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

Re: [Ifeffit] Large Enot values
by Paul Bingham 13 Jun '10

13 Jun '10

Thanks Shelly. I have tried doing as you suggest, shifting manually the value of E0 by +10 eV in Athena before fitting in Artemis. Thankfully the delta E of the new fit is close to zero which I think means that the theory and the data do agree, i.e. I am fitting the first shell with the correct atom type. I am still a little unclear as to why such a large energy shift might arise and will look into this further. Any tips or suggestions would again be very welcome and I would very much appreciate it if you can send me a copy of your book chapter which you mentioned. Best Regards Paul. -- 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 Quoting 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. Re: Large Enot values (shelly Kelly) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 11 Jun 2010 09:18:33 -0500 > From: "shelly Kelly" <dr.sdkelly(a)gmail.com> > To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Large Enot values > Message-ID: <4c1245c4.9d90d80a.567d.3528(a)mx.google.com> > Content-Type: text/plain; charset="utf-8" > > Hi  paul: > > Have you tried to shift eo in athena by 10 ev? If you have and the fit still > gives a large deltaE then the theory and the data do not agree.  DeltaE > changes the spectra most strongly at low k, so another thing to try is to > increase kmin in the ft.  > > You can also use the theory to help remove the background in athena.  If > you have tried all these and it doesn't work.  I'd try a different > theory.  Either a different se oxide or a different atom type. > > Of course my book chapter goes over how to do these thing. I'll send you a > copy if you ask.  I've also posted example athena projects > on xafs.org. > > Good luck. > > > > -- Sent from my Palm Pr? > On Jun 8, 2010 5:55 PM, Paul Bingham <p.a.bingham(a)sheffield.ac.uk> > wrote: > > Thanks Bruce, > > > > I agree that the Se-O bond lengths are short but in SeO2, and Na2SeO3 as > Se4+ > > "standards" there are Se-O bond lengths average around 1.7A. For example when > I > > run feff on the SeO2 cif file it gives 1 Se-O bond at 1.623A and 2 at > 1.793A, > > averaging at roughly 1.7A. > > > > I'm confident that the XANES I have for this sample show that the Se is > pretty > > much all present as Se4+ and I think the first shell is very likely to > consist > > of oxygens. > > > > I also tried another shell from the same feff as included in the data I > sent, > > using O1_1 instead of O2_1 and the fit including Delr still points to an > > average Se-O bond length of about 1.7A with an Enot of around 10. > > > > I will try fitting with feffs based on different cif files with some > different > > Se-O bond lengths, but if you have any other suggestions I'd be grateful. > > > > Thanks very much for your advice - it's appreciated. > > > > Regards > > > > Paul. > > -- > > 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 > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > >

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Re: [Ifeffit] Large Enot values
by Paul Bingham 11 Jun '10

11 Jun '10

Thanks Bruce, I agree that the Se-O bond lengths are short but in SeO2, and Na2SeO3 as Se4+ "standards" there are Se-O bond lengths average around 1.7A. For example when I run feff on the SeO2 cif file it gives 1 Se-O bond at 1.623A and 2 at 1.793A, averaging at roughly 1.7A. I'm confident that the XANES I have for this sample show that the Se is pretty much all present as Se4+ and I think the first shell is very likely to consist of oxygens. I also tried another shell from the same feff as included in the data I sent, using O1_1 instead of O2_1 and the fit including Delr still points to an average Se-O bond length of about 1.7A with an Enot of around 10. I will try fitting with feffs based on different cif files with some different Se-O bond lengths, but if you have any other suggestions I'd be grateful. Thanks very much for your advice - it's appreciated. Regards Paul. -- 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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Scott Calvin PhD Thesis
by María Elena Montero Cabrera 09 Jun '10

09 Jun '10

Hello to all! Would you tell me, please, how to obtain Scott Calvin PhD Thesis, or, at least, his e-mail? I am reading a paper whose reference 30th is that document, and I have already spent 3 hours navigating by university libraries without any success. Thank you very much for any help, regards -- María Elena Dra. María Elena Montero Cabrera Departamento de Medio Ambiente y Energía Centro de Investigación en Materiales Avanzados (CIMAV) Miguel de Cervantes 120, Compl. Ind. Chihuahua Chihuahua CP 31109, Chih. México Tel (614) 4391123

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NACSSC - two more days for oral presentation abstracts
by Carlo Segre 09 Jun '10

09 Jun '10

Hello All: The deadline for oral presentations abstracts for the 1st North American Core Shell Spectroscopy Conference is just 2 days away! The conference will feature a symposium in honor of Ed Stern and is an ideal place for graduate students and postdocs to present their results. Please see the conference web page and the attached announcement. http://www.dxcicdd.com/cssc We urge you to consider attending the conference and submitting an abstract. Carlo Segre & Daniel Haskel

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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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