[Ifeffit] Data file for Arrojadite with screenshots

Barton, David (DG) DGBarton at dow.com
Fri Apr 16 09:18:11 CDT 2010


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 at millenia.cars.aps.anl.gov
[mailto:ifeffit-bounces at millenia.cars.aps.anl.gov] On Behalf Of
Jatinkumar Rana
	Sent: Friday, April 16, 2010 3:45 AM
	To: ifeffit at 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 at 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" <timjoku at uni-bonn.de>
<mailto:timjoku at uni-bonn.de> 
		To: ifeffit at millenia.cars.aps.anl.gov
		Subject: Re: [Ifeffit] Emission spectra of Cobalt
(Timna-Josua Kuehn)
		Message-ID: <201004142207.06319.timjoku at uni-bonn.de>
<mailto:201004142207.06319.timjoku at 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 <joshua.j.kas at gmail.com>
<mailto:joshua.j.kas at 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"
<timjoku at uni-bonn.de> <mailto:timjoku at 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
<jatinkumar.rana at helmholtz-berlin.de>
<mailto:jatinkumar.rana at helmholtz-berlin.de> 
		To: ifeffit at millenia.cars.aps.anl.gov
		Subject: [Ifeffit] EXAFS related querry
		Message-ID: <4BC70F86.6020808 at helmholtz-berlin.de>
<mailto:4BC70F86.6020808 at 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 <bravel at bnl.gov>
<mailto:bravel at bnl.gov> 
		To: XAFS Analysis using Ifeffit
<ifeffit at millenia.cars.aps.anl.gov>
<mailto:ifeffit at millenia.cars.aps.anl.gov> 
		Subject: Re: [Ifeffit] EXAFS related querry
		Message-ID: <201004151001.09115.bravel at bnl.gov>
<mailto:201004151001.09115.bravel at 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
		
		  


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