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

Dodgy Edge Steps
by LACHLAN MACLEAN 03 May '08

03 May '08

Hi All Long-term lurker, first time poster. I've recently collected some EXAFS data with a large edge step (~3.4) and for some reason didn't pick up on it until it was too late. I've been told that ideally we would want an edge step of 1 and anything above ~1.5-2 is too high. I'm wondering if there is a way to salvage the dataset in order to compare it with EXAFS data that I collected from two other samples (all three are supposed to be synthetic goethite). The first two samples that I want to compare have edge steps of about 0.35. I know Athena allows one to adjust the edge step but wonder how appropriate this is and how much change this would cause the EXAFS data? Trying to adjust the edge step from 3.4 down to ~1 or so seems to be quite a jump. I'm curious whether there is a way to salvage this data rather than wait until the next beamrun. Any help would be appreciated. Cheers Lachlan

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job posting: beamline scientist at GSECARS / APS
by Matt Newville 03 May '08

03 May '08

Hi Folks, GSECARS is looking for a beamline scientist with a good background in x-ray absorption / related spectroscopies to work at the APS. See the posting at http://xafs.org/Jobs (or read below) for more details, including how to apply for this position. --Matt Job Posting: Beamline Scientist, Center for Advanced Radiation Sources (CARS), The University of Chicago University of Chicago Job Requistion # 079054 The Center for Advanced Radiation Sources (CARS) of the University of Chicago has a Beamline Scientist position available at the GeoSoilEnviroCARS (GSECARS) synchrotron research facility at the Advanced Photon Source (APS), Argonne National Laboratory, in Argonne, Illinois. This full-time position requires a Ph.D. in geology, environmental science, chemistry, physics or a related field and synchrotron radiation experience applying x-ray absorption spectroscopy and x-ray fluorescence techniques in earth and environmental science research. The successful candidate will (1) conduct research on the chemical properties of earth and environmental materials using large sample instruments and x-ray microprobes; (2) participate in the development of analytical instrumentation and techniques; and (3) provide partial support for and collaborate with scientific users from the earth and environmental communities who conduct research using the GSECARS synchrotron beamlines. The successful candidate will have excellent relevant computer, organizational, verbal and written communication skills, and must be able to work effectively both independently and as a team member. Candidates must be able to satisfy requirements for access to Argonne National Laboratory. Applications must be made on-line: Go to http://jobopportunities.uchicago.edu/ and search for Job Requistion # 079054. Applications must include a curriculum vitae, cover letter, statement of research interests, and list of publications, along with three professional references. This posting will be closed when the position is filled. The University of Chicago is an Equal Opportunity/Affirmative Action Employer.

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Re: [Ifeffit] Using the amplitude reduction factor as a linearcombination fitting parameter
by Frenkel, Anatoly 01 May '08

01 May '08

There are a few points in your description that puzzle me. Have you collected not one but a series of spectra where some external condition (e.g., temperature, concentration, time, pH etc) were varied? If not, PCA cannot be used if only one spectrum was collected containing a mixture of two species. Such spectrum would have only one component, of course - itself. Next, assuming you did use PCA for a series of spectra, without having XANES and/or EXAFS data of test compounds how were you able to deconvolute abstract components that PCA generates into the two species that have meening of XANES or EXAFS data? Without test compounds such deconvolution is not possible unless you used not PCA but a linear combination fit of some sort... And, finally, if you used test compounds that could be reliably reproduced by your 2 principal components, why do you need to do anything else? They are your two species. Please clarify. Anatoly ----- Original Message ----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov <ifeffit-bounces(a)millenia.cars.aps.anl.gov> To: ifeffit(a)millenia.cars.aps.anl.gov <ifeffit(a)millenia.cars.aps.anl.gov> Sent: Tue Apr 29 03:06:28 2008 Subject: [Ifeffit] Using the amplitude reduction factor as a linearcombination fitting parameter I have recently collected EXAFS spectra of uranium on a FeS2 surface. Using principal component analysis of the XANES and k3-weighted EXAFS spectra, I have found that there are two uranium species which compose the spectra. As a first tentative guess, I believe these two uranium species are uraninite (UO2(c)) and a uranyl species. I would like now to fit the fourier transform functions (real parts and magnitudes) using the theoretical paths and path degeneracies created by feff, and use the amplitude reduction factor S02 as a fitting parameter to derive the relative amounts of the two uranium species in my samples. Normally, this S02 is taken as a constant (between 0.7 and 1.0), and the path degeneracies are fitted. So normally, S02 is not really a fitting parameter (some papers derive it even with theoretical functions). However, given the fact that S02 and N are completely correlated, I think it is justified to use this approach. Can someone comment on this? Many thanks in advance, Christophe SCK·CEN Disclaimer http://www.sckcen.be/emaildisclaimer.html

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LDOS calculations
by Rajdeep Saha 30 Apr '08

30 Apr '08

Hi All, This question concerns the Feff8 program. So this may not be the appropriate site, however I would greatly appreciate if I could get some feedback. I calculate the DOS of TiO_2 anatase system using FEFF8 and then compare the results with benchmark calculations done using VASP. Apparently, the FEFF results are no where near the VASP results. I was wondering if somebody could take a look at my input file and suggest some improvements. I am absolutely new to EXAFS, and anybody's help would be greatly appreciated. Thanks, Rajdeep Saha. The input file is as follows; TITLE anatase HOLE 1 1.0 CONTROL 1 1 1 0 0 0 PRINT 0 0 0 0 0 0 RPATH 5.5 LDOS -18 0 0.01 SCF 6.21 POTENTIALS 0 8 O 1 22 Ti 2 8 O ATOMS 5.67630000 5.67630000 14.27190000 1 Ti 5.67630000 5.67630000 4.75730000 1 Ti 5.67630000 3.78420000 16.65055000 1 Ti 5.67630000 3.78420000 7.13595000 1 Ti 5.67630000 1.89210000 14.27190000 1 Ti 5.67630000 1.89210000 4.75730000 1 Ti 5.67630000 0.00000000 16.65055000 1 Ti 5.67630000 0.00000000 7.13595000 1 Ti 3.78420000 5.67630000 11.89325000 1 Ti 3.78420000 5.67630000 2.37865000 1 Ti 3.78420000 3.78420000 9.51460000 1 Ti 3.78420000 3.78420000 0.00000000 1 Ti 3.78420000 1.89210000 11.89325000 1 Ti 3.78420000 1.89210000 2.37865000 1 Ti 3.78420000 0.00000000 9.51460000 1 Ti 3.78420000 0.00000000 0.00000000 1 Ti 1.89210000 5.67630000 14.27190000 1 Ti 1.89210000 5.67630000 4.75730000 1 Ti 1.89210000 3.78420000 16.65055000 1 Ti 1.89210000 3.78420000 7.13595000 1 Ti 1.89210000 1.89210000 14.27190000 1 Ti 1.89210000 1.89210000 4.75730000 1 Ti 1.89210000 0.00000000 16.65055000 1 Ti 1.89210000 0.00000000 7.13595000 1 Ti 0.00000000 5.67630000 11.89325000 1 Ti 0.00000000 5.67630000 2.37865000 1 Ti 0.00000000 3.78420000 9.51460000 1 Ti 0.00000000 3.78420000 0.00000000 1 Ti 0.00000000 1.89210000 11.89325000 1 Ti 0.00000000 1.89210000 2.37865000 1 Ti 0.00000000 0.00000000 9.51460000 1 Ti 0.00000000 0.00000000 0.00000000 1 Ti 5.67630000 5.67630000 16.25188826 2 O 5.67630000 5.67630000 12.29191174 2 O 5.67630000 5.67630000 6.73728826 2 O 5.67630000 5.67630000 2.77731174 2 O 5.67630000 3.78420000 18.63053826 2 O 5.67630000 3.78420000 14.67056174 2 O 5.67630000 3.78420000 9.11593826 2 O 5.67630000 3.78420000 5.15596174 2 O 5.67630000 1.89210000 16.25188826 2 O 5.67630000 1.89210000 12.29191174 2 O 5.67630000 1.89210000 6.73728826 2 O 5.67630000 1.89210000 2.77731174 2 O 5.67630000 0.00000000 18.63053826 2 O 5.67630000 0.00000000 14.67056174 2 O 5.67630000 0.00000000 9.11593826 2 O 5.67630000 0.00000000 5.15596174 2 O 3.78420000 5.67630000 13.87323826 2 O 3.78420000 5.67630000 9.91326174 2 O 3.78420000 5.67630000 4.35863826 2 O 3.78420000 5.67630000 0.39866174 2 O 3.78420000 3.78420000 17.04921174 2 O 3.78420000 3.78420000 11.49458826 2 O 3.78420000 3.78420000 7.53461174 2 O 3.78420000 3.78420000 1.97998826 2 O 3.78420000 1.89210000 13.87323826 2 O 3.78420000 1.89210000 9.91326174 2 O 3.78420000 1.89210000 4.35863826 2 O 3.78420000 1.89210000 0.39866174 2 O 3.78420000 0.00000000 17.04921174 2 O 3.78420000 0.00000000 11.49458826 2 O 3.78420000 0.00000000 7.53461174 2 O 3.78420000 0.00000000 1.97998826 2 O 1.89210000 5.67630000 16.25188826 2 O 1.89210000 5.67630000 12.29191174 2 O 1.89210000 5.67630000 6.73728826 2 O 1.89210000 5.67630000 2.77731174 2 O 1.89210000 3.78420000 18.63053826 2 O 1.89210000 3.78420000 14.67056174 2 O 1.89210000 3.78420000 9.11593826 2 O 1.89210000 3.78420000 5.15596174 2 O 1.89210000 1.89210000 16.25188826 2 O 1.89210000 1.89210000 12.29191174 2 O 1.89210000 1.89210000 6.73728826 2 O 1.89210000 1.89210000 2.77731174 2 O 1.89210000 0.00000000 18.63053826 2 O 1.89210000 0.00000000 14.67056174 2 O 1.89210000 0.00000000 9.11593826 2 O 1.89210000 0.00000000 5.15596174 2 O 0.00000000 5.67630000 13.87323826 2 O 0.00000000 5.67630000 9.91326174 2 O 0.00000000 5.67630000 4.35863826 2 O 0.00000000 5.67630000 0.39866174 2 O 0.00000000 3.78420000 17.04921174 2 O 0.00000000 3.78420000 11.49458826 2 O 0.00000000 3.78420000 7.53461174 2 O 0.00000000 3.78420000 1.97998826 2 O 0.00000000 1.89210000 13.87323826 2 O 0.00000000 1.89210000 9.91326174 2 O 0.00000000 1.89210000 4.35863826 2 O 0.00000000 1.89210000 0.39866174 2 O 0.00000000 0.00000000 17.04921174 2 O 0.00000000 0.00000000 11.49458826 2 O 0.00000000 0.00000000 7.53461174 2 O 0.00000000 0.00000000 1.97998826 0 O

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Using the amplitude reduction factor as a linear combination fitting parameter
by Bruggeman Christophe 30 Apr '08

30 Apr '08

I have recently collected EXAFS spectra of uranium on a FeS2 surface. Using principal component analysis of the XANES and k3-weighted EXAFS spectra, I have found that there are two uranium species which compose the spectra. As a first tentative guess, I believe these two uranium species are uraninite (UO2(c)) and a uranyl species. I would like now to fit the fourier transform functions (real parts and magnitudes) using the theoretical paths and path degeneracies created by feff, and use the amplitude reduction factor S02 as a fitting parameter to derive the relative amounts of the two uranium species in my samples. Normally, this S02 is taken as a constant (between 0.7 and 1.0), and the path degeneracies are fitted. So normally, S02 is not really a fitting parameter (some papers derive it even with theoretical functions). However, given the fact that S02 and N are completely correlated, I think it is justified to use this approach. Can someone comment on this? Many thanks in advance, Christophe ---------- SCK-CEN Disclaimer --------- http://www.sckcen.be/emaildisclaimer.html

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Re: [Ifeffit] Using the amplitude reduction factor as alinearcombination fitting parameter
by Frenkel, Anatoly 29 Apr '08

29 Apr '08

An option could be, if you collected just one spectrum, to construct 1st shell EXAFS data for each compound using FEFF and use a linear combination option of Athena to see if there is any value of the mixing fraction of these two theoretical compounds that resemble good fit. You will still need to know the best fit value of S02 obtained previously from standard uranium compounds and use same sigma2 for all U-O bonds. You can define your fitting range using large value of kmin to emphasize the first shell signal better, and do fititing in k space with k-weighting of 1 for the same reason. It can all be done witinin Athena. Anatoly ----- Original Message ----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov <ifeffit-bounces(a)millenia.cars.aps.anl.gov> To: ifeffit(a)millenia.cars.aps.anl.gov <ifeffit(a)millenia.cars.aps.anl.gov> Sent: Tue Apr 29 10:23:10 2008 Subject: Re: [Ifeffit] Using the amplitude reduction factor as alinearcombination fitting parameter There are a few points in your description that puzzle me. Have you collected not one but a series of spectra where some external condition (e.g., temperature, concentration, time, pH etc) were varied? If not, PCA cannot be used if only one spectrum was collected containing a mixture of two species. Such spectrum would have only one component, of course - itself. Next, assuming you did use PCA for a series of spectra, without having XANES and/or EXAFS data of test compounds how were you able to deconvolute abstract components that PCA generates into the two species that have meening of XANES or EXAFS data? Without test compounds such deconvolution is not possible unless you used not PCA but a linear combination fit of some sort... And, finally, if you used test compounds that could be reliably reproduced by your 2 principal components, why do you need to do anything else? They are your two species. Please clarify. Anatoly ----- Original Message ----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov <ifeffit-bounces(a)millenia.cars.aps.anl.gov> To: ifeffit(a)millenia.cars.aps.anl.gov <ifeffit(a)millenia.cars.aps.anl.gov> Sent: Tue Apr 29 03:06:28 2008 Subject: [Ifeffit] Using the amplitude reduction factor as a linearcombination fitting parameter I have recently collected EXAFS spectra of uranium on a FeS2 surface. Using principal component analysis of the XANES and k3-weighted EXAFS spectra, I have found that there are two uranium species which compose the spectra. As a first tentative guess, I believe these two uranium species are uraninite (UO2(c)) and a uranyl species. I would like now to fit the fourier transform functions (real parts and magnitudes) using the theoretical paths and path degeneracies created by feff, and use the amplitude reduction factor S02 as a fitting parameter to derive the relative amounts of the two uranium species in my samples. Normally, this S02 is taken as a constant (between 0.7 and 1.0), and the path degeneracies are fitted. So normally, S02 is not really a fitting parameter (some papers derive it even with theoretical functions). However, given the fact that S02 and N are completely correlated, I think it is justified to use this approach. Can someone comment on this? Many thanks in advance, Christophe SCK·CEN Disclaimer http://www.sckcen.be/emaildisclaimer.html _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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compiling ifeffit on 64 bit linux
by Matthew Ginder-Vogel 22 Apr '08

22 Apr '08

Hello, I'm trying to compile Ifeffit on a 64 bit CentOS 4 machine and am having a few problems. I can get PGPLOT to compile without error by following bruce's prior directions to edit the makefile for pgplot http://cars9.uchicago.edu/pipermail/ifeffit/2005-September/002018.html I then compile Ifeffit using ./configure CC="cc -fPIC" FFLAGS="-g -O2 -fPIC" and everything seems to work okay, but when i try and run IFEFFIT at the command line it get this error [root@cluster ifeffit-1.2.10]# ifeffit ifeffit: error while loading shared libraries: libpgplot_iff.so: cannot open shared object file: No such file or directory [root@cluster ifeffit-1.2.10]# If I compile Ifeffit without PGPLOT support then Ifeffit runs without any problems. Does anyone have any advice? Thanks, Matt -- ******************************************* Matthew Ginder-Vogel Post Doctoral Researcher Center for Critical Zone Research Environmental Soil Chemistry University of Delaware http://ag.udel.edu/SoilChem/gindervogel.html (302) 831-0608 mattgv(a)udel.edu *******************************************

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problems with automatic update of ifeffit on Windows
by Stefan Mangold 18 Apr '08

18 Apr '08

Hello all, we have some start-up delays (1 min) during some start-up's of the programs of the ifeffit packages. The systems are Windows XP systems. It seems, that the software can't connect to the update Server. Since our IT-Staffs deny to help to open the respective ports in the firewall, if I can't specify them, I search here for help. Can anybody specify the ports (out and in), which need to be open. Is there also an option to turn the update process off? Thanks in advance Stefan Mangold -- Dr. Stefan Mangold Institut für Synchrotronstrahlung Forschungszentrum Karlsruhe Tel.: +49-7247-826073

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problems with automatic update of ifeffit on Windows
by Dominik Samuelis 18 Apr '08

18 Apr '08

Hi Stefan, > we have some start-up delays (1 min) during some start-up's of the > programs of the ifeffit packages. The systems are Windows XP systems. > It seems, that the software can't connect to the update Server. Since > our IT-Staffs deny to help to open the respective ports in the > firewall, if I can't specify them, I search here for help. Can anybody > specify the ports (out and in), which need to be open. the port which needs to be open for automatic updates is the usual port for http access: 80/tcp (out). runner.exe just issues a regular http request to "http://cars9.uchicago.edu/~ifeffit/updates//current.dat", with a timeout specified by timeout_connect. As this port might be already open on your machines, the delays could also be caused by temporary network issues, either on your or on cars9 side. All the automatic update stuff is configured in %IFEFFIT_DIR%/config/updater.ini . You have several options of decreasing waiting time, either by decreasing timeout_connect and timeout_test, or by setting timestamp to some future unix date, e.g. 1500000000.00. This effectively disables automatic updates till May 2017 (which possibly doesn't matter, as it seems, that automatic updates weren't used since 2006, roughly corresponding to the ifeffit1.2.9 release for Windows XP). You could of course use less offensive settings for the timestamp. It's easy to compute, since it's just the seconds from 1-Jan-1970. Cheers, dominik -- Dipl.-Ing. Dominik Samuelis samuelis(a)pc.rwth-aachen.de Physikalische Chemie I RWTH Aachen University Phone: +49-241-80-94840 Fax: +49-241-80-92128 Landoltweg 2 52074 Aachen Germany

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Proposal for a U.S. XAFS conference
by Carlo Segre 17 Apr '08

17 Apr '08

Hello All: Next year is the IXS meeting but for two years after that , there will be no conference dedicated to XAS for another 3 years. I have been looking into establishing a topical meeting (with the focus changing from year to year) in the United States in years that IXS is not being held. The first one of these would be 2010. My proposal is to associate the meeting with the Denver X-ray Conference (DXC) which is held in Colorado in early August. The advantages of association with this conference is that the people who organize the DXC are able and willing to take care of all the logistics (conference fees, rooms, hotel, etc.) and there would only be a need to have a scientific organizing group. In fact, the DXC has been host to several satellite meetings: lst year the fiber diffraction community held a session and this year, there is a parallel conference on stress analysis. Since XAS is an x-ray technique, I think that it would be a good fit. I have discussed this with the DXC organizers and they have indicated a willingness to be involved. The advantages of running such a conference is that there would be an XAS outlet for students to be involved with that would not be too expensive to attend in the years of no IXS. I am intending this message primarily for list members in the US (apologies to everyone else!) and I would appreciate any comments you might have about this idea before I begin to set it in motion. If Matt is OK with the conversation continuing on the list we can keep the replies public but if he prefers not to clog the list, please contact me directly. Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre(a)iit.edu http://www.iit.edu/~segre segre(a)debian.org

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