Re: refinement

[Le Bail Armel]

Nice job !Happy new year.Armelenvoyé : 6 janvier 2023 à 12:36de : Frank Girgsdies à : KULDEEP SINGH <2019phdph...@curaj.ac.in>, rietveld_l@ill.frobjet : Re: refinementDear Kuldeep,First of all, a refinement (I suppose you mean Rietveld refinement?) requires a crystal structure model, which in turn requires that you have a rather precise knowledge about the identity/composition of the crystalline phase you want to refine. XRD is not an elemental analysis method, and perovskite structures can be formed with many, many elements. Unfortunately, you forgot to mention what elements your material is composed of.I tired an identification anyway, using the latest edition of the PDF-4+ database. However, despite the fact that the pattern looks definitely perovskite-like, there was no match close enough. Trying to tune the lattice parameters of some better candidate structures revealed that something is weird about your pattern, as the positions of related reflections do not agree with each other.Then I tried to shift the pattern on a trial-and-error basis and found that it has in fact a severe zero shift of more than 0.4 degrees 2theta. It could also be a serious sample height (a.k.a. displacement) error, since these two errors are rather similar in effect. However, in order to refine a displacement correction, I would need to know your goniometer radius.I performed a Le Bail fit assuming a GdFeO3 type structure (in setting Pbnm) and obtained a reasonable fit yielding the following lattice parameters:a = 5.26617(12) Åb = 5.62135(16) Åc = 7.48743(19) Åzero error = -0.4428(8) deg. 2thetaWith this zero error information, I went back to the PDF search.Based on that, my best guess is that your sample could be Ho(Cr0.5Mn0.5)O3.Best wishes and Happy New Year,Frank GirgsdiesOn 23.12.2022 06:16, KULDEEP SINGH wrote:Hi all,please help to refine this simple data of perovskite i am stuck in it.angle 20-80step size 0.01wavelength 1.5404*Kuldeep Singh**Research Scholar**Department of PhysicsCentral University of Rajasthan**Bandarsindri-305817**District-Ajmer, Rajasthan*ᐧ++Please do NOT attach files to the whole list Send commands to  eg: HELP as the subject with no body textThe Rietveld_L list archive is on http://www.mail-archive.com/rietveld_l@ill.fr/Please do NOT attach files to the whole list Send commands to  eg: HELP as the subject with no body textThe Rietveld_L list archive is on http://www.mail-archive.com/rietveld_l@ill.fr/++
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Re: refinement

[Frank Girgsdies]

Dear Kuldeep,

First of all, a refinement (I suppose you mean Rietveld refinement?) 
requires a crystal structure model, which in turn requires that you have 
a rather precise knowledge about the identity/composition of the 
crystalline phase you want to refine. XRD is not an elemental analysis 
method, and perovskite structures can be formed with many, many 
elements. Unfortunately, you forgot to mention what elements your 
material is composed of.


I tired an identification anyway, using the latest edition of the PDF-4+ 
database. However, despite the fact that the pattern looks definitely 
perovskite-like, there was no match close enough. Trying to tune the 
lattice parameters of some better candidate structures revealed that 
something is weird about your pattern, as the positions of related 
reflections do not agree with each other.
Then I tried to shift the pattern on a trial-and-error basis and found 
that it has in fact a severe zero shift of more than 0.4 degrees 2theta. 
It could also be a serious sample height (a.k.a. displacement) error, 
since these two errors are rather similar in effect. However, in order 
to refine a displacement correction, I would need to know your 
goniometer radius.
I performed a Le Bail fit assuming a GdFeO3 type structure (in setting 
Pbnm) and obtained a reasonable fit yielding the following lattice 
parameters:

a = 5.26617(12) Å
b = 5.62135(16) Å
c = 7.48743(19) Å
zero error = -0.4428(8) deg. 2theta

With this zero error information, I went back to the PDF search.
Based on that, my best guess is that your sample could be Ho(Cr0.5Mn0.5)O3.

Best wishes and Happy New Year,
Frank Girgsdies




On 23.12.2022 06:16, KULDEEP SINGH wrote:

Hi all,
please help to refine this simple data of perovskite i am stuck in it.
angle 20-80
step size 0.01
wavelength 1.5404
*Kuldeep Singh*
*Research Scholar*
*Department of Physics
Central University of Rajasthan
*
*Bandarsindri-305817*
*District-Ajmer, Rajasthan*
ᐧ

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Re: refinement

[KULDEEP SINGH]

Ok Sir, I will take care of it, next time
Thank you

On Fri, Dec 23, 2022, 13:06 Alan W Hewat 
wrote:

> "Please do NOT attach files to the whole list".
> This message appears immediately before the file you attached to the whole
> list. If you do it again, you will be removed from the list. Please read
> the instructions for your refinement program and try again. If you really
> are stuck, say something specific about the problem you have. What
> experience do you have? If you are a student, get help first from your
> local professor or another colleague.
>
> Best wishes to all for the end of year celebrations, and a happy New Year.
>
> Alan
> 
> Dr Alan Hewat, NeutronOptics
> Grenoble, FRANCE (from phone)
> alan.he...@neutronoptics.com
> +33.476984168 VAT:FR79499450856
> http://NeutronOptics.com/hewat
> ___
>
>
> On Fri, 23 Dec 2022, 06:17 KULDEEP SINGH, <2019phdph...@curaj.ac.in>
> wrote:
>
>> Hi all,
>> please help to refine this simple data of perovskite i am stuck in it.
>> angle 20-80
>> step size 0.01
>> wavelength 1.5404
>> *Kuldeep Singh*
>> *Research Scholar*
>>
>>
>> *Department of PhysicsCentral University of Rajasthan*
>> *Bandarsindri-305817*
>> *District-Ajmer, Rajasthan*
>> ᐧ
>> ++
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>> ++
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>>
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Re: refinement

[Alan W Hewat]

"Please do NOT attach files to the whole list".
This message appears immediately before the file you attached to the whole
list. If you do it again, you will be removed from the list. Please read
the instructions for your refinement program and try again. If you really
are stuck, say something specific about the problem you have. What
experience do you have? If you are a student, get help first from your
local professor or another colleague.

Best wishes to all for the end of year celebrations, and a happy New Year.

Alan

Dr Alan Hewat, NeutronOptics
Grenoble, FRANCE (from phone)
alan.he...@neutronoptics.com
+33.476984168 VAT:FR79499450856
http://NeutronOptics.com/hewat
___


On Fri, 23 Dec 2022, 06:17 KULDEEP SINGH, <2019phdph...@curaj.ac.in> wrote:

> Hi all,
> please help to refine this simple data of perovskite i am stuck in it.
> angle 20-80
> step size 0.01
> wavelength 1.5404
> *Kuldeep Singh*
> *Research Scholar*
>
>
> *Department of PhysicsCentral University of Rajasthan*
> *Bandarsindri-305817*
> *District-Ajmer, Rajasthan*
> ᐧ
> ++
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> text
> The Rietveld_L list archive is on
> http://www.mail-archive.com/rietveld_l@ill.fr/
> ++
>
>
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refinement

[KULDEEP SINGH]

Hi all,
please help to refine this simple data of perovskite i am stuck in it.
angle 20-80
step size 0.01
wavelength 1.5404
*Kuldeep Singh*
*Research Scholar*


*Department of PhysicsCentral University of Rajasthan*
*Bandarsindri-305817*
*District-Ajmer, Rajasthan*
ᐧ


Sheet1.dat
Description: Binary data
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Re: refinement

[Le Bail Armel]

Your pattern match well with Bixbyite (plus some impurity)http://www.crystallography.net/cod/9007522.htmlUsing FPSM http://nanoair.dii.unitn.it:8080/sfpm/BestArmelenvoyé : 15 septembre 2022 à 18:37de : KULDEEP SINGH <2019phdph...@curaj.ac.in>à : rietveld_l@ill.frobjet : refinementAnybody can provide me Rietveld refinement of the following data.angle 10-90scane step 0.01Pyrochlore compound Fe2Mn2O7Kuldeep SinghResearch ScholarDepartment of PhysicsCentral University of RajasthanBandarsindri-305817District-Ajmer, Rajasthanᐧ++Please do NOT attach files to the whole list Send commands to  eg: HELP as the subject with no body textThe Rietveld_L list archive is on http://www.mail-archive.com/rietveld_l@ill.fr/++
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refinement

[KULDEEP SINGH]

Anybody can provide me Rietveld refinement of the following data.
angle 10-90
scane step 0.01
Pyrochlore compound
Fe2Mn2O7


*Kuldeep Singh*
*Research Scholar*


*Department of PhysicsCentral University of Rajasthan*
*Bandarsindri-305817*
*District-Ajmer, Rajasthan*
ᐧ


fmo.DAT
Description: Binary data
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[SUSPECTED SPAM] refinement

[KULDEEP SINGH]

Hi all, I want to know that the spinel and pyrochlore Wyckoff positions may
be the same?
*Kuldeep Singh*
*Research Scholar*


*Department of PhysicsCentral University of Rajasthan*
*Bandarsindri-305817*
*District-Ajmer, Rajasthan*
ᐧ
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Regarding form factor refinement

[Archna Sagdeo]

Dear Rietvelders,
While fitting the anomalous x-ray diffraction pattern, I am not able to
refine the form factor of the element, about the edge of which x-ray
diffraction measurements have been performed. I am able to give the
parameters f' and f" from the option pattern->user scattering parameter, if
I use the edit pcr option, in Fullprof. It would be nice if anybody can
help me in this regard.

Regards
Archna

Dr. Archna  Sagdeo
Scientific Officer
Synchrotrons Utilization Section
Raja Ramanna Centre for Advanced Technology
Indore-13
INDIA
Ph: 91-731-2442126; 2442512; 2442124 (O)
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Powder Diffraction and Rietveld Refinement School 2020

[EVANS, IVANA R.]

Dear All,

The biennial Powder Diffraction & Rietveld Refinement School at Durham 
University will take place 29th March-2nd April 2020.

The information about the School content and format, practical information 
(deadlines and fees) and the application link are available at:

https://community.dur.ac.uk/john.evans//webpages/pdrr_school.htm<https://community.dur.ac.uk/john.evans/webpages/pdrr_school.htm>

As in previous years, we will offer a combination of lectures covering the 
theoretical aspects of powder diffraction and Rietveld refinement, 
classroom-based "by-hand" problem sessions/tutorials and extensive hands-on 
practical sessions using a variety of modern software packages.

Topics to be covered will include:

  *   Data collection strategies for X-ray and neutron diffraction
  *   Constant-wavelength and time-of-flight diffraction
  *   Modelling peak shapes (including microstructure analysis)
  *   Indexing powder patterns
  *   Rietveld, Le Bail and Pawley fitting methods
  *   X-ray and neutron combined Rietveld refinements
  *   Restrained refinements
  *   Rigid body refinements
  *   A number of more specialised and advanced optional topics (ab-initio 
structure solution, parametric and symmetry distortion mode refinements)

Lectures will be given by Prof. John Evans, Prof. Ivana Evans, Dr. Jeremy 
Cockcroft and Prof. Andy Fitch.

Best wishes,
Ivana Evans


Ivana Radosavljevic Evans
Professor in Structural/Materials Chemistry
Royal Society - Leverhulme Senior Research Fellow
Durham University
Department of Chemistry
Durham DH1 3LE, U.K.
Phone: (0191) 334-2594
www.dur.ac.uk/chemistry/research/academic-groups/i.r.evans/<http://www.dur.ac.uk/chemistry/research/academic-groups/i.r.evans/>
Twitter: @ivana_evans


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Re: Simultaneous refinement of multiple atoms sharing same site

[Jean-Marc Joubert]

Dear Ahmed,
two different things should be distinguished:
- the physical possibility do the refinement
- the mathematical way do implement the constraints in eg Fullprof

Concerning the first point, as it has already been pointed out, it is 
not possible to refine site occupancies of two atoms sharing the same 
site from a single X-ray or neutron data set. This is basically because, 
from a single dataset, you will get _one _(nuclear or electron) density 
from which you cannot get _two _site occupancies (an infinite number of 
combinations of the three elements can give the same density). However, 
this is possible if you have two datasets eg X-ray+neutron or two X--ray 
datasets, one of which using anomalous (or resonant) diffraction. In the 
two datasets, the relative contrasts between the elements should be 
different to insure higher accuracy.


Concerning the second point, yes it is possible. Let's name the three 
elements A, B and C. You may divide the atom A into two lines: A1 and 
A2. For the program, it does not matter if you have one A on position 
xyz or 0.5 A (A1) on xyz plus 0.5 A (A2) on xyz. Then you can set the 
constraints: A1 occupancy +11.00, A2 occupancy +21.00, B occupancy 
-11.00, C occupancy -21.00. Please note that it is not a restraint, it 
is a constraint maintaining the full occupancy of the site and the 
result will be exact. If the mechanism involves the distribution of A,B 
and C on different sites, the technique may be applied to constraint the 
overall composition of A, B, C. Eg. with two sites, put on the second 
site A1 -11.00, A2 -21.00, B +11.00, C +21.00. Of course, the initial 
values of the occupancies should be set correctly.


The technique has been described in my paper: J.-M. Joubert, R. Cerný, 
M. Latroche, A. Percheron-Guégan, K. Yvon, Site occupancies in LaNi5 
three-substituted compound determined by means of multiwavelength X-ray 
powder diffraction., J. Appl. Crystallogr. 31 (1998) 327-332.


And it allows to solve very complex substitution schemes such as 
refining 3 atoms distributed on 5 sites with overall composition 
constraint such as in K. Yaqoob, J.-C. Crivello, J.-M. Joubert, 
Comparison of the site occupancies determined by combined Rietveld 
refinement and by DFT calculations: the example of the ternary Mo-Ni-Re 
s phase, Inorg. Chem. 51 (5) (2012) 3071-3078.


Kind regards.
/Jean-Marc



Le 31/08/2019 à 16:44, Ahmed Subrati a écrit :

Dear all,

I wanted to ask how three atoms, sharing the same xyz position, could 
be refined in terms of their occupancies /via /FullProf. We know that 
for the case of two atoms, the first atom is set as 11.0 and the 
second one as -11.0 so that their sum is unity, but how would be the 
case for three atoms.


Thank you very much.

King regards,
Ahmed Subrati
PhD student
NanoBioMedical Centre | Adam Mickiewicz University in Poznan, Poland

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--
Jean-Marc Joubert
Chimie Métallurgique des Terres Rares
Institut de Chimie et des Matériaux Paris-Est
UMR 7182 CNRS-Université Paris-Est Créteil
2-8 rue Henri Dunant, 94320 Thiais, France
Laboratory's page:http://www.icmpe.cnrs.fr/spip.php?rubrique70
phone/fax: 33 1 49 78 13 44/12 03
Researcher ID: A-1259-2013, ORCID: -0001-7266-1850
email :joub...@icmpe.cnrs.fr  
personal page:http://www.icmpe.cnrs.fr/spip.php?article632


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Re: Simultaneous refinement of multiple atoms sharing same site

[Matthew Rowles]

Our chemical engineers like to make perovskites with about 6 elements in
two sites for their solid state fuel cells...

On Mon, 2 Sep. 2019, 16:15 Le Bail Armel,  wrote:

> If more than 2 atoms sharing the same site, then fire the chemist...
>
> Armel
> ++
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Re: Simultaneous refinement of multiple atoms sharing same site

[Le Bail Armel]

If more than 2 atoms sharing the same site, then fire the chemist...
Armel
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Re: Simultaneous refinement of multiple atoms sharing same site

[Daniel M . Többens]

Adding a little bit to the previous answers,

aside from using neutron diffraction, on can also use anomalous 
diffraction close to the absorption edge of the respective chemical 
elements. This requires a synchrotron source in most cases (unless one 
happens to have just the right exotic X-ray tube). Anomalous scattering 
changes the scattering power of the elements, too, adding extra 
information quite similar to the neutron case. In principle this can be 
done for each chemical species involved in the site disorder, thus 
allowing to refine simultaneously all occupation factors independently.


In praxis such a refinement will be ridiculously unstable in most cases.

Fullprof in particular allows, in addition to the hard parameter 
coupling you mentioned in the initial mail below, soft linear 
restraints. For this you put NLI = 1 (or higher, for multiple 
restraits), and add a CHEMCOMP line at the very end of the .pcr-file. 
This looks like this:


!  Set of  1 linear restraints:
!  Identifier, number of coeff., value, sigma / List of coeff & Parameters
Chemcomp  3   28.00    0.10  -> Current 
calculated value:    27.81

  1.  8   2.  9   1.  10

This example would be for three parameters P8, P9, P10 to be coupled in 
a way that their values are P8 + 2.0*P9 + P10 = 28.0. Negative 
multiplier are also possible. This chemcomp approach is quite flexible 
and allows to restrict the refinement to total composition or charge 
neutrality. If you use the same parameter number multiple times in your 
refinement, make sure which value is selected.


Good Luck,
Daniel Többens
On 31 Aug 2019, at 16:44, Ahmed Subrati <mailto:assubr...@hotmail.com>> wrote:


Dear all,

I wanted to ask how three atoms, sharing the same xyz position, could 
be refined in terms of their occupancies/via/FullProf. We know that 
for the case of two atoms, the first atom is set as 11.0 and the 
second one as -11.0 so that their sum is unity, but how would be the 
case for three atoms.


Thank you very much.

King regards,
Ahmed Subrati
PhD student
NanoBioMedical Centre | Adam Mickiewicz University in Poznan, Poland
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Re: Simultaneous refinement of multiple atoms sharing same site

[Ahmed Subrati]

Dear all,

Thank you very much for your prompt and kind suggestions.

Best regards,
Ahmed Subrati

From: Luca Lutterotti 
Sent: Monday, September 2, 2019 7:22 AM
To: Ahmed Subrati ; rietveld_l@ill.fr 
Subject: Re: Simultaneous refinement of multiple atoms sharing same site

With 3 atoms, as Larry and Alan explain it cannot be done unless you have 
additional info (e.g. chemical info). In our lab, if the three atoms or at 
least 2 are in the range for XRF, we do a combined XRD+XRF refinement.

Luca

---Luca 
Lutterotti
Dipartimento di Ingegneria Industriale, Universita' di Trento,
via Sommarive, 9, 38123 Trento, Italy

e-mail address : luca.luttero...@unitn.it<mailto:luca.luttero...@ing.unitn.it>
Maud page : http://maud.radiographema.com<http://maud.radiographema/>

Phone number :+39-0461-28-2414
XRD lab:: +39-0461-282434
Fax : +39-0461-28-1977





On 31 Aug 2019, at 16:44, Ahmed Subrati 
mailto:assubr...@hotmail.com>> wrote:

Dear all,

I wanted to ask how three atoms, sharing the same xyz position, could be 
refined in terms of their occupancies via FullProf. We know that for the case 
of two atoms, the first atom is set as 11.0 and the second one as -11.0 so that 
their sum is unity, but how would be the case for three atoms.

Thank you very much.

King regards,
Ahmed Subrati
PhD student
NanoBioMedical Centre | Adam Mickiewicz University in Poznan, Poland
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Re: Simultaneous refinement of multiple atoms sharing same site

[Luca Lutterotti]

With 3 atoms, as Larry and Alan explain it cannot be done unless you have 
additional info (e.g. chemical info). In our lab, if the three atoms or at 
least 2 are in the range for XRF, we do a combined XRD+XRF refinement.

Luca

---Luca 
Lutterotti
Dipartimento di Ingegneria Industriale, Universita' di Trento,
via Sommarive, 9, 38123 Trento, Italy

e-mail address : luca.luttero...@unitn.it <mailto:luca.luttero...@ing.unitn.it>
Maud page : http://maud.radiographema.com <http://maud.radiographema/>

Phone number :+39-0461-28-2414
XRD lab:: +39-0461-282434
Fax : +39-0461-28-1977





> On 31 Aug 2019, at 16:44, Ahmed Subrati  wrote:
> 
> Dear all,
> 
> I wanted to ask how three atoms, sharing the same xyz position, could be 
> refined in terms of their occupancies via FullProf. We know that for the case 
> of two atoms, the first atom is set as 11.0 and the second one as -11.0 so 
> that their sum is unity, but how would be the case for three atoms.
> 
> Thank you very much.
> 
> King regards,
> Ahmed Subrati
> PhD student
> NanoBioMedical Centre | Adam Mickiewicz University in Poznan, Poland
> ++
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> http://www.mail-archive.com/rietveld_l@ill.fr/ 
> <http://www.mail-archive.com/rietveld_l@ill.fr/>
> ++

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Re: Simultaneous refinement of multiple atoms sharing same site

[Leonid Solovyov]

>how three atoms, sharing the same xyz position, could be refined in terms of 
>their occupancies via FullProf

One of many possible options is to set 11.0 for one atom and -10.5 for the two 
others.

***
Leonid A. Solovyov
Institute of Chemistry and Chemical Technology
660036, Akademgorodok 50/24, Krasnoyarsk, Russia
http://sites.google.com/site/solovyovleonid
***






On Saturday, August 31, 2019, 9:46:50 PM GMT+7, Ahmed Subrati 
 wrote: 







Dear all,





I wanted to ask how three atoms, sharing the same xyz position, could be 
refined in terms of their occupancies via FullProf. We know that for the case 
of two atoms, the first atom is set as 11.0 and the second one as -11.0 so that 
their sum is unity, but how would be the case for three atoms.





Thank you very much.





King regards,

Ahmed Subrati


PhD student

NanoBioMedical Centre | Adam Mickiewicz University in Poznan, Poland


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Re: Simultaneous refinement of multiple atoms sharing same site

[Alan Hewat]

Even with neutron diffraction :-) you can only refine the scattering power
(length) of each site. When you refine the occupancy of two atoms on a
single site you are adding additional "information" by assuming that the
site is fully occupied by one or the other. That may be true, or not. If
the scattering power changes significantly with wavelength (or angle with
x-rays) you may obtain the necessary additional information.

But can you do a chemical or other quantitative analysis to determine the
relative proportions of eg cations ? Neutron activation analysis may also
be possible. Don't believe that everything can be determined by powder
diffraction :-)

Alan
__
   Dr Alan Hewat, NeutronOptics, Grenoble, FRANCE
   from my telephone
 +33.476.98.41.68
http://www.NeutronOptics.com/hewat
__

On Sat, 31 Aug 2019, 19:59 Larry Finger,  wrote:

> On 8/31/19 9:44 AM, Ahmed Subrati wrote:
> > Dear all,
> >
> > I wanted to ask how three atoms, sharing the same xyz position, could be
> refined
> > in terms of their occupancies /via /FullProf. We know that for the case
> of two
> > atoms, the first atom is set as 11.0 and the second one as -11.0 so that
> their
> > sum is unity, but how would be the case for three atoms.
>
> It does not matter what program you use. If you have X-ray data, and were
> to
> normalize the scattering curve for each type of atom by dividing by the
> atomic
> number, the curves would very nearly overlap. The minute differences would
> be
> the only information allowing you to determine those occupancies uniquely.
> If
> you merely constrain the sum of the occupancies, and the composition of
> the
> sample, the results will converge to nonsense results because the errors
> in the
> data would overwhelm those small differences.
>
> If you had neutron scattering data, then you might be able to do it,
> depending
> on how different the scattering for the 3 types of nuclei.
>
> Your only possibility is to add additional constraints. Perhaps average
> bond
> lengths will provide such information, or there may be other information
> available for your material. In any case, the diffraction data will not be
> sufficient for Reitveld, or single-crystal data.
>
> Larry
> ++
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> ++
>
>
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Re: Simultaneous refinement of multiple atoms sharing same site

[Larry Finger]

On 8/31/19 9:44 AM, Ahmed Subrati wrote:

Dear all,

I wanted to ask how three atoms, sharing the same xyz position, could be refined 
in terms of their occupancies /via /FullProf. We know that for the case of two 
atoms, the first atom is set as 11.0 and the second one as -11.0 so that their 
sum is unity, but how would be the case for three atoms.


It does not matter what program you use. If you have X-ray data, and were to 
normalize the scattering curve for each type of atom by dividing by the atomic 
number, the curves would very nearly overlap. The minute differences would be 
the only information allowing you to determine those occupancies uniquely. If 
you merely constrain the sum of the occupancies, and the composition of the 
sample, the results will converge to nonsense results because the errors in the 
data would overwhelm those small differences.


If you had neutron scattering data, then you might be able to do it, depending 
on how different the scattering for the 3 types of nuclei.


Your only possibility is to add additional constraints. Perhaps average bond 
lengths will provide such information, or there may be other information 
available for your material. In any case, the diffraction data will not be 
sufficient for Reitveld, or single-crystal data.


Larry
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++

Simultaneous refinement of multiple atoms sharing same site

[Ahmed Subrati]

Dear all,

I wanted to ask how three atoms, sharing the same xyz position, could be 
refined in terms of their occupancies via FullProf. We know that for the case 
of two atoms, the first atom is set as 11.0 and the second one as -11.0 so that 
their sum is unity, but how would be the case for three atoms.

Thank you very much.

King regards,
Ahmed Subrati
PhD student
NanoBioMedical Centre | Adam Mickiewicz University in Poznan, Poland
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++

RE: Mixed refinement Topas example

[Cline, James Dr. (Fed)]

François,

Somewhat more than slightly curious: Why do you want to use Topas in GUI mode?

Jim


James P. Cline
Materials Measurement Science Division  
National Institute of Standards and Technology
100 Bureau Dr. stop 8520 [ B113 / Bldg 217 ]
Gaithersburg, MD 20899-8523    USA
james.cl...@nist.gov
(301) 975 5793

-Original Message-
From: rietveld_l-requ...@ill.fr  On Behalf Of Luzia 
Germann
Sent: Friday, November 02, 2018 9:17 AM
To: rietveld_l@ill.fr
Subject: Re: Mixed refinement Topas example

Hey François,

You can find an example (with input file) on John's wonderful webpage under the 
following page:

https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fcommunity.dur.ac.uk%2Fjohn.evans%2Ftopas_workshop%2Ftutorial_combined.htmdata=02%7C01%7Cjames.cline%40nist.gov%7Cb56878acaf134a6fdd5a08d640c58634%7C2ab5d82fd8fa4797a93e054655c61dec%7C1%7C0%7C636767614451670425sdata=Yhn2S6ldVw2lvbtDMOTT%2Fza6gjO0I73iBncJDpdM1tw%3Dreserved=0

There are also other, really cool tutorials, worth checking out!

Best,
Luzia

Quoting François Goutenoire :

> Dear Rietveld users,
>
> I am starting with Topas5.0 commercial, and I would like to do a mixed 
> X-Ray-Neutron refinement directly on GUI mode.
>
> Does anyone can send me an example of *.PRO file or even an *.INP file 
> to to the refinement in launch mode.
>
> The neutron data are with constant wavelength.
>
> Thanks in advance.
>
> --
> **
> ***
> Pr. Francois GOUTENOIRE
> e-mail: francois.gouteno...@univ-lemans.fr
> Tel: 02.43.83.33.54
> FAX: 02.43.83.35.06
> Skype Entreprise visio conférence
> Département des Oxydes et Fluorures
> Institut des Molécules et des Matériaux du Mans IMMM - UMR CNRS 6283 
> Université du Maine - Avenue Olivier Messiaen
> F-72085 Le Mans Cedex 9
> FRANCE
> **
> ***
> Formation Rietveld CNRS 2019
> https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcnrsf
> ormation.cnrs.fr%2Fstage.php%3Fstage%3D19089data=02%7C01%7Cjames.
> cline%40nist.gov%7Cb56878acaf134a6fdd5a08d640c58634%7C2ab5d82fd8fa4797
> a93e054655c61dec%7C1%7C0%7C636767614451670425sdata=aYdg0gg%2FhTWw
> hBPMBfn9u5lmxXKDwNh70ZDih8OOMNk%3Dreserved=0
> Formation SAXS et Réflectivités pour couches minces et matériaux 
> nanostructurés.
> https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcnrsf
> ormation.cnrs.fr%2Fstage.php%3Fstage%3D19093data=02%7C01%7Cjames.
> cline%40nist.gov%7Cb56878acaf134a6fdd5a08d640c58634%7C2ab5d82fd8fa4797
> a93e054655c61dec%7C1%7C0%7C636767614451670425sdata=99Myif%2B0dBbc
> r1r8Plgg4y163Ma8RhxdKeE0nwbCl6k%3Dreserved=0
> Bibliographie
> https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fschol
> ar.google.fr%2Fcitations%3Fhl%3Dfr%26user%3DqC-lmN4J%26view_op%3Dl
> ist_works%26authuser%3D1%26sortby%3Dtitledata=02%7C01%7Cjames.cli
> ne%40nist.gov%7Cb56878acaf134a6fdd5a08d640c58634%7C2ab5d82fd8fa4797a93
> e054655c61dec%7C1%7C0%7C636767614451670425sdata=mjclfF1FR4s57RbKD
> Wxo44qGjopbhhQodIFwaFBP8jc%3Dreserved=0
> https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Forcid
> .org%2F-0001-5339-3002data=02%7C01%7Cjames.cline%40nist.gov%7
> Cb56878acaf134a6fdd5a08d640c58634%7C2ab5d82fd8fa4797a93e054655c61dec%7
> C1%7C0%7C636767614451670425sdata=QNZFU9f7yP419SlmuOagzo18rGclVUVv
> dxeSExIH5A0%3Dreserved=0
>
>
>
> ---
> L'absence de virus dans ce courrier électronique a été vérifiée par le 
> logiciel antivirus Avast.
> https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.a
> vast.com%2Fantivirusdata=02%7C01%7Cjames.cline%40nist.gov%7Cb5687
> 8acaf134a6fdd5a08d640c58634%7C2ab5d82fd8fa4797a93e054655c61dec%7C1%7C0
> %7C636767614451670425sdata=bepY%2FppDj96pLQ8j1swH8o2S%2BtyysqDg0O
> XEdCwVw2k%3Dreserved=0



--
Luzia S. Germann
Scientific Service Group Diffraction
Max-Planck-Institute for Solid State Research Heisenbergstr. 1
70569 Stuttgart
Germany

Phone: +49 711 689-1506

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Re: Mixed refinement Topas example

[Luzia Germann]

Hey François,

You can find an example (with input file) on John's wonderful webpage  
under the following page:


http://community.dur.ac.uk/john.evans/topas_workshop/tutorial_combined.htm

There are also other, really cool tutorials, worth checking out!

Best,
Luzia

Quoting François Goutenoire :


Dear Rietveld users,

I am starting with Topas5.0 commercial, and I would like to do a  
mixed X-Ray-Neutron refinement directly on GUI mode.


Does anyone can send me an example of *.PRO file or even an *.INP  
file to to the refinement in launch mode.


The neutron data are with constant wavelength.

Thanks in advance.

--
*
Pr. Francois GOUTENOIRE
e-mail: francois.gouteno...@univ-lemans.fr
Tel: 02.43.83.33.54
FAX: 02.43.83.35.06
Skype Entreprise visio conférence
Département des Oxydes et Fluorures
Institut des Molécules et des Matériaux du Mans
IMMM - UMR CNRS 6283
Université du Maine - Avenue Olivier Messiaen
F-72085 Le Mans Cedex 9
FRANCE
*
Formation Rietveld CNRS 2019
https://cnrsformation.cnrs.fr/stage.php?stage=19089
Formation SAXS et Réflectivités pour couches minces et matériaux  
nanostructurés.

https://cnrsformation.cnrs.fr/stage.php?stage=19093
Bibliographie
https://scholar.google.fr/citations?hl=fr=qC-lmN4J_op=list_works=1=title
https://orcid.org/-0001-5339-3002



---
L'absence de virus dans ce courrier électronique a été vérifiée par  
le logiciel antivirus Avast.

https://www.avast.com/antivirus




--
Luzia S. Germann
Scientific Service Group Diffraction
Max-Planck-Institute for Solid State Research
Heisenbergstr. 1
70569 Stuttgart
Germany

Phone: +49 711 689-1506

++
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++

Mixed refinement Topas example

[François Goutenoire]

Dear Rietveld users,

I am starting with Topas5.0 commercial, and I would like to do a mixed 
X-Ray-Neutron refinement directly on GUI mode.


Does anyone can send me an example of *.PRO file or even an *.INP file 
to to the refinement in launch mode.


The neutron data are with constant wavelength.

Thanks in advance.

--
*
Pr. Francois GOUTENOIRE
e-mail: francois.gouteno...@univ-lemans.fr
Tel: 02.43.83.33.54
FAX: 02.43.83.35.06
Skype Entreprise visio conférence
Département des Oxydes et Fluorures
Institut des Molécules et des Matériaux du Mans
IMMM - UMR CNRS 6283
Université du Maine - Avenue Olivier Messiaen
F-72085 Le Mans Cedex 9
FRANCE
*
Formation Rietveld CNRS 2019
https://cnrsformation.cnrs.fr/stage.php?stage=19089
Formation SAXS et Réflectivités pour couches minces et matériaux nanostructurés.
https://cnrsformation.cnrs.fr/stage.php?stage=19093
Bibliographie
https://scholar.google.fr/citations?hl=fr=qC-lmN4J_op=list_works=1=title
https://orcid.org/-0001-5339-3002



---
L'absence de virus dans ce courrier électronique a été vérifiée par le logiciel 
antivirus Avast.
https://www.avast.com/antivirus
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++

Re: The development of powder profile refinement...

[Larry Finger]

On 08/10/2018 10:55 AM, Alan Hewat wrote:
Thanks Henk (and Bob). It's a story that must be quite common in science. Humans 
like to simplify, and identify with heros. Humanity teaches us that we stand on 
the shoulders of others. Few discoveries, especially in science, are made by a 
single individual.


Profile Refinement was perhaps an idea "whose time had come" with the 
application of computers. But the stroke of genius was to refine the structure 
directly from the data points, rather than first refine structure factors. Even 
that may have been simply because computers at that time could only handle a 
limited number of parameters.


A fascinating story. Alan.


Henk,

I agree with Alan that you told a fascinating story, and not what I was 
expecting. It is always a temptation to give yourself more credit than an 
unbiased observer might allow. This case represents a most egregious instance.


To show the state of early computing, one of the graduate students in 
Crystallography in the Geology Department at the University of Minnesota when I 
started in 1962, was awarded a PhD for writing a computer program to calculate 
powder patterns! This was on a Univac 1103 with capabilities similar to that of 
the computer described in Bob and Henk's article. With such limited 
capabilities, you had to choose the problem with considerable care.


By the time I graduated 5 years later, the University had a CDC 6600 
"supercomputer", which had the blazing speed of 3 megaFLOPS (double precision)! 
For comparison, this is roughly the performance of an x86 machine with an 0.7 
GHz clock!!


Larry

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Re: The development of powder profile refinement...

[Alan Hewat]

Thanks Henk (and Bob). It's a story that must be quite common in science.
Humans like to simplify, and identify with heros. Humanity teaches us that
we stand on the shoulders of others. Few discoveries, especially in
science, are made by a single individual.

Profile Refinement was perhaps an idea "whose time had come" with the
application of computers. But the stroke of genius was to refine the
structure directly from the data points, rather than first refine structure
factors. Even that may have been simply because computers at that time
could only handle a limited number of parameters.

A fascinating story. Alan.

On 9 August 2018 at 12:32,  wrote:

> Bob van Laar and I wrote an article about the development of the powder
> Profile Refinement at the Reactor Centre Netherlands. This method is later
> called Rietveld refinement. We show that there were three persons involved
> in this enterprise, Bert Loopstra for the idea, Bob van Laar for the
> mathematical treatment and Hugo Rietveld for the computer program, rather
> than one. For all users of the method it will be interesting to read.
>
> The article (Acta Cryst. (2018). A74, 88-92) is Open Access and can be
> downloaded from: http://journals.iucr.org/a/issues/2018/02/00/ib5058/
> ib5058.pdf
>
> At the moment it is the most read article of Acta Cryst. A of the last 6
> months: http://178.33.252.149/a/services/mostread.html
>
> Kind greetings,
> Henk Schenk
>
__
*   Dr Alan Hewat, NeutronOptics, Grenoble, FRANCE *
 +33.476.98.41.68
http://www.NeutronOptics.com/hewat
__
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2018 Powder Diffraction & Rietveld Refinement School, Durham

[EVANS, IVANA R.]

Dear All,

The biennial Powder Diffraction & Rietveld Refinement School at Durham 
University will take place 8-12th April 2018.

The applications deadline is approaching - online applications can be submitted 
until the end of next week, 19 January 2018, at the School website: 
community.dur.ac.uk/john.evans/webpages/riet_register.htm<https://community.dur.ac.uk/john.evans/webpages/riet_register.htm>

As in previous years, we will offer a combination of lectures covering the 
theoretical aspects of powder diffraction and Rietveld refinement, 
classroom-based "by-hand" problem sessions/tutorials and extensive hands-on 
practical sessions using a variety of modern software packages.

Topics to be covered will include:

  *   Data collection strategies for X-ray and neutron diffraction
  *   Constant-wavelength and time-of-flight diffraction
  *   Modelling peak shapes (including microstructure analysis)
  *   Indexing powder patterns
  *   Rietveld, Le Bail and Pawley fitting methods
  *   X-ray and neutron combined Rietveld refinements
  *   Restrained refinements
  *   Rigid body refinements
  *   A number of more specialised and advanced optional topics (ab-initio 
structure solution, parametric and symmetry-mode refinements)

Lectures will be given by Prof. John Evans, Dr. Ivana Evans, Dr. Jeremy 
Cockcroft and Prof. Andy Fitch.

Best wishes,
Ivana Evans


Dr. Ivana Radosavljevic Evans
Associate Professor/Reader in Structural/Materials Chemistry
Durham University
Department of Chemistry
Durham DH1 3LE, U.K.
Office: CG 244
Phone: (0191) 334-2594
www.dur.ac.uk/chemistry/research/academic-groups/i.r.evans/<http://www.dur.ac.uk/chemistry/research/academic-groups/i.r.evans/>


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++

2018 Powder Diffraction & Rietveld Refinement School, Durham

[EVANS, IVANA R.]

Dear All,

The biennial Powder Diffraction & Rietveld Refinement School at Durham 
University will take place 8-12th April 2018.

As in previous years, we will offer a combination of lectures covering the 
theoretical aspects of powder diffraction and Rietveld refinement, 
classroom-based "by-hand" problem sessions/tutorials and extensive hands-on 
practical sessions using a variety of modern software packages.

Topics to be covered will include:

  *   Data collection strategies for X-ray and neutron diffraction
  *   Constant-wavelength and time-of-flight diffraction
  *   Modelling peak shapes (including microstructure analysis)
  *   Indexing powder patterns
  *   Rietveld, Le Bail and Pawley fitting methods
  *   X-ray and neutron combined Rietveld refinements
  *   Restrained refinements
  *   Rigid body refinements
  *   A number of more specialised and advanced optional topics (ab-initio 
structure solution, parametric and symmetry-mode refinements)

Lectures will be given by Prof. John Evans, Dr. Ivana Evans, Dr. Jeremy 
Cockcroft and Prof. Andy Fitch.

Online applications can be submitted until 19 January 2018 at the Powder 
Diffraction & Rietveld Refinement School 2018 website: 
community.dur.ac.uk/john.evans/webpages/riet_register.htm<https://community.dur.ac.uk/john.evans/webpages/riet_register.htm>

Best wishes,
Ivana Evans


Dr. Ivana Radosavljevic Evans
Associate Professor/Reader in Structural/Materials Chemistry
Durham University
Department of Chemistry
Durham DH1 3LE, U.K.
Office: CG 244
Phone: (0191) 334-2594
www.dur.ac.uk/chemistry/research/academic-groups/i.r.evans/<http://www.dur.ac.uk/chemistry/research/academic-groups/i.r.evans/>


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++

Announcement of 2017 school "Modern Methods in Rietveld Refinement and Structural Analysis"

[Khalifah, Peter]

We are pleased to announce that the third annual "Modern Methods in Rietveld 
Refinement for Structural Analysis" school will be held from June 18-23, 2017, 
at Oak Ridge National Laboratory in close partnership with the Shull-Wollan 
Center Joint Institute for Neutron Sciences (University of Tennessee and ORNL) 
and Bruker-AXS.

The primary goal of this school is to teach participants Rietveld refinement 
and other methods for evaluating crystal structures from powder diffraction 
data with an emphasis on data collected on US national user facility beamlines 
optimized for structural analysis such as the 11-BM, 17-BM, and 11-ID-B 
synchrotron beamlines at the APS of Argonne National Laboratory, the POWGEN and 
NOMAD time-of-flight neutron diffraction beamlines at the SNS of Oak Ridge 
National Laboratory, and the XPD synchrotron beamline at the NSLS-II of BNL.  
The combination of advances in instrumentation and in software algorithms now 
allow many challenging structural problems to be resolved solely from powder 
diffraction data, and an up-to-date instruction in modern methods will be 
provided.  This course will emphasize traditional solid state compounds 
(non-molecular), and will use the TOPAS software as the platform for Rietveld 
refinement (complementary trial license will be provided to participants).

There will be a special secondary emphasis this year on the complementary use 
of pair distribution function (PDF) data to carry out small-box refinements for 
average unit cells, highlighting the new functionality of the TOPAS software to 
carry out both Rietveld and PDF refinements.  Both NOMAD (neutron PDF) and 
11-ID-B (synchrotron PDF) beamline scientists will be present as instructors at 
the course, and there will be an opportunity for participants to have data 
suitable for both Rietveld and PDF refinement collected on their own sample at 
both synchrotron and neutron beamlines.

Confirmed 2017 instructors include Prof. Peter Khalifah (SBU), Prof. Cora Lind 
(U. Toledo), Dr. Katharine Page (ORNL, NOMAD), Dr. Ashfia Huq (ORNL, POWGEN), 
Dr. Jue Liu (ORNL), Dr. Karena Chapman (ANL, 11-ID-B), Dr. Saul Lapidus (ANL, 
11-BM), Dr. Wenqian Xu (ANL, 17-BM), and Dr. Nathan Henderson (Bruker-AXS).

Further general information about the course is available through the website: 
https://sites.google.com/a/stonybrook.edu/mmrrsa-portal/. The application for 
this year can be directly accessed at: http://conference.sns.gov/mmrrsa.

There will be no registration fee associated with this course.  There are 
ongoing fundraising efforts to additionally support some or all of the lodging 
and meal expenses of most or all participants in this program.  All travel 
expenses will be the responsibility of participants.

While this course is open to all applicants, priority will be given to Ph.D. 
students and post-doctoral researchers from North American institutions.  
Completed applications should be received by March 31, 2017, although later 
applications may still be considered.


Dr. Peter Khalifah, kp...@bnl.gov<mailto:kp...@bnl.gov>

Associate ProfessorChemist
Dept. of Chemistry Dept. of Chemistry
Stony Brook University Brookhaven National Laboratory
Stony Brook, NY 11794-3400 Upton, NY 11973-5000

Office: 447 Grad. ChemistryOffice: Bldg 555, Rm 340
Phone: (631)632-7796   Phone: (631)344-7689
Fax: (631)632-7960 Fax: (631)344-5815
Web page: https://sites.google.com/a/stonybrook.edu/pgk/home

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++

RE: Refinement of birnessite type layered manganese oxides

[Marine Reynaud]

Dear Nadya, 

I would recommend the use of the program FAULTS to refine powder diffraction 
data of your birnessite-type layered manganese oxides containing stacking 
faults. 

FAULTS is indeed a program developed for the refinement of diffraction data of 
materials with planar defects, and in particular layered materials having 
stacking faults. This program is included in the FullProf Suite 
(https://www.ill.eu/sites/fullprof/ ) and it is also available as a separate 
program at this webpage:  http://www.cicenergigune.com/faults .

We have recently published a paper describing the program FAULTS, including 
several examples of refinements: in particular a sample layered oxide Li2PtO3 
which presents stacking faults and a sample of gamma-MnO2 which is an 
intergrowth of pyrolusite and ramsdellite structures. You can find this article 
here: http://scripts.iucr.org/cgi-bin/paper?kc5049 (Casas-Cabanas et al. J 
Appl. Cryst 216, 49, p2259-2269).

If you need more information about FAULTS, or some support, do not hesitate to 
contact us at fau...@cicenergigune.com 

Best regards

Marine 


Marine Reynaud
Post-Doctoral Researcher
Structure and Surface Analysis

CIC Energigune
Parque Tecnológico
C/ Albert Einstein, 48
01510 Miñano (Álava)
Spain

Tel: +34 945 297 108 or +34 911 922 137 ext. 380
E-mail: mreyn...@cicenergigune.com

www.cicenergigune.com


-Mensaje original-
De: rietveld_l-requ...@ill.fr [mailto:rietveld_l-requ...@ill.fr] En nombre de 
GREGORKIEWITZ MICHAEL Enviado el: martes, 17 de enero de 2017 16:50
Para: Nayda Patricia Arias Duque
CC: rietveld_l@ill.fr
Asunto: Re: Refinement of birnessite type layered manganese oxides

dear Nayda,

a bit late, but may be still useful for you:

we worked on Rietveld refinement of a birnessite impurity considering various 
stacking types - without much success, but in our ms you can find references to 
different models, and a quite surprising result for our "birnessite" sample.

Our article is free access and can be found in Acta Cryst B dec 2016 or on 
researchgate.

Best

Miguel


---
michele gregorkiewitz
Dip Scienze Fisiche, della Terra e dell'Ambiente Università di Siena via 
Laterina 8, I-53100 Siena gre...@unisi.it, +39'0577'233810


Il 2016-12-22 00:51 Nayda Patricia Arias Duque ha scritto:
> Hello .
> 
> I am trying to refine birnessite type layered manganese oxides and I 
> want to know how can I identify stacking faults on this type of 
> materials?.
> 
> Thank you in advance for your information,
> 
> Best Regards and Merry Christmas
> 
> Nayda Patricia Arias Duque
> PhD Candidate in Chemical Engineering
> Nanostructured and Functional Materials Laboratory National University 
> of Colombia- Manizales Campus www.unal.edu.co [1]
> 
> Links:
> --
> [1] http://www.unal.edu.co
> ++
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> <alan.he...@neutronoptics.com> Send commands to <lists...@ill.fr> eg:
> HELP as the subject with no body text The Rietveld_L list archive is 
> on http://www.mail-archive.com/rietveld_l@ill.fr/
> ++
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++

Re: Refinement of birnessite type layered manganese oxides

[GREGORKIEWITZ MICHAEL]

dear Nayda,

a bit late, but may be still useful for you:

we worked on Rietveld refinement of a birnessite impurity considering 
various stacking types - without much success, but in our ms you can 
find references to different models, and a quite surprising result for 
our "birnessite" sample.


Our article is free access and can be found in Acta Cryst B dec 2016 or 
on researchgate.


Best

Miguel


---
michele gregorkiewitz
Dip Scienze Fisiche, della Terra e dell'Ambiente
Università di Siena
via Laterina 8, I-53100 Siena
gre...@unisi.it, +39'0577'233810


Il 2016-12-22 00:51 Nayda Patricia Arias Duque ha scritto:

Hello .

I am trying to refine birnessite type layered manganese oxides and I
want to know how can I identify stacking faults on this type of
materials?.

Thank you in advance for your information,

Best Regards and Merry Christmas

Nayda Patricia Arias Duque
PhD Candidate in Chemical Engineering
Nanostructured and Functional Materials Laboratory
National University of Colombia- Manizales Campus
www.unal.edu.co [1]

Links:
--
[1] http://www.unal.edu.co
++
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++
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++

Refinement of birnessite type layered manganese oxides

[Nayda Patricia Arias Duque]

Hello .

I am trying to refine birnessite type layered manganese oxides and I want
to know how can I identify stacking faults on this type of materials?.

Thank you in advance for your information,

Best Regards and Merry Christmas

Nayda Patricia Arias Duque
PhD Candidate in Chemical Engineering
Nanostructured and Functional Materials Laboratory
National University of Colombia- Manizales Campus
www.unal.edu.co
++
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++

Second announcement: Powder Diffraction & Rietveld Refinement School, Durham 2016

[EVANS I.R.]

Dear All,

The biennial Powder Diffraction & Rietveld Refinement School at Durham 
University will take place 10-14th April 2016.

As in previous years, we will offer a combination of lectures covering the 
theoretical aspects of powder diffraction and Rietveld refinement, 
classroom-based "by-hand" problem sessions/tutorials and extensive hands-on 
practical sessions using a variety of modern software packages. Topics to be 
covered will include:

  *   Data collection strategies for X-ray and neutron diffraction
  *   Constant wavelength and time of flight diffraction
  *   Modelling peak shapes (including microstructure analysis)
  *   Indexing powder patterns
  *   Rietveld, Le Bail and Pawley fitting methods
  *   X-ray and neutron combined Rietveld refinements
  *   Restrained refinements
  *   Rigid body refinements
  *   A number of more specialised and advanced optional topics (ab-initio 
structure solution, parametric and symmetry-mode refinements)

Lectures will be given by Prof. John Evans, Dr. Ivana Evans, Dr. Jeremy 
Cockcroft and Prof. Andy Fitch.

Online applications can be submitted until 22nd January 2016, at the Powder 
Diffraction & Rietveld Refinement School 2016 website: 
http://community.dur.ac.uk/john.evans/webpages/pdrr_school_2016.htm

Best wishes,
Ivana Evans


Dr. Ivana Radosavljevic Evans
Reader in Structural/Materials Chemistry
Department of Chemistry
Durham University
Durham DH1 3LE, U.K.
Office: CG 244
Phone: (0191) 334-2594
Fax: (0191) 384-4737
www.dur.ac.uk/chemistry/research/academic-groups/i.r.evans/<http://www.dur.ac.uk/chemistry/research/academic-groups/i.r.evans/>


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++

2016 Powder Diffraction & Rietveld Refinement School, Durham

[EVANS I.R.]

Dear All,

The biennial Powder Diffraction & Rietveld Refinement School at Durham 
University will take place 10-14th April 2016.

As in previous years, we will offer a combination of lectures covering the 
theoretical aspects of powder diffraction and Rietveld refinement, 
classroom-based "by-hand" problem sessions/tutorials and extensive hands-on 
practical sessions using a variety of modern software packages.
Topics to be covered will include:

  *   Data collection strategies for X-ray and neutron diffraction
  *   Constant wavelength and time of flight diffraction
  *   Modelling peak shapes (including microstructure analysis)
  *   Indexing powder patterns
  *   Rietveld, Le Bail and Pawley fitting methods
  *   X-ray and neutron combined Rietveld refinements
  *   Restrained refinements
  *   Rigid body refinements
  *   A number of more specialised and advanced optional topics (ab-initio 
structure solution, parametric and symmetry-mode refinements)

Lectures will be given by Prof. John Evans, Dr. Ivana Evans, Dr. Jeremy 
Cockcroft and Prof. Andy Fitch.

Online applications can be submitted until 22nd January 2016, at the Powder 
Diffraction & Rietveld Refinement School 2014 website: 
http://community.dur.ac.uk/john.evans/webpages/pdrr_school_2016.htm

Best wishes,
Ivana Evans


Dr. Ivana Radosavljevic Evans
Reader in Structural/Materials Chemistry
Department of Chemistry
Durham University
Durham DH1 3LE, U.K.
Office: CG 244
Phone: (0191) 334-2594
Fax: (0191) 384-4737
www.dur.ac.uk/chemistry/research/academic-groups/i.r.evans/<http://www.dur.ac.uk/chemistry/research/academic-groups/i.r.evans/>


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++

Need Your Help in Structure Refinement

[Sirous Khabbazabkenar (Student)]

Dear All,

Hope my e-mail finds you well.

I am a beginner in Rietveld Analysis and I am working on structure
refinement of my powder diffraction data.

For structure refinement of my XRD data ( taken from pure ZnO powder) what
I realized is, I should perform a Pawley refinement. It actually gives me
some refined lattice parameters that I have to use them in the next step
i.e refining the atomic positions. Therefore, I am under the assumption
that once I performe a pawley refinement, then I have to save it as an
input file to use in the lunch mode. right?

One of my basic questions ( sorry if it is too basic) is that  when I want
to start refining the atomic positions, should I already create the rigid
body myself in the editor section of the TOPAS? or it will be created by
its own when I use my Pawley refinement results in the lunch mode?

If I need to create the rigid body myself, then how can I make the created
rigid body to be refined when I start the refinement in TOPAS?

I was wondering if any of you could explain how to take the last step i.e
refining the general atomic positions using my previous pawley refinement
results.

Thanks in advance,
Sirous.

-- 
*Sirous Khabbaz Abkenar*

*Ph.D. Student, Materials Science  Engineering,*
*Faculty of Engineering and Natural Sciences,*
*Sabanci University,*
*Tuzla, Istanbul, 34956 Turkey*
*khabbazabke...@sabanciuniv.edu khabbazabke...@sabanciuniv.edu*
*Tell: +90 507 094 7291 %2B90%20507%20094%207291*
++
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++

RE: information for rietveld refinement

[Sitepu, Husinsyah]

Dear All,

Could you please provide the information on low density materials, which has a 
specific gravity from 0.2 to 0.5 (or. The density 0.2 to 0.5 gr/cc).

If you are aware the crystal structure of date seed powder, could you please 
send it to me.

Thanks, and best wishes

Husin


Husin Sitepu, 
PhDhttp://scholar.google.com/citations?hl=enuser=cUTV8HkJview_op=list_workspagesize=100
Saudi Aramco
Research and Development Center
Technical Services Division
Advanced Analysis Unit
Bld. 2296, Room: GB-110
Phone: 876-3050
Email: sitep...@aramco.commailto:sitep...@aramco.com
http://scholar.google.com/citations?hl=enuser=cUTV8HkJview_op=list_workspagesize=100




From: alan.he...@gmail.com [mailto:alan.he...@gmail.com] On Behalf Of Alan Hewat
Sent: Wednesday, July 16, 2014 9:43 AM
To: rietveld_l@ill.fr
Subject: Re: information for rietveld refinement

 Im student researcher I need  a guidelines for refinement structure double 
 perovskite
 using fullprof or other software in case to reduce Factors and than draw 
 structures

Dear Colleague.

It is difficult to reply to such a general query. You could start by reading 
the FullProf manual and tutorials on 
https://www.ill.eu/sites/fullprof/php/tutorials.html :-)

The first question is the symmetry (space group). Do a google search for:
https://www.google.com/webhp?q=%22double+perovskite%22+symmetry
Then look in particular at the free articles on http://www.researchgate.net/ 
(3rd link)

To search for examples of double perovskites, try http://www.ill.fr/ Log on as 
demo and search for Element=O6 and ElementCount=3 i.e.
http://icsd.ill.eu/icsd/index.php?action=Searchelements=o6elementc=3

If you then click on the formula eg Cu (Nb2 O6) the structure will be drawn 
using Java in a new window. (You must install Java in your browser and give it 
permission to run).

You can download the CIF files, calculate bond lengths, draw the powder 
patterns etc by clicking on those buttons.

I hope this will get you started, but then I suggest you join the Rietveld 
mailing list, which has over 1000 members who can advise you about specific 
problems. To join, send an email to lists...@ill.frmailto:lists...@ill.fr 
with the title:
SUBSCRIBE Rietveld_L your name and lab

With kind regards, Alan Hewat (Rietveld list manager)
__
   Dr Alan Hewat, NeutronOptics, Grenoble, FRANCE
alan.he...@neutronoptics.commailto:alan.he...@neutronoptics.com 
+33.476.98.41.68
http://www.NeutronOptics.com/hewat
__



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This Email may not be disclosed or forwarded to anyone else without 
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Email in error, please notify the sender immediately and delete all copies from 
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++

Re: Quantification and rietveld refinement

[gwilherm . nenert]

Dear Nelson Duarte,

Within the help system of HighScore Plus you will find various tutorial 
examples about Rietveld analyses.
Just press the F1-key at any stage in the program to invoke the help 
system.

These tutorials will guide you step by step.  In particular I would 
recommend you to look at the following chapters within the help file:
6. Analysis/Rietveld Analysis and 8. Practical/ Practice Rietveld analysis

We tried to contact you personally by email, but have not yet received an 
answer. 
Please feel free to contact your local PANAlytical representatives at any 
time, they will help you further or will get you in touch with a 
specialist. 

Sincerely yours,

Gwilherm Nénert 
  
Gwilherm Nénert - Product Marketing XRD 
 
PANalytical B.V. 
Lelyweg 1 (7602 EA) 
PO Box 13 
7600 AA Almelo 
CoC Registration No. 06069492, Enschede, The Netherlands 
T   +31 546 534 520
M   +31 612726178
gwilherm.nen...@panalytical.com
www.panalytical.com


 PANalytical
get insight  

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If you are not the intended recipient, you are hereby notified that any 
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From:   Nelson nelson.dua...@ipn.pt
To: rietveld_l@ill.fr, 
Date:   09/05/2014 06:47 PM
Subject:Quantification and rietveld refinement
Sent by:rietveld_l-requ...@ill.fr



Dear rietvelds
 
I have some samples, all with the same two phases: alumina and crocoite 
(PbCrO4) (electrochemical bath). I use Cobalt radiation. Indexing, I use 
always the same two ICDD files, 74-0323 for alumina and 73-1332 for 
crocoite. I use software High score plus. Can i use the semiquantification 
of software for know the quantification of each phase betwen the samples.
Wuhere i can find the right cif files for this two phases, for introduce 
in High score plus and made Rietveld refinement.
Where i can find a manual or exemples of how to make a rietveld refinement 
of this XRD.
I don´t have experience of rietveld analysis.
 
Thanks in advances 
Best regrds
Nelson++
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text
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http://www.mail-archive.com/rietveld_l@ill.fr/
++


++
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++

RE: Quantification and rietveld refinement

[Whitfield, Pamela S.]

You would be well advised to do some background reading on microabsorption as 
it will be pretty bad with those two phases and limit the accuracy you may 
realistically expect in your quantification

Pam

From: rietveld_l-requ...@ill.fr [mailto:rietveld_l-requ...@ill.fr] On Behalf Of 
Nelson
Sent: Friday, September 05, 2014 12:44 PM
To: rietveld_l@ill.fr
Subject: Quantification and rietveld refinement

Dear rietvelds

I have some samples, all with the same two phases: alumina and crocoite 
(PbCrO4) (electrochemical bath). I use Cobalt radiation. Indexing, I use always 
the same two ICDD files, 74-0323 for alumina and 73-1332 for crocoite. I use 
software High score plus. Can i use the semiquantification of software for know 
the quantification of each phase betwen the samples.
Wuhere i can find the right cif files for this two phases, for introduce in 
High score plus and made Rietveld refinement.
Where i can find a manual or exemples of how to make a rietveld refinement of 
this XRD.
I don´t have experience of rietveld analysis.

Thanks in advances
Best regrds
Nelson
++
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++

Quantification and rietveld refinement

[Nelson]

Dear rietvelds

 

I have some samples, all with the same two phases: alumina and crocoite
(PbCrO4) (electrochemical bath). I use Cobalt radiation. Indexing, I use
always the same two ICDD files, 74-0323 for alumina and 73-1332 for
crocoite. I use software High score plus. Can i use the semiquantification
of software for know the quantification of each phase betwen the samples.

Wuhere i can find the right cif files for this two phases, for introduce in
High score plus and made Rietveld refinement.

Where i can find a manual or exemples of how to make a rietveld refinement
of this XRD.

I don´t have experience of rietveld analysis.

 

Thanks in advances 

Best regrds

Nelson

++
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Send commands to lists...@ill.fr eg: HELP as the subject with no body text
The Rietveld_L list archive is on http://www.mail-archive.com/rietveld_l@ill.fr/
++

Re: Quantification and rietveld refinement

[Leopoldo Suescun]

Prezado Nelson,

You can find CIF files for both alumina and crocoite phases at the
Crystallography Open Database (www.crystallography.net) looking for
chemical elements.

An excellent set of educational material on Rietveld refinement using
GSAS+EXPGUI at the APS-11BM site (
http://www.aps.anl.gov/Xray_Science_Division/Powder_Diffraction_Crystallography/)
and additional resources at http://11bm.xray.aps.anl.gov/resources.html.

If you don´t have experience with Rietveld analysis and no-one to ask for
advice it may be a painful path to walk alone but there are many books that
can be of help such as The Rietveld Method by RA Young or Fundamentals
of Powder Diffraction and Structural Characterization of Materials by
Pescharsky and Zavalij... but attending a Rietveld course (such as ICDD
Clinics for example) may be of help to start.

Finally, but maybe of advanced level, be very careful when extracting
weight percentages for both phases from your refinements, if you don´t have
perfect control or knowledge of particle sizes for both phases, since the
huge difference in absorption coefficients among them may make
microabsorption an issue on your quantification work.

Best of luck
Leo




2014-09-05 13:43 GMT-03:00 Nelson nelson.dua...@ipn.pt:

 Dear rietvelds



 I have some samples, all with the same two phases: alumina and crocoite
 (PbCrO4) (electrochemical bath). I use Cobalt radiation. Indexing, I use
 always the same two ICDD files, 74-0323 for alumina and 73-1332 for
 crocoite. I use software High score plus. Can i use the semiquantification
 of software for know the quantification of each phase betwen the samples.

 Wuhere i can find the right cif files for this two phases, for introduce
 in High score plus and made Rietveld refinement.

 Where i can find a manual or exemples of how to make a rietveld refinement
 of this XRD.

 I don´t have experience of rietveld analysis.



 Thanks in advances

 Best regrds

 Nelson

 ++
 Please do NOT attach files to the whole list alan.he...@neutronoptics.com
 
 Send commands to lists...@ill.fr eg: HELP as the subject with no body
 text
 The Rietveld_L list archive is on
 http://www.mail-archive.com/rietveld_l@ill.fr/
 ++





-- 
Dr. Leopoldo Suescun
Prof. Agr (Assoc. Prof.) de Física   Tel: (+598) 29290705/29249859
Cryssmat-Lab./DETEMA Fax: (+598) 29241906*
Facultad de Quimica, Universidad de la Republica
  ,_.
  |  \
  |   v-
 ,' \
 |  (
 \__Montevideo, Uruguay

En pleno disfrute del Año Internacional de la Cristalografía 2014 (
http://www.iycr2014.org ),  (http://www.cristalografia2014.fq.edu.uy)
++
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++

Re: Quantification and rietveld refinement

[David L. Bish]

Dear Nelson,

You can also often find structures of interest in the American 
Mineralogist Crystal Structure database 
(http://rruff.geo.arizona.edu/AMS/amcsd.php). Both of your phases are 
listed numerous times in this data base, and you can download cif files. 
The database is freely available.


Regards,

Dave

On 9/5/2014 1:34 PM, Leopoldo Suescun wrote:

Prezado Nelson,

You can find CIF files for both alumina and crocoite phases at the 
Crystallography Open Database (www.crystallography.net 
http://www.crystallography.net) looking for chemical elements.


An excellent set of educational material on Rietveld refinement using 
GSAS+EXPGUI at the APS-11BM site 
(http://www.aps.anl.gov/Xray_Science_Division/Powder_Diffraction_Crystallography/) 
and additional resources at http://11bm.xray.aps.anl.gov/resources.html.


If you don´t have experience with Rietveld analysis and no-one to ask 
for advice it may be a painful path to walk alone but there are many 
books that can be of help such as The Rietveld Method by RA Young or 
Fundamentals of Powder Diffraction and Structural Characterization of 
Materials by Pescharsky and Zavalij... but attending a Rietveld 
course (such as ICDD Clinics for example) may be of help to start.


Finally, but maybe of advanced level, be very careful when extracting 
weight percentages for both phases from your refinements, if you don´t 
have perfect control or knowledge of particle sizes for both phases, 
since the huge difference in absorption coefficients among them may 
make microabsorption an issue on your quantification work.


Best of luck
Leo




2014-09-05 13:43 GMT-03:00 Nelson nelson.dua...@ipn.pt 
mailto:nelson.dua...@ipn.pt:


Dear rietvelds

I have some samples, all with the same two phases: alumina and
crocoite (PbCrO4) (electrochemical bath). I use Cobalt radiation.
Indexing, I use always the same two ICDD files, 74-0323 for
alumina and 73-1332 for crocoite. I use software High score plus.
Can i use the semiquantification of software for know the
quantification of each phase betwen the samples.

Wuhere i can find the right cif files for this two phases, for
introduce in High score plus and made Rietveld refinement.

Where i can find a manual or exemples of how to make a rietveld
refinement of this XRD.

I don´t have experience of rietveld analysis.

Thanks in advances

Best regrds

Nelson


++
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HELP as the subject with no body text
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++





--
Dr. Leopoldo Suescun
Prof. Agr (Assoc. Prof.) de Física   Tel: (+598) 29290705/29249859
Cryssmat-Lab./DETEMA Fax: (+598) 29241906*
Facultad de Quimica, Universidad de la Republica
  ,_.
  |  \
  |   v-
 ,' \
 |  (
 \__Montevideo, Uruguay

En pleno disfrute del Año Internacional de la Cristalografía 2014 
(http://www.iycr2014.org ),  (http://www.cristalografia2014.fq.edu.uy)


--
David L. Bish
Department of Geological Sciences
Indiana University
1001 E. 10th St.
Bloomington, IN 47405
812-855-2039

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++

Re: information for rietveld refinement

[Alan Hewat]

 Im student researcher I need  a guidelines for refinement structure
double perovskite
 using fullprof or other software in case to reduce Factors and than draw
structures

Dear Colleague.

It is difficult to reply to such a general query. You could start by
reading the FullProf manual and tutorials on
https://www.ill.eu/sites/fullprof/php/tutorials.html :-)

The first question is the symmetry (space group). Do a google search for:
https://www.google.com/webhp?q=%22double+perovskite%22+symmetry
Then look in particular at the free articles on http://www.researchgate.net/
(3rd link)

To search for examples of double perovskites, try http://www.ill.fr/ Log on
as demo and search for Element=O6 and ElementCount=3 i.e.
http://icsd.ill.eu/icsd/index.php?action=Searchelements=o6elementc=3

If you then click on the formula eg Cu (Nb2 O6) the structure will be drawn
using Java in a new window. (You must install Java in your browser and give
it permission to run).

You can download the CIF files, calculate bond lengths, draw the powder
patterns etc by clicking on those buttons.

I hope this will get you started, but then I suggest you join the Rietveld
mailing list, which has over 1000 members who can advise you about specific
problems. To join, send an email to lists...@ill.fr with the title:
SUBSCRIBE Rietveld_L your name and lab

With kind regards, Alan Hewat (Rietveld list manager)
__
*   Dr Alan Hewat, NeutronOptics, Grenoble, FRANCE *
alan.he...@neutronoptics.com +33.476.98.41.68
http://www.NeutronOptics.com/hewat
__
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++

RE: Site occupancies refinement (Many Thanks)

[NAVEED ZAFAR]

Dear Dr Peter Stephens, Dr. Martin Fisch and Dr. Noberto Masciocchi,
Many thanks for your reply and useful tips.In particularcomments from Dr. 
Noberto M. and for sparing time in rearranging my .INP file.
Best regards,
Dr Naveed Zafar Ali

Subject: Re: Site occupancies refinement
Date: Mon, 28 Apr 2014 08:00:50 -0400
From: peter.steph...@stonybrook.edu
To: naveed...@hotmail.com
CC: rietveld_l@ill.fr

You seem to be confusing beq (thermal parameter) with site occupancy.  At a 
start, I would think that the site would have the same thermal parameter for 
either atom, and refine occupancies that sum to unity.  For example,
site A1 occ Fe feocc .9 x 0 y 0 z Az .055 beq Abeq 2site A2 occ Ru =1-feocc; x 
0 y 0 z  =Az; beq =Abeq;will put Fe and Ru in the same site, refine the iron 
occupancy (feocc), common z coordinate (Az), and give them the same isotropic 
thermal parameter (Abeq).
You could imagine that the lighter atom could have a larger thermal parameter, 
but it would be very hard to determine that from powder data because it would 
be strongly correlated with site occupancy, etc.

**Peter W. StephensProfessor, Department of Physics and 
AstronomyAssociate Dean for Curriculum, College of Arts and Sciences
Stony Brook University(631) 
632-8156http://mini.physics.sunysb.edu/~pstephensPlease update your records to 
my new email: peter.steph...@stonybrook.edu



On Mon, Apr 28, 2014 at 7:39 AM, NAVEED ZAFAR naveed...@hotmail.com wrote:






Dear Rietvelders, I was actually doing the site (occupancy) refinement using 
TOPAS 4.1 software.While studying the effect of doping on one crystallographic 
site.

We normally refine the sites of interest employ the following 
methodology.Consider e.g., Pervoskite structure (ABO3) as an example.If we wish 
to dope the A site in ABO3,
and to confirm whether doping was successful or not, we normally refinethe 
occupancies in the following way.
For example.We refine occupancies like occupancy of original site A   =beq1
occupancy of dopant   site A`  
=1-beq1
If the refinemnent goes well, all the crystallogrhic occupancies should merge 
to a single constant value,
those crystallographic sites which are fully occupied should give [occ=1] and 
those doped should yield net occupancies [occ (A + A`= 1].
Can anyone share or suggest,why the Beq (isotropic temperature factor) values 
are going to huge,??
at the end of such a refinement. Which otherwise should be around [ 
Beq=Uiso*8pi^2].
Also if possible share  .pro file (GUI mode or Launch mode) of such a 
refinemnet or some literature.

Best regards,Dr. Naveed Zafar Ali
  

++

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++





  ++
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++

Site occupancies refinement

[NAVEED ZAFAR]

Dear Rietvelders, I was actually doing the site (occupancy) refinement using 
TOPAS 4.1 software.While studying the effect of doping on one crystallographic 
site.
We normally refine the sites of interest employ the following 
methodology.Consider e.g., Pervoskite structure (ABO3) as an example.If we wish 
to dope the A site in ABO3,and to confirm whether doping was successful or not, 
we normally refinethe occupancies in the following way.
For example.We refine occupancies like occupancy of original site A   =beq1 
occupancy of dopant   site A`  =1-beq1
If the refinemnent goes well, all the crystallogrhic occupancies should merge 
to a single constant value,those crystallographic sites which are fully 
occupied should give [occ=1] and those doped should yield net occupancies [occ 
(A + A`= 1].
Can anyone share or suggest,why the Beq (isotropic temperature factor) values 
are going to huge,??at the end of such a refinement. Which otherwise should be 
around [ Beq=Uiso*8pi^2].
Also if possible share  .pro file (GUI mode or Launch mode) of such a 
refinemnet or some literature.
Best regards,Dr. Naveed Zafar Ali
  ++
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Send commands to lists...@ill.fr eg: HELP as the subject with no body text
The Rietveld_L list archive is on http://www.mail-archive.com/rietveld_l@ill.fr/
++

Re: Site occupancies refinement

[Peter Stephens]

You seem to be confusing beq (thermal parameter) with site occupancy.  At a
start, I would think that the site would have the same thermal parameter
for either atom, and refine occupancies that sum to unity.  For example,
site A1 occ Fe feocc .9 x 0 y 0 z Az .055 beq Abeq 2
site A2 occ Ru =1-feocc; x 0 y 0 z  =Az; beq =Abeq;
will put Fe and Ru in the same site, refine the iron occupancy (feocc),
common z coordinate (Az), and give them the same isotropic thermal
parameter (Abeq).
You could imagine that the lighter atom could have a larger thermal
parameter, but it would be very hard to determine that from powder data
because it would be strongly correlated with site occupancy, etc.


**
Peter W. Stephens
Professor, Department of Physics and Astronomy
Associate Dean for Curriculum, College of Arts and Sciences
Stony Brook University
(631) 632-8156
http://mini.physics.sunysb.edu/~pstephens
Please update your records to my new email: peter.steph...@stonybrook.edu


On Mon, Apr 28, 2014 at 7:39 AM, NAVEED ZAFAR naveed...@hotmail.com wrote:



 *Dear Rietvelders,*
  I was actually doing the site (occupancy) refinement using TOPAS 4.1
 software.
 While studying the effect of doping on one crystallographic site.

 We normally refine the sites of interest employ the following methodology.
 Consider e.g., Pervoskite structure (ABO3) as an example.
 If we wish to dope the A site in ABO3,
 and to confirm whether doping was successful or not, we normally refine
 the occupancies in the following way.

 For example.
 We refine occupancies like occupancy of original site A   =beq1
 occupancy of dopant   site A`  =1-beq1

 If the refinemnent goes well, all the crystallogrhic occupancies
 should merge to a single constant value,
 those crystallographic sites which are fully occupied should give [occ=1]
 and those doped should yield net occupancies [occ (A + A`= 1].

 Can anyone share or suggest,
 why the Beq (isotropic temperature factor) values are going to huge,??
 at the end of such a refinement. Which otherwise should be around [
 Beq=Uiso*8pi^2].

 Also if possible share  .pro file (GUI mode or Launch mode) of such a
 refinemnet or some literature.

 Best regards,
 *Dr. Naveed Zafar Ali*


 ++
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 text
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 http://www.mail-archive.com/rietveld_l@ill.fr/
 ++



++
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++

Powder Diffraction and Rietveld Refinement School, Durham 2014

[EVANS I.]

Dear All,

The biennial Powder Diffraction  Rietveld Refinement School will take place at 
Durham University, 30th March - 3rd April March 2014.

As in previous years, the course will offer a combination of lectures covering 
the theoretical aspects of powder diffraction and Rietveld refinement, problem 
sessions/tutorials and extensive hands-on practical sessions using a variety of 
modern software packages.
Topics to be covered will include:

  *   Data collection strategies for X-ray and neutron diffraction
  *   Constant wavelength and time of flight diffraction
  *   Modelling peak shapes
  *   Indexing powder patterns
  *   Rietveld, Le Bail and Pawley fitting methods
  *   X-ray and neutron combined Rietveld refinement
  *   Restrained refinements
  *   Rigid body refinements

Lectures will be given by Prof. John Evans, Dr. Ivana Evans, Dr. Jeremy 
Cockcroft and Prof. Andy Fitch.

For any information not covered on the School website please contact Ivana 
Evans 
(ivana.radosavlje...@durham.ac.ukmailto:ivana.radosavlje...@durham.ac.uk).

Online applications can be submitted until 20th January 2014 at the Powder 
Diffraction  Rietveld Refinement School 2014 website: 
http://community.dur.ac.uk/john.evans/webpages/pdrr_school_2014.htm.


Best wishes,
Ivana Evans



Dr. Ivana Radosavljevic Evans
Senior Lecturer in Structural/Materials Chemistry
Department of Chemistry
Durham University
Durham DH1 3LE, U.K.
Office: CG 244
Phone: (0191) 334-2594
Fax: (0191) 384-4737
www.dur.ac.uk/chemistry/research/academic-groups/i.r.evans/http://www.dur.ac.uk/chemistry/research/academic-groups/i.r.evans/


++
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++

RE: What is a good sequence for refinement of (U,V,W) of a multiphase sample ?

[Maxim V. Lobanov]

For our LaB6 sample (from local Russian authority) and with my machine (Rigaku 
Miniflex II) I found Y=0.0497 (with Fullprof); X refines to essentially zero.

Long ago I did the same with Bruker D8 Advance and NIST SRM 660a.
What I dug out from my old files is that the picture was essentially the same:
Y=0.0323 and X refines to zero.

Maybe this helps...

Sincerely,
Maxim.


-Original Message-
From: Huy LE-QUOC [mailto:huy.le-q...@lpsc.in2p3.fr] 
Sent: Monday, February 08, 2010 1:51 PM
To: Maxim V. Lobanov
Subject: Re: What is a good sequence for refinement of (U,V,W) of a multiphase 
sample ?

Maxim V. Lobanov a écrit :
 Actually, V and W reflect instrumental broadening - so better to be refined 
 globally or fixed at the values refined with a standard (LaB6 or similar).
 U is a mixture of instrumental contribution and Gaussian strain broadening 
 term - so, can de different for three phases. But practically for such 
 difficult multiphase situation maybe indeed it would be better to refine it 
 globally, at least for intermediate refinements.
 Generally, it makes sense also to refine Gaussian size broadening 
 [~1/cos^2(theta)], usually denoted P or Z (software-dependent).

 Sincerely,
 Maxim.

 ---
 Dr. Maxim Lobanov
 Head of RD Department
 Huntsman-NMG
 mailto: m_loba...@huntsman-nmg.com

 -Original Message-
 From: gre...@unisi.it [mailto:gre...@unisi.it] 
 Sent: Wednesday, February 03, 2010 6:10 PM
 To: rietveld_l@ill.fr
 Subject: Re: What is a good sequence for refinement of (U,V,W) of a 
 multiphase sample ?

 you better refine uvw globally for the sample and then Lorentzian x and y 
 individually for each phase. uvw should be constant for a given 
 diffractometer setting and you might get it from an independent refinement 
 of a standard.

 best

 miguel


 On 3 Feb 2010 at 15:41, Huy LE-QUOC wrote:

   
 Dear Rietvelders,

 I'm currently doing Rietveld refinements (with FullProf) for a 
 multiphase sample whose 3 phases with space groups Fm3m, P63/m and 
 I41a/md. The problem is the reflections of these 3 phases are very 
 superposed and hence I have found that their (U,V,W) refined parameters 
 seem to be very correlated.

 I have read somewhere that for each phase we should begin refine W, then 
 V and finally U. But I don't know in my case whose 3 phases having their 
 own  (U, V, W) we should follow which sequence ? First refine (U, V, W) 
 of the strongest phase and then for others phases? Or should we refine 
 simultaneously W for all phases and then V and U for all phases? 


 Do anyone of you have any experience on this case ?

 Thank you in advance for your kindly helps.

 Best regards,

 ---
 Huy LE-QUOC,
 Doctorant
 LPSC/CNRS - Centre de Recherche Plasmas-Matériaux-Nanostructures
 et Institut Néel/CNRS
 53 rue des Martyrs, Grenoble 38026, FRANCE


 

 --
 Miguel Gregorkiewitz
 Dip Scienze della Terra, Università
 via Laterina 8, I-53100 Siena, Europe
 fon +39'0577'233810 fax 233938
 email gre...@unisi.it




   
Dear Miguel,

Thank you for your kindly help. In fact, I'm trying with the refinement 
of a LaB6 standard to find out the instrumental values of line profile. 
For this purpose, I have selected the Thompson-Cox-Hastings pseudo-Voigt 
peak shape (Npr = 7 in FulProf) but I'm a little confused with the fact 
that: should I refine just only 3 parameters (U, V, W) and let X and Y 
which corresponds to strain broadening and size broadening, 
respectively, equal zero (because we don't have these effects with LaB6 
standard, I think) ? Or I still have to refine both (U, V, W) and then 
(X, Y) even for LaB6 standard ?

Thanks in advance for your any help with this question.

Best regards,

Huy LE-QUOC,

RE: What is a good sequence for refinement of (U,V, W) of a multiphase sample ?

[Alan Hewat]

 I have found that their (U,V,W) refined parameters seem to be very
correlated.

The Cagliotti formula FWHM**2=W+V.tan(theta)+U.tan**2(theta) with
parameters U,V,W represents instrument line width FWHM as a function of
scattering angle 2.theta for a conventional neutron powder
diffractometer.

This function may approximate line broadening in other situations, but
really you should use more appropriate parameters for broadening due to
particle size and strain, or other types of diffractometer. See the
FullProf manual for alternatives. Particle size and strain may be
different for different phases, and even for different crystallographic
axes. Such effects may not be seen for low resolution neutron
diffractometers.

Since Cagliotti's formula is a quadratic equation, U,V,W will naturally be
strongly correlated if there is no clear minimum in the line width as a
function of angle. You can remove this correlation by simply fixing the
angle for this minimum i.e. by differentiation and requiring that
V=-2U.tan(theta) where 2.theta is approximately the monochromator angle
for a conventional neutron diffractometer.
__
Dr Alan Hewat, NeutronOptics, Grenoble, FRANCE
alan.he...@neutronoptics.com +33.476.98.41.68
  http://www.NeutronOptics.com/hewat
__

What is a good sequence for refinement of (U,V,W) of a multiphase sample ?

[Huy LE-QUOC]

Dear Rietvelders,

I'm currently doing Rietveld refinements (with FullProf) for a 
multiphase sample whose 3 phases with space groups Fm3m, P63/m and 
I41a/md. The problem is the reflections of these 3 phases are very 
superposed and hence I have found that their (U,V,W) refined parameters 
seem to be very correlated.


I have read somewhere that for each phase we should begin refine W, then 
V and finally U. But I don't know in my case whose 3 phases having their 
own  (U, V, W) we should follow which sequence ? First refine (U, V, W) 
of the strongest phase and then for others phases? Or should we refine 
simultaneously W for all phases and then V and U for all phases? 
  


Do anyone of you have any experience on this case ?

Thank you in advance for your kindly helps.

Best regards,

---
Huy LE-QUOC,
Doctorant
LPSC/CNRS - Centre de Recherche Plasmas-Matériaux-Nanostructures
et Institut Néel/CNRS
53 rue des Martyrs, Grenoble 38026, FRANCE

Re: What is a good sequence for refinement of (U,V,W) of a multiphase sample ?

[gregor]

you better refine uvw globally for the sample and then Lorentzian x and y 
individually for each phase. uvw should be constant for a given 
diffractometer setting and you might get it from an independent refinement 
of a standard.

best

miguel


On 3 Feb 2010 at 15:41, Huy LE-QUOC wrote:

 Dear Rietvelders,
 
 I'm currently doing Rietveld refinements (with FullProf) for a 
 multiphase sample whose 3 phases with space groups Fm3m, P63/m and 
 I41a/md. The problem is the reflections of these 3 phases are very 
 superposed and hence I have found that their (U,V,W) refined parameters 
 seem to be very correlated.
 
 I have read somewhere that for each phase we should begin refine W, then 
 V and finally U. But I don't know in my case whose 3 phases having their 
 own  (U, V, W) we should follow which sequence ? First refine (U, V, W) 
 of the strongest phase and then for others phases? Or should we refine 
 simultaneously W for all phases and then V and U for all phases? 

 
 Do anyone of you have any experience on this case ?
 
 Thank you in advance for your kindly helps.
 
 Best regards,
 
 ---
 Huy LE-QUOC,
 Doctorant
 LPSC/CNRS - Centre de Recherche Plasmas-Matériaux-Nanostructures
 et Institut Néel/CNRS
 53 rue des Martyrs, Grenoble 38026, FRANCE
 
 

--
Miguel Gregorkiewitz
Dip Scienze della Terra, Università
via Laterina 8, I-53100 Siena, Europe
fon +39'0577'233810 fax 233938
email gre...@unisi.it

RE: What is a good sequence for refinement of (U,V,W) of a multiphase sample ?

[Maxim V. Lobanov]

Actually, V and W reflect instrumental broadening - so better to be refined 
globally or fixed at the values refined with a standard (LaB6 or similar).
U is a mixture of instrumental contribution and Gaussian strain broadening term 
- so, can de different for three phases. But practically for such difficult 
multiphase situation maybe indeed it would be better to refine it globally, at 
least for intermediate refinements.
Generally, it makes sense also to refine Gaussian size broadening 
[~1/cos^2(theta)], usually denoted P or Z (software-dependent).

Sincerely,
Maxim.

---
Dr. Maxim Lobanov
Head of RD Department
Huntsman-NMG
mailto: m_loba...@huntsman-nmg.com

-Original Message-
From: gre...@unisi.it [mailto:gre...@unisi.it] 
Sent: Wednesday, February 03, 2010 6:10 PM
To: rietveld_l@ill.fr
Subject: Re: What is a good sequence for refinement of (U,V,W) of a multiphase 
sample ?

you better refine uvw globally for the sample and then Lorentzian x and y 
individually for each phase. uvw should be constant for a given 
diffractometer setting and you might get it from an independent refinement 
of a standard.

best

miguel


On 3 Feb 2010 at 15:41, Huy LE-QUOC wrote:

 Dear Rietvelders,
 
 I'm currently doing Rietveld refinements (with FullProf) for a 
 multiphase sample whose 3 phases with space groups Fm3m, P63/m and 
 I41a/md. The problem is the reflections of these 3 phases are very 
 superposed and hence I have found that their (U,V,W) refined parameters 
 seem to be very correlated.
 
 I have read somewhere that for each phase we should begin refine W, then 
 V and finally U. But I don't know in my case whose 3 phases having their 
 own  (U, V, W) we should follow which sequence ? First refine (U, V, W) 
 of the strongest phase and then for others phases? Or should we refine 
 simultaneously W for all phases and then V and U for all phases? 

 
 Do anyone of you have any experience on this case ?
 
 Thank you in advance for your kindly helps.
 
 Best regards,
 
 ---
 Huy LE-QUOC,
 Doctorant
 LPSC/CNRS - Centre de Recherche Plasmas-Matériaux-Nanostructures
 et Institut Néel/CNRS
 53 rue des Martyrs, Grenoble 38026, FRANCE
 
 

--
Miguel Gregorkiewitz
Dip Scienze della Terra, Università
via Laterina 8, I-53100 Siena, Europe
fon +39'0577'233810 fax 233938
email gre...@unisi.it

Problem with the refinement of spinel structures

[muhammad ali]

dear all
when we are using the FULLPROF software for the rietveld refinement of  spinel 
structure, the refinement stops because of errot of singular matrix. As the 
corresponding  space space group is 
Fd-3m (space group with inversion center), what should be done to overcome this 
problem?
thanks in anticipation


  

Powder Diffraction Rietveld Refinement School 2010: deadline reminder

[EVANS I.]

Dear All,

Just a reminder of the approaching applications deadline (31st December)
for the Powder Diffraction and Rietveld Refinement School in Durham, UK.

The EPSRC/IUCr/PCG-SCMP supported biennial Powder Diffraction and
Rietveld Refinement School will take place at Durham University, 18th -
22nd April 2010. The course will offer a combination of lectures
covering the theoretical aspects of powder diffraction and Rietveld
refinement, problem sessions/tutorials and extensive hands-on practical
sessions using a variety of modern software packages. 

Topics to be covered will include: 

* Data collection strategies for X-ray and neutron diffraction 

* Constant wavelength and time of flight diffraction 

* Modelling peak shapes 

* Indexing powder patterns 

* Rietveld, Le Bail and Pawley fitting methods 

* X-ray and neutron combined Rietveld refinement 

* Restrained refinements 

* Rigid body refinements

Examples and tutorials will cover both extended and molecular systems.
Lectures will be given by Prof. John Evans, Dr. Ivana Evans, Dr. Jeremy
Cockroft and Prof. Andy Fitch. 

Student bursaries will be available to contribute to local costs or
travel expenses of applicants from UK academic institutions. We will
also offer a number of IUCr bursaries to overseas students.

For further information and informal inquiries about the School please
contact Ivana Evans (ivana.radosavlje...@durham.ac.uk).

Online applications can be submitted until 31st December 2009, at the
Powder Diffraction and Rietveld Refinement  School 2010 website:
http://www.dur.ac.uk/john.evans/webpages/pcg_rietveld_school_2010.htm

 

Ivana Evans

 

 



Dr. Ivana Radosavljevic Evans

Lecturer in Structural/Materials Chemistry

Department of Chemistry

Durham University

Durham DH1 3LE, U.K.

Office: CG 244

Phone: (0191) 334-2594

Fax: (0191) 384-4737



 

RE: Rietveld refinement in TOPAS with parallel beam geometry

[Cline, James Dr.]

Patrick,


From: Patrick Price [patrickpric...@gmail.com]
Sent: Friday, December 04, 2009 6:30 AM
To: Rietveld_l@ill.fr
Subject: Rietveld refinement in TOPAS with parallel beam geometry

Since this is my first post I will start with a brief introduction. My
name is Patrick Price and I am in my second year of graduate school.
My thesis work involves the investigation of phase equilibria in
perovskites.

I am using a Bruker D8 Discover diffractometer with parallel beam
geometry. The diffractometer has a Cu K-alpha X-Ray source with a Si
Gobel mirror and a Ge monochromator giving a parallel beam
monochromatic x-ray source.

This instrument description doesn't make sense.

Regards,

Jim


 The receiving side has Soller slits and a
Tl-doped NaI point detector. I am trying to teach myself how to use
TOPAS to PROPERLY analyze my data using Rietveld refinement
techniques.

I have recently taken a scan of the NIST line profile 660 LaB6
standard followed by scans of my perovskite powders using a step size
of 0.02 degrees and scan time of 4 seconds.

Most of the articles I have read are specific to convergent/divergent
beam geometries and I do not know how much of that information
transfers to parallel beam geometries. If anyone could help me answer
the following questions I would greatly appreciate it. These questions
mainly address which parameters should be refined with the LaB6
standard when using parallel beam geometry.
1.  I need to use the scan of the LaB6 powders to characterize the
contributions of the instrument to the diffraction profile. Starting
with the emission profile, TOPAS asks for the wavelength, the Area,
and the Lorentz Half Width. First, I assume the wavelength I should be
the more recent Cu Ka wavelength of 0.154059 nm instead of 0.154056
nm. Second, does Cu Ka have a definite Lorentz HW and “Area” or should
these parameters be refined with the LaB6 diffraction pattern?
2.  Since I have a Ge monochromater I assume the Lorentz polarization
factor should be fixed at 27.3 (Is this correct?). Obviously the
lattice parameters and atomic positions would be fixed.
3.   I read that you should NOT refine both the zero shift error and
sample displacement, and since it is parallel beam I only refine the
zero shift error. Should I refine surface roughness, absorption, or
sample tilt with the LaB6? (Currently I do not refine these)
4.  Am I correct in assuming that I do not have any EQUITORIAL
convolutions (e.g. from slits, FDS, beam spill, VDS) since it is
parallel beam geometry? What about TUBE TAILS?
5.  I am using the Finger_et_al  method to refine the AXIAL
convolutions, however I often get a large error associated with the S
value (sample length), even when my GOF is decent (1.45). Do any of
you know why this would happen?
6.  Should I refine the “Scale” or scale factor. (Currently I do)
7.  IMPORTANT: Originally I was refining the crystallite size but it
always refined to a very small value (~300nm), where as NIST claims
660 LAB6 should have a mean grain size of a few microns or more. I
assume this happens because the TOPAS is accounting for instrument
caused peak broadening by making the crystallite size smaller than it
actually is in the software. However, when I do refine the grain size
I do get a better fit. Should I leave this unchecked, refine it, or
fix it at a reasonable value of ~2500 nm.

In summary, currently I am only refining the Lorentz HW and “Area” in
the emission profile, zero shift error, the Finger parameters (S  H),
the scale factor, and nothing else.
I am unsure if I should be refining anything else such as the
crystallite size, tube tails and other forms of equatorial
convergence, or if there is something else that is important which I
am disregarding completely. I am also unsure if I am correct in
refining Lorentz HW and area in the emission profile.
Sorry if I got a little long winded; I just wanted to give enough
detail so people could answer. Thank you in advance for your help.
Patrick




James P. Cline
Ceramics Division   
National Institute of Standards and Technology
100 Bureau Dr. stop 8520 [ B113 / Bldg 217 ]
Gaithersburg, MD 20899-8523USA
jcl...@nist.gov
(301) 975 5793
FAX (301) 975 5334

Re: Rietveld refinement in TOPAS with parallel beam geometry

[Patrick Price]

Sorry about the confusion on the instrument configuration. I am new to
the field of x-ray diffraction. Hopefully this helps.
The Bruker D8 uses reflection geometry and a THETA : THETA goniometer,
where the x-ray source and detector can be move simultaneously on the
arms of the goniometer.  The x-ray source is Cu and is directed at a
Bruker multipurpose Si Gobel mirror which reflects a parallel beam of
Cu K-alpha (12) radiation at a 2-bounce Ge(022) analyzer crystal.  As
I understand it, the analyzer crystal filters our the K-alpha 2 peak,
producing monochromatic K-alpha 1radiation. There are no soller slits
on the primary side of the instrument. The beam is directed at the
specimen and the diffracted beam passes through a set of soller slits
and then to the point detector.
Thanks,
Patrick

On Fri, Dec 4, 2009 at 5:59 AM, Cline, James Dr. james.cl...@nist.gov wrote:
 Patrick,

 
 From: Patrick Price [patrickpric...@gmail.com]
 Sent: Friday, December 04, 2009 6:30 AM
 To: Rietveld_l@ill.fr
 Subject: Rietveld refinement in TOPAS with parallel beam geometry

 Since this is my first post I will start with a brief introduction. My
 name is Patrick Price and I am in my second year of graduate school.
 My thesis work involves the investigation of phase equilibria in
 perovskites.

 I am using a Bruker D8 Discover diffractometer with parallel beam
 geometry. The diffractometer has a Cu K-alpha X-Ray source with a Si
 Gobel mirror and a Ge monochromator giving a parallel beam
 monochromatic x-ray source.

 This instrument description doesn't make sense.

 Regards,

 Jim


  The receiving side has Soller slits and a
 Tl-doped NaI point detector. I am trying to teach myself how to use
 TOPAS to PROPERLY analyze my data using Rietveld refinement
 techniques.

 I have recently taken a scan of the NIST line profile 660 LaB6
 standard followed by scans of my perovskite powders using a step size
 of 0.02 degrees and scan time of 4 seconds.

 Most of the articles I have read are specific to convergent/divergent
 beam geometries and I do not know how much of that information
 transfers to parallel beam geometries. If anyone could help me answer
 the following questions I would greatly appreciate it. These questions
 mainly address which parameters should be refined with the LaB6
 standard when using parallel beam geometry.
 1.      I need to use the scan of the LaB6 powders to characterize the
 contributions of the instrument to the diffraction profile. Starting
 with the emission profile, TOPAS asks for the wavelength, the Area,
 and the Lorentz Half Width. First, I assume the wavelength I should be
 the more recent Cu Ka wavelength of 0.154059 nm instead of 0.154056
 nm. Second, does Cu Ka have a definite Lorentz HW and “Area” or should
 these parameters be refined with the LaB6 diffraction pattern?
 2.      Since I have a Ge monochromater I assume the Lorentz polarization
 factor should be fixed at 27.3 (Is this correct?). Obviously the
 lattice parameters and atomic positions would be fixed.
 3.       I read that you should NOT refine both the zero shift error and
 sample displacement, and since it is parallel beam I only refine the
 zero shift error. Should I refine surface roughness, absorption, or
 sample tilt with the LaB6? (Currently I do not refine these)
 4.      Am I correct in assuming that I do not have any EQUITORIAL
 convolutions (e.g. from slits, FDS, beam spill, VDS) since it is
 parallel beam geometry? What about TUBE TAILS?
 5.      I am using the Finger_et_al  method to refine the AXIAL
 convolutions, however I often get a large error associated with the S
 value (sample length), even when my GOF is decent (1.45). Do any of
 you know why this would happen?
 6.      Should I refine the “Scale” or scale factor. (Currently I do)
 7.      IMPORTANT: Originally I was refining the crystallite size but it
 always refined to a very small value (~300nm), where as NIST claims
 660 LAB6 should have a mean grain size of a few microns or more. I
 assume this happens because the TOPAS is accounting for instrument
 caused peak broadening by making the crystallite size smaller than it
 actually is in the software. However, when I do refine the grain size
 I do get a better fit. Should I leave this unchecked, refine it, or
 fix it at a reasonable value of ~2500 nm.

 In summary, currently I am only refining the Lorentz HW and “Area” in
 the emission profile, zero shift error, the Finger parameters (S  H),
 the scale factor, and nothing else.
 I am unsure if I should be refining anything else such as the
 crystallite size, tube tails and other forms of equatorial
 convergence, or if there is something else that is important which I
 am disregarding completely. I am also unsure if I am correct in
 refining Lorentz HW and area in the emission profile.
 Sorry if I got a little long winded; I just wanted to give enough
 detail so people could answer. Thank you in advance for your help

Powder Diffraction Rietveld Refinement School 2010

[EVANS I.R.]

Dear All,

The EPSRC/IUCr/PCG-SCMP supported biennial Powder Diffraction and
Rietveld Refinement School will take place at Durham University, 18th -
22nd April 2010. The course will offer a combination of lectures
covering the theoretical aspects of powder diffraction and Rietveld
refinement, problem sessions/tutorials and extensive hands-on practical
sessions using a variety of modern software packages. 

Topics to be covered will include: 

* Data collection strategies for X-ray and neutron diffraction 

* Constant wavelength and time of flight diffraction 

* Modelling peak shapes 

* Indexing powder patterns 

* Rietveld, Le Bail and Pawley fitting methods 

* X-ray and neutron combined Rietveld refinement 

* Restrained refinements 

* Rigid body refinements

Examples and tutorials will cover both extended and molecular systems.
Lectures will be given by Prof. John Evans, Dr. Ivana Evans, Dr. Jeremy
Cockroft and Prof. Andy Fitch. 

Student bursaries will be available to contribute to local costs or
travel expenses of applicants from UK academic institutions. We will
also offer a number of IUCr bursaries to overseas students.

For further information and informal inquiries about the School please
contact Ivana Evans (ivana.radosavlje...@durham.ac.uk).

Online applications can be submitted until 31st December 2009, at the
Powder Diffraction and Rietveld Refinement  School 2010 website:
http://www.dur.ac.uk/john.evans/webpages/pcg_rietveld_school_2010.htm

 

Ivana Evans

 



Dr. Ivana Radosavljevic Evans

Lecturer in Structural/Materials Chemistry

Department of Chemistry

Durham University

Durham DH1 3LE, U.K.

Office: CG 244

Phone: (0191) 334-2594

Fax: (0191) 384-4737



 

model based structure refinement

[muhammad ali]

dear all
if the sufficient knowledge about the structure is known(eg. lattice 
parameters, space group, approximate atomic positions etc), then what must be 
the stategy to solve similar structures.

i m working on soft ferrites which have spinel structureand space group Fd-3m.

i have made a lot of literature survey, but i cannot find the proper guidance 
about it

thanks in anticipation 


  

plotting sequential fullprof refinement

[Joost van Duijn]

Hi,
 
I am fitting some variable temperature data using the sequential refinement 
option in Fullprof on a Mac and was wondering if anybody has tried this and if 
so how they mannaged to plot the data from the corresponding *.seq file. The 
seq button in winplotr-2006 to do this does not appear to work in the Mac 
version.

Thanks in advance for your help.

Cheers,
Joost


  

Re: LP factor in the Rietveld refinement

[Nicolae Popa]

Right, but specially for students- beginners we must  be much, let say, 
didactic


LP means (Lorentz) * (Polarisation)
What is important in Rietveld refinement when a lot of mirrors  
monochromators are present is how they change (Polarization)
because (Lorentz) is changed by adding factors independent on hkl, then 
entering in the scaling factor


Presuming the same scattering plane for all scatterers the polarization 
factor is:



pol = SIN(PSI)**2 + COS(PSI)**2*COS(2*TET1)**2*COS(2*TET2)**2 
*.*COS(2*TETm)**2*COS(2*TETb)**2



where   TET1, TET2, ., TETm   are the Bragg angles at monochromator 1, 
2, ,m


and where  TETb  is the Bragg angle at  sample  (depending on hkl)

and where PSI  is the angle between polarization  vector of the incident 
beam - IF it is TOTALLY POLARIZED!!! - and the scattering plane;


If the incident beam is NOT POLARIZED the averages of both SIN(PSI)**2 and 
COS(PSI)**2  result in 1/2.


If the incident beam is partially polarized one replace for example 
SIN(PSI)**2  by  P0 , consequently COS(PSI)**2 = 1 - P0  and one refine P0


If the geometry is much complicated (different scattering planes for 
different monochromators) pol should be calculated for the given


geometry  by applying successively the known formula (see a book of 
electrodynamics, e.g.. Landau)


Ej+1 = (Ej X u)Xu  and taking at the END:  |E(last)|**2 / |E0|**2 (X 
means vectorial product)


where Ej is the electric field vector in the beam scattered j times and  u 
is the unit vector along the scattered beam j+1


Best wishes,

Nicolae Popa




- Original Message - 
From: Leonid Solovyov l_solov...@yahoo.com

To: rietveld_l@ill.fr
Sent: Sunday, July 26, 2009 9:05 AM
Subject: RE: LP factor in the Rietveld refinement



In principle, the LP correction for a multi-bounce monochromator is similar 
to that for a single-crystal one with the same crystal type and reflection 
indexes (or diffraction angle).
The exact LP value depends, as well, on the crystal perfection (mosaicity) 
and for supremely precise measurements one might consider refining the LP 
value as was mentioned by Kurt and Peter. Besides the angular range, the 
correlation with thermal parameters, and the instrument alignment, one more 
problem of the LP refinement is the correct choice of the atomic scattering 
curves in accordance with the oxidation states which might be not quite 
obvious in general.


Leonid

***
Leonid A. Solovyov
Institute of Chemistry and Chemical Technology
660049, K. Marx 42, Krasnoyarsk , Russia
www.icct.ru/eng/content/persons/Sol_LA
www.geocities.com/l_solovyov
***

--- On Sun, 7/26/09, Peter Y. Zavalij pzava...@umd.edu wrote:


From: Peter Y. Zavalij pzava...@umd.edu
Subject: RE: LP factor in the Rietveld refinement
To: rietveld_l@ill.fr
Date: Sunday, July 26, 2009, 5:03 AM
That's right. LP refinement works
just fine within TOPAS but angular range
as wide as possible is needed. If it is up to 140-150 deg.
2thteta LP does
not correlate much with thermal parameters. Refined LP is
not exact but very
close.

Peter Zavalij

X-ray Crystallographic Center
University of Maryland
College Park, MD

Office: (301)405-1861
Lab: (301)405-3230
Fax: (301)314-9121




-Original Message-
From: Kurt Leinenweber [mailto:ku...@asu.edu]
Sent: Saturday, July 25, 2009 8:53 PM
To: alor...@unex.es;
Leonid Solovyov
Cc: rietveld_l@ill.fr
Subject: RE: LP factor in the Rietveld refinement

Hi all,

I haven't actually DONE this, so maybe I shouldn't put my 2
cents in, but
can't you refine the polarization factor by using a
standard such as Y2O3
and fixing the structure and thermal parameters of the
standard while
refining the polarization angle?

The angle so obtained should agree with what the theory
tells you for your
diffractometer configuration, but it seems more comforting
to verify it by a
measurement.

- Kurt



From: alor...@unex.es
[mailto:alor...@unex.es]
Sent: Sat 7/25/2009 1:29 PM
To: Leonid Solovyov
Cc: rietveld_l@ill.fr
Subject: Re: LP factor in the Rietveld refinement



In this context:

What about the LP for a Goebel mirror followed by a
4-bounce or 2-bounce
primary monochromator?

Best regards

angel l. ortiz








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This message was checked by NOD32 antivirus system.
http://www.eset.com

Re: LP factor in the Rietveld refinement

[Leonid Solovyov]

As far as I know, for X-ray mirrors the LP angle is near zero.

Leonid

***
 Leonid A. Solovyov
 Institute of Chemistry and Chemical Technology
 660049, K. Marx 42, Krasnoyarsk , Russia
 www.icct.ru/eng/content/persons/Sol_LA
 www.geocities.com/l_solovyov
***

--- On Sat, 7/25/09, chu...@hkusua.hku.hk chu...@hkusua.hku.hk wrote:

 From: chu...@hkusua.hku.hk chu...@hkusua.hku.hk
 Subject: Re: LP factor in the Rietveld refinement
 To: Ross H Colman ucca...@ucl.ac.uk
 Cc: rietveld_l@ill.fr
 Date: Saturday, July 25, 2009, 4:16 AM
 Dear Ross,
 
 How about the LP factor/monochromator angle if using Gobel
 mirror in  
 my D8 system?
 
 Thanks!
 
 stephen
 
 


  

Re: LP factor in the Rietveld refinement

[alortiz]

In this context:

What about the LP for a Goebel mirror followed by a 4-bounce or 2-bounce
primary monochromator?

Best regards

angel l. ortiz


 As far as I know, for X-ray mirrors the LP angle is near zero.

 Leonid

 ***
  Leonid A. Solovyov
  Institute of Chemistry and Chemical Technology
  660049, K. Marx 42, Krasnoyarsk , Russia
  www.icct.ru/eng/content/persons/Sol_LA
  www.geocities.com/l_solovyov
 ***

 --- On Sat, 7/25/09, chu...@hkusua.hku.hk chu...@hkusua.hku.hk wrote:

 From: chu...@hkusua.hku.hk chu...@hkusua.hku.hk
 Subject: Re: LP factor in the Rietveld refinement
 To: Ross H Colman ucca...@ucl.ac.uk
 Cc: rietveld_l@ill.fr
 Date: Saturday, July 25, 2009, 4:16 AM
 Dear Ross,

 How about the LP factor/monochromator angle if using Gobel
 mirror in 
 my D8 system?

 Thanks!

 stephen

Re: LP factor in the Rietveld refinement

[chuisy]

Dear Ross,

How about the LP factor/monochromator angle if using Gobel mirror in  
my D8 system?


Thanks!

stephen


- Message from ucca...@ucl.ac.uk -
Date: Thu, 23 Jul 2009 09:52:55 +0100
From: Ross H Colman ucca...@ucl.ac.uk
Reply-To: Ross H Colman ucca...@ucl.ac.uk
 Subject: Re: LP factor in the Rietveld refinement
  To: rietveld_l@ill.fr



Dear all,

Just to be complete, the Topas technical reference manual also gives the
LP values for a few other common monchromators:
Pg109
Values for most common monochromators (Cu radiation) are:
Ge : 27.3
Graphite : 26.4
Quartz : 26.6

Regards
Ross Colman



Ross Colman

G19 Christopher Ingold Laboratories

University College London

Department of Chemistry

20 Gordon Street

London

WC1H 0AJ

Phone: +44 (0)20 7679 4636

Internal: 24636

Email:  ross.col...@ucl.ac.uk





- End message from ucca...@ucl.ac.uk -

RE: LP factor in the Rietveld refinement

[Leonid Solovyov]

Dear Angel,

In general, the LP correction angle is the diffraction angle (2theta) of the 
monochromator crystal. If the primary monochromator is Si(111) then the angle 
is 28.44 for CuK_alpha1.

Best regards,
Leonid

***
 Leonid A. Solovyov
 Institute of Chemistry and Chemical Technology
 660049, K. Marx 42, Krasnoyarsk , Russia
 www.icct.ru/eng/content/persons/Sol_LA
 www.geocities.com/l_solovyov
***

--- On Thu, 7/23/09, alor...@unex.es alor...@unex.es wrote:

 From: alor...@unex.es alor...@unex.es
 Subject: RE: LP factor in the Rietveld refinement
 To: Leonid Solovyov l_solov...@yahoo.com
 Cc: rietveld_l@ill.fr
 Date: Thursday, July 23, 2009, 7:00 AM
 Dear All,
 
 In this scenario, which should be the number for LP in
 Topas if ones has a
 D8 with a primary monochromator for pure CuKalpha1?
 
 thanks for the response,
 
 angel l. ortiz
 



  

AW: LP factor in the Rietveld refinement

[Hinrichsen, Bernd]

One intensity correction that is perhaps more realistic is surface roughness. 
This does have a vaguely similar angular dependence to the LP correction. This 
correction is generally only applied to highly absorbing samples in 
Bragg-Brentano (or generally reflection) setups. This would seem to be the case 
for the LaB6 measurement mentioned by Peter.

Greetings
Bernd


-Ursprüngliche Nachricht-
Von: Peter Y. Zavalij [mailto:pzava...@umd.edu]
Gesendet: Donnerstag, 23. Juli 2009 05:52
An: rietveld_l@ill.fr
Betreff: RE: LP factor in the Rietveld refinement

Well... the situation with LP is not so simple. Using TOPAS for refinement
data collected on D8 advance with Ni-filter and LynxEye detector I observe
the following:
- For all samples LP=0 is OK and gives the best fit as it should be by the
book.
- HOWEVER for LaB6 standard LP=0 yields very poor fit for several high angle
reflections (120 deg. 2theta) while LP=90 gives perfect fit. The difference
in R factors 12% and 4% cannot be simply ignored...

Can anyone explain this?


Peter Zavalij

X-ray Crystallographic Center
University of Maryland
College Park, MD

Office: (301)405-1861
Lab: (301)405-3230
Fax: (301)314-9121




-Original Message-
From: Ross Williams [mailto:ross.willi...@curtin.edu.au]
Sent: Wednesday, July 22, 2009 8:43 PM
To: Jon Wright; xiu...@ualberta.ca
Cc: rietveld_l@ill.fr
Subject: RE: LP factor in the Rietveld refinement

Hi Xiujun,

Jon is correct, but to answer your question fully, the angle is used in an
equation to scale the peaks as function of 2theta.

If you look in the Technical Reference Manual of TOPAS states that the LP
factor (for x-rays) is given by

LP = (1 + cos(2th)^2 cos(2th_m)^2) / (cos(theta) sun(theta)^2)

2th_m is the angle mentioned by Jon, ie 26.4° when using Cu Kalpha  with a
graphic monochromator, 0° when using unpolarised beam, and 90° for full
polarised.

Or in TOPAS macro language : scale_pks = (1 + Cos(CeV(c,v) Deg)^2 Cos(2
Th)^2) /(Sin(Th)^2 Cos(Th));

The Technical Reference has a derivation of the LP equation above and
compares it to parameters used in GSAS and Fullprof.

Kind Regards,

Ross



+

Ross Williams
PhD Student
Centre for Materials Research
Department of Imaging and Applied Physics
Curtin University of Technology
GPO Box U1987 Perth WA 6845
Western Australia
Phone: +61 (0)8 9266 4219
Fax: +61 (0)8 9266 2377
Email:   ross.willi...@curtin.edu.au






-Original Message-
From: Jon Wright [mailto:wri...@esrf.fr]
Sent: Thursday, 23 July 2009 5:26 AM
To: xiu...@ualberta.ca
Cc: rietveld_l@ill.fr
Subject: Re: LP factor in the Rietveld refinement

Sounds like the parameter is the monochromator angle you would need to
use to convert an unpolarised beam into a beam with the polarisation
state you have (eg, 90 degrees gives 100% polarised). Don't confuse this
with the actual monochromator angle at the synchrotron, as the bean is
usually polarised before it reaches the monochromator anyway. With some
packages you can set the monochromator roll angle to put the
polarisation in the right plane, depending which way up an area detector
was mounted.

Good luck,

Jon

xiu...@ualberta.ca wrote:
 Hello, everyone,

 I have some questions about the refinement in Topas.

 When we put the instrument parameters, we always include the LP
 factor, and set it to a constant value. I thought LP factor is a
 function of theta and not a constant value, so my question is what
 exact the constant value means. Why for unpolarized radiation, it is
 equal to 0, and for synchrotron radiation it is equal to 90. Sorry to
 throw so many questions.

 Thank a lot for any help.

 Xiujun Li
 Master Student
 Advanced Materials and Processing Laboratory
 Chemical and Materials Engineering
 University of Alberta
 Edmonton, Alberta, Canada T6G 2G6
 Phone: 1-780-492-0701



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Re: Refinement of spiral magnetic structure from neutron powder diffraction

[Alexander Barcza]

Dear Ross,

Thanks for your reply. Sorry for being so exclusive in my initail mail, of
course I should have included everyone! The title of PhD student also
applies to me.

I've seen a talk about SARAh by Andrew Wills at ISIS and was impressed by
it. Therefore I've already downloaded it but didn't succeed in using it yet.

The problem is actually already at the beginning:
In my GSAS file I created a second phase with P1 and just copied the atoms
of the main phase over.

I loaded that file by clicking GSAS Controls, Load GSAS EXP file

How do I then define the MAT file?

Sorry, it must be obvious but I can't find it. I am happy to read some
documentation but couldn't find any on the website (
http://www.chem.ucl.ac.uk/people/wills/index.html).

Thanks again for your help
Alex



2009/7/23 Ross H Colman ucca...@ucl.ac.uk

 Dear Alex,

 You addressed your email to experts on magnetic refinement so I
 apologise if I am the only person to reply for I am a lowly PhD student.

 I am afraid I am not going to answer your questions directly but instead
 point you to the program that I use for magnetic refinements. Its free
 software available on CCP14 called SARAh. It allows you to input your
 magnetic atom sites, space group and k-vector then has the ability to
 modify your fullprof pcr file depending on how you wish to do the
 refinement.

 The process is a little involved, as it uses representational theory to
 reduce your problem to symmetry allowed structures, rather than freely
 refining all variables, but it has step by step instructions and I think
 there are even some online help videos for using it now.

 Available from:
 www.CCP14.ac.uk  or
 www.chem.ucl.ac.uk/people/wills/index.html

 Best regards and good luck
 Ross Colman


  Dear experts on magnetic refinement,
 
  We recently got some nice data on GEM, ISIS and I was able to get a
 decent
  structural fit using GSAS and FullProf.
 
  Now I would like to refine the magnetic structure but this is my first
  time
  so I struggle to give FullProf what it wants.
 
  Since I'm a novice treating the magnetic data I'd have some general
  questions about the input (which I attached below). The general structure
  of
  the pcr file seems to be OK, because it is read by FP but unfortunately
 in
  the current form leads to a singular matrix. I'm sure I've done something
  wrong with the input parameters.
 
  Here is a quick outline of what I want to achieve:
  There are two magnetic ions in the structure. Mn and Co, but Co has a
 very
  small moment (we know that from neutron diffraction from the 80's). The
  moments seem to order in two incommensurate spiral structures (one for Mn
  and one for Co) with the k-vector along c-axis. I thought it is best to
  include a separate purely magnetic phase in FP. Would you agree and if
 yes
  can I still do a multi-bank refinenment?
 
  Here is the snippet from the pcr file which was inspired by Ho2Cu2O5, an
  example from the FP webpage (questions below):
 
 --
  CoMnSi(magnetic
  reflection)
 
  !
  !Nat Dis Mom Jbt  Isy Str FurthATZ Nvk More
 2   0   0 -1-1  0   0  0.   2   1
  !Jvi Jdi Hel Sol Mom Ter
   3   0   0   0   0   0
  !Contributions (0/1) of this phase to the  6 patterns (FOR simplicity I
  deleted all but the first pattern to get started)
   1
  !Irf Npr Jtyp  Nsp_Ref Ph_Shift for Pattern#  1
-1  13   -1  0  0
  ! Pr1Pr2Pr3   Brind.   Rmua   Rmub   Rmuc for Pattern#  1
0.000  0.000  1.000  1.000  0.000  0.000  0.000
  P -1  --Space group symbol
  !Nsym Cen Laue MagMat
 4   1 31
  !
  SYMM  x,y,z
  MSYM  u,v,w,0.0
  SYMM -x,-y,z+1/2
  MSYM  u, v,-w,0.0
  SYMM  x+1/2,-y+1/2,z
  MSYM -u,v,-w,0.0
  SYMM -x+1/2,y+1/2,z+1/2
  MSYM  u,-v,-w,0.0
  !
  !Atom   Typ   Mag VekXYZ Biso   Occ  Rm
  Rphi  Rtheta
  !   Im   Iphi   Ithetabeta11   beta22   beta33   MagPh
  Co1 MCO2 1   1   0.15609  0.25000  0.05324  0.0   1.0
  0.323.0
  45.0
 
  220.00 0.00   230.00   280.00  0.00   0.0
  0.0   0.0
0.0  0.0  0.0  0.0  0.0   0.0
   0.00 0.00 0.00 0.00 0.00  0.00
  Mn1 MMN2 1   2   0.02093  0.25000  0.68070  0.0   1.0
  3.1 178.0
  13.0
 
   0.00 0.00 0.00 0.00  0.00
  0.0  0.0  0.0
0.0  0.0  0.0  0.0  0.0   0.0
   0.00 0.00 0.00 0.00 0.00  0.00
  !--- Profile Parameters for Pattern #  1
  !  Scale   Extinc  Bov Str1 Str2 Str3Strain-Model
4.8798   0.   0.   0.   0.   0.   0
  1.0 0.00 0.00 0.00 0.00 0.00
  ! Sig-2

Re: AW: LP factor in the Rietveld refinement

[David Lee]

I have a question about the surface roughness.The LaB6 powders  
that I have seen are
very finely ground and produce very flat, smooth samples. Is the  
roughness connected
with the absorption?   I'm thinking along the lines that a low  
absorbing, rough sample
might not look as rough to an x-ray beam as a high absorbing,  
smoother sample.


Thanks,

David Lee, Ph.D.
DTLee Scientific, llc
http://www.dtlee.com
614-562-6230

On Jul 23, 2009, at 5:23 AM, Hinrichsen, Bernd wrote:

One intensity correction that is perhaps more realistic is surface  
roughness. This does have a vaguely similar angular dependence to  
the LP correction. This correction is generally only applied to  
highly absorbing samples in Bragg-Brentano (or generally reflection)  
setups. This would seem to be the case for the LaB6 measurement  
mentioned by Peter.


Greetings
Bernd


-Ursprüngliche Nachricht-
Von: Peter Y. Zavalij [mailto:pzava...@umd.edu]
Gesendet: Donnerstag, 23. Juli 2009 05:52
An: rietveld_l@ill.fr
Betreff: RE: LP factor in the Rietveld refinement

Well... the situation with LP is not so simple. Using TOPAS for  
refinement
data collected on D8 advance with Ni-filter and LynxEye detector I  
observe

the following:
- For all samples LP=0 is OK and gives the best fit as it should be  
by the

book.
- HOWEVER for LaB6 standard LP=0 yields very poor fit for several  
high angle
reflections (120 deg. 2theta) while LP=90 gives perfect fit. The  
difference

in R factors 12% and 4% cannot be simply ignored...

Can anyone explain this?


Peter Zavalij

X-ray Crystallographic Center
University of Maryland
College Park, MD

Office: (301)405-1861
Lab: (301)405-3230
Fax: (301)314-9121




-Original Message-
From: Ross Williams [mailto:ross.willi...@curtin.edu.au]
Sent: Wednesday, July 22, 2009 8:43 PM
To: Jon Wright; xiu...@ualberta.ca
Cc: rietveld_l@ill.fr
Subject: RE: LP factor in the Rietveld refinement

Hi Xiujun,

Jon is correct, but to answer your question fully, the angle is used  
in an

equation to scale the peaks as function of 2theta.

If you look in the Technical Reference Manual of TOPAS states that  
the LP

factor (for x-rays) is given by

LP = (1 + cos(2th)^2 cos(2th_m)^2) / (cos(theta) sun(theta)^2)

2th_m is the angle mentioned by Jon, ie 26.4° when using Cu Kalpha   
with a
graphic monochromator, 0° when using unpolarised beam, and 90° for  
full

polarised.

Or in TOPAS macro language : scale_pks = (1 + Cos(CeV(c,v) Deg)^2  
Cos(2

Th)^2) /(Sin(Th)^2 Cos(Th));

The Technical Reference has a derivation of the LP equation above and
compares it to parameters used in GSAS and Fullprof.

Kind Regards,

Ross



+

Ross Williams
PhD Student
Centre for Materials Research
Department of Imaging and Applied Physics
Curtin University of Technology
GPO Box U1987 Perth WA 6845
Western Australia
Phone: +61 (0)8 9266 4219
Fax: +61 (0)8 9266 2377
Email:   ross.willi...@curtin.edu.au






-Original Message-
From: Jon Wright [mailto:wri...@esrf.fr]
Sent: Thursday, 23 July 2009 5:26 AM
To: xiu...@ualberta.ca
Cc: rietveld_l@ill.fr
Subject: Re: LP factor in the Rietveld refinement

Sounds like the parameter is the monochromator angle you would need to
use to convert an unpolarised beam into a beam with the polarisation
state you have (eg, 90 degrees gives 100% polarised). Don't confuse  
this

with the actual monochromator angle at the synchrotron, as the bean is
usually polarised before it reaches the monochromator anyway. With  
some

packages you can set the monochromator roll angle to put the
polarisation in the right plane, depending which way up an area  
detector

was mounted.

Good luck,

Jon

xiu...@ualberta.ca wrote:

Hello, everyone,

I have some questions about the refinement in Topas.

When we put the instrument parameters, we always include the LP
factor, and set it to a constant value. I thought LP factor is a
function of theta and not a constant value, so my question is what
exact the constant value means. Why for unpolarized radiation, it is
equal to 0, and for synchrotron radiation it is equal to 90. Sorry to
throw so many questions.

Thank a lot for any help.

Xiujun Li
Master Student
Advanced Materials and Processing Laboratory
Chemical and Materials Engineering
University of Alberta
Edmonton, Alberta, Canada T6G 2G6
Phone: 1-780-492-0701




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Re: Refinement of spiral magnetic structure from neutron powder diffraction

[Andrew Wills]

Dear Alex

The MAT file is generated from the symmetry analysis calculations  
using SARAh-Representational Analysis (there are video help files to  
show you how to do this).


 If you are setting up a refinement in GSAS, you can use SARAh Refine  
to set up the magnetic phase for you. There are 2 options:


1) you set up the phase, make it magnetic and put in an atom with a  
moment on it to make sure it works. Select GSAS Controls/Insert  
magnetic atoms , to overwrite this atom with all the atoms for your P1  
magnetic structure. (this is required so that SARAh can match the atom  
to its moment orientation


2) Use SARAh Refine to set up the magnetic phase for you.
-To do this, delete all the atoms in the P1 phase, then delete the  
phase itself. Run Powpref to make sure it works.

-Then Select GSAS Controls/Make magnetic phase (Fully automatic)
-Define the nuclear phase that will be used as a template for the  
magnetic phase's lattice parameters, profile, etc

-Define the form factors of the different moments

-The phase will now be set up for you. (If there are problems with  
this, let me know and I'll try to fix them)


Refining the structure is then based on selecting the basis vectors  
and firing off reverse-Monte Carlo cycles. There is no need to define  
red/black symmetries in GSAS as the moment orientations are all looked  
after by SARAh. Start with selecting the basis vectors of a single  
irreducible representation, and then combining them if that fails to  
fit your data. It is important to learn to read basis vectors and what  
they correspond to- SARAh has some help files to help you get to grips  
with this.


A word on GSAS vs Fullprof:
GSAS can only handle a magnetic structure that can be defined by a  
unit cell. So, your incommensurate structure would need to be close to  
a lock-in value to work, i.e. (0 0 0.32) is close to (0 0 1/3). That  
said, the definition of the magnetic structure can be very simple, a  
set of moments in P1, so setting understanding what it all means is  
quite unambiguous.


FullProf has a k vector and is far more flexible in the ways in which  
magnetic structures can be defined. This flexibility can make it hard  
to set up a magnetic phase. SARAh -Refine tries to deal with most of  
these problems for you (see the video help for the entire process),  
but it is sometimes less obvious to see what is happening in the pcr  
file.


If you have any questions, feel free to get in contact. Good luck!

Andrew

ps/ to see the SARAh documentation- install SARAh (which contains  
SARAh-Representational Analysis and SARAh-Refine) on a windows  
computer (including macs with parallels or vmfusion), and look in the  
help menu



On 23 Jul 2009, at 12:27, Alexander Barcza wrote:


Dear Ross,

Thanks for your reply. Sorry for being so exclusive in my initail  
mail, of course I should have included everyone! The title of PhD  
student also applies to me.


I've seen a talk about SARAh by Andrew Wills at ISIS and was  
impressed by it. Therefore I've already downloaded it but didn't  
succeed in using it yet.


The problem is actually already at the beginning:
In my GSAS file I created a second phase with P1 and just copied the  
atoms of the main phase over.


I loaded that file by clicking GSAS Controls, Load GSAS EXP file

How do I then define the MAT file?

Sorry, it must be obvious but I can't find it. I am happy to read  
some documentation but couldn't find any on the website (http://www.chem.ucl.ac.uk/people/wills/index.html 
).


Thanks again for your help
Alex



2009/7/23 Ross H Colman ucca...@ucl.ac.uk
Dear Alex,

You addressed your email to experts on magnetic refinement so I
apologise if I am the only person to reply for I am a lowly PhD  
student.


I am afraid I am not going to answer your questions directly but  
instead

point you to the program that I use for magnetic refinements. Its free
software available on CCP14 called SARAh. It allows you to input your
magnetic atom sites, space group and k-vector then has the ability to
modify your fullprof pcr file depending on how you wish to do the
refinement.

The process is a little involved, as it uses representational theory  
to

reduce your problem to symmetry allowed structures, rather than freely
refining all variables, but it has step by step instructions and I  
think

there are even some online help videos for using it now.

Available from:
www.CCP14.ac.uk  or
www.chem.ucl.ac.uk/people/wills/index.html

Best regards and good luck
Ross Colman


 Dear experts on magnetic refinement,

 We recently got some nice data on GEM, ISIS and I was able to get  
a decent

 structural fit using GSAS and FullProf.

 Now I would like to refine the magnetic structure but this is my  
first

 time
 so I struggle to give FullProf what it wants.

 Since I'm a novice treating the magnetic data I'd have some general
 questions about the input (which I attached below). The general  
structure

 of
 the pcr file

Re: Refinement of spiral magnetic structure from neutron powder diffraction

[Alexander Barcza]

Dear Andrew,

First, thank you very much for taking the time for this really detailed and
helpful answer. It is very much appreciated and I hope that I can give some
useful feedback besides consuming your time.

Just to let you know, I run everything in vmware fusion on a mac (but it
should be exactly the same as native Windows).

When I installed SARAh a desktop icon was created that launched SARAh-refine
but I didn't 'know anything' of SARAh-representational analysis.That's fine
because a beginner would click on the video tutorial button immediately.
This however doesn't do anything in my version (7.1.3). I guess it should
open a browser and go to the some webpage. Anyway, that's just a minor
detail and I figured out that going to
ftp://ftp.bcc.ac.uk/pub/users/uccaawi/ has all the tutorials.

They are really excellent and I could easily understand how all individual
parts of the software are used (of course the underlying representational
analysis much less so)!

Since we suspect from earlier neutron powder diffraction that the magn
structure is incomm I decided to work with Fullprof.

So off I went and created the MAT file with Pnma as the underlying crystal
structure, one Mn atom in a Wyckoff 4c position (for simplicity I neglected
Co moments) and a 'guess' (or rather a value from literature) for k (0 0
tau). The creation of the files was smooth and I was able to load the MAT
file in SARAh-refine.  For a simple start I selected all the basis functions
with the common IR gama(1) and created the pcr file.

As the next step I copied the relevant information from sarah62.pcr into
my.pcr . Please note that the 'phase header' is slightly different in my pcr
because ultimately I want to refine multi-bank patterns from GEM. Therefore
some parameters (such as  Irf Npr Jtyp   Pr1Pr2Pr3 ) are defined
individually for each bank on a separate line. I don't know if that's
crucial for describing my problem but I thought I'll mention it. The rest of
the magnetic phase information was, however, copied from sarah62.pcr as a
second phase into my.pcr.

For a start I fixed all parameters except the C coefficients (set the value
to 1.00 and the code to 1.00) as explained in the tutorial.
Running Fullprof results in some pattern calculation BUT unfortunately the
scale factor is off so much that the magnetic phase is a factor 10 more
intense than the nuclear phase. Refining the scale factor (either for the
magn phase or the nuc phase) doesn't help. Neither does setting it to some
fixed large value to compensate the scaling difference.

I was wondering whether this is a known problem or whether you'd have any
guesses as to what I might be doing wrong. If you want to see any files
please let me know. I'm more than happy to send them.

The possibility to solve a magnetic structure from basic principles such as
group theory and RA seems very appealing and unbiased to me so I hope that
there is a solution to problems arising on the way.

Once again I'm very grateful for your help and time.

Alex





2009/7/23 Andrew Wills a.s.wi...@ucl.ac.uk

 Dear Alex
 The MAT file is generated from the symmetry analysis calculations using
 SARAh-Representational Analysis (there are video help files to show you how
 to do this).

  If you are setting up a refinement in GSAS, you can use SARAh Refine to
 set up the magnetic phase for you. There are 2 options:

 1) you set up the phase, make it magnetic and put in an atom with a moment
 on it to make sure it works. Select GSAS Controls/Insert magnetic atoms ,
 to overwrite this atom with all the atoms for your P1 magnetic structure.
 (this is required so that SARAh can match the atom to its moment
 orientation

 2) Use SARAh Refine to set up the magnetic phase for you.
 -To do this, delete all the atoms in the P1 phase, then delete the phase
 itself. Run Powpref to make sure it works.
 -Then Select GSAS Controls/Make magnetic phase (Fully automatic)
 -Define the nuclear phase that will be used as a template for the magnetic
 phase's lattice parameters, profile, etc
 -Define the form factors of the different moments

 -The phase will now be set up for you. (If there are problems with this,
 let me know and I'll try to fix them)

 Refining the structure is then based on selecting the basis vectors and
 firing off reverse-Monte Carlo cycles. There is no need to define red/black
 symmetries in GSAS as the moment orientations are all looked after by SARAh.
 Start with selecting the basis vectors of a single irreducible
 representation, and then combining them if that fails to fit your data. It
 is important to learn to read basis vectors and what they correspond to-
 SARAh has some help files to help you get to grips with this.

 A word on GSAS vs Fullprof:
 GSAS can only handle a magnetic structure that can be defined by a unit
 cell. So, your incommensurate structure would need to be close to a lock-in
 value to work, i.e. (0 0 0.32) is close to (0 0
 1/3). That said, the definition

RE: LP factor in the Rietveld refinement

[Ross Williams]

Hi Xiujun,

Jon is correct, but to answer your question fully, the angle is used in an 
equation to scale the peaks as function of 2theta. 

If you look in the Technical Reference Manual of TOPAS states that the LP 
factor (for x-rays) is given by

LP = (1 + cos(2th)^2 cos(2th_m)^2) / (cos(theta) sun(theta)^2)

2th_m is the angle mentioned by Jon, ie 26.4° when using Cu Kalpha  with a 
graphic monochromator, 0° when using unpolarised beam, and 90° for full 
polarised.

Or in TOPAS macro language : scale_pks = (1 + Cos(CeV(c,v) Deg)^2 Cos(2 Th)^2) 
/(Sin(Th)^2 Cos(Th));

The Technical Reference has a derivation of the LP equation above and compares 
it to parameters used in GSAS and Fullprof.

Kind Regards,

Ross 



+

Ross Williams
PhD Student
Centre for Materials Research
Department of Imaging and Applied Physics
Curtin University of Technology
GPO Box U1987 Perth WA 6845
Western Australia
Phone: +61 (0)8 9266 4219
Fax: +61 (0)8 9266 2377
Email:   ross.willi...@curtin.edu.au






-Original Message-
From: Jon Wright [mailto:wri...@esrf.fr] 
Sent: Thursday, 23 July 2009 5:26 AM
To: xiu...@ualberta.ca
Cc: rietveld_l@ill.fr
Subject: Re: LP factor in the Rietveld refinement

Sounds like the parameter is the monochromator angle you would need to 
use to convert an unpolarised beam into a beam with the polarisation 
state you have (eg, 90 degrees gives 100% polarised). Don't confuse this 
with the actual monochromator angle at the synchrotron, as the bean is 
usually polarised before it reaches the monochromator anyway. With some 
packages you can set the monochromator roll angle to put the 
polarisation in the right plane, depending which way up an area detector 
was mounted.

Good luck,

Jon

xiu...@ualberta.ca wrote:
 Hello, everyone,

 I have some questions about the refinement in Topas.

 When we put the instrument parameters, we always include the LP 
 factor, and set it to a constant value. I thought LP factor is a 
 function of theta and not a constant value, so my question is what 
 exact the constant value means. Why for unpolarized radiation, it is 
 equal to 0, and for synchrotron radiation it is equal to 90. Sorry to 
 throw so many questions.

 Thank a lot for any help.

 Xiujun Li
 Master Student
 Advanced Materials and Processing Laboratory
 Chemical and Materials Engineering
 University of Alberta
 Edmonton, Alberta, Canada T6G 2G6
 Phone: 1-780-492-0701

RE: LP factor in the Rietveld refinement

[Leonid Solovyov]

Dear Peter,

Of course the LP correction can't be sample-dependent and for your 
configuration LP=0 should be Ok for all samples. It seems that you have an 
intensity loss at high-angles that may be partly compensated by LP=90. Possible 
reason may be in a misalignment of the anti-scattering slits or screen (knife) 
if you use them.

Best regards,
Leonid

***
 Leonid A. Solovyov
 Institute of Chemistry and Chemical Technology
 660049, K. Marx 42, Krasnoyarsk , Russia
 www.icct.ru/eng/content/persons/Sol_LA
 www.geocities.com/l_solovyov
***

--- On Thu, 7/23/09, Peter Y. Zavalij pzava...@umd.edu wrote:

From: Peter Y. Zavalij pzava...@umd.edu
Subject: RE: LP factor in the Rietveld refinement
To: rietveld_l@ill.fr
Date: Thursday, July 23, 2009, 4:52 AM

Well... the situation with LP is not so simple. Using TOPAS for refinement
data collected on D8 advance with Ni-filter and LynxEye detector I observe
the following: 
- For all samples LP=0 is OK and gives the best fit as it should be by the
book.
- HOWEVER for LaB6 standard LP=0 yields very poor fit for several high angle
reflections (120 deg. 2theta) while LP=90 gives perfect fit. The difference
in R factors 12% and 4% cannot be simply ignored...

Can anyone explain this?


Peter Zavalij 

X-ray Crystallographic Center
University of Maryland
College Park, MD

Office: (301)405-1861
Lab: (301)405-3230
Fax: (301)314-9121



  

RE: LP factor in the Rietveld refinement

[alortiz]

Dear All,

In this scenario, which should be the number for LP in Topas if ones has a
D8 with a primary monochromator for pure CuKalpha1?

thanks for the response,

angel l. ortiz


 Dear Peter,

 Of course the LP correction can't be sample-dependent and for your
 configuration LP=0 should be Ok for all samples. It seems that you have an
 intensity loss at high-angles that may be partly compensated by LP=90.
 Possible reason may be in a misalignment of the anti-scattering slits or
 screen (knife) if you use them.

 Best regards,
 Leonid

 ***
  Leonid A. Solovyov
  Institute of Chemistry and Chemical Technology
  660049, K. Marx 42, Krasnoyarsk , Russia
  www.icct.ru/eng/content/persons/Sol_LA
  www.geocities.com/l_solovyov
 ***

 --- On Thu, 7/23/09, Peter Y. Zavalij pzava...@umd.edu wrote:

 From: Peter Y. Zavalij pzava...@umd.edu
 Subject: RE: LP factor in the Rietveld refinement
 To: rietveld_l@ill.fr
 Date: Thursday, July 23, 2009, 4:52 AM

 Well... the situation with LP is not so simple. Using TOPAS for refinement
 data collected on D8 advance with Ni-filter and LynxEye detector I observe
 the following:
 - For all samples LP=0 is OK and gives the best fit as it should be by the
 book.
 - HOWEVER for LaB6 standard LP=0 yields very poor fit for several high
 angle
 reflections (120 deg. 2theta) while LP=90 gives perfect fit. The
 difference
 in R factors 12% and 4% cannot be simply ignored...

 Can anyone explain this?


 Peter Zavalij 

 X-ray Crystallographic Center
 University of Maryland
 College Park, MD

 Office: (301)405-1861
 Lab: (301)405-3230
 Fax: (301)314-9121

postdoc jobs in nanostructure determination and refinement

[Simon Billinge]

Hi Everyone,

I have two post-doc searches open in my group right now in
nanostructure refinement and determination using neutron/x-ray total
scattering and PDF analysis.

The first is located at Brookhaven National Lab and is more
experimental.  The posting is here:
https://jobs.bnl.gov/psc/Jobs/EMPLOYEE/HRMS/c/HRS_HRAM.HRS_CE.GBL

The second is located at Columbia University and is a position in the
DANSE project.  It is mostly computational, developing and applying
advanced software for powder diffraction and PDF analysis. The posting
is here:
http://academicjobs.columbia.edu/applicants/Central?quickFind=51512


I look forward to hearing from  interested people!  To apply for the
position(s) you should follow instructions at the links above.  If you
want more info, please feel free to contact me directly (don't reply
to the list!) at sb2896atcolumbia.edu.  More information about our
work and our publications can be found at http://nirt.pa.msu.edu/ (the
page is fairly up to date, though it hasn't been ported over to
Columbia yet!)

Best wishes,

Simon
--
Prof. Simon Billinge
Applied Physics  Applied Mathematics
Columbia University
500 West 120th Street
Room 200 Mudd, MC 4701
New York, NY 10027
Tel: (212)-854-2918 (o) 851-7428 (lab)

Condensed Matter and Materials Science
Brookhaven National Laboratory
P.O. Box 5000
Upton, NY 11973-5000
(631)-344-5387

email: sb2896 at columbia dot edu
home: http://nirt.pa.msu.edu/

RIET: Re: I am a newcome, how can I begin my rietveld refinement analysis

[Lachlan Cranswick]

Moderate self citation alert follows - the practical notes from the 
Canadian Powder Diffraction Workshop give starting practical on
fitting using GSAS which might help guide starting refinements
if you following the manual examples.

  http://www.cins.ca/cpdw/notes.html

Lachlan.


At 08:11 AM 11/30/2008 +0800, Mingtao Li wrote:
Hi, everyone,
  I am a newcome to Rietveld refinement. Actually I am a student
majored in photocatalytic splitting water for hydrogen production. We
want to analysis the structures of our photocatalysts via rietveld
method. For that purpose we got a X'pert Pro diffractionmeter from
Panalytica about 3 years ago. But rietveld is too difficult to start.
Now I have read some books and downloaded some programs from ccp14
such as fullprof, checkcell and so on. Also I have tested some
examples. However I am still confused. How can I determine the initial
value of some parameters such as U, V and W. Maybe I need a
Instrumental Resolution Function file, but how can set that file?

Can anybody give me some advice about this?

thanks a million.

-- 
Mingtao Li
State Key Laboratory of Multiphase Flow in Power Engineering
School of Energy and Power Engineering
Xi'an Jiaotong University
Xi'an, 710049
P.R.China
Tel: +86-29-8266 8296
Fax: +86-29-8266 9033
Email: [EMAIL PROTECTED]



---
Lachlan M. D. Cranswick
Contact outside working hours /
  Coordonnees en dehors des heures de travail:
NEW E-mail / courriel:  lachlanc *at* magma.ca
Home Tel: (613) 584-4226 ; Cell/mobile: (613) 401-6254
WWW: http://lachlan.bluehaze.com.au/
P.O. Box 2057, Deep River, Ontario, Canada, K0J 1P0

(please use clear titles in any Email - otherwise messages might
accidentally get put in the SPAM list due to large amount of junk
Email being received. If you don't get an expected reply to any
messages, please try again.)

(Essayez d'utiliser des titres explicites - sans quoi vos messages
pourraient aboutir dans un dossier de rebuts, du fait de la quantite
tres importante de pourriels recue. Si vous n'obtenez pas la reponse
attendue, merci de bien vouloir renvoyer un message.)

I am a newcome, how can I begin my rietveld refinement analysis

[Mingtao Li]

Hi, everyone,
 I am a newcome to Rietveld refinement. Actually I am a student
majored in photocatalytic splitting water for hydrogen production. We
want to analysis the structures of our photocatalysts via rietveld
method. For that purpose we got a X'pert Pro diffractionmeter from
Panalytica about 3 years ago. But rietveld is too difficult to start.
Now I have read some books and downloaded some programs from ccp14
such as fullprof, checkcell and so on. Also I have tested some
examples. However I am still confused. How can I determine the initial
value of some parameters such as U, V and W. Maybe I need a
Instrumental Resolution Function file, but how can set that file?

Can anybody give me some advice about this?

thanks a million.

-- 
Mingtao Li
State Key Laboratory of Multiphase Flow in Power Engineering
School of Energy and Power Engineering
Xi'an Jiaotong University
Xi'an, 710049
P.R.China
Tel: +86-29-8266 8296
Fax: +86-29-8266 9033
Email: [EMAIL PROTECTED]

Re: I am a newcome, how can I begin my rietveld refinement analysis

[Leonid Solovyov]

At the
initial stage you don’t need precise values of U, V, and W. You may set U=0,
V=0, and W equal to the squared FWHM of the highest peak.

 



Leonid


*
 
Leonid A. Solovyov
 
Institute of Chemistry and Chemical Technology
 
660049, K. Marx 42, Krasnoyarsk, Russia
 
www.icct.ru/eng/content/persons/Sol_LA

  www.geocities.com/l_solovyov

*
--- On Sun, 11/30/08, Mingtao Li [EMAIL PROTECTED] wrote:

Hi, everyone,
 I am a newcome to Rietveld refinement. Actually I am a student
majored in photocatalytic splitting water for hydrogen production. We
want to analysis the structures of our photocatalysts via rietveld
method. For that purpose we got a X'pert Pro diffractionmeter from
Panalytica about 3 years ago. But rietveld is too difficult to start.
Now I have read some books and downloaded some programs from ccp14
such as fullprof, checkcell and so on. Also I have tested some
examples. However I am still confused. How can I determine the initial
value of some parameters such as U, V and W. Maybe I need a
Instrumental Resolution Function file, but how can set that file?

Can anybody give me some advice about this?

thanks a million.

-- 
Mingtao Li
State Key Laboratory of Multiphase Flow in Power Engineering
School of Energy and Power Engineering
Xi'an Jiaotong University
Xi'an, 710049
P.R.China
Tel: +86-29-8266 8296
Fax: +86-29-8266 9033
Email: [EMAIL PROTECTED]



  

Re: PDF refinement pros and cons

[Jonathan Wright]

Hi Alan,

I also find it hard to understand the rationale behind this approach. 
G(r) can suffer from fourier truncation artifacts due to the finite q 
range of the data, but there seems to be no such limitation in a model. 
Isn't there a risk of fitting to truncation ripples with G(r)?


As for computational costs, Bricogne has explained this somewhat better 
than I can in section 1.3.4.4.4 (.5 and .7) of International Tables 
Volume B (reciprocal space). To paraphrase; when N.Nhkl is huge an FFT 
helps. The reciprocal space R factors (and gradients) can be found via 
an FFT of an electron density map with cost savings for large problems.


Not having a unit cell for liquids and amorphous materials does present 
a conceptual problem, which seems to need the Debye formula, see eg:


http://srs.dl.ac.uk/arch/dalai/Formula.html

It seems that function is mainly used for small angle scattering, where 
the q range is too small to make a pdf. The distance histogram method 
mentioned there also looks interesting for computational speeds.


Looking forwards to hearing some more opinions...

All the best,

Jon



AlanCoelho wrote:


HI all

Looking at the Pair Distribution Function and refinement I come away 
with the following:


Fitting in real space (directly to G(r)) should be equivalent to 
fitting to reciprocal space except for a difference in the cost 
function. Is this difference beneficial in any way. In other words 
does the radius of convergence increase or decrease.


The computational effort required to generate G(r) is proportional to 
N^2 where N is the number of atoms within the unit cell. The 
computational effort for generating F^2 scales by N.Nhkl where Nhkl is 
the number of observed reflections. Is there a speed benefit in 
generating G(r) - my guess is that it’s about the same. Note, 
generating G(r) by first calculating F and then performing a Fourier 
transform is not considered.


In generating the observed PDF there’s an attempt to remove 
instrumental and background effects. In reciprocal space these 
unwanted effects are implicitly considered. This seems a plus for the 
F^2 refinement.


From my simple understanding of the process, there seems to be good 
qualitative information in a G(r) pattern but can someone help in 
explaining the benefit of actually refining directly to G(r).


Cheers

Alan

RE: PDF refinement pros and cons

[Michael Glazer]

Alan
I think you are misunderstanding what the PDF method is used for. The
idea is to fourier transform directly the whole range of scattering
including peaks and background (after removing artifacts in the
background due to the diffractometer, air scattering etc).  In a highly
ordered crystal structure most of the diffracted intensity resides in
the peaks, and there is little background. In such a case normal
structure factor refinement  to get the crystal structure is the way to
go. However in a disordered structure there is a contribution to the
background and then the PDF method is useful to obtain local information
about atoms (it is a bit like the results of NMR or EXAFS). Thus for
instance if we have a structure in say a hexagonal symmetry with an atom
displaced along [001], we can find this using the  usual structure
factor methods which gives the AVERAGE crystal structure. However in the
example I am thinking of we also find a very large aniotropic
displacement parameter for this atom suggesting that the atom is not
actually displaced along [001] but at the unit cell level is slightly
displaced off this direction. PDF methods then show that the distance
between this atom and its nearest neighbours is consistent with the
off-axis displacement rather than for the atom being actually along
[001]. 
 
Sp the point is that the PDF method is useful for looking at local order
whereas the structure factor method is for average structures. Note byt
the way that there is no phase problem for the  PDF method.
The main problems with the PDF are
1. Being able to account properly for extraneous background so that the
remaining background which we need truly represents the crystal
2. The need for very high Q in order to obtain suficient resolution. The
use of copper radiation for example does not give sufficientky high Q
and so one needs generally to use vedry short wavelengths from a
synchrotron or use time of flight neutrons.
Mike Glazer
 

Fwd: PDF refinement pros and cons

[Simon Billinge]

Sorry, this got bounced last night so I am resending.

-- Forwarded message --
From: Simon Billinge [EMAIL PROTECTED]
Date: Thu, Jun 12, 2008 at 9:30 PM
Subject: Fwd: PDF refinement pros and cons
To: rietveld_l@ill.fr


Hi Alan, greetings to the Antipodes.

Fitting F(Q) and G(r) should give identical results if the model has
the same degrees of freedom in both spaces and the data are fit over
the same range, however:

To get G(r) we typically Fourier transform data over a Q-range up to
25-50  A-1 and we take Bragg and Diffuse scattering weighted by
inverse form-factor squared and by Q (the high-Q information is
therefore heavily weighted.  This means that to be fitting the
equivalent function in Q-space the fit should be made over the same
wide range of Q with the same Q-weighting.This is not typically
(ever?) done.


The Q-space model also has to fit the Bragg and diffuse scattering at
the same time.  This is possible in a kind of big-box scenario as
used in RMC type modeling where you can have correlated regions of
local order that extend only over a few angstroms or nm (and RMC fits
sometimes do fit in Q-space) maybe superimposed on a crystalline
background.  By fitting in real-space it is possible to separate the
local from the average structure by fitting G(r) over different
ranges.  r-dependent fits are now quick and becoming more common.
This is a computationally efficient way of getting information on the
local structure.

Finally, G(r) is a very intuitive function and the physical meaning is
often quite direct, so people like it.

Structural parameters tend to be differently correlated, and as Alan
points out the convergence may be different (though it is not clear
that it is better in real-space), but these things argue for fits to
be done in _both_ real and reciprocal space, if the above mentioned
difficulties can be overcome.  This is the approach of RMCProfile, for
afficionados of big-box modeling.  Pure real-space fitting with PDFgui
or (TOPASpdf Alan?) allows small-box crystallographic type models to
be applied to the study of local structure.  Both approaches can lead
to the physical insight we are after.

Those are my thoughts,

Simon


-- Forwarded message --
From: AlanCoelho [EMAIL PROTECTED]
Date: Thu, Jun 12, 2008 at 8:17 PM
Subject: PDF refinement pros and cons
To: rietveld_l@ill.fr


HI all



Looking at the Pair Distribution Function and refinement I come away
with the following:



Fitting in real space (directly to G(r)) should be equivalent to
fitting to reciprocal space except for a difference in the cost
function. Is this difference beneficial in any way. In other words
does the radius of convergence increase or decrease.



The computational effort required to generate G(r) is proportional to
N^2 where N is the number of atoms within the unit cell.  The
computational effort for generating F^2 scales by N.Nhkl where Nhkl is
the number of observed reflections. Is there a speed benefit in
generating G(r) - my guess is that it's about the same. Note,
generating G(r) by first calculating F and then performing a Fourier
transform is not considered.



In generating the observed PDF there's an attempt to remove
instrumental and background effects. In reciprocal space these
unwanted effects are implicitly considered. This seems a plus for the
F^2 refinement.



From my simple understanding of the process, there seems to be good
qualitative information in a G(r) pattern but can someone help in
explaining the benefit of actually refining directly to G(r).



Cheers

Alan




--
Prof. Simon Billinge
Applied Physics  Applied Mathematics
Columbia University
500 West 120th Street
Room 200 Mudd, MC 4701
New York, NY 10027
Tel: (212)-854-2918

Condensed Matter and Materials Science
Brookhaven National Laboratory
P.O. Box 5000
Upton, NY 11973-5000

email: sb2896 at columbia dot edu
home: http://nirt.pa.msu.edu/



-- 
Prof. Simon Billinge
Applied Physics  Applied Mathematics
Columbia University
500 West 120th Street
Room 200 Mudd, MC 4701
New York, NY 10027
Tel: (212)-854-2918

Condensed Matter and Materials Science
Brookhaven National Laboratory
P.O. Box 5000
Upton, NY 11973-5000

email: sb2896 at columbia dot edu
home: http://nirt.pa.msu.edu/

RE: PDF refinement pros and cons

[AlanCoelho]

Thanks all for the PDF explanations

I think I'm beginning to understand. To summarise what we know:

- PDF for powder data is a Patterson function (as Alan Hewat stated) in one
dimension that plots the histogram of atom separation

- It will show quite nicely the short range order and then possible disorder
longer range (eg. Rotated bucky balls)


There seems to be a few issues:

1) PDF refinement on long range ordered crystals is the same as Rietveld
refinement and little benefit if any is obtained by fitting to G(r)
directly. It's useful however to view a PDF to ascertain whether there's
disorder even in the event of a good Rietveld fit. 

2) A nano-sized crystal, as Vincent mentioned, can be modelled by arranging
the atoms such that it's G(r) matches the observed PDF. This can be done
with disregard to lattice parameters and periodicity in general.

3) a mix of (1) and (2) as in regularly arranged bucky balls but with the
balls randomly rotated.


The ability to do number (2) is what can't be done with normal Rietveld
refinement as a disordered object has no periodicity and no Bragg peaks.
Arranging atoms in space to form an object with disregard to lattice
parameters and space groups can yield a G(r) to match an observed PDF.
However even very small crystals would have 10s of thousands of atoms. Its
seems difficult to try and determine atomic positions of such an object from
a PDF.

It may be worthwhile to look at what the glass community has done (the Debye
Formula - thanks Jon - still reading).

The main point that is still confusing me is whether current PDF analysis
considers an object (or should) or is it the case that most materials are
periodic (with an enlarged unit cell) with parts of the cell being
disordered.

Cheers
Alan

Re: PDF refinement pros and cons

[Martin Dove]

Dear all

I have to weigh in here as someone who has been using total scattering  
measurements for some while now.


I suggest that since this is a crystallography mail list I should  
restrict discussion to crystals and not amorphous or nano-crystalline  
materials.


What Bragg diffraction gives is the single-particle distribution  
functions. Typically Rietveld refinement gives something like the mean  
position of an atom. When you calculate bond lengths, you are actually  
calculating the distance between mean positions.


On the other hand, PDF gives you the what it says, namely a pair  
distribution function that is a histogram of instantaneous distances  
between atoms, which is a fundamentally different quantity from the  
mean positions between atoms.


Now if you have a simple crystal (let us say NaCl) where the atoms are  
vibrating harmonically, the mean of the instantaneous distances  
between atoms obtained from Rietveld, which we can write as Na–Cl,  
is not going to differ from the distances between mean positions  
obtained from a PDF analysis, which we can write as Na–Cl; in this  
case you don't gain much. But, if you have a lot of disorder that is  
not harmonic, then the distance between mean positions is not in any  
way related to the actual instantaneous bond lengths. We saw this  
clearly from our measurements of quartz. In this case, as quartz goes  
through the phase transition, the distance between the mean Si and O  
positions, Si–O, decreases a lot on heating through the phase  
transition, whereas the mean instantaneous interatomic distance from  
pdf, namely Si–O, doesn't appear to change at all through the phase  
transition (as you might expect). We see Si–O  Si–O, as you  
would expect, with the difference increasing on heating, but the  
difference vanishing on cooling down to 0 K (again as you would expect).


There are many interesting cases where the local structure is not a  
mere reflection of the long-range order, and for these a combination  
of pdf and Rietveld is great. I would stress that we are convinced  
that one should use the information contained in the Bragg peaks  
explicitly as well as the information contained within the total  
scattering (Bragg peaks + diffuse scattering background).


I would make a small number of additional comments:
1. Background corrections are critical, but are doable. The downside  
is that to get good data you do have to measure for some hours on an  
instrument like GEM at ISIS
2. You need to go to high Q. GEM lets us get to 50 Å^–1. By  
comparison, measuring on Cu Kalpha out to theta = 90° only gets to Q  
of 8 Å^–1. The requirement to go to high Q is to reduce truncation  
ripples and to improve real-space resolution. Signals are weak at  
higher Q, hence the need for longer counting times.
3. The ability to go to high Q means you could collect a lot of data.  
The huge quantities of data this would mean in 3d from a single  
crystal are unviable to work with, and hence powders are the only real  
option. But just as Rietveld has shown that powders are okay for  
structure, we have found that powder in total scattering are okay if  
your questions are not too ambitious.
4. The pdf from total scattering is actually not the same as the  
Patterson, since the Patterson is constructed only from the Bragg peaks.
5. We use Reverse Monte Carlo to analyse our data, fitting not only to  
the total scattering and pdf but also to the Bragg peaks. Since Bragg  
peaks have hkl indices, this enables us to recover some 3d  
information. RMC ignites debate; my view is that it works.


Bottom line is that there are classes of scientific problem for which  
a proper PDF analysis gives you very new insights. And it no longer  
needs to be a specialist tool.


Best wishes

Martin Dove

On 13 Jun 2008, at 09:39, Favre-Nicolin Vincent wrote:


Hi,

 I've only begun to look at pdf, but it seems to me that pdf is only  
really

interesting if you want to model non-crystalline material (or
nano-crystalline), so that there is no long-range periodicity  
(limited size,
defects on the borders, large strain, variation in composition,...),  
and
therefore the F^2 calculation is not even on option. The reason I've  
begun to
look at pdf is that I'm working on a sample with nano-columns that  
are (at
best !) 3 or 4 nm in diameter - we're still looking for the Bragg  
peaks !


 From a computationnal point of view, I think it takes in practice  
much more
time to compute the pdf - indeed it is N^2, but N does not even  
correspond to
a single unit cell (or sub-unit if centered/centro), but the entire  
object
(if nano-sized). If the pdf is computed for a truly crystalline  
compound, it
can be reduced to N_asym * N_shell (atoms in the asym unit cell /  
asym in the

shell of radius corresponding to the largest d you're interested in).

Vincent
--
Vincent Favre-Nicolin   http://vincefn.net
Université Joseph Fourier

Re: PDF refinement pros and cons

[Matteo Leoni]

just my two cents.. even if I'm aware that times are not yet mature for a 
comparison of this type.


There is lot of enthusiasm behind the use of the PDF approach and the 
number of symposia in conferences, as well as the number of talks on the 
subject is increasing day after day... the true question is: if we're 
given the same dataset (experimental data I mean), what can we get out of 
the two approaches? And what's the advantage of one versus the other?
The furher question is: PDF or total scattering? The two things IMHO are 
different, even if there is a general (unjustified) belief that they're 
the same, cause in the PDF approach the whole information in the pattern 
in used. Well, you can do total pattern analysis without using a PDF 
approach (I do it weekly): you just need the right tools!
This said, with lab data forget about PDF... perhaps with a silver or a 
tungsten tube you can get futher in reciprocal space but... other methods 
are the winners here! You can do a Debye analysis, no problem in that, but 
in that case you fit on the data and not on the PDF (the PDF is an 
intermediate byproduct).
With synchrotron data: a pattern employed to obtain the PDF should be of 
such a quality that it can be easily used also as is in a Rietveld (or 
alternative) approach. What's different there:

- in order to fit the background, the PDF approach considers features
  ignored by most (if not all) Rietveld people (proper account for
  background allows Bragg+dffuse scattering to be considered)
  This is a problem of the Rietveld approach where a peak is any bell-shaped
  function and background is a well behaving polynomial.
  This is a weakness that can be easily accounted for!
- the PDF approach suffers of truncation problems (check any published PDF
  and you'll see the ringing...). The higher the ringing, the higher the
  indetermination in the positions and intensity of maxima (other reason
  for the need of high q data). We know we have access to synchrotrons or
  neutrons but that's not routine work for everyone!
- the Rietveld approach is not suited for problems showing 3D periodicity.
  You can account for that in simple cases by reducing the symmetry of the
  problem and considering the streaking effects as Bragg effects showing
  anisotropic broadening (fcc/hcp, bcc/orthorhombic cases can be easily
  worked out). Also in this case, alternatives exist to deal with
  problems where structure and microstructure interplay, fully considering
  Bragg and diffuse scattering even with lab data (DIFFaX+ is one of them)
  without transforming the data into PDF. The Rietveld method is not
  thought to solve all crystallographic problems!
  For sure if you have a PDF then you can visually see the effect that in
  the diffraction pattern can be well hidden!
- microstructural effects.. well that's interesting: Rietveld is usually
  rough there (exceptions exists where a WPPM approach has been attached
  some structural information, or where proper microstructural models
  have been imported into the Rietveld). The PDF approach isstill
  lacking here and this is where things will come out in the next future

much more can be added here but in the end my opinion is that there is no 
winner and for sure I won't leave reciprocal space methods to fully jump 
on the train of real space ones. On the other hand I still keep an eye on 
real space methods as, for their inner nature, are more intuitive as they 
are directly related to the object we like to study: after all, atoms are 
positioned in real space
There is a loser, though: anyone using those approaches as black 
boxes (believing they work cause they spite out some result). I'd go for 
the best of the two worlds (direct / reciprocal) when data quality allows 
for that, and in any case for the most suited to my need (I'd not use 
Rietveld when I have some structure/microstructure interplay, or use the 
PDF when I have nanocrystalline materials). And I'd use both and compare 
the results when I can do it!


Not having a unit cell for liquids and amorphous materials does present a 
conceptual problem, which seems to need the Debye formula, see eg:


http://srs.dl.ac.uk/arch/dalai/Formula.html

It seems that function is mainly used for small angle scattering, where the q 
range is too small to make a pdf. The distance histogram method mentioned 
there also looks interesting for computational speeds.


I'd skip the amorphous/liquids case. And I do not agree on the last 
sentence, but that's another story. Skipping the true small angle 
region, the Debye approach allows modelling the whole powder diffraction 
pattern up to any q value
The Debye approach is somewhat intermediate: instead of massaging the data 
to get the PDF out, you work bottom up, building a diffraction pattern via 
the true PDF (not an RDF) calculated from a real space object.
Yes, there are several tricks to get it fast (histogram and distance 
binning/harvesting are among them, but 

RE: PDF refinement pros and cons

[Whitfield, Pamela]

I'm only going to stick my big toe in here on a practical note for
lab-based studies.
I managed to get the Bruker Vantec detector to work with MoKa quite
nicely for some non-ambient work and decided to see if I could get
useful data for PDF from some battery cathode materials (I think it was
up to 17A-1 or so).  The PSD means the data collection time is more
reasonable to get low noise and the data did show the metal-oxygen bond
splitting that was supposed to be there from synchrotron studies.  
Next step is AgKa for a more demanding non-ambient application I'm
working on so I'll find out if the Vantec works or whether an high
energy optimized Si-strip detector is the way to go.  Should be fun!

Pam

-Original Message-
From: Matteo Leoni [mailto:[EMAIL PROTECTED] 
Sent: June 13, 2008 8:18 AM
To: Jonathan Wright
Cc: rietveld_l@ill.fr
Subject: Re: PDF refinement pros and cons

just my two cents.. even if I'm aware that times are not yet mature for
a 
comparison of this type.

There is lot of enthusiasm behind the use of the PDF approach and the 
number of symposia in conferences, as well as the number of talks on the

subject is increasing day after day... the true question is: if we're 
given the same dataset (experimental data I mean), what can we get out
of 
the two approaches? And what's the advantage of one versus the other?
The furher question is: PDF or total scattering? The two things IMHO are

different, even if there is a general (unjustified) belief that they're 
the same, cause in the PDF approach the whole information in the
pattern 
in used. Well, you can do total pattern analysis without using a PDF 
approach (I do it weekly): you just need the right tools!
This said, with lab data forget about PDF... perhaps with a silver or a 
tungsten tube you can get futher in reciprocal space but... other
methods 
are the winners here! You can do a Debye analysis, no problem in that,
but 
in that case you fit on the data and not on the PDF (the PDF is an 
intermediate byproduct).
With synchrotron data: a pattern employed to obtain the PDF should be of

such a quality that it can be easily used also as is in a Rietveld (or 
alternative) approach. What's different there:
- in order to fit the background, the PDF approach considers features
   ignored by most (if not all) Rietveld people (proper account for
   background allows Bragg+dffuse scattering to be considered)
   This is a problem of the Rietveld approach where a peak is any
bell-shaped
   function and background is a well behaving polynomial.
   This is a weakness that can be easily accounted for!
- the PDF approach suffers of truncation problems (check any published
PDF
   and you'll see the ringing...). The higher the ringing, the higher
the
   indetermination in the positions and intensity of maxima (other
reason
   for the need of high q data). We know we have access to synchrotrons
or
   neutrons but that's not routine work for everyone!
- the Rietveld approach is not suited for problems showing 3D
periodicity.
   You can account for that in simple cases by reducing the symmetry of
the
   problem and considering the streaking effects as Bragg effects
showing
   anisotropic broadening (fcc/hcp, bcc/orthorhombic cases can be easily
   worked out). Also in this case, alternatives exist to deal with
   problems where structure and microstructure interplay, fully
considering
   Bragg and diffuse scattering even with lab data (DIFFaX+ is one of
them)
   without transforming the data into PDF. The Rietveld method is not
   thought to solve all crystallographic problems!
   For sure if you have a PDF then you can visually see the effect that
in
   the diffraction pattern can be well hidden!
- microstructural effects.. well that's interesting: Rietveld is usually
   rough there (exceptions exists where a WPPM approach has been
attached
   some structural information, or where proper microstructural models
   have been imported into the Rietveld). The PDF approach isstill
   lacking here and this is where things will come out in the next
future

much more can be added here but in the end my opinion is that there is
no 
winner and for sure I won't leave reciprocal space methods to fully jump

on the train of real space ones. On the other hand I still keep an eye
on 
real space methods as, for their inner nature, are more intuitive as
they 
are directly related to the object we like to study: after all, atoms
are 
positioned in real space
There is a loser, though: anyone using those approaches as black 
boxes (believing they work cause they spite out some result). I'd go for

the best of the two worlds (direct / reciprocal) when data quality
allows 
for that, and in any case for the most suited to my need (I'd not use 
Rietveld when I have some structure/microstructure interplay, or use the

PDF when I have nanocrystalline materials). And I'd use both and compare

the results when I can do it!

 Not having a unit cell for liquids and amorphous

Re: PDF refinement pros and cons

[Alan Hewat]

Martin gives a good example for which interesting new information was
obtained from the PDF function - the fact that the Si-O bond lengths do
not change during a structural transition in quartz.

But quartz is a rather special case. First of all quartz is simple enough
that the Si-O distances might actually be measured directly from the PDF -
this cannot often be the case.

Second quartz is a material that exhibits strong librational motion of
small rigid units (associated with the transition) and unless such
libration is correctly modelled (using spherical harmonics in a periodic
structural model) this is a textbook example of Rietveld refinement
under-estimating bond lengths by trying to fit a banana-shaped
distribution with an ellipsoid. With a correct model for libration you
would also obtain correct bond lengths by refinement from the Bragg peaks
alone. As Martin says, the Bragg peaks describe the average periodic
structure, which in this case consists of banana-shaped O-distributions
at constant distance from Si.

Let's not quibble over whether the PDF and Patterson functions are the
same or not; in 1935 Patterson didn't have a computer and could only
measure Bragg peaks. What he described is the instantaneous electron
density folded with itself, which is precisely the definition of the PDF
today. If you obtain this as he did by Fourier transforming the Bragg
intensities (F**2) you do ignore correlations that are non-periodic with
the lattice, but he had no choice.

Much is made of total scattering implying that modulations in the
background bring essential new information to PDF not available to
Rietveld. Total scattering was in fact advocated for Rietveld refinement
by Sabine 20+ years ago - see Young's book on the Rietveld method. (Sabine
wrote the first neutron paper with Rietveld (Nature 1961) and coined the
term Rietveld Refinement). A better example of the interest of background
scattering might be anti-ferroelectric perovskite transitions (Mike:-),
where atom displacements doubling the cell manifest as diffuse scattering
between peaks.

Of course if we *define* Rietveld refinement as Bragg peak refinement, we
restrict its power. I would define Rietveld refinement as direct
refinement of the structural parameters (atom positions etc) to fit the
observed data (without first extracting structure factors or performing
other intermediate operations, which was usual before Rietveld).

I still think that Fourier transforming the total scattering, and then
refining against that, cannot do more than refining against the total
scattering directly. Martin almost says as much when he talks about RMC.
The original question I think, was whether there is any computational
advantage in Fourier transforming the data before refining. Probably not.

Alan.
__
Dr Alan Hewat, NeutronOptics, Grenoble, FRANCE
[EMAIL PROTECTED] +33.476.98.41.68
  http://www.NeutronOptics.com/hewat
__

Re: PDF refinement pros and cons

[Martin Dove]

To continue ...

On 13 Jun 2008, at 14:37, Alan Hewat wrote:


Martin gives a good example for which interesting new information was
obtained from the PDF function - the fact that the Si-O bond lengths  
do

not change during a structural transition in quartz.

But quartz is a rather special case. First of all quartz is simple  
enough
that the Si-O distances might actually be measured directly from the  
PDF -

this cannot often be the case.


Yes indeed, it is a special case. Which is really my point. In many  
cases the traditional Rietveld approach is exactly what is needed.  
Others may have different opinions, but in my view the overhead of  
collecting and analysing total scattering data is too high for  
anything other than the special cases. The special cases are more  
common in our research than the name might suggest, but you might  
expect that given the nature of research!


I realise that your special case point here concerns the simplicity of  
the quartz structure. This is a valid point, but actually the short- 
range distances can be understood for rather more complicated cases  
than quartz. It is certainly the case though that PDF analysis will  
run out of steam when even the short-range peaks overlap too much, but  
fortunately lots of examples present interest science challenges  
without this problem.




Second quartz is a material that exhibits strong librational motion of
small rigid units (associated with the transition) and unless such
libration is correctly modelled (using spherical harmonics in a  
periodic

structural model) this is a textbook example of Rietveld refinement
under-estimating bond lengths by trying to fit a banana-shaped
distribution with an ellipsoid. With a correct model for libration you
would also obtain correct bond lengths by refinement from the Bragg  
peaks

alone. As Martin says, the Bragg peaks describe the average periodic
structure, which in this case consists of banana-shaped O- 
distributions

at constant distance from Si.


Yes, this is true. Many materials though have these sorts of units, or  
at least, many materials that give rise to interesting physical  
phenomena such as negative thermal expansion and phase transitions do.


What I would comment on is that in such cases one should indeed do any  
structure analysis with a proper single-atom distribution function,  
such as a banana shape, rather than trying to force a standard thermal  
ellipsoid model. However, my point is that this tells you one thing,  
but it won't give you the pair distribution function, and for some  
studies (the special cases) you might want scientific insight from the  
pair distribution as well as (not instead of) the single-particle  
distribution function.




Let's not quibble over whether the PDF and Patterson functions are the
same or not; in 1935 Patterson didn't have a computer and could only
measure Bragg peaks. What he described is the instantaneous electron
density folded with itself, which is precisely the definition of the  
PDF

today. If you obtain this as he did by Fourier transforming the Bragg
intensities (F**2) you do ignore correlations that are non-periodic  
with

the lattice, but he had no choice.

Much is made of total scattering implying that modulations in the
background bring essential new information to PDF not available to
Rietveld. Total scattering was in fact advocated for Rietveld  
refinement
by Sabine 20+ years ago - see Young's book on the Rietveld method.  
(Sabine
wrote the first neutron paper with Rietveld (Nature 1961) and coined  
the
term Rietveld Refinement). A better example of the interest of  
background
scattering might be anti-ferroelectric perovskite transitions  
(Mike:-),
where atom displacements doubling the cell manifest as diffuse  
scattering

between peaks.

Of course if we *define* Rietveld refinement as Bragg peak  
refinement, we

restrict its power. I would define Rietveld refinement as direct
refinement of the structural parameters (atom positions etc) to fit  
the
observed data (without first extracting structure factors or  
performing

other intermediate operations, which was usual before Rietveld).


One indeed has to be very careful about semantics (or just 'names 'in  
less subtle cases). If you define Patterson functions as only  
involving the Bragg peaks, it is different from PDF. If you define  
Patterson as from the whole pattern (including diffraction), then  
indeed you formally have the PDF.


The one thing that I would stress about semantics concerns  
understanding the difference between the information content of the  
Bragg peaks and the information content of the Bragg + diffuse  
scattering, ie the difference in the information content of long-range  
order and short-range order. And I would stress that it is about  
understanding the difference in information, and not about judging  
whether one is better than the other. Where I think that the  
differences are useful is when you

Re: PDF refinement pros and cons

[Robert Von Dreele]

Let's see if this gets through. I recently moved to APS  my official 
e-mail address changed but not my public one ([EMAIL PROTECTED]).

OK, my comments on PDF vs/and Rietveld refinement.
First both techniques use the same raw data; one directly  the other 
after a lot of corrections (some perhaps dubious) and a few Fourier 
transforms.
Why dubious? Because it is not clear that the signal not in the Bragg 
peaks actually belongs to the crystalline part of the sample. All powder 
samples have a considerable amount of surface area and that surface 
structure can make a substantial contribution to the total scattering. 
Moreover, the material may contain a substantial amorphous (glassy!) 
fraction not associated with the crystalline powder particles at all - 
that depends on the preparation. So unless one knows that the crystal 
structure as obtained in a first-pass Rietveld refinement has problems 
(e.g. peculiar bond lengths), doing a PDF may give quite an erroneous 
view of the structure because it can not discriminate between the 
various possible sources of diffuse scattering. If a PDF is then done to 
try and work out what the local structure is around these problem 
areas; that local structure model can be used as a disorder model for a 
better Rietveld refinement (constraints/restraints may be needed to be 
sure the refinement focuses on the parameters of interest!). Remember 
the disorder does affect the Bragg intensities and should, in principle, 
be subject to proper modeling. BTW that is what folks did before 
Rietveld refinement was invented - go see an old paper (~1970, I think) 
by Cheetham, et al. on defect fluorites.
We've heard several references to the Debye equations. I hope all 
realize that these have been a part of GSAS for a very long time, first 
as alternative background functions and later as separate diffuse 
scattering contributions. BobThere are some complexities here - have a 
look at the relevant section in the GSAS Manual - having to do with the 
nature of the local defect giving rise to the diffuse scattering so 
there are 3 different functional forms for this in GSAS. I'm not sure 
the now conventional PDF analysis considers these effects in full.
It is also worth noting that a substantial contribution under all the 
Bragg peaks comes from 1st order phonon scattering - this is ignored in 
both Rietveld refinement and PDF analysis. An old study of nickel by 
Colin Winsor showed that the effective thermal motion derived from a 
(now named) Rietveld refinement is off by ~10% due to this extra 
contribution.
I fully agree with Alan's definition of Rietveld Refinement; I usually 
describe it as a curve fitting to the entire powder diffraction 
profile (Bragg peaks and diffuse scattering/background).

Bob
Alan Hewat wrote:

Martin gives a good example for which interesting new information was
obtained from the PDF function - the fact that the Si-O bond lengths do
not change during a structural transition in quartz.

But quartz is a rather special case. First of all quartz is simple enough
that the Si-O distances might actually be measured directly from the PDF -
this cannot often be the case.

Second quartz is a material that exhibits strong librational motion of
small rigid units (associated with the transition) and unless such
libration is correctly modelled (using spherical harmonics in a periodic
structural model) this is a textbook example of Rietveld refinement
under-estimating bond lengths by trying to fit a banana-shaped
distribution with an ellipsoid. With a correct model for libration you
would also obtain correct bond lengths by refinement from the Bragg peaks
alone. As Martin says, the Bragg peaks describe the average periodic
structure, which in this case consists of banana-shaped O-distributions
at constant distance from Si.

Let's not quibble over whether the PDF and Patterson functions are the
same or not; in 1935 Patterson didn't have a computer and could only
measure Bragg peaks. What he described is the instantaneous electron
density folded with itself, which is precisely the definition of the PDF
today. If you obtain this as he did by Fourier transforming the Bragg
intensities (F**2) you do ignore correlations that are non-periodic with
the lattice, but he had no choice.

Much is made of total scattering implying that modulations in the
background bring essential new information to PDF not available to
Rietveld. Total scattering was in fact advocated for Rietveld refinement
by Sabine 20+ years ago - see Young's book on the Rietveld method. (Sabine
wrote the first neutron paper with Rietveld (Nature 1961) and coined the
term Rietveld Refinement). A better example of the interest of background
scattering might be anti-ferroelectric perovskite transitions (Mike:-),
where atom displacements doubling the cell manifest as diffuse scattering
between peaks.

Of course if we *define* Rietveld refinement as Bragg peak refinement, we
restrict its power. I would define

RE: PDF refinement pros and cons

[Yokochi, Alexandre]

Pam and all,

I too have been looking at materials using in house lab data.  Using an
Ag rotating anode (I actually used Ag-k beta for simplicity of the lack
of peak splitting) and an MSC curved imaging plate, and very long
exposures we got data we found quite useful.  However, I stopped playing
in that particular corner of the sandbox a while ago to focus on other
stuff (more process engineering than materials science related) and
would be interested in learning what's new in lab based data.

Alex Y


Dr. Alexandre (Alex) F. T. Yokochi
Assistant Professor
Department of Chemical Engineering
Oregon State University
Corvallis, OR 97331-2702

Voice:  (541) 737-9357
Fax:  (541) 737-4600
http://oregonstate.edu/~yokochia

 -Original Message-
 From: Whitfield, Pamela [mailto:[EMAIL PROTECTED]
 Sent: Friday, June 13, 2008 6:26 AM
 To: Matteo Leoni; Jonathan Wright
 Cc: rietveld_l@ill.fr
 Subject: RE: PDF refinement pros and cons
 
 I'm only going to stick my big toe in here on a practical note for
 lab-based studies.
 I managed to get the Bruker Vantec detector to work with MoKa quite
 nicely for some non-ambient work and decided to see if I could get
 useful data for PDF from some battery cathode materials (I think it
was
 up to 17A-1 or so).  The PSD means the data collection time is more
 reasonable to get low noise and the data did show the metal-oxygen
bond
 splitting that was supposed to be there from synchrotron studies.
 Next step is AgKa for a more demanding non-ambient application I'm
 working on so I'll find out if the Vantec works or whether an high
 energy optimized Si-strip detector is the way to go.  Should be fun!
 
 Pam
 

Re: PDF refinement pros and cons

[Olga Smirnova]

Dear all,

 Let's see if this gets through. I recently moved to APS  my official
 e-mail address changed but not my public one ([EMAIL PROTECTED]).
 OK, my comments on PDF vs/and Rietveld refinement.

...

 I fully agree with Alan's definition of Rietveld Refinement; I usually
 describe it as a curve fitting to the entire powder diffraction 
 profile (Bragg peaks and diffuse scattering/background).
 Bob

Myself feel safer in the reciprocal space.
Let's ask Hugo Rietveld what is 'profile matching' then.
If some body suggests to fit the total scattering data directly to a
set of interatomic distances, that must be not Hugo Rietveld.

Best wishes,
OS

PDF refinement pros and cons

[AlanCoelho]

HI all

 

Looking at the Pair Distribution Function and refinement I come away with
the following:

 

Fitting in real space (directly to G(r)) should be equivalent to fitting to
reciprocal space except for a difference in the cost function. Is this
difference beneficial in any way. In other words does the radius of
convergence increase or decrease.

 

The computational effort required to generate G(r) is proportional to N^2
where N is the number of atoms within the unit cell.  The computational
effort for generating F^2 scales by N.Nhkl where Nhkl is the number of
observed reflections. Is there a speed benefit in generating G(r) - my guess
is that it's about the same. Note, generating G(r) by first calculating F
and then performing a Fourier transform is not considered. 

 

In generating the observed PDF there's an attempt to remove instrumental and
background effects. In reciprocal space these unwanted effects are
implicitly considered. This seems a plus for the F^2 refinement.

 

From my simple understanding of the process, there seems to be good
qualitative information in a G(r) pattern but can someone help in explaining
the benefit of actually refining directly to G(r).

 

Cheers

Alan

 

1/Yo**2 weighting scheme in Rietveld refinement

[Franz Werner]

Dear Rietvelders

I just stumbled on the paper Weighting Scheme for the Minimization Function in 
Rietveld Refinement (H. Toraya, http://dx.doi.org/10.1107/S0021889897011096) 
where w=1/Yo**2 is proposed (By using the new weighting scheme, the accuracy 
of positional parameters of the test sample was significantly improved relative 
to the weight function 1/Yo, which weights the medium and strong intensities 
more heavily, is in accordance with statistical theory and gives a better 
overall fit between the observed and calculated powder patterns.).

Does anyone have experience with this weighting scheme?

Thanks for your advise.

Franz Werner
-- 
Psst! Geheimtipp: Online Games kostenlos spielen bei den GMX Free Games! 
http://games.entertainment.gmx.net/de/entertainment/games/free

Re: 1/Yo**2 weighting scheme in Rietveld refinement

[Brian H. Toby]

On Mar 14, 2008, at 5:41 AM, Franz Werner wrote:

w=1/Yo**2 [weighting] is proposed (By using the new weighting  
scheme, the accuracy of positional parameters of the test sample  
was significantly improved relative to the weight function 1/Yo,  
which weights the medium and strong intensities more heavily, is in  
accordance with statistical theory and gives a better overall fit  
between the observed and calculated powder patterns.).



I'll give my stock comment in response. For fitting of data with only  
statistical errors, you obtain the smallest uncertainties on the fit  
parameters when weighting is w = sigma**-2. This requires that you  
know the experimental uncertainties (no image plates or other non- 
quanta counting detectors). Further, if your data have only  
statistical errors, then chi**2 ~= 1. Any other weighting scheme is  
effectively throwing away data.


In cases where there are non-statistical error sources, then you do  
gain by down-weighting the data most effected by systematic errors.  
However, be aware that the systematic error you are choosing to  
reject could be trying to tell you that really would want to know:  
e.g. the model you are using is incomplete or even wrong.


If you have reason to believe that your measurements are inaccurate  
in a particular way (for example uncorrected deadtime, sample  
roughness, or funky peak shapes, etc) it might make sense to change  
the weighting function, but I personally don't think there is a  
generic source of error in all diffraction measurements that would  
make it appropriate to use the same weighting change for all types of  
data and materials.


Brian

Powder Diffraction and Rietveld Refinement School, Durham

[Ivana R Evans]

Dear All,

On behalf of the Physical Crystallography Group of the British 
Crystallographic Association, I am pleased to announce the Powder 
Diffraction and Rietveld Refinement School at Durham University, 30th 
March-3rd April 2008. Lectures will be given by Jeremy Cockcroft, Andy 
Fitch, John Evans and Ivana Evans. There will also be small group 
tutorials and a large number of practical hands-on computer sessions.


Topics to be covered will include:

· Data collection strategies for X-ray and neutron diffraction
· Constant wavelength and time of flight diffraction
· Modelling peak shapes
· Indexing powder patterns
· Rietveld, Le Bail and Pawley fitting methods
· X-ray and neutron combined Rietveld refinement
· Extended solids and molecular systems
· Restrained refinements
· Rigid body refinements

Accommodation will be at a Durham College and lectures/computer 
workshops will be held in the Chemistry Department.


We have managed to raise significant sponsorship from EPSRC, PCG and 
IUCr, and will be able to offer a significant number of bursaries to the 
UK students and a smaller number of bursaries to overseas participants.


The number of participants is limited and applications are accepted 
online, via the school website: 
http://www.dur.ac.uk/john.evans/webpages/pcg_rietveld_school_2008.htm.


For more information please email [EMAIL PROTECTED]  or 
[EMAIL PROTECTED]



Dr. Ivana Radosavljevic Evans
Academic Fellow in Structural/Materials Chemistry
Department of Chemistry
University of Durham
Science Site
Durham DH1 3LE, U.K.
Office: CG 244
Phone: (0191) 334-2594
Fax: (0191) 384-4737
www.dur.ac.uk/ivana.radosavljevic

Parameters in Rietveld refinement

[Alan Hewat]

Forwarded from Mike Glazer:

I think that very often people tend to overlook what is in fact the
primary purpose of Rietveld: it is to get structural parameters out that
have some meaning. The Rietveld method consists of two sets of
refinement variables. First of all you have the structural parameters
(atomic positions, displacement parameters, site occupation etc) and
secondly instrumental type parameters whose purpose is to enable fitting
of the profiles. In my experience playing around with different line
shapes and profile parameters (within reason) usually has a relatively
minor effect on the structural parameters, especially atomic positions.

What they do however is to make the profile fit look nicer and give you
lower R factors. And then everyone feels happier. However, the
importance of Rietveld is in the structural parameters that you get out.

The meanings of the instrumental parameters are fairly obtuse as this is
where most of the errors end up. The U V W parameters of Cagliotti are
meaningless. To see this, the next time you do a refinement with U V and W
take a look at the correlation matrix between these parameters:

you will see that they are invariably almost 100% correlated. That is why
in fact you are probably better to fix one and refine just two.

It for this reason also that I have little faith in the meaning of refined
parameters such as preferred orientation, except perhaps in some very
rough sense.

Mike Glazer
_
Dr Alan Hewat, ILL Grenoble, FRANCE [EMAIL PROTECTED]fax+33.476.20.76.48
+33.476.20.72.13 (.26 Mme Guillermet) http://www.ill.fr/dif/people/hewat/
_



Alan
I wanted to send the 
following to the Rietveld group but it was rejected. Any 
ideas?


I think that very often people tend to overlook what is in fact the primary 
purpose of Rietveld: it is to get structural parameters out that have some 
meaning. The Rietveld method consists of two sets of refinement variables. First 
of all you have the structural parameters (atomic positions, displacement 
parameters, site occupation etc) and secondly instrumental type parameters whose 
purpose is to enable fitting of the profiles. In my experience playing around 
with different line shapes and profile parameters (within reason) usually has a 
relatively minor effect on the structural parameters, especially atomic 
positions.
What they do however is to make the profile fit look nicer and give you lower 
R factors. And then everyone feels happier. However, the importance of Rietveld 
is in the structural parameters that you get out.
The meanings of the instrumental parameters are fairly obtuse as this is 
where most of the errors end up. The U V W parameters of Cagliotti are 
meaningless. To see this, the next time you do a refinement with U V and W take 
a look at the correlation matrix between these parameters:
you will see that they are invariably almost 100% correlated. That is why in 
fact you are probably better to fix one and refine just two.
It for this reason also that I have little faith in the meaning of refined 
parameters such as preferred orientation, except perhaps in some very rough 
sense.
Mike Glazerattachment: Glaciernbsp;Bkgrd.jpg

commensurate modulated crystal structure refinement in Fullprof

[Bridges, Craig]

Dear All,
 I am wondering if someone could possibly provide me with a working sample 
*.pcr file for commensurate modulated crystal structure refinement. I have been 
struggling to get a file working using the manual, so far with limited success. 
Editpcr has helped, but there appear to be no example files for this (Jbt=15) 
in the ~50 or more sample files provided with Fullprof. A file, or any advice, 
would be very much appreciated.
 
Regards,
Craig Bridges
McMaster University

Re: Problems using TOPAS R (Rietveld refinement)

[Joerg Bergmann]

Dear Lubomir Smrock,

linear pattern analysis is _not_ Rietveld, this was a common QPA
method prior to Rietveld QPA. In a Rietvel QPA, one must refine
the lattice parameter at least. And that makes it nonlinear.
Depending on the sample, one may decide to add more nonlinear 
details to the refinement. Of course, additional knowledge
about the phases in the sample is welcome. For example: Stacking 
faults in clay minerals are known to be common from single crystal
or electron microscopy investigations. Some phases are known to 
have sheet- or needle-like shape, e.g. from scanning electron 
microscopy; therefore anisotropic, hkl-dependant line broadening
and/or strong preferred orientation must be concerned. Only
seldom such phases real structure is derived from the pattern
itself. But knowing them Rietveld QPA must introduce and refine 
them for good results.

Regards

Joerg Bergmann, Dresden


Am Mittwoch, den 21.03.2007, 07:50 +0100 schrieb Lubomir Smrcok:
 Gentlemen,
 I've been listening for a week or so and I am really wondering what do you
 want to get ... Actually you are setting up a refinement, whose results
 will be, at least, inaccurate. I am always surprised by attempts to refine
 crystal structure of a disordered sheet silicate from powders, especially
 when it is known it hardly works with single crystal data. Yes, there are
 several models of disorder, but who has ever proved they are really good ?
 I do not mean here a graphical comparison of powder patterns with a
 calculated trace, but a comparison of structure factors or integrated
 intensities. (Which ones are to be selected is well described in the works
 of my colleague, S.Durovic and his co-workers.)
 As far as powders are concerned, all sheet silicates suffer from
 prefered orientation along 001. Until you have a pattern taken in a
 capillary or in transmission mode, this effect will be dominating and you
 can forget such noble problems like anisotropic broadening.
 
 Last but not least : quantitative phase analysis by Rietveld is (when only
 scale factors are on) nothing else but multiple linear regression. There
 is a huge volume of literature on the topic, especially which variables
 must, which should and which could be a part of your model.
 I really wonder why the authors of program do not add one option called
 QUAN, which could, upon convergence of highly sophisticated non-linear
 L-S, fix all parameters but scale factors and run standard tests or factor
 analysis. One more diagonalization is not very time consuming, is it ? To
 avoid numerical problems, I'd use SVD.
 This idea is free and if it helps people reporting 0.1% MgO (SiO2) in a
 mixture  of 10 phases to think a little of the numbers they are getting, I
 would only be happy :-)
 Lubo
 
 P.S. Hereby I declare I have never used Topas and I am thus not familiar
 with all its advantages or disadvantages compared to other codes.
 
 
 On Wed, 21 Mar 2007, Reinhard Kleeberg wrote:
 
  Dear Leandro Bravo,
  some comments below:
 
  Leandro Bravo schrieb:
 
  
   In the refinement of chlorite minerals with well defined disordering
   (layers shifting by exactly b/3 along the three pseudohexagonal Y
   axis), you separate the peaks into k = 3.n (relative sharp, less
   intensive peak) and k #61625; 3.n (broadened or disappeared
   reflections). How did you determined this value k = 3.n and n =
   0,1,2,3..., right?
  
  The occurence of stacking faults along the pseudohexagonal Y axes causes
  broadening of all reflections hkl with k unequal 3n (for example 110,
  020, 111..) whereas the reflections with k equal 3n remain unaffected
  (001, 131, 060, 331...). This is clear from geometric conditions, and
  can be seen in single crystal XRD (oscillation photographs, Weissenberg
  photographs) as well in selected area electron diffraction patterns. The
  fact is known for a long time, and published and discussed in standard
  textbooks, for example *Brindley, G.W., Brown, G.:  Crystal Structures
  of Clay Minerals and their X-ray Identification. Mineralogical Society,
  London, 1980.*
 
   First, the chlorite refinement.
  
   In the first refinement of chlorite you used no disordering models and
   used ´´cell parameters`` and ´´occupation of octahedra``. So you
   refined the lattice parameters and the occupancy of all atoms?
 
  Yes, the lattice parameters.
  Only the occupation/substitution of atoms with significant difference in
  scattering power can be refined in powder diffraction. In case of
  chlorites, the substitution Fe-Mg at the 4 octahedral positions can be
  refined.
 
  
   In the second refinement, you use na anisotropic line broadening ´´in
   the traditional way``. So you used a simple ellipsoidal model and/or
   spherical harmonics?
  
  Simple ellipsoidal model, assuming very thiny platy crystals. But it was
  clear that this model must fail, see above the known fact of disorder in
  layer stacking. And from microscopy it is clear that the crystals

Re: Problems using TOPAS R (Rietveld refinement)

[Reinhard Kleeberg]

Dear colleagues,
sorry, my mail should go directly to Leandro, but I used this damned 
reply buttom...
My answer was related to Leandro's questions regarding these line 
broadening models. I realised that Leandro is going on to apply a 
Rietveld program for phase quantification, including kaolinite and later 
other clay minerals. I only tried to express my personal experience, 
that any inadequate profile description of a clay mineral will surely 
cause wrong QPA results, nothing else. This is a practical issue, and it 
is only partially related to structure refinement. Lubomir Smrcok is 
definitely right that other things like PO are frequently biasing a QPA 
result, but for the most of these problems working solutions do exist. 
But I disagree that anisotropic line broadening is a noble problem. In 
clay mineral mixtures, it is essentially to fit the profiles of the 
single phases as best as one can, to get any reasonable QPA result in 
a +-5 wt% interval. On the other hand, for the QPA purpose it is not so 
much important to find any sophisticated description of the 
microstructure of a phase. But the model should be flexible enough to 
cover the variablility of the profiles in a given system, and, on the 
other hand, stabil enough (not over-parametrised) to work in mixtures. 
The balancing out of these two issues could be the matter of an endless 
debate. And here I agree again, a better, more stable minimisation 
algorithm can help to keep a maximum of flexibility of the models.

Best regards
Reinhard Kleeberg

Lubomir Smrcok schrieb:


Gentlemen,
I've been listening for a week or so and I am really wondering what do you
want to get ... Actually you are setting up a refinement, whose results
will be, at least, inaccurate. I am always surprised by attempts to refine
crystal structure of a disordered sheet silicate from powders, especially
when it is known it hardly works with single crystal data. Yes, there are
several models of disorder, but who has ever proved they are really good ?
I do not mean here a graphical comparison of powder patterns with a
calculated trace, but a comparison of structure factors or integrated
intensities. (Which ones are to be selected is well described in the works
of my colleague, S.Durovic and his co-workers.)
As far as powders are concerned, all sheet silicates suffer from
prefered orientation along 001. Until you have a pattern taken in a
capillary or in transmission mode, this effect will be dominating and you
can forget such noble problems like anisotropic broadening.

Last but not least : quantitative phase analysis by Rietveld is (when only
scale factors are on) nothing else but multiple linear regression. There
is a huge volume of literature on the topic, especially which variables
must, which should and which could be a part of your model.
I really wonder why the authors of program do not add one option called
QUAN, which could, upon convergence of highly sophisticated non-linear
L-S, fix all parameters but scale factors and run standard tests or factor
analysis. One more diagonalization is not very time consuming, is it ? To
avoid numerical problems, I'd use SVD.
This idea is free and if it helps people reporting 0.1% MgO (SiO2) in a
mixture  of 10 phases to think a little of the numbers they are getting, I
would only be happy :-)
Lubo

P.S. Hereby I declare I have never used Topas and I am thus not familiar
with all its advantages or disadvantages compared to other codes.


On Wed, 21 Mar 2007, Reinhard Kleeberg wrote:

 


Dear Leandro Bravo,
some comments below:

Leandro Bravo schrieb:

   


In the refinement of chlorite minerals with well defined disordering
(layers shifting by exactly b/3 along the three pseudohexagonal Y
axis), you separate the peaks into k = 3.n (relative sharp, less
intensive peak) and k #61625; 3.n (broadened or disappeared
reflections). How did you determined this value k = 3.n and n =
0,1,2,3..., right?

 


The occurence of stacking faults along the pseudohexagonal Y axes causes
broadening of all reflections hkl with k unequal 3n (for example 110,
020, 111..) whereas the reflections with k equal 3n remain unaffected
(001, 131, 060, 331...). This is clear from geometric conditions, and
can be seen in single crystal XRD (oscillation photographs, Weissenberg
photographs) as well in selected area electron diffraction patterns. The
fact is known for a long time, and published and discussed in standard
textbooks, for example *Brindley, G.W., Brown, G.:  Crystal Structures
of Clay Minerals and their X-ray Identification. Mineralogical Society,
London, 1980.*

   


First, the chlorite refinement.

In the first refinement of chlorite you used no disordering models and
used ´´cell parameters`` and ´´occupation of octahedra``. So you
refined the lattice parameters and the occupancy of all atoms?
 


Yes, the lattice parameters.
Only the occupation/substitution of atoms with significant difference in
scattering power can be refined

RE: Problems using TOPAS R (Rietveld refinement)

[AlanCoelho]

Clay people

I think the single crystal analysis of clays is interesting. I have not read
the literature but in determining the intensities is overlap of the dots
considered as I would have expected the dots to be very much smeared (5 to
10 degrees 2Th in my experience). If yes the fitting in two dimension would
be better.

Thus the question to ask is how accurate can QPA be for clays if the
intensities can be accurately obtained; is this an open question or is the
book closed on this. If as Reinhard Kleeberg mentioned that some directions
are unaffected then it would seem plausible that something can be gained
especially if one of those models work. 

Also, TOPAS simply offers a means of describing the peak shapes using a hkl
dependent spherical harmonics. From my experiences it seems to work. Like
Lubomir Smrcok remarked getting the intensities is critical. 

Another important point, again as Lubomir Smrcok mentioned, is preferred
orientation. If there's very strong preferred orientation then the peak
shapes will be affected due to axial divergence as well; it best to remove
preferred orientation.

Cheers
Alan



-Original Message-
From: Reinhard Kleeberg [mailto:[EMAIL PROTECTED] 
Sent: Wednesday, 21 March 2007 7:48 PM
To: rietveld_l@ill.fr
Subject: Re: Problems using TOPAS R (Rietveld refinement)

Dear colleagues,
sorry, my mail should go directly to Leandro, but I used this damned reply
buttom...
My answer was related to Leandro's questions regarding these line broadening
models. I realised that Leandro is going on to apply a Rietveld program for
phase quantification, including kaolinite and later other clay minerals. I
only tried to express my personal experience, that any inadequate profile
description of a clay mineral will surely cause wrong QPA results, nothing
else. This is a practical issue, and it is only partially related to
structure refinement. Lubomir Smrcok is definitely right that other things
like PO are frequently biasing a QPA result, but for the most of these
problems working solutions do exist. 
But I disagree that anisotropic line broadening is a noble problem. In
clay mineral mixtures, it is essentially to fit the profiles of the single
phases as best as one can, to get any reasonable QPA result in a +-5 wt%
interval. On the other hand, for the QPA purpose it is not so much important
to find any sophisticated description of the microstructure of a phase. But
the model should be flexible enough to cover the variablility of the
profiles in a given system, and, on the other hand, stabil enough (not
over-parametrised) to work in mixtures. 
The balancing out of these two issues could be the matter of an endless
debate. And here I agree again, a better, more stable minimisation algorithm
can help to keep a maximum of flexibility of the models.
Best regards
Reinhard Kleeberg

Lubomir Smrcok schrieb:

Gentlemen,
I've been listening for a week or so and I am really wondering what do 
you want to get ... Actually you are setting up a refinement, whose 
results will be, at least, inaccurate. I am always surprised by 
attempts to refine crystal structure of a disordered sheet silicate 
from powders, especially when it is known it hardly works with single 
crystal data. Yes, there are several models of disorder, but who has ever
proved they are really good ?
I do not mean here a graphical comparison of powder patterns with a 
calculated trace, but a comparison of structure factors or integrated 
intensities. (Which ones are to be selected is well described in the 
works of my colleague, S.Durovic and his co-workers.) As far as powders 
are concerned, all sheet silicates suffer from prefered orientation 
along 001. Until you have a pattern taken in a capillary or in 
transmission mode, this effect will be dominating and you can forget 
such noble problems like anisotropic broadening.

Last but not least : quantitative phase analysis by Rietveld is (when 
only scale factors are on) nothing else but multiple linear 
regression. There is a huge volume of literature on the topic, 
especially which variables must, which should and which could be a part of
your model.
I really wonder why the authors of program do not add one option called 
QUAN, which could, upon convergence of highly sophisticated 
non-linear L-S, fix all parameters but scale factors and run standard 
tests or factor analysis. One more diagonalization is not very time 
consuming, is it ? To avoid numerical problems, I'd use SVD.
This idea is free and if it helps people reporting 0.1% MgO (SiO2) in a 
mixture  of 10 phases to think a little of the numbers they are 
getting, I would only be happy :-) Lubo

P.S. Hereby I declare I have never used Topas and I am thus not 
familiar with all its advantages or disadvantages compared to other codes.


On Wed, 21 Mar 2007, Reinhard Kleeberg wrote:

  

Dear Leandro Bravo,
some comments below:

Leandro Bravo schrieb:



In the refinement of chlorite minerals with well defined

RE: Re: Problems using TOPAS R (Rietveld refinement)

[Whitfield, Pamela]

I have to disagree with that; at least on a practical front with lab XRD.  I 
have done measurements myself with samples containing large portlandite plates 
(granted, not a silicate but lovely-looking plates in a SEM) for quantitative 
analysis.  The whole point of the work was to see if capillary measurements 
would be worth it if the normal sample prep techniques would change the nature 
of the sample.  The reflection measurements had awful orientation, but the 
portlandite spherical harmonics PO coefficients for the capillary data gave a 
texture index of 1, i.e. an ideal powder.  The diffraction optics and detector 
were identical for reflection and transmission.  The capillary data actually 
gave better quantitative results than the reflection.  A reason might be that 
if the grains are large enough to orientate significantly they might be big 
enough to cause microabsorption effects that are best avoided (the Brindley 
correction assumes spherical particles so plates are a bit of a headache).
 
It's just a thought, but the orientation in neutron and X-ray data might differ 
due to the difference in sample container size and orientation.  Neutron cans 
are often mounted vertically and are pretty big so there won't be much 
advantage over reflection as the material settles.  Lab capillaries are usually 
mounted horizontally and the capillary diameter is often quite small in 
relation to the grain size (compared to neutron sample cans). All bets are off 
for wollastonite though!
 
I will shut up at this point as I trying to avoid doing clay analysis!
 
Pam

-Original Message-
From: David L. Bish [mailto:[EMAIL PROTECTED] 
Sent: March 21, 2007 9:11 AM
To: rietveld_l@ill.fr
Subject: Re: Problems using TOPAS R (Rietveld refinement)


One often hears of attempts to eliminate preferred orientation in 
diffraction patterns of layer silicates using transmission measurements.  Keep 
in mind that if PO is a problem in reflection geometry, it will also affect 
transmission measurements, in a manner potentially similar to flat-plate 
samples.  We did some TOF neutron measurements on phyllosilicates a few years 
ago with what amounts to capillary sample holders, and preferred orientation 
was a significant problem.  If a material orients, it will do so in all mounts 
unless steps are taken to minimize it.

Dave

At 07:50 AM 3/21/2007 +0100, you wrote:


Gentlemen,
I've been listening for a week or so and I am really wondering 
what do you
want to get ... Actually you are setting up a refinement, 
whose results
will be, at least, inaccurate. I am always surprised by 
attempts to refine
crystal structure of a disordered sheet silicate from powders, 
especially
when it is known it hardly works with single crystal data. Yes, 
there are
several models of disorder, but who has ever proved they are 
really good ?
I do not mean here a graphical comparison of powder patterns 
with a
calculated trace, but a comparison of structure factors or 
integrated
intensities. (Which ones are to be selected is well described 
in the works
of my colleague, S.Durovic and his co-workers.)
As far as powders are concerned, all sheet silicates suffer 
from
prefered orientation along 001. Until you have a pattern taken 
in a
capillary or in transmission mode, this effect will be 
dominating and you
can forget such noble problems like anisotropic broadening.

Last but not least : quantitative phase analysis by Rietveld 
is (when only
scale factors are on) nothing else but multiple linear 
regression. There
is a huge volume of literature on the topic, especially which 
variables
must, which should and which could be a part of your model.
I really wonder why the authors of program do not add one 
option called
QUAN, which could, upon convergence of highly sophisticated 
non-linear
L-S, fix all parameters but scale factors and run standard 
tests or factor
analysis. One more diagonalization is not very time consuming, 
is it ? To
avoid numerical problems, I'd use SVD.
This idea is free and if it helps people reporting 0.1% MgO 
(SiO2) in a
mixture  of 10 phases to think a little of the numbers they are 
getting, I
would only be happy :-)
Lubo

P.S. Hereby I declare I have never used Topas and I am thus not 
familiar
with all its advantages or disadvantages compared to other 
codes

RE: Problems using TOPAS R (Rietveld refinement)

[AlanCoelho]

Lubo

SVD as you mentioned does avoid numerical problems as does other methods
such as the conjugate gradient method. SVD minimizes on the residuals |A x -
b| after solving the matrix equation A x = b.

I would like to point out however that errors obtained from the covariance
matrix are an approximation. The idea of fixing parameters as in SVD when a
singular value is encountered is also a little arbitrary as it requires the
user setting a lower limit.

The A matrix is formed at a point in parameter space; when there are strong
correlations (as SVD would report) then that point in space changes from one
refinement to another after modifying the parameter slightly.

If derivatives are numerically calculated, as is the case for convolution
parameters, then the A matrix becomes a function of how the derivative are
calculated; forward difference approximation for example gives different
derivatives than both forward and backwards if the step size in the
derivative is appreciable. For most convolutions and numerical derivatives
in general then it needs to be appreciable for good convergence.

Rietveld people may want to look at the re-sampling technique known as the
bootstrap method of error determination. It gives similar errors to the
covariance matrix when the correlations are weak; the maths journals are
full of details. It requires some more computing time but it actually gives
the distribution. And yes TOPAS has the bootstrap method; other code writers
may wish to investigate it.

Cheers
Alan



 

-Original Message-
From: Lubomir Smrcok [mailto:[EMAIL PROTECTED] 
Sent: Wednesday, 21 March 2007 5:50 PM
To: rietveld_l@ill.fr
Subject: Re: Problems using TOPAS R (Rietveld refinement)

Gentlemen,
I've been listening for a week or so and I am really wondering what do you
want to get ... Actually you are setting up a refinement, whose results
will be, at least, inaccurate. I am always surprised by attempts to refine
crystal structure of a disordered sheet silicate from powders, especially
when it is known it hardly works with single crystal data. Yes, there are
several models of disorder, but who has ever proved they are really good ?
I do not mean here a graphical comparison of powder patterns with a
calculated trace, but a comparison of structure factors or integrated
intensities. (Which ones are to be selected is well described in the works
of my colleague, S.Durovic and his co-workers.)
As far as powders are concerned, all sheet silicates suffer from
prefered orientation along 001. Until you have a pattern taken in a
capillary or in transmission mode, this effect will be dominating and you
can forget such noble problems like anisotropic broadening.

Last but not least : quantitative phase analysis by Rietveld is (when only
scale factors are on) nothing else but multiple linear regression. There
is a huge volume of literature on the topic, especially which variables
must, which should and which could be a part of your model.
I really wonder why the authors of program do not add one option called
QUAN, which could, upon convergence of highly sophisticated non-linear
L-S, fix all parameters but scale factors and run standard tests or factor
analysis. One more diagonalization is not very time consuming, is it ? To
avoid numerical problems, I'd use SVD.
This idea is free and if it helps people reporting 0.1% MgO (SiO2) in a
mixture  of 10 phases to think a little of the numbers they are getting, I
would only be happy :-)
Lubo

P.S. Hereby I declare I have never used Topas and I am thus not familiar
with all its advantages or disadvantages compared to other codes.


On Wed, 21 Mar 2007, Reinhard Kleeberg wrote:

 Dear Leandro Bravo,
 some comments below:

 Leandro Bravo schrieb:

 
  In the refinement of chlorite minerals with well defined disordering
  (layers shifting by exactly b/3 along the three pseudohexagonal Y
  axis), you separate the peaks into k = 3.n (relative sharp, less
  intensive peak) and k #61625; 3.n (broadened or disappeared
  reflections). How did you determined this value k = 3.n and n =
  0,1,2,3..., right?
 
 The occurence of stacking faults along the pseudohexagonal Y axes causes
 broadening of all reflections hkl with k unequal 3n (for example 110,
 020, 111..) whereas the reflections with k equal 3n remain unaffected
 (001, 131, 060, 331...). This is clear from geometric conditions, and
 can be seen in single crystal XRD (oscillation photographs, Weissenberg
 photographs) as well in selected area electron diffraction patterns. The
 fact is known for a long time, and published and discussed in standard
 textbooks, for example *Brindley, G.W., Brown, G.:  Crystal Structures
 of Clay Minerals and their X-ray Identification. Mineralogical Society,
 London, 1980.*

  First, the chlorite refinement.
 
  In the first refinement of chlorite you used no disordering models and
  used ´´cell parameters`` and ´´occupation of octahedra``. So you
  refined the lattice parameters

Re: Problems using TOPAS R (Rietveld refinement)

[Omotoso, Oladipo]

My limited experience with X-ray capillary measurements of ultra fine clay 
minerals suggests that you could have significant preferred orientation along 
the b* axis.  It is actually a good way of determining aspect ratios in 
phyllosilicates. 

 

Dipo Omotoso



From: Whitfield, Pamela [mailto:[EMAIL PROTECTED] 
Sent: Wednesday, March 21, 2007 7:51 AM
To: rietveld_l@ill.fr
Subject: RE: Re: Problems using TOPAS R (Rietveld refinement)

 

I have to disagree with that; at least on a practical front with lab XRD.  I 
have done measurements myself with samples containing large portlandite plates 
(granted, not a silicate but lovely-looking plates in a SEM) for quantitative 
analysis.  The whole point of the work was to see if capillary measurements 
would be worth it if the normal sample prep techniques would change the nature 
of the sample.  The reflection measurements had awful orientation, but the 
portlandite spherical harmonics PO coefficients for the capillary data gave a 
texture index of 1, i.e. an ideal powder.  The diffraction optics and detector 
were identical for reflection and transmission.  The capillary data actually 
gave better quantitative results than the reflection.  A reason might be that 
if the grains are large enough to orientate significantly they might be big 
enough to cause microabsorption effects that are best avoided (the Brindley 
correction assumes spherical particles so plates are a bit of a headache).

 

It's just a thought, but the orientation in neutron and X-ray data might differ 
due to the difference in sample container size and orientation.  Neutron cans 
are often mounted vertically and are pretty big so there won't be much 
advantage over reflection as the material settles.  Lab capillaries are usually 
mounted horizontally and the capillary diameter is often quite small in 
relation to the grain size (compared to neutron sample cans). All bets are off 
for wollastonite though!

 

I will shut up at this point as I trying to avoid doing clay analysis!

 

Pam

-Original Message-
From: David L. Bish [mailto:[EMAIL PROTECTED] 
Sent: March 21, 2007 9:11 AM
To: rietveld_l@ill.fr
Subject: Re: Problems using TOPAS R (Rietveld refinement)

One often hears of attempts to eliminate preferred orientation in 
diffraction patterns of layer silicates using transmission measurements.  Keep 
in mind that if PO is a problem in reflection geometry, it will also affect 
transmission measurements, in a manner potentially similar to flat-plate 
samples.  We did some TOF neutron measurements on phyllosilicates a few years 
ago with what amounts to capillary sample holders, and preferred orientation 
was a significant problem.  If a material orients, it will do so in all mounts 
unless steps are taken to minimize it.

Dave

At 07:50 AM 3/21/2007 +0100, you wrote:



Gentlemen,
I've been listening for a week or so and I am really wondering what do 
you
want to get ... Actually you are setting up a refinement, whose 
results
will be, at least, inaccurate. I am always surprised by attempts to 
refine
crystal structure of a disordered sheet silicate from powders, 
especially
when it is known it hardly works with single crystal data. Yes, there 
are
several models of disorder, but who has ever proved they are really 
good ?
I do not mean here a graphical comparison of powder patterns with a
calculated trace, but a comparison of structure factors or integrated
intensities. (Which ones are to be selected is well described in the 
works
of my colleague, S.Durovic and his co-workers.)
As far as powders are concerned, all sheet silicates suffer from
prefered orientation along 001. Until you have a pattern taken in a
capillary or in transmission mode, this effect will be dominating and 
you
can forget such noble problems like anisotropic broadening.

Last but not least : quantitative phase analysis by Rietveld is (when 
only
scale factors are on) nothing else but multiple linear regression. 
There
is a huge volume of literature on the topic, especially which variables
must, which should and which could be a part of your model.
I really wonder why the authors of program do not add one option called
QUAN, which could, upon convergence of highly sophisticated non-linear
L-S, fix all parameters but scale factors and run standard tests or 
factor
analysis. One more diagonalization is not very time consuming, is it ? 
To
avoid numerical problems, I'd use SVD.
This idea is free and if it helps people reporting 0.1% MgO (SiO2) in a
mixture  of 10 phases to think a little of the numbers they are 
getting, I
would only be happy :-)
Lubo

RE: Re: Problems using TOPAS R (Rietveld refinement)

[Whitfield, Pamela]

Makes sense with ultra-fines.  My portlandite grains were 5 microns upwards.
I'm working to avoid ultra-fines even harder than the bigger stuff :-)
 
Pam



From: Omotoso, Oladipo [mailto:[EMAIL PROTECTED]
Sent: Wed 21/03/2007 10:47 AM
To: rietveld_l@ill.fr
Subject: Re: Problems using TOPAS R (Rietveld refinement)



My limited experience with X-ray capillary measurements of ultra fine clay 
minerals suggests that you could have significant preferred orientation along 
the b* axis.  It is actually a good way of determining aspect ratios in 
phyllosilicates. 

 

Dipo Omotoso



From: Whitfield, Pamela [mailto:[EMAIL PROTECTED] 
Sent: Wednesday, March 21, 2007 7:51 AM
To: rietveld_l@ill.fr
Subject: RE: Re: Problems using TOPAS R (Rietveld refinement)

 

I have to disagree with that; at least on a practical front with lab XRD.  I 
have done measurements myself with samples containing large portlandite plates 
(granted, not a silicate but lovely-looking plates in a SEM) for quantitative 
analysis.  The whole point of the work was to see if capillary measurements 
would be worth it if the normal sample prep techniques would change the nature 
of the sample.  The reflection measurements had awful orientation, but the 
portlandite spherical harmonics PO coefficients for the capillary data gave a 
texture index of 1, i.e. an ideal powder.  The diffraction optics and detector 
were identical for reflection and transmission.  The capillary data actually 
gave better quantitative results than the reflection.  A reason might be that 
if the grains are large enough to orientate significantly they might be big 
enough to cause microabsorption effects that are best avoided (the Brindley 
correction assumes spherical particles so plates are a bit of a headache).

 

It's just a thought, but the orientation in neutron and X-ray data might differ 
due to the difference in sample container size and orientation.  Neutron cans 
are often mounted vertically and are pretty big so there won't be much 
advantage over reflection as the material settles.  Lab capillaries are usually 
mounted horizontally and the capillary diameter is often quite small in 
relation to the grain size (compared to neutron sample cans). All bets are off 
for wollastonite though!

 

I will shut up at this point as I trying to avoid doing clay analysis!

 

Pam

-Original Message-
From: David L. Bish [mailto:[EMAIL PROTECTED] 
Sent: March 21, 2007 9:11 AM
To: rietveld_l@ill.fr
Subject: Re: Problems using TOPAS R (Rietveld refinement)

One often hears of attempts to eliminate preferred orientation in 
diffraction patterns of layer silicates using transmission measurements.  Keep 
in mind that if PO is a problem in reflection geometry, it will also affect 
transmission measurements, in a manner potentially similar to flat-plate 
samples.  We did some TOF neutron measurements on phyllosilicates a few years 
ago with what amounts to capillary sample holders, and preferred orientation 
was a significant problem.  If a material orients, it will do so in all mounts 
unless steps are taken to minimize it.

Dave

At 07:50 AM 3/21/2007 +0100, you wrote:



Gentlemen,
I've been listening for a week or so and I am really wondering what do 
you
want to get ... Actually you are setting up a refinement, whose 
results
will be, at least, inaccurate. I am always surprised by attempts to 
refine
crystal structure of a disordered sheet silicate from powders, 
especially
when it is known it hardly works with single crystal data. Yes, there 
are
several models of disorder, but who has ever proved they are really 
good ?
I do not mean here a graphical comparison of powder patterns with a
calculated trace, but a comparison of structure factors or integrated
intensities. (Which ones are to be selected is well described in the 
works
of my colleague, S.Durovic and his co-workers.)
As far as powders are concerned, all sheet silicates suffer from
prefered orientation along 001. Until you have a pattern taken in a
capillary or in transmission mode, this effect will be dominating and 
you
can forget such noble problems like anisotropic broadening.

Last but not least : quantitative phase analysis by Rietveld is (when 
only
scale factors are on) nothing else but multiple linear regression. 
There
is a huge volume of literature on the topic, especially which variables
must, which should and which could be a part of your model.
I really wonder why the authors of program do not add one option called
QUAN, which could, upon convergence of highly sophisticated non-linear
L-S, fix all parameters but scale factors and run standard tests

Re: Problems using TOPAS R (Rietveld refinement)

[Reinhard Kleeberg]

Dear Leandro Bravo,
some comments below:

Leandro Bravo schrieb:



In the refinement of chlorite minerals with well defined disordering 
(layers shifting by exactly b/3 along the three pseudohexagonal Y 
axis), you separate the peaks into k = 3.n (relative sharp, less 
intensive peak) and k #61625; 3.n (broadened or disappeared 
reflections). How did you determined this value k = 3.n and n = 
0,1,2,3..., right?


The occurence of stacking faults along the pseudohexagonal Y axes causes 
broadening of all reflections hkl with k unequal 3n (for example 110, 
020, 111..) whereas the reflections with k equal 3n remain unaffected 
(001, 131, 060, 331...). This is clear from geometric conditions, and 
can be seen in single crystal XRD (oscillation photographs, Weissenberg 
photographs) as well in selected area electron diffraction patterns. The 
fact is known for a long time, and published and discussed in standard 
textbooks, for example *Brindley, G.W., Brown, G.:  Crystal Structures 
of Clay Minerals and their X-ray Identification. Mineralogical Society, 
London, 1980.*



First, the chlorite refinement.

In the first refinement of chlorite you used no disordering models and 
used ´´cell parameters`` and ´´occupation of octahedra``. So you 
refined the lattice parameters and the occupancy of all atoms?


Yes, the lattice parameters.
Only the occupation/substitution of atoms with significant difference in 
scattering power can be refined in powder diffraction. In case of 
chlorites, the substitution Fe-Mg at the 4 octahedral positions can be 
refined.




In the second refinement, you use na anisotropic line broadening ´´in 
the traditional way``. So you used a simple ellipsoidal model and/or 
spherical harmonics?


Simple ellipsoidal model, assuming very thiny platy crystals. But it was 
clear that this model must fail, see above the known fact of disorder in 
layer stacking. And from microscopy it is clear that the crystals are 
much too large to produce significant line broadening from size effects. 
You can see this for a lot of clay minerals: If the ellipsoidal 
crystallite shape model would be ok, the 00l reflections would have the 
broadest lines, and the 110, 020 and so on should be the sharpest ones. 
But this is not true in practice, mostly the hkl are terribly broadenend 
and smeared, but the 00l are still sharp.


The last refinement, describing a real structure. You used for the 
reflections k #61625; 3.n (broadened peaks) a ´´rod-like intensity 
distribution``, with the rod being projected by the cosine of the 
direction on the diffractogram. You used also the lenghts of the rods 
as a parameter, so as the dimension of the rods for 0k0 with k 
#61625; 3.n. I would like to know how did you ´´project`` these rods 
and use them in the refinement.


For the k = 3.n reflections, you used an anisotropic broadening model 
(aniso crystallyte size) and and isotropic broadening model 
(microstrain broadening). But you said that crystallite size is an 
isotropic line broadening in my kaolinite refinement and I should not 
use it. So I use or not the cry size?


Yes, we used an additional ellipsoidal broadening in order to describe 
any potential thinning of the crystals. But this broadening model was 
not significant because the broadening was dominated by the stacking 
faults. A microstrain makes sense because of natural chlorits are 
sometimes zoned in their chemical composition and a distribution of the 
lattice constants may occur.
In one of your mails you mentioned crysize gave reasonable numbers with 
low error, and from that I assumed you looked only on the errors of the 
isotropic crysize as defined in Topas. You must know what model you did 
apply. But it is clear that any crysize model is inadequate to 
describe the line broadening of kaolinite.



Now the kaolinite refinement.

In the first refinement was used fixed atomic positions and a 
conventional anisotropic peak broadening. This conventional 
anisotropic peak broadening would be the simple ellipsoidal model 
and/or spherical harmonics?!


Only ellipsoidal model, assuming a platy crystal shape, see above. Only 
for comparision.




After that you use the introduced model of disorfering. Is this model 
the same of the chlorite (rods for k #61625; 3.n and microstrain 
broadening and anisotropic crystallite size?


Not exactly the same like in chlorite, because the disorder in kaolinite 
is much more complicated like in chlorites. See also the textbook cited 
above, and extensive works of Plancon and Tchoubar. Thus, most of the 
natural kaolinites show stacking faults along b/3 as well as along a, 
and additional random faults. Thus, more broadening parameters had to be 
defined, and this is not completely perfect until now. See the 
presentation I sent you last week.


Best regards

Reinhard Kleeberg
begin:vcard
fn:Reinhard Kleeberg
n:Kleeberg;Reinhard
org;quoted-printable:TU Bergakademie Freiberg;Institut f=C3=BCr Mineralogie
adr