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

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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