[Ifeffit] EXAFS simulations
Frommer Jakob
jakob.frommer at env.ethz.ch
Sun Oct 26 16:32:42 CDT 2008
Ciao Sebastiano,
did you use the mu-column of the xmu.dat? If so, the main difference between the chi.dat and the xmu.dat is that the mue_0 (as calculated by FEFF) is already subtracted in the former while it needs to be subtracted by Athena in the latter. Some of the difficulties you mentioned are thus due to problems of Athena to do a decent background (i.e. mue_0 and normalization) processing if there is no pre-edge region. Thus the effect of changing the absorption energy in Cu Bulk 4 from 8988.430eV to 8988.431eV is not caused by a *wrong* Enot but by a change in the edge-jump of almost 50% (due to a different *pre-edge*). Thus using the chi.dat seems to be the better (i.e. more reproducible) choice in this case (a precautionary note though: the mue_0 as calculated by FEFF will most likely differ between the central and the peripheral atoms; this may be part of the cluster-effect or an artifact (I assume that this is only a problem in the XANES region but I don't know, so you should check this by plotting the single mue_0).
HTH
Jakob
___________________________________________________
Jakob Frommer
Soil Chemistry Group
Institute of Biogeochemistry and Pollutant Dynamics,
ETH Zürich
Universitätstrasse 16,
CHN F19
CH - 8092 Zürich
Tel: +41 44 632 87 58
Fax: +41 44 633 11 18
web: http://www.ibp.ethz.ch/research/soilchemistry
________________________________
From: ifeffit-bounces at millenia.cars.aps.anl.gov on behalf of ifeffit-request at millenia.cars.aps.anl.gov
Sent: Fri 10/24/2008 09:57
To: ifeffit at millenia.cars.aps.anl.gov
Subject: Ifeffit Digest, Vol 68, Issue 21
Send Ifeffit mailing list submissions to
ifeffit at millenia.cars.aps.anl.gov
To subscribe or unsubscribe via the World Wide Web, visit
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
or, via email, send a message with subject or body 'help' to
ifeffit-request at millenia.cars.aps.anl.gov
You can reach the person managing the list at
ifeffit-owner at millenia.cars.aps.anl.gov
When replying, please edit your Subject line so it is more specific
than "Re: Contents of Ifeffit digest..."
Today's Topics:
1. Re: Fit XANES spectra using Athena (Adam Webb)
2. EXAFS simulations (Cammelli Sebastiano)
----------------------------------------------------------------------
Message: 1
Date: Fri, 24 Oct 2008 07:39:55 +0200
From: Adam Webb <adam.webb at desy.de>
Subject: Re: [Ifeffit] Fit XANES spectra using Athena
To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
Message-ID: <49015FAB.5060802 at desy.de>
Content-Type: text/plain; charset=ISO-8859-1
Hi Jenny,
I don't know what exactly you are trying to do so I can't say which
method is better but I can make a comment.
It all comes down to the number of independent variables. The Gaussian
and step functions are independent of each other. The heights, widths
and positions can all be adjusted. In the linear combination you change
everything together so for example, the ratio of the peak height and the
step height doesn't change. The result is that you need more spectra to
get the same number of degrees of freedom as in the least-squares peak fit.
Cheers,
Adam
Jenny Cai wrote:
> Hello everyone,
>
> Sorry for bothering you again.
>
> I am using least-squares peak fit and linear combination fit to analyze
> my samples. I have spent tons of time on it, and it really makes me
> crazy. Why can't I get consistent results from these two methods?
>
> Please see the attached file. Both of these methods work well
> individually, but linear combination fit always need more peaks than
> peak fit to get an 'ok' fitting. Should I stick on one method for all my
> samples, no matter what results the other one gives? It is confusing me
> so much. Could anyone help me out?
>
> Thank you in advance for your help!
>
>
> Jenny
>
>
------------------------------
Message: 2
Date: Fri, 24 Oct 2008 09:57:35 +0200
From: "Cammelli Sebastiano" <Sebastiano.Cammelli at psi.ch>
Subject: [Ifeffit] EXAFS simulations
To: <ifeffit at millenia.cars.aps.anl.gov>
Message-ID:
<AD99CE4B84C4D3468F69B0E4FB345D5804A5E78C at MAILBOX0A.psi.ch>
Content-Type: text/plain; charset="us-ascii"
Dear IFFEFIT user
I do some EXAFS simulations (FEFF8.4) of small pure Cu clusters (fcc
bulk structure) and then I try to compare them with experimental data.
The simulations are performed on all the shells, then all the
contribution are added according to the number of atoms per shell (so
the total xmu of a cluster of 19 atoms is = [xmu0+12*xmu1+6*xmu2]/19
where xmu0 is the xmu of the atom in the center of the cluster and xmu1
of the atoms in the first shell and xmu2 for the second shell).
The first and obvious result concerns the peaks amplitude of the FT
which is proportional to the number of atoms involved in the
simulations. I have calculated the EXAFS spectra from the xmu.dat files.
As you know in EXAFS simulations there is not pre-edge so finally is not
easy to find the right value of E0.
In the Athena.prj file I attached you can easily see this effect
changing the absorption energy of Cu Bulk 4 from 8988.430eV to
8988.431eV. The amplitude of the first peak of the FT changes from 100
to 60! In order to overcome this problem I recalculated the FT using the
chi.dat and not the xmu.dat.
In the Athena file you can find the 8 simulations based on the xmu.dat
(and they are called Cu bulk 1.... Cu bulk 8) and on the chi.dat (called
CHI_Cu bulk 1....8). Of course they refer to the same cluster and they
were calculated in the same way.
Since these simulations, calculated on the Chi.dat, are very different
from those calculated on xmu.dat, some questions rise. Moreover if you
compare the FT of the simulations Chi_Cu bulk 5 and Chi_Cu Bulk 6 you
can see that the amplitude of the first peak is larger for the smaller
cluster.
1. Should I use the spectra I got from the xmu.dat or
from the chi.dat?
2. Are the difference between Chi_Cu 5 and Chi Cu 6
(even if small) due to the E0 calculation?
3. How shall I behave if the first derivative of some
simulations does not show a peak where it is "reasonably" expected
(compare Cu Bulk 4 and Cu Bulk 7)
4. Do you have any other suggestions?
Thank you in advance for any suggestion,
Best regards
Sebastiano Cammelli
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20081024/13e238ff/attachment.html
-------------- next part --------------
A non-text attachment was scrubbed...
Name: athena_Cu.prj
Type: application/octet-stream
Size: 34413 bytes
Desc: athena_Cu.prj
Url : http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20081024/13e238ff/attachment.obj
------------------------------
_______________________________________________
Ifeffit mailing list
Ifeffit at millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
End of Ifeffit Digest, Vol 68, Issue 21
***************************************
More information about the Ifeffit
mailing list