Re: [Ifeffit] how to obtain average vacancy files?

31 May 2012

      Dear friends from the Ifeffit list, specially Sebastiano and Bruce,

Thank you very much for your advices. Here I am giving you a better
explanation of the physical problem we are facing, and then I´ll give the
approach we will try to follow now.

We are working on a 50-50 Cr-Fe maghemite, which structure is known by high
resolution XRD and Rietveld method. The synthesis of such a maghemite is
difficult and some magnetic properties are being measured.  We know, also,
that pure Fe maghemite structure at T=10 K has ordered vacancies. We are
trying to verify by XAFS if the local environment of Cr or Fe absorbers
reflects ordered vacancies.

With the aid of crystallographic codes we modeled the various vacancy
configurations, including the one corresponding to the ordered Fe maghemite
structure. By the Rietveld analysis and by the XANES Cr spectrum we know
that Cr occupies only octahedral sites. We have tried to fit with Artemis
the experimental Cr and Fe EXAFS spectra, comparing them with one model of
the ordered vacancies structure. The results are not the best, and then we
“suspect” that the model of ordered vacancies is not the good one.

 As I have written before, our idea was to obtain “average vacancies” FEFF
files and to work with the fully occupied magnetite structure, but with
some kind of “gray” atoms. These gray atoms would be the average of
vacancies and Cr or Fe atoms in octahedral sites. After your comments, it
seems too difficult to obtain the corresponding FEFF functions.

As a way for testing the disordered model, we are now working on the much
easier problem of fitting the magnetite structure to our EXAFS spectra and
to obtain the corresponding interatomic distances and amplitudes. We hope
their interpretation will be also easier than before.

Thanks a lot again for your attention. Best regards

Maria Elena

2012/5/31 
...
Dear friends:
Thank you very much for your kind answers. Believe me, now I am in a
hurry, and I hope this evening I'll answer with more details.
Regards
Maria Elena
Enviado desde mi oficina móvil BlackBerry® de Telcel
-----Original Message-----
From: Bruce Ravel 
Sender: ifeffit-bounces@millenia.cars.aps.anl.gov
Date: Thu, 31 May 2012 09:33:29
To: XAFS Analysis using Ifeffit
Reply-To: XAFS Analysis using Ifeffit 
Subject: Re: [Ifeffit] how to obtain average vacancy files?
On Tuesday, May 29, 2012 10:31:43 PM María Elena Montero Cabrera wrote:
...
Dear friends,
I am trying to fit with Artemis, not very successfully, a maghemite
structure. The main difficulty seems to be the vacancies in the
structure.
My idea, following a recently given Bruce’s advice to a person in this
list, is to obtain “average vacancies” FEFF files and to work with the
fully occupied magnetite structure. I wanted to obtain each file for a
given vacancy configuration in the first coordination sphere and then to
multiply the obtained functions by the weight of each configuration and
summ them all. I had the hope of doing this by using the feff00nn.dat
files
that I have used when working with SixPack, some years ago.
Surprisingly, I
couldn’t find the Artemis’ corresponding  feff00nn.dat files at any
folder.
What can I do?
There are two questions here.  I'll answer the second one first.
It would be reasonable to say that the whole point of Artemis is to
free the user from having to manage the feffNNNN.dat files.  They get
stashed in an out-of-the-way location so that the user can focus on
creating a fitting model rather than keep track of many (dozens,
hundreds,...) of little text files.
You are not very clear about what, exactly, your confusion is in terms
of the vacancy thing.  So I can only make a guess.
In general, vacancies are hard to model in Feff.  In any case, it is
may be imporssible to do a good job of modeling a vacancy with a
/single/ Feff calculation.  The reason is the same as the reason as
for dopants -- Feff requires that every point in the cluster be
occupied by only one kind of thing -- i.e. an atom or nothing.  In
general, you cannot know how to distribute the vacancy in the small
cluster represented in the feff.inp file.
The word "vacancy" makes much more sense in a crystallographic context
where the structure is averaged over 10^23 atoms.  In an EXAFS
context, you have to figure out how to model both of the main effects
of missing atom:
* Reduction in coordination
* Change in the distances to other neighboring atoms due to
  relaxation around the missing atom.
I think that, if you spend some time reading papers by the folks who
answer questions around here, you will find that the prefered approach
to solving a problem involving vacancies is to run Feff on the
"native" structure, then to parameterize the fit in such a way that
models the coordinaton reduction and the changes in bond lengths.
That is, I see dealing with a problem like yours as a modeling problem
in Artemis, not as a problem requiring a clever use of Feff.
For starters, read some of Scott Calvin's papers on mixed ferrites to
understand how he approached the problem of mixed occupancy.
B
--
Bruce Ravel  ------------------------------------ bravel@bnl.gov
National Institute of Standards and Technology
 Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2
 Building 535A
 Upton NY, 11973
Homepage:    http://xafs.org/BruceRavel
 Software:    https://github.com/bruceravel
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-- 
María Elena

Dra. María Elena Montero Cabrera
Centro de Investigación en Materiales Avanzados (CIMAV)
Miguel de Cervantes 120, Compl. Ind. Chihuahua
Chihuahua CP 31109, Chih. México
Tel (614) 4391123