- 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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Re: [Ifeffit] ATHENA: \\\"you have not used any memory yet\\\"
by Claire Gervais 23 Jul '10

23 Jul '10

Hello, You are right, this is exactly by googling that I have found that I was not alone to have this problem! I did change the fonts to have all windows entirely visible, but it did not improve. Still stuck with no OK in view. Indeed, it seems that the application waits for me. I am in Gnome, but I don't think it's the point, otherwise it would work under Windows in Virtualbox, no...? I am not an expert in GUI however. Claire ------------------------------------- > > 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 ------------------------------------

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Ei component
by Abhijeet Gaur 17 Jul '10

17 Jul '10

Hi all My question is about Ei component taken for the problem of poor energy resolution. How it can be calculated using measured energy resolution ? How Ei can be calculated using a known sample, such as a foil for which we have comparable spectra on a beamline with better energy resolution ? With regards Abhijeet Gaur Vikram University Ujjain, India

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Re: [Ifeffit] Neg SS
by Abhijeet Gaur 16 Jul '10

16 Jul '10

Hi Thanks for the quick response. As per the data collection range is concerned, we have limitation of 300eV above the edge. I think I had done data processing in Athena right. I know that the peak at position less than 1 Angs can not be real but I am unable to remove it by data processing in Athena. As per the model is concerned I am attaching herewith feff calculation result and the XRD results for different bondlengths of the sample. By comparing them it seems that model is right. On the other hand poor energy resolution is also one of the reasons for this kind of results. I had alraedy read about this Ei component earlier in papers, but I am unable to follow the procedure like how to calculate it using a known standard. From where I can get literature related to this? It will be really helpfull. With regards Abhijeet Gaur

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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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