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

C and N NEXAFS normalization
by Peter Nico 08 Jun '10

08 Jun '10

Hello All, I am looking for thoughts and opinions regarding the best way to approach post-edge fitting and normalization of C and N NEXAFS data. I know soft x-rays aren't exactly the focus of the list, but it is still the best access to a lot of people with a lot of XAS knowledge, and I would be very interested in your opinions. Obviously, linear or quad curve fitting followed by normalization is standard and well accepted for hard x-ray spectra. However, as far as I can tell there is no such accepted norm of C and N NEXAFS treatment. I have seen that some groups use a single point normalization, e.g. 310 for the case of C, and simply divide through the entire spectrum with this value. Other groups take the min and max value of the spectrum and map it onto a 0 to 1 scale. Neither of these approaches seems satisfactory to me for data with obvious backgrounds like those attached. While these data are not perfect, it seems like they should definitely be useable. My thought is why not do a 'standard' hard x-ray type normalization like that shown with an e0 set to the theoretical ionization potential for C or N. I understand that this has problems with the potential of including tailing sigma* transitions or first EXAFS oscillations in the background region because it doesn't extend far enough beyond the edge. However, it seems to me an approach like this must be 'less-wrong' than the more simplistic methods mentioned above and capable of yielding useful data. Thoughts, comments, jeers? --Peter

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Large Enot values
by Paul Bingham 08 Jun '10

08 Jun '10

Hi, I have been struggling with a tricky problem and cannot resolve it - hopefully someone out there can help! I have collected fluorescence XANES and EXAFS at the Se K-edge and I'm currently trying to fit the EXAFS (see attached files). The XANES agrees very well with a number of my standards and shows that the vast majority, if not all, of the Se is present in this material (an amorphous oxide-based system) as Se4+. I have tried to fit the EXAFS using a single Se-O path from a range of cif files (the simplest being SeO2). Other ions than O present incorrect bond lengths and I am convinced the first shell is oxygen. I can obtain a decent fit in terms of most parameters, as long as I disregard the consistently high value of Enot. Guidelines indicate that Enot should be less than about 5(ish), but I consistently get values of 10-12 when I try to fit my spectra, of which one is present in the attached files. I have checked my background subtraction and tried as many different options, changes and tweaks that I know or can find suggested (too many to list here) but I cannot obtain a fit with Enot below about 10 and so I ask my colleagues out there who are more experienced than I with EXAFS - can anyone shed any light on (a) the potential cause/s and (b) any potential solution/s? Thanks in advance for your time. Best Regards Paul Bingham -- Dr. Paul Bingham Immobilisation Science Laboratory Dept. of Engineering Materials University of Sheffield Mappin Street Sheffield S1 3JD UK Email: p.a.bingham(a)sheffield.ac.uk Direct Line: (0114) 2225473

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Re: [Ifeffit] Ifeffit Digest, Vol 88, Issue 4
by Jatinkumar Rana 08 Jun '10

08 Jun '10

Dear Dominik, Thank you so very much for your detailed explanation about the effects of particle size on XAFS spectra. Warm wishes, Rana On 07.06.2010 19:00, ifeffit-request(a)millenia.cars.aps.anl.gov wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)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(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)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. particle size effects on XAFS spectra (Jatinkumar Rana) > 2. Re: particle size effects on XAFS spectra (Dominik Samuelis) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 07 Jun 2010 14:49:33 +0200 > From: Jatinkumar Rana<jatinkumar.rana(a)helmholtz-berlin.de> > To: Ifeffit users<ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] particle size effects on XAFS spectra > Message-ID:<4C0CEADD.8040600(a)helmholtz-berlin.de> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Dear Users, > > I am working with the EXAFS technique for the characterization of my > powder sample. I must admit that i am very much new to the technique and > its analysis. I have read many tutorials on preparing sample for XAFS > measurement (both transmission and fluoroscence). However, i am dealing > with the powder having particle size much more smaller than one > absorption length. > > I would like to know will it create any destructive effect on my XAFS > spectra ?? > > Many thanks in advance... > > Warm wishes, > Rana > > > ------------------------------ > > Message: 2 > Date: Mon, 07 Jun 2010 15:21:14 +0200 > From: Dominik Samuelis<d.samuelis(a)fkf.mpg.de> > To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] particle size effects on XAFS spectra > Message-ID:<4C0CF24A.10407(a)fkf.mpg.de> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Dear Rana, > > yes, it will have effects on your XAFS spectra, but not really > destructive. EXAFS only really vanishes if you have isolated atoms. As > long as your particles still have several hundred atoms with some > coordination shell-like ordering, EXAFS oscillations will show up. > > However, the amplitude of the XAFS signals will be smaller than in bulk > material, due to the lower average coordination number of the central > atoms. If you e.g. have 5 nm particles (some 2000 atoms), already almost > half of the atoms (~800) is sitting on the particle surface and > therefore has a reduced coordination number. > > There's a wealth of information in literature where people actually use > this effect for determining the particle size from XAFS. > > Another thing to keep in mind is that often it's not really clear how > the surfaces of a particle looks like chemically - there might be > adsorbates, or even passivation layers. If you're e.g. doing EXAFS on > untreated 5nm Si particles, you can't really expect to see anything > close to bulk Si, because the top layer might be SiO2 > > Best regards, > Dominik > > > > On 07.06.2010 14:49, Jatinkumar Rana wrote: > >> Dear Users, >> >> I am working with the EXAFS technique for the characterization of my >> powder sample. I must admit that i am very much new to the technique and >> its analysis. I have read many tutorials on preparing sample for XAFS >> measurement (both transmission and fluoroscence). However, i am dealing >> with the powder having particle size much more smaller than one >> absorption length. >> >> I would like to know will it create any destructive effect on my XAFS >> spectra ?? >> >> Many thanks in advance... >> >> Warm wishes, >> Rana >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> > >

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particle size effects on XAFS spectra
by Jatinkumar Rana 07 Jun '10

07 Jun '10

Dear Users, I am working with the EXAFS technique for the characterization of my powder sample. I must admit that i am very much new to the technique and its analysis. I have read many tutorials on preparing sample for XAFS measurement (both transmission and fluoroscence). However, i am dealing with the powder having particle size much more smaller than one absorption length. I would like to know will it create any destructive effect on my XAFS spectra ?? Many thanks in advance... Warm wishes, Rana

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1st North American Core Shell Spectroscopy Conference
by Carlo Segre 04 Jun '10

04 Jun '10

Hello All: Please share this announcement with anyone whom you feel might be interested. I am positive that I am not getting this out to the entire core shell spectroscopy community. The abstract deadline has been extended until June 1 for oral presentations. ---- Conference Announcement ---- 1st North American Core Shell Spectroscopy Conference to be held jointly with the 59th Denver X-ray Conference 2-6 August 2010 Ι Denver Marriott Tech Center Hotel, Denver, CO <https://resweb.passkey.com/Resweb.do?mode=welcome_ei_new&eventID=1454471> The first North American Core Shell Spectroscopy Conference will be held jointly with the 59th Denver X-Ray Conference, 2-6 August 2010. The conference will feature poster sessions as well as oral presentations and students, in particular are encouraged to participate with oral presentation submissions. All topics relating to core shell spectroscopy are welcome, including: · X-ray Absorption Spectroscopy · X-ray Fluorescence Spectroscopy / Fluorescence Mapping · Resonant Inelastic X-ray Scattering / X-ray Raman Scattering · X-ray Magnetic Circular Dichroism The conference will feature a special session and dinner in honor of Ed Stern. The list of invited speakers for this special session includes Dr. Mali Balasubramanian, Argonne National Laboratory Prof. Jerry Seidler, University of Washington Prof. Anatoly Frenkel, Yeshiva University Dr. Ken Kemner, Argonne National Laboratory Prof. John Rehr, University of Washington Prof. Michael Paesler, North Carolina State University The other invited speakers are: Dr. Corwin Booth, Lawrence Berkeley National Laboratory Prof. James Penner-Hahn, University of Michigan Prof. Daryl Crozier - Simon Fraser University Prof. Bruce Bunker - University of Notre Dame Prof. Trevor Tyson - New Jersey Institute of Technology Dr. Joshua Kas - University of Washington Dr. Simon Bare - UOP LLC Participants will be able to attend Denver X-Ray Conference Sessions being held in adjacent rooms. Details of the oral presentation sessions will be posted on the DXC web site <http://www.dxcicdd.com/default.htm> as they are available. Students are able to register for a reduced cost, are eligible for special student room rates <http://www.dxcicdd.com/10/details.htm#studentrooms>, and may apply for funding <http://www.dxcicdd.com/10/files/2010-DXC-Student-Travel-Grant-application.p…> to attend the conference. Abstract submissions for oral presentations will be open until June 1 and can be made on the Denver X-Ray Conference web site by selecting the "Submit Abstract for the Joint Meeting with the North American Core Shell Spectroscopy Conference" link on the left side of the page (the 8th button down) or directly at the abstract submission page <http://www.dxcicdd.com/cssc/cssc_abstract.asp>. For more information, visit http://www.dxcicdd.com or contact: Denise Flaherty, Conference Coordinator flaherty(a)icdd.com<mailto:flaherty@icdd.com> ICDD 12 Campus Boulevard Newtown Square, PA 19073 -- Carlo U. Segre -- Professor of Physics Associate Dean for Graduate Admissions, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre(a)iit.edu http://www.iit.edu/~segre segre(a)debian.org

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plots from athena
by Saugata Datta 31 May '10

31 May '10

Hello, if you can help me with this question: I am trying to plot directly from athena via powerpoint for a publication/manuscript quality plot., I read a message posted that " "If you want to adjust things like fonts and line sizes on the plot for publication, then you have the option to save the plot as a metafile from the PGPlot window and import it into PowerPoint. Then convert the metafile into a drawing object with the "ungroup" feature. From this point you can change fonts, line shapes, colors, etc. to get the plot how you want it to look for publication. You can then re-save that slide as a picture (gif, tiff, metafile, etc) to be imported into the manuscript. This can get time intensive, but it's an alternative if all you want to do is adjust fonts and line colors/sizes. One caveat though, don't change the data! You can easily and unknowingly change the data if you're not careful (performing an action on one part of the drawing object without realizing another is highlighted for example) so always compare the final product to the original to make sure it's the same"... But I cannot find where the PGPlot window is., if you can kindly help. Say I want to plot six standards plotted /stacked one on top of the other in one figure, with correct seuqnce of legend? Can I do this without exporting to excel??? Thanks again... Saugata _________________________________________________________________ The New Busy think 9 to 5 is a cute idea. Combine multiple calendars with Hotmail. http://www.windowslive.com/campaign/thenewbusy?tile=multicalendar&ocid=PID2…

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Exporting derivative data
by Paul Bingham 31 May '10

31 May '10

Hi, I wonder if you can help: I'm using Athena to process some XANES data and wish to export the derivative data so that I can use a package such as Excel to prepare the data for publication. However, the derivative data that is presented visually in the graphics window is a much cleaner, smoother data set than the one I get when I export it in either deriv Mu(E) or deriv Norm(E). I tried the smoothing option in Data-Smooth mu(E) with 3 iterations and again with 10 iterations on the interpolative smoothing. Both gave far noisier data than the data shown in the Graphics window. Please can you tell me how to get exported derivative data that will be (more or less) the same as that shown in the graphics window? Basically I' hoping for WYSIWYG if that's possible? Any thoughts or suggestions would be very welcome and thanks for your time. -- Dr. Paul Bingham Postdoctoral Research Associate Immobilisation Science Laboratory Dept. of Engineering Materials University of Sheffield Mappin Street Sheffield S1 3JD UK Email: p.a.bingham(a)sheffield.ac.uk Direct Line: (0114) 2225473

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the use of constraints
by Kellie Aldi 28 May '10

28 May '10

Hi, I have a question on the use of constraints and restraints in EXAFS data fitting. I am using SixPack to build a model for the EXAFS of some synthetic layered transition metal (TM) oxides with relatively large amounts of layer vacancies. I am refining the occupancy of the layer TM site, from which I can determine the amount of layer vacancies. I want to include a parameter in this model that refines the number of these vacancies that are capped by interlayer TM (something that can happen in these structures), but I am having difficulty in deciding a responsible way to define the parameters of this variable. I am modifying the intensity of the interlayer TM scattering paths with a parameter fcap = (1-focc)*percap where focc is the refined occupancy of the layer TM site, and percap is the percentage of vacancies, "1-focc", that are capped by interlayer TM. However, just letting percap float, the value goes greater that 1... which, as a percentage, does not make much sense physically in my model. So I want to keep the value of this between 0 and 1. I have tried what was suggested on the IFEFFIT frequently asked questions page regarding constraints and restraints. I don't feel comfortable simply using a constraint and forcing the value to be between 0 and 1 using the suggested min/max idiom. I like better the idea of penalizing a fit when percap is outside of a defined range and thus "encouraging" the fit to settle percap somewhere inside this range. But in trying to use the restraint idea, including the fix suggested by Matt Newville for only penalizing the fit outside of the min/max range, percap still goes slightly above 1 (about 1.02) and in my results I get a value for the "penalty" that I am unsure how to interpret. Can this value be used to understand why the restraint still allows the value of percap to be outside of the defined "ideal" range? I am trying to understand how the restraint that Matt Newville defined in the link in the restraints/constraints FAQ works, but I am relatively new to EXAFS modeling and thus shaky on my skills at defining these parameters and knowing how certain math functions can be used. Are there any other help sections or guides that might address the use of such restraints? Or any suggestions on how to re-define this restraint? I would greatly appreciate any suggestions/input! Thanks, Kellie Aldi

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athena an widows 7
by Matthias Bauer 28 May '10

28 May '10

Dear all, i have a problem with running athena on windows 7. I can open the program, but when I try to open a file, just by clicking "open" the interfaces closes and only the graph window remains open. Does anyone encounter the same problem or even has a solution? Many thanks, matthias Dr. Matthias Bauer Inst. f. Technische Chemie und Polymerchemie Karlsruhe Institute of Technology (KIT) - Campus Süd Engesserstrasse 18 76131 Karlsruhe email: matthias.bauer(a)kit.edu phone: +49 721 608 4320

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athena an windows 7
by Matthias Bauer 28 May '10

28 May '10

Dear all, i have a problem with running athena on windows 7. I can open the program, but when I try to open a file, just by clicking "open" the interfaces closes and only the graph window remains open. Does anyone encounter the same problem or even has a solution? Many thanks, matthias Dr. Matthias Bauer Karlsruhe Institute of Technologie - Campus Süd Inst. für Technische Chemie und Polymerchemie Engesserstrasse 18 76128 Karlsruhe email: matthias.bauer(a)kit.edu phone: 0049 721 608 4320

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fitting
by mohamed sobhy 26 May '10

26 May '10

----- Forwarded Message ---- From: mohamed sobhy <bakhshwan1981(a)yahoo.com> To: ifeffit(a)millenia.cars.aps.anl.gov Sent: Thu, May 20, 2010 4:14:18 PM Subject: [Ifeffit] fitting Dear all thanks for your help and explanation about the background I fitted my data after removing the background and in the attached file I got this fitting, although all the values are good but I think the coordination number should be less than 8 (for the first shell) due to irradiation. So how can I get the right coordination number? How to improve the fitting of second shell? thanks _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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co-ordination number for given shell
by Jatinkumar Rana 25 May '10

25 May '10

Dear Ifeffit users, I am working on EXAFS analysis of a mineral Arrojadite. It has very very complicated crystal structure. I have measured EXAFS in fluoresence mode on Mn and Fe edge. The mineral contains Mn and Fe as divalent cations distributed over 7 different atomic positions e.g. 3 different Mn atomic position (Mn1, Mn2 and Mn3) and 4 different Fe position (Fe4, Fe5, Fe6, Fe7). My question is : How do i know that How many paths should i take into consideration to fit 1st shell, 2nd shell and 3rd shell.. ?? I have rough idea that the first shell is octahedral Oxygen ions. I tried fitting first shell taking into account first 6 Oxygen paths and it gave reasonably good fit to first shell. But the confusion is how to consider paths for 2nd Shell, 3rd shell....etc. Your feedback is highly appreciated. P.S. I have attached artemis file (both Fe and Mn edge) with this mail for your reference. Best regards, Jatin

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Re: [Ifeffit] calibrating and aligning samples for LCF
by Monson, Todd 24 May '10

24 May '10

I have XAFS data from several Fe nanoparticle samples as well as some Fe and Fe oxide standards collected during two different months. I would like to fit the Fe nanoparticle data using LCF and the Fe & Fe oxide standards. Data collected from Fe foil during the two months have been calibrated in energy. What is the best way to calibrate or align the other nanoparticle samples and standards collected during both of these sessions prior to doing LCF? Thanks, Todd -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Saturday, May 22, 2010 11:00 AM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 87, Issue 28 Send Ifeffit mailing list submissions to ifeffit(a)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(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)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. XANES and DOS calculations (Joanna Czapla) ---------------------------------------------------------------------- Message: 1 Date: Sat, 22 May 2010 17:21:41 +0200 From: Joanna Czapla <czapla.asia(a)gmail.com> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] XANES and DOS calculations Message-ID: <AANLkTimVJVPZoDKuU0NW8GEr9wdrrOI7OyfaAeOxSzMN(a)mail.gmail.com> Content-Type: text/plain; charset=windows-1252 Dear Feff Users, first of all I must admit that I am a total beginner and probably there are some things which I don?t understand very well. I need to make XANES and DOS calculations for K-edge of sulfur and then compare them with experiment. I use feff 8.4. First, I started from inorganic compounds such as CdS. I generated feff.inp file in ATOMS and first run feff with default values (generated by ATOMS). The fit wasn?t perfect so I started to change parameters-FMS and SCF but there was so significant improvement. I can only add that others fit are even worse. My question is which parameter I should change or which card should I add to make XANES calculations better? Maybe you can recommend any paper? The second question is about DOS calculations. I took the pDOS functions for each atom, set Fermi level from ldosNN files, but the main peaks are below this level and I don?t have any correspondence with XANES spectrum. For other compounds I have the same problem. Should I add any extra shift? I will be grateful for your advice. Regards Joanna Czapla I add the original feff.inp file generated by ATOMS: * This feff8 input file was generated by WebAtoms 1.8 (Atoms 3.0beta10) * Atoms written by and copyright (c) Bruce Ravel, 1998-2001 TITLE name: CdS (greenockite) (cubic zinc sulfide structure) TITLE formula: CdS TITLE sites: Cd1,S1 TITLE refer1: wyckoff 1,III,110 TITLE refer2: TITLE schoen: TITLE notes1: cubic zinc sulfide structure * S K edge energy = 2472.0 eV EDGE K S02 1.0 * pot xsph fms paths genfmt ff2chi CONTROL 1 1 1 1 1 1 PRINT 1 0 0 0 0 0 *** ixc=0 means to use Hedin-Lundqvist * ixc [ Vr Vi ] EXCHANGE 0 *** Radius of small cluster for *** self-consistency calculation *** A sphere including 2 shells is *** a good choice *** l_scf = 0 for a solid, 1 for a molecule * r_scf [ l_scf n_scf ca ] SCF 4.0 *** Upper limit of XANES calculation. *** This *must* be uncommented to *** make Feff calculate full multiple *** scattering rather than a path expansion * kmax [ delta_k delta_e ] XANES 4.0 *** Radius of cluster for Full Multiple *** Scattering calculation *** l_fms = 0 for a solid, 1 for a molecule * r_fms l_fms FMS 5.54240 0 *** Energy grid over which to calculate *** DOS functions * emin emax eimag LDOS -30 20 0.1 *** for EXAFS: RMAX 8.0 and uncomment *** the EXAFS card RPATH 0.1 *EXAFS 20 POTENTIALS * ipot Z element l_scmt l_fms stoichiometry 0 16 S 2 2 0.001 1 48 Cd 3 3 4 2 16 S 2 2 4 ATOMS * this list contains 87 atoms * x y z ipot tag distance 0.00000 0.00000 0.00000 0 S1 0.00000 0 -1.45450 1.45450 1.45450 1 Cd1 2.51927 1 1.45450 -1.45450 1.45450 1 Cd1 2.51927 2 1.45450 1.45450 -1.45450 1 Cd1 2.51927 3 -1.45450 -1.45450 -1.45450 1 Cd1 2.51927 4 2.90900 2.90900 0.00000 2 S1 4.11395 5 -2.90900 2.90900 0.00000 2 S1 4.11395 6 2.90900 -2.90900 0.00000 2 S1 4.11395 7 -2.90900 -2.90900 0.00000 2 S1 4.11395 8 2.90900 0.00000 2.90900 2 S1 4.11395 9 -2.90900 0.00000 2.90900 2 S1 4.11395 10 0.00000 2.90900 2.90900 2 S1 4.11395 11 0.00000 -2.90900 2.90900 2 S1 4.11395 12 2.90900 0.00000 -2.90900 2 S1 4.11395 13 -2.90900 0.00000 -2.90900 2 S1 4.11395 14 0.00000 2.90900 -2.90900 2 S1 4.11395 15 0.00000 -2.90900 -2.90900 2 S1 4.11395 16 4.36350 1.45450 1.45450 1 Cd1 4.82403 17 1.45450 4.36350 1.45450 1 Cd1 4.82403 18 -4.36350 -1.45450 1.45450 1 Cd1 4.82403 19 -1.45450 -4.36350 1.45450 1 Cd1 4.82403 20 1.45450 1.45450 4.36350 1 Cd1 4.82403 21 -1.45450 -1.45450 4.36350 1 Cd1 4.82403 22 -4.36350 1.45450 -1.45450 1 Cd1 4.82403 23 -1.45450 4.36350 -1.45450 1 Cd1 4.82403 24 4.36350 -1.45450 -1.45450 1 Cd1 4.82403 25 1.45450 -4.36350 -1.45450 1 Cd1 4.82403 26 -1.45450 1.45450 -4.36350 1 Cd1 4.82403 27 1.45450 -1.45450 -4.36350 1 Cd1 4.82403 28 5.81800 0.00000 0.00000 2 S1 5.81800 29 -5.81800 0.00000 0.00000 2 S1 5.81800 30 0.00000 5.81800 0.00000 2 S1 5.81800 31 0.00000 -5.81800 0.00000 2 S1 5.81800 32 0.00000 0.00000 5.81800 2 S1 5.81800 33 0.00000 0.00000 -5.81800 2 S1 5.81800 34 -4.36350 4.36350 1.45450 1 Cd1 6.34002 35 4.36350 -4.36350 1.45450 1 Cd1 6.34002 36 -4.36350 1.45450 4.36350 1 Cd1 6.34002 37 -1.45450 4.36350 4.36350 1 Cd1 6.34002 38 4.36350 -1.45450 4.36350 1 Cd1 6.34002 39 1.45450 -4.36350 4.36350 1 Cd1 6.34002 40 4.36350 4.36350 -1.45450 1 Cd1 6.34002 41 -4.36350 -4.36350 -1.45450 1 Cd1 6.34002 42 4.36350 1.45450 -4.36350 1 Cd1 6.34002 43 1.45450 4.36350 -4.36350 1 Cd1 6.34002 44 -4.36350 -1.45450 -4.36350 1 Cd1 6.34002 45 -1.45450 -4.36350 -4.36350 1 Cd1 6.34002 46 5.81800 2.90900 2.90900 2 S1 7.12557 47 -5.81800 2.90900 2.90900 2 S1 7.12557 48 2.90900 5.81800 2.90900 2 S1 7.12557 49 -2.90900 5.81800 2.90900 2 S1 7.12557 50 5.81800 -2.90900 2.90900 2 S1 7.12557 51 -5.81800 -2.90900 2.90900 2 S1 7.12557 52 2.90900 -5.81800 2.90900 2 S1 7.12557 53 -2.90900 -5.81800 2.90900 2 S1 7.12557 54 2.90900 2.90900 5.81800 2 S1 7.12557 55 -2.90900 2.90900 5.81800 2 S1 7.12557 56 2.90900 -2.90900 5.81800 2 S1 7.12557 57 -2.90900 -2.90900 5.81800 2 S1 7.12557 58 5.81800 2.90900 -2.90900 2 S1 7.12557 59 -5.81800 2.90900 -2.90900 2 S1 7.12557 60 2.90900 5.81800 -2.90900 2 S1 7.12557 61 -2.90900 5.81800 -2.90900 2 S1 7.12557 62 5.81800 -2.90900 -2.90900 2 S1 7.12557 63 -5.81800 -2.90900 -2.90900 2 S1 7.12557 64 2.90900 -5.81800 -2.90900 2 S1 7.12557 65 -2.90900 -5.81800 -2.90900 2 S1 7.12557 66 2.90900 2.90900 -5.81800 2 S1 7.12557 67 -2.90900 2.90900 -5.81800 2 S1 7.12557 68 2.90900 -2.90900 -5.81800 2 S1 7.12557 69 -2.90900 -2.90900 -5.81800 2 S1 7.12557 70 -7.27250 1.45450 1.45450 1 Cd1 7.55780 71 -1.45450 7.27250 1.45450 1 Cd1 7.55780 72 7.27250 -1.45450 1.45450 1 Cd1 7.55780 73 1.45450 -7.27250 1.45450 1 Cd1 7.55780 74 4.36350 4.36350 4.36350 1 Cd1 7.55780 75 -4.36350 -4.36350 4.36350 1 Cd1 7.55780 76 -1.45450 1.45450 7.27250 1 Cd1 7.55780 77 1.45450 -1.45450 7.27250 1 Cd1 7.55780 78 7.27250 1.45450 -1.45450 1 Cd1 7.55780 79 1.45450 7.27250 -1.45450 1 Cd1 7.55780 80 -7.27250 -1.45450 -1.45450 1 Cd1 7.55780 81 -1.45450 -7.27250 -1.45450 1 Cd1 7.55780 82 -4.36350 4.36350 -4.36350 1 Cd1 7.55780 83 4.36350 -4.36350 -4.36350 1 Cd1 7.55780 84 1.45450 1.45450 -7.27250 1 Cd1 7.55780 85 -1.45450 -1.45450 -7.27250 1 Cd1 7.55780 86 END 2010/5/21 <ifeffit-request(a)millenia.cars.aps.anl.gov>: > Send Ifeffit mailing list submissions to ? ? ? > ?ifeffit(a)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(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at ? ? ? > ?ifeffit-owner(a)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. fitting (mohamed sobhy) > ? 2. update error in Windows 7 (pkraal(a)geo.uu.nl) ? 3. Re: update > error in Windows 7 (Laurent Menard) ? 4. Re: update error in Windows 7 > (Bryan Gauntt) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 20 May 2010 14:14:18 -0700 (PDT) > From: mohamed sobhy <bakhshwan1981(a)yahoo.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] fitting > Message-ID: <725080.73390.qm(a)web50302.mail.re2.yahoo.com> > Content-Type: text/plain; charset="us-ascii" > > Dear all thanks for your help and explanation about the background I > fitted my data after removing the background and in the attached file > I got this fitting, although all the values are good but I think the coordination number should be less than 8 (for the first shell) due to irradiation. > So how can I get the right coordination number? > How to improve the fitting of second shell? > thanks > > > > -------------- next part -------------- An HTML attachment was > scrubbed... > URL: > <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/201005 > 20/4d94da82/attachment.html> > > ------------------------------ > > Message: 2 > Date: Fri, 21 May 2010 12:09:24 +0200 > From: pkraal(a)geo.uu.nl > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] update error in Windows 7 > Message-ID: > ? ? ? ?<3ded096a7acb18ecc34d49196967ce21.squirrel(a)webmail.geo.uu.nl> > Content-Type: text/plain;charset=iso-8859-1 > > Dear sir or madam, > > I am using IFEFFIT on a Windows 7 system. When the runner informs that > updates are available, I select to download and install them. Then, > the first package is downloaded, but during expanding and installation > of this package the update basically stops and the runner gives an > error associated with access to bin/athena.exe. Windows 7 (like Vista > pretty easily stressed when you try to change software) does not > inform me that a program is trying to change the system or whatever, > so I don't know what to do. Is there anybody out there with similar > problems and maybe, even better, a solution? > > Regards and many thanks, > > Peter Kraal. > > > > ------------------------------ > > Message: 3 > Date: Fri, 21 May 2010 09:23:38 -0400 > From: "Laurent Menard" <menard(a)email.unc.edu> > To: "'XAFS Analysis using Ifeffit'" > ? ? ? ?<ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] update error in Windows 7 > Message-ID: <01cb01caf8e8$d2cc0e90$78642bb0$(a)unc.edu> > Content-Type: text/plain; ? ? ? charset="US-ASCII" > > Peter, > > You need to make sure you have permission in Windows to write to the > IFEFFIT folder. ?If I remember correctly all you have to do is right > click on the IFEFFIT folder, select Properties. ?Go to the Security > Tab and then select the Edit button. ?Make sure that under Users all > of the "allow" boxes are checked then click OK. ?IFEFFIT should > install the updates the next time it checks for updates. > > Regards, > Laurent > > > > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov > [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of > pkraal(a)geo.uu.nl > Sent: Friday, May 21, 2010 6:09 AM > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] update error in Windows 7 > > Dear sir or madam, > > I am using IFEFFIT on a Windows 7 system. When the runner informs that > updates are available, I select to download and install them. Then, > the first package is downloaded, but during expanding and installation > of this package the update basically stops and the runner gives an > error associated with access to bin/athena.exe. Windows 7 (like Vista > pretty easily stressed when you try to change software) does not > inform me that a program is trying to change the system or whatever, > so I don't know what to do. Is there anybody out there with similar > problems and maybe, even better, a solution? > > Regards and many thanks, > > Peter Kraal. > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > ------------------------------ > > Message: 4 > Date: Fri, 21 May 2010 09:26:01 -0400 > From: Bryan Gauntt <bdg160(a)psu.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] update error in Windows 7 > Message-ID: > ? ? ? ?<AANLkTikFXm8cspcd65cHnFcT7R9MN78Gf8gjwBAY6oWB(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Dear Peter, > I found that setting both Artemis and Athena to run in compatibility > mode (XP Service Pack 3) did the trick for me. ?You can do this by > locating the executables in the start menu and right clicking them. > Select "properties" and then the "compatibility" tab. Under > "compatibility mode" select the box next to "Run this program in > compatibility mode," and then select Windows XP (Service Pack 3) from > the drop-down list. > > Best of luck, > Bryan Gauntt > > On Fri, May 21, 2010 at 6:09 AM, ?<pkraal(a)geo.uu.nl> wrote: >> Dear sir or madam, >> >> I am using IFEFFIT on a Windows 7 system. When the runner informs >> that updates are available, I select to download and install them. >> Then, the first package is downloaded, but during expanding and >> installation of this package the update basically stops and the >> runner gives an error associated with access to bin/athena.exe. >> Windows 7 (like Vista pretty easily stressed when you try to change >> software) does not inform me that a program is trying to change the >> system or whatever, so I don't know what to do. Is there anybody out >> there with similar problems and maybe, even better, a solution? >> >> Regards and many thanks, >> >> Peter Kraal. >> >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> > > > > -- > Bryan D. Gauntt > > PhD Candidate > Department of Materials Science and Engineering > 274 Materials Research Lab > Penn State University > (814) 574-2751 > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 87, Issue 27 > *************************************** > ------------------------------ _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit End of Ifeffit Digest, Vol 87, Issue 28 ***************************************

2 1

XANES and DOS calculations
by Joanna Czapla 22 May '10

22 May '10

Dear Feff Users, first of all I must admit that I am a total beginner and probably there are some things which I don’t understand very well. I need to make XANES and DOS calculations for K-edge of sulfur and then compare them with experiment. I use feff 8.4. First, I started from inorganic compounds such as CdS. I generated feff.inp file in ATOMS and first run feff with default values (generated by ATOMS). The fit wasn’t perfect so I started to change parameters-FMS and SCF but there was so significant improvement. I can only add that others fit are even worse. My question is which parameter I should change or which card should I add to make XANES calculations better? Maybe you can recommend any paper? The second question is about DOS calculations. I took the pDOS functions for each atom, set Fermi level from ldosNN files, but the main peaks are below this level and I don’t have any correspondence with XANES spectrum. For other compounds I have the same problem. Should I add any extra shift? I will be grateful for your advice. Regards Joanna Czapla I add the original feff.inp file generated by ATOMS: * This feff8 input file was generated by WebAtoms 1.8 (Atoms 3.0beta10) * Atoms written by and copyright (c) Bruce Ravel, 1998-2001 TITLE name: CdS (greenockite) (cubic zinc sulfide structure) TITLE formula: CdS TITLE sites: Cd1,S1 TITLE refer1: wyckoff 1,III,110 TITLE refer2: TITLE schoen: TITLE notes1: cubic zinc sulfide structure * S K edge energy = 2472.0 eV EDGE K S02 1.0 * pot xsph fms paths genfmt ff2chi CONTROL 1 1 1 1 1 1 PRINT 1 0 0 0 0 0 *** ixc=0 means to use Hedin-Lundqvist * ixc [ Vr Vi ] EXCHANGE 0 *** Radius of small cluster for *** self-consistency calculation *** A sphere including 2 shells is *** a good choice *** l_scf = 0 for a solid, 1 for a molecule * r_scf [ l_scf n_scf ca ] SCF 4.0 *** Upper limit of XANES calculation. *** This *must* be uncommented to *** make Feff calculate full multiple *** scattering rather than a path expansion * kmax [ delta_k delta_e ] XANES 4.0 *** Radius of cluster for Full Multiple *** Scattering calculation *** l_fms = 0 for a solid, 1 for a molecule * r_fms l_fms FMS 5.54240 0 *** Energy grid over which to calculate *** DOS functions * emin emax eimag LDOS -30 20 0.1 *** for EXAFS: RMAX 8.0 and uncomment *** the EXAFS card RPATH 0.1 *EXAFS 20 POTENTIALS * ipot Z element l_scmt l_fms stoichiometry 0 16 S 2 2 0.001 1 48 Cd 3 3 4 2 16 S 2 2 4 ATOMS * this list contains 87 atoms * x y z ipot tag distance 0.00000 0.00000 0.00000 0 S1 0.00000 0 -1.45450 1.45450 1.45450 1 Cd1 2.51927 1 1.45450 -1.45450 1.45450 1 Cd1 2.51927 2 1.45450 1.45450 -1.45450 1 Cd1 2.51927 3 -1.45450 -1.45450 -1.45450 1 Cd1 2.51927 4 2.90900 2.90900 0.00000 2 S1 4.11395 5 -2.90900 2.90900 0.00000 2 S1 4.11395 6 2.90900 -2.90900 0.00000 2 S1 4.11395 7 -2.90900 -2.90900 0.00000 2 S1 4.11395 8 2.90900 0.00000 2.90900 2 S1 4.11395 9 -2.90900 0.00000 2.90900 2 S1 4.11395 10 0.00000 2.90900 2.90900 2 S1 4.11395 11 0.00000 -2.90900 2.90900 2 S1 4.11395 12 2.90900 0.00000 -2.90900 2 S1 4.11395 13 -2.90900 0.00000 -2.90900 2 S1 4.11395 14 0.00000 2.90900 -2.90900 2 S1 4.11395 15 0.00000 -2.90900 -2.90900 2 S1 4.11395 16 4.36350 1.45450 1.45450 1 Cd1 4.82403 17 1.45450 4.36350 1.45450 1 Cd1 4.82403 18 -4.36350 -1.45450 1.45450 1 Cd1 4.82403 19 -1.45450 -4.36350 1.45450 1 Cd1 4.82403 20 1.45450 1.45450 4.36350 1 Cd1 4.82403 21 -1.45450 -1.45450 4.36350 1 Cd1 4.82403 22 -4.36350 1.45450 -1.45450 1 Cd1 4.82403 23 -1.45450 4.36350 -1.45450 1 Cd1 4.82403 24 4.36350 -1.45450 -1.45450 1 Cd1 4.82403 25 1.45450 -4.36350 -1.45450 1 Cd1 4.82403 26 -1.45450 1.45450 -4.36350 1 Cd1 4.82403 27 1.45450 -1.45450 -4.36350 1 Cd1 4.82403 28 5.81800 0.00000 0.00000 2 S1 5.81800 29 -5.81800 0.00000 0.00000 2 S1 5.81800 30 0.00000 5.81800 0.00000 2 S1 5.81800 31 0.00000 -5.81800 0.00000 2 S1 5.81800 32 0.00000 0.00000 5.81800 2 S1 5.81800 33 0.00000 0.00000 -5.81800 2 S1 5.81800 34 -4.36350 4.36350 1.45450 1 Cd1 6.34002 35 4.36350 -4.36350 1.45450 1 Cd1 6.34002 36 -4.36350 1.45450 4.36350 1 Cd1 6.34002 37 -1.45450 4.36350 4.36350 1 Cd1 6.34002 38 4.36350 -1.45450 4.36350 1 Cd1 6.34002 39 1.45450 -4.36350 4.36350 1 Cd1 6.34002 40 4.36350 4.36350 -1.45450 1 Cd1 6.34002 41 -4.36350 -4.36350 -1.45450 1 Cd1 6.34002 42 4.36350 1.45450 -4.36350 1 Cd1 6.34002 43 1.45450 4.36350 -4.36350 1 Cd1 6.34002 44 -4.36350 -1.45450 -4.36350 1 Cd1 6.34002 45 -1.45450 -4.36350 -4.36350 1 Cd1 6.34002 46 5.81800 2.90900 2.90900 2 S1 7.12557 47 -5.81800 2.90900 2.90900 2 S1 7.12557 48 2.90900 5.81800 2.90900 2 S1 7.12557 49 -2.90900 5.81800 2.90900 2 S1 7.12557 50 5.81800 -2.90900 2.90900 2 S1 7.12557 51 -5.81800 -2.90900 2.90900 2 S1 7.12557 52 2.90900 -5.81800 2.90900 2 S1 7.12557 53 -2.90900 -5.81800 2.90900 2 S1 7.12557 54 2.90900 2.90900 5.81800 2 S1 7.12557 55 -2.90900 2.90900 5.81800 2 S1 7.12557 56 2.90900 -2.90900 5.81800 2 S1 7.12557 57 -2.90900 -2.90900 5.81800 2 S1 7.12557 58 5.81800 2.90900 -2.90900 2 S1 7.12557 59 -5.81800 2.90900 -2.90900 2 S1 7.12557 60 2.90900 5.81800 -2.90900 2 S1 7.12557 61 -2.90900 5.81800 -2.90900 2 S1 7.12557 62 5.81800 -2.90900 -2.90900 2 S1 7.12557 63 -5.81800 -2.90900 -2.90900 2 S1 7.12557 64 2.90900 -5.81800 -2.90900 2 S1 7.12557 65 -2.90900 -5.81800 -2.90900 2 S1 7.12557 66 2.90900 2.90900 -5.81800 2 S1 7.12557 67 -2.90900 2.90900 -5.81800 2 S1 7.12557 68 2.90900 -2.90900 -5.81800 2 S1 7.12557 69 -2.90900 -2.90900 -5.81800 2 S1 7.12557 70 -7.27250 1.45450 1.45450 1 Cd1 7.55780 71 -1.45450 7.27250 1.45450 1 Cd1 7.55780 72 7.27250 -1.45450 1.45450 1 Cd1 7.55780 73 1.45450 -7.27250 1.45450 1 Cd1 7.55780 74 4.36350 4.36350 4.36350 1 Cd1 7.55780 75 -4.36350 -4.36350 4.36350 1 Cd1 7.55780 76 -1.45450 1.45450 7.27250 1 Cd1 7.55780 77 1.45450 -1.45450 7.27250 1 Cd1 7.55780 78 7.27250 1.45450 -1.45450 1 Cd1 7.55780 79 1.45450 7.27250 -1.45450 1 Cd1 7.55780 80 -7.27250 -1.45450 -1.45450 1 Cd1 7.55780 81 -1.45450 -7.27250 -1.45450 1 Cd1 7.55780 82 -4.36350 4.36350 -4.36350 1 Cd1 7.55780 83 4.36350 -4.36350 -4.36350 1 Cd1 7.55780 84 1.45450 1.45450 -7.27250 1 Cd1 7.55780 85 -1.45450 -1.45450 -7.27250 1 Cd1 7.55780 86 END 2010/5/21 <ifeffit-request(a)millenia.cars.aps.anl.gov>: > Send Ifeffit mailing list submissions to > ifeffit(a)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(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)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. fitting (mohamed sobhy) > 2. update error in Windows 7 (pkraal(a)geo.uu.nl) > 3. Re: update error in Windows 7 (Laurent Menard) > 4. Re: update error in Windows 7 (Bryan Gauntt) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 20 May 2010 14:14:18 -0700 (PDT) > From: mohamed sobhy <bakhshwan1981(a)yahoo.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] fitting > Message-ID: <725080.73390.qm(a)web50302.mail.re2.yahoo.com> > Content-Type: text/plain; charset="us-ascii" > > Dear all thanks for your help and explanation about the background > I > fitted my data after removing the background and in the attached file I > got this fitting, although all the values are good but I think the coordination number should be less than 8 (for the first shell) due to irradiation. > So how can I get the right coordination number? > How to improve the fitting of second shell? > thanks > > > >

1 0

update error in Windows 7
by pkraal＠geo.uu.nl 21 May '10

21 May '10

Dear sir or madam, I am using IFEFFIT on a Windows 7 system. When the runner informs that updates are available, I select to download and install them. Then, the first package is downloaded, but during expanding and installation of this package the update basically stops and the runner gives an error associated with access to bin/athena.exe. Windows 7 (like Vista pretty easily stressed when you try to change software) does not inform me that a program is trying to change the system or whatever, so I don't know what to do. Is there anybody out there with similar problems and maybe, even better, a solution? Regards and many thanks, Peter Kraal.

3 2

fitting
by mohamed sobhy 20 May '10

20 May '10

Dear all thanks for your help and explanation about the background I fitted my data after removing the background and in the attached file I got this fitting, although all the values are good but I think the coordination number should be less than 8 (for the first shell) due to irradiation. So how can I get the right coordination number? How to improve the fitting of second shell? thanks

1 0

question about E0
by Janeth Lozano 20 May '10

20 May '10

Hi everybody, My question is about the E0, i am making fits where the E0 final is some high, around 8eV, i tried to change the feff calculation with the card EXCHANGE to lower the E0 but it did not work, after the fit i obtained the same E0 around 8 eV, what can i do to improve the E0 around 5 eV, any suggestion? Distance and sigmas are reasonable but my E0 not at all Thanks Janeth Lozano PhD Student mlozano(a)mda.cinvestav.mx

4 3

small screens and my software
by Bruce Ravel 17 May '10

17 May '10

Hi all, Today I received a very common question. An Athena user had just purchased a new laptop and Athena did not display properly on the small screen. When reading in a file, the "OK" button on the column selection dialog was off the bottom of the screen. This question comes up with enough regularity that I wrote a FAQ entry about how to work around this problem. See question 14 at http://cars9.uchicago.edu/ifeffit/FAQ/HoraeQuestions Regards, B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

2 2

Sample Charging
by Pralay K. Santra 15 May '10

15 May '10

Hi, I am performing EXAFS experiments on semiconductor nanoparticles. As these samples are highly insulating, they will be charged under the X-ray radiation. Does this charging effect the EXAFS signal (transmission as well as the fluorescence)? If yes, how can one can remove this charging effect? Will it be good enough to mix the sample with graphite and perform the EXAFS? With regards, Pralay. -- Research Student Prof D. D. Sarma's Group (http://sscu.iisc.ernet.in/DDSarma) Solid State and Structural Chemistry Unit Indian Institute of Science Bangalore 560 012 INDIA Ph No: +91 80 2293 2336 (Extn: 2052) Fax No: +91 80 2360 1310 Mob No: +91 9845123219

1 0

Re: [Ifeffit] Differences between fluorescence and transmission of the same sample
by Ditty Dixon 14 May '10

14 May '10

---------- Forwarded message ---------- From: Ditty Dixon <ditty.dixon(a)gmail.com> Date: Fri, May 14, 2010 at 4:35 PM Subject: Re: Ifeffit Digest, Vol 87, Issue 18 To: ifeffit(a)millenia.cars.aps.anl.gov Hello Carlo, Thank you so much. We already tried with other catalyst like RuSe and CoSe. What was more exiting for me was the similarity between the data for anode pellet, cathode removed, and fluo data(attachment). Actually we want to generate exact conditions in a Direct Methanol fuel cell (methanol crossover and starvation), so we still like to keep both pt system there. Thank you once again, Ditty On Fri, May 14, 2010 at 3:09 PM, <ifeffit-request(a)millenia.cars.aps.anl.gov>wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)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(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)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: fitting (Iztok Ar?on) > 2. Re: Differences between fluorescence and transmission of the > same sample (Carlo Segre) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 14 May 2010 08:59:20 +0200 > From: Iztok Ar?on <iztok.arcon(a)ung.si> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] fitting > Message-ID: <4BECF4C8.2090302(a)ung.si> > Content-Type: text/plain; charset="iso-8859-2"; Format="flowed" > > Dear Mohamed, > > There is an example of CeO2 EXAFS analysis, taking into account > background problems, > in the following paper: > *J. Pade?nik Gomil?ek, I. Kozjek-?kofic, N. Bukovec, A. Kodre > */X-ray absorption study of CeO2 and Ce/V mixed oxide thin films > obtained by sol-gel deposition. /* > *Thin solid films, vol. 446, issue 1, (2004) 117-123. > regards > Iztok Arcon > > mohamed sobhy wrote: > > > Dear all > > I am trying to use artemis to do fitting to CeO2. But really I cant > > get the right way to do that. > > During the fitting, I am using amp as set and change in N degeneracy > > of the path. attached is the best fit i got but it still not good and > > the chi-square is 41.109065479 > > so can you suggest me what to do > > > > thanks > > > > Mohamed > > > > > >------------------------------------------------------------------------ > > > >_______________________________________________ > >Ifeffit mailing list > >Ifeffit(a)millenia.cars.aps.anl.gov > >http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > > > -- > Iztok Arcon > University of Nova Gorica > Vipavska 13, POB 301 > 5001 Nova Gorica, Slovenia > > tel: +386 5 331 5227 > fax: +386 5 331 5240 > e-mail: iztok.arcon(a)ung.si > http://www.ung.si/~arcon <http://www.ung.si/%7Earcon> > http://www.ung.si/~arcon/xas <http://www.ung.si/%7Earcon/xas> > >

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Re: [Ifeffit] Ifeffit Digest, Vol 87, Issue 18
by Ditty Dixon 14 May '10

14 May '10

Hello Carlo, Thank you so much. We already tried with other catalyst like RuSe and CoSe. What was more exiting for me was the similarity between the data for anode pellet, cathode removed, and fluo data(attachment). Actually we want to generate exact conditions in a Direct Methanol fuel cell (methanol crossover and starvation), so we still like to keep both pt system there. Thank you once again, Ditty On Fri, May 14, 2010 at 3:09 PM, <ifeffit-request(a)millenia.cars.aps.anl.gov>wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)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(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)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: fitting (Iztok Ar?on) > 2. Re: Differences between fluorescence and transmission of the > same sample (Carlo Segre) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 14 May 2010 08:59:20 +0200 > From: Iztok Ar?on <iztok.arcon(a)ung.si> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] fitting > Message-ID: <4BECF4C8.2090302(a)ung.si> > Content-Type: text/plain; charset="iso-8859-2"; Format="flowed" > > Dear Mohamed, > > There is an example of CeO2 EXAFS analysis, taking into account > background problems, > in the following paper: > *J. Pade?nik Gomil?ek, I. Kozjek-?kofic, N. Bukovec, A. Kodre > */X-ray absorption study of CeO2 and Ce/V mixed oxide thin films > obtained by sol-gel deposition. /* > *Thin solid films, vol. 446, issue 1, (2004) 117-123. > regards > Iztok Arcon > > mohamed sobhy wrote: > > > Dear all > > I am trying to use artemis to do fitting to CeO2. But really I cant > > get the right way to do that. > > During the fitting, I am using amp as set and change in N degeneracy > > of the path. attached is the best fit i got but it still not good and > > the chi-square is 41.109065479 > > so can you suggest me what to do > > > > thanks > > > > Mohamed > > > > > >------------------------------------------------------------------------ > > > >_______________________________________________ > >Ifeffit mailing list > >Ifeffit(a)millenia.cars.aps.anl.gov > >http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > > > -- > Iztok Arcon > University of Nova Gorica > Vipavska 13, POB 301 > 5001 Nova Gorica, Slovenia > > tel: +386 5 331 5227 > fax: +386 5 331 5240 > e-mail: iztok.arcon(a)ung.si > http://www.ung.si/~arcon <http://www.ung.si/%7Earcon> > http://www.ung.si/~arcon/xas <http://www.ung.si/%7Earcon/xas> > >

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Differences between fluorescence and transmission of the same sample
by Ditty Dixon 14 May '10

14 May '10

Hello ifeffit users, I am working in the area of In-situ XAS analysis of Fuel cell catalyst. The heart of the fuel cell, MEA(membrane electrode assembly) consist of nafion membrane and the catalyst sprayed on both sides which act as Cathode and Anode(the whole max thickness 1mm). I have a system where Platinum is a common metal catalyst for both anode and cathode, with anode made of alloy of Pt and Ru(nano) ,and Cathode pure Pt(both 2mg/cm2 metal loading). An In-situ transmission XAS measurements on such a system gives no information as the transmission signal will contain both Pt signal from anode and cathode and two different process taking place oxidation and reduction. So we deal with the situation by removing the catalyst from one side. But when we did our measurements in fluorescence(without removing any catalyst) we got two different signals when we turned the cell 180 degree. If the anode was facing the fluo detector we got characteristic signal for Pt/Ru alloy(dampening in FT) and when cathode was facing, that of pure Pt. Is this a solution to separate the signals from anode and cathode without removing any catalyst?. I have attached the file for the fluorescence measurements for my MEA. Thanks in Advance, Ditty On Wed, May 5, 2010 at 5:43 PM, <ifeffit-request(a)millenia.cars.aps.anl.gov>wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)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(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)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: Differences between fluorescence and transmission of the > same sample (Bruce Ravel) > 2. Re: Ifeffit Digest, Vol 87, Issue 4 (Bruce Ravel) > 3. Differences between fluorescence and transmission of the same > sample (Andrew Campos) > 4. Re: Differences between fluorescence and transmission of the > same sample (Ditty Dixon) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 5 May 2010 10:30:18 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Differences between fluorescence and > transmission of the same sample > Message-ID: <201005051030.18579.bravel(a)bnl.gov> > Content-Type: Text/Plain; charset="iso-8859-15" > > Andrew, > > I suspect that you are seeing what Grant refers to in his tutorials as > "leakage". That is, your transmission data appears to my eye to be > what happens when you have a wide spread in sample thickness under the > beam, ranging from gaps to very thick particles. > > If you go to > > http://gbxafs.iit.edu/training/tutorials.html > > And follow the link to the "Sample preparation" presentation, the > effect of leakage is shown on slide 16. > > On the following slide, Grant points out that this thickness effect > always reduces amplitudes. That is the case above the edge for your > data. And if you normalize data distorted in that way, you end up > with an artificially enhanced pre-edge peak, again as in your data. > > My US$0.02, > B > > > On Wednesday 05 May 2010 09:55:16 am Andrew Campos wrote: > > Hi everyone, > > > > My lab mates are running in-situ H2 reduction of Cobalt/SiO2 catalysts > > using the Co K-edge and are obtaining differences between the > > fluorescence and transmission signals. The in-situ cell does have > > quite a bit of sample thickness (2-3 mm approx) and I was wondering if > > the fluorescence signal only has a penetration depth of a few > > micrometers. If this is the case that would explain it where the side > > that is further away from the heating element is more oxidized than > > the rest of the sample. > > > > Has anyone run into this problem before? We're using the basic > > furnace/cryostat unit (in-situ cell manufactured by the exafsco) and a > > 13 element fluorescence detector (germanium diode). > > > > I appreciate any insight into the issue, I have attached a > > fluorescence and transmission spectrum collected at the same time > > where the transmission and fluorescence are in the .prj file. > > > > Thanks so much! > > Andrew > > > > -- > > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 > Building 535A > Upton NY, 11973 > > My homepage: http://xafs.org/BruceRavel > EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/<http://cars9.uchicago.edu/%7Eravel/software/exafs/> > > > ------------------------------ > > Message: 2 > Date: Wed, 5 May 2010 10:39:14 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Ifeffit Digest, Vol 87, Issue 4 > Message-ID: <201005051039.14501.bravel(a)bnl.gov> > Content-Type: Text/Plain; charset="iso-8859-1" > > On Wednesday 05 May 2010 07:56:47 am baran yildirim wrote: > > My problem is similar; I am trying to simulate a doped crystal > > (different than chp 10 in Atemis doc, this time impurity atom is > > subjected to XAS) and the host is similar to inverse-spinel type: > > include both tetrahedral and octahedral sites in its structure. The > > dopant may settle in tetrahedral or octahedral sites. > > Indeed. Similar enough that you also should read the paper by Scott > Calvin that I suggested to Maria Elena. > > > 1- I managed to simulate the doped structure as changing the FEFF inp > > file manually (first I run Atoms as if impurity ions settle in all > > sites and then keep it in 0 potential and change the 1st potential > > with the original atom) and did it for both sites, thus i have 2 batch > > of paths and then fit it. It seems it works (Question: Do you think > > what i am doing is logical? or any other suggestion? ) > > I think that's a good approach. > > Question 15 at > > http://cars9.uchicago.edu/ifeffit/FAQ/FeffitModeling > > gives a bit more information. The link to the page authored by Scott > is quite useful. > > > > 2- But problems do not end :) Another problem is impurity ion may > > take different valences: it can be trivalent or divalent. In FEFF 9.0 > > i found kinda solution using ION command, it doesnt do what i > > exactly want but i can get some idea on what happens if the charge > > distribution changes. But unfortunately, i cant try it in ARTEMIS > > since i can not install FEFF 9.0 in ARTEMIS. As far as i understood > > the program structure is changed completely. But I didnt give up :)I > > generated the chi file in FEFF 9.0 and load it in ARTEMIS and continue > > to analyze but the results are not promising. (Question: Is there any > > way to run it together? and any suggestion in changing the valance? ) > > Artemis does not support Feff9 at this time. > > I actually have not played around with Feff9 yet, myself, so I won't > be able to help with the rest. Perhaps one of the Seattlites can help > .... > > B > > > -- > > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 > Building 535A > Upton NY, 11973 > > My homepage: http://xafs.org/BruceRavel > EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/<http://cars9.uchicago.edu/%7Eravel/software/exafs/> > > > ------------------------------ > > Message: 3 > Date: Wed, 5 May 2010 11:24:16 -0400 > From: Andrew Campos <acampo2(a)tigers.lsu.edu> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Differences between fluorescence and transmission > of the same sample > Message-ID: > <z2md94177571005050824k8abda3a0n708eaada202fdc6e(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dr. Ravel, > > Thanks so much for the link and the advice! I appreciate it greatly. I > will advise my lab mates as such and may have to only use the > fluorescence data if that is indeed the case. > > I also included the file where the lower temperature is included and > you might come to the same conclusion. The samples that I ran were > pre-sieved, and the ones included in the .prj file aren't so that > should be pursued prior to running the experiment. If they crush the > particle and sieve the sample, I think that we can be more certain > that this is not the case. This was very helpful! > > Andrew >

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fitting
by mohamed sobhy 14 May '10

14 May '10

Dear all I am trying to use artemis to do fitting to CeO2. But really I cant get the right way to do that. During the fitting, I am using amp as set and change in N degeneracy of the path. attached is the best fit i got but it still not good and the chi-square is 41.109065479 so can you suggest me what to do thanks Mohamed

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Debye model on Artemis
by Kleber Daum Machado 12 May '10

12 May '10

Hi Matt, Concerning the third cumulant, my problem is to use a particular model for it. Some articles (Frenkel and Rehr, PRB 48 (1993) 585; Araujo et al, PRB 74 (2006) 184102) show how to use the Einstein model on Artemis, since these articles show the expressions that should be defined for sigma^2(T) and C3(T) for this model in Artemis (eqs. 11 and 18 of Frenkel and eqs. 2 and 3 of Araujo). In fact, I have already tested them on my analysis, using the eins function for sigma^2 and defining the C3(T) expression given in those articles in Artemis. I'd like to test Debye model too, and my problem is to use Debye model for sigma^2(T) and C3(T). For sigma^2(T) Artemis has the debye function already predefined. I'd like to use/write an expression for C3(T) considering Debye model, but I didn't find anything about such expression on the literature. Kleber

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Debye model on artemis
by Kleber Daum Machado 11 May '10

11 May '10

I'd like to use the third cumulant option in Artemis, but considering the Debye model. Artemis has a Debye function for the second cumulant (Debye-Waller factor) but not to the third. How could this be done in Artemis? Kleber

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