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

Re: [Ifeffit] ATHENA: \"you have not used any memory yet\"
by Bruce Ravel 14 Jul '10

14 Jul '10

On Wednesday, July 14, 2010 10:45:45 am you wrote: > Thank you for answering me. > > What I mean with stalled it that the cursor is "running" when it is on the > main Athena window, everything is gray and no file appears on the right (in > the group list). > > And, I do not see any OK button in the "data columns" window... I know that > my laptop has a small screen, but I have checked at the whole window > (moving around with ALT F7) and there is really no OK button. GUI > problem...? > > I will try on another 64bit system and will let you know. > Claire, Please use the mailing list. That way, others can find solutions to problems by doing a google search. Is your problem related to question 13 at http://cars9.uchicago.edu/ifeffit/FAQ/HoraeQuestions Are you a KDE user? The "everything is grey" could be a kwin visual cue that the application is waiting for input that you cannot find because the column selection dialog is off the bottom of the screen. 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/

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Negative ss problem
by Abhijeet Gaur 14 Jul '10

14 Jul '10

Hi all, I read the discussion on negative Debye waller factor. As per the discussion the negative value of this factor shows that the model has shortcomings, so it should be corrected. I am also getting the same problem while fitting one of my samples. It is a Cu complex whose EXAFS data is taken at Dispersive EXAFS beamline at RRCAT, Indore, India. In the complex the nearest neighbours of Copper atom are Nitrogen and Oxygen. I am getting a very good fit upto 3rd shell but the problem is that all ss parameters are coming negative. I checked the model it seem correct. Also I am getting a peak below 1 Angs which is also getting fitted but I am not able to get that whether it is a real or due to some noise. I am attaching herewith the results of data analysis and fitting. Thanks in advance With regards Abhijeet Gaur Vikram University Ujjain, INDIA

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Re: [Ifeffit] Negative ss problem
by Chris Patridge 14 Jul '10

14 Jul '10

Hello, It seems to me that you have some more problems than just ss values. The data collection range seems a little short just ~300 eV past the edge. Amp is quite high and delr is very large. I am an expert by no means but I might suggest that you have the wrong model. The model is trying to compensate for high R space magnitude by making amp above 1 and ss negative. Have you considered your data processing in Athena? Did you use the default settings? I would guess Cu-O bonds might be too short for the presets in Athena. How did you check your model? Buena salud, Chris Patridge On Jul 14, 2010, at 2:59 AM, Abhijeet Gaur <abhijeetgaur9(a)gmail.com> wrote: > Hi all, > I read the discussion on negative Debye waller factor. As > per the discussion the negative value of this factor shows that the > model has shortcomings, so it should be corrected. > I am also getting the same problem while fitting one of my > samples. It is a Cu complex whose EXAFS data is taken at Dispersive > EXAFS beamline at RRCAT, Indore, India. > In the complex the nearest neighbours of Copper atom are > Nitrogen and Oxygen. > I am getting a very good fit upto 3rd shell but the problem > is that all ss parameters are coming negative. I checked the model > it seem correct. > Also I am getting a peak below 1 Angs which is also getting > fitted but I am not able to get that whether it is a real or due to > some noise. > I am attaching herewith the results of data analysis and > fitting. > Thanks in advance > With regards > Abhijeet Gaur > Vikram University > Ujjain, INDIA > <Cu complex fitting results.doc> > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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ATHENA: "you have not used any memory yet"
by Claire Gervais 13 Jul '10

13 Jul '10

Hello, I have recently installed ATHENA on my laptop (Lenovo X200) and runs into trouble when I try to open a file: The "data column" window opens well, and the plot is there but then I am stalled. At the bottom of the main window is written: "you have not used any memory yet" I know that a previous thread was written on it ([Ifeffit] A problem with Athena from 2008) but it seems to remain an open issue... Here is my configuration: OS: Ubuntu Jaunty AMD64 Athena version: 0.8.059 Ifeffit version: 1.2.11d I have also tried with a previous Athena version, and on WindowsXP via Virtualbox. The problem remains. My data file is according to ATHENA standard (i.e. # for comments followed by columns). If you have any idea, I would be delighted to read it! Thanks, Claire ---------------------------------------------------------------------- Claire Gervais PhD Chemistry & Material Sciences, Visiting scientist Smithsonian Museum Conservation Institute Museum Support Center 4210 Silver Hill Road Suitland, Maryland 20746 USA Web: http://www.claire-et-net.ch ---------------------------------------------------------------------

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Vanadium center fitting issues
by Christopher Allen 10 Jul '10

10 Jul '10

Hi, I wanted to get some advice on a vanadium centered material I’ve been trying to fit for quite a while w/ repeated failure. Based on XRD and electrochemistry I’m pretty confident in the material/model, and I have the input file for the material. The first shell out to 2.2 angstroms in R space is a distorted VO6 w/ bond lengths ranging from 1.6 to 2.2 angstroms, similar to the V2O5 which has been discussed on the mailing list recently (July 7th). The last two peaks from 2.2 to 3.3 angstroms presumably include 4 V-P and 1 more V-O single scattering paths. (the best fit I could get on the 4V-P/1V-O used only the first of these two peaks.) With regards to the first shell fitting, is it appropriate to be grouping the V-O bonds in terms of 1 short, 4 medium, and 1 long bond distance to cut down on variables? I noticed in the V2O5 previously discussed, that he used one ss and delr term for all 6 V-O paths, but I guess that just means making some assumptions that any variations in ss and delr are isotropic throughout. Is that correct? I’ve had real issues w/ those peaks representing V-P/V-O from 2-3.3 angstroms so I wonder if it’s unreasonable to try and extract this information based on the k space or if possible thats not what I have there. Could it be that I need to account for the two inequivalent V centers? (In that case, wouldn’t the number of variables be doubled?) Thanks for any comments, Chris -- Chris Allen Northeastern University Center for Renewable Energy Technology 317 Egan Research Center 360 Huntington Ave. Boston, MA 02115 617-373-5630

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3 Year XAFS Postdoc Position at The University of Manchester
by Sven L.M. Schroeder 08 Jul '10

08 Jul '10

Dear colleagues Robert Dryfe and I have been awarded funding for a postdoctoral XAFS position, for a 3 year appointment to study metal nanoparticle deposition and growth at liquid-liquid interfaces: http://www.jobs.ac.uk/job/ABI341/research-associate/ This NSF- and EPSRC-supported project will make use of facilities at DIAMOND and the APS, in close collaboration with Mark Schlossman from University of Illinois at Chicago, who will lead on interfacial diffraction and X-ray reflectivity measurements on the same systems. More information about the project is available here: http://gow.epsrc.ac.uk/ViewGrant.aspx?GrantRef=EP/H047786/1 Applications or informal enquiries can be directed to myself or Robert Dryfe. Best wishes Sven -- Dr Sven L.M. Schroeder (mailto:s.schroeder@manchester.ac.uk) Head of Research / Reader School of Chemical Engineering and Analytical Science (CEAS) The University of Manchester, Manchester M13 9PL, United Kingdom http://www.ceas.manchester.ac.uk http://www.slmslab.info Also at: School of Chemistry, The University of Manchester, Manchester M13 9PL, United Kingdom Tel +44 (161) 306 4502 Fax +44 (161) 306 8867 Office: Room C57 (Jackson's Mill) DISCLAIMER The views expressed within this message are those of the sender, not those of The University of Manchester or one of its Departments. While all emails and attachments are scanned for viruses before sending, we cannot accept any responsibility for viruses, so please scan all emails and attachments. This email is intended for the addressee only. If you are not the intended recipient, please notify the sender and delete this email immediately. END OF MESSAGE

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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 07 Jul '10

07 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 07 Jul '10

07 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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