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

Re: [Ifeffit] updating Athena in Windows 7
by Monson, Todd 14 Aug '10

14 Aug '10

My difficulty in updating Athena was indeed a permissions problem. After following Laurent's suggestions, I was able to edit and save the updater.ini file as well as successfully download and install the updates to Athena while starting up the program. Thanks for all the help! Todd ---------------------------------------------------------------------- Message: 1 Date: Wed, 11 Aug 2010 07:13:23 -0500 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] updating Athena in Windows 7 (Matt Newville) Message-ID: <AANLkTin3bADHAyZX8g2jRZ5WvcJvKOhPF1mGS0qFMwCF(a)mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Hi Todd, That sounds like a permissions problem to me. Some account needs to be able to write to that file.... If updating the updater.ini file is not working, and Laurent's suggestions don't let you edit that file, you could also try downloading and installing the update zip files by hand. This is a bit more work (compared to editing updater.ini!), but the description at http://cars9.uchicago.edu/ifeffit/IfeffitOnWindows/WinUpdater guides you through it. Hope that helps, --Matt ------------------------------ _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit End of Ifeffit Digest, Vol 90, Issue 6 **************************************

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PYTHON scripting on MacOS & XP
by Brugger, Joel (SAM) 14 Aug '10

14 Aug '10

We used python scripting in 2005 (Win XP). However trying to get back into it we ran into trouble: - We're now using MacOS X, but could not find a python wrapper in the current iXAFS or IFEFFIT installs; is python scripting supported on the mac at all? - We then tried to get back to the PC version, only to discover that the wrapper also seems to be absent from the latest install. Can you please help us to get going again with python scripting? If this option is not supported anymore, can you recommend an alternative? Thanks, Joel & Barbara

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two measurements of the same compound in different beam-lines
by María Elena Montero Cabrera 13 Aug '10

13 Aug '10

Hi all! I have performed two independent XAFS measurements of Cr K-edge of the same Fe-Cr sample at two different beam-lines at SSRL. I have obtained the Fe-K edge data only once. The quality of data are different in each measurement. However, I cannot average spectra from different Cr-K measurements, and I don't know if I could take somehow advantage from having almost twice the information for the Cr- K adge, or I have to use only the better quality data and discard the other. What do you advice? If I can use both measurements, how can I do the fitting in Artemis? Thank you very much and all take care -- 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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S K-edge of CdS(ZnOOH) Thin Films
by Kevin McPeak 13 Aug '10

13 Aug '10

Hi all, On Aug 22nd I will acquiring S K-edge XANES spectra (at APS 9-BM) of CdS(ZnOOH) thin films that I have grown in my lab. The films are grown in such a way that their composition and thickness vary as a function of position. View the following pdfs for details on thickness and composition: http://dunx1.irt.drexel.edu/~kmm333/cdzns/figure1.pdf http://dunx1.irt.drexel.edu/~kmm333/cdzns/figure3.pdf The idea is to take scans at various position along the middle of the substrate and observe how the different amounts of oxygen affect the Sulfur species present. Foreseeable issues are: 1). The CdS(ZnOOH) films are deposited on FTO (250 nm F:SnO2 film deposited on 2 mm of soda lime glass). There is 0.2 wt% SO3 (0.05 at% S) in the glass according to the manufacturer. We will run a scan on the bare FTO before starting work on CdS(ZnOOH), hopefully the SO3 in the glass is below the detection level. 2). If the SO3 in the glass is an issue I also have a sample where the CdS(ZnOOH) film is deposited on <100> Silicon. In earlier work I tried using this sample at the Cd and Zn K-edge at the APS 10-BM (to reduce scatter from the glass) but I ended up getting Bragg peaks in the spectra. Outside of spinning the substrate (not really an option here) do you have any suggestions for avoiding the Si Bragg peaks? I read one paper where they discussed deglitching but I am not sure how well that would go over with reviewers. Furthermore, grazing-incidence is not an option at 9-BM. All of the measurements above either have been (Cd and Zn) or will be (S) acquired in fluorescence. I am meeting with the beamline scientist to discuss this next Thursday but I figured it was a good idea to get input from the list as well. Any advice is most appreciated. Regards, Kevin McPeak kmm333(a)drexel.edu 312.371.5477 -- PhD Candidate Chemical Engineering Drexel University

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Fwd: Windows 7?
by Bruce Ravel 12 Aug '10

12 Aug '10

Hi all, This afternoon I was asked the following: > They are talking here to move us all from XP to Window 7... I checked on > your website and Athena is compatible with XP, Windows 2000, Windows > 95/98/ME but there is no mention of Window 7. Is it also adapted for > Window 7? Not having used Windows 7 myself, I don't have a lot to say. I know that everything worked OK with Vista, so I presume that the same is true of 7. Would anyone else like to comment to Suzanne on this issue? Thanks, 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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amplitude values too high (>>100%)
by Edgar Macias 11 Aug '10

11 Aug '10

Hello, I am looking for some help on trying to understand what is wrong with our data. We are very impressed with the high values of amplitude (up to 390.24) that we got working with Artemis and we know are wrong. Hope somebody could help us and take a look into these files, we will appreciate it. Thank you in advance!

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Re: [Ifeffit] updating Athena in Windows 7 (Matt Newville)
by Monson, Todd 11 Aug '10

11 Aug '10

Matt, I tried resetting the timestamp to 0 under: Ifeffit\config\updater.ini. However, I could not save the changed updater.ini file. I verified that I have administrator privileges on my computer. Could something else be preventing me from updating the updater.ini file and in turn updating Athena? Todd Date: Wed, 28 Jul 2010 07:37:52 -0500 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] updating Athena in Windows 7 Message-ID: <AANLkTinxBX3aCXUGdN5XZCajMuK5gWCyftb9N-6YvpVz(a)mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Hi Todd, On Mon, Jul 26, 2010 at 3:39 PM, Monson, Todd <tmonson(a)sandia.gov> wrote: > 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? You can change the file current.dat in C:\Program Files\Ifeffit\config. It probably reads 013 right now, and you could change that to 012 or even lower. That will cause an update the next time ifeffit looks for updates, which only happens when one of the programs starts and if the time in Ifeffit\config\updater.ini is past. To force a check for updates the next time ifeffit runs, change updater.ini to read timestamp = 0 In general, I believe this should work for Windows 7 (I have access to two Windows 7 64-bit machines, and all seems to be working on them, though I admit to not stressing them too much). So, as you say, I would also guess that the trouble you had was "only" permission issues. But, please let us know how it goes, Sorry for the trouble, --Matt ------------------------------ _______________________________________________ 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 19 ***************************************

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How to analyze this data
by Elsa E. Sileo 10 Aug '10

10 Aug '10

I have some measurements at the As edge of As(V) adsorbed onto pure goethite (alfa-FeOOH), Mn partially substituted Goethite (alfa-Mn,Fe.OOH), Al substituted goethite (alfa-Al,FeOOH) and Mn and Al goethite (alfa-Al,Mn,FeOOH) The EXAFS signals change from one spectrum to another. I have refined the distances As-Fe on pure goethite, but when I try to refine Mn-FeOOH or Al,FeOOH, the analysis gets more difficult because As forms different complexes with Al and Fe. Unfortunately for me is almost impossible to have the pure phases alfa-MnOOH or alfa-AlOOH, and measured the As adsorbed. How can I analyze the spectra and have some knowledge about the As-surface complexes formed? Thanks, Elsa Dra. Elsa E. Sileo Solidos Inorganicos INQUIMAE - Dto. Qca. Inorganica, Analitica y Qca. Fisica; FCEN, UBA Int. Güiraldes 2160, Pabellón 2, Piso 3, Ciudad Universitaria - C1428EHA CABA - Argentina Tel: (54 11) 4576 3380 ext. 113 Fax: (54 11) 4576 3341 e-mail: sileo(a)qi.fcen.uba.ar

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Re: [Ifeffit] Physical meaning of POLARIZATION card 0 0 1
by Joshua Kas 06 Aug '10

06 Aug '10

Does this POL card > setting mean that the electric vector is along the z/c axis of the > crystal axis? Not quite. FEFF doesn't really know about crystal symmetry. The coordinates in the POLARIZATION card are the same as those in the feff.inp file under the ATOMS card. If the c axis of the crystal happens to be along the z direction, then POLARIZATION 0 0 1 sets the electric field vector along the c axis. You will have to look at the coordinates in the feff.inp to figure out which direction the c axis is. I may be wrong, but I think atoms/webatoms puts the c-axis in the z direction by default. Cheers, Josh Kas > I did read the Feff manual and the POL card but I am > still confused how to relate these to the crystal structure and > orientation. > > Thank you all in advance, > > -- > Chris Patridge > PhD. Candidate > Dept. of Chemistry > SUNY University at Buffalo > Buffalo, NY 14260 > Contact: 315-529-0501 > >

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Physical meaning of POLARIZATION card 0 0 1
by Chris Patridge 06 Aug '10

06 Aug '10

Hello everyone, I am working on modeling HfO2 using L3 Hf edge data. Using the default Feff input generated in Artemis, there is some significant mismatch between the data and theory so I augmented the Feff file by adding the POLARIZATION card setting the values of x y z to (0 0 1). Summing the theoretical paths in this calculation looked much closer and fitting the theory gives the results pasted in the text file. Does this POL card setting mean that the electric vector is along the z/c axis of the crystal axis? I did read the Feff manual and the POL card but I am still confused how to relate these to the crystal structure and orientation. Thank you all in advance, -- Chris Patridge PhD. Candidate Dept. of Chemistry SUNY University at Buffalo Buffalo, NY 14260 Contact: 315-529-0501

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