12/9/2017 CCP14 Homepage - Single Crystal and Powder Diffraction - Methods, Problems, Solutions and Tutorials - Doing Le Bail

il (whole pattern structur

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Methods, Problems and Solutions - and Tutorials

GSAS (General Structure Analysis System) Rietveld powder diffraction and Single Crystal software

Doing Le Bail (whole pattern structureless) fitting in GSAS via Brian Toby's EXPGUI
interface as part of setting up for a combined X-ray / Neutron Rietveld refinement
The CCP14 Homepage is at http://www.ccp14.ac.uk

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[The reference to use for GSAS in any resulting publications is: A.C. Larson and R.B. Von Dreele, "General Structure Analysis System
(GSAS)", Los Alamos National Laboratory Report LAUR 86-748 (1994).]

[The reference to cite in any resulting publications for using EXPGUI is: B. H. Toby, EXPGUI, a graphical user interface for GSAS, J.
Appl. Cryst. (2001). 34, 210-213]

This example is Orthorhombic Lead Sulphate used in the first Rietveld Round Robin organised by Rod Hill under the auspices of the IUCr
Commission on Powder Diffraction.

Click here to download a zipped file of the PbSO4 GSAS XRD and Neutron data - as well as
the Parameter files

The main strategy here is to a) add the phase of interest (PbSO4), then b) add both XRD and
Neutron histograms then c) followed by Le Bail fitting both datasets together.

As noted below, Le Bail fitting in GSAS can go very easily if you use the EXPGUI "Fit
Background Graphically" feature.

Information on Brian Toby's EXPGUI, with installation instructions for UNIX and MS-
Windows can be obtained via the following webpages. Make sure you have the latest Beta
version for the best results (personal opinion).

EXP GUI Homepage

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CCP14 Canadian EXP GUI Homepage Mirror

Run EXPGUI and goto the directory with the diffraction data and PRM files for the neutron
and powder diffractometers. Enter a new file name and press READ to create a new EXP file.
(of course you can open and edit an existing GSAS EXP file)

When prompted, create the new EXP file, then provide the title information leading to the 2nd
EXPGUI screen.

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Click on the Phases Tab to present the following screen image, then click on the Add Phase
Tab

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Then input the Spacegroup and Cell information then click Add then continue to lead back to
the Phase Tab with the cell and spacegroup information (but no atom information) :

S.G., a, b, c, al, be, ga := P n m a 8.472940 5.393338 6.953579 90.0000 90.0000 90.0000

(if you have the structure information in PowderCell or CIF format, you can easily importn all
the structure information).

Now (if convenient) add the starting structure (or at least a dummy atom) using the Add
Atoms GUI interface. Leading to the second screen image below.
PB PB1 .187427 .250000 .167072 1.00 .025
S S2 .066713 .250000 .684284 1.00 .025
O O3 -.092390 .250000 .595179 1.00 .025
O O4 .193956 .250000 .543152 1.00 .025
O O5 .081057 .027005 .808874 1.00 .025

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Now click on the Histogram GUI interface and the Add New Histogram Icon for in this case
to starting adding the first X-ray diffractogram. Then browse and select the Data file and PRM
file and click Add to continue.

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Note: It is quite common for GSAS instrument parameter files to have incomplete or incorrect
information. Thus always check that the parameters displayed by EXPGUI make sense. In this
case, you will have to correct the Ratio (of Alpha 1 and 2) to 0.5 and reset the Zero (offset) to
0. Also check that the wavelength(s) are correct.

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Now repeat the same sequence to add in the Neutron dataset and parameter file via the Add
New Histogram Icon. As there are two Banks/Sets defined by this particular instrument
parameter file, select the one that is appropriate (in this case Number 1).

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To enable Le Bail mode fitting for the two datasets, select the LS Controls tab, click on the
XC histogram (XRD dataset 1) and then click on Equally Weighted Le Bail Method. Now
select the NC histogram (Neutron dataset 2) and then click on Equally Weighted Le Bail
Method.

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Now run POWPREF and then GENLES and slowly release parameters as per normal to fit
the data (remember to turn off the Scale Factor as by default this may be left on). This can also
be very easily done in EXPGUI using point and click.

From Brian Toby: Personally, I would also suggest setting the cycles to zero & running
GENLES 2-4 times.
Also from Brian Toby:
My recommendation for a LeBail refinement scheme would be (1) to fit 2
background terms/histogram, (2) then unit cell, (3) then zero, (4) then
neutron wavelength (5) then more background terms until the fit is good
(6) then profile terms. On occasion I need to fix the bkg terms while I
refine the profile terms. BTW, I never refine the FCJ S/L & H/L terms. I
will probably need to rerun POWPREF once or twice through this scheme
and after I do this, I rerun GENLES a few times with zero cycles until
the Rwp's settle down.

The value of BKGEDIT comes in if one of two things happen: the Le Bail
fit does weird things with intensities, rather than draw the background
where it should be, or the background is sufficiently complex that one
cannot start the LeBail w/o a reasonable background.

Set background, wavelength and two-theta offset in the Histogram tab; Profile parameters in
the Profile Tab; UNIT Cell in the Phase tab.

Hints that you can ignore if you have better ideas:

Refine Unitcell and zero offset for the XRD data and refine Wavelength and zero offset
for the neutron data.
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For the profile function: try using Type 3 profile - Pseudo Voight with FCJ assymmetry
correction for both the XRD and Neutron data.

Running Powpref resets the Le Bail intensities. Normally you would not want to reset the
Le Bail intensities as then you would have to fix most parameters to allow the Le Bail
intensities to refit in a stable manner.

Fitting Background while Le Bailing in GSAS ---- Use the

EXPGUI "Fit Background Graphically" feature - it is
totally brilliant!
(This will normally fix most of the difficulties Le Bailing in GSAS)

If having a problem fitting the background, you may like to use the very nifty and almost life
saving EXPGUI manual Background Point selection and editing feature. (you then fit a
Chebyshev to this and save back into the GSAS EXP file where you have the option of refining
or fixing the background). This "Fit Background Graphically" feature is accessed via Edit
Background in the Histogram Tab. (if you have not done this before, refer to tutorial
runthrough on Using EXPGUI, BKGEDIT and GSAS to manually define a background using
Chebyshev Polynomial coefficients.

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Fit the profile until you are happy. Then turn on the Rietveld option for both Histograms to
start refining the structure. Following is the Le Bail fit for the Neutron pattern. If you have
difficulties with Le Bail fitting Alpha_1,2 XRD data, you may want to turn the Rietveld option
back on(?). Refer below to possible reasons why you may be experiencing difficulty here with
GSAS.

If you have trouble fitting a powder XRD profile, refer to Difficulty in profiling Powder XRD
data in GSAS, Peak Cutoff values and the influence of Powpref

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From the Structure Solution from Powder Diffractometry List:

At 12:44 07/09/99 -0500, Jaap Vente wrote:
>On Tue, 7 Sep 1999, Peter Y. Zavalij wrote:
>
>> > Lachlan wrote :
>> > A belated reply on the topic of Le Bail extraction
>> > in GSAS:
>> >
>> There is small problem with LeBail extraction in GSAS:
>> alpha1 and alpha2 components are refined independently...
>>
>
>
>Yes I found that as well, but thought that I had made a mistake somewhere.
>I think it is a major problem though. Bob could you please fix that?

Not sure if Bob has subscribed to this list. The way this problem
was fixed in ARIT was to consider the two structure factor amplitudes
independently derived from the alpha 1 and 2 components, then
to make them both equal to the mean value, after each new
iteration. I did not find a better way. This is the reason why
Rp is more slowly decreasing when dealing with alpha1+2 than
with alpha 1 alone.

In FORTRAN, this operation corresponds to :

( see in ARIT source at http://sdpd.univ-lemans.fr/arit.html )

In ITER subroutine :
make both structure factors equal to the mean

DO 1 I=1,NN
IF(ICH(I).EQ.0)GO TO 1
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SOMH=FNUU(I)+FNUU(ICH(I))
FNUU(I)=SOMH/2.
FNUU(ICH(I))=FNUU(I)
1 CONTINUE

In the MAIN program, IHC is the order

of the alpha2 component in the hkl list :

DO 4 I=1,NN-1
IHC(I)=0
IF(ICC(I).EQ.5)GO TO 4
DO 3 J=I+1,NN
IF(ICC(J).NE.5)GO TO 3
IF(ICO(I).NE.ICO(J))GO TO 3
IF(HHH(1,I).NE.HHH(1,J).OR.HHH(2,I).NE.HHH(2,J).OR.
1HHH(3,I).NE.HHH(3,J))GO TO 3
IHC(I)=J
GO TO 4
3 CONTINUE
4 CONTINUE

Best,

Armel

PS : To subscribe, send an e-mail to sdpd-subscribe@egroups.com

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