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

Transmission EXAFS sample
by Jatinkumar Rana 19 Nov '10

19 Nov '10

Dear all, I have very basic question about the sample preparation for EXAFS. It is well understood and proven by several researchers that the optimum amount of sample (per unit area) required for EXAFS is determined by the fact that the total absorbtion of the entire sample above the absorption edge (of interest) should be between 2 to 2.5, more precisely, it should be 2.3. The reason which forces me to put this question to a mailing list is that, i treat my sample through a process which yields only few percentage of the total amount of sample required for EXAFS. I would prefer to measure EXAFS in transmission mode with samples prepared on several layers of Kapton tape which are bound together to ensure pinhole free sample. My questions are : -- Can my sample be only few percentage of the "actual amount" (i.e. calculated based on above fact) required, and still i can perform transmission EXAFS ? How would this affect my data ? (I guess, it will be heavily dominated by noise) -- What if, i have required amount of sample but since material's density is so high that it yields only small volume of powder (for a given weight), that it can not be covered up on multiple layers of Kapton tape to ensure pinhole-free sample ? I look forward to any comments or suggestions as this would help me improvise the quality of my data. With best regards, Jatin -- Jatinkumar Rana Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Institut für angewandte Materialforschung FI-1 Mikrostruktur Hahn-Meitner-Platz 1 D-14109 Berlin Germany Tel: +49 30 8062-43217 Fax: +49 30 8062-43059 eMail: jatinkumar.rana(a)helmholtz-berlin.de **************************************************************************************** Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Vorsitzender des Aufsichtsrats: Prof. Dr. Dr. h.c. mult. Joachim Treusch Stellvertretende Vorsitzende: Dr. Beatrix Vierkorn-Rudolph Geschäftsführer: Prof. Dr. Anke Rita Kaysser-Pyzalla, Prof. Dr. Dr. h.c. Wolfgang Eberhardt, Dr. Ulrich Breuer Sitz der Gesellschaft: Berlin Handelsregister: AG Charlottenburg, 89 HRB 5583

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Re: [Ifeffit] Origin of terminology "self-absorption"
by Scott Calvin 17 Nov '10

17 Nov '10

I tried a few searches, but rapidly get lost in other uses of the term. My guess is we borrowed it from some other spectroscopy, much the way we borrowed "Debye-Waller factor" from XRD, and then proceeded to change its meaning. But it would be nice to be able to track that down. --Scott Calvin Faculty at Sarah Lawrence College Currently on sabbatical at Stanford Synchrotron Radiation Laboratory On Nov 16, 2010, at 10:54 AM, Matthew Marcus wrote: > It's definitely a misnomer. I use "overabsorption" and encourage > others to do so. I suppose to track it down would require going > back over the seminal papers on the subject. > mam > > On 11/16/2010 10:19 AM, Scott Calvin wrote: >> Hi all, >> >> As some of you know, I'm currently working on a textbook on XAFS >> analysis. Because of that, I'm going to occasionally pose some >> questions for the list that may seem a bit random. I hope none of >> you mind me using the list in this way; the questions may seem to >> come out of left field, but I think they will still be of interest >> to many. >> >> With that said, here's my question for today: >> >> What is the origin of the use of "self-absorption" to describe the >> suppression of fine-structure observed in thick, concentrated >> samples measured in fluorescence? I understand the physics of the >> effect itself, my question is the curious wording. Compared to a >> thin concentrated sample, the effect might better be described as >> "saturation," while compared to a thick dilute sample, it's >> actually related to a lack of absorption by other elements. >> >> --Scott Calvin >> Faculty at Sarah Lawrence College >> Currently on sabbatical at Stanford Synchrotron Radiation Laboratory >> _______________________________________________ >> 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

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UO2 thin films on STO
by mohamed sobhy 16 Nov '10

16 Nov '10

Dear All I would like to grow UO2 thin films on STO (SrTiO3) substrate but I found that Sr K-edge 16105 and U L3-edge is 17166. Do you think there will be any interference? Best, Mohamed

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Origin of terminology "self-absorption"
by Scott Calvin 16 Nov '10

16 Nov '10

Hi all, As some of you know, I'm currently working on a textbook on XAFS analysis. Because of that, I'm going to occasionally pose some questions for the list that may seem a bit random. I hope none of you mind me using the list in this way; the questions may seem to come out of left field, but I think they will still be of interest to many. With that said, here's my question for today: What is the origin of the use of "self-absorption" to describe the suppression of fine-structure observed in thick, concentrated samples measured in fluorescence? I understand the physics of the effect itself, my question is the curious wording. Compared to a thin concentrated sample, the effect might better be described as "saturation," while compared to a thick dilute sample, it's actually related to a lack of absorption by other elements. --Scott Calvin Faculty at Sarah Lawrence College Currently on sabbatical at Stanford Synchrotron Radiation Laboratory

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help
by Aaron Yevick 11 Nov '10

11 Nov '10

Hi all, I downloaded Artemis twice, from both cars.uchicago and sourceforge. Both times I downloaded the latest, 1.2.11.exe. When it installed, I opened Artemis and was prompted to install several updates. I clicked Install Updates, and both times it says: downloading fetching update 10 (iff_010.zip).... downloaded iff_010.zip OK. expanding file iff_010.zip and goes no further in an hour. I quit. When it runs, along the bottom it says the version is 0.8.012 (c) 2002-2008, which I was told is not the latest version (is that true?) My operating system is Windows 7 Professional. Can anybody offer suggestions as to why this happens? Does it matter if I don't have these updates? Aaron

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Re: [Ifeffit] something is wrong with Ruthenium-Oxygen bond amplitudes
by Scott Calvin 05 Nov '10

05 Nov '10

Hi Maria, What was the physical form of the samples (powder, thin film, etc.) and how were they measured (transmission, fluorescence, ...)? Sometimes this kind of thing can stem from sample/beamline/data effects. --Scott Calvin Sarah Lawrence College On Nov 5, 2010, at 5:50 PM, María Elena Montero Cabrera wrote: > Hello friends, > > Hopping someone could help us. We are having some problems in > fitting Ru K-edge in a Ruthenium-cuprate sample on Artemis, with > path functions obtained using FEFF 8.4, where we got amplitude > values of less than 0.50 for Ru-O first shells. We think this value > probably is wrong, although there are some publications where some > oxygen deficiency is studied and recorded as true. The ATOMS input > data was found to be ok due to the Rietveld analysis results told us > these are good. The reason we think we may be wrong with something > during the fitting appeared because we tried to fit our reference > sample of RuO2 (measured under same conditions as the experiment of > Ru-Cu at SSRL) and we came to the same results, even worst, of > amplitude lower than 0.40. We are attaching the Artemis files so you > can take a look on it and give us some light to continue with our > analysis. > Thanking in advance, take care

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something is wrong with Ruthenium-Oxygen bond amplitudes
by María Elena Montero Cabrera 05 Nov '10

05 Nov '10

Hello friends, Hopping someone could help us. We are having some problems in fitting Ru K-edge in a Ruthenium-cuprate sample on Artemis, with path functions obtained using FEFF 8.4, where we got amplitude values of less than 0.50 for Ru-O first shells. We think this value probably is wrong, although there are some publications where some oxygen deficiency is studied and recorded as true. The ATOMS input data was found to be ok due to the Rietveld analysis results told us these are good. The reason we think we may be wrong with something during the fitting appeared because we tried to fit our reference sample of RuO2 (measured under same conditions as the experiment of Ru-Cu at SSRL) and we came to the same results, even worst, of amplitude lower than 0.40. We are attaching the Artemis files so you can take a look on it and give us some light to continue with our analysis. Thanking in advance, take care -- María Elena Dra. María Elena Montero Cabrera 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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Re: [Ifeffit] feff question
by Joshua Kas 04 Nov '10

04 Nov '10

Hi George, The obsolete warning is probably not a big deal, however, the compilation should be tested since compiling with gfortran has not been well tested for feff7. If you can get an old version of g77, you won't have issues. Otherwise, I would use the following command when running gfortran. gfortran -finit-local-zero -o feff702 feff702.f This may not work with your version of gfortran (-finit-local-zero is not in the manual) but if it does, the compiled feff will be less likely to have runtime errors. Cheers, Josh Kas I installed gfortran-4.2.3.dmg file on top of the gfortran-42-5577.pkg and > can now see "gfortran" in '/usr/local/bin'. I am also able to compile > simple > fortran code, but when I attempt to run Feff7 I get the following message: > > bash-3.2$ /usr/local/bin/gfortran -o feff702 feff702.f > feff702.f:12161.72: > > if (den.eq.0) pause 'failure in polint' > 1 > Warning: Obsolete: PAUSE statement at (1) > feff702.f:12226.72: > > if (den.eq.0) pause 'failure in polint' > 1 > Warning: Obsolete: PAUSE statement at (1) > bash-3.2$ > > Any idea as to what the problem is now? > > Thank you, > George > > > > On Wed, Nov 3, 2010 at 3:45 PM, Matt Newville <newville(a)cars.uchicago.edu > >wrote: > > > Hi George, > > > > On Wed, Nov 3, 2010 at 2:37 PM, George Sterbinsky > > <GeorgeSterbinsky(a)u.northwestern.edu> wrote: > > > I've also noticed that there is not a file or directory called gfortran > > in > > > '/usr/local/bin'. This is what made me think I may also need to install > > the > > > gfortran-4.2.3.dmg file. If I do not see a file or directory called > > gfortran > > > in '/usr/local/bin' does this indicate that gfortran is not installed? > Is > > it > > > possible that gfortran-42-5577.pkg placed it somewhere else? > > > > Yes, those are all possible. You need to install gfortran, find out > > where it is, and then run it to compile and link feff702 into an > > executable. It sounds like you might want to get a local unix-savvy > > person who can help you.... > > > > --Matt > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > >

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feff question
by George Sterbinsky 03 Nov '10

03 Nov '10

Hi, I am hoping someone can explain to me how to run Feff 7 on a mac (OSX version 10.5.8) starting from the feff702.f file. Thank you, George

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Scripting - Python
by Andrew Korinda 01 Nov '10

01 Nov '10

I'm looking to introduce some scripting routines to some of my EXAFS fitting work. Looking around I ran across the Python module and downloaded that. The shell works fine, as does enter commands directly into Ifeffit, however I'm not getting the read and write commands to work from within Python scripts. Example: iff.ifeffit("read_data(C:\Program Files\Ifeffit\examples\Ifeffit\data\cu10k.chi,group=c)") returns -1. >From this experience I have some questions: ~First does anyone have some debugging tips for cross talk problems? The Fortran return values are fine, but would returning the echo_buffer or a log file be more helpful? ~Secondly, Does anyone have any example Python scripts for Ifeffit that they would like to share? I'm new to Python and haven't done programming for a while and I'd like to get a better idea of what's all possible, and how. I was looking at Matt Newville's message back in 2008 about defining a library for Athena in Python and his 2001 paper but couldn't find much else. ~Finally, would I be better off coding in Perl and using Demeter? Thanks everyone, Andy Korinda Notestein Lab Chemical & Biological Engineering Northwestern University

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