Lesson 6

BGMN & Profex

Nicola Döbelin
RMS Foundation, Bettlach, Switzerland

January 14 – 16, 2015, Bern, Switzerland

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

http://www.bgmn.de/program.html

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BGMN Control File (*.sav)

device.geq
Interpolated peak profile
sample.lst
Results
sample.xy
Measured scan Refinement control file

RUN REFINEMENT sample.par

sample.sav sample.out
structure-A.str «BGMN.EXE sample.sav»
Peak list

structure-B.str

Wavelength sample.dia
structure-C.str Polarization Refined diffraction pattern
Model structures
2θ range
Files referenced in the
refinement control file
Sample displacement

Additional global parameters

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Profex

Graphical User Interface (GUI) for BGMN

Developer: Nicola Döbelin (private)

License: GPL (open source)
Platforms: Windows XP / Vista / 7 / 8
Linux
Mac 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

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

Profex

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Lesson 6: Example 1

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Lesson 6: Example 1

Cubix-ads-10mm.geq

Select:
betaTCP.str
Hydroxylapatite.str

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Lesson 6: Example 1

BGMN control file

was created

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 BGMN Control File (*.sav)

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

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

Context Help:
Place Cursor on a key word
Press «F1»

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Lesson 6: Example 1

Run the refinement

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Lesson 6: Example 1

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Lesson 6: Example 2

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

Corundum: good
Fluorite: bad

What is wrong? Suggestions?

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 Lesson 6: Example 2

1200
Peak position: correct
1000
Integrated intensity: correct (?)
800
Peak-broadening: wrong
600

400
Intensity [cts]

200

-200

-400
Specific for Fluorite phase.
-600
Can be fixed in file «fluorite.str»
-800
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BGMN Structure Files (*.str)
«Open all project STR files»

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 BGMN Structure Files (*.str)

PHASE=Fluorite // 04-002-2191 Phase name // Database reference

SpacegroupNo=225 HermannMauguin=F4/m-32/m // Space group number & H-M symbol
PARAM=A=0.5463_0.54^0.55 // Unit Cell: a axis (nm)
RP=4 k1=0 k2=0 PARAM=B1=0_0^0.003 PARAM=GEWICHT=0.1_0 // Peak profile parameters
d=10 // Mean particle size (µm), optional
GOAL=GrainSize(1,1,1) //
GOAL=my // Goals (optional, these values are
reported in the results file)
GOAL=d //
GOAL:fluorite=GEWICHT*ifthenelse(ifdef(d),exp(my*d*3/4),1)
E=CA+2 Wyckoff=a TDS=0.0041
List of atomic positions
E=F-1 Wyckoff=c TDS=0.0062

Full notation:
E=CA+2(1) Wyckoff=a x=0.0 y=0.0 z=0.0 TDS=0.0041

Element Wyckoff sequence Thermal displacement parameter

(Biso [nm2])
Site occupancy Fractional coordinates

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 BGMN Structure Files (*.str)

Right mouse button

PHASE=Fluorite // 04-002-2191
SpacegroupNo=225 HermannMauguin=F4/m-32/m //
on a parameter:
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

Fix parameter: Refined parameter: Refined parameter with limits:

A=0.5463 PARAM=A=0.5463 PARAM=A=0.5463_0.54^0.55

Name Value Release for Name Starting value Release for Name Starting Lower Upper
refinement refinement value limit limit

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 Lesson 6: Example 2

PHASE=Fluorite // 04-002-2191
In Lesson 6, Example 2,
SpacegroupNo=225 HermannMauguin=F4/m-32/m //
PARAM=A=0.5463_0.54^0.55 //
peak broadening was not
RP=4 k1=0 k2=0 PARAM=B1=0_0^0.003 PARAM=GEWICHT=0.1_0 // fitted correctly
d=10 //
GOAL=GrainSize(1,1,1) //
GOAL=my // Peak shape is
GOAL=d //
controlled here
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: peak broadening caused by crystallite size

k2: peak broadening caused by micro-strain

See http://www.bgmn.de/variables.html#real for RP=4 and k1=0

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 Lesson 6: Example 2

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

Change:
RP=4 k1=0 k2=0 PARAM=B1=0_0^0.003 PARAM=GEWICHT=0.1_0 //

To:
RP=4 k1=0 k2=0 PARAM=B1=0_0^0.03 PARAM=GEWICHT=0.1_0 //

Repeat Refinement

Better, but not

perfect.
Is there microstrain?

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Lesson 6: Example 2

Change:
RP=4 k1=0 k2=0 PARAM=B1=0_0^0.03 PARAM=GEWICHT=0.1_0 //

To:
RP=4 k1=0 PARAM=k2=0_0 PARAM=B1=0_0^0.03 PARAM=GEWICHT=0.1_0 //

Repeat Refinement

Better, but still

not perfect.

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Lesson 6: Example 2

Preferred Orientation / Texture:

- Refine «GEWICHT» anisotropically:
- Right mouse button on GEWICHT
- «Refine anisotropically»

Changes:
RP=4 k1=0 PARAM=k2=0_0 PARAM=B1=0_0^0.03 PARAM=GEWICHT=0.1_0 //

To:
RP=4 k1=0 PARAM=k2=0_0 PARAM=B1=0_0^0.03 GEWICHT=SPHAR4 //

Repeat Refinement

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Lesson 6: Example 2

Our refinement strategy:

1. Unit cell dimensions
2. Weight fractions
3. Crystallite sizes
4. Micro-strain of Fluorite Released manually
5. Texture of Fluorite

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Lesson 6: Example 2

Results in *.LST file

Summary table

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Summary: Structure Files (*.str)

- 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)

Refinements are «fine tuned» by editing Structure Files:

Commonly: Rarely:
- Set reasonable upper and lower limits - Control structural parameters:
- Control peak broadening - atomic coordinates
- Control texture / preferred orientation - site occupancies
- thermal displacement parameters

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Structure Databases

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

Create control file for first scan

Instrument: cubix-ads-10mm
Phase 1: betaTCP
Phase 2: hydroxylapatite

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Lesson 6: Example 3 - Batch Refinement

Sav file created for first scan

But not for the other scans

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Lesson 6: Example 3 - Batch Refinement

«Copy Control File»

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Lesson 6: Example 3 - Batch Refinement

• Copies the control file to

all projects
• Adjusts all input/output
file names

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Lesson 6: Example 3 - Batch Refinement

Start Batch Refinement

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Lesson 6: Example 3 - Batch Refinement

Export Summary of all Projects

to Spread Sheet (*.csv)

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Lesson 6: Example 3 - Batch Refinement

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User Manual

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