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

questions concerning paper
by s440697＠stud.uni-goettingen.de 23 May '08

23 May '08

Hello, i have some questions concerning the xafs-formula in this paper (attached): "Theoretical approaches to x-ray absorption fine structure" (July 2000). The author explained on page 625 and 626 the parameters of this formula. I think, most of you have read this paper. I don't understand the meaning of lambda(k), the author wrote "... and lambda(k) is the energy-dependent XAFS mean free path (not to be confused with the de Broglie wavelength)." My question is, the mean free path whereof? The propagating photoelektron(wave) or the (back)scattered waves? In the next sentence, what is the overall amplitude factor S_0^2? How is it defined? In conjunction with question one i don't understand the expression in the next paragraph for the term e^{-2R/lambda}. The author wrote: "The decay of the wave (which wave does he mean?) due to the mean free path or finite lifetime (what does he mean?, finite lifetime of the emitted and propagating photoelektron wave?) [including core-hole lifetime] of the photoelectron is captured by ..." Is it right, that the emitted photoelektron is detectable outside the sample? Another parameter is the phase factor phi = arg f(k) "...reflects the quantum-mechanical wavelike nature of the backscattering." Please explain me the meaning of this parameter. At the bottom of this page the author wrote: "...the Debye-Waller factor, which is given to a good approximation by e^{-2 sigma^2 k^2}." In this context he refers to figure 8, where k^2 chi(k) vs. k is plotted. I don't understand this context because there is no chi in the approximation for the Debye-Waller factor. Where comes the chi here? I would be very grateful for any help you would offer to me. Thank you very much for your help and time. sincerely yours, E.Bosman --------------------------------- Eckhard Bosman e.bosman(a)stud.uni-goettingen.de +49 (0)551-39-14441 Raum: E0.104 Institut für Röntgenphysik Friedrich-Hund-Platz 1 37077 Göttingen Germany

5 5

Re: [Ifeffit] questions concerning paper
by Frenkel, Anatoly 22 May '08

22 May '08

We should ask John Rehr to rename FEFF to Odysseus. It makes both physical and mythological sense. Anatoly ----- Original Message ----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov <ifeffit-bounces(a)millenia.cars.aps.anl.gov> To: Ravel, Bruce; XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Sent: Thu May 22 14:30:38 2008 Subject: Re: [Ifeffit] questions concerning paper I loved it also, thanks Matt :-) May i cite your Odysseus explanation in my diploma thesis? ;) -------- Original-Nachricht -------- > Datum: Thu, 22 May 2008 12:40:01 -0400 > Von: Bruce Ravel <bravel(a)bnl.gov> > An: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Betreff: Re: [Ifeffit] questions concerning paper > > Matt, > > That was awesome! I **loved** the Odysseus explanation of the exafs > equation. Quite possibly the best Ifeffit mailing list post ever. > > 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/ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- GMX startet ShortView.de. Hier findest Du Leute mit Deinen Interessen! Jetzt dabei sein: http://www.shortview.de/?mc=sv_ext_mf@gmx _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

1 0

2008 APS XAFS School
by Matt Newville 16 May '08

16 May '08

Hi Everyone, The application form for the 2008 APS XAFS School is now open: http://cars9.uchicago.edu/xafs_school/2008 Details about this year's APS XAFS School are at http://xafs.org/Workshops/APS2008 --Matt PS: Starting sometime yesterday (and currently), mail from outside APS to this list is being bounced by an APS firewall. If you have sent mail to this list and had it bounce, please be patient. I'll post a message when the mailing list is back up.

4 4

iron L edges
by Bruce Ravel 16 May '08

16 May '08

Hi everyone, I have just spent a fruitless half hour with google scholar trying to find a paper that publishes Fe L2,3 edge spectra (not K -- I have those!) of the FeOOH species goethite and lepidocrocite. Can anyone point me in the right direction? Thanks a million! 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/

3 2

feff8.4 LDOS number of energy points
by Rajmund Bacewicz 12 May '08

12 May '08

Hi all, In a Windows version of FEFF8.4, LDOS is calculated in 401 energy points, that is extremely time consuming. Is it possible to change it to a smaller number of points (e.g. 101 points like in FEFF8.2)? Regards Rajmund -- List przeskanowano programem ArcaMail, ArcaVir 2006 przeskanowano 2008-05-12 10:29:02, silnik: 2005.12.01 12:00:00, bazy: 2008.05.04 14:32:29 This message has been scanned by ArcaMail, ArcaVir 2006 scanned 2008-05-12 10:29:02, engine: 2005.12.01 12:00:00, base: 2008.05.04 14:32:29 http://www.arcabit.com

2 1

XANES Background removal and Normalization
by Jens Kruse 10 May '08

10 May '08

Hi there, I have some P L2/L3-edge XANES spectra. I am not sure how to remove the background and normalize these data. Due to the fact that the pre edge and the post edge region is not very flat the the edge-step normalization using AUTOBK dose not work very well. CLNORM background subtraction seems to work better in some case. But some spectra get partly negative values after CLNORM (see .prj attached). So my questions are: 1:Is CLNORM the best choice in my case, especially when I plan to do linear combination fitting with these data? 2: Athena needs the knowledge of the absorbing atom an the edge to use CLNNORM, but the spectra contain both L3 an L2. So, which edge do I have to choose L3 or L2? 3: Would it be also correct to use a Victoreen-Fit for the pre edge without any further normalization and than do the linear combination fitting? Or do I have to normalize spectra in general when I am doing linear combination fitting, to eliminate effects of different concentrations of the absorbing atom in the mixtures? thanks, a lot for your help jens

1 0

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

5 4

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.

1 0

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

3 2

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

2 1

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

3 4

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

1 0

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 *******************************************

2 2

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

3 2

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

1 0

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

3 2

Inability to plot in any space other than E
by Andrew Connelly 14 Apr '08

14 Apr '08

Hello, I have some EXAFS data at the S K-edge which all merges very nicely but I can't plot it under anything other than E. The other options are faded out along with all Fourier transform options, Rbkg etc. Is this a comment on the quality of the data (its not great)?! Or is it something else, the other plotting options work fine on other data (at other edges) I have. Any help / advice great fully received. Andy

4 3

Reading individual data columns with ifeffit
by Matthew Ginder-Vogel 04 Apr '08

04 Apr '08

Hello all, When reading data files using the read_data command in ifeffit is there a way to specify which columns of data will be read? I have very long data files and run into array size problems when I try and read the entire file. However, if I could read only columns 1, 2, and 3 rather than all 5 data columns I think my problem would be solved. I think narray may be the command to use, but I'm not sure how to implement it and couldn't find anything in the ifeffit manual. 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 *******************************************

3 2

FW: Brainteaser
by Anatoly Frenkel 04 Apr '08

04 Apr '08

I think this answer is as good as the correct one! Anatoly. -----Original Message----- From: Woicik, Joseph [mailto:woicik@bnl.gov] Sent: Friday, April 04, 2008 3:28 PM To: anatoly.frenkel(a)yu.edu Subject: RE: Brainteaser oh, i got it, you right clicked when you should have left clicked..... _____

1 0

2007 APS XAFS School
by Julie Olmsted Cross 04 Apr '08

04 Apr '08

The on-line application for the 2007 APS XAFS School is now available at xafs.org http://www.xafs.org/Workshops/APS2007 ~^^~^~^~~^~^~^~^~^~^~^~^~~^~^~ Julie O. Cross Advanced Photon Source Argonne National Lab 9700 South Cass Ave., Bldg. 401/B4204 Argonne IL 60439 tel: 630 327 7825 fax: 630 252 0580 ~^^~^~^~~^~^~^~^~^~^~^~^~~^~^~

5 9

FW: Brainteaser
by Anatoly Frenkel 04 Apr '08

04 Apr '08

-----Original Message----- From: Matthew Marcus [mailto:mamarcus@lbl.gov] Sent: Thursday, April 03, 2008 9:57 PM To: anatoly.frenkel(a)yu.edu Subject: Re: [Ifeffit] Brainteaser Sorry about jumping in too quickly. I've had this very thing happen to me so I recognize the sharp edge rise. Maybe I should have replied privately to give others a chance to weigh in, or put ***spoiler warning - possible solution **** in the subject line. My apologies to all! mam ----- Original Message ----- From: Anatoly Frenkel <mailto:frenkel@bnl.gov> To: 'Matthew Marcus' <mailto:MAMarcus@lbl.gov> ; anatoly.frenkel(a)yu.edu ; 'XAFS Analysis using <mailto:ifeffit@millenia.cars.aps.anl.gov> Ifeffit' Sent: Thursday, April 03, 2008 6:52 PM Subject: RE: [Ifeffit] Brainteaser I apologize to everyone who Matthew did not even give a chance to think but the excuse is that Matthew is really good! It was a saturation of the I_t current amplifier. Another sign of that is too sharp a rise of the edge right after the pre-edge - it is when the I_t signal drops below the saturation limit. A comment: the last time NSLS had 20h of stored beam lifetime was in the 20th century, I think, but it is besides the point. Anatoly -----Original Message----- From: Matthew Marcus [mailto:mamarcus@lbl.gov] Sent: Thursday, April 03, 2008 9:30 PM To: anatoly.frenkel(a)yu.edu; XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Brainteaser The most obvious explanation for why the post-edge scans line up and the pre-edges don't is that the transmission chamber current amp or V/F is saturated and reads a fixed value below the edge. As the ring current decays, I0 goes down while It is fixed below the edge, so ln(I0/It) decreases as observed. With this explanation, and noting that ln(I0/It) decreased by about 0.05 in an hour, I infer that the stored-beam lifetime is ~20hr. mam ----- Original Message ----- From: Anatoly Frenkel <mailto:frenkel@bnl.gov> To: anatoly.frenkel(a)yu.edu ; 'XAFS Analysis using <mailto:ifeffit@millenia.cars.aps.anl.gov> Ifeffit' Sent: Thursday, April 03, 2008 6:13 PM Subject: [Ifeffit] Brainteaser Attached is a brainteaser which I think is cute. Too late for the April fool's day but still... Some comments: three consecutive scans of the same sample were taken in this order: scan 1, 2 and 3. Duration: 30 minutes per scan. If these data look unusual to you please tell us why and what could've happened in this experiment. Those of you who send first three correct answers will be acknowledged! Anatoly _____ _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

1 0

saving a window function in Athena/Artemis
by van der Veen Renske 27 Mar '08

27 Mar '08

Hi! Could anyone tell me whether it is possible to save a specific window function together with the data in either Athena or Artemis? Another general question: how can I easily search for specific key words in the archive folders of the mailing list (without going through them individually)? Thanks & happy new year to you all! Renske Renske M. van der Veen PhD student Chergui Group EPFL Paul Scherrer Institut Swiss Light Source WSLA/210 5232 Villigen PSI Switzerland Phone: +41 56 310 5362 Fax: +41 56 310 3171 E-mail: renske.vanderveen(a)psi.ch Web: http://lsu.epfl.ch http://femto.web.psi.ch

5 6

Colin L Beswick/East-US/ExxonMobil is out of the office.
by colin.l.beswick＠exxonmobil.com 25 Mar '08

25 Mar '08

I will be out of the office starting 03/25/2008 and will not return until 03/26/2008. My response to your message may be delayed.

1 0

X-ray absorption measurements for Fluorescence detection.
by 沛昌蔡 24 Mar '08

24 Mar '08

Dear Authors: The Athena, Artemis fitting programs is suitable for X-ray absorption measurements for Fluorescence detection mode? Because transmission have different physical describing with Fluorescence mode. Or maybe you have more descriptions about Fluorescense detection mode fitting about X-ray absorption measurement? Thanks for your time and help! Pei ___________________________________________________________________ 付費才容量無上限？Yahoo!奇摩電子信箱2.0免費給你，信件永遠不必刪！ - 馬上體驗！

3 2

Re: [Ifeffit] about TkAtoms
by Bruce Ravel 17 Mar '08

17 Mar '08

Yordy, I am CCing my answer to the Ifeffit mailing list, which is the most appropriate place for this sort of thing. > 1.I would like to know why the TkAtoms software is not in the installation > last versions of IFFEFIT packages or maybe I dont find or dont know how to > do it? I would like to know is there is any way to download a package with > TkAtoms included in it to install in WindowsXP? See question 5 on this page of the Ifeffit FAQ: http://cars9.uchicago.edu/iffwiki/FAQ/RunningFeff > 2. Is there any software to transform .cif files to .inp files? I think this question is answered above as well. Both Artemis and the command line version of Atoms read a CIF file and convert to a feff.inp file. In Artemis, use the normal "open file" dialog and select a CIF file. If it is a properly structured CIF file, Artemis will recognize it as such and do the right thing with it. Go ahead and post questions on the mailing list if you have any further problems. Here's the URL if you are not already a member: http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Regards, B > > Thanks very much, Yordy > > Yordy E. Licea Fonseca > Laboratório de Catálise Heterogênea > Dept. de Físico-Química > Rio de Janeiro, RJ, CEP 21.949-909 > Brasil -- 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/

1 0