Jatin,
This is an issue with the challenge of dealing with occupancy factors of
less than one in ATOMS. When you plot this crystal structure in a
visualization program you quickly notice there are overlapping atoms
with different identities. Of course this is why they put in occupancy
factors into the crystal structure file. For example, if you look at
the last two lines or your crystal file:
O 0.13830 0.00130 0.23150 O27 0.500
F 0.13830 0.00130 0.23150 F 0.500
you will notice that the O and F have exactly the same coordinates and
50% occupancy. The big question is how to deal with this complexity
and build an appropriate model. There have been several discussions in
the past on this mailing list that you should read. I am definitely not
an expert in this type of analysis so I can provide no additional help,
but some others may chime in.
Dave Barton
________________________________
From: ifeffit-bounces@millenia.cars.aps.anl.gov
[mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of
Jatinkumar Rana
Sent: Friday, April 16, 2010 3:45 AM
To: ifeffit@millenia.cars.aps.anl.gov
Subject: [Ifeffit] Data file for Arrojadite with screenshots
Dear Bruce,
Thank you very much for your reply.
I used structural file from ICSD database
(http://icsd.ill.eu/icsd/index.php?action=Details&id[]=50276). I have
attached the same file with this mail also.
The following screenshot shows the core atom (Fe) i selected to
get scattering paths.
The following screenshot shows the actual problem : The
Degeneracy (Deg : N) is 1 or 2 for all the paths which is not true from
the structure.
Many more thanks in advance.
Best regards,
Jatin
On 15.04.2010 19:00, ifeffit-request@millenia.cars.aps.anl.gov
wrote:
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Today's Topics:
1. Re: Emission spectra of Cobalt (Timna-Josua Kuehn)
(Timna-Josua Kuehn)
2. EXAFS related querry (Jatinkumar Rana)
3. Re: EXAFS related querry (Bruce Ravel)
----------------------------------------------------------------------
Message: 1
Date: Wed, 14 Apr 2010 22:07:06 +0200
From: "Timna-Josua Kuehn"
mailto:timjoku@uni-bonn.de
To: ifeffit@millenia.cars.aps.anl.gov
Subject: Re: [Ifeffit] Emission spectra of Cobalt
(Timna-Josua Kuehn)
Message-ID: <201004142207.06319.timjoku@uni-bonn.de>
mailto:201004142207.06319.timjoku@uni-bonn.de
Content-Type: text/plain; charset="iso-8859-1"
Hi Joshua,
thanks for this explanation of the XES command. I was
not aware of it.
However, I can not find the data file of the XES
simulation yet, although no
error is reportet! There is some file called
"xsect.dat", where something
about "em" is written, but there are no XES spectra in
it. Does one have to
process this file's data or even some more files?
Regards
Timna-Josua Kuehn
Date: Mon, 12 Apr 2010 11:19:17 -0700
From: Joshua Kas
mailto:joshua.j.kas@gmail.com
Hi Timna,
The energy arguments for the XES in FEFF84 are
energies of the valence
electron relative to vacuum, so emin should be a
negative number.
Try
XES -20 0 0.3
This should capture at least some of the XES.
You can play with emin to get
the range right. Note that the number of energy
points in FEFF84 is fixed,
and if you specify a small energy step (the
third parameter) you will not
achieve the full range that you specify.
Cheers,
Josh Kas
Date: Mon, 12 Apr 2010 12:47:11 +0200
From: "Timna-Josua Kuehn"
mailto:timjoku@uni-bonn.de
Dear all,
I am trying to simulate Cobalt Kbeta
emission spectra. Actually I just
exchanged the XANES card with XES, as is
explained and set emin = 7700 eV
and
emax = 7800 eV with estep = 100 to
calculate the whole Co Kbeta line at
7649.43 eV.
But I do not find a file that contains
the emission data. I am thankful
for each helpful advice.
Best regards
Timna
Timna-Josua Kuehn (PhD student)
Synchrotron Radiation Group
Institute of Physics
University of Bonn
Germany
------------------------------
Message: 2
Date: Thu, 15 Apr 2010 15:07:18 +0200
From: Jatinkumar Rana
mailto:jatinkumar.rana@helmholtz-berlin.de
To: ifeffit@millenia.cars.aps.anl.gov
Subject: [Ifeffit] EXAFS related querry
Message-ID: <4BC70F86.6020808@helmholtz-berlin.de>
mailto:4BC70F86.6020808@helmholtz-berlin.de
Content-Type: text/plain; charset=ISO-8859-1;
format=flowed
Dear Bruce,
I am trying to fit EXAFS data for Arrojadite (a
naturally occuring
phosphate mineral) measured on Fe-edge.
When i load crystallogrphic file in to FEFF, i get
Degeneracy (N) for
all path as 1 or 2. I know from the crystal structure of
Arrojadite that
it is not true.
Kindly help me in solving this problem.
Best regards,
Jatin
------------------------------
Message: 3
Date: Thu, 15 Apr 2010 10:01:09 -0400
From: Bruce Ravel
mailto:bravel@bnl.gov
To: XAFS Analysis using Ifeffit
mailto:ifeffit@millenia.cars.aps.anl.gov
Subject: Re: [Ifeffit] EXAFS related querry
Message-ID: <201004151001.09115.bravel@bnl.gov>
mailto:201004151001.09115.bravel@bnl.gov
Content-Type: Text/Plain; charset="iso-8859-1"
On Thursday 15 April 2010 09:07:18 am Jatinkumar Rana
wrote:
Dear Bruce,
I am trying to fit EXAFS data for Arrojadite (a
naturally occuring
phosphate mineral) measured on Fe-edge.
When i load crystallogrphic file in to FEFF, i
get Degeneracy (N) for
all path as 1 or 2. I know from the crystal
structure of Arrojadite that
it is not true.
Kindly help me in solving this problem.
Best regards,
Jatin
As I say here:
http://cars9.uchicago.edu/ifeffit/BruceRavel/FormLetters/HelpRequest
"Remember that if you do not provide enough information
to reproduce the
problem on my own computer, there will be little I can
do to help you. As I
explain on that page, you should send along a project
file, a data file, a
screenshot -- something that helps to explain your
problem."
In this case, you would be much more likely to get a
useful response from
someone on the mailing list were you to include the
crystal data you are
working from.
B
