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1. STR View Hide Structure Displays the structure in the Structure Viewer see section 5 Create hki Is phase Creates a hkl_Is phase adopting the refinement model as used for Rietveld refinement Delete Structure Deletes the selected Structure item Paste INP to Node Selections Supports pasting of information in INP format from the clipboard DOC M88 EXX065 V4 2 01 2009 44 TOPAS User s Manual The Sites item The Sites item contains the following information concerning atomic sites Parameter name Remarks e Site Customizable site name e Xx y z Fractional atomic coordinates e Atom X ray data Chemical species atom ion determining the scattering factor Neutron data Chemical symbol isotope to determine the scattering length Both can be selected from a drop down list e Occ Site occupancy factor 0 lt Occ lt 1 e Beg Isotropic temperature factor Note A comparison of atomic positions is performed in the generation of the unique positions with a tolerance in fractional coordinates of 10 When entering a fractional coordinate for a special position such as 1 3 1 6 etc it is mandatory to enter a fraction in the form of an equation such as 1 3 1 6 etc in the Codes page instead of entering a value with re occuring digits such as 0 3333 0 1666 etc in the Values page as shown in Fig 4 14 The correct parameter value will be calculated automatically from the equation and displayed in
2. TOPAS User s Manual 31 The shortcut menu of the Emission Profile item offers the following options e Load Emission Profile e Save Emission Profile e Add Emission Line e Paste INP to Node Selections Supports pasting of information in INP format from the clipboard Selected emission rows can be deleted using the DEL key For laboratory diffractometer systems a selection of predefined emission profiles is available in the LAM directory covering the most common anode target materials For other target materials as well as for synchrotron and neutron sources it is necessary to define a suitable emission profile For accurate work it is necessary to refine on the emission profile shape using e g the NIST SRM 660a LaB standard 4 2 2 2 Background Two background functions are provided Fig 4 5 a Chebychev polynomial of any order and a 1 X function gt Parameters F2 H En Background Apt Text sod raw 0E Emission Profile Use Value Code Error ca pe e Background Chebychey jwe 0E Instrument Order 5 qH Corrections 1 Bka Ca a i A Miscellaneous Structures hkl Phases da0 Pb5D4 Coefficent Error o Paste INP to NodeSelections 0 DO DO DO DO Fig 4 5 Background item with its associated data grid The shortcut menu of the Background item offers the following option e Paste INP to Node Selections Supports pasting of information in INP format from the clipboard 4 2
3. 20 Q 2z d and d for the x axis and y linear Sart y square root and Ln y logarithmic for the y axis e Display of observed calculated difference and background data e Display of calculated intensities for individual single peaks or phases e Animated display of the profile fitting process For Whole Powder Pattern Decomposition Pawley and LeBail method and Rietveld refinement the following additional items are displayed e hkl markers at the bottom e the phase name plus relative phase amounts in the upper right part of the window DOC M88 EXX065 V4 2 01 2009 12 Available menu commands and toolbar icons are Menu View X Axis Scale Linear Q d spacing View Y Axis Scale Linear Sqrt y Ln y View Curves Calculated View Curves Background View Curves Difference View Curves Single Peaks View Show hkl Ticks n a Icon apx TOPAS User s Manual Result Sets the x axis scale to X Q d Sets the y axis scale to y Sqrt y Ln y Displays hides calculated curves Displays hides background curves Displays hides difference curves Displays hides single peaks Displays hides hkl ticks phase names and amounts View previous next Scan Window using LMB RMB Further features for Whole Powder Pattern Decomposition Pawley and LeBail method and Rietveld refinement are View Show hkl Ticks must be on e When moving the mouse onto the
4. Fig 4 16 Preferred Orientation item The shortcut menu of the Preferred Orientation item offers the following option e Paste INP to Node Selections Supports pasting of information in INP format from the clipboard DOC M88 EXX065 V4 2 01 2009 TOPAS User s Manual 47 The Str Output item Allows for the output of the following structure details Fig 4 17 e Generate Bondlengths Errors lf checked bondlengths and bondangles will be calculated Additionally errors for bondlengths and bondangles will be provided if Calculate Errors has been turned on in the Fit menu or in the Refinement Options Dialog section 3 3 7 The results will be displayed in the Bondlengths page e Consider Lattice Parameters in Errors lf checked lattice parameter errors will be considered for calculation of bondlength and bondangle errors e Generate CIF Output for Structure lf checked crystal structure details will be generated in CIF format and displayed in the CIF Str Output page e Generate FCF Output lf checked structure factor details will be generated in FCF format and displayed in the FCF Output page An example bond lengths output is as follows Guan OLEU ZwaAS TAS O22 0 Ze25143 362063 O20 Z 46045 LODO DRE AS The first line gives the distance between the sites Y1 and O2 The first number in the second line gives the distance between sites Y1 and O2 The third number of 88 083 gives the angle between the vectors Y1 to O1 and Y1 to O2 T
5. 3 4 5 l 7 8 9 A oO SI NAL NI NEN val mou MM om di di da da fi ajajajajajajaja ja BA swe 73 45 eforf2 909 67 15 63709 9380 66 72 EFBAFI 100 66 21 EFBB48 o6 63 3 EFEBOB 623 64 95 270019 125 64 59 mele etal Sam 64 25 270017 500 63 61 52 8003 67 6559 54 0591 by 6279 by 6092 67 6546 r etait r 6541 oy 6571 40 6577 81 2736 40 6570 61 5038 ail alley raul eit 81 3139 81347 51 2793 55 iiil gt Gof vs Volume Details for selected 26 FO FFOF contribution removed from observed and calculated rali A 0 BS Z 0 418257 3 92 29 0 0082 81 3133 81 3133 73 0449 90 90 li Select previous Select next Sort by Gol decreasing Sort by UN Gol decreasing Sort by Yolume Sort by selected columns Save to ND file Paste INF to NodeSelections h m h hr aa tj npo anlJlJ tj n Mee wo NM OM ee Oo yn Cow mM oO Wr me KI eR l 50 40 Be 31 ZE ZE ed z3 ZI ZO z0 de 63968 6567 4213 PLE 3454 oov6 3483 473 5101 5555 3283 do B245 5207 415Z 0620 4295 5314 5622 3291 V B da dc l BZ 0994 0668 0544 081Z 0583 0521 040z 0444 OW Wo Ww Wo me hoe eR ZThe 5835 3746 4763 531Z 1674 ZIOS Z975 4205 Psa B435 3495 ZTha 9665 4687 1590 Z036 Z565 4120 PES 5364 341Z ZTha 0 O ook O O O O O O O Fig 4 24 Indexing range with its
6. 4 3 Printing and reporting Any data grid information can be copied to the clipboard or transferred to the TopasEditor or Microsoft Word if available using the shortcut menu of the data grid shown in Fig 4 27a Available options are Copy all selection Copies the full page or the selection to the clipboard Copy all selection create TopasEditor document Launches the TopasEditor and transfers the full page or the selection into a new document in RTF format Copy all selection create Word document Launches Microsoft Word if available and transfers the full page or the selection into a new document in DOC format based on the currently defined document template default is TOPAS DOT DOT file topas dot Allows to define a document template file for Microsoft Word if available This feature allows for the creation of customized reports with for example user defined headers footers page numbering and more Note Topas dot does not contain macros however to use DOT files containing macros the security level of Microsoft Word for opening files must be set to either low not recommended or medium if set to high any macros will be automatically disabled For more information please refer to the Microsoft Word user s manual Additionally any contents of text fields including the Text and Report Format page as well as the Bondlengths CIF Str Output and FCF Str Output pages can be saved as plain ASCII files or printed on the
7. INP is set by the menu command Launch Set INP File Input files contain all information for controlling TOPAS in Launch Mode and can be modified by a text editor for details please refer to the Technical Reference manual Notepad is set as the default editor user specified can be made permanently active by selecting Launch Editor Editing can be performed by selecting Launch Edit INP File ln Launch mode refinement results are always written to an output file OUT which has the same format as the INP file The output file can be inspected by selecting Launch Edit OUT File As in Launch Mode the refinement will be completely controlled by the input file the following windows in the Working Area will have no effect e Peak Search Dialog section 3 3 4 e Peak Details Dialog section 3 3 5 e Parameters Window section 4 Scans loaded from Launch mode are placed into the Parameters Window for graphical display purposes Editing of these entries has no bearing on the fitting process which is controlled entirely from the INP file Note It is possible to work in GUI and Launch Mode at the same time Once an input file is set the Launch button in the Fit Window allows for the switching between GUI and Launch Mode DOC M88 EXX065 V4 2 01 2009 66 TOPAS User s Manual 9 REFERENCES Bergmann J Kleeberg R Haase A amp Breidenstein B 2000 Advanced Fundamental Parameters Model for Improved Profile Analysis Ma
8. J Appl Cryst 20 pp 467 474 Le Bail A Duroy H amp Fourquet J L 1988 Ab initio Structure Determination of LiSbWOg by X Ray Powder Diffraction Mat Res Bull 23 447 452 March A 1932 Mathematische Theorie der Regelung nach der Korngestalt bei affiner Deformation Z Krist 81 285 297 Pawley G S 1981 Unit cell refinement from powder diffraction scans J Appl Cryst 14 357 361 Pitschke W Mattern N amp Hermann H 1993 ncorporation of microabsorption corrections in Rietveld analysis Powder Diffraction 8 4 223 228 Rietveld H M 1967 Line profiles of neutron powder diffraction peaks for structure refinement Acta Cryst 22 151 152 Rietveld H M 1969 A profile refinement method for nuclear and magnetic structures J Appl Cryst 2 65 71 Savitzky A amp Golay M J E 1964 Smoothing and differentiation of data by simplified least squares procedures Analytical Chemistry 36 1627 1639 DOC M88 EXX065 V4 2 01 2009 TOPAS User s Manual Suortti P 1972 Effects of porosity and surface roughness on the x ray intensity reflected from a powder specimen J Appl Cryst 5 325 331 DOC M88 EXX065 V4 2 01 2009 67 68 TOPAS User s Manual DOC M88 EXX065 V4 2 01 2009
9. e If several datasets are loaded in several Scan Windows the data of minimized as well as closed windows will not be fitted e f several datasets are loaded in several Scan Windows and one of these windows is maximized then only the data within the maximized window are fitted e lf the menu switch Fit Fit Zoomed is selected only the data points displayed in the Scan Window are used for fitting All data outside the zoomed area are ignored 3 3 Views related to the Scan Window 3 3 1 Quick Zoom Window Always displays the complete scan which is particularly useful if the Scan Window only displays a zoomed area Inside of the Quick Zoom Window a zoom rectangle represents the actually displayed data range within the active Scan Window It allows a modification of the zoomed area by grabbing one of the red lines with the mouse and moving it A double click on the Quick Zoom Window resets the Scan Window to full scale DOC M88 EXX065 V4 2 01 2009 16 TOPAS User s Manual 3 3 2 Weight Percent Pie Chart Window Displays a weight percent pie chart providing quantitative analysis results 3 3 3 Chart Options Dialog This dialog Fig 3 1 is linked to the shortcut menu of the Scan Window RMB and provides two pages allowing to copy and print the chart as well as to define properties of the chart title and axes Settings can be saved in STARTUP DEF see the Technical Reference manual with the exception of the x and y axis limits
10. which cannot be kept as defaults Note Definition of Y1 or Y2 axis limits requires them to be unfixed gt Chart Options Aa Set as Defaults E Chart Title Font Size L Pbsotd raw A Chart Area Font Size E Show Legend gt Chart Options Print Print Setup to Clipboard as Metafile to Clipboard as Bitma 2Th Degrees 10 0 01 A Title Font Size Counts E Minimumi Masimum 0 Labels Min Step Font Size 0 01 Fig 3 1 Chart Options Dialog DOC M88 EXX065 V4 2 01 2009 TOPAS User s Manual 17 3 3 4 Peak Search Dialog Note GUI mode only Offers an automatic peak search according to Savitzky 8 Golay 1964 Fig 3 2 Kaz peaks can be removed automatically Peak search w Remove K Alpha 2 Peaks 0 Intensity Ratio Tolerance 5 Fosition Tolerance 2 i Fig 3 2 Peak Search Dialog e Peak Width Peak search parameter Should correspond approximately to the peak halfwidth e Noise Threshold Peak search parameter Defines the minimum intensity of a peak A noise threshold of one corresponds to a noise level of two sigma e Remove K Alpha 2 Peaks Removes Ka peaks automatically Intensity Ratio Tolerance and Position Tolerance define a window to recognice Ka peaks DOC M88 EXX065 V4 2 01 2009 18 TOPAS User s Manual 3 3 5 Peak Details Dialog Note GUI mode only Allows the insertion of different peak types as well as the direct editing of peak parameter val
11. 15 20 25 30 35 40 45 50 55 60 65 70 75 x 40 98266 y 3337 846 d 2 200439 Fig 1 2 Schematic representation of the GUI Launch Kernel architecture of TOPAS DOC M88 EXX065 V4 2 01 2009 4 TOPAS User s Manual 1 3 2 Features available in GUI and Launch Mode Table 1 1 gives an overview about the functionality of TOPAS in GUI and Launch Mode For more details refer to the Technical Reference manual Table 1 1 Functionality of TOPAS Features marked with GUI are available in GUI Mode Features not available in TOPAS P are marked with P Features Profile Fitting Methods and Related Applications Single line up to Whole Powder Pattern Fitting GUI Indexing LSI Index LP Search GUI Whole Powder Pattern Decomposition Pawley method LeBail method GUI Rietveld structure refinement P GUI Quantitative Rietveld analysis P GUI Structure determination Simulated annealing Charge Flipping electron density display gt Measurement Data and Refinement Parameters Laboratory and synchrotron X ray data constant wavelength and TOF neutron data GUI Variable Counting Time VCT GUI Single crystal data P Combined refinement of X ray and neutron powder data P GUI Combined refinement of powder and single crystal data H Non dependence on X ray data all kinds of XY data can be fitted GUI Support of non equidistant x axis steps GUI Support of negative x axis values GUI Refines simultaneously on any number of diffraction p
12. Bko Structures hkl Phases Goniometer radii PbSod Primary radius mm Secondary radius mm Equatorial Conyvolutions Point detector Receiving Slit Width ram FDS Shape anglef Add Structure Beam spill sample lengl YOS irradiated length m YOS Scale Intensity Capillary Linear PSD Tube Tails LEN LAN NAS Load d la DIF LD Save if displayed obs Ycale DI Phases Bh Arial Convolutions Replace Scan Data Full Axial Model Reverse data and make s asis positive Source length mm Delete Range Sample length mm Paste INP to Node S elections RS length mon x Fig 4 2 Range item with its associated data grid showing the All Range Dependent page All range dependent parameter values and codes can be viewed and manipulated in this data grid as well as in the respective second level items The shortcut menu of the Range item offers the following options for file types and formats refer to the Technical Reference manual Add Structure Adds an empty structure default values are predefined in the file STR DEF see the Technical Reference manual Add Peaks Phase Adds an empty peaks phase default peak type is fundamental parameters Add hkl Phase Adds an empty hkl phase default values are predefined in the file HKLI DEF see the Technical Reference manual Load STR s Loads structure information from STR file s Load CIF s Loads structure information from CIF file s Load INP PAR Loads information f
13. Create Indexing Range Creates a new range for indexing see section 4 2 3 If peaks wavelengths are present then they are placed into the indexing range e Create Pawley Range Creates a Pawley range adopting the refinement model as used for profile fitting e Delete Peaks Phase Deletes the selected Peak Phase item e Paste INP to Node Selections Supports pasting of information in INP format from the clipboard 4 2 2 7 hkl Phase hkl Phase items Fig 4 12 provide all parameters required for Whole Powder Pattern Decomposition including both the Pawley and the Le Bail method The data grid comprises the following pages Phase Details Peak Type hki Is and Additional Convolutions The 3rd level item Indexing Details provides for multiple Pawley or Le Bail refinements It is specific for LSI Indexing and described in section 4 2 3 gt Parameters F2 Global Phase Details Peak Type e hkls Is Additional Convolutions Rpt Test LT ext B PFbsodraw EI Emission Profile Lise Value Code Error Min Max a Background Use Phase jw I Instrument Le Bail H Corrections Delete hkls on Refinemer w Miscellaneous LP Search m a4 LI Structures hkl Phases FESDO4 jj Indexing Details Spacegroup Fob nom 6 9500000 0 0000000 B 4700000 0 0000000 5 3900000 0 0000000 o Fix a Cry Size Cry size L inm W 100 0 a 0 0 Cry size G inm 200 0 Refine L ol IB nm 0 000 Lyal FWHM nm l 0 000
14. Grid The Toolbar offers the following menu commands and toolbar icons to display or hide the various windows and dialogs Menu View Quick Zoom View Pie Chart View Parameters Window View Peak Details Window View Options Window Fit Fit Window View Search Peaks Tools New Rigid Body Shortcut F2 F3 F4 FS Result Displays hides Quick Zoom Window Displays hides Pie Chart Windows Displays hides the Parameters Window Displays hides the Peak Details Dialog Displays hides the Options Dialog Displays hides the Fit Window Displays hides the Peak search Dialog Displays hides the Rigid Editor Window Body Editor DOC M88 EXX065 V4 2 01 2009 TOPAS User s Manual 11 3 THE SCAN WINDOW 3 1 Common features in GUI Mode and in Launch Mode 3 1 1 Display In TOPAS an unlimited number of data sets can be loaded and refined simultaneously The data can be displayed in one single Scan Window default or in individual Scan Windows which can be tiled horizontally and vertically cascaded and closed within the Working Area using the appropriate Window menu commands lf there are no Scan Windows then a Scan Window is created when a scan in loaded Closing a Scan Window does not unload its data The data can be redisplayed by selecting Window One Scan per Window The following features concern the data displayed in the Scan Window e Axes scales comprise x
15. Options Dialog section 3 3 3 for defining various chart properties such as labels ticks and fonts which can be saved as default Charts can be printed directly or copied to the clipboard Delete Selection Deletes selected peaks and excluded regions Delete Nearest Peak F9 Deletes the peak nearest to the actual mouse position DOC M88 EXX065 V4 2 01 2009 TOPAS User s Manual 15 Note As it is not possible in Launch Mode to graphically insert peak and excluded regions the Delete Selection and Delete Nearest Peak F9 will have no effect in Launch Mode see also section 3 2 3 2 Features available in GUI Mode only The following features are available in GUI Mode only as in Launch Mode the refinement is completely controlled by the input file e Graphical peak treatment such as manual peak insertion automatic peak search and the editing of peak properties e Display of peak markers and profile parameters for single peaks e Highlighting the intensity distribution of a peak with a bold line as the mouse is moved over its peak marker e Graphical insertion of excluded regions e Selection of peaks and excluded regions with the mouse pressing the CTRL key allows multi selection e Deletion of the selection with the DEL key With respect to the fitting process it is important to understand the following features of the Scan Window in GUI Mode e In general all datasets in visible Scan Windows are fitted simultaneously
16. a selection cursor All peaks in the selection area are marked by a dashed line Selected regions are marked with dashed patterns Selected peaks and excluded regions can be deleted with the DEL key or using the shortcut menu see section 3 1 3 In addition selected peaks can be manipulated using the Peak Details Window Note Zooming and panning also work while fitting DOC M88 EXX065 V4 2 01 2009 14 TOPAS User s Manual Available menu commands and toolbar icons are Menu Icon Result View Dont fix Y1 Lak Does not fix Y1 Fix Y1 to zero Lu Fixes Y1 to zero Fix Y1 to min value Lust Fixes Y1 to the minimum count value View kai Dont fix Y2 FI Does not fix Y2 Fix Y2 to max value Lak Fixes Y2 to the maximum count value View Horizontal Scroll Bar n a Displays hides the horizontal scroll bar View Unzoom n a Resets to the full X and Y scale n a P Compresses the x axis left right using the left right mouse buttons 3 1 3 Shortcut menu options the RMB anywhere in the Scan Window will open a shortcut menu offering access to the following features Set X1 X2 Y1 Y2 to Mouse Position Sets the x and y axis limits to the actual mouse position Note Fixed Y1 or Y2 axis limits will be automatically unfixed to allow setting of Y1 and Y2 Reset Axies to Previous Resets to the previously zoomed region Unzoom Resets axies to the full X and Y scale Edit Print Chart Options Opens the Chart
17. associated data grid showing the Solutions page and detailed results for the selected solution TOPAS C Topas4 Tutorial Index svd ex2 pro Indexing File View Fit DS M BOUSYRANB Io fe Launch Tools Window Help 7 600 110 0l12 7400 lo 21 7 200 7 000 6 800 J O 1 00 030 02 6 600 6400 6 200 6 000 5 800 5 600 5400 5200 5 000 4800 4600 4400 4200 4000 3 800 3 600 3400 3 200 3 000 TON 2 800 2 600 2 4004 2 2004 2 0004 1 800 goes 1 000 W 800 600 2 Did 24 26 3 2 Naya 34 3 6 w ye 3 8 4 MA AN ka Li dik Aka AN N 42 44 46 1 600 1 400 j j 1 2004 Mainau POPE f L 5 2 Laat A wel 54 5 6 5 8 6 x 2 875478 5576 527 Press Ctrl ke Fig 4 25 Scan Window showing a stick pattern for the selected solution overlaid with the observed line positions and the associated powder pattern DOC M88 EXX065 V4 2 01 2009 56 TOPAS User s Manual Shortcut menu options of the Results page are e Select previous Selects the previous solution e Select next Selects the next solution e Sort by Gof decreasing sorts the indexing results by decreasing goodness of fit e Sort by UNI Gof decreasin
18. blue color Not adhering to this convention may lead to severely wrong refinement results y site No x z Atom Occ Beg 1 zn A 0 33333 0 66667 0 00000 Znt 1 0 25 0 0 0 35333 0 66667 0 38260 O 2 l 0 5 Site Np x z Atom acc Beg 1 n UER 1 3 2 3 T An 2 Fix iT 2 iS D 1 3 213 a O 2 Fix ia Fig 4 14 Sites item data grids showing the Values a and Codes page b for a structure example requiring atomic coordinates provided in form of equations Note The Fit Window drops a warning if a coordinate is closer than 0 001A to particular special positions as shown in Fig 4 15 Although there is an increasing probability with increasing structure size that a general position may be close to a special position by chance a cross check is always strongly recommended DOC M88 EXX065 V4 2 01 2009 TOPAS User s Manual Interface Mode Fit Zoomed ON am m0 gt mt NEN Warning fractional atomic coordinate of 0 3333 is close to the special position value of 1 3 Recurring le ce atomic coordinates such as 0 3333 should be entered as x 1 3 Number of equivalent positions 12 Number of independent parameters 18 Number of hkls generated for C iTopas4isqip 3ml sq 43 0 Time 0 05 Rwp 772 080 0 000 MC 0 00 0 Interface Mode Fit Zoomed ON 45 Fig 4 15 Fit Window showing a warning for a coordinate closer than 0 001A to a 1 3 special position Shortcut menu options of the Sites ite
19. default printer Fig 4 27b Save to TXT file Saves the full text field or the selection to a plain ASCII file Print directly sends the full text field or the selection to the default printer a Copy allfselection Copy allfselection Copy aliselection create TopasEditor document det aliselection create TopasEditor document Copy alliselection create Word document Copy alliselection create Word document DOT File topas dot DOT File topas dot Save to TAT file Print directly b Fig 4 27 Shortcut menu of the data grid showing available options for a grid pages and b text fields DOC M88 EXX065 V4 2 01 2009 TOPAS User s Manual 59 5 THE STRUCTURE VIEWER Note Not available in TOPAS P The Structure Viewer allows to view crystal structures Fig 5 1 and 3D electron densities including atom picking Fig 5 2 As a refinement continues the structure viewer is updated providing animated refinement in 3D MQOYSOVEHBZHIBZKBOv E Fig 5 1 Structure Viewer window with crystal structure Rietveld refinement DOC M88 EXX065 V4 2 01 2009 60 TOPAS User s Manual MQOVYDHIDIEZSLOIZKABOSEO9 Fig 5 2 Structure Viewer window displaying a 3D electron density map obtained from Charge Flipping including automatic atom picking results In GUI Mode the Structure Viewer can be opened using the shortcut menu item View Hide Structure of the Structure item see section 4 2 2 8 In Launch Mode the str
20. is the direct editing capability of peak parameter values and refinement codes in the Scan Window A mouse click LMB on the text displayed nearby the peak using the left mouse button will open an edit field which allows to change parameter values or refinement codes Any changes have to be confirmed using the Enter key DOC M88 EXX065 V4 2 01 2009 TOPAS User s Manual 19 For changing the values of a peak group there are three buttons on the bottom of the Peak Details Window e All Win Overwrites the values of all peaks in the active Scan Window with the value in the edit field Note A change of the peak position moves all peaks to the same position e All Wins Same as All Win but changes will be applied to all peaks in all Scan Windows e Selections Changes are applied to all selected peaks in the active Scan Window 3 3 6 Options Dialog Provides several mouse controlled modes Fig 3 4 Of these only Capture will have an effect in Launch mode all other options are intended for use in GUI mode only Options F4 Insert Peak Capture Manipulate x Manipulate y Exclude Region Select Ctrl key Fig 3 4 Options Dialog e Arrow Normal mouse operation for Zooming and panning e Insert Peak Shows the Peak Details Dialog and switches the mouse to peak insertion mode e Capture Any observed or calculated data including difference plots in a Scan Window can be captured by the mouse After clicking on the diag
21. lines removal attempt successful e Status 4 Impurity lines removal attempt successful In the Scan Window for the selected solution a stick pattern is overlaid with the observed line positions dashed red lines indicate theoretical peak positions not matched with an observed line dashed blue lines indicate unindexed observed peaks The associated powder pattern can be overlaid as well Fig 4 25 gt Parameters F2 1 1 Global Indexing Solutions RptTest tf Text eee Indexing Data Solutions Fipt Text l Z 69711 5785 73 45 52 8003 40 6577 a EE r2 96967 15 SO 6 6559 81 2736 a 63709 9380 6672 AN 54 0591 40 6570 a EFBAFI 168 56 21 D r 6279 81 5036 6 a a 9 l ERE eles 6530 AE hapa a 61 5167 arogl eres atest r 6546 o1 3141 270019 125 64 069 alll 0r GD 81 3139 270950 344 64 25 6 6541 8l a427 270017 500 63 61 Sa 67 65071 81 2799 4 gt E JE EEE TARE T an nan e n Perret y Si n T ie Select previous Select next Sort by Gof decreasing Sort by UINIG ofdecreasing Sort by Yolume Sort by selected columns Save to ND file of i eri gee eee T Bh Paste INP to Node S elections 500 000 4 000 000 1 500 000 Fig 4 23 Indexing range with its associated data grid showing the Solutions page and the goodness of fit Gof versus volume plot DOC M88 EXX065 V4 2 01 2009 TOPAS User s Manual gt Parameters F Er Global m E Use 5g Sts UNI 1 2
22. original sample Wt in Spiked sample and Wt in Original sample respectively DOC M88 EXX065 V4 2 01 2009 50 TOPAS User s Manual gt Parameters F2 Global monn Values Errors Degree of crystallinity Apt T ext Dem cpd3raw Values Enors FptText DI Emission Profile witt Rietye Use WEY of Spik wt in Spiked Wk in Origins Cell Mass Background 44 050 wo 30 790 30 790 0 000 611 765 0E Instrument i 28 297 0 000 19 765 28 558 312 300 CE Corrections inci 27 6235 0 000 19 295 27 079 162 775 0 Miscellaneous GH Structures hkl Phases 0E Quantitative SG Lattice parameters 9 Brindley conection Spherice fg Display SEE c Corundum Wks in Spiked sample 30 150 0 000 a Fluorite Wks in Original sample 43 563 0 000 a 6 Zincite HJ Peaks Phase UII valye Error ji gt Paste INP to NodeSelections Fig 4 19 Quantitative item showing the Values page with its associated datagrid The Degree of crystallinity page Allows the calculation of the degree of crystallinity of a sample on request see Fig 4 20 Note that degree of crystallinity calculations can be performed using Peak Phases hkl Phases and Structures in any combination the number of which used for modeling both crystalline and amorphous contributions is not limited gt Parameters F2 pan anes En Deges ofc Fae alues Errors Degree of crystallinity Apt Test cpd 3 raw CA Emission P
23. z matrix z matrix z matrix Editor Main View Fig 6 1 Rigid Body Editor DOC M88 EXX065 V4 2 01 2009 Zr Zr 2x zr Zr zr RRR RRR 90 02 90 90 02 180 90 02 270 180 02 0 64 TOPAS User s Manual 7 THE ESSENTIAL HELP WINDOW The Essential Help window Fig 7 1 can be displayed as a startup window and allows to display user defined information It will display all RTF files found in the TOPAS4 Essential Help directory RTF files can be created with e g MicroSoft Word The Help Essential Help menu can be used to display and close the Essential Help window TOPAS EE File View Fit Launch Tools Window Help SA Sei x PbEAPUSe yFHAVE Loe Fx yA yea Special Positions tis mandatory to enter a fractional coordinate for a special position in the form of an equation such as 1 3 1 6 etc inthe Codes page instead of entering a value with re occuring digits such as 0 3333 0 1666 etc inthe Values page The correct parameter value will be calculated automatically from the equation and displayed in blue color For more details refer to the User s Manual Not adhering to this convention may lead to severely wrong refinement results Fig 7 1 Essential Help window DOC M88 EXX065 V4 2 01 2009 TOPAS User s Manual 65 6 OPERATION IN GUI AND LAUNCH MODE The GUI Mode is active by default Launch Mode becomes active if an input file
24. 2 3 Instrument Provides for the definition of the instrument function For instruments operating in divergent beam geometry the Fundamental Parameters Approach is available in the DOC M88 EXX065 V4 2 01 2009 32 TOPAS User s Manual Divergent beam page Fig 4 6 other instrument geometries can be empirically modelled some more functions are offered in the Additional Convolutions page Fig 4 7 Note that both the Divergent beam and the Additional Convolutions page provide different shortcut menus gt Parameters F2 t Global Additional Convolutions B Pbsod raw Emission Profile Use Value 0E Background Goniometer radii 0E Instrument Primary radius mm 173 LI Corrections Secondary radius mm 173 Ca Miscellaneous Equatorial Convolutions Structures hkl Phases ao PbSO4 Code Error Point detector Capillary Linear PSD Tube Tails Axial Conyolutions Full Axial Model Finger_et_al Load Instrument Details Simple Axial Model mm Save Instrument Details Paste INP to NodesSelections Fig 4 6 Instrument item with its associated data grid showing the Divergent beam page Note Point detector Capillary Linear PSD Tube Tails Full Axial Model and Finger_et_al are Use dependent expand collapse grid items gt Parameters F2 Global z MM Di Divergent beam Additional Convolutions Emission Profile i 0 Background Lorentzian 1 Cos Th w 005 Fix 9 Instrument 0E Corrections 9 Miscellaneo
25. Bruker AXS GmbH DIFFRAC TOPAS e TOPAS 4 2 User Manual XRD think forward The reproduction transmission or use of this document or its contents is not permitted without express written authority Offenders will be liable for damages All rights reserved We have checked the contents of this manual for agreement with the hardware and software described Since deviations cannot be precluded entirely we cannot guarantee full agreement However the data in this manual are reviewed regularly and any necessary corrections are included in subsequent editions Suggestions for improvement are welcome All configurations and specifications are subject to change without notice Order no DOC M88 EXX065 V4 2 Updated Jan 15 2009 2003 2009 Bruker AXS GmbH Karlsruhe Germany All trademarks and registered trademarks are the sole property of their respective owners Printed in the Federal Republic of Germany Bruker AXS GmbH stliche Rheinbriickenstr 49 76187 Karlsruhe Germany Tel 49 721 595 28 88 Fax 49 721 595 45 87 info brukeraxs de www brukeraxs com Contents I CONTENTS t INTRODUCTION accen 1 AeA TOPAS OVV O oi tt tl ad ka ant de n n kt n a Ba oke a ake a ooo ka 1 1 2 WAS VS ORAS P iii acces cease easier eee a e e ee koka l k 1 1 3 TOPAS TO IJCUFOS bet kt ate tant n thse tine k kk ty n t et ti 2 t31 GUrand Launch Moda teat te kitel bio koke le a k ka l ee a ie ea 2 1 3 2 Featur
26. DIF or UXD files for all selected files providing a link to the ICDD PDF via DIFFRAC EVA and SEARCH e Replace Scan Data for Selected Files Allows to exchange scan data for selected files to be refined using the same refinement model e Reverse data and make X axis positive Allows the use of data obtained from scans in negative x axis regions e Paste INP to Node Selections Supports pasting of information in INP format from the clipboard 4 2 2 Range item s For each range loaded an additional Range item is created and labelled using the file name of the measurement data file For multi range RAW files an additional range number is appended to the range label Ranges can be enabled or disabled using the checkbox next to the range node Range dependent second level items of the Range item are e Emission Profile section 4 2 2 1 e Background section 4 2 2 2 e Instrument section 4 2 2 3 e Corrections section 4 2 2 4 e Miscellaneous section 4 2 2 5 Additionally the following items may be displayed as well e Peak Phase section 4 2 2 6 e hkl Phase section 4 2 2 7 e Structure section 4 2 2 8 e Structures hkl Phases section 4 2 2 9 An Indexing range is a specialized 1st level Range item and described in section 4 2 3 DOC M88 EXX065 V4 2 01 2009 28 TOPAS User s Manual gt Parameters F2 0E Emission Profile a Background Background 0 Instrument Chebychev _ Corrections Order 0 Miscellaneous 1
27. PAS the tree only contains the Global item which is a permanent first level item and allows defining of global refinement settings such as the convergence criterion For each scan Range loaded additional first level items Range items are created For single line up to Whole Powder Pattern Fitting Whole Powder Pattern Decomposition and Rietveld analysis so called Peak Phases hkl Phases and Structures respectively are added as range dependent items second level items to a selected Range item Using the checkbox displayed next to the tree node phases can be set to use or no use for the refinement The Global item is most useful when more than one scan is loaded It allows the simultaneous viewing and manipulation of refinement parameters common to ranges some of the possibilities include the defining of parameter values and constraints across ranges as well as the loading of a common source emission profile or structural data into all or selected ranges Most tree items have shortcut menus via the RMB The contents of these menus are also mirrored in the Grid Tab Options Box see Fig 2 3 which can be used alternatively 1 Peak Phases hkl Phases and Structures all represent phases and are related to the keywords x o do hkl and str respectively see the Technical Reference manual DOC M88 EXX065 V4 2 01 2009 24 TOPAS User s Manual 4 1 2 The data grid The data grid contains refinement parameters and codes as w
28. Reference manual Fig 1 2 provides a schematic representation of the GUI Launch Kernel architecture of TOPAS The Scan Window with its zooming and panning functionality is available in both modes of operation The same is true for the Fit Window with its kernel output Note the possibility to exchange data between GUI and Launch An input file exported from GUI is fully compatible to Launch Mode This is not true vice versa due to the extended functionality available in Launch Mode It is up to the user to import only input files into GUI which contain valid statements Otherwise TOPAS will throw an exception DOC M88 EXX065 V4 2 01 2009 TOPAS User s Manual 3 Parameters Window Editor VA Lister c Topas4 Tutorial AlVO4 alvo4 rietveld inp File Edit Options Help Parameters F2 oun stwctue Peak Type rte AdionaConvoktns RoTes E Emission Profile E Background E Instrument rp 6 rp dash tr up 6 r wp dash r_exp 8 r exp dash gof 6 weighted Durbin Watson a Corrections 6 5414400 Q 0000000 Miscellaneous 7 7597500 0 0000000 39 Structures hkl Phases E p rt a avo4s 9 1357200 0 0000000 xX O E Sites 96 18452 E Preferred Orientation 107 2379 0 RAW alvo4 i CuKka1 6 681 Input File Radius 266 5 LP Factor 27 3 Simple Axial Model B 12 E Str Output 101 401 M 0 001 Cry size L nm 200 0 Refine Zero_Error 8 Cry size G nm 200 0 Re
29. Scale page provides an overview about all loaded structures and hkl phases which can be included or excluded from the refinement using the Use checkbox in front of the Phase Name field see Fig 4 18 Refineable microstructure parameters can be accessed in the Cry Size L Cry Size G Strain L and Strain G pages for information about the microstructure parameters refer to the Technical Reference manual 3rd level items are e Quantitative See below e SG Lattice Parameters Displays lattice parameters for all phases included in the refinement e Brindley Correction Spherical Particles Corrects microabsorption effects for spherical particles Brindley 1945 e Display Allows customization of display properties including colors data point size and line width for each range DOC M88 EXX065 V4 2 01 2009 TOPAS User s Manual 49 gt Parameters F Kax a D8 8486 raw 1 ia Emission Profile Use Phase Name Use vale Code Error Min Mex Background C35 monoclinic ll 1e 006 sc cosmo 0 II Instrument C25 beta MUM W 12 005 ac cesbm 0 Corrections C3A cubic M le 007 se ciacut La Miscellaneous C4AF W 1e005 scctaf 0 SO ES Me LISE Periclase w 0 0001 sc periclad Quantitative W 1e 005 cao D SQ Lattice parameters Brindley correction Spherice Display 2 e Se E C34 cubic Use Phase Name Use Value Code Error Min fq C4AF C35 monoclinic l W ie 006 sc_casmo0 A Periclase C25 beta MUMB W ie 005 s
30. Strain Strain L w ool a 0 Strain G Di Refine O e 0 00000 0 00000 Wht Rietveld 0 000 0 000 WE of Spiked 0 000 Cell Mass 0 000 0 000 Cell volume 43 o O00000 Fix 0 00000 R Bragg 0 000 Save Phase m E Create str phase 4 Delete hkl Phase Paste INP to NodesSelections Fig 4 12 hkl Phase item with its associated data grid showing the Phase Details page DOC M88 EXX065 V4 2 01 2009 40 TOPAS User s Manual The Phase Details page offers the following refinement parameters and options Parameter name Use Phase Le Bail Delete hkis on Refinement LP Search Spacegroup a b c alpha beta gamma Scale Cry Size Cry Size L Cry Size G LVolI IB LVol FWHM Strain Strain L Strain G e0 Wt Rietveld Wt of Spiked Wt in Spiked sample Wt in Original sample Cell Mass Cell Vol R Bragg Remarks Includes or excludes the phase from the refinement If checked the Le Bail method will be used for refinement of peak intensities lf checked default the current hkls will be replaced by new hkls calculated for the actual spacegroup and data range everytime a new refinement is started refined intensities will be lost This option should be used if the spacegroup or the data range has been changed lf checked LP Search indexing will search the correct lattice parameters starting from dummy values LP Search will test a single crystal system which is defined by
31. Updating can be started again using the Keep X2 at max X toolbar icon an unzoom operation will show the whole Rwp plot again Icon Shortcut Result gt n a Update the Rwp plot after each iteration and keep X2 at N p the maximum x axis limit When working in GUI mode the Fit Window caption will change to Interface Mode and additionally display the Fit Zoomed status which is either ON or OFF and can be set in the Refinement Options Dialog see below In Launch Mode the Fit Window caption will change to Launch Mode and additionally display the input file name The Rwp plot window copies the content of the Fit Window caption At the end of a refinement due to convergence or by user intervention the Start Step Stop and Break Cycle buttons are hidden The Refinement Converged dialog at the end of refinement is modeless and allows inspection of the refinement results before accepting any changes The horizontal toolbar offers the following options Icon Shortcut Result n a Displays or hides the text and or the Rwp plot AM F6 Starts the refinement JM F Performs one refinement iteration rod Shift F8 Stops the refinement 23 n a Cancels the current refinement cycle ac r n a Animation of the graphics in the Scan Window on off a vi n a Shows the Refinement Options Dialog Fd n a Switches between GUI Mode and Launch Mode The Refinement Options Dialog Fig 3 6 offers several options to control the refin
32. ated peaks is displayed in the Aki s page including the following parameters h k l m multiplicity d 20 and F structure factor The Additional Convolutions page provides for empirical modelling of the observed line profile shapes its options are identical to the Additional Convolutions page of the Instrument item see section 4 2 2 3 DOC M88 EXX065 V4 2 01 2009 TOPAS User s Manual 43 gt Parameters F2 o B Pbsodraw 1 Emission Profile Use Value Code Error Min Background Lise Phase II Instrument Spacegroup Pbnm Corrections 6 9590000 0 0000000 kin 6 4820000 a 00000an Structures hkl Phases mi pe 5 6 Pb5d4 Sites 0 0001 a Preferred Orientation fg Str Output Cry size L nim Cry size G nm L ol IB nm Lyol FWHM nim Save Structure in STA format Strain i Strain L Strain 6 el x 100 0 m 200 0 Refine 0 000 0 000 O 01 a O 1 Retine 0 00000 0 00000 Wks Rietveld 0 000 0 000 Wks oF Spiked 0 000 Cell Mass 0 000 0 000 Cell volume 843 0 00000 0 00000 Cry LAC fern 0 000 0 000 Cry Density giem 3 0 000 0 000 R Bragg 0 000 Paste INF to NodeSelections B BEB Bee Fig 4 13 Structure item with its associated data grid showing the Structure page Note A single mouse click LMB on a selected Structure item allows direct editing of its label Shortcut menu options of the Structure item are Save Structure in STR Format saves the selected Structure item in INP format
33. atterns with any number of peaks GUI any number of datapoints and any number of parameters Refines on any number of structures per diffraction pattern with any number of sites per GUI structure and atoms per site All parameters can be fixed refined constrained and restrained GUI Quantitative Phase Analysis Support of spiking and calibration methods GUI Quantification of phases with partial or no known crystal structures GUI Brindley microabsorption correction GUI Degree of crystallinity analysis GUI Peak Shape Models Analytical profile fitting GUI Profile functions PVII Modified PV TCHZ type PV Voigt GUI Asymmetry SPV SPVII for single line fitting GUI Simple and Full Axial Models Cheary amp Coelho 1998a b GUI Finger asymmetry correction Finger et al 1994 GUI Crystallite size determination by Scherrer method GUI Direct convolution approach GUI Measured instrument functions GUI Fundamental Parameters Approach GUI Standardless crystallite size and strain analysis GUI Refinable instrument parameters GUI Determination of mean sample absorption coefficient and sample thickness GUI Tube tails correction GUI Support of user defined convolutions GUI DOC M88 EXX065 V4 2 01 2009 TOPAS User s Manual Background Models Chebychev polynomial of n th order Single peaks PV SPV PVII SPVII Gauss Lorentz Voigt FPA 1 x type background Modulated background Preferred Orientation Models March Dollase Spher
34. available together with their shortcuts respectively toolbar icons if existing e Toolbar Displays the most important commands in form of icons for fast access e Working Area Contains all elements needed for profile fitting such as observed and calculated data fit parameters and fit results which are displayed in separated views e Status Bar Displays some context sensitive help information and the x and y coordinates of the data cursor in the active Scan Window which is described in section 3 Menubar Toolbars Working Area Status Bar Fig 2 1 TOPAS screen DOC M88 EXX065 V4 2 01 2009 TOPAS User s Manual The Working Area serves as a container for the following views Scan Window The Scan Window Fig 2 2 is the actual field of operation and is available in both the GUI and the Launch Mode The following views are related to it e Quick Zoom Window e Weight Percent Pie Chart Window e Chart Options Dialog e Peak Search Dialog GUI mode only e Peak Details Dialog GUI mode only e Options Dialog most options available in GUI mode only e Fit Window with its Refinement Options Dialog The Scan Window is described in section 3 Parameters Window GUI mode only The Parameters Window represents all refinement parameters available in GUI Mode by a hierarchically organized tree view Fig 2 3 It can be docked at the left right top or bottom of the Working Area and is described
35. c_czsbm0 8 Free Lime C34 cubic W 1e 007 sc _c3acuto CHAF W 1e 005 sc chaf 0 Periclase W 00001 sc_periclad W 1e 005 sc_cao D an n kon a n Free Lime pa ma lt i Paste INP to Kade Selection MARE Free Lime Fig 4 18 Structures hkl Phases item with its associated datagrid The shortcut menu of the Structures hkl Phases item offers the following option e Paste INP to Node Selections Supports pasting of information in INP format from the clipboard The Quantitative item data grid comprises the following pages Values and Degree of crystallinity The Values page The Values page displays quantitative phase amounts for all phases included in the refinement see Fig 4 19 As X ray powder diffraction is only sensitive to crystalline materials any amorphous component of a sample is not considered and is instead included in the background model by default the relative weight fractions of the crystalline phases are normalized to 100 By adding a known weight of an internal standard to the sample spiking the amount of the amorphous phase may be measured directly Furthermore absolute weight fractions will be obtained for all phases A single phase can be declared as a spike phase by checking the Use checkbox and providing its weighed phase amount Wt of Spike Absolute weight percents for all crystalline phases and the amorphous compound are then calculated for both the spiked and the
36. cellaneous 2 ra CITopas4Tutorial Qa D8 8486 raw LA Display 3 MO CiTopas4iTutorial QalD8 8487 raw AN Structureshkl Phases All Peaks M D8 6485 raw B D6 5456 raw D8 8497 raw Create Indexing Range Load Emission Profile for Selected Files Load STR s for Selected Files Load CIF s for Selected Files Load INP FAR for Selected Files Load d_Is DIF USD for Selected Files Replace Scan Data for Selected Files Reverse data and make x axis positive for 5 Paste INP to Node Selections Fig 4 1 Global item with its associated data grid The shortcut menu of the Global item offers the following options for file types and formats refer to the Technical Reference manual e Create Indexing Range Creates a range for indexing see section 4 2 3 e Load Emission Profile for Selected Files Loads a source emission profile from a LAM file for all selected files e Load STR s for Selected Files Loads structure information from STR file s for all selected files e Load CIF s for Selected Files Loads structure information from CIF file s for all selected files DOC M88 EXX065 V4 2 01 2009 TOPAS User s Manual 27 e Load INP PAR for Selected Files Loads information from INP and PAR file s for all selected files while PAR files are intended for instrument parameters only with INP files any keywords and macros supported by the GUI can be loaded e Load d_ls DIF UXD for Selected Files Loads peak information from
37. combination with the Capillary convolution instrument page see section 4 2 2 3 DOC M88 EXX065 V4 2 01 2009 TOPAS User s Manual 37 The shortcut menu of the Corrections item offers the following option e Paste INP to Node Selections Supports pasting of information in INP format from the clipboard 4 2 2 5 Miscellaneous Provides the following options Fig 4 10 Parameter name Remarks e Convolution Steps An integer corresponding to the number of calculated data points per measured data point It may be useful to increase this number when numerical instabilities are introduced This can happen when a particular convolution has a small effect on the profile shape or when the measurement step is large e Start X Finish X Used to limit the refined X range independent on zooming e Fixed WL Neutron Signals the use of neutron atomic scattering lengths The Excl Regions page allows for a definition of an unlimited number of excluded regions which may overlap Options of the shortcut menu are e Add Excluded Region Adds an excluded region e Paste INP to Node Selections Supports pasting of information in INP format from the clipboard Selected excluded region rows can be deleted using the DEL key 4 Parameters F2 iscellaneous Degree of crystallinity Apt T ext een Ppt Te E mission Profile Use Value Code Error Min 1 Background Cony Steps 1 Ap I Instrument Start EC A Corrections risk 2 M 160 Misc
38. ctometers J Res Natl Inst Stand Technol 109 1 25 Kern A Coelho A A amp Cheary R W 2004 Convolution based profile fitting Diffraction Analysis of the Microstructure of Materials edited by Mittemeijer E J amp Scardi P Materials Science Springer ISBN 3 540 40510 4 17 50 Indexing Coelho A A 2003 Indexing of powder diffraction patterns by iterative use of singular value decomposition J Appl Cryst 36 86 95 Coelho A A amp Kern A 2005 Discussion of the indexing algorithms within TOPAS CPD Newsletter 32 43 45 Structure determination Coelho A A 2000 Whole Profile Structure Solution from Powder Diffraction Data using Simulated Annealing J Appl Cryst 33 899 908 Coelho A A 2007 A charge flipping algorithm incorporating the tangent formula for solving difficult structures Acta Cryst A36 400 406 DOC M88 EXX065 V4 2 01 2009 TOPAS User s Manual 7 2 ELEMENTS OF THE USER INTERFACE The TOPAS graphical user interface is intended for working in both GUI and Launch Mode Refinements in GUI Mode require input to a Parameters Window refinements in Launch Mode are controlled by an INP format file Consequently several windows and dialogs used in GUI mode will be not available or have no effect in Launch Mode The TOPAS screen Fig 2 1 consists of the following elements e Menubar Contains the names of submenus which provide lists of all commands
39. d if the refinement is far from the global minimum Use Extrapolation Often increases the convergence rate if used with Line Minimization Interface and Launch Mode Graphics Response Time Defines the update frequency of the Scan Window and the Rwp plot window Reducing the update frequency will leave more CPU time for numerical calculations DOC M88 EXX065 V4 2 01 2009 TOPAS User s Manual 23 4 THE PARAMETERS WINDOW 4 1 Elements of the Parameters Window The Parameters Window Fig 2 3 provides access to all refinement parameters available in GUI Mode It consists of a hierarchal tree view of refinement models and a data grid containing the associated refinement parameters and parameter attributes For details about any refinement parameters and parameter attributes please refer to the Technical Reference manual The command Window Clone Parameters Window clones the Parameters Window which is useful for viewing different parameter types simultaneously For example parameter values and their codes can be viewed simultaneously with two Parameter Windows in cases where one Parameter Window displays only one type of these types at a time The number of cloned Parameters Windows is not restricted 4 1 1 The tree view Displays a dynamic tree essentially representing all contributions to scan data coming from the source the instrument and the sample which may consist of one or more crystallographic phases After starting TO
40. e basic difference between TOPAS and its variant TOPAS P is illustrated Note that the Whole Powder Pattern Decomposition and Indexing methods are implemented in both TOPAS and TOPAS P DOC M88 EXX065 V4 2 01 2009 2 TOPAS User s Manual Single Line Fitting Local Pattern Fitting Whole Powder Pattern Fitting Indexing N LSI Index LP Search TOPAS P Whole Powder Pattern Decomposition Pawley method LeBail method TOPAS Rietveld structure refinement Quantitative Rietveld Analysis Ab initio structure solution Simulated annealing Charge Flipping Fig 1 1 Schematic representation of the basic differences between the functionality of TOPAS and TOPAS P 1 3 TOPAS features 1 3 1 GUI and Launch Mode TOPAS supports two modes of operation 1 A Graphical User Interface mode for parameter input GUI Mode 2 Direct editing of an input file Launch Mode In GUI Mode refinements are controlled using a Graphical User Interface for parameter input Operation in Launch Mode gives access to the full functionality of TOPAS including structure determination see section 1 3 2 In Launch Mode input to the kernel is through an input file INP Advantageous is the possibility to include user defined parameters and models into the refinement Knowledge of the simple but extremely powerful TOPAS macro and equation language is required for details refer to the Technical
41. ell as range and phase dependent display properties such as colors data point size and line width The contents of the data grid are related to the tree item selected it consists of a varying number of pages dependent on the type as well as amount of information to be displayed In the folllwing some general information about the data grid is provided for a detailed description of all data grid pages refer to section 4 2 In the data grid for each tree item there is at least one grid page containing refinement parameters and codes and the Rpt Text page which when selected expands to the Report Format Text and Grid pages Selecting the Grid page switches back to the last used grid page Elements of the grid page Each grid page allows the selection of parameters for refinement and to define their parameter attributes including Use Value Code Error Min Max e Use Boolean switch to indicate the use of the parameter for refinement e Value The parameters value If the parameter is to be refined the parameter value will be updated with the refined value after each refinement cycle e Code Can be either e a switch indicating independent refinement of the parameter Refine or e a switch indicating that the parameter is not to be refined Fix or e auser defined name given to the parameter e an equation also in terms of other parameters e Error The parameters error esd e Min Max User defined limits fo
42. ellaneous Fixed WL Neutron LI Structures hkl Phases 438 Pb5D4 Excl Regions Add Excluded Region Paste INF to NodeSelections Fig 4 10 Miscellaneous item with its associated data grid The Degree of crystallinity page allows degree of crystallinity calculations see section 4 2 2 9 DOC M88 EXX065 V4 2 01 2009 38 TOPAS User s Manual 4 2 2 6 Peak Phase Peak Phase items provide all parameters required for single line up to Whole Powder Pattern Fitting The first Peak Phase item will be created automatically if a peak has been inserted manually or if a peak search has been performed Peak Phase items can also be created manually using the shortcut menu see below With more than one Peak Phase item present additional peaks either inserted manually or found by peak search will be moved to the selected Peak Phase item A new Peak Phase item is always created when importing a peak list d l values from a DIF or a UXD file Individual peaks of a Peak Phase can be of the type FP PV PVII SPV and SPVII Furthermore there are several grid pages related to microstructure parameters as well as another Additional Convolutions page For information about the microstructure parameters refer to the Technical Reference manual The Additional Convolutions page provides for empirical modelling of the observed line profile shapes its options are identical to the Additional Convolutions page of the nstrument it
43. em see section 4 2 2 3 gt Parameters F2 Global Min Max maram CA Emission Profile LyobPwHM nm ef Additional Convolutions Background Type Lise Pasitian Area cry size L ncry size G ir Strain L Strain G 1 ae SPY IY 21 37935 6840 6 200 0 200 0 0 1 0 1 ONeCHOnS 0I Miscellaneous Peaks SPY Crystalline DE Peaks SPY Hide peak sticks Save Phase Save Peaks as DIF file Change to d_l phase Create Indexing Range Create Pawley range Delete Peaks Phase Paste INP to Node S elections Fig 4 11 Peak Phase items The associated data grid only shows the profile function specific refinement parameters which are different for the peak types FP PV PVII SPV and SPVII The peak type can be changed for each peak at any time using the Type combo box refined profile parameters will be lost The Use checkbox enables disables individual peaks A single mouse click LMB on a selected Peak Phase item allows direct editing of its label Shortcut menu options of the Peak Phase item are e Hide peak sticks Show peak sticks Hides or shows peak sticks for individual peak phases e Save Phase Saves the selected Peak Phase item in INP format DOC M88 EXX065 V4 2 01 2009 TOPAS User s Manual 39 e Save Peaks as DIF file Saves all peaks of the selected Peak Phase item as a d l list in DIF format e Change to d Is phase Change to xo_Is phase Switches between display of 20 and d values e
44. ement mainly in GUI mode Note All options provided in the Interface Mode section of the Refinement Options Dialog will have no effect in Launch Mode as the refinement will be completely controlled by the input file DOC M88 EXX065 V4 2 01 2009 22 TOPAS User s Manual gt Refinement Options Interface Mode Calculate Errors Fit Zoomed Fe Verbose mode for Kernel output Continue After Convergence Randomize as a function of Errors a Mo Normal Equations Use Line Minimization L OT st lt i Use Extrapolation Interface and Launch Mode a Pa Graphics Response Time secs wf Ok Fig 3 6 Refinement Options Dialog Interface Mode Calculate Errors Calculates errors if checked Fit Zoomed If checked only the zoomed region will be fitted Verbose mode for Kernel output Toggles kernel output in the text field between verbose and brief Continue After Convergence Refinement is continued after convergence Randomize as a function of Errors Useful if Continue After Convergence is used Performs a random parameter change based on its error and then continues the refinement No Normal Equations Prevents the use of normal equations in the minimization routine useful if only effects of line minimization are sought Use Line Minimization Invokes the use of line minimization Faster convergence and often to a lower minima is observe
45. es available in GUI and Launch Mode cccecececccececceeeceueeeaceneaeas 4 14 TOPAS FOfOFONCES w swen titan ta an dad cade ak a ka tk n n a kk n a a ke a n a n e a a e a n e 6 2 ELEMENTS OF THE USER INTERFACE 0 ht vit teat atanta aaa aatanaasansosassonansanaosansonannn 7 3 THE SCAN WINDOW sis eitiei 5 6tstinettitoletanottit sti tata taa tata at l ala lk 11 3 1 Common features in GUI Mode and in Launch Mode cccccecececeeeeeees 11 De ket ASON AY Aaa teknik sik kf a kk ki an idan n a n a nated aan fai a Genta eestor ii 11 3 1 2 Y axis limits Zooming panning and selecting rl rvrvortoreorooroooenoonoononnonos 13 3413 SAONEUE MENW OPOS bwete kaw wii aw gi kn a w w ba ko ea po e ki a kaz a yan ka 14 3 2 Features available in GUI Mode Only ccccescceseceeeeeeeeeeeeeeeeeeseeeseeesenesenes 15 3 3 Views related to the Scan WINCOW 0 ka tete teke a ennan ant ananaataraaaasaneseosanessosanannnnanann 15 BOU Quek ZOOM VV MICO MW ke ik a aa ik ve ki kk A A e e ese ave 15 3 3 2 Weight Percent Pie Chart WINdOW cccccccecccececeeeeeeseeeceeceeeceeeeeesaeesaues 16 329 0 Chart ODMOMS DIAG tet yn tit ata a kita e a tattered a a kw l a ai at a 16 Jwe Peak S FCN DISO ae beat EAEE 17 29 9 PEAK DELANS DIGIOG siacesscadsanssandnasisandsandnandnaddaneanes s k na da vR ede VARE RATE e RETA DA PRIM A ARAAA 18 JO OBNONS DIAO ab eten oka kt ken et deel et ke en bek en ek enn p in tal den kte k
46. fine 0 lt bkg 8668668 Lyol 18 nm 0 000 l Import STR P 1 L ol FWHM nm 0 000 kK q Strain me x x phase name A1U04 a 6 54144 Strain L LI 0 1 Input File a 7 75975 Strain G L Nou a 9 13572 F 0 00000 a 96 18452 0 000 a 107 23793 a 161 46699 Save Structure in STR format 0 000 View Hide Structure Create hki s phase Delete Structure Paste INP to Node Selections Cry Density ajem43 am ae A11 x 6 74912 z 6 40696 Al2 x 0 46427 6 215 62 A13 x 6 95983 8 00680 u1 x 6 99779 A 6 74677 v2 x G 6 19746 6 34449 val Ya Data Exchange Data Exchange Kernel Parameters Window Kernel Input File N fo Fit Window TOPAS alvo4 raw TI Jindow elp Non linear least squares c 1992 2007 Alan A Coelho e View Fit Launch Too pe ap os Aa ma A SA OU ae Ta Number of independent parameters 74 LAN F a e N D me ou iy x Loading xyz s for P l from file C Topas4 sq p l sg Space group P l is centrosymmetric 10 500 Number of equivalent positions 2 Number of independent parameters 74 10 000 Number of hkls generated for C Topas4 sg p l sg 530 Time s 74 128 0 000 z 0 9 500 Tine m 6 983 67 146 Time 3 175 1 808 9 000 Time e 816 0 359 Time A 788 0 028 8 500 Time A 786 0 001 Time 786 0 000 8 000 Kernel m Output 7 000 6 500 6 000 5 500 5 000 4 500 4 000 3 500 3 000 2 500 Scan 2 000 Window 1 500 1 000 500 bay 0 bi vi Pry Li y 500 5 10
47. g Sorts the indexing results by decreasing number of unindexed lines goodness of fit e Sort by Volume sorts the indexing results by volume e Sort by selected columns sorts by the selected columns e Save to NDX file Saves the indexing results into an NDX file e Paste INP to Node Selections Supports pasting of information in INP format from the clipboard Multiple Pawley Le Bail refinements hkl Phase items provide all parameters required for whole powder pattern decomposition including both the Pawley and the Le Bail method The dependent Indexing Details item allows fully automatic Pawley or Le Bail refinement of all selected solutions of an indexing run The Indexing Details page is similar to the Results page of the Indexing range and contains the same information additionally Rwp is obtained after Pawley or Le Bail refinements The Ref checkbox is used to flag solutions to be refined and is cleared automatically after refinement repeated refinements are possible For multiple Pawley Le Bail refinements it is not necessary to provide any space group and lattice parameter information in the Phase Details page of the hkl Phase item these fields are automatically completed For each selected solution Rwp the refined zero point error as well as refined lattice parameters are provided after termination of refinement DOC M88 EXX065 V4 2 01 2009 TOPAS User s Manual gt Parameters F2 Global eszadd 0E Emi
48. g options for the 3D display of electron densities and offers atom picking capabilities with or without symmetry consideration Clicking the RMB anywhere in the Structure Viewer will open a shortcut menu offering access to the following features e Set rotation position at geometric center e Set rotation position at atom under mouse e Set rotation position at eye e Keep rotation position at center of view e Show connecting atoms for selection e Hide selection e New polygon connecting selected atoms e Show connecting atoms e Hide connecting atoms e isolate atom polyhedra under mouse DOC M88 EXX065 V4 2 01 2009 62 TOPAS User s Manual 6 THE RIGID BODY EDITOR Note Not available in TOPAS P The Rigid Body Editor Fig 6 1 provides for creation viewing and editing of rigid bodies and structures It can load and save files in INP format INP STR RGD furthermore cloud files CLD can be loaded for details refer to the Technical Reference manual The top Browser area can be displayed hidden using the Load Hide menu item the Preview area offers a preview for the currently selected file read only One or more files can be loaded into the Main View area LMB double click on file name The associated rigid body structure definition is displayed in the Editor area at the left of the Main View area The Loaded page in the Options box provides an overview about all loaded files selected i
49. he first number on the third line contains the distance between sites Y1 and O3 The second number in the third line contains the angle between the vectors Y1 to O3 and Y1 to O2 The third number in line three contains the angle between the vectors Y1 to O3 and Y1 to O1 Thus bond lengths correspond to the first number in each line and bond angles start from the second number The numbers after the site name and after the character corresponds to the site equivalent position as found in the SG space group files found in the SG directory DOC M88 EXX065 V4 2 01 2009 48 TOPAS User s Manual gt Parameters F2 TES S04 ak 0E Emission Profile EE Background Generate Bond lengths ferrors 0E Instrument Consider Lattice parameters in errors Lai Corrections Generate CIF outpuk For structure LI Miscellaneous Structures hkl Phases 5 61 Fb504 Preferred Orientation Str Dutput Generate FCF output Paste INF to NodeSelections Fig 4 17 Str Output item with its associated data grid The shortcut menu of the Str Output item offers the following option e Paste INP to Node Selections Supports pasting of information in INP format from the clipboard 4 2 2 9 Structures hkl Phases Allows viewing and manipulating of refinement parameters and options common to all structures and hkl phases Fig 4 18 The data grid associated to the Structures hkl Phases item comprises the following pages The
50. ical Harmonics Anisotropic Refinement Models Peak broadening Peak shifts Preferred orientation Temperature factors GUI GUI GUI GUI Constraints and Restraints Any linear and non linear constraints Penalty functions Can be applied to all refineable parameters Bondlength restraints Anti Bump Parabola lattice energy minimization user defined Rigid and soft bodies with all parameters refineable Rigid body editor PPP GUI Minimization Procedures Marquarat BFGS method Line minimisation Extrapolation Sparse matrix method Miscallenous Extensive macro language support of user defined refinement parameters and refinement models Fully automated operation possible GUI GUI GUI GUI GUI Single crystal data are not available in GUI Mode DOC M88 EXX065 V4 2 01 2009 TOPAS User s Manual 1 4 TOPAS references For publication of results obtained with TOPAS the following references can be used For general use of TOPAS Bruker AXS 2008 TOPAS V4 General profile and structure analysis software for powder diffraction data User s Manual Bruker AXS Karlsruhe Germany Convolution based profile fitting fundamental parameters approach Cheary R W amp Coelho A A 1992 A fundamental parameters approach to X ray line profile fitting J Appl Cryst 25 109 121 Cheary R W Coelho A A amp Cline J P 2004 Fundamental Parameters Line Profile Fitting in Laboratory Diffra
51. in section 4 The Parameters Window has no effect in Launch Mode Structure Viewer Rigid Body Editor Window not available in TOPAS P The Structure Viewer Rigid Body Editor Window allows to view crystal structures and 3D electron densities and provides for creation and editing of rigid bodies It can be docked at the left right top or bottom of the Working Area and is described in section 5 DOC M88 EXX065 V4 2 01 2009 TOPAS User s Manual Quick Zoom Zoom Rectangle Window TOPAS le View dow Help Scan Window 1 DSS BS US7 oy ea scan Window 2 ge Scan Window 3 fen scan Window 4 _ 2 active Weight Percent Pie Chart Window Wt Rietveld hkl Marker Corundum 14 56 Fluorite 53 01 Yo Zincite 3243 Yo Options F4 Peak Details Insert Peak i Capture Dialog Manipulate x Manipulate y Exclude Region Select Ctrl key Options Dialog Fit Window Interface Mode Number of hkls generated for C Topas4 sgq pbnm sg 384 0 Time 0 11 Rvp 82 625 0 000 MC 0 00 0 l Time 0 20 Rwp 51 660 30 965 MC 0 14 l 2 Time 0 33 Rup 28 924 22 736 MC 0 04 1 3 Time 0 42 Rvp 15 476 13 448 MC 0 01 l 4 Time 0 48 Rwp 10 900 4 575 MC 0 01 l 5 Time 0 53 Rup 10 184 0 716 MC 0 04 1 6 Time 0 69 Rup 10 138 0 046 MC 0 01 1 7 Time 0 73 Rup 10 103 0 035 MC 0 00 l 8 Time 0 80 Rwp 10 099 0 004 MC 0 70 l Refinement Options 7 P Interface M
52. ing correction functions gt Parameters F2 Global BP FPbsot raw I Emission Profile Background Inistrument Corrections A Miscellaneous Structures hkl Phases A PbS04 Paste INP to NoderSelections Cylindrical sample 5 abine Use Value Code Error Min Peak shift Zero error won a Sample displacement mm O Refine Intensity Corrections LP Factor W 26 37 Fix Surface Rghnss Pitschke e Surface Rghnss Suortti Sample Conyolutions Absorption tlicm 100 Refine Sample Tilt mm Mo Refine Fig 4 8 Corrections item with its associated data grid showing the Corrections page Note Absorption is a Use dependent expand collapse grid item Parameter name e Zero Error e Sample Disp e LP Factor e Surface Rghnss Pitschke e Surface Rghnss Suortti e Absorption e Sample Thickness e Scale Intensity e Sample Tilt Remarks Zero point error in 20 Sample displacement in mm Lorentz Polarisation factor using the monochromator angle in 20 Allows surface roughness intensity corrections according to Pitschke et al 1993 Allows surface roughness intensity corrections according to Suortti 1972 Linear absorption coefficient used for adjusting the peak shape cm Sample thickness in mm in the direction of the scattering vector Peak intensity correction for absorption effects Sample tilt in mm DOC M88 EXX065 V4 2 01 2009 36 TOPAS User s Manua
53. it detector slit width mm Fixed Divergence Slit angle Sample length mm for beam overflow related profile shape correction Beam overflow related intensity correction Irradiated sample length in beam direction for Variable Divergence Slits mm 1 sin 0 intensity correction for Variable Divergence Slits Diameter of the capillary Linear Absorption Coefficient 1 cm Angular range window size in Fixed Divergence Slit angle Sample length mm for beam overflow related profile shape correction Beam overflow related intensity correction Tube tails correction Bergmann 2000 Width of the tube filament mm Length of the left tail negative mm Length of the right tail mm Fractional height of the tube tails relative to the main beam Accurate model for describing peak asymmetry Length of the tube focus mm Length of the irradiated sample mm Receiving Slit length mm Primary Soller slit angle Secondary Soller slit angle Refer to the Technical Reference manual Simplified model for describing peak asymmetry Simplified model for describing peak asymmetry DOC M88 EXX065 V4 2 01 2009 34 TOPAS User s Manual Shortcut menu options of the Divergent beam page are e Load Instrument Details Loads instrument details from a PAR file e Save Instrument Details Saves instrument details to a PAR file e Paste INP to Node Selections Supports pasting of information in INP format fr
54. l The Lorentz Polarisation factor for unpolarized radiation is 90 e g X ray diffractometers without any monochromator and 0 for fully polarized radiation e g synchrotron radiation Values for most common monochromators Cu radiation are e Ge 27 3 e Graphite 26 4 e Quartz 26 6 There is no polarization factor for neutron data and thus the angle for Lorentz Polarization should be set to 90 this gives the Lorentz only part The shortcut menu of the Corrections item offers the following option e Paste INP to Node Selections Supports pasting of information in INP format from the clipboard The Cylindrical Sample Sabine page The Cylindrical Sample Sabine page Fig 4 9 provides two correction functions related to capillaries gt Parameters F2 Global Corrections Cylindrical sample Sabine Ret T ext en Conections Cy ple Sabine ipt Text E Emission Profile Use Value Code Error Min Max 2Th correction Ei Refine O I Background LI Instrument Intensity correction ie Refine 0 L orrechons Miscellaneous Structures hkl Phases 1an Pb5D4 Paste INP to NodeSelections Fig 4 9 Corrections item with its associated data grid showing the Cylindrical sample Sabine page Parameter name Remarks e 2Th correction Allows a 20 correction for cylindrical samples e Intensity correction Allows an intensity correction for cylindrical samples Note Both corrections should not be used in
55. lable using the shortcut menu This allows for example for the easy creation of files with particular refinement results such as various peak versus intensity lists xyz lists of atomic coordinates A detailed description of the shortcut menu options is provided in section 4 2 3 Import of grid data The GUI supports general pasting of information in INP format from the clipboard into tree nodes or selected grid items This provides for extremely convenient and fast duplication exchange of any refinement data The Report Format and Text pages Contains the content of the grid pages in the form of differently formatted text Note As for the grid the contents of the Report Format and Text pages is dependent on the selected tree item The Text page represents the grid content as plain text in INP format and is useful for learning the INP format of TOPAS It also faciliates the setup of INP files via copying amp pasting of selected text The Report Format page displays the grid page contents in the form of a formatted report The contents of both the Report Format and Text page can be copied to the clipboard saved to a TXT file printed directly or transferred to the TopasEditor or Microsoft Word if available using the shortcut menu see section 4 2 3 4 2 Tree items and their associated data grid pages 4 2 1 Global item The Global item Fig 4 1 allows viewing and manipulating of both global refinement settings as well as refine
56. m are Add Site Before Current Site Adds a new site before the current site Add Site at Bottom Adds a new site at the bottom of the list Add Atom at Current Site Adds a new atom at the current site Paste INP to Node Selections Supports pasting of information in INP format from the clipboard DOC M88 EXX065 V4 2 01 2009 46 TOPAS User s Manual The Preferred Orientation item The Preferred Orientation item Fig 4 16 offers two models for preferred orientation correction 1 March Dollase March 1932 preferred orientation correction for up to two directions hkls provided in the Aki field needs to be separated with spaces as shown in Fig 4 16 2 A correction for preferred orientation effects using a spherical harmonics series its coefficients can be viewed and manipulated in the Coefficients page The Order parameter corresponds to the order of the spherical harmonics series which must be an even integer ranging from 2 to 8 gt Parameters F2 Global PO March Dollase Rpt Test tT ext B Posod raw C Emission Profile hk Use Value Code Error Background Direction 1 oo1 W il Refine O 0E Instrument Direction 2 Ei Refine 0 Corrections Fraction Dir 1 0 5 Refine 0 LI Micelaneous Structures hkl Phases lt 4 0 Pb504 II Sites PO Spherical Harmonics Coefficients Ii Preferred Orientation Name Use Order LI Str Output 1 osh_47bS2ich8 6c 4 Paste INF to Node S elections
57. m calculations Optionally each line can be weighted and typically observed line intensities serve as weights The Good parameter which can be used only once indicates that the corresponding d spacing is not an impurity line A single use of Good on a high d Spacing decreases the number of possible solutions and hence speeds up the indexing process DOC M88 EXX065 V4 2 01 2009 TOPAS User s Manual 53 gt Parameters F2 Global Use The Use Weighting Good 1 966476 195 7783 2 465681 18 03186 3 15902 107 9634 3 20356 14 4943 3 206518 6 802709 3 411992 VI FI ot DI 24 41587 3 036389 6 451032 3 94119 16 5969 4 246764 10 69863 4 6538 226 0719 4 74166 13 65 758 4 945118 15 92032 5 056488 40 24849 5 084931 3 016471 5 139916 T e06 5217920 34 51916 aso 95 65892 D 427500 42 3550 5 606178 7 026954 5 795913 56861435 6 013195 254 1447 6 105054 24 99227 6 172267 11 36425 s ai om an AE Add data Set data a d Set data as 2Th Paste dz from Clipboard Paste 7 he from Clipboard Paste drl from Clipboard Paste 27 hy ls from Clipboard 4 41 41 4 41 4 4 41 41 4 4 4 4 4 4 41 4 41 4 41 4 4 ss 4 4 41 4 41 4 4 41 4 lt 1 4 4 lt E 4 lt 1 41 4 4 4 4 sis BHEBBEB BEB NO A A Ree ee eee eee Fig 4 22 Indexing range with its associated data grid showing the Data page Shortcut menu options of the Data page are e Add data Adds a new line at the bottom of the li
58. ment parameters and codes across all loaded ranges Global refinement settings are provided in the Global items data grid including calculated step size for XY type measurement data convolution steps the global convergence criterion and the maximum number of iterations to be performed With more than one scan data file loaded the Global item represents a transposition of the Range item contents where all refinement parameters common to all ranges can be viewed and manipulated individually as well as simultaneously Selected ranges can be turned on off at once DOC M88 EXX065 V4 2 01 2009 26 TOPAS User s Manual Second level items of the Global item are e Background section 4 2 2 2 e Instrument section 4 2 2 3 e Corrections Convolutions section 4 2 2 4 e Miscellaneous section 4 2 2 5 e Display Additionally the following items may be displayed as well e All Peaks section 4 2 2 6 e All Structures hkl Phases section 4 2 2 9 The Display item provides for customization of display properties including colors data point size and line width for each range Note The Global Defaults page allows for the definition of program defaults for the display properties with the exception of the observed data color which cannot be kept as default to prevent ambiguity gt Parameters F2 E Ex e r ACRA DAN E Instrument Display Path Corrections Convolution 1 jw CH Topas4i TutoriallQatD8 8488 raw LI Mis
59. mines the maximum number of solutions kept Defines space group s to be used for indexing Defines x0 in the reciprocal lattice equation see the index_x0 keyword in the Technical Reference manual Defines Bravais lattices to be used for indexing Note that indexing can be performed on both selected space groups and Bravais lattices simultaneously DOC M88 EXX065 V4 2 01 2009 52 TOPAS User s Manual gt Parameters F2 EEE E lndexirg wavelength A Zero error Max zero error in 2Th Max 27h error for UNI Max ratio Nc Mo Max number solutions Try space groups Set x0 from The Bravais lattices ta include Orthorhombic F Orthorhombic 1 Orthorhombic lt Orthorhombic P Manaclinic C Cubic I Cubic P Trigonal Hexagonal R Trigonal Hexagonal F Clone Indexing Range Tetragonal I Delete Indexing Range Tetragonal P Paste INP to Node Selections Manaclinic P a 4 4 4 4 4 a a Triclinic Fig 4 21 Indexing range with its associated data grid showing the Indexing page Shortcut menu options of the ndexing page are e Clone Indexing Range Clones the selected indexing range e Delete Indexing Range Deletes the selected indexing range e Paste INP to Node Selections Supports pasting of information in INP format from the clipboard The Data page contains the d or 20 values to be used for indexing Fig 4 22 The Use parameter allows including or excluding individual lines fro
60. n OU DON 19 BI FIL IMOONW sinon kad rit bett ke bibi kek kaki kek eee deataucidhatsnchatatseaiahobauakstatds 20 4 THE PARAMETERS WINDOW 2 0 cccccccccccccscesceccecsccenencsccncsncensccenenesneecsnesneess 23 4 1 Elements of the Parameters Window ccccecsccececcecsccsccncecencsceanenesaeanseeanes 23 A kok PAT MON 26sieje so diodasino kone ten ane ee n desas die debi kondane sipa rete 23 AeA Oooo k Le 6 EYES scr scent tine FY A Seems ore Mart VE FE WE eee etre cee PAF Na 24 4 2 Tree items and their associated data grid Pages rereerreerosrasasonnnnn 25 AZA GIOD NON RRR ene On Rn OA CORA ane Oe Cane mT EA NA Can a in oi Ste eT A 25 ZZ PRAMS MENN SY kb tat ea ei an EO 27 A293 MOENG FWA A E E eae eae rare eee 51 4 3 PRINTING ANA F PON A f kav ti ou k k n kk ik ka kk e ka kk ak a kk ka kk a a kk ao a a 58 57 THE SIRUCTURE VIEWER 5e ee ti fi koute ct kat kn ote ARRE 59 6 THE RIGID BODY EDIT OR 45 ket it tal ti tk ta a a ak n ei isk 62 7 THE ESSENTIAL HELP WINDOW e kk tt kk knn nana nannan ana aeaaaasaasosassanaosensosensonannnn 64 8 OPERATION IN GUI AND LAUNCH MODE 0 tt tete ee ata ataraasassosassessosessosensonannnn 65 QV REFERENCES areas mmo ee k n ie at te A 66 DOC M88 EXX065 V4 2 01 2009 TOPAS User s Manual intentionally left blank DOC M88 EXX065 V4 2 01 2009 TOPAS User s Manual 1 1 INTRODUCTION 1 1 TOPAS overview TOPAS is a graphics based profile a
61. nalysis program built around a general non linear least squares fitting system TOPAS integrates various types of X ray and neutron diffraction analyses by supporting all profile fit methods currently employed in powder diffractometry e Single line fitting up to Whole Powder Pattern Fitting e Indexing using the LSI Indexing and LP Search methods Coelho 2003 Coelho amp Kern 2005 e Whole Powder Pattern Decomposition according to Pawley 1981 and Le Bail et al 1988 in the following referred to as Pawley method and Le Bail method e Rietveld structure refinement Rietveld 1967 1969 and quantitative Rietveld analysis Hill amp Howard 1987 e Ab initio structure determination using simulated annealing Coelho 2000 and Charge Flipping Coelho 2007 methods 1 2 TOPAS vs TOPAS P For applications which do not require the full features of TOPAS an additional variant has been developed TOPAS P TOPAS P is designed for profile analysis of powder data without reference to a crystal structure model This includes Single Line Fitting up to Whole Powder Pattern Fitting Whole Powder Pattern Decomposition Pawley and LeBail methods and Indexing LSI Index and LP Search methods Applications include the determination of accurate profile parameters line positions integrated intensities peak widths and shapes standardless microstructure analysis indexing as well as lattice parameter refinement In Fig 1 1 th
62. ode pinn Calculate Errors minn i a 5 Fit Zoomed ATEN J P verbose mode for Kernel output i Continue After Convergence E Randomize as a function of Errors P No Normal Equations P Use Line Minimization P Use Extrapolation E Interface and Launch Mode P Graphics Response Time secs Refinement Options Dialog Fig 2 2 Scan Windows with related views DOC M88 EXX065 V4 2 01 2009 Cry size L nm Cry size G nm Strain L Strain G BEB NO MSO lv Remove K Alpha 2 Peak Intensity Ratio Tolerance X Position Tolerance n AOE ORE AERE Dor a ae he _ L Peak Search Dialog 10 TOPAS User s Manual Parameters BEES Cie Window Global akodraw Parameter Tree fg Emission Profile E Background E Instrument D Corrections 9 Miscellaneous H 0 Structures hkl Phases 3 6 Avo4 E Sites 9 Preferred Orientation E Str Output Save Structure in STR format View Hide Structure Create hkl_Is phase Delete Structure Paste INP to Node Selections a Fig 2 3 Parameters Window Grid Tab Options Box Seles ode Error 6 5414400 0 0000000 7597500 0 0000000 9 1357200 0 0000000 96 18452 107 2379 101 401 0 001 lt Cry size L nm Cry size G nm Lyol IB nm Lyol FWHM nm Strain Strain L Strain G E EEE Bee Cell volume A43 0 00000 Cry LAC 1 cm 0 000 Cry Density glcem3 0 000 R Bragg 0 000 Data
63. om the clipboard The Additional Convolutions page Provides for empirical modelling of instrument functions Available convolutions include the Hat Lorentzian Gaussian Circles Exponential and One on X convolutions to be selected from the Conv Type combo box Predefined angular dependencies are Constant 1 Cos Th Tan Th and Sin 2 Th to be selected from the 27h Dependence combo box alternatively user defined angular dependencies can be provided in the form of equations Shortcut menu options of the Additional Convolutions page are e Load Instrument Details Loads instrument details from a PAR file e Save Instrument Details Saves instrument details to a PAR file e Add Convolution Adds an additional convolution Convolution type and angular dependence can be defined using the Conv Type and 2Th Dependence combo boxes Additionally it offers quick access to the following important convolutions e Add Hat 1 cos Th dependence e Add Lorentzian 1 cos Th dependence e Add Gaussian 1 cos Th dependence e Add Hat Tan Th dependence e Add Lorentzian Tan Th dependence e Add Gaussian Tan Th dependence selected additional convolution rows can be deleted using the DEL key e Paste INP to Node Selections Supports pasting of information in INP format from the clipboard DOC M88 EXX065 V4 2 01 2009 TOPAS User s Manual 4 2 2 4 Corrections The Corrections page 35 The Corrections page Fig 4 8 provides the follow
64. phase name the intensity distribution of this particular phase will be shown using a bold line Additionally the hkl markers for this particular phase are highlighted using small triangles at the bottom of the markers When moving the mouse onto the hkl markers the cursor will always lock on to the nearest hkl marker which makes it easier to select closely spaced hkl s After lock on the marker will be highlighted using a small triangle at the top of the marker and some hkl information will be displayed For systematic overlaps of non symmetry equivalent reflections all possible hkl s will be shown DOC M88 EXX065 V4 2 01 2009 TOPAS User s Manual 13 3 1 2 Y axis limits Zooming panning and selecting Y axis limits Y axis minimum Y1 and maximum limits Y2 can be fixed or unfixed using the Fix Y1 and Fix Y2 toolbar icons Fixing options include fixing of Y1 to zero as well as to the minimum count value and Y2 to the maximum count value Fixing Y1 and or Y2 affects both the zooming and panning behaviour as described below Zooming Can can be performed in both the Scan Window and the Quick Zoom Window section 3 3 1 Zooming is performed by pressing the LMB at the upper left position of the targeted zoom area and dragging the mouse to define the zoom area By doing the same backwards the axies are reset to the full X and Y scale Zooming and unzooming is also possible by pressing and scrolling the mouse wheel For zooming ou
65. r fitting to negative 20 values e For LAM cursor Switches the mouse cursor to a multi line Cursor representing the different emission lines of the current emission profile Fig 4 4 e Lam for Bragg angle Only for expert users refer to the Technical Reference manual e Calculate Lam Only for expert users refer to the Technical Reference manual DOC M88 EXX065 V4 2 01 2009 30 TOPAS User s Manual 4 Parameters F2 7 Yates Codes Ens Min Max Options J Ret Tex 0E Background 1 534753 Instrument 1 540596 0 Corrections 1 541055 SS Miscellaneous 1 544410 H O Structures hkl Phases aif PbSod 1 544721 WE A 1 534753 Load Emission Profile 1 540596 Save Emission Profile 1 541058 Add Emission Line 1 544410 Paste INP to Node Selections 1 544721 Fig 4 3 Emission Profile item with its associated data grid showing a list of emission lines of the current emission profile here CuKa5 TOPAS lebailsh raw File View Fit Launch Tools Window Help SH Tams a x 70 0004 e500 TA 55000 50 000 45 0004 anoo 25000 20 000 25000 20 0004 15 000 10 000 5 0004 46 5 46 75 47 47 25 47 5 ATIS 48 48 25 48 x 47 48431 46537 23 d 1 913207 Fig 4 4 With For Lam cursor switched on a multi line cursor representing the different emission lines of the current emission profile here CuKa5 will be shown DOC M88 EXX065 V4 2 01 2009
66. r the parameter value For more details about parameters and parameter attributes refer to the Technical Reference manual A double click on the code field will switch the code from Refine to Fix and vice versa If a user defined parameter name has been defined the character will be placed in front of the parameter name or removed respectively The colors used in the grid have the following meaning e Parameter values with a grey background are read only e Parameter values with a white background can be modified by the user The text color is dependent on its code e Black text The parameter is fixed e Red text The parameter is refined e Blue text The parameter is calculated from an equation DOC M88 EXX065 V4 2 01 2009 TOPAS User s Manual 25 Selection in the grid Rows or columns can be selected by clicking the row or column heading Adjacent rows or columns can be selected by either dragging across the row or column headings or by selecting the first row or column and then holding down SHIFT and selecting the last row or column Nonadjacent rows or columns can be selected by selecting the first row or column and then holding down CTRL and selecting the other rows or columns The complete grid can be selected by clicking the Select All button of the grid at the top left of the grid Export of grid data The grid page contents can be copied to the clipboard or transferred to the TopasEditor or Microsoft Word if avai
67. ram line a new Scan Window is opened which contains the captured data This feature allows for the export of any calculated data in a separate data file e Manipulate X Allows the movement of a selected scan in the positive or negative x direction This feature is useful for comparing different data sets or for visualisation of 20 errors Note The data set in memory which constitute loaded data is directly manipulated the original data file remains unchanged Subsequent calculations are performed on the modified data DOC M88 EXX065 V4 2 01 2009 20 TOPAS User s Manual e Manipulate Y Similar to Manipulate X but in the y direction Note The data set in memory which constitute loaded data is directly manipulated the original data file remains unchanged Subsequent calculations are performed on the modified data e Exclude Region Allows the exclusion of selected data ranges from calculations Excluded regions are defined with the mouse by clicking and dragging An unlimited number of excluded regions are allowed including the case of overlap e Select Allows the selection of peaks and excluded regions in the Scan Window 3 3 Fit Window This is the central place for controlling the refinement process Fig 3 5 It basically consists of a text field and a plot window and is a normal top level window by default which can be docked at the left right top or bottom of the Working Area Note If the Fit Window is docked then i
68. rofile Background Calculate Degree of crystallinit Instrument Crystalline area 969430219 LY Corrections Amorphous area 2272 79411 La Miscellaneous Degree of crystallinity 35 81 0079734 Structures hkl Phases 0 Quantitative SG Lattice parameters 0 Brindley correction Spherice fy Display Phase Name Amorphous Area Corundurm A L Fluorite 2704 38889 Zincite i 2577 63886 J Peaks Phase inci 4411 657443 Peaks Phase 0 z272 79411 ki m gt Paste INP to Kade Selection Fig 4 20 Quantitative item showing the Degree of crystallinity page with its associated datagrid DOC M88 EXX065 V4 2 01 2009 4 2 3 Indexing TOPAS User s Manual 51 Indexing provides access to all LSI Index relevant parameters and options in GUI Mode The Indexing range data grid Fig 4 21 comprises the following pages Indexing Data and Solutions The Indexing page offers the following parameters and options Parameter name Wavelength A Zero error Max zero error in 2Th Max 2Th error for UNI Max ratio Nc No Max number solutions Try space groups Set x0 from 2Th Bravais lattices to include Remarks Wavelength used for indexing Includes a zero error calculation Excludes solutions with zero errors larger than the given value Lines with a 20 error larger than the given value will be considered as unindexed UNI Determines the maximum ratio of the number of calculated to observed lines Deter
69. rom INP and PAR file s while PAR files are intended for instrument parameters only with INP files any keywords and macros supported by the GUI can be loaded Load d_Is DIF UXD Loads peak information from DIF or UXD files providing a link to the ICDD PDF via DIFFRAC EVA and SEARCH DOC M88 EXX065 V4 2 01 2009 TOPAS User s Manual 29 Save if displayed Yobs Ycalc Diff Phases Bkg Output of plot data Allows to save observed calculated difference background and individual phase intensity data in a comma separated text file for plot generation using 3rd party software Data is saved according to the y axis scaling and the x axis is changed to the selected 20 d Q Replace Scan Data Allows to exchange scan data for selected files to be refined using the same refinement model Reverse Data and make X axis positive Allows the use of data obtained from scans in negative x axis regions Delete Range Deletes the selected range Paste INP to Node Selections Supports pasting of information in INP format from the clipboard 4 2 2 1 Emission profile Gives the ability to add and delete emission lines Fig 4 3 which form the emission profile of the X ray source The Options page contains the following options Option Remarks e Ymin on Ymax Determines the x axis extent to which peak tails are calculated cut off e No Th dependence Defines an emission profile that is 20 independent Allows the use of non X ray data o
70. ssion Profile Background 0E Instrument fg Corrections Miscellaneous 3j Structures hkl Phases 4aq hkl Phase Indexing Details C Indexing Load ND file Paste Indexing details Sort by Awp Sort by Gol decreasing Sort by UN Gol decreasing Sort by volume Sort by selected columns Paste INP to Node S elections Indexing Details Apt T ent Ref Sg 4 4141 41 4 4 41 4 i 2 3 4 5 6 7 8 s Rip vs Yolume ke SE ai BAN Ayo 73 45 270061 625 65 59 EFABOS A1 67 54 ERE LA 69709 9386 6G F EE felipe sa avai he 270954 781 65 32 1 000 000 52 8803 1 500 000 67 6601 67 6610 67 6303 54 0591 67 6592 67 6530 57 Fig 4 26 Indexing Details page showing a multiple Pawley refinement of selected indexing solutions The solution highlighted by a blue bar is currently being refined on For solutions not refined yet Rwp IS displayed as 999 Shortcut menu options of the Indexing Details page are e Load NDX file Loads previously saved indexing results e Paste Indexing details Pastes indexing details from clipboard e Sort by Rwp sorts the indexing results by Rwe e Sort by Gof decreasing sorts the indexing results by decreasing goodness of fit e Sort by UNI Gof decreasing Sorts the indexing results by decreasing number of unindexed lines goodness of fit e Sort by Volume Sorts the indexing results by volume DOC M88 EXX065 V4 2 01 2009 58 TOPAS User s Manual
71. st e Set data asd Defines given peak positions as d values e Set data as 2Th Defines given peak positions as 20 values e Paste ds from Clipboard Pastes a list of peak positions from the clipboard and defines them as d values e Paste 2Ths from Clipboard Pastes a list of peak positions from the clipboard and defines them as 20 values e Paste d is from Clipboard Pastes a list of peak positions vs intensities from the clipboard Defines peak positions as 20 values and intensities as weights e Paste 2Th ls from Clipboard Pastes a list of peak positions vs intensities from the clipboard Defines peak positions as 20 values and intensities as weights e Paste INP to Node Selections Supports pasting of information in INP format from the clipboard The Solutions page contains the results of the current indexing run For each solution the following information is listed space group proposal Sg status Sts number of unindexed lines UNI volume Vol goodness of fit Gof zero point error Zero and lattice parameters Furthermore a goodness of fit versus volume plot as well as DOC M88 EXX065 V4 2 01 2009 54 TOPAS User s Manual detailed information about the selected solution are available Fig 4 23 and Fig 4 24 The possible values and meanings of status Sts are e Status 1 Weighting applied as defined in Coelho 2003 e Status 2 Zero error attempt applied e Status 3 Zero error attempt successful and impurity
72. t Sci Forum 347 349 303 308 Brindley G W 1945 The effect of grain or particle size on X ray reflections from mixed powders and alloys considered in relation to the quantitative determination of crystalline substances by X ray methods Phil Mag 36 347 369 Cheary R W amp Coelho A A 1998a Axial divergence in a conventional X ray powder diffractometer l Theoretical foundations J Appl Cryst 31 851 861 Cheary R W amp Coelho A A 1998b Axial divergence in a conventional X ray powder diffractometer II Implementation and comparison with experiment J Appl Cryst 31 862 868 Coelho A A 2000 Whole Profile Structure Solution from Powder Diffraction Data using Simulated Annealing J Appl Cryst 33 899 908 Coelho A A 2003 Indexing of powder diffraction patterns by iterative use of singular value decomposition J Appl Cryst 36 86 95 Coelho A A 2007 A charge flipping algorithm incorporating the tangent formula for solving difficult structures Acta Cryst A36 400 406 Coelho A A amp Kern A 2005 Discussion of the indexing algorithms within TOPAS CPD Newsletter 32 43 45 Finger L W Cox D E amp Jephcoat A P 1994 A correction for powder diffraction peak asymmetry due to axial divergence J Appl Cryst 27 892 900 Hill R J amp Howard C J 1987 Quantitative phase analysis from neutron powder diffraction data using the Rietveld method
73. t cannot be maximised or minimised Interface Mode Fit Zoomed ON El gt mt el ew gt Number of independent parameters Number of equivalent positions 8 Number of independent parameters 30 Number of hkl5 generated for C Topas4 sg pbnm sg 384 Q Time 0 11 Rwp 633 309 0 000 HC 0 00 0 l Time 0 19 Rwp 258 652 377 657 MC 0 00 l Z Time 0 23 75 394 180 258 MC 0 00 l 3 Time 0 28 15 977 59 417 MC 0 00 l 4 Time 0 33 11 569 4 408 MC 0 02 1 5 Time 0 38 10 616 0 953 MC 0 08 1 6 Time 0 42 10 209 0 407 MC 0 02 l 8 efi Time 0 48 10 170 0 040 MC 0 07 l Time 0 56 10 169 0 001 MC 2 37 3 nement converged Interface Mode Fit Zoomed ON Fig 3 5 Fit Window The text field provides information about the refinement process such as some space group information number of independent parameters and details about the refinement iterations including iteration number elapsed time Rw as well as Rwp difference and the number of Marquardt cycles MC The plot window shows an Rwp plot versus refinement cycle which is updated after each iteration This window offers the same zooming and panning possibilities as the Scan Window additionally similar toolbar icons as well as a shortcut menu RMB are available For these options refer to sections 3 1 2 and 3 1 3 When zooming into the Rwp plot updating stops in order to allow examination of the Zoomed region DOC M88 EXX065 V4 2 01 2009 TOPAS User s Manual 21
74. t the X scale can be compressed using the Compress toolbar icon The previously zoomed region can be reset using the shortcut menu command Reset Axies to Previous section 3 1 3 Alternatively the rectangle in the Quick Zoom Window allows a modification of the zoomed area by grabbing one of the red lines with the mouse and moving it A double click on the Quick Zoom Window resets the Scan Window to full scale Note If Y1 or Y2 have been fixed to the minimum or maximum count value respectively the y axis limits will be automatically adjusted to the lowest and highest count value within the Zoomed x region X and Y limits can also be set directly to discrete values using either the shortcut menu or the chart options dialog both described in section 3 1 3 Panning Possible in both the Scan Window and the Quick Zoom Window By pressing the RMB and moving the mouse the zoomed area is moved over the data range horizontally and vertically note vertical panning requires Y1 and Y2 to be unfixed Horizontal panning is also possible by scrolling the mouse wheel or by using the horizontal scroll bar which is displayed if View Horizontal Scroll Bar has been selected Note When panning horizontally with fixed Y1 and Y2 the y axis limits will be automatically adjusted while moving the zoomed region along the x axis Selecting Performed similar to zooming with the CTRL key pressed simultaneously During movement the mouse cursor changes into
75. tems can be unloaded using the Del key The Editor allows creation of new modification of loaded rigid bodies or structures The Main View is updated on using the Update menu item or by pressing Alt F1 New rigid bodies or modifications can be saved using the Save and Save As options The First Guess Z matrix menu item can be used to convert a rigid body definition given in Cartesian or fractional coordinates into a more useful internal coordinate description a Z matrix representation of this description is provided in a temporary output window The Add torsion angle menu item allows to introduce a refineable torsion angle along two selected atoms The Main View offers most of the features and options available in the Structure Viewer see section 5 DOC M88 EXX065 V4 2 01 2009 TOPAS User s Manual Rigid Body Editor Browser Options C Topas4 rigid Z Octahedra rgd EE c system ec gt Topas4 Dy 2Giidene od w Z Octahedra rad C Z6 H6 rgd ID Z C6 10d O Z Cube rad ii Z Octshedra rad O zrozinp O Z Square rad O ZTetrahedron rgd IM Z8 Crad pru r 2 min 1 8 max 2 2 g rigid s z_matrix z matrix z matrix z matrix z matrix z matrix z matrix Zr ol 02 03 04 05 06 Preview RRR Wou MON NON la la Load Hide Update Alt F1 First quess 2 matrix Add torsion angle prn r 2 min 1 8 max 2 2 rigid Z_matrix z matrix Z matrix Z matrix
76. the space group provided Typically the space group will correspond to one that is of lowest symmetry with the particular crystal system tested i e for triclinic put space group number 1 for monoclinic put 3 and so forth Space group symbol or space group number When selecting the field a drop down button opens a dialog for space group selection Lattice parameters Spacegroup depend symmetry constraints are automatically applied including removal of redundant lattice parameters from the grid Scale factor Microstructure parameters related to crystallite size refer to the Technical Reference manual Microstructure parameters related to strain refer to the Technical Reference manual Relative phase amount Weighed phase amount if phase is used as a spike see also section 4 2 2 9 Absolute phase amount in the spiked sample after considering amorphous phase amounts Absolute phase amount in the original sample after considering amorphous phase amounts Cell mass Cell volume R Bragg value DOC M88 EXX065 V4 2 01 2009 TOPAS User s Manual 41 The Peak Type page allows selection of the profile shape function available functions are FP PV Mod PV_TCHZ and PVII For information about these profile shape functions and their parameters refer to the Technical Reference manual A list of all generated peaks is displayed in the Aki s page including the following parameters h k I m multiplicity d 26 and intensit
77. ucture dependent keyword view_structure can be used see the Technical Reference manual structures 3D electron densities can be freely rotated by pressing the LMB and dragging the mouse Zooming is performed by pressing the RMB and dragging the mouse To rotate a structure 3D electron density around an axis perpendicular to the computer screen press both the Shift key and the LMB and the drag the mouse The sensitivity of rotation decreases as the mouse position moves away from the center of the window and allows precise positioning of objects DOC M88 EXX065 V4 2 01 2009 TOPAS User s Manual 61 The Structure Viewer comprises the following icons and actions Icon m jm L S i m IJSBRANTS ETNE Yo Result Switches between Structure Viewer and Rigid Body Editor windows Displays in perspective or orthogonal view Displays the lighting options Displays viewing options incl rotation and translation dialogs Wiggles the view about an axis perpendicular to the computer screen Displays hides the unit cell walls Displays hides atom names Displays hides balls Displays atoms in their expected size Displays hides sticks connecting atoms Displays hides polygons Display multiple unit cells Clip atoms appearing outside of the unit cell Display clipping planes and clipping dialog Temporary Output window Displays selected atoms in z matrix format Cloud Options dialog Displays viewin
78. ues and refinement codes in the Scan Window Fig 3 3 Peaks inserted into the Scan Window will be of the peak type selected in the left column It is possible to insert different peak types into the same powder pattern For each peak inserted a peak marker is displayed In addition near to the top of the peak marker some peak properties such as profile parameter values or refinement codes for the associated peak can be shown depending on the selections in the second and third column of the Peak Details Dialog Peak Details F3 Fig 3 3 Peak Details Dialog When opening the Peak Details Dialog the cursor will change to peak insertion mode The form of the cursor unambiguously reflects the selected peak type A mouse click using the left mouse button in the Scan Window will insert a peak when the Peak Details Dialog is open Peaks can also be inserted anytime even when the Peak Details Window is closed by pressing the CTRL key when clicking the left mouse button Peak insertion is assisted by the Bouncing Ball feature The color of the Ball follows the scan that it is on When more that one range is displayed then the scan with the bouncing ball is selected for peak insertion the Bouncing Ball feature automatically selects the scan closest to the cursor If the scan with the Bouncing Ball has more than one peaks phase then the user is prompted to select the a peaks phase from the tree view An important feature of the Peak Details Dialog
79. us Structures hkl Phases Heide Pb5D4 Load Instrument Details Save Instrument Details Add Convolution Add Hat 1 Cos Th dependence Add Lorentzian 1 Cos Th dependence Add Gaussian 1 Cos Th dependence Add Hat Tan Th dependence Add Lorentzian Tan Th dependence Add Gaussian Tan Th dependence Paste INP ta Node S elections Fig 4 7 Instrument item with its associated data grid showing the Additional Convolutions page with one example convolution added DOC M88 EXX065 V4 2 01 2009 TOPAS User s Manual The Divergent beam page 33 Contains all instrument details necessary to model the instrument function using the Fundamental Parameters Approach This includes the following refinement models Parameter name Goniometer radii e Primary Radius e Secondary Radius Equatorial Convolutions e Point detector e Receiving Slit Width e FDS Shape Angle e Beam spill sample length e Correct Intensity e VDS Irradiated Length e VDS Scale Intensity e Capillary e Diameter e LAC e Linear PSD e 2Th angular range e FDS Shape Angle e Beam spill sample length e Correct Intensity e Tube Tails e Source Width e Z1 e Z2 e Fraction Axial Convolutions e Full Axial Model e Source Length e Sample Length e RS Length e Prim Soller e Sec Soller e N Beta e Finger_et_al e Simple Axial Model Remarks Primary goniometer circle radius mm Secondary goniometer circle radius mm Receiving Sl
80. y Individual hkls can be excluded from refinement using their Use checkbox The Additional Convolutions page provides for empirical modelling of the observed line profile shapes its options are identical to the Additional Convolutions page of the Instrument item see section 4 2 2 3 Note A single mouse click LMB on a selected hkl Phase item allows direct editing of its label Shortcut menu options of the hkl Phase item are e Save Phase Saves the selected hk Phase item in INP format e Create str Phase Creates a Structure item adopting the crystal structure and microstructure model as used for Pawley Le Bail fitting e Delete hkl Phase Deletes the selected hkl Phase item e Paste INP to Node Selections Supports pasting of information in INP format from the clipboard 4 2 2 8 Structure Note Not available in TOPAS P Structure items Fig 4 12 provide all parameters required for Rietveld structure refinement as well as for quantitative Rietveld analysis The Structure dependent items Sites PO March Dollase PO Spherical Harmonics and Str Output are described below The Structure item data grid comprises the following pages Structure Peak Type hkl_Is and Additional Convolutions DOC M88 EXX065 V4 2 01 2009 42 TOPAS User s Manual The Structure page contains the following structure information Parameter name Use Phase Spacegroup a b c alpha beta gamma Scale Cry Size Cry Size L Cr
81. y Size G LVolI IB LVol FWHM Strain Strain L Strain G e0 Wt Rietveld Wt of Spiked Wt in Spiked sample Wt in Original sample Cell Mass Cell Vol Cry Linear Absorption Coeff Cry Density R Bragg Remarks Includes or excludes the phase from the refinement Space group symbol or space group number When selecting the field a drop down button allows to open a dialog for space group selection Lattice parameters Spacegroup depend symmetry constraints are automatically applied including removal of redundant lattice parameters from the grid Scale factor Microstructure parameters related to crystallite size refer to the Technical Reference manual Microstructure parameters related to strain refer to the Technical Reference manual Relative phase amount Weighed phase amount if phase is used as a spike see also section 4 2 2 9 Absolute phase amount in the spiked sample after considering amorphous phase amounts Absolute phase amount in the original sample after considering amorphous phase amounts Cell mass Cell volume Phase linear absorption coefficient for a packing density of 1 Phase X ray density for a packing density of 1 R Bragg value The Peak Type page allows selection of the profile shape function available functions are FP PV Mod PV_TCHZ and PVII For information about these profile shape functions and their parameters refer to the Technical Reference manual A list of all gener

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