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: Send Ifeffit mailing list submissions to ifeffit@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@millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner@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: 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