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: Nicola Döbelin (private)
License: GPL v2 or later (open source)
Founded in: 2003
Platforms: Windows XP / Vista / 7 / 8 / 10
Linux
Mac OS X 10.7 -10.11 (64bit)
Rietveld Backends: BGMN, Fullprof.2k
Website: http://profex.doebelin.org
Current stable version: 3.11.0
History
3
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
First Use
4
Profex
First Use
5
«Dock Windows»
Can be re-arranged
(drag & drop)
Stacked
Floating
Closed
(opened from
«Window» menu)
«Open Graph File»
Load Scan File
6
Select correct file format
First Use: Example 1
7
Scan File = «Project»
Scans in File
Plot area
(press «shift» for
help window)
First Use: Example 1
8
Identify phases from
internal database
First Use: Example 1
9
Create Refinement Control File
First Use: Example 1
10
Choose correct
instrument
configuration
Select phases
(HAp is pre-selected)
First Use: Example 1
11
New BGMN Refinement
Control File was generated
First Use: Example 1
12
Run the refinement
First Use: Example 1
13
Plot display changed from *.raw file
to *.dia (= refinement result)
First Use: Example 1
14
Left mouse button:
Zoom / unzoom
Right mouse button:
Context menu
Current discrepancy
value Rwp
Lowest expected
discrepancy value Rexp
Acceptable
discrepancy value 1.5·Rexp
(customizable)
First Use: Example 1
15
First Use: Example 1
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Add another phase
First Use: Example 1
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Select Whitlockite
Control file already
exists, don’t generate
a new default file
Click «OK» and re-run
the refinement
First Use: Example 1
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Phase Quantities:
95.55 (± 0.13) wt-% Hydroxyapatite
4.45 (± 0.13) wt-% Whitlockite
χ2 = 1.625
First Use: Example 1
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*.lst file with detailed
refinement results
opened automatically
Features of Profex (I)
20
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
Features of Profex (II)
21
Instrument config file
Structure files
Handled by Profex:
Conversion of raw scan
XRDML XY
Automatic file names
of output files
GOALs for phase
quantification
Features of Profex (III)
22
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
Features of Profex (IV)
23
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
Optimizing the Refinement
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Rietveld Refinement = Curve Fitting
𝑦 = 𝑎𝑥 + 𝑏
𝐹ℎ𝑘𝑙 = 𝑓0 ∙ 𝑒−𝐵∙sin2 𝜃𝜆2 ∙ 𝑒2𝜋𝑖(ℎ𝑥+𝑘𝑦+𝑙𝑧)
1
𝑑=𝑏2𝑐2ℎ2 sin2 𝛼 + 𝑐2𝑎2𝑘2 sin2 𝛽 + 𝑎2𝑏2𝑙2 sin2 𝛾 + 2𝑎𝑏𝑐2ℎ𝑘 cos 𝛼 cos 𝛽 − cos 𝛾 + 2𝑎𝑏2𝑐ℎ𝑙(cos 𝛼 cos 𝛾 − cos 𝛽 ) + 2𝑎2𝑏𝑐𝑘𝑙(cos 𝛽 cos 𝛾 − cos 𝛼 )
𝑎2𝑏2𝑐2(1 − cos2 𝛼 − cos2 𝛽 − cos2 𝛾 − 2 cos 𝛼 cos 𝛽 cos(𝛾))
𝑊𝑎 =𝑆𝑎 ∙ 𝑍𝑀𝑉 𝑎 ∙ 𝑢𝑚
∗
𝐾
a = slope
b = y intercept
Phase quantities:
Relative peak intensities:
Lattice plane spacing:
θ = asin(𝜆
2𝑑) Peak position:
User decides which parameters to
fit to measured diffraction pattern
Optimizing the Refinement
25
Right-click on line «STRUC[1]=Hydroxyapatite.str»
And select
«Open File»
Optimizing the Refinement
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Alternatively click
«Open all Project Structure Files»
Opens both structure files
BGMN Control / Structure File Syntax
27
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)
Optimizing the Refinement
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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
Toggling Parameter Refinement States
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Isotropic parameters Anisotropic parameters
Texture
Fix A=0.9424
Fix B1=0
GEWICHT=SPHAR0
Refined with limits PARAM=A=0.9424_0.9404^0.9444
Refined isotropically PARAM=B1=0_0^0.01
GEWICHT=SPHAR2
Refined without limits PARAM=A=0.9424
Refined anisotropically
B1=ANISO^0.01
GEWICHT=SPHAR4
F6
F5
F5
F6
Optimized Refinement
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Done!
Close Project
Optimized Refinement
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Further optimizations:
- Additional phase MgO
- Substitutions
- Thermal displacement parameters
Example 2: Batch Refinement
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1. Set Format
2. Select and
open all files
Series of measurements of the same sample
Example 2: Batch Refinement
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One Project per File
Example 2: Batch Refinement
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1. Add
«Hydroxyapatite»
and
«Whitlockite»
2. Run the refinement
Example 2: Batch Refinement
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Satisfactory results
Use the same project settings
for all other datasets
Example 2: Batch Refinement
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Identical control file
was created
«Run Batch Refinement»
Will process all open projects
Example 2: Batch Refinement
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Follow the progress
Example 2: Batch Refinement
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Export results of all
open projects
Exported Global GOALs
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Sort by «Parameter/Goal»
Exported Global GOALs
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Easy to compute
mean and standard deviations
Refined Chemical Composition
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Open «Window Chemistry»
Make sure the Quantity GOALs are assigned correctly
Normalized to 100%
Normalized to
refined phase quantity
Total sample compo-
sition available
Create CIF files from refined structures
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Export CIF files
Drawing Structures
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http://jp-minerals.org/vesta/en/
Exporting Diffraction Patterns
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1. Display the Plot Area
2. Select «Save As…»
Diffraction Data Formats
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ASCII Free format (*.xy)
for import in
Excel, Origin, etc.
Diffraction Data Formats
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Scalable Vector
Graphics (*.svg)
for import in Illustrator,
CorelDRAW, Inkscape etc.
Diffraction Data Formats
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Print to PDF (PDF printer required)
Mass Export (to printer, PDF, SVG)
Profex
More «Behind the Scenes» information
in «Lesson 8: Crystal Structures»
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http://profex.doebelin.org
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