lesson 8 crystal structure models -...
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Lesson 8
Crystal Structure Models
Nicola Döbelin
RMS Foundation, Bettlach, Switzerland
October 03 – 05, 2016, Maastricht, NL
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BGMN Project Structure
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device.geq
sample.xy
sample.sav structure-A.str
structure-B.str
structure-C.str
Interpolated peak profile
Refinement control file Measured scan
Model structures
sample.lst
Files referenced in the
refinement control file
sample.par
sample.out
sample.dia
RUN REFINEMENT
Results
Peak list
Refined diffraction pattern
Additional global parameters
Wavelength
Polarization
2θ range
Sample displacement
…
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Profex Structure and Device File Database
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Profex Structure and Device File Database
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Profex Structure and Device File Database
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«Help About Profex…» «Edit Preferences… BGMN»
Databases can be changed to a network share.
Structures added by one user become available to others.
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Public Structure Databases
6
- STR files shipped with Profex (created manually by the Profex developer)
- http://www.bgmn.de/download-structures.html (created manually by BGMN team)
- Create manually from:
- ICSD (http://www.fiz-karlsruhe.de/icsd.html)
- PDF-4+ (http://www.icdd.com/)
- American Mineralogist Structure Database
(http://rruff.geo.arizona.edu/AMS/amcsd.php)
- Crystallography Open Database COD
(http://www.crystallography.net/)
- Cambridge Crystallographic Data Centre
(http://beta-www.ccdc.cam.ac.uk/pages/Home.aspx)
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AMCSD
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AMCSD: Downloading CIF Files
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Download CIF file
Watch out for high-temp and
high-pressure datasets
!
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CIF File Format
9
CIF (Crystallographic
Information File) Format:
- Standardized file format
- Contains structural information
- Contains references
- Specification available
at http://www.iucr.org
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CIF Format Specification
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http://www.iucr.org/resources/cif/dictionaries
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Problems with CIF Files
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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
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Profex CIF Import
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«File Import Structure File…»
«Examples/Lesson 6/Vaterite.cif»
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Profex CIF Import
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Best Case: No Questions asked = automatic import
«Save STR» to Structures database directory
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Profex CIF Import
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Profex could not assign the CIF HM symbol «P m c n»
to BGMN’s full notation.
«+ Add Files Aragonite.cif»
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Profex CIF Import
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«Save STR» to Structures database directory
No further input required
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Profex CIF Import
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«+ Add Files Calcite.cif»
Space Group Number for «R -3 c» is missing.
Found elsewhere: 167
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Profex CIF Import
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BGMN’s full notations for SG #167
Seems to match. Click «OK»
Read from CIF file
Supported by BGMN
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Profex CIF Import
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BGMN’s full notations for SG #167
Two settings for R-32/c:
- Trigonal
- Rhombohedral
Check CIF file which one is correct
(here: Trigonal)
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Profex CIF Import
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Warning: Missing Wyckoff symbols
Empty!
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Profex CIF Import
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«Help BGMN SPACEGRP.DAT»
Select Number 167, Trigonal setting, and browse all Wyckoff positions.
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Profex CIF Import
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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
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Profex CIF Import
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Rescan Structures Directory
and index new files
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Import from ICDD PDF4+ XML Format
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«File Save PDF Card»
in «ICDD XML Files» Format
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Import from ICDD PDF4+ XML Format
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In Profex: «File Import Structure File…»
«Examples/Lesson 6/Vaterite.cif»
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Import from ICDD PDF4+ XML Format
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Remove spaces and underscores
from quantity GOAL:
GOAL:Calcite_syn=…
GOAL:Calcite=…
«Save STR» to Structures database directory
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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
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Device Files
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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
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Device Files
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http://www.bgmn.de
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Device Files
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http://www.bgmn.de
Recommended: Modify an existing instrument
configuration
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Device Files
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Meaningful names were given
(model, detector, divergence slit
mode, …)
Pick one that seems to match your
instrument configuration
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Device Files
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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
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Device Files
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Get instrument parameters from:
- Measurement software
- Configuration page
- Instrument user manual
- …
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Device Files
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…
- labels on
apertures
- Or measure!
(better than nothing)
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Tutorial on http://profex.doebelin.org
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