Lesson 6 Profex Graphical User Interface for BGMN and Fullprof

Transcription

1 Lesson 6 Profex Graphical User Interface for BGMN and Fullprof Nicola Döbelin RMS Foundation, Bettlach, Switzerland June 07 09, 2017, Oslo, N

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

3 History 2003: Start of development as an alternative GUI for Fullprof.2k For personal use only Linux only 2006: Major rewrite Support for Windows 2012: Support for BGMN Rietveld Backend added 2013: First public release 2014: Support for Mac OS X 3

4 First Use Profex 4

5 First Use «Dock Windows» Can be re-arranged (drag & drop) Stacked Floating Closed (opened from «Window» menu) 5

6 Load Scan File «Open Graph File» Select correct file format 6

7 First Use: Example 1 Scan File = «Project» Scans in File Plot area (press «shift» for help window) 7

8 First Use: Example 1 Identify phases from internal database 8

9 First Use: Example 1 Create Refinement Control File 9

10 First Use: Example 1 Choose correct instrument configuration Select phases (HAp is pre-selected) 10

11 First Use: Example 1 New BGMN Refinement Control File was generated 11

12 First Use: Example 1 Run the refinement 12

13 First Use: Example 1 Plot display changed from *.raw file to *.dia (= refinement result) 13

14 First Use: Example 1 Left mouse button: Zoom / unzoom Right mouse button: Context menu Current discrepancy value R wp Acceptable discrepancy value 1.5 R exp (customizable) Lowest expected discrepancy value R exp 14

15 First Use: Example 1 15

16 First Use: Example 1 Add another phase 16

17 First Use: Example 1 Control file already exists, don t generate a new default file Select Whitlockite Click «OK» and re-run the refinement 17

18 First Use: Example 1 Phase Quantities: (± 0.13) wt-% Hydroxyapatite 4.45 (± 0.13) wt-% Whitlockite χ 2 =

19 First Use: Example 1 *.lst file with detailed refinement results opened automatically 19

20 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 20

21 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 21

22 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 22

23 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: Do not force Profex to use different file names than the auto-generated ones 23

24 Optimizing the Refinement Rietveld Refinement = Curve Fitting Phase quantities: Relative peak intensities: W a = S a ZMV a u m K F hkl = f 0 e B sin2 θ λ 2 e 2πi(hx+ky+lz) y = ax + b a = slope b = y intercept Lattice plane spacing: 1 d = b2 c 2 h 2 sin 2 α + c 2 a 2 k 2 sin 2 β + a 2 b 2 l 2 sin 2 γ + 2abc 2 hk cos α cos β cos γ + 2ab 2 chl(cos α cos γ cos β ) + 2a 2 bckl(cos β cos γ cos α ) a 2 b 2 c 2 (1 cos 2 α cos 2 β cos 2 γ 2 cos α cos β cos (γ)) Peak position: θ = asin ( λ 2d ) User decides which parameters to fit to measured diffraction pattern 24

25 Optimizing the Refinement Right-click on line «STRUC[1]=Hydroxyapatite.str» And select «Open File» 25

26 Optimizing the Refinement Opens both structure files Alternatively click «Open all Project Structure Files» 26

27 BGMN Control / Structure File Syntax X=0 Parameter X is fixed at the value 0 X is not refined PARAM=X=0 Parameter X is initialized with the value 0 X is released for refinement PARAM=X=0_-1^1 Parameter X is initialized with the value 0 X is released for refinement X can vary between -1 and 1 X=ANISO^1 Parameter X is initialized with the value 0 X is released for anisotropic refinement X can vary between 0 and 1 (e.g. size of the crystallites) 27

28 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 28

29 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 29

30 Optimized Refinement Done! Close Project 30

31 Optimized Refinement Further optimizations: - Additional phase MgO - Substitutions - Thermal displacement parameters 31

32 Example 2: Batch Refinement Series of measurements of the same sample 2. Select and open all files 1. Set Format 32

33 Example 2: Batch Refinement One Project per File 33

34 Example 2: Batch Refinement 1. Add «Hydroxyapatite» and «Whitlockite» 2. Run the refinement 34

35 Example 2: Batch Refinement Satisfactory results Use the same project settings for all other datasets 35

36 Example 2: Batch Refinement Identical control file was created «Run Batch Refinement» Will process all open projects 36

37 Example 2: Batch Refinement Follow the progress 37

38 Example 2: Batch Refinement Export results of all open projects 38

39 Exported Global GOALs Sort by «Parameter/Goal» 39

40 Exported Global GOALs Easy to compute mean and standard deviations 40

41 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 41

42 Create CIF files from refined structures Export CIF files 42

43 Drawing Structures 43

44 Exporting Diffraction Patterns 1. Display the Plot Area 2. Select «Save As» 44

45 Diffraction Data Formats ASCII Free format (*.xy) for import in Excel, Origin, etc. 45

46 Diffraction Data Formats Scalable Vector Graphics (*.svg) for import in Illustrator, CorelDRAW, Inkscape etc. 46

47 Diffraction Data Formats Print to PDF (PDF printer required) Mass Export (to printer, PDF, SVG) 47

48 Profex More «Behind the Scenes» information in «Lesson 8: Crystal Structures» 48

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