Lesson 8 Crystal Structure Models

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1 Lesson 8 Crystal Structure Models Nicola Döbelin RMS Foundation, Bettlach, Switzerland June 07 09, 2017, Oslo, N

2 BGMN Project Structure device.geq Interpolated peak profile sample.lst sample.xy Measured scan Refinement control file Results structure-a.str sample.sav RUN REFINEMENT sample.par sample.out Peak list structure-b.str structure-c.str Model structures Wavelength Polarization 2θ range sample.dia Refined diffraction pattern Files referenced in the refinement control file Sample displacement Additional global parameters 2

3 Profex Structure and Device File Database 3

4 Profex Structure and Device File Database 4

5 Profex Structure and Device File Database «Help About Profex» «Edit Preferences BGMN» Databases can be changed to a network share. Structures added by one user become available to others. 5

6 Public Structure Databases - STR files shipped with Profex (created manually by the Profex developer) - (created manually by BGMN team) - Create manually from: - ICSD ( - PDF-4+ ( - American Mineralogist Structure Database ( - Crystallography Open Database COD ( - Cambridge Crystallographic Data Centre ( 6

7 AMCSD 7

8 AMCSD: Downloading CIF Files Watch out for high-temp and high-pressure datasets! Download CIF file 8

9 CIF File Format CIF (Crystallographic Information File) Format: - Standardized file format - Contains structural information - Contains references - Specification available at 9

10 CIF Format Specification 10

11 Problems with CIF Files Problems with CIF files: 1. May be (and very often ARE) incomplete 2. May use non-standard atomic settings 3. Must be converted to STR format for BGMN With Profex: For complete CIF files: automatic import For incomplete CIF files: semi-automatic import 11

12 Profex CIF Import «File Import Structure File» «Examples/Lesson 6/Vaterite.cif» 12

13 Profex CIF Import Best Case: No Questions asked = automatic import «Save STR» to Structures database directory 13

14 Profex CIF Import «+ Add Files Aragonite.cif» Profex could not assign the CIF HM symbol «P m c n» to BGMN s full notation. 14

15 Profex CIF Import No further input required «Save STR» to Structures database directory 15

16 Profex CIF Import «+ Add Files Calcite.cif» Space Group Number for «R -3 c» is missing. Found elsewhere:

17 Profex CIF Import BGMN s full notations for SG #167 Read from CIF file Supported by BGMN Seems to match. Click «OK» 17

18 Profex CIF Import BGMN s full notations for SG #167 Two settings for R-3 2 /c: - Trigonal - Rhombohedral Check CIF file which one is correct (here: Trigonal) 18

19 Profex CIF Import Warning: Missing Wyckoff symbols Empty! 19

20 Profex CIF Import «Help BGMN SPACEGRP.DAT» Select Number 167, Trigonal setting, and browse all Wyckoff positions. 20

21 Profex CIF Import Ca at 0,0,0: Wyckoff=b C at 0,0,1/4: Wyckoff=a O at x,0,1/4: Wyckoff=e Fill in manually Save STR to Structure Database directory 21

22 Profex CIF Import Rescan Structures Directory and index new files 22

23 Import from ICDD PDF4+ XML Format «File Save PDF Card» in «ICDD XML Files» Format 23

24 Import from ICDD PDF4+ XML Format In Profex: «File Import Structure File» «Examples/Lesson 6/Vaterite.cif» 24

25 Import from ICDD PDF4+ XML Format Remove spaces and underscores from quantity GOAL: GOAL:Calcite_syn= GOAL:Calcite= «Save STR» to Structures database directory 25

26 Summary: STR Files If no *.str file is available: Download CIF file from public database (COD, AMCSD, ICSD) Or export XML file from PDF-4+ database Convert to *.str format with Profex Fix *.str file manually if necessary Save to «Structures» directory in Profex-BGMN- Bundle 26

27 Device Files BGMN uses Fundamental Parameters Approach (FPA) to model peak shapes Very detailed description of instrument configuration required Wrong Instrument Config = Wrong peak shapes = wrong refinement results (particularly crystallite sizes and micro-strain) = poor fits 27

28 Device Files 28

29 Device Files Recommended: Modify an existing instrument configuration Incomplete feature (don t use) Edit existing configuration 29

30 Device Files Meaningful names were given (model, detector, divergence slit mode, ) Pick one that seems to match your instrument configuration 30

new name Acknowledge the warning message

31 Device Files Verify / modify each line (bundled files are well documented) Verify «Control» and «Calculations» options If unsure, leave unchanged «Save As» under a new name Acknowledge the warning message about file names Click «Run» Wait for completion 31

32 Device Files Get instrument parameters from: - Measurement software - Configuration page - Instrument user manual - 32

33 Device Files - labels on apertures - Or measure! (better than nothing) 33

34 Tutorial on 34

Documentation on http://www.bgmn.de http://bgmn.

35 Documentation on

Lesson 4 Crystal Structure Files

Lesson 4 Crystal Structure Files Nicola Döbelin RMS Foundation, Bettlach, Switzerland March 3, 2015, Lyon, France Repetition: BGMN Project Structure device.geq Interpolated peak profile sample.lst sample.xy