Re: Problems using TOPAS R (Rietveld refinement)

2007-03-16 Thread Reinhard Kleeberg

Dear Leandro,
some comments:
Leandro Bravo schrieb:

I know that refining the atoms positions is ´´too much´´, exagerated. 
But is the only way I can make the calculated DRX pattern fit with the 
measured one. There must a problem in the instrument details since I´m 
using Fundamental Parameters (FP) for peak shape, the values I put in 
the instrument description play a major role in FP, am I right?


No. The misfit in your Rietveld refinement of kaolinite you get by using 
published atomic coordinates and temperature factors does definitely not 
arise from wrong published structure date and probably not significantly 
from any error in your instrumental parameters.  Kaolinite diffraction 
pattern can not be described by simple isotropic line broadening as you 
tried by the crystallite size parameter. The different types and 
amounts of stacking faults in kaolinite are the reason for different 
kinds of smearing of the reciprocal lattice points. It makes no sense 
to refine atomic coordinates and temperature factors in an ideal cell to 
get a better Rwp of a disordered structure: One will of course get a 
better fit, but this is reached by variations of intensity by 
meaningless atomic positions.


I made a new scan, of the same sample, with range from 10° to 80°, 
step size 0,02 and count time 4 seconds. The old one was from 5° to 
120,° maybe it is prejudicing the background refining.


Tomorrow I´m gonna to scrap this old pattern and work with the new 
one. I´m having a good response refining the calcite and teh dolomite 
in the sample only refining lattice parameters, cry size and beq. I 
think that refining this is what we can call a ´´normal refining 
method``. Now the kaolinite...


The major problem is that I have a sample from a laterite with 
hydroxyapatite, calcite, dolomite, vermiculite and other phases. The 
vermiculite is very alterated and in the DRX pattern we can confuse it 
with other ``layered silicates``, it will be a huge problem. But I 
will only put my hands on these samples after finishing with the 
kaolinite. 


Altered vermiculite is probably a mixed-layered clay mineral? If yes, 
I'm in doubt that you can quantify this by the Rietveld method. See:


Omotoso, O., McCarty, D.K., Hillier, S., Kleeberg, R. (2006) Some 
successful approaches to quantitative mineral analysis as revealed by 
the 3^rd Reynolds Cup contest. Clays and Clay Minerals, 54 (6),  751-763.


One question, these ´´models`` and ´´trials`` that you talk about 
regarding the kaolinite is used in the CIF part of the refinement, am 
I right?! It´s not a part of the TOPAS itself. right?


I think he CIF part you are referring is from the database you used 
(ICSD), right? These data refer to the ideal cell. One must introduce 
any models regarding line broadening or supercell coordinates into your 
structure model (*.str ?) what is used in your refinement. You will not 
find such models in a crystallographic database, specific formulations 
are necessary, depending on your disorder problem and on the 
capabilities of your Rietveld program. 
Best regards


Reinhard



Thank you,

Leandro

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RE: RE: Exporting GSAS powplot data

2007-03-16 Thread Duncan, Jo
Once again, many thanks... Anyone know how to do the same using TOPAS
academic?

 

Cheers

 

Jo.

 

 



From: Leopoldo Suescun [mailto:[EMAIL PROTECTED] 
Sent: 15 March 2007 15:08
To: rietveld_l@ill.fr
Subject: RE: Exporting GSAS powplot data

 

Dear Jo,

 

Works very nicely in LIVEPLOT but you can still do it in POWPLOT. After
you choose your graphic output (any of them would be the same), the next
screen offers option A which is an ascii file written using the selected
options. If you have only one histogram you will still need to select it
by typing H 1 before being able to write the output file. If you want
to change x-axis units, toggle on tickmarks, etc you will also need to
do it before saving the pattern.

If trying to export a conventional X-ray pattern that was the only one
included in the refinement I would typicaly type:

 

C (choose graphic output for visualization)

N (I don't want to save graphic output in ps or eps format)

H 1 D M T  (select histogram 1, show difference curve, show tickmarks,
use 2theta as x-axis units)

P (plot the pattern in the screen, check that everything looks like I
expected)

A (export the pattern as it is shown, you'll be asked to enter an
8-character name without extension and the file will be saved as
NAME.TXT)

 

IMHO LIVEPLOT makes a nicer treatment of the tickmarks giving a separate
x-axis/phase list of positions. Easier to handle when you have more than
one phase with significant peak overlap.

Hope this helps.

Leo

Dr. Leopoldo Suescun
Postodoctoral Appointee
Materials Science Division - Bldg 223 - Rm D217
Argonne National Laboratory
9700 S. Cass Ave., Argonne, IL 60439
Phone: 1 (630) 252 9760
Fax: 1 (630) 252 
URL: http://www.msd.anl.gov/groups/nxrs/personnel/suescun/index.html 

 

 



From: Brian H. Toby [mailto:[EMAIL PROTECTED] 
Sent: Thursday, March 15, 2007 9:41 AM
To: rietveld_l@ill.fr
Subject: Re: Exporting GSAS powplot data

You can also export from liveplot in a few different formats including
.csv for use in a spreadsheet. I am open to suggestions on other ASCII
formats for data export -- but be prepared to research that format so
you can tell me exactly what needs to be written. 

 

Brian 

 

On Mar 15, 2007, at 8:21 AM, Duncan, Jo wrote:





Hello RR people. How can I extract the information in powplot (in GSAS)
for use in another package e.g. excel ? i.e. how can I get the x and y
values of Refined pattern, histogram and residual?

Many thanks

Jo

 

 

Brian H. Toby, Ph.D. office: 630-252-5488

Materials Characterization Group Leader, Advanced Photon Source

9700 S. Cass Ave, Bldg. 433/D003 work cell: 630-327-8426 

Argonne National Laboratory secretary (Marija): 630-252-5453

Argonne, IL 60439-4856 e-mail: brian dot toby at anl dot gov