December 2005 - Ifeffit - millenia.cars.aps.anl.gov

Debye-Waller factors for metal oxides ?
by Ian James Drake 16 Apr '09

16 Apr '09

Hi, There is little discussion over the significance of fitted Debye-Waller factors (ss2) found for metal centers in metal oxides of heterogeneous catalysts. I am searching for a better way of determining how reasonable these values are in the fits I get. 1. Are phenomenological models like the correlated Debye model and Einstein model appropriate? It seems that Debye temperatures are hard to find for oxides. 2. Is there an equivalent value for ss2 in x-ray crystallography data that I can refer to for comparison in these materials? What should I look for in reviewing published x-ray crystallographic data? 3. Is the temperature dependence reported for the ss2 for some metals (like Cu and Al) similar to their respective oxides? For example, in Debye-Waller factor calculations reported for Al metal by R.C.G Killean (in J.Phys.F: Metal Phys., v. 4, pg. 1908, 1974), the ss2 changes by a factor of three between 25C and 300C. Would I expect a factor of three increase in crystalline zeolites (AlO4 structural units). 4. Specific to my work: I have studied Al containing oxides at temperatures between 25 and 300 C. I would like to quantify coordination changes by doing EXAFS fitting of the Al K-edge data. The EXAFS was taken at temperature and I observe no change in the broadening of the data. Likewise, the fitting shows no sensitivity in the Debye-Waller factor. It is nearly constant at 0.001 A over the temperatures of interest. Since ss2 and the coordination number (CN) are correlated, I would like a way to bind the error on the fitted CN by modeling real physical changes in the Debye-Waller factors. Do you have any suggestions? Looking forward to your thoughts. Ian Drake Graduate Student UC Berkeley

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New Method for Normalization?
by Barton, David (DG) 30 Mar '09

30 Mar '09

XANES Aficionados, I know most users on this list are hard-core EXAFS analysts, but some of us use XANES analysis to decipher mixed phases or use it to get structural clues when data quality isn't sufficient for EXAFS analysis. Anyway, I have a question for those interested in quantitative analysis of XANES or those that are willing to offer an opinion on methods to normalize raw spectra to get reliable, repeatable comparisons of near-edge features. Has anyone considered using the methods of Penner-Hahn to normalize their data to get reliable intensities of near-edge features? The reference to their method of normalization is below: J. Synchrotron Rad. (2005). 12, 506-510 [doi:10.1107/S0909049504034193] "A method for normalization of X-ray absorption spectra" T.-C. Weng, G. S. Waldo and J. E. Penner-Hahn It is my understanding the Ifeffit uses a linear function to remove the pre-edge and a quadratic for the post-edge and that the Athena's flatten is a subtraction of these functions. This is an excellent method under most scenarios since the background is usually fairly smooth and can be well approximated by a quadratic equation. Personally, I have had only a few rare cases where the quadratic function on the post-edge was not sufficient to reliably normalize the data and in those cases a third-order polynomial was sufficient. Does anyone else have an opinion on using alternative normalization routines? Dave _________________________________ David Barton The Dow Chemical Company

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Artemis- Loading up error
by Zohair Hussain 17 Apr '06

17 Apr '06

Hi! I recently had to install ifeffit software package on our network computer. The first time I ran Artemis I was asked to update which I did. However, Artemis did not start after that. The error message that I got is shown in the attached figures artemis-error1a and 1b. Please note that only Artemis doesn't work, all the other softwares (Athena, Hephaestus, TKAtoms etc.) work fine. I tried running the .bat file from the Ifeffit folder but that didn't work either. I also tried to run the artemis.exe file and received the error shown in figure "artemis-error2". Later I unisntalled and re-installed Ifeffit and chose not to do the updates and Artemis is now running fine. I was wondering if anyone has any idea why this is so or if there is a way around installing the updates and still being able to use Artemis??? Thanks, Zohair

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RE: [Ifeffit] my problem
by Scott Calvin 19 Dec '05

19 Dec '05

Hi Tadej, I agree with the general drift of Anatoly's comment--this is what Shelly meant by saying it sounds like a tough problem! But I think it came off sounding a little more harsh than I suspect Anatoly meant it to be, particularly considering some of the systems he himself has examined! Anatoly's description is fair IF only a nearest-neighbor fit is performed. But it's possible that inequivalent sites have very different environments at greater Reff, particularly since niobium is so much heavier than oxygen! For example, there's been a lot of work done that shows that there is a screamingly large difference in the EXAFS spectra of A and B sites in the spinel structure (Vince Harris did a lot of this, for example). In such a case, Artemis is able to find the site occupancy without too much trouble, using a strategy such as Shelly explained. Of course, =seven= freely-floating sites sounds likely to yield nonsense fits. It would help if you could use some physical intuition to try to simplify the problem, at least at first. Consider also using the "restraint" feature in Artemis/Ifeffit liberally in your early fits to keep the fit from wandering off into nonsensical territory. --Scott Calvin Sarah Lawrence College At 12:14 PM 12/15/2005, Anatoly wrote: >boundary="----_=_NextPart_001_01C6019A.F6711239" > >You cannot resolve these sites from EXAFS analysis. Even if you had >only 2 inequivalent sites of the same central atom with occupancies >N1 and N2, you would not be able to resolve N1 and N2 in the fit >because different Nb atoms would have similar environments (e.g., 4 >and 6 oxygens), and they will have similar Nb-O distances around >each site. The best you can do is to try to fit the first nearest >neighbor peak as an average Nb-O contribution (if it is a well >isolated peak) and try to make use of sigma2 that may turn out to be >larger than in some well known Nb oxide reference that you should >analyze first. > >Anatoly > >Dear collegues, > >my name is Tadej Rojac and I'm writing from the Institute Jozef >Stefan in Ljubljana, Slovenia. I work in the Department of >electronic ceramics. Actually, I'm working on a EXAFS spectra with >Artemis. What I am trying to do is mainly to describe an EXAFS >spectrum with a model concerning the structure of Nb2O5. I'm working >togheter with prof. Iztok Arcon, who is a specialist in the field. >My main problem is that I have to do some suppositions. In fact >Nb2O5 structure is quite complicated. It is composed of seven >different Nb positions which I took into account using 7 feffs in >Artemis. I don't know the exact occupancies of the seven positions. >In order to make the search easier I did at first a supposition >that all the occupancies must be positive, which is realistic. I set >this with the command "abs" in each feff file. Secondly, I need to >supose that the sum of all occupancies is 1. In that way the search >for the result is much easier, otherwise I get the sum greater than >one, which, for sure, is not the case. My question is how can I do >that? For example, if the occupancies are O1, O2, O3, O4, O5, O6 and >O7 and I define them with a starting value (let use say the same, so >1/7) than I can do O = O1+O2+O3+O4+O5+O6+O7. Finally I need to do O >=1, but here Artemis doesn't want to define the same parameter (O in >this case) twice. So, how can I insert the conditions, that the sum >of all the occupancies is 1, into Artemis? I hope you can help me.

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(no subject)
by Victor Krayzman 19 Dec '05

19 Dec '05

Hi Bruce, This is Victor Krayzman. I haven't seen you for ten years. Currently I am at NIST as a guest scientist. Besides other codes I work with Athena and Artemis and I have some troubles with Artemis. (It runs under Windows 2000) Last time I read a data file, made two FEFF calculations, read one more data file and made three FEFF calculations for it. Then I saved project, quit Artemis, open it again and tried to read the saved project. I found only data files and two FEFF calculations for the first data set. FEFF calculations for the second set disappeared. I met the same situation some time ago. To fix the problem I had to reinstall the Artemis. But now I have got the same thing. Could you help me? I attached the saved project and the message in a window. Thank you. Best regards to Ed. Sincerely. Victor

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RE: [Ifeffit] Pd data
by Barton, David (DG) 19 Dec '05

19 Dec '05

Sorry I meant to include that. The file at DND-CAT is a bit unwieldy. The key is: Col 4=energy, Col 25=Io, Col 26=It. Dave > -----Original Message----- > From: Kelly, Shelly D. [mailto:SKelly@anl.gov] > Sent: Monday, December 19, 2005 12:13 PM > To: XAFS Analysis using Ifeffit > Subject: RE: [Ifeffit] Pd data > > > Hi Dave, > > Thanks a bunch for the data file. Could I trouble you for a > key for the columns within the file? > > Shelly > > Shelly Kelly Bldg 203 RM E113 > Skelly(a)anl.gov Argonne National Laboratory > 630-252-7376 9700 S Cass Ave > www.mesg.anl.gov Argonne, IL 60439 > > > > > > -----Original Message----- > > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit- > > bounces(a)millenia.cars.aps.anl.gov] On Behalf Of Barton, David (DG) > > Sent: Monday, December 19, 2005 10:11 AM > > To: 'XAFS Analysis using Ifeffit' > > Subject: RE: [Ifeffit] Pd data > > > > Shelly, > > > > Attached is a Pd foil data set. It was only collected out > to k=16A-1, > > otherwise the data looks great. Data was collected with > Si111 mono at > > DND-CAT (APS-ANL). > > > > Dave > > > > -----Original Message----- > > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit- > > bounces(a)millenia.cars.aps.anl.gov] On Behalf Of Kelly, Shelly D. > > Sent: Monday, December 19, 2005 10:38 AM > > To: XAFS Analysis using Ifeffit > > Subject: [Ifeffit] Pd data > > > > > > Hello friends, > > > > Does anyone have Pd foil data or know of an EXAFS study that models > the > > data beyond the first shell? I have some data but it > doesn't seem to > > correspond to the crystallographic structure of Pd. I'm suspicious > that > > something about the foil sample caused the structure to become > non-ideal. > > > > Thanks > > Shelly > > > > > > > > > > > _______________________________________________ > 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] Pd data
by Kelly, Shelly D. 19 Dec '05

19 Dec '05

Hi Dave, Thanks a bunch for the data file. Could I trouble you for a key for the columns within the file? Shelly Shelly Kelly Bldg 203 RM E113 Skelly(a)anl.gov Argonne National Laboratory 630-252-7376 9700 S Cass Ave www.mesg.anl.gov Argonne, IL 60439 > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit- > bounces(a)millenia.cars.aps.anl.gov] On Behalf Of Barton, David (DG) > Sent: Monday, December 19, 2005 10:11 AM > To: 'XAFS Analysis using Ifeffit' > Subject: RE: [Ifeffit] Pd data > > Shelly, > > Attached is a Pd foil data set. It was only collected out to k=16A-1, > otherwise the data looks great. Data was collected with Si111 mono at > DND-CAT (APS-ANL). > > Dave > > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit- > bounces(a)millenia.cars.aps.anl.gov] On Behalf Of Kelly, Shelly D. > Sent: Monday, December 19, 2005 10:38 AM > To: XAFS Analysis using Ifeffit > Subject: [Ifeffit] Pd data > > > Hello friends, > > Does anyone have Pd foil data or know of an EXAFS study that models the > data beyond the first shell? I have some data but it doesn't seem to > correspond to the crystallographic structure of Pd. I'm suspicious that > something about the foil sample caused the structure to become non-ideal. > > Thanks > Shelly > > > >

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RE: Ifeffit Digest, Vol 34, Issue 18
by Vivek Srinivasamurthi 19 Dec '05

19 Dec '05

Shelly, Sorry, forgot to attach the file before.. vivek -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Monday, December 19, 2005 11:12 AM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 34, Issue 18 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. Pd data (Kelly, Shelly D.) 2. RE: Pd data (Barton, David (DG)) ---------------------------------------------------------------------- Message: 1 Date: Mon, 19 Dec 2005 09:37:47 -0600 From: "Kelly, Shelly D." <SKelly(a)anl.gov> Subject: [Ifeffit] Pd data To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <A7B9B5614B54BE48B378DAE209FECC30ABE841(a)ROCKY.anl.gov> Content-Type: text/plain; charset="us-ascii" Hello friends, Does anyone have Pd foil data or know of an EXAFS study that models the data beyond the first shell? I have some data but it doesn't seem to correspond to the crystallographic structure of Pd. I'm suspicious that something about the foil sample caused the structure to become non-ideal. Thanks Shelly

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RE: Ifeffit Digest, Vol 34, Issue 18
by Vivek Srinivasamurthi 19 Dec '05

19 Dec '05

Shelly, Attached is a Pd nanoparticle sample on a carbon support. The data was taken upto 18 k-space. It also has a Pd foil in the reference channel. The data was collected with a Si(111) monochromator at BNL-NSLS -X18B. Vivek -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Monday, December 19, 2005 11:12 AM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 34, Issue 18 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. Pd data (Kelly, Shelly D.) 2. RE: Pd data (Barton, David (DG)) ---------------------------------------------------------------------- Message: 1 Date: Mon, 19 Dec 2005 09:37:47 -0600 From: "Kelly, Shelly D." <SKelly(a)anl.gov> Subject: [Ifeffit] Pd data To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <A7B9B5614B54BE48B378DAE209FECC30ABE841(a)ROCKY.anl.gov> Content-Type: text/plain; charset="us-ascii" Hello friends, Does anyone have Pd foil data or know of an EXAFS study that models the data beyond the first shell? I have some data but it doesn't seem to correspond to the crystallographic structure of Pd. I'm suspicious that something about the foil sample caused the structure to become non-ideal. Thanks Shelly

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RE: [Ifeffit] Pd data
by Barton, David (DG) 19 Dec '05

19 Dec '05

Shelly, Attached is a Pd foil data set. It was only collected out to k=16A-1, otherwise the data looks great. Data was collected with Si111 mono at DND-CAT (APS-ANL). Dave -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Kelly, Shelly D. Sent: Monday, December 19, 2005 10:38 AM To: XAFS Analysis using Ifeffit Subject: [Ifeffit] Pd data Hello friends, Does anyone have Pd foil data or know of an EXAFS study that models the data beyond the first shell? I have some data but it doesn't seem to correspond to the crystallographic structure of Pd. I'm suspicious that something about the foil sample caused the structure to become non-ideal. Thanks Shelly

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