June 2010 - Ifeffit - millenia.cars.aps.anl.gov

Re: [Ifeffit] Ifeffit Digest, Vol 88, Issue 12
by Jatinkumar Rana 27 Jul '10

27 Jul '10

Dear Darek, Sorry for the late response. To fit the "first shell" the No.of independent points and No.of variables which i use are as follows: I use deltaK=11, deltaR = 1.1 so No.of independent points are 8 and No.of variables are 4 (i.e. N, e0, delr, and ss2) I set s02=0.9. Best regards, Rana On 14.06.2010 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. XAFS fitting with multiple atomic sites of absorbing atom > (Jatinkumar Rana) > 2. ODP: XAFS fitting with multiple atomic sites of absorbing > atom (Zajac, Dariusz A.) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 14 Jun 2010 12:00:27 +0200 > From: Jatinkumar Rana<jatinkumar.rana(a)helmholtz-berlin.de> > To: Ifeffit users<ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] XAFS fitting with multiple atomic sites of > absorbing atom > Message-ID:<4C15FDBB.1050203(a)helmholtz-berlin.de> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Dear users, > > I have measured XAFS spectra on Mn and Fe edge on my material. The > material contains 3 different atomic positions for Mn and 4 different > atomic positions for Fe. > > Initially, I tried fitting Fe-edge/Mn-edge spectra using indiviual Fe/Mn > atomic position one-by-one (i.e. first take one Fe/Mn position, > calculate Feff paths, consider certain paths to fit specific R-range, > then take another Fe/Mn position and do the same) but the fit was not > good visually and in terms of goodness of fit parameters. > > Then, i tried fitting Fe-edge/Mn-edge spectra, taking into account all > Fe/Mn atomic position together i.e. I separately calulated Feff paths > for each Fe/Mn atomic position and summed up related paths from each > Feff calculation for fitting a specific R-range. (The assumption being, > the experimental Fe-edge/Mn-edge XAFS spectra has varying contribution > from all Fe/Mn atomic position in crystal structure). > > Anybody in the group could comment about my approach to fit such problem ? > > Is there any specific strategy to fit such problem ? > > I would be thankful if you could suggest some literature available on > such problems. > > Thanks in advance. > > Best regards, > Rana > > > ------------------------------ > > Message: 2 > Date: Mon, 14 Jun 2010 13:34:18 +0200 > From: "Zajac, Dariusz A."<dariusz.zajac(a)desy.de> > To: "XAFS Analysis using Ifeffit"<ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] ODP: XAFS fitting with multiple atomic sites of > absorbing atom > Message-ID: > <35E004AD6290A7438FCA34BBF325F41601206741(a)ADXV2.win.desy.de> > Content-Type: text/plain; charset="iso-8859-2" > > > Dear Rana, > could you specify how many independent data points and variables you have and you use for fitting? > thnx > darek > > -----Wiadomo?? oryginalna----- > Od: ifeffit-bounces(a)millenia.cars.aps.anl.gov w imieniu Jatinkumar Rana > Wys?ano: Pn 2010-06-14 12:00 > Do: Ifeffit users > Temat: [Ifeffit] XAFS fitting with multiple atomic sites of absorbing atom > > Dear users, > > I have measured XAFS spectra on Mn and Fe edge on my material. The > material contains 3 different atomic positions for Mn and 4 different > atomic positions for Fe. > > Initially, I tried fitting Fe-edge/Mn-edge spectra using indiviual Fe/Mn > atomic position one-by-one (i.e. first take one Fe/Mn position, > calculate Feff paths, consider certain paths to fit specific R-range, > then take another Fe/Mn position and do the same) but the fit was not > good visually and in terms of goodness of fit parameters. > > Then, i tried fitting Fe-edge/Mn-edge spectra, taking into account all > Fe/Mn atomic position together i.e. I separately calulated Feff paths > for each Fe/Mn atomic position and summed up related paths from each > Feff calculation for fitting a specific R-range. (The assumption being, > the experimental Fe-edge/Mn-edge XAFS spectra has varying contribution > from all Fe/Mn atomic position in crystal structure). > > Anybody in the group could comment about my approach to fit such problem ? > > Is there any specific strategy to fit such problem ? > > I would be thankful if you could suggest some literature available on > such problems. > > Thanks in advance. > > Best regards, > Rana > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 88, Issue 12 > *************************************** > > >

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can sigma square ever be less than zero?
by Chris Patridge 29 Jun '10

29 Jun '10

Hello all, I am working on W L3 edge data. W is acting as a substitution dopant in vanadium dioxide at rather low concentration. In a past mailing conversation discussing Feff6 overestimation of E0 for heavier elements it was mentioned that the E0 could be past the rising edge due to the white line from W data. Well using this comment I aligned data using the theory method well explained by Shelly Kelly SnO2 example. Literature suggests W approximates WO2 cubic structure locally instead of the VO2 unit structure. Then fitting the first oxygen coordination shell paths which are well isolated from the other paths, it gives reasonable values for amplitude and enot of 0.77 (0.17) and -1.14 (3.06) respectively. delr is -0.067 (0.028) and then ss comes out to -0.00036 (0.00414). Can ss be negative if the uncertainty brings it above 0? Thank you all, Chris Patridge PhD Candidate Department of Chemistry NSC 405 SUNY Buffalo 315-529-0501

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Postdoctoral position open
by Mukerjee, Sanjeev 28 Jun '10

28 Jun '10

Dear Members, I have an opening for a postdoctoral position in my research group and center starting in August of 2010. The position will be for two years with renewal option at the end of the first. Qualification for this position is a recent Ph.D in physics or chemistry in the field related to synchrotron spectroscopy. Most important would be to have good experience conducting in situ x-ray absorption studies including EXAFS data analysis. We will train the person on other more specific aspects of the spectroscopy as conducted by the research group. Proficiency in basic electrochemistry including classical methods are a must. Please apply with resume and one or two key publications to me personally as soon as possible. We promise a very vibrant research environment and opportunity to develop a portfolio for future career options such as academic positions. This includes training in proposal writing and teaching graduate level courses. In addition this position carries competitive salary and benefits. Sincerely Sanjeev Mukerjee (Professor) Department of Chemistry and Chemical Biology Director of the Northeastern University Center for Renewable Energy Technology (NUCRET) Northeastern University, 360 Huntington Avenue, Boston, MA 02115 Phone (617) 373 2382 Fax (617) 373 8949 URL: www.northeastern.edu/nucret www.northeastern.edu/leap

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Help with artemis!
by JESUS ISAAC AGUIRRE QUIROZ 24 Jun '10

24 Jun '10

Hi everyone, i'm using a macbook with mac OSX. I'm trying to open some files in artemis (just starting) I can open the Cu010k file from the examples folder but when i try to open the respective atoms file (a friend of mine was able to open these files with no problems on windows xp) but artemis shows a message saying "artemis trapped one or more errors! Error message dumped to screen" and nothing happens. I tried to build up the atoms file starting with a blank page and introducing all respective values but it still shows the same error. I'm thinking i may have an old version or I may have missed something about the installation because i had some problems with athena and now i'm working with artemis and i can't even get started. Thanks for your help and advice... _________________________________________________________________ Enciende tu hotness con Hotmail www.hotmailhotness.com.mx

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Sodium uranate fit problem
by Andy Connelly 23 Jun '10

23 Jun '10

Hello all, I've been following this mailing list for ages and have learnt a lot, thank you. Now I have a problem and am hoping someone can help. I have some really nice sodium uranate (Na2U2O7) data from the NSLS (X23A2) that I collected (embarrassingly) a couple of years ago. I have been trying to fit it and have never managed to get a satisfactory fit even to the first shell. >From the literature there should be 2 uranyl oxygens and 6 equatorial oxygens. If I fit these paths I get an amp (S02) value of 0.32 and negative sigma squared values (ss). I have tried to add paths from the second shell to reduce this amp value but no success. I do not believe that this value is real but I cannot find any problem in the background or in the fit. I have found similar problems for lithium uranate and some glass samples, all of which should have similar uranium coordinations. I can bring ss into a more sensible value but amp is always very low. I have tried several different .cif files for different uranate or uranyl systems and they all give roughly the same result. I have found similar problems with some data I collected at Daresbury on a different Na2U2O7 sample so I do not think it is the sample or the beamline. Does anyone have any thoughts why this might be so? Any help or suggestions would be most appreciated. Thank you all in advance, Best regards Andy Connelly

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distinct crystal positions for the absorber atom
by Chris Patridge 22 Jun '10

22 Jun '10

Hello everyone, I am working on fitting the first shell of a double layer vanadium oxide material. The data is V K edge data with 3 scans merged. There is two positions for vanadium in the unit structure with equal occupancy. I started modeling using equal weighting between the 2 feff calculations for each unique vanadium. Setting amp*0.5 seems straight forward. The first shell consists of oxygen coordinated and the next shell is dominated by the vanadium of the adjacent edge sharing polyhedra. Feff0 appears to give a better fit by itself with lower uncertainties than using both model in concert or Feff1 by itself. Can this problem lie in the fact that the bond lengths are quite short (1.6 A) for V-O and discerning the background and signal causes an error? I feel reasonably confident in the crystallography. I pasted the fit results below and included bmps and artemis file there. If there is something suspect please let me know or if you have a suggestion. Thank you all in advance, Christopher Patridge PhD Candidate SUNY University at Buffalo Dept of Chemistry 315-529-0501 Independent points = 7.691406250 Number of variables = 4.000000000 Chi-square = 2503.896487489 Reduced Chi-square = 678.304233648 R-factor = 0.029837426 Measurement uncertainty (k) = 0.000474272 Measurement uncertainty (R) = 0.000888467 Number of data sets = 1.000000000 Guess parameters +/- uncertainties (initial guess): amp = 0.8044660 +/- 0.1118000 (1.0000) enot = -1.9212800 +/- 1.8083430 (0.0000) ssO = 0.0001680 +/- 0.0018760 (0.0030) alpha = 0.0011620 +/- 0.0078840 (0.0000)

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XAFS fitting with multiple atomic sites of absorbing atom
by Jatinkumar Rana 14 Jun '10

14 Jun '10

Dear users, I have measured XAFS spectra on Mn and Fe edge on my material. The material contains 3 different atomic positions for Mn and 4 different atomic positions for Fe. Initially, I tried fitting Fe-edge/Mn-edge spectra using indiviual Fe/Mn atomic position one-by-one (i.e. first take one Fe/Mn position, calculate Feff paths, consider certain paths to fit specific R-range, then take another Fe/Mn position and do the same) but the fit was not good visually and in terms of goodness of fit parameters. Then, i tried fitting Fe-edge/Mn-edge spectra, taking into account all Fe/Mn atomic position together i.e. I separately calulated Feff paths for each Fe/Mn atomic position and summed up related paths from each Feff calculation for fitting a specific R-range. (The assumption being, the experimental Fe-edge/Mn-edge XAFS spectra has varying contribution from all Fe/Mn atomic position in crystal structure). Anybody in the group could comment about my approach to fit such problem ? Is there any specific strategy to fit such problem ? I would be thankful if you could suggest some literature available on such problems. Thanks in advance. Best regards, Rana

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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 10 Jun '10

10 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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