0.

Expgui /GSAS

GSAS:
Allen C. Larson and Robert B. Von Dreele, Los Alamos National Laboratory, Los Alamos

Expgui:
Brian H. Toby, NIST Center for Neutron Research

Platforms:
Windows, Linux, SGI/Irix, Mac. Freeware for academic use

Download
CCP14 - Homepage: http://www.ccp14.ac.uk/solution/gsas/

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0. Expgui /GSAS

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0. Expgui /GSAS
A typical command line interface...

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1. Setting up an experiment I

Selecting a working directory for *.gsa, *.ins and *.cif files

Creating a new (empty) experiment file

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1. Setting up an experiment II

Providing an overall title Whatever you like...

Expgui screen with created experiment file

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2. Adding a phase I

The Phase panel: Manual definition or import of supported crystallographic data formats

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2. Adding a phase II

Lattice parameters after import

Always check for possible errors! Eg.: Here R-3c in hexagonal setting with centering vectors For rhombohedral setting: R -3 c R

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2. Adding a phase III

The final structure

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3. Adding powder diffraction data I

Histogram = diffraction pattern Panel also used to modify pattern related parameters like: diffractometer constants (eg. wavelength), the background function and terms.

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3. Adding powder diffraction data II

Useable data range can be checked by running RAWPLOT

After "Add" EXPTOOL automatically performs a check. Final display (no errors) will look like this:

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4. Changing the background function I

More than 10 background functions implemented in GSAS Default: Cosine fourier series (3 parameters) Check Refine background for background refinement by GENLES Damping: 0 1 9 (100% shift applied) (90% shift applied) (10% shift applied)

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4. Changing the background function II

Fit background graphically invokes BKGEDIT (useful for difficult cases) Choosing Shifted Chebyschnew function with 6 parameters Arbitrary starting values (including 0) is usually OK

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5. Scale factor and background refinement I

Scaling panel: 1 overall scale factor 1 scale factor for each phase

LS Controls panel: Lowering the initial number cycles Check Extract Fobs Run POWPREF
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5. Scale factor and background refinement II

POWPREF run

Default Step back message after any changes (Switch off in options)

Last POWPREF run noted in history Everything ready for refinement: Run GENLES

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5. Scale factor and background refinement III

Refinement of 7 parameters

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5. Scale factor and background refinement III

Refinement of 7 parameters wRp: Chi: 99% => 72% 258 => 134 (Shifts insignificant if < esd)
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Parameter shifts: 854 (!!) => 0

6. Plotting the initial fit I

GSAS: POWPLOT Expgui: LIVEPLOT Significant differences!!

Reflection tickmarks for each phase by 1, 2, .... (or Tickmarks in File) Fit becomes worse at higher angles!

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6. Plotting the initial fit II

Zoom in with left mouse button (ROI corners)

Low angles: Lattice parameters not OK Peak widths OK BUT:

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6. Plotting the initial fit III

High angles: Fit becomes worse! (positions, peak widths)

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7. Fitting the unit cell I

Calculated peaks are in the range of experimental ones => Unit cell fitting possible Phase panel: Check refine cell

LS controls panel: Increase number of refinement cycles (eg. : 6) Run GENLES

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7. Fitting the unit cell II

Significant improvement! Chi, wRp, Liveplot

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7. Fitting the unit cell III

Significant peak changes: Run POWPREF

Not necessary but: New GENLES fit: Chi drops to 60 (Better indexing)

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8. Refine Zero correction I

Histogram panel: Check Refine zero Run GENLES

Note: - Zero refinement preferably for parallel beam instruments (eg. synchrotron) - For parafocusing geometries (Bragg-Brentano): - Refinement of sample displacement - if needed also: Sample transparency
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8. Refine Zero correction II

Small fit improvements: wRp: 51% -> 48% (More precise lattice constants)

Zero shift changed: 0.04 -> 1.73 Means: 0.4 x 10-2 -> 1.73 x 10-2 degrees 2Theta (!)

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9. Initial Fitting of profile parameters I

Normally: Improvement of crystallographic model But here: High angle fit not really good! Shape: Profile parameters Intensities: Model, temperature factor Background: Too few parameters

Profile panel: Choose profile function Here: Gaussian with refinement of all three Cagliotti terms (U, V, W) Run GENLES

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9. Initial Fitting of profile parameters II

Significant fit improvement: wRp: 48% -> 40%

BUT: Model profiles truncated Reason: No POWPREF run after peak changes! Profiles became broader -> not enough data points in peak computation
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9. Initial Fitting of profile parameters III

After re-running POWPREF and GENLES: Slight improvements wRp and Chi

Significant improvements for profiles at high angles Intensities still do not fit...

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10. Refine coordinates and Overall Uiso I

Intensities still do not fit: Crystallographic model is somehow inadequate...

Here: Introduce a constraint Group atoms to share a common temperature factor (displacement parameter) Constraint panel -> New constraint

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10. Refine coordinates and Overall Uiso II

Overall displacement factor due to data/parameter ratio Factor can be set by multiplier

Constraints in Expgui: coordinates, displacement, profile parameters More constraints in EXPEDIT Set refinement flags for coordinates and displacement (X, U)
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10. Refine coordinates and Overall Uiso III

The result: Great impact on refinement: wRp goes down to 8% Chi goes down to 2

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11. Finishing up (Expert refinements) I

Here: Neutron data with regular peak shapes (!) 1) Apply individual displacement parameters (delete constraint)

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11. Finishing up (Expert refinements) II

Here: Neutron data with regular peak shapes (!) 1) Apply individual displacement parameters (delete constraint)

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11. Finishing up (Expert refinements) III

Here: Neutron data with regular peak shapes (!) 2) Change background function (Refine additional parameters) 3) Change profile function (Instrument parameter file contains default parameters. Complete description in GSAS manual)

Types: 1: Simple Gaussian peak shapes, poor asymmetry correction; appropriate for CW neutrons only. 2: Pseudo-Voigt function, poor asymmetry correction; good for refinements where low-angle peaks are not significant 3: Similar to type 2, except this includes the Finger-Cox-Jephcoat asymmetry correction. Good even with significant low angle peaks. 4: Similar to type 3, except this includes the Stephens model for anisotropic strain broadening (where different classes of reflections have different widths
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11. Finishing up (Expert refinements) IV

Here: Neutron data with regular peak shapes (!) 2) Change background function (Refine additional parameters) 3) Change profile function (Instrument parameter file contains default parameters.) Press Current to take current refinement parameters

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11. Finishing up (Expert refinements) V

3) Change profile function Set Cagliotti-parameters UVW as refinable

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11. Finishing up (Expert refinements) VI

Run: GENLES POWPREF GENLES => Small improvements of fitting parameters

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11. Finishing up (Expert refinements) VII

Run: GENLES POWPREF GENLES => Small improvements of fitting parameters Turn on Cumulative Chi-squared in LIVEPLOT options menu to check evaluation

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