February 2008 - Ifeffit - millenia.cars.aps.anl.gov

sorting files in Athena
by Dominik Samuelis 22 Feb '08

22 Feb '08

Hi Dariusz, > I use Iffefit under Win XP, and every time when I open (import) more > files I have them in such order: 1, 11, 12, 13, ... , 19, 2, 20, 21, 22, > ... , 29, 3, 30, 31 ... etc. > So, my question is if there is some "hidden" way to sort automatically > files during importing or in the menue. Do you know something about? Is > the sorting lexigraphical (from Windows)? this is a typical problem with the Windows file selection dialog. Windows always puts the file, which is currently selected, at the first position of the files list. Now, when you're shift-clicking on your last file, you automatically select this one. That's why file 31 is in first position. The easiest workaround for this issue is to select your files backwards, i.e. first click on file 31, then shift-click on file 1. Now, with HASYLAB files, it gets a little more complicated, due to filenames like scan_00001rxx, where xx is the scan number during a QEXAFS scan. I usually just open them in two chunks, one with xx=1-9 and then xx=10-99. This way, you can use the lexical sorting of Windows. Cheers, dominik -- Dipl.-Ing. Dominik Samuelis samuelis(a)pc.rwth-aachen.de Physikalische Chemie I RWTH Aachen University Phone: +49-241-80-94840 Fax: +49-241-80-92128 Landoltweg 2 52074 Aachen Germany

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theoretical EXAFS spectra
by Mustafa Hussein 22 Feb '08

22 Feb '08

Dear all, I am doing a Car-Parinello MD simulation, and I want to generate an EXAFS spectrum using the MD trajectory data. I am not familiar with the realm of XAS data analysis software. I need to know what software to use (FEFF, IFEFFIT, etc, what is the difference?) and is there some interface that helps me to build input files easily (I am having very little time)? and some other plotting commands that can produce nice plots? any help is appreciated Sincerely, Mustafa Mustafa Hussein Muhammad Independent Research Student Quantum Chemistry Senior Undergraduate Faculty of Pharmacy Minia University Minia 61511, Egypt Cell: + (20) 10 187 6193 --------------------------------- Looking for last minute shopping deals? Find them fast with Yahoo! Search.

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sorting files in Athena
by Zajac, Dariusz 22 Feb '08

22 Feb '08

Hi, I can not find one small thing - sorting files in Athena - it makes me crazy ;) I work with QEXAFS data - usualy few tens of files or even more. Files are named in such way: "file_name"rXX.fio where XX is next file number (1, 2, 3, ... ,10, 11, 12, ... , 20, 21, etc.). I use Iffefit under Win XP, and every time when I open (import) more files I have them in such order: 1, 11, 12, 13, ... , 19, 2, 20, 21, 22, ... , 29, 3, 30, 31 ... etc. So, my question is if there is some "hidden" way to sort automatically files during importing or in the menue. Do you know something about? Is the sorting lexigraphical (from Windows)? another problem which apears, is the limitation of the memmory... thanks for answer and greetings kicaj ------------------------------------------------------------------------ Zajac Dariusz A. Deutsches Elektronen-Synchrotron -Hasylab phone: +49-40-8998-2932 Notkestr. 85 fax: +49-40-8998-2787 22607 Hamburg e-mail: Germany ------------------------------------------------------------------------

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Re: [Ifeffit] problem with feff.inp
by Matt Newville 21 Feb '08

21 Feb '08

It looks like the SCF calculation is having a hard time with the new potential. The input file you sent only has atoms out to 2.48 Ang (though perhaps you truncated it when posting???), but the SCF 4 0 30 0.2 1 in your feff.inp means to make a self-consistent potential out to 4 Ang. Without any atoms out that far, I can imagine it would have problems. I think you'll probably need a larger cluster than a single shell for a reasonable XANES simulation. Hope that helps, --Matt

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problem with feeff.inp
by Sebastiano Cammelli 21 Feb '08

21 Feb '08

Dear I have some problem with a very easy simulation. Everytime I try to introduce a potential with more elements, for instance POTENTIALS 0 26 Fe 1 26 Fe 2 29 Cu the program stops the simulation with a message that I do not understand and that is attached to this mail. This 'weird' behavior does not happen with a monoatomic potential like POTENTIALS 0 26 Fe 1 26 Fe and in this second case everything works perfectly. I would be very glad if you will have any suggestion. Thank you in advance Sebastiano Cammelli

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problem with feff.inp
by Sebastiano Cammelli 21 Feb '08

21 Feb '08

Dear I have some problem with some very easy simulations with FEFF. Everytime I introduce a second element in the matrix in this way POTENTIALS 0 26 Fe 1 26 Fe 2 29 Cu the simulation does not work and it stops with a message that you can read in the attached document. But the program works perfectly with the monoatomic potential POTENTIALS 0 26 Fe 1 26 Fe I do not understand what there is written in the feff-message, so I will appreciate any suggestion. Thank you in advance for your precious help. Sebastiano Cammelli

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Background Subtraction
by Aimee Morey 07 Feb '08

07 Feb '08

Dear All, I don't know if I am just overlooking this feature in Athena, but I would like to view my pre- and post-edge lines for background subtraction along with my experimental data. Is this feature possible with this software and does anyone have a suggestion on how to do this? Any help would be greatly appreciated, Aimee -- Aimee M. Morey Graduate Assistant Department of Chemistry, U-3060 University of Connecticut 55 North Eagleville Rd Storrs, CT 06269-3060 Phone # (860) 486 - 6567 Fax # (860) 486 - 2981 "All you need is love, but a little chocolate now and then doesn't hurt" - Lucy van Pelt (Peanuts)

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