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From application to framework driven computing solutions: The present and future of TOF single crystal diffraction at IS

From application to framework driven computing solutions: The present and future of TOF single crystal diffraction at ISIS (a “super user” perspective). A. Daoud-Aladine M.J. Gutmann, L.C Chapon. PSD4C workshop, Paris, November 2008. Outline. Present : the SXD2001 package .

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From application to framework driven computing solutions: The present and future of TOF single crystal diffraction at IS

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  1. From application to framework driven computing solutions: The present and future of TOF single crystal diffraction at ISIS (a “super user” perspective) A. Daoud-Aladine M.J. Gutmann, L.C Chapon PSD4C workshop, Paris, November 2008

  2. Outline Present : the SXD2001 package TOF Laue diffraction: specificities Presentation of SXD2001 Two typical success stories Illustrative examples of typical difficulties/limitations: Viewing/understanding 3D data coverage Optimizing the data collection strategy for the integration of magnetic Bragg intensities Future solutions : The Mantid project The framework concept Plans for deployment on Single crystal software

  3. kf ki SXD w TOF Laue diffraction: specificity 2D visualization (summed in TOF) 90°(2) sample kf 37°-det 90°-det 37°(3) ki 1D visualization of single spectra • - 11x(64x64) ZnS pixelated AREA detectors with each pixel recording a 1D ~2000 bins TOF spectrum • 1 Data set ~ 70 Mbytes (compressed) • 3D data sets in (x,z,time) (0 -12 0)

  4. TOF Laue diffraction: specificity Reciprocal space (Q) Instrument view (kf) TOF scan  l scan  Q scan 1 Data set ~ 70 Mbytes (compressed) 2D visualization (summed in TOF) Q=kf(l)-ki 1/lmin 90°-det 37°-det 90°-det 1/lmax 1D visualization of single spectra 90°-det tilted down by 45° (0 -12 0) Picture made with Ewald3D, a Matlab utility. Non-trivial Q-coverage due to 1) The non-equatorial geometry 2) The goniometry 3) Detector gaps

  5. Before post data processing Data analysis software: SXD2001 A data reduction software Bragg Scattering (integration) Produces HKL lists for supported packages: SHELX,GSAS,FULLPROF JANA2000 (New, JANA2006) 37°-det 90°-det 80-90% common tasks already present in SXD2001! (0 -12 0) Reciprocal space mapping (binning in Q, hkl-space…) Binary/ASCII files for internal/external visualisation

  6. Outline Present : the SXD2001 package TOF Laue diffraction: specificities Presentation of SXD2001 Two typical success stories Illustrative examples of typical difficulties/limitations: Viewing/understanding 3D data coverage Optimizing the data collection strategy for the integration of magnetic Bragg intensities Future solutions : The Mantid project The framework concept Plans for deployment on Single crystal software

  7. ISIS raw data access encapsulated in so-called “open GENIE” dll’s provided by the computing group • Calculations, GUI, plotting 100% written in the IDL application language in order to satisfy 2 essential user wishes : • Need for GUI-based applications • Beneficiate from high level built in plotting tools • Derived from (not portable) and historical Fortran/Vax code SXD98 • Much enhanced capabilities • Complete analysis route from raw data to structure factors and/or reciprocal space exploration • Stand-alone package • Dynamically extended according to user’s wishes M.J. Gutmann A brief history of SXD2001

  8. M.J. Gutmann SXD2001:Peak integration • Choice of three algorithms • Shoebox • Dynamic box • 3D Gauss ellipsoid • Information about resolution used • Gives directly F2 • Propagation vectors can be used • Manual integration • Graphical diagnostic

  9. M.J. Gutmann SXD2001:Reciprocal space sections • Calculation of volumes in reciprocal space • Flexible slicing • Markers for space-group allowed, magnetic, incommensurate reflections • Laue symmetry averaging • Export to ASCII files • Movie through volume

  10. Outline Present : the SXD2001 package TOF Laue diffraction: specificities Presentation of SXD2001 Two typical success stories Illustrative examples of typical difficulties/limitations: Viewing/understanding 3D data coverage Optimizing the data collection strategy for the integration of magnetic Bragg intensities Future solutions : The Mantid project The framework concept Plans for deployment on Single crystal software

  11. Success story-I: Proton migration in urea phosphoric acid 200 K 150 K 175 K 300 K 225 K 100 K 275 K 325 K 350 K 375 K 250 K Protonated Old data/Old software Recent data/SXD2001 ~5000 reflections ~8200 reflections Same result on deuterated urea phosphoric acid C C Wilson, K Shankland & N Shankland (2001). Z Krist, 216, 303-306 C. Spanswick, C. R. Pulham, University of Edinburgh A. Parkin, C. C. Wilson, University of Glasgow No planning here required for getting large numbers of unique “anonymous” Bragg reflections + some necessary redundancy: experiment made using 5~6 “STANDARD” goniometry settings

  12. Success story-II: Quantitative diffuse scattering modeling Rebinned data Correct magnitudes of thermal displacements arise from the fitting of the diffuse scattering T. R. Welberry, D. J. Goossens et al. J. Appl. Cryst. 36, 1440 (2003) Scattering resulting from a theoretical distorted atom configuration, obtained from a spring model, whose force constants are refined against the data

  13. Outline Present : the SXD2001 package TOF Laue diffraction: specificities Presentation of SXD2001 Two typical success stories Illustrative examples of typical difficulties/limitations: Viewing/understanding 3D data coverage Optimizing the data collection strategy for the integration of magnetic Bragg intensities Future solutions : The Mantid project The framework concept Plans for deployment on Single crystal software

  14. Viewing/understanding 3D data coverage One single crystal orientation (say, w=10) 2D-sliced representation of the coverage of the (b*,c*) plane 3D schematic representation Goniometry settings 3 2 1 Choice of plane Det 4 4 6 5 Det 3 Gap Gap 10 Det 5 9

  15. Viewing/understanding 3D data coverage TWO single crystal orientation (say, w=10, and w=-30) Data “merged” indistinctly Recall : one orientation result Det 4 Det 4 Det 3 Det 3 ? Det 5 Det 5

  16. Viewing/understanding 3D data coverage TWO single crystal orientation (say, w=10, and w=-30) Info recovered only in 3D view Data “merged” indistinctly Det 4 3 4 Det 3 6 Det 6 5 Det 5

  17. Outline Present : the SXD2001 package TOF Laue diffraction: specificities Presentation of SXD2001 Two typical success stories Illustrative examples of typical difficulties/limitations: Viewing/understanding 3D data coverage Optimizing the data collection strategy for the integration of magnetic Bragg intensities Future solutions : The Mantid project The framework concept Plans for deployment on Single crystal software

  18. INDEX CELL refinement Final UB for each frame/crystal Peak integration Reciprocal space plotting using various methods Selection of planes for diffuse scattering analysis How many and which GONIO setting(s)? Instrument coords? w1 w2 w3 w4 From one HKL… ? The “reverse” problem PEAKSEARCH Find CELL w1 Next Run/ Orientiation Refine UB with more reflections Goniometer angles setting <=> 1 data set w2 w3 Absorption/extinction corrections Separate outputs Improve ext/abs as model improves Export to GSAS etc. Export to ASCII files Merged HKL Lists with redondancy ie. for hkl’s measured more than once Iobs(w1,l1) ≠ Iobs(w2,l2) Refinement in GSAS, SHELX, etc Diffuse modelling Data “merged” indistinctly UB/goniometry Info lost! Visualisation of structure ORTEP etc Each HKL, each Q-point, can be in several data corresponding to different “orientations”

  19. EX: Magnetic diffraction Lots of “holes” of coverage at low Q’s TbMn2O5 at T=30K To solve the (T=30K) magnetic structure, a simulated annealing algorithm was used with single-crystal data to search for starting configurations. The phases were then fixed while the magnitude and directions of the moments were refined by Rietveld analysis of the [final model on] powder data (Fig. 4), which are more complete at low momentum transfer k=(1/2 0 1/4) k=(1/2 0 1/4) “Standard settings” w=-150 w=-130 w=-110 w=-90 w=-70 w=-50 L. Chapon et al. PRL(2004)

  20. EX: Magnetic diffraction TbMn2O5 at T=27K HKL list with Propagation vectors can be used (FullProf Convention) k=(1/2 0 1/4) k=(1/2 0 1/4) YMn2O5 at T=27K “Standard settings” w=-150 w=-130 w=-110 w=-90 w=-70 w=-50 Rnuc = 10% (not shown) Rmag = 20% w=-149 w= -89 w= -54 w= -29 w= 4 w= 97 ~170 reflections I>3s L. Chapon et al. PRL(2004) A. Daoud-Aladine, M. Gutmann, L. Chapon, P. G. Radaelli

  21. Outline Present : the SXD2001 package TOF Laue diffraction: specificities Presentation of SXD2001 Two typical success stories Illustrative examples of typical difficulties/limitations: Viewing/understanding 3D data coverage Optimizing the data collection strategy for the integration of magnetic Bragg intensities (reverse problem: hkl => angles) Future solutions : The Mantid project The framework concept Plans for deployment on Single crystal software

  22. MantidManipulation and Analysis Toolkit for ISIS data Nick Draper 05/11/2008

  23. Project Aims • Aims • To provide a framework for Data Analysis that is not instrument or technique/dependent. • Support multiple target platforms (Windows, Linux). • Easily extensible by Instruments Scientists/Users. • Freely redistributable to visiting scientists. • Provide low-level functionalities for • Scripting • Visualization • Data transformation • Implementing Algorithms • Virtual Instrument Geometry

  24. Architectural Design - Overview Instrument log files MantidScript Command line & Scripting interface Mantid Framework RAW data files API Algorithms Workspaces MantidPlot Graphing and analysis NEXUS data files Matlab Interface DAE direct access User Defined User Defined Future Instrument specific UI Future Instrument specific UI

  25. Geometry Problem: How to maintain & visualise an accurate and fast representation of complex objects • Mesh Based • Easy, fast visualization • Poor computational accuracy & performance • Hard to define complex shapes • Surface Based • Hard, slow visualization • Good computational accuracy & performance • Easy to define objects using CSG

  26. Geometry • Constructive Solid Geometry • Building of complex shapes fromintersections, unions and differencesof common primitives • Easily understood by users • Hybrid geometric model GNU Triangulated Surface Library • Surface CSG • Used for • Definition • Calculations • Mesh • Used for • Visualization • Approximation

  27. Instrument Visualisation Instrument.exe

  28. User Extensible • Doesn’t have the algorithm you need? • Add it yourself Plugin.exe

  29. Outline Present : the SXD2001 package TOF Laue diffraction: specificities Presentation of SXD2001 Two typical success stories Illustrative examples of typical difficulties/limitations: Viewing/understanding 3D data coverage Optimizing the data collection strategy for the integration of magnetic Bragg intensities (reverse problem: hkl => angles) Future solutions : The Mantid project The framework concept Plans for deployment on Single crystal software : peak search done!

  30. INDEX CELL refinement Final UB for each frame/crystal Peak integration Reciprocal space plotting using various methods Selection of planes for diffuse scattering analysis The data analysis flowchart Indexation: Semi interactive Single dataset treatment => Creates an indexation file containing refined UB’s for one ore more than one crystals and the goniometer angles for each raw file PEAKSEARCH Find CELL Next Run/ Orientiation Refine UB with more reflections Integration/binning: Data treatment sequentially done using many raw files and indexation files Absorption/extinction corrections Improve ext/abs as model improves Export to GSAS etc. Export to ASCII files Refinement in GSAS, SHELX, etc Diffuse modelling Limit of the SXD “black box” Visualisation of structure ORTEP etc

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