==== Setting Up an Experiment EXPGUI

8/13/2019 ==== Setting Up an Experiment EXPGUI

1/19

11

CKWP13

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

DownloadCCP14 - Homepage:

http://www.ccp14.ac.uk/solution/gsas/

CKWP13

0. Expgui /GSAS


2/19

22

CKWP13

0. Expgui /GSAS

A typical command line interface...

CKWP13

1. Setting up an experiment I

Selecting a working directory for

*.gsa, *.ins and *.cif files

Creating a new (empty) experiment

file


3/19

33

CKWP13

1. Setting up an experiment II

Providing an overall title

Whatever you like...

Expgui screen with created

experiment file

CKWP13

2. Adding a phase I

The Phase panel:

Manual definition or import of

supported crystallographic data

formats


4/19

44

CKWP13

2. Adding a phase II

Lattice parameters after import

Always check for possible errors!

Eg.:

Here R-3c in hexagonal settingwith centering vectors

For rhombohedral setting:

R -3 c R

CKWP13

2. Adding a phase III

The final structure


5/19

55

CKWP13

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.

CKWP13

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:


6/19

66

CKWP13

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 (100% shift applied)

1 (90% shift applied)

9 (10% shift applied)

CKWP13

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


7/19

77

CKWP13

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

CKWP13

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


8/19

88

CKWP13

5. Scale factor and background refinement III

Refinement of 7 parameters

CKWP13

5. Scale factor and background refinement III

Refinement of 7 parameters

wRp: 99% => 72%

Chi: 258 => 134

Parameter shifts: 854 (!!) => 0 (Shifts insignificant if < esd)


9/19

99

CKWP13

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!

CKWP13

6. Plotting the initial fit II

Zoom in with left mouse button

(ROI corners)

Low angles:

Lattice parameters not OK

Peak widths OK

BUT:


10/19

1010

CKWP13

6. Plotting the initial fit III

High angles:

Fit becomes worse!

(positions, peak widths)

CKWP13

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


11/19

1111

CKWP13

7. Fitting the unit cell II

Significant improvement!

Chi, wRp, Liveplot

CKWP13

7. Fitting the unit cell III

Significant peak changes:

Run POWPREF

Not necessary but:

New GENLES fit: Chi

drops to 60

(Better indexing)


12/19

1212

CKWP13

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

CKWP13

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 (!)


13/19

1313

CKWP13

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 functionHere: Gaussian with refinement of all

three Cagliotti terms (U, V, W)

Run GENLES

CKWP13

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


14/19

1414

CKWP13

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...

CKWP13

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


15/19

1515

CKWP13

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)

CKWP13

10. Refine coordinates and Overall Uiso III

The result:

Great impact on refinement:

wRp goes down to 8%

Chi goes down to 2


16/19

1616

CKWP13

11. Finishing up (Expert refinements) I

Here:

Neutron data with regular peak shapes (!)

1)

Apply individual displacement parameters

(delete constraint)

CKWP13

11. Finishing up (Expert refinements) II

Here:


1)

Apply individual displacement parameters

(delete constraint)


17/19

1717

CKWP13

11. Finishing up (Expert refinements) III

Here:


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

CKWP13

11. Finishing up (Expert refinements) IV

Here:


2) Change background function

(Refine additional parameters)


(Instrument parameter file contains defaultparameters.)

Press Current to take current refinement

parameters


18/19

1818

CKWP13

11. Finishing up (Expert refinements) V


Set Cagliotti-parameters UVW as refinable

CKWP13

11. Finishing up (Expert refinements) VI

Run:

GENLES

POWPREF

GENLES

=> Small improvements of fitting

parameters


19/19

CKWP13

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

Documents

==== Setting Up an Experiment EXPGUI