September 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 16 Apr '06

16 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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writing beam time proposals
by Bruce Ravel 08 Dec '05

08 Dec '05

Hi folks, Yesterday I received an interesting question about writing beam time proposals. I know that proposal review panel members at least from APS and NSLS are readers of this mailing list (perhaps other synchrotrons as well), so I thought it would be interesting to start a thread on proposal writing strategies. The fellow who sent me mail asked: My question is, since I am a student, should my advisor be the official PI applying for time or should I be the PI? Is there any advantage one way or the other? In principle, I think it should not matter. Beam time should be awarded to a quality proposal. What advice do you all have for this proposal writer? What has your experience in applying for beam time? BTW, this fellow had been a student in a recent XAS summer school. I suggested he mention that in his proposal. Regards, B -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advance Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

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Runner.exe Network Error
by Barton, David (DG) 28 Sep '05

28 Sep '05

Bruce and Matt, I am running the Ifeffit 1.2.8 on a Win2000 box and I having several issues with the startup of Athena/Artemis when I am not connected to a network. First thing is that all programs run fine when I am connected to the internet. So the obvious workaround for me is to just make sure that I have an open network connection before running Athena/Artemis. However, it would be nice if the auto-update feature in "Runner.exe" would still let me run Athena/Artemis when I wasn't connected to the network, basically just ignore looking for an update when I don't have a network connection. The errors that I get in the Runner.exe.log are below. There are two different cases shown. The first set of errors are when I have a connection to my local network, but have not yet logged onto the firewall that lets me out onto the internet. The second set of errors comes up when I unplug the network connection completely. Hope these help. NETWORK CONNECTION NO INTERNET CONNECTION ----------------------------------------- Traceback (most recent call last): File "runner.py", line 753, in ? File "runner.py", line 184, in __init__ File "runner.py", line 275, in LookForUpdates File "runner.py", line 299, in read_web_version File "urllib.pyc", line 76, in urlopen File "urllib.pyc", line 181, in open File "urllib.pyc", line 306, in open_http File "urllib.pyc", line 319, in http_error File "urllib.pyc", line 565, in http_error_302 File "urllib.pyc", line 580, in redirect_internal File "urllib.pyc", line 181, in open File "urllib.pyc", line 306, in open_http File "urllib.pyc", line 319, in http_error File "urllib.pyc", line 616, in http_error_401 File "urllib.pyc", line 624, in retry_http_basic_auth File "urllib.pyc", line 650, in get_user_passwd File "urllib.pyc", line 658, in prompt_user_passwd NO NETWORK CONNECTION -------------------------------------- File "runner.py", line 753, in ? File "runner.py", line 184, in __init__ File "runner.py", line 275, in LookForUpdates File "runner.py", line 302, in read_web_version Dave _________________________________ David Barton The Dow Chemical Company

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getting chi(r) information out of command line IFEFFIT
by Sean X. Luo 28 Sep '05

28 Sep '05

Hello all. It's been a while since I've written on the mailing list about this project, but it's come up that I need everyone's general input. Just a brief overview of the project: I am working with Scott Calvin to simultaneously fit 12 data sets in the command line of IFEFFIT, and I need to somehow get the chi(r) information for the fit out of the command line. I've tried around with the "show" command and the different permutations possible with that, but whenever I type in "show(fit.r, fit.chir_real)" (which is our guess right now on how to get the information I need out of the command line), it gives me the error that the arrays fit.r and fit.chir_real does not exist, or something along those lines. Does anyone else have any idea on how to run this? Thanks in advance, - Sean.

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RE: [Ifeffit] Fe oxide
by Kelly, Shelly D. 26 Sep '05

26 Sep '05

Hi Juro, I had some fun playing with this project file. I hope you don't mind. Here is a list of suggestions. 1st: Don't use the paths that are less than 0.1 Angstroms apart. 1st-b: If you don't know the CN set it to ONE and then vary just the amplitude. There is a degen box multiplied by a amp box. Degen should be one. 2st: set the values for CN, and s2, while letting delr vary 3rd. Let the CN and delr vary. You will find that the Fe path around 3 Ansgroms isn't needed. 4th. Make sure your fit range and data ranges are appropriate. 5th. Add as much constraints as you think is reasonable. First Oxygen coordination number should be 6 or 4 total. I thought 6 worked well. 6th. Fit the data with k-weight of 1,2, and 3, to get the uncertainties smaller. Take a look at the project file. I think that this model or one like it might work. You need a separate S02 value from the Amp value. Amp should be S02*Amp. I didn't add a S02 part. You should get that from a known standard measured on the same beamline. S02 should be between 0.70 and 1.0. So the CN reported are likely a bit too big. Good luck, 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 60440 > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit- > bounces(a)millenia.cars.aps.anl.gov] On Behalf Of Juraj Majzlan > Sent: Monday, September 26, 2005 8:46 AM > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Fe oxide > > Hello, > > I am trying to fit an EXAFS spectrum of an X-ray amorphous > Fe precipitate. In a model (goethite), there are Fe atoms > at 3.02, 3.29, and 3.45 A. Fitting the two most distant > shells of iron gives strange results. Fitting them > simultaneously gives very high amplitudes (32, -66) which > cancel each other (fig. 1) and produce a beautiful and > unreasonable fit (fig. 2). > > Fitting them separate gives small ('reasonable') > amplitudes, but the distance (dr) have very high > uncertainties, e.g., dr = 0.12 +- 20.3. > > Can I expect to resolve these three Fe shells or is it > asking too much? > > I am also attaching the Artemis file, but will appreciate > any comments and suggestions. > > Juro Majzlan > > > ---------------------------------- > Juraj Majzlan > Institute of Mineralogy and Petrology > Albert-Ludwig-University of Freiburg > Albertstrasse 23b > Freiburg, D-79104, Germany > telephone +49-761-203-6416 > fax +49-761-203-6407 > http://www.minpet.uni-freiburg.de/sites/personen/majzlan.html

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Fe oxide
by Juraj Majzlan 26 Sep '05

26 Sep '05

Hello, I am trying to fit an EXAFS spectrum of an X-ray amorphous Fe precipitate. In a model (goethite), there are Fe atoms at 3.02, 3.29, and 3.45 A. Fitting the two most distant shells of iron gives strange results. Fitting them simultaneously gives very high amplitudes (32, -66) which cancel each other (fig. 1) and produce a beautiful and unreasonable fit (fig. 2). Fitting them separate gives small ('reasonable') amplitudes, but the distance (dr) have very high uncertainties, e.g., dr = 0.12 +- 20.3. Can I expect to resolve these three Fe shells or is it asking too much? I am also attaching the Artemis file, but will appreciate any comments and suggestions. Juro Majzlan ---------------------------------- Juraj Majzlan Institute of Mineralogy and Petrology Albert-Ludwig-University of Freiburg Albertstrasse 23b Freiburg, D-79104, Germany telephone +49-761-203-6416 fax +49-761-203-6407 http://www.minpet.uni-freiburg.de/sites/personen/majzlan.html

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problems on running the windows 1.2.8 ifeffit version
by M Ceolin 23 Sep '05

23 Sep '05

Dear Bruce et al. I just installed the new 1.2.8 for windows version of ifeffit and I am experiencing problems to run any of the programs associated (arthemis, athena, etc.). I installed the programs in a Win98 machine where the previous versions of IFEFFIT were running. I took care of adding the suggested line to the config.sys file and installed the program in c:\ifeffit (as suggested). However, both, starting from the icons in the desktop, from the applications installed at c:\ifeffit\bin or from the menu at the start, the runner program (installed with the pakage) send an error message forcing to abort the run. The message says: (sorry, in spanish) Este programa ha efectuado una operacion no admitida y sera interrumpido (in the datails window says) RUNNER provoco un error de pagina no valida en el modulo MSVCRT.DLL de 017f:7801274b. etc. (registry numbers). Could you comment the point and, perhaps, suggest a solution ?. Yours. Marcelo Ceolin. *************************************** Dr. Marcelo Ceolin Centro Regional de Estudios Genomicos UNLP-AUGM Av. Calchaqui km 23,5 (4to piso) (1888) Florencio Varela Argentina Tel/Fax: +54-11-42758100 e-mail 1: mceolin(a)creg.org.ar e:mail 2: mrceolin(a)yahoo.com.ar WEB: www.creg.org.ar *************************************** PLEASE NOTE THAT THE E-MAIL ADDESSS mceolin(a)gwdg.de IS NO LONGER AVAILABLE. USE ONE OF THE ADDRESSES ABOVE. --------------------------------- 1GB gratis, Antivirus y Antispam Correo Yahoo!, el mejor correo web del mundo Abrí tu cuenta aquí

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RE: [Ifeffit] writing beam time proposals
by Frenkel, Anatoly 23 Sep '05

23 Sep '05

I rate proposals on the merit but it a former XAFS school student is a research group member it makes me happier. Anatoly -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov on behalf of Matt Newville Sent: Fri 9/23/2005 12:06 PM To: Carlo Segre; XAFS Analysis using Ifeffit Cc: Subject: Re: [Ifeffit] writing beam time proposals In my opinion, it is better for the student or post-doc to write the beamtime proposal and be listed as PI, with the advisor listed somewhere on the proposal Many proposal foms have a checkbox for 'is this work part of a thesis', and that is definitely monitored (at least at the APS, but I'd imagine it to be true at other facilities), even if it is not formalized. There is usually an eagerness for bringing new students (and new post-docs and new faculty members) to the syncrotrons. Also, in my experience reading beamtime proposals now and then, students and post-docs do a better job at writing them <wink>. Even f the professor is listed first (and many groups do this!), I would suggest that the student/post-doc actually write the proposal and have the advisor look it over before submitting. Other advice for writing proposals: - communicate with the beamline scientist to make sure the work is feasible and appropriate. - write it to convince someone in a *different field* why the experiment is important. - include references to previous work to show that you know the field. --Matt _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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