Lesson 6 Profexprofex.doebelin.org/wp-content/uploads/2017/06/Lesson-6.pdf · Lesson 6 Profex...

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

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Select correct file format

First Use: Example 1

7

Scan File = «Project»

Scans in File

Plot area

(press «shift» for

help window)


8

Identify phases from

internal database


9

Create Refinement Control File


10

Choose correct

instrument

configuration

Select phases

(HAp is pre-selected)


11

New BGMN Refinement

Control File was generated


12

Run the refinement


13

Plot display changed from *.raw file

to *.dia (= refinement result)


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)


15


16

Add another phase


17

Select Whitlockite

Control file already

exists, don’t generate

a new default file

Click «OK» and re-run

the refinement


18

Phase Quantities:

95.55 (± 0.13) wt-% Hydroxyapatite

4.45 (± 0.13) wt-% Whitlockite

χ2 = 1.625


19

*.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


25

Right-click on line «STRUC[1]=Hydroxyapatite.str»

And select

«Open File»


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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)


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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


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One Project per File


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1. Add

«Hydroxyapatite»

and

«Whitlockite»

2. Run the refinement


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Satisfactory results

Use the same project settings

for all other datasets


36

Identical control file

was created

«Run Batch Refinement»

Will process all open projects


37

Follow the progress


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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.


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Scalable Vector

Graphics (*.svg)

for import in Illustrator,

CorelDRAW, Inkscape etc.


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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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