[Ifeffit] how to obtain average vacancy files?

elena.montero at cimav.edu.mx elena.montero at cimav.edu.mx
Thu May 31 16:34:31 CDT 2012

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.
Maria Elena 
Enviado desde mi oficina móvil BlackBerry® de Telcel

-----Original Message-----
From: Bruce Ravel <bravel at bnl.gov>
Sender: ifeffit-bounces at millenia.cars.aps.anl.gov
Date: Thu, 31 May 2012 09:33:29 
To: XAFS Analysis using Ifeffit<ifeffit at millenia.cars.aps.anl.gov>
Reply-To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
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.



 Bruce Ravel  ------------------------------------ bravel at 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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