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

Re: [Ifeffit] Ifeffit Digest, Vol 89, Issue 17
by Jatinkumar Rana 28 Jul '10

28 Jul '10

Hello Darek, Thank you so much for your reply. Yes, i can rely on model, we have performed reitveld refinement to get the crystallographic data. To my knowledge, there should not be any other phases. Your suggestion is quite right. Somehow, i have to constrain my parameters (to reduce the no. of parameters) and try to fit it. However, I would like to ask you following questions. I am confused about the term "Delta E0" what is the theoretical meaning of that in terms of photoelectron interactions ? If you have multiple atomic sites of absorbing atom, should "Delta E0" be same for all of them (assuming all absorbing atoms are at same oxidizing state) ? I am looking forward to your comments.. Best regards, Rana On 27.07.2010 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. updating Athena in Windows 7 (Monson, Todd) > 2. ODP: Ifeffit Digest, Vol 88, Issue 12 (Zajac, Dariusz A.) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 26 Jul 2010 14:39:00 -0600 > From: "Monson, Todd"<tmonson(a)sandia.gov> > To: "ifeffit(a)millenia.cars.aps.anl.gov" > <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] updating Athena in Windows 7 > Message-ID: > <AC050BA7EAC9A34E9A05BC31C3AA2E8B183C0D11B5(a)ES02SNLNT.srn.sandia.gov> > Content-Type: text/plain; charset="us-ascii" > > On Saturday, while starting up Athena, I was informed that there was an update to Athena available. I tried installing the update but failed. I am afraid this is due to some user permission issue in windows 7. How can I try to reinstall the update and ensure that it works? > Thanks, > Todd > > Todd Monson > Sandia National Labs > Nanomaterials Sciences > P.O. Box 5800, MS 1415 > Albuquerque, NM 87185-1415 > (505) 845-2129 > Fax: (505) 844-5470 > >

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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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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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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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