profile function Check this option if Profex should automatically change the profile parameters of BGMN Structure files str The files will be modified when they are copied from the structure database to the project directory by calling Edit Add Phase If this option is disabled the profile parameters will no
70. s have not been indexed before hkl indices will be calculated on the fly when the structure is selected On modern computers this only takes a second or two Afterwards the hkl positions will be buffered and be available instantly The buffer can be cleared as described in section e 1 3 Note that the double click function described in section b 3 is only available for indexed reference structures Reset reference structure This button will reset the reference structure dropdown menu and hide reference hkl lines After resetting no structure will be pre selected in the Add Phase dialog anymore Search and index new reference structures Pressing this button will scan the structure database directory for new STR files and index all new files The reference structures become imme diately available in all projects 5 6 Menu Structure 5 6 1 File Open Text File Ctrl O Opens a file in a text editor If a project with the same name as the text file s base name is already open the file is opened in this project Else a new project is created If the text file is a control or results file Profex will automatically locate all other control and results files of the same project as well as the scan file and open them too Non existing files are ignored BGMN structure files str are always opened in the currently shown project regardless of the project name Open Graph File Ctrl G Opens a scan file in the graph page If a co
71. several occasions when modifying the control file content E g after creating a default control file or after applying a control file from another project 60 Start Create VAL file Convert displayed scan file to xy VAL n file exists on hard disk Launch BGMN re finement process Figure 22 Immediately before running the refinement process Profex checks whether the VAL file referenced in the control file exists on the hard disk If not a xy file will be created from the currently displayed scan file 61 A Bundle File Structure A 1 Windows Profex BGMN Bundle 3 5 0 zip BGMNwin BGMN EX MakeGEQ EXE 1 Profex 3 5 0 Devices Instrument 1 sav Instrument l ger Instrument l geq Instrument 1 tpl Instrument 2 sav I see Structures Structure 1 str Structure 2 str I Presets Preset 1 pfp Preset 2 pfp 4 profex exe te ee A 2 Mac OS X Profex BGMN Bundle 3 5 0 dmg Profex BGMN profex app BGMNwin bgmn makegeg BGMN Templates Devices Instrument 1 sav Instrument 1 ger Instrument 1 geq Instrument 1 tpl Instrument 2 sav ill Structures i Structure 1 str 62 otr cture 2 stt Presets Preset 1 Preset 2 SU 1 1 oo o A 3 Linux No bundle is available for Linux 63 Ref
72. sv See section 8 3 for more information Export Chemistry Writes the calculated chemical composition to a semicolon separated spread sheet csv See section 8 3 for more information Refinement Presets Lists all refinement presets to create refinement control files Select one of them to apply the preset to the current project See section for more information on refinement presets Save as Refinement Preset Creates a new refinement preset from the currently loaded project See section 7 4 for more information on refinement presets 5 6 5 Run Run Refinement F9 Starts the refinement of the currently shown project Run Batch Refinement F10 Starts a batch refinement of all open projects Abort Current Refinement Ctrl C Aborts refinement of the currently shown project In batch refinement mode all projects scheduled for batch refinement will be unscheduled If the cur rently shown project is not running but scheduled it will be unscheduled but the remaining batch refinement will not be interrupted In either case refinements started outside of the batch will not be interrupted Abort All Refinemet Shift Ctrl C Aborts all running projects and batches If more projects than the currently shown one are affected the user will be asked for confirmation 28 5 6 6 Instrument New Configuration Read some hardware information from Bruker RAW V4 Bruker BRML V5 and PANalytical XRDML files to create a BGMN instrument config
73. t and copy to the clipboard 5 Special paste it into the word processor or presentation program for example as an extended metafile 43 8 1 5 Fityk Session FIT Fityk scripts can be opened directly with the program Fityk 11 version 0 9 8 or later This export filter was specifically designed for phase quantification of calcium phosphate phases for medical devices according to the standard procedure described in ASTM F2024 10 It may not be of much use for anyone not performing this specific analysis The Fityk Session export offers several different export modes Entire File will write the entire measured range to a script All other modes are described in more detail Corundum 104 peak This export mode is to be used with the corundum reference data set It will export the range from 34 0 to 36 2 20 around the corundum 1 0 4 peak Running the script in Fityk will fit a linear function to the background signal Afterwards it will integrate the intensities lobs Ipackground from 34 4 to 35 9 and print the result This is the corundum reference intensity to be used for ASTM F2024 10 b TCP range This mode which is to be used with the CaP data set will export the range from 27 0 to 35 0 20 Running the script in Fityk will fit a linear function to the background and PearsonVII functions to all peaks except B TCP 0 2 10 and then integrate the difference be tween all fitted curves and the observed curve from 30 5
74. t be changed Profile Function RP Specify the RP n parameter Scaling GEWICHT Specify the GEWICHT parameter Choose SPHARn for refinement of preferred orientation or ISOTROPIC for untextured samples 33 Lorenzian Size Broadening B1 Specify B1 enter ANISO for anisotropic crystallite sizes Check refine to refine this parameter Gaussian Size Broadening k1 Specify k1 Check refine to refine this parameter Micro Strain k2 Specify k2 enter ANISO4 for anisotropic micro strain Check refine to refine this parameter GOALs Add Default Goals Check this option if a set of default goals is to be added to each copied BGMN Structure file str Specify the goals in the text field below Example GrainSize 1 1 1 Micro Absorption Correction Add Correction for Micro Absorption Check this option if a correction for micro absorption Brindlay correction shall be added to each copied structure file Default Function If checked the correction formula is hard coded to a default function Custom Function Check this line and enter a custom correction function if a correction formula other than the default one shall be used 6 3 3 CIF File Handling CIF to STR Conversion Upper and Lower Limits for Cell Parameters Specifies the range for upper and lower limits of unit cell parameters to be added automatically to BGMN Structure files str created from CIF files 6 3 4 Summary Table Output Global Parameters a
75. tached window back into the main window to dock it 17 Closing Opening Dockable windows can be closed by clicking on the close button x in the title bar To open it again use the menu Window in the main window s menu bar 5 2 1 Projects This list shows all open projects and their current status Click on a project to view it in the plot and editor area Most actions from the menu and toolbar will apply to the currently shown project Projects can be edited while another project is refining Multiple projects can be refined at a time but refinement may be slow depending on CPU power and number of CPU cores Running a batch refinement see section 5 6 5 will allow to refine all open projects in a sequence rather than parallel 5 2 2 Plot options This list shows all scans loaded in the currently shown project To change the scans drawing style color line style line width refer to the graph preferences discussed in section 6 2 Names of scans cannot be changed they depend on the names read from the scan files Visibility of each scan can be changed by checking or unchecking the box in front of the scan name For refined scans Profex distinguishes between main scans usually Lobs cater Iaify and the background curve as well as phase patterns All phase patterns can be toggled on or off at once by using the function View Show Hide phase patterns This change is persistent and applies to all open projects It is a
76. tes Presets Graphs Fil BGMN Font Sans Serif 11 pt ile Extensions Fullprof File Extensions associated with BGMN dia sav Ist par val Appearance and Behaviour v Convert raw scans to XY format Default ProjectType BGMN v Performance Toolbar Layout Icons only M Number of CPU cores used by BGMN Automatic Y Multi Scan Files Show individual Scans v Default Wavelength 1 540560 A Always use default Wavelength ok cancel a Set the default project type to BGMN b Select the BGMN executable files as well as structure device and preset database directories Figure 2 Manual configuration of the BGMN backend in Profex 3 3 Using WINE on Linux Profex supports running the Windows version of BGMN on Linux using WINE In that case a BGMNwin directory from a Windows installation can be copied to any location on a Linux system The executable files of the BGMN backend will then be called BGMN EXE MAKEGEQ EXE GEOMET EXE OUTPUT EXE and GERTEST EXE Checking the box Run in WINE and entering the WINE executable in the configuration dialog Fig 2 which is usually usr bin wine will let Profex call the BGMN backend in WINE However for performance reasons it is recommended to use the native Linux version of BGMN if available 3 4 Structure Device and Preset Database Profex supports databases for crystal structures device configurations and refinement presets for the BGMN
77. the first occurrence will be removed In that case the option Delete STR Files will be ignored until the last reference to this file was removed from the control file 7 3 Project organization When working with several datasets projects at a time it is important to understand how Profex Add Phase function handles structure and instrument files in the background By default the Add Phase dialog will copy selected structure and instrument files to the lo cation of the currently loaded scan file as shown in Fig It will check whether a file with the same name is already present If yes the present file will not be overwritten unless the option overwrite existing files was activated for structure files and generate default control file was activated manually for instrument files Since several raw scan files can be located in the same directory a structure file will only be present once even if it was added multiple times for each project Modifying removing or over writing this structure file will affect all projects within this directory Fig 11 If common structure files are not desired there are several options to avoid shared access by multiple projects e Distribute the raw scans on several sub directories as shown in Fig The Add Phase dialog will have to be called for each project separately but each project will receive it s own copy of the instrument and structure files 37 e Manually mana
78. to 31 5 20 This integrated intensity will be used to quantify B TCP in the sample CaO range This mode will export the range from 36 0 to 38 8 20 Running the script in Fityk will fit a linear function to the background and integrate the difference Igy Ipackground from 37 0 to 38 5 20 This integrated intensity will be used to quantify CaO HA range This mode will export the range from 37 5 to 59 5 20 Running the script in Fityk will fit a linear function to the background and integrate the intensities lobs Ibackgrouna in the range from 38 5 to 59 0 20 to quantify hydroxyapatite All CaP ranges to separate files This mode will export all three ranges 6 TCP CaO HA ana lyzed with the CaP sample to separate files 8 2 Printing to PDF On most operating systems a PDF printer is available It allows direct export of the graph to a PDF file Prepare the graph as described at the beginning of this section but use File gt Print instead of the save as function Use the printer dialog to write the output to a PDF file The layout and functions are platform specific If line widths are too fine or too wide change the printing line width in the preferences as described in section 6 2 PDF files can be used directly in IATgX Other word processors may need the same conversion as described for SVG files 8 3 Refinement results At the end of a refinement Profex shows a summary of global parameters and GOALs as well
79. ub directories working directory scan_1 sav dataset 1 STRUC 1 structure_l str _scan_l sav STRUC 2 structure_2 str structure_l str structure 2 str scan_2 sav dataset 2 STRUC l1 sstructure d str scan_2 sav STRUC 2 structure_2 str structure l str structure 2 str Manually renamed structure files working directory scan_1 sav scan_l sav STRUC 1 structure_la str Scan 2 sav STRUC 2 structure_2a str I structure ta Str _structure 2a str scan_2 sav Structure 1b str STRUC 1 structure lb str structure 2b str STRUC 2 structure_2b str Structure files in sub directories working directory scan_1 sav iLLScan l sav STRUC 1 strFiles_l structure_l str _scan_2 sav STRUC 2 strFiles_l structure_2 str strFiles_l p str scan 2 sav structure 2 str STRUC 1 strFiles 2 structure l str L strFiles 2 STRUC 2 strFiles_2 structure_2 str structure_l str we Str a File structure b Control file content Figure 11 Projects and structure files can be organized in different ways depending on whether structure and instrument files shall be shared or not 39 other lt textfile gt dots lt textfile gt lt other gt and lt other gt lt binaryfile gt dots lt binaryfile gt lt other
80. ulated anisotropic values are not supported by the CIF format 49 KG Select Space Group Number 2 x Number of Space Group R 3 c 167 X Supported Settings R 32 c R 32 c c No space group setting found ww y Choose the correct Setting for Space Group R 3 c HermannMauguin R 32 c Setting 1 UniqueAxis c Lattice Trigonal fig OK Cancel OK Cancel a Space group number b Space group setting Figure 14 Importing a CIF file If no space group number is found in the CIF file it has to be entered manually in dialog a If more than one setting for the space group is available it has to be choosen manually from dialog b Isotropic B Isotropic B is the format supported by BGMN However BGMN uses a different unit than normally provided in the CIF file Automatic conversion therefore performs the following conversion Biso nm 0 01 Biso Anisotropic B Anisotropic Bj are converted to isotropic B values in the expected unit 12 1 x _ xk Biso nm 0 01 3 Y Bie a AiAj j i with reciprocal lattice parameters a and real lattice parameters A A Anisotropic U Anisotropic U are converted to Uequiv using the expression 12 Ueguio 3 25 Uija 8j 213 1 J with reciprocal lattice parameters a A and real lattice parameters A A Ugeguiv is con verted to Biso by the following equation Isotropic Uegquiv Isotropic Uequiv values are converted to isotropic B
81. um 32 92 0 00 0 00 0 00 Fluorite fluorite surr 0 00 20 07 13 60 0 00 LiF liffsum 0 00 0 00 12 99 20 42 Total 32 92 20 07 26 59 20 42 b Figure 12 Chemical composition of the sample Quantity goals must be selected by the user If no quantity goals were selected a each phase will be normalized to 100 If the goals describing the phases quantities were assigned b the total bulk composition of the sample will be calculated too needs to know the relative quantity of each phase which is normally calculated as a global goal Profex will attempt to identify the correct Quantity Goal by comparing global goal names with the phase name If a goal name of format phase_name some_stringisfound with phase name matching the phases PHASE variable case insensitive the goal will be automatically selected Else no Quantity Goal will be selected and the user will have to select it manually As an example the following Quantity Goal will be recognized and assigned automatically because the phase name and goal name match matching is case insensitive STR file PHASE Corundum GOAL corundum GEWICHT SAV file GOAL 1 corundum sum But the following Quantity Goal will not be recognized automatically because the phase name and goal name do not match The user will have to select it manually STR file PHASE Corundum GOAL A1203 GEWICHT SAV file GOAL 1 A1203 sum Once a valid Quantity G
82. uration file from scratch Other raw data formats are not supported Usually several variable required by BGMN will still not be available from the raw data files and will thus have to be entered manually See section 12 for more information Edit Configuration Opens a dialog to process BGMN instrument configurations See section 12 for more information 5 6 7 Window Projects Shows or hides the Projects list window Plot Options Shows or hides the Plot Options window Refinement Protocol Shows or hides the Refinement Protocol window Global Parameters and GOALs Shows or hides the summary table window for global parameters and goals Local Parameters Shows or hides the summary table window for local parameters and goals Chemistry Shows or hides the table showing the refined chemical composition in oxide form Context Help Shows or hides the context help display 5 6 8 Help Context Help F1 Shows the context help of the keyword under the text cursor The Context Help window View menu must be shown to display the context help BGMN Variables Opens a web browser showing the BGMN variables documentation page BGMN SPACEGRP DAT Opens a dialog to browse spacegroups and atomic positions sup ported by BGMN Mouse and Keyboard Commands Shows a dialog with mouse and keyboard commands for plot windows About Profex Shows information about Profex 29 6 Preferences 6 1 General 6 1 1 Editor Font S
83. vice configuration and structure file has been stored in the databases section B 4 the program is ready for a first refinement 1 10 11 Click File Open Graph or alternatively press Ctrl G or the corresponding button in the main tool bar In the opening file dialog set the file formal at the bottom to the format of your raw scan file and open the file The scan will be loaded as a new project Double click on the strongest peak or select a reference structure from the reference structure dropdown menu to identify your main phase Click Edit gt Add Phase or press F8 or the corresponding button in the project tool bar create a control file The dialog shown in Fig 10 will be shown Select your instrument configuration from the dropdown menu your phase from the struc tures list it may be pre selected and verify that the option Generate default control file is active Then click OK Click Run Run Refinement F9 or click the corresponding button in the refinement tool bar Wait for the refinement to complete If more phases are present repeat steps 4 7 but make sure the option Generate default control file is not active anymore If the refinement is complete click File Export Global Parameters and GOALs or press Ctrl E or the corresponding button in the project tool bar to export the results to a CSV file Optionally also click
84. will be applied by default when creating a new file set from the database An example is shown below All device file names structure files scan files and the various output files will be filled in automatically by Profex The automatic processes running in the background when using the Add Phase dialog are illustrated in Fig 4 More information on the Add Phase dialog can be found in section Theoretical instrumental function VERZERR Wavelength LAMBDA CU Phases oe oe Measured data AL 1 Minimum Angle 2theta WMIN 10 Maximum Angle 2theta WMAX 60 Result list output LIST Peak list output OUTPUT Diagram output DIAGRAMM Global parameters for zero point and sample displacement EPS1 0 PARAM 1 EPS2 0_ 0 001 0 001 betaratio 0 NTHREADS 2 PROTOKOLL Y lt o o9 oe oe If the template file contains a reference to a scan file containing a measured background curve UNT myBackground xy the background file should be stored in the device database directory too Profex will copy it to the project directory when creating a new refinement control file The background scan file will not be converted It must be stored in a format natively supported by BGMN The recommended format is ASCII XY 3 4 4 Refinement Preset Files A refinement preset file allows to quickly create a control file with a certain device configuration file and a set of structu
85. will be shown as a comment in the Add Phase dialog The following lines show an example of the file lime str PHASE Ca0 04 007 9734 SpacegroupNo 225 HermannMauguin F4 m 32 m PARAM A 0 4819 0 4771 0 4867 RP 4 k1 0 k2 0 B1 ANISO 0 01 GEWICHT SPHAR2 GOAL GrainSize 1 1 1 GOAL CaO GEWICHT ifthenelse ifdef d exp myxdx3 4 1 E CA 2 Wyckoff a x 0 0000 y 0 0000 z 0 0000 TDS 0 00350000 E 0 2 Wyckoff b x 0 5000 y 0 5000 z 0 5000 TDS 0 00440000 3 4 2 STR File Handling Depending on where structure files are obtained from created manually exported from databases converted downloaded shared with others they may contain different profile parameters RP B1 k1 k2 GEWICHT etc Altering these files in the structure file database will also affect other users accessing the same database and may thus not be desired Profex offers a feature to modify the structure files while copying them from the database to the working directory Choose Edit Preferences BGMN STR File Handling to access the settings Fig B The individual options on this page are explained in more detail in section 6 3 2 3 4 3 Device Configuration Files For each device configuration Profex expects to find four different files in the device database directory These file names are supposed to have the same file name but different file extensions Fig 4 sav Containing the description of the device c

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