Lesson 6 - Profex and...
Transcript of Lesson 6 - Profex and...
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Lesson 6
BGMN & Profex
Nicola DöbelinRMS Foundation, Bettlach, Switzerland
January 14 – 16, 2015, Bern, Switzerland
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Rietveld Refinement Software BGMN
BGMN:
- Fundamental Parameters Approach
- Free for academic use
- Device independent
- Very robust automatic refinement strategy
- Slightly less steep learning curve
- Powerful scripting language
- Multi-Platform
- Multi-threaded
Visit: http://www.bgmn.de for tutorials and documentation
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BGMN Website
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http://www.bgmn.de/program.html
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BGMN Control File (*.sav)
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device.geq
sample.xy
sample.savstructure-A.str
structure-B.str
structure-C.str
Interpolated peak profile
Refinement control fileMeasured scan
Model structures
sample.lst
Files referenced in the
refinement control file
sample.parsample.out
sample.dia
RUN REFINEMENT
«BGMN.EXE sample.sav»
Results
Peak list
Refined diffraction pattern
Additional global parameters
Wavelength
Polarization
2θ range
Sample displacement
…
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Profex
Graphical User Interface (GUI) for BGMN
Developer: Nicola Döbelin (private)
License: GPL (open source)
Platforms: Windows XP / Vista / 7 / 8LinuxMac OS X 10.6.8-10.9.2 (64bit)
Rietveld Backends: BGMN, Fullprof.2k
Website: http://profex.doebelin.org
Current stable version: 3.3.1
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History
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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
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First Use
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Profex
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Lesson 6: Example 1
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Lesson 6: Example 1
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Cubix-ads-10mm.geq
Select:
betaTCP.strHydroxylapatite.str
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Lesson 6: Example 1
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BGMN control filewas created
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BGMN Control File (*.sav)
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What Profex does in the background:
- Generate a control file
- Adjust file names in control file
- Copy all selected structure files
from local DB to location of scan file
- Copy instrument configuration
files from local DB to location
of the scan file
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Profex
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With Profex:
1. Load scan file
2. Use «Add 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
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Lesson 6: Example 1
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Context Help:
Place Cursor on a key word
Press «F1»
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Lesson 6: Example 1
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Run the refinement
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Lesson 6: Example 1
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Lesson 6: Example 2
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1. Open Graph File: «Examples\Lesson 6\Example 2\lesson6-ex2.file1.xrdml»
2. Click «Add a phase» (+)
a) Select instrument: «pw1800-fds»
b) Select Phases:«AL2O3-Corundum»«Fluorite»
3. Run the refinement
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Lesson 6: Example 2
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Lesson 6: Example 2
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Corundum: good
Fluorite: bad
What is wrong? Suggestions?
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27 28 29
-800
-600
-400
-200
0
200
400
600
800
1000
1200
Inte
nsity [cts
]
Lesson 6: Example 2
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Peak position: correct
Integrated intensity: correct (?)
Peak-broadening: wrong
Specific for Fluorite phase.
Can be fixed in file «fluorite.str»
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BGMN Structure Files (*.str)
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«Open all project STR files»
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BGMN Structure Files (*.str)
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PHASE=Fluorite // 04-002-2191
SpacegroupNo=225 HermannMauguin=F4/m-32/m //
PARAM=A=0.5463_0.54^0.55 //
RP=4 k1=0 k2=0 PARAM=B1=0_0^0.003 PARAM=GEWICHT=0.1_0 //
d=10 //
GOAL=GrainSize(1,1,1) //
GOAL=my //
GOAL=d //
GOAL:fluorite=GEWICHT*ifthenelse(ifdef(d),exp(my*d*3/4),1)
E=CA+2 Wyckoff=a TDS=0.0041
E=F-1 Wyckoff=c TDS=0.0062
Phase name // Database reference
Space group number & H-M symbol
Unit Cell: a axis (nm)
Peak profile parameters
Mean particle size (µm), optional
Goals (optional, these values arereported in the results file)
List of atomic positions
Full notation:
E=CA+2(1) Wyckoff=a x=0.0 y=0.0 z=0.0 TDS=0.0041
Element
Site occupancy
Wyckoff sequence
Fractional coordinates
Thermal displacement parameter(Biso [nm2])
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BGMN Structure Files (*.str)
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PHASE=Fluorite // 04-002-2191
SpacegroupNo=225 HermannMauguin=F4/m-32/m //
PARAM=A=0.5463_0.54^0.55 //
RP=4 k1=0 k2=0 PARAM=B1=0_0^0.003 PARAM=GEWICHT=0.1_0 //
d=10 //
GOAL=GrainSize(1,1,1) //
GOAL=my //
GOAL=d //
GOAL:fluorite=GEWICHT*ifthenelse(ifdef(d),exp(my*d*3/4),1)
E=CA+2 Wyckoff=a TDS=0.0041
E=F-1 Wyckoff=c TDS=0.0062
A=0.5463
Fix parameter:
Name Value
PARAM=A=0.5463
Refined parameter:
Name Starting valueRelease forrefinement
PARAM=A=0.5463_0.54^0.55
Refined parameter with limits:
Name Startingvalue
Release forrefinement
Lowerlimit
Upperlimit
Right mouse buttonon a parameter:
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Lesson 6: Example 2
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PHASE=Fluorite // 04-002-2191
SpacegroupNo=225 HermannMauguin=F4/m-32/m //
PARAM=A=0.5463_0.54^0.55 //
RP=4 k1=0 k2=0 PARAM=B1=0_0^0.003 PARAM=GEWICHT=0.1_0 //
d=10 //
GOAL=GrainSize(1,1,1) //
GOAL=my //
GOAL=d //
GOAL:fluorite=GEWICHT*ifthenelse(ifdef(d),exp(my*d*3/4),1)
E=CA+2 Wyckoff=a TDS=0.0041
E=F-1 Wyckoff=c TDS=0.0062
In Lesson 6, Example 2, peak broadening was not
fitted correctly
Peak shape iscontrolled here
See http://www.bgmn.de/variables.html#real for RP=4 and k1=0
B1: peak broadening caused by crystallite size
k2: peak broadening caused by micro-strain
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Lesson 6: Example 2
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PHASE=Fluorite // 04-002-2191
SpacegroupNo=225 HermannMauguin=F4/m-32/m //
PARAM=A=0.5463_0.54^0.55 //
RP=4 k1=0 k2=0 PARAM=B1=0_0^0.003 PARAM=GEWICHT=0.1_0 //
d=10 //
GOAL=GrainSize(1,1,1) //
GOAL=my //
GOAL=d //
GOAL:fluorite=GEWICHT*ifthenelse(ifdef(d),exp(my*d*3/4),1)
E=CA+2 Wyckoff=a TDS=0.0041
E=F-1 Wyckoff=c TDS=0.0062
B1: refined, but limited to the range 0.000 – 0.003 (upper limit may be too strict)
k2: micro strain effect, not refined (necessary?)
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Lesson 6: Example 2
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RP=4 k1=0 k2=0 PARAM=B1=0_0^0.003 PARAM=GEWICHT=0.1_0 //
Change:
To:
RP=4 k1=0 k2=0 PARAM=B1=0_0^0.03 PARAM=GEWICHT=0.1_0 //
Repeat Refinement
Better, but notperfect.
Is there microstrain?
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Lesson 6: Example 2
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RP=4 k1=0 k2=0 PARAM=B1=0_0^0.03 PARAM=GEWICHT=0.1_0 //
Change:
To:
RP=4 k1=0 PARAM=k2=0_0 PARAM=B1=0_0^0.03 PARAM=GEWICHT=0.1_0 //
Repeat Refinement
Better, but stillnot perfect.
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Lesson 6: Example 2
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RP=4 k1=0 PARAM=k2=0_0 PARAM=B1=0_0^0.03 PARAM=GEWICHT=0.1_0 //
Changes:
To:
RP=4 k1=0 PARAM=k2=0_0 PARAM=B1=0_0^0.03 GEWICHT=SPHAR4 //
Repeat Refinement
Preferred Orientation / Texture:
- Refine «GEWICHT» anisotropically:
- Right mouse button on GEWICHT
- «Refine anisotropically»
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Lesson 6: Example 2
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Our refinement strategy:
1. Unit cell dimensions
2. Weight fractions
3. Crystallite sizes
4. Micro-strain of Fluorite
5. Texture of Fluorite
Released manually
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Lesson 6: Example 2
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Results in *.LST file
Summary table
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Summary: Structure Files (*.str)
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- Structure file database (*.str) is stored in
…\Profex-BGMN-Bundle-3.3.1\Profex\Structures
- Copied by Profex to the location of the scan file
- They contain:
- Space group information
- Unit cell dimensions
- Profile parameters
- Scaling (weight fraction)
- List of atoms (element, SOF, Wyckoff sequence, fract. coordinates, TDS)
- Optional «Goals»: Results / values printed to the results file (*.lst)
- Release parameters for refinement:
- «PARAM=»
- Optionally (recommended!): «_lowerLimit» and «^upperLimit»
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Summary: Structure Files (*.str)
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Refinements are «fine tuned» by editing Structure Files:
Commonly:
- Set reasonable upper and lower limits
- Control peak broadening
- Control texture / preferred orientation
Rarely:
- Control structural parameters:
- atomic coordinates
- site occupancies
- thermal displacement parameters
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Structure Databases
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STR files included in Profex bundle(created manually by Nicola Doebelin)
http://www.bgmn.de/download-structures.html
More on Structure Files:
Lesson 8: Creating Structure Files
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Lesson 6: Example 3 - Batch Refinement
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Lesson 6: Example 3 - Batch Refinement
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Create control file for first scanInstrument: cubix-ads-10mm
Phase 1: betaTCPPhase 2: hydroxylapatite
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Lesson 6: Example 3 - Batch Refinement
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Sav file created for first scan
But not for the other scans
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Lesson 6: Example 3 - Batch Refinement
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«Copy Control File»
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Lesson 6: Example 3 - Batch Refinement
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• Copies the control file toall projects
• Adjusts all input/outputfile names
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Lesson 6: Example 3 - Batch Refinement
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Start Batch Refinement
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Lesson 6: Example 3 - Batch Refinement
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Export Summary of all Projectsto Spread Sheet (*.csv)
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Lesson 6: Example 3 - Batch Refinement
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User Manual
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