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

background fitting functions in Artemis
by Chris Patridge 07 Jul '10

07 Jul '10

Hello all, If a background is difficult to remove due to short paths lengths, can a background fitting be used in the Artemis fit? I have a large data range giving near two times the ind points even when including the background function. After fitting the data, it gave a number of correlations some of which are negative. The parameters give reasonable values and uncertainties and I feel confident about the model. I know the fit is not great but can I use this as the starting point or is the background just giving me a large fudge factor? Thank you, Chris Patridge

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Clarification needed on the structured 2nn peak
by Varadarajan Sridharan 06 Jul '10

06 Jul '10

Greetings to all I am a beginner to EXAFS. Recently I had carried out Cd K-edge EXAFS measurements on Cd1-xCaxO solid solution. The end members CdO and CaO belong to same crystal structure Fm-3m. I had analysed the spectrum with Atthena and fitted with Arthemis. I am attaching the Athena project file (***.prj) and that of Arthemis project file (***.apr) for your reference. Athena: As per the crystal structure of CdO, the first nearest neighbour is at 2.345 A corresponding to Cd-O1 inter atomic distance and 2nn distance is 3.3.16 A corresponding to Cd-Cd1 inter atomic distance. Though I am able get the first peak in chi(R) plot at expected position, I am having some problems for the second peak. The second peak has features; main one and a shoulder. The main peak itself appears at lower R compared to expected one. Intensity of the shoulder increases with Ca substitution at the expense of main peak itself. Can any one comment on this? My predicament: If I associate, based on the structure of second peak, bimodal distribution for the Cd-Cd1 interatomic distance, the difference of 0.4 A is 11%. This value gives me an uneasy feeling. Is it possible to accommodate this difference within the setting of F m-3m? OR It is due the multi scattering is the problem? Arthemis: For CdO: The k^3 weighted chi fitting, I agree is far from satisfaction. Std of delR is a bothering point. I had included 20 paths. Even for the CdO with F m-3m, the calculated second peak has a shoulder at lower R. I could see a small contribution from path 4. But I am not sure if that is all. How to float the individual GDS parameter for each and every path? What can be done to improve the fitting? Thanking you all in advance Varadarajan Sridharan ---------------------------------- Condensed matter Physics Division Materials Science division Indira Gandhi Centre for Atomic Research Kalpakkam 603 102 India

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Re: [Ifeffit] Ifeffit Digest, Vol 89, Issue 3
by Varadarajan Sridharan 06 Jul '10

06 Jul '10

Dear Matt, I agree to your point. AS of now I am not attempting to fit the Ca substituted system for two reasons 1.I am specifically looking for the "cause" for the structure in the second peak. The structure is present in the calculated CdO Chi(R) plot itself. 2. Apart from that when I tried to put in Ca in the ATOM, Ca is not at all appearing in the list after running ATOM. Can you help me out in this matter as well. Thanking you ---- Varadarajan Sridharan On Tue, Jul 6, 2010 at 10:30 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: Clarification needed on the structured 2nn peak > (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 6 Jul 2010 07:52:16 -0500 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Clarification needed on the structured 2nn peak > Message-ID: > <AANLkTinjUxHwVBBkCBiONWnNNptLnpSKpI9mnri3HbBv(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Dear Varadarian, > > I didn't look at your attachments, but have you considered that there > might be some Cd-Ca in the second shell? I didn't see what value of > x you had in Cd(1-x)CaxO, but if the oxides form a solid solution one > might naively expect the second shell to have (1-x) Cd and x Ca > coordination. Ca and Cd scatter photoelectrons differently enough > to be distinguishable in the EXAFS. It might be that there is extra > disorder too, say if the typical Cd-Ca distance was different from the > typical Cd-Cd distance. > > Cheers, > > --Matt > > On Tue, Jul 6, 2010 at 7:29 AM, Varadarajan Sridharan > <varadu.sridh(a)gmail.com> wrote: > > Greetings to all > > > > ?? I am a beginner to EXAFS. > > > > ? Recently I had carried out Cd K-edge EXAFS? measurements on Cd1-xCaxO > > solid solution. The end members CdO and CaO belong to same crystal > structure > > Fm-3m. > > > > ?? I had analysed the spectrum with Atthena and fitted with Arthemis. I > am > > attaching the Athena project file (***.prj) and that of Arthemis project > > file (***.apr) for your reference. > > > > Athena: > > > > ?? As per the crystal structure of CdO, the first nearest neighbour is at > > 2.345 A corresponding to Cd-O1 inter atomic distance and 2nn distance is > > 3.3.16 A corresponding to Cd-Cd1 inter atomic distance. Though I am able > get > > the first peak in chi(R) plot at expected position, I am having some > > problems for the second peak. The second peak has features; main one and > a > > shoulder. The main peak itself appears at lower R compared to expected > one. > > Intensity of the shoulder increases with Ca substitution at the expense > of > > main peak itself. > > > > ??????????? Can any one comment on this? > > > > ???? My predicament: If I associate, based on the structure of second > peak, > > bimodal distribution for the Cd-Cd1 interatomic distance, the difference > of > > 0.4 A is 11%. This value gives me an uneasy feeling. Is it possible to > > accommodate this difference within the setting of F m-3m? > > > > ????????????????????????????????? OR > > > > ???????????????????????????????? It is due the multi scattering is the > > problem? > > > > Arthemis: > > > > For CdO: ?The k^3 weighted chi fitting, I agree is far from satisfaction. > > Std of delR is a bothering point. I had included 20 paths. Even for the > CdO > > with F m-3m, the calculated second peak has a shoulder at lower R. I > could > > see a small contribution from path 4. But I am not sure if that is all. > > > > How to float the individual GDS parameter for each and every path? What > can > > be done to improve the fitting? > > > > Thanking you all in advance > > > > Varadarajan Sridharan > > > > ---------------------------------- > > > > Condensed matter Physics Division > > > > Materials Science division > > > > Indira Gandhi Centre for Atomic Research > > > > Kalpakkam 603 102 > > > > India > > > > _______________________________________________ > > 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 89, Issue 3 > ************************************** >

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XAFS Postdoc position at HASYLAB
by Welter, Edmund 01 Jul '10

01 Jul '10

Dear colleagues, at the Hamburger Synchrotron Strahlungslabor (HASYLAB) a postdoc position in the XAFS business is available. For more information please follow: http://www.desy.de/v2/docs/1275482643-e.pdf The main tasks of the successful applicant will be the operation of the X1 XAFS-beamline, to take care of our industrial XAFS users and last but not least DESY is strongly encouraging postdocs to work in their own field of science. If you have questions about this mail or the available position please do not reply to the mailing list, but contact me directly instead. Best regards, Edmund Welter

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can sigma square ever be less than zero?
by Chris Patridge 28 Jun '10

28 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 22 Jun '10

22 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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