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
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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 > 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 
Maud page : http://maud.radiographema.com 

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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> subject with no body text
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> 
> ++

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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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