Lesson 3 Profex Graphical User Interface for BGMN and Fullprof

Transcription

1 Lesson 3 Profex Graphical User Interface for BGMN and Fullprof Nicola Döbelin RMS Foundation, Bettlach, Switzerland March 01 02, 2016, Freiberg, Germany

2 Background Information Developer: License: Founded in: 2003 Nicola Döbelin (private) GPL v2 or later (open source) Platforms: Windows XP / Vista / 7 / 8 / 10 Linux Mac OS X (64bit) Rietveld Backends: Website: Current stable version: BGMN, Fullprof.2k 2 March 01 02, 2016, Freiberg, Germany

3 History 2003: Start of development as an alternative GUI for Fullprof.2k For personal use only (my PhD) Linux only 2006: Major rewrite Support for Windows 2012: Support for BGMN Rietveld Backend added 2014: Support for Mac OS X 3 March 01 02, 2016, Freiberg, Germany

4 First Use Profex 4 March 01 02, 2016, Freiberg, Germany

5 First Use «Dock Windows» Can be re-arranged (drag & drop) Stacked Floating Closed (opened from «Window» menu) 5 March 01 02, 2016, Freiberg, Germany

6 Load Scan File «Open Graph File» Select correct file format 6 March 01 02, 2016, Freiberg, Germany

7 First Use: Example 1 Scan File = «Project» Plot area (press «shift» for help window) Scans in File 7 March 01 02, 2016, Freiberg, Germany

8 First Use: Example 1 Identify phases from internal database 8 March 01 02, 2016, Freiberg, Germany

9 First Use: Example 1 Create Refinement Control File 9 March 01 02, 2016, Freiberg, Germany

10 First Use: Example 1 Choose correct instrument configuration Select phases (HAp is pre-selected) 10 March 01 02, 2016, Freiberg, Germany

11 First Use: Example 1 New BGMN Refinement Control File was generated 11 March 01 02, 2016, Freiberg, Germany

12 First Use: Example 1 Run the refinement 12 March 01 02, 2016, Freiberg, Germany

13 First Use: Example 1 Plot display changed from *.raw file to *.dia (= refinement result) 13 March 01 02, 2016, Freiberg, Germany

14 First Use: Example 1 Add another phase 14 March 01 02, 2016, Freiberg, Germany

15 First Use: Example 1 Control file already exists, don t generate a new default file Select Whitlockite Click «OK» and re-run the refinement 15 March 01 02, 2016, Freiberg, Germany

16 First Use: Example 1 Phase Quantities: (± 0.13) wt-% Hydroxyapatite 4.46 (± 0.13) wt-% Whitlockite 16 March 01 02, 2016, Freiberg, Germany

17 First Use: Example 1 *.lst file with detailed refinement results opened automatically 17

18 Features of Profex (I) What Profex does in the background: - Generate a control file - Copy all selected structure files from local DB to location of scan file - Copy instrument configuration file from local DB to location of scan file - Adjust file names in control file - Converts Raw Scan format to XY format for BGMN - Convert file formats (Windowx Unix/Mac) - Adjusts GOALs for phase quantification 18 March 01 02, 2016, Freiberg, Germany

19 Features of Profex (II) Handled by Profex: Instrument config file Structure files Conversion of raw scan XRDML XY Automatic file names of output files GOALs for phase quantification 19 March 01 02, 2016, Freiberg, Germany

20 Features of Profex (III) With Profex: 1. Load scan file 2. Use «Append phase» dialog to select phases, instrument, and generate control file 3. Run refinement No need to: - Copy structure / device files - Change any file names - Convert scan files* * for supported scan file formats 20 March 01 02, 2016, Freiberg, Germany

21 Features of Profex (IV) Advantages: - Very efficient workflow for many use cases - Automatic batch refinements - Easier learning curve Disadvantages: - Restrictions in choice of file names - Restrictions in terms of custom calculations (Refinement should work, but summary table may be wrong) 21 March 01 02, 2016, Freiberg, Germany

22 Optimizing the Refinement Right-click on line «STRUC[1]=Hydroxyapatite.str» And select «Open File» 22 March 01 02, 2016, Freiberg, Germany

23 Optimizing the Refinement Opens both structure files Alternatively click «Open all Project Structure Files» 23 March 01 02, 2016, Freiberg, Germany

24 Optimizing the Refinement In «hydroxyapatite.str» right-click on «k2=0» and select «refine isotropically» Alternatively: Place cursor on «k2=0» and press: F6: fix isotropic anisotropic F5: anisotropic isotropic fix 24 March 01 02, 2016, Freiberg, Germany

25 Toggling Parameter Refinement States Isotropic parameters Anisotropic parameters Texture F6 Fix A= Fix B1=0 GEWICHT=SPHAR0 F5 Refined with limits PARAM=A=0.9424_0.9404^ Refined isotropically PARAM=B1=0_0^0.01 GEWICHT=SPHAR2 F6 Refined without limits PARAM=A= Refined anisotropically B1=ANISO^0.01 GEWICHT=SPHAR4 F5 25 March 01 02, 2016, Freiberg, Germany

26 Optimized Refinement Done! Close Project 26 March 01 02, 2016, Freiberg, Germany

27 Example 2: Batch Refinement Series of measurements of the same sample 2. Select and open all files 1. Set Format 27 March 01 02, 2016, Freiberg, Germany

28 Example 2: Batch Refinement One Project per File 28 March 01 02, 2016, Freiberg, Germany

29 Example 2: Batch Refinement 1. Add «Hydroxyapatite» and «Whitlockite» 2. Run the refinement 29 March 01 02, 2016, Freiberg, Germany

30 Example 2: Batch Refinement Satisfactory results Use the same project settings for all other datasets 30 March 01 02, 2016, Freiberg, Germany

31 Example 2: Batch Refinement Identical control file was created «Run Batch Refinement» Will process all open projects 31 March 01 02, 2016, Freiberg, Germany

32 Example 2: Batch Refinement Follow the progress 32 March 01 02, 2016, Freiberg, Germany

33 Example 2: Batch Refinement Export results of all open projects 33 March 01 02, 2016, Freiberg, Germany

34 Exported Global GOALs Sort by «Parameter/Goal» 34 March 01 02, 2016, Freiberg, Germany

35 Exported Global GOALs Easy to compute mean and standard deviations 35 March 01 02, 2016, Freiberg, Germany

36 Refined Chemical Composition Open «Window Chemistry» Normalized to 100% Make sure the Quantity GOALs are assigned correctly Normalized to refined phase quantity Total sample composition available 36 March 01 02, 2016, Freiberg, Germany

37 Create CIF files from refined structures Export CIF files 37 March 01 02, 2016, Freiberg, Germany

38 Drawing Structures 38 March 01 02, 2016, Freiberg, Germany

39 Exporting Diffraction Patterns 1. Display the Plot Area 2. Select «Save As» 39 March 01 02, 2016, Freiberg, Germany

40 Diffraction Data Formats ASCII Free format (*.xy) for import in Excel, Origin, etc. 40 March 01 02, 2016, Freiberg, Germany

41 Diffraction Data Formats Scalable Vector Graphics (*.svg) for import in Illustrator, CorelDRAW, Inkscape etc. 41 March 01 02, 2016, Freiberg, Germany

42 Diffraction Data Formats 42 March 01 02, 2016, Freiberg, Germany

43 Profex More «Behind the Scenes» information in «Lesson 6: Crystal Structures» 43 March 01 02, 2016, Freiberg, Germany

44 44 March 01 02, 2016, Freiberg, Germany