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

charge transfer
by Bruce Ravel 05 Jan '09

05 Jan '09

Hi all, The following message from Jeong Eun Suk was not delivered correctly to the mailing list. Fortunately, I noticed the problem and am forwarding it along now. B Original message: what does charge transfer mean in FEFF? I cant understand what the number of charge transfer like 0.058, -0.073 means. The number indicate the number of electron in atom? If anybody knows it, please answer Charge transfer: iph charge(iph) 0 0.058 1 -0.073 2 0.072 -- 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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Problem running Feff through Artemis on Mac OS
by Aaron Slowey 02 Jan '09

02 Jan '09

Hello, I have Artemis running on intel Mac OS 10.4 and am unable to get FEFF to run by using Artemis. I have changed the preferences in the 'atoms' submenu to have feff_version as 7 and template as feff7 and then I have, under the 'feff' submenu, the path to my feff executable, specifically "/Users/aslowey/feff/feff7.exe" I tried removing the .exe -- no go. Then I reverted back to Artemis' default settings (feff version 6) and it still didn't work. I relocated both the feff.inp and feff executable in the same folder, but this also failed. In all cases, the Artemis palettes window opens to the Messages tab with red text that Artemis configured incorrectly...incorrect value of feff->feff_executable. Is there something about Mac OS that FEFF can't work? - Aaron Slowey

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subscription
by 穆鑫 30 Dec '08

30 Dec '08

Hello: I want to subscribe the Ifeffit . Thanks! Happy New year!

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How to identify N and O atoms in the first coordinate
by mzhu＠udel.edu 22 Dec '08

22 Dec '08

Hello all, Merry Christmas! I have some samples of heavy metal sorption on bacterial biofilm. I want to figure out what elements are coordinated with the heavy metal in the first coordinate. Since the oxygen and nitrogen have similar scattering factors, how can I differetiate them? Using shell-by-shell fitting or linear combination fitting with standards? Thanks. Best wishes, Mengqiang Zhu ----------------------- Mengqiang Zhu Ph.D Candidate Environmental Soil Chemistry Department of Plant and Soil Sciences University of Delaware 152 Townsend Hall Newark, DE 19716 http://ag.udel.edu/soilchem/zhu.html

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Re: [Ifeffit] How to identify N and O atoms in the first coordinate
by Frenkel, Anatoly 20 Dec '08

20 Dec '08

The fact that PCA tells between known Ni-N and Ni-O complexes by adding one more component when the wrong complex is added (N to O or vice versa) does not mean that there is specific fingerprinting sensitivity to N or O. One needs to demonstrate first that all Ni-N pairs have similar distances and disorder, regardless of their chemical surrounding, and that the same is true for Ni-O. Only in that case your PCA results indeed mean that the Ni sorbed biofilm have both types of bonds. Otherwise you cannot prove that it is Ni-N plus Ni-O vs. a situation where there are two unique types of Ni-O that have not been matched to your Ni-O standard and may thus fool you in thinking that one of them is due to Ni-N instead. Thus, before you conclude that, you should verify whether various Ni-N and Ni-O complexes have same pair properties. From your description it appears not to be the case since you have two components (not one) for your oxygen ligands and nitrogen ligands. Anatoly ----- Original Message ----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov <ifeffit-bounces(a)millenia.cars.aps.anl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Sent: Fri Dec 19 18:39:24 2008 Subject: Re: [Ifeffit] How to identify N and O atoms in the first coordinate Hello Anatoly, Thanks for your reply. I could not do it as the literature you mentioned since I do not have detailed structural information as they do. I am wondering if the following method can be justified to indentify nitrogen atoms: 1) EXAFS data of 7 nickel oxygen-coordinated organic and inorganic complexes in which nickel only coordinates to oxygen atoms from carboxyl group, phosphoryl group and water molecules. 2) Fourier back transformation of the peak from 1-2 aus. in R+ delta-R space. This R range must cover the scattering peaks from both nitrogen and oxygen. Then chi functions of these complexes are obtained. 3) A principal component anlaysis (PCA) was performed over the oxygen-coordinated dataset of the chi functions obtained in the step (2). PCA analysis indicated two major components based on the IND values. 4)Then chi functions of two nitrogen-coordinated nickel complexes was obtained using the same method as step 2). It is certain that nitrogen atoms are coordinated to the nickel in the first shell in addition to oxygen atoms. 5) A target transformaiton of the chi function of two nitrogen-coordinated nickel complexes using oxygen-coordianted dataset resulted in the SPOIL values close to 5. Addition of one of the two complexes to the group of nickel complexes in PCA, PCA resulted in 3 components. These indicate that they have different coordination environment to the oxygen-coordinated nickel complexes. It is expected because they have nitrogen in the first shell. 6) A target transformation conducted on a sample of nickel-sorbed biofilm (back fourier transformed chi function in 1-2 aus.) resulted in the value close to 5. It means that the sample can not be represented by the nickel organic group, either. Since the first shell only can have two types of atoms, oxgen and nitrogen. If the nickel sorbed on biofilm can not be represented by the nickel oxygen-coordinated organic group which only has oxygen in the frist shell, it must have nitrogen atoms in the first shell. Also, linear square fitting of the Ni_biofilm with the nitrogen-coordinated complexes resulted in the better goodness than other oxygen-coordinated complexes. Thus, the nitrogen must exist in the first shell of Ni_biofilm sample. Do you think this method is reasonable? Best wishes, Mengqiang Zhu ----------------------- Mengqiang Zhu Ph.D Candidate Environmental Soil Chemistry Department of Plant and Soil Sciences University of Delaware 152 Townsend Hall Newark, DE 19716 http://ag.udel.edu/soilchem/zhu.html ---- Original message ---- >Date: Fri, 19 Dec 2008 16:34:36 -0500 >From: ifeffit-bounces(a)millenia.cars.aps.anl.gov (on behalf of "Frenkel, Anatoly" <frenkel(a)bnl.gov>) >Subject: Re: [Ifeffit] How to identify N and O atoms in the first coordinate >To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov>, <ifeffit(a)millenia.cars.aps.anl.gov> > >Dear Mengqiang, > >To the best of my knowledge, in most cases Nitrogen cannot be discerned from Oxygen as a nearest neighbor since their scattering properties are similar. Thus, if you want to solve an "inverse" problem ("Which type of neighbors do I have") you cannot do it. However, if you believe you have some knowledge about the type of metal-oxygen bonding: either M=O or a M-O or a M-OH or a M-OH2 (the first one is the shortest and the strongest, the others may have similar interatomic distances but different bond strengths), you can advance somewhat. > >If you have a certain number of distinct models you want to compare the data against, it can be done via a linear combination fitting, or by direct algebraic extraction of any given type of the pair contribution from the data, as described, for example here: > >E. Poverenov, I. Efremenko, A. I. Frenkel, Y. Ben-David, L. J. W. Shimon, G. Leitus, J. M. L. Marin, D. Milstein. A terminal Pt(IV)-oxo complex bearing no stabilizing electron withdrawing ligands and exhibiting diverse reactivity. Nature 255, 1093-1096, 2008. > >See supplementary info to that article for specific details. >Regards, >Anatoly > > >________________________________ > >From: ifeffit-bounces(a)millenia.cars.aps.anl.gov on behalf of mzhu(a)udel.edu >Sent: Fri 12/19/2008 4:20 PM >To: ifeffit(a)millenia.cars.aps.anl.gov >Subject: [Ifeffit] How to identify N and O atoms in the first coordinate > > > >Hello all, > Merry Christmas! > I have some samples of heavy metal sorption on bacterial biofilm. I want to figure out what elements are coordinated with the heavy metal in the first coordinate. Since the oxygen and nitrogen have similar scattering factors, how can I differetiate them? Using shell-by-shell fitting or linear combination fitting with standards? Thanks. > >Best wishes, > >Mengqiang Zhu > > > > > > > >----------------------- >Mengqiang Zhu >Ph.D Candidate >Environmental Soil Chemistry >Department of Plant and Soil Sciences >University of Delaware >152 Townsend Hall >Newark, DE 19716 >http://ag.udel.edu/soilchem/zhu.html >_______________________________________________ >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 _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Re: [Ifeffit] Problems with feff and crystallographic data (Now with bug report)
by Gregory Merchan 19 Dec '08

19 Dec '08

Hi Hashem, Atoms doesn't handle the occupancy data in the CIF file. See this page for more info: http://cars9.uchicago.edu/iffwiki/FAQ/FeffitModeling#head-b273ecfd19542ec82… I assume you see a message like this one that I see: This warning indicates a problem in the Atoms list. For some reason you have atoms that are separated by than 0.93 Angstroms (or 1.75 Rydberg). If you look on the Atoms tab in Artemis when you open the CIF file, you should see that the co-ordinates for Mg and Al are all 0.00000 ; i.e., all Atoms sees is that they are in the same place. Bruce, here's two bug reports: 1. The warning message above is missing the word "less", as in "separated by _less_ than 0.93 Angstroms" 2. It's an extensive message but doesn't mention this kind of problem. If you want to drive yourself mad with interface stuff, you could catch and highlight these errors on input and disable the controls they affect until the input is corrected. A tricky part of that is making sure the user knows what the highlighting means and has a clue about how to fix the error without - say - throwing up a talking paperclip. A sort of "heavy tooltip" ("lead balloon"?) could be shown - placed so as not to obscure the relevant controls - with a brief message, a way to get to the more help, and dismissal button. An automatic fade out might be nice, not sure. So long as the bad input exists, there should be a way to get the message back, like mousing over the highlighted input or the disabled controls. I don't know of any cross-platform toolkit that makes that kind of thing easy. Cheers, Greg On Thu, Dec 18, 2008 at 10:04 PM, Hashem Stietiya <mstiet2(a)lsu.edu> wrote: > Hello! > > > > I was using Artemis to run feff and generate paths from hydrotalcite. > However, it failed to run and an error message indicated that there is > something wrong with the crystallographic data. I used the crystallographic > data of hydrotalcite from different sources, but encountered the same > problem. Can you please help identify the problem and run feff? > > > > Please find attached the crystallographic data for hydrotalcite. > > > > I appreciate your help. > > > > Regards, > > Hashem Stietiya > > Louisiana State University > > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > >

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Error bars reported in the curve-fitting analysis in Artemis
by Hiroshi Oji 19 Dec '08

19 Dec '08

Dear all, Could someone tell me how the uncertainities in the fitted variables are estimated in the curve-fitting analysis in Artemis? Thank you very much in advance for your help. Hiroshi Oji -- ========================================================= 　Hiroshi Oji, Dr. Industrial Application Division Japan Synchrotron Radiation Research Institute (JASRI) 1-1-1 Kouto, Sayo-cho Sayo-gun, Hyogo 679-5198 JAPAN E-mail oji-h(a)spring8.co.jp =========================================================

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Problems with feff and crystallographic data
by Hashem Stietiya 19 Dec '08

19 Dec '08

Hello! I was using Artemis to run feff and generate paths from hydrotalcite. However, it failed to run and an error message indicated that there is something wrong with the crystallographic data. I used the crystallographic data of hydrotalcite from different sources, but encountered the same problem. Can you please help identify the problem and run feff? Please find attached the crystallographic data for hydrotalcite. I appreciate your help. Regards, Hashem Stietiya Louisiana State University

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New windows update
by Matt Newville 17 Dec '08

17 Dec '08

Hi Folks, Bruce and I put together a new Windows updater, and it is now posted and available for download. This should fix several small problems with athena and artemis. It should also fix problems that several people have noticed with the previous update. After the update, the versions should be Athena 0.8.058 Artemis 0.8.013 Ifeffit 1.2.11c If you have any trouble with this update not working to install and run the latest versions, please let us know. --Matt

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fitting ReO2
by Edward L. Kunkes 16 Dec '08

16 Dec '08

Hi everyone, I am trying to do a first shell fit of ReO2 – where there are 2 different Re-O distances in the first coordination shell. Does anyone have an .atoms file or structural information for this material that they would be willing to share ? Thank you very much for your help. -Edward Kunkes Research Assistant Department of Chemical Engineering University of Wisconsin-Madison

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how can i call the function of Athena or Artemis in Python
by goodhei8＠gmail.com 05 Dec '08

05 Dec '08

Such as I want to call calibrate or merge function of Athena in python. Can python glue them together? any document? Jack Song

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How to generate ATOMS file
by milena filadelpho coutinho 04 Dec '08

04 Dec '08

Dear all, I have a simple question.I would like to generate input file (ATOMS) to IFEFFIT. What I have to do? I am still begining my application in EXAFS. thanks Milena. _________________________________________________________________ Confira vídeos com notícias do NY Times, gols direto do Lance, videocassetadas e muito mais no MSN Video! http://video.msn.com/?mkt=pt-br

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remove text
by Guvenc Akgul (gakgul) 02 Dec '08

02 Dec '08

dear all, i have a simple question.I would like to remove texts on graphics window at athena.what can i do this?? thanks guvenc

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Re: [Ifeffit] about wolframite crystallographic file (Ravel, Bruce)
by Yordy Licea Fonseca 26 Nov '08

26 Nov '08

Hi all, In my case, Artemis version 0.8.012 (c), the error in Echo is just: "Artemis trapped one or more errors! Error message dumped to screen." Thank you very much, the problem is solved the way Dominik and Carl have suggested. Best regards, Yordy 2008/11/17 <ifeffit-request(a)millenia.cars.aps.anl.gov> > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. Re: about wolframite crystallographic file (Ravel, Bruce) > 2. Re: about wolframite crystallographic file (Dominik Samuelis) > 3. Re: about wolframite crystallographic file (Ponader, Carl W Dr) > 4. Re: [PGPLOT build problem] Upgrading to ifeffit-1.2.11b on > Ubuntu from source (Mauro Rovezzi) > 5. Re: [PGPLOT build problem] Upgrading to ifeffit-1.2.11b on > Ubuntu from source (Carlo Segre) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 17 Nov 2008 09:16:25 -0500 > From: "Ravel, Bruce" <bravel(a)bnl.gov> > Subject: Re: [Ifeffit] about wolframite crystallographic file > To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <8FA2653072F45348BC6E32FEB95CDC62D3D1(a)exchangemb5.bnl.gov> > Content-Type: text/plain; charset="iso-8859-1" > > > Yordy, > > I'll look into this when I get a chance, but that might not be until later > in the week (I am on travel at the moment). > > B > > -- > Bruce Ravel ----------------------------------- bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Methods Group at Brookhaven National Laboratory > Building 535A > Upton NY, 11973 > > My homepage: http://cars9.uchicago.edu/~ravel > EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/ > > > > > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov on behalf of Yordy Licea > Fonseca > Sent: Sat 11/15/2008 6:36 PM > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] about wolframite crystallographic file > > Hi all, > > As soon as I load this attached CIF crystallographic file from ISCD in > Artemis0.8.012 the software says: > "Artemis trapped one or more errors! Error message dumped to screen." > I can`t go on runnig Atoms as it seems to be a problem with the file. I > have > read the suggestion made in FAQ, but I can not manage to find the error. > Could you help me, please? > It would be nice once the problem been fixed to add this structure to > Matt's > atoms.inp database. > > Thanks you very much, Yordy > > -- > Yordy E. Licea Fonseca > Departamento de F?sico-Qu?mica > Instituto de Qu?mica-IQ/UFRJ > Laborat?rio de Cat?lise Heterog?nea > Rio de Janeiro, RJ, CEP 21.949-909 > Brasil > Email: yliceafonseca(a)gmail.com > >

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Re: [Ifeffit] Hexagonal WO3 (Carlo Segre)
by Yordy Licea Fonseca 26 Nov '08

26 Nov '08

Hi Carlo and Ying, Does it means that if the sample is a random solid solution at experimental temperature, in principle, you would be able to simulate the EXAFS spectra whichever be the Mo/W ratio in the second shell coordination in the Feff.inp, am I right? Thanks, Yordy 2008/11/18 <ifeffit-request(a)millenia.cars.aps.anl.gov> > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. Re: [PGPLOT build problem] Upgrading to ifeffit-1.2.11b on > Ubuntu from source (Matt Newville) > 2. Ifeffit 1.2.11c (was Re: [PGPLOT build problem] Upgrading to > ifeffit-1.2.11b on Ubuntu from source) (Matt Newville) > 3. Re: Ifeffit 1.2.11c (was Re: [PGPLOT build problem] Upgrading > to ifeffit-1.2.11b on Ubuntu from source) (Carlo Segre) > 4. Re: Ifeffit 1.2.11c (was Re: [PGPLOT build problem] Upgrading > to ifeffit-1.2.11b on Ubuntu from source) (Matt Newville) > 5. Hexagonal WO3 (Ying Zhou, Anorganisch-Chemisches Inst.) > 6. Re: Hexagonal WO3 (Carlo Segre) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 17 Nov 2008 12:30:20 -0600 > From: "Matt Newville" <newville(a)cars.uchicago.edu> > Subject: Re: [Ifeffit] [PGPLOT build problem] Upgrading to > ifeffit-1.2.11b on Ubuntu from source > To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: > <b8522e3d0811171030o2db1e183va43b9dcb4d99705e(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi, > > This is my fault... and I apologize for the sloppiness and for being > late in fixing this. I've been mixing 'development/testing' and > 'production' versions, and haven't been very good at keeping them > cleanly separated. I think I have this mostly under control now, > but I will have to work on a decent "test suite". > > I think I found another reason to make a 1.2.11c version too, that the > mixing of "devel" and "production" > caused an experiment in how fitting was done to be the default, so > that the reported chi-square doesn't actually match the documentation > (instead of summing real and imaginary parts, it sums real and > magnitude components of the misfit, which is part of an experiment to > see how Feff8.5 worked for XAFS. Using Magnitude as well Phase for > another way to report chi-square and misfits is potentially a useful > approach, but it's not what is documented. Anyway, mixing devel and > production versions like this (for the past couple years, really) is > very sloppy on my part, and I apologize again. > > I actually have an ubuntu box now, though I built pgplot from source, > and have never made a .deb file. > There is a new source kit at > http://cars.uchicago.edu/~ifeffit/src/ifeffit-1.2.11c.tar.gz I'll > post this to sourceforge this afternoon, and I'll also make a new DLL > for Windows and post all of these on the download page. I'll also make > a new updater for Windows. > > --Matt > > > On Mon, Nov 17, 2008 at 10:07 AM, Mauro Rovezzi <rovezzi(a)esrf.fr> wrote: > > Carlo Segre wrote: > >> > >> Hi Mauro: > >> > >> I have now produced a package of ifeffit 1.2.11b. It is in Debian > >> unstable and available for Ubuntu intrepid and jaunty in my repository > >> > >> deb http://debian-xray.iit.edu intrepid main contrib non-free > > > > Carlo, > > > > Thank you very much for the package. > > > > Actually, I was able to build/install ifeffit 1.2.11b from source but > > not able to build than the Perl/Python wrappers and so no Horae&Friends > > from Bruce SVN. > > > > Well, now I have "pgplot5", "ifeffit", "perl-ifeffit" and > > "python-ifeffit" from binaries and "libperlxray" "horae" and "demeter" > > built from source (Bruce SVN). > > > > Everything seems fine but I still do not understand why ifeffit 1.2.11 > > has all these "IFF str = *" output as stated also by Gareth in his > > "Ifeffit 1.2.11b terminal output" post. Is it normal? > > > > Cheers, > > Mauro > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > > > ------------------------------ > > Message: 2 > Date: Mon, 17 Nov 2008 17:06:35 -0600 > From: "Matt Newville" <newville(a)cars.uchicago.edu> > Subject: [Ifeffit] Ifeffit 1.2.11c (was Re: [PGPLOT build problem] > Upgrading to ifeffit-1.2.11b on Ubuntu from source) > To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: > <b8522e3d0811171506h438ba6abke90121bbb1744818(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi Folks, > > I've uploaded source kits for Ifeffit 1.2.11c to the cars.uchicago.edu > and sourceforge.net download sites. > > I have a Windows dll made for this bug fix version. If anyone is > interested, this is currently at > http://cars.uchicago.edu/~ifeffit/updates/011/bin/ifeffit_12.dll > > This should be a drop-in replacement for the > IFEFFIT_DIR\bin\ifeffit_12.dll on your system. > Artemis.exe will not be updated from this dll, as it has this dlls > "compiled in". Bruce will have to make a new Artemis.exe, and then > we'll make a automatic update. > > Sorry for all the trouble, > > --Matt > > > On Mon, Nov 17, 2008 at 12:30 PM, Matt Newville > <newville(a)cars.uchicago.edu> wrote: > > Hi, > > > > This is my fault... and I apologize for the sloppiness and for being > > late in fixing this. I've been mixing 'development/testing' and > > 'production' versions, and haven't been very good at keeping them > > cleanly separated. I think I have this mostly under control now, > > but I will have to work on a decent "test suite". > > > > I think I found another reason to make a 1.2.11c version too, that the > > mixing of "devel" and "production" > > caused an experiment in how fitting was done to be the default, so > > that the reported chi-square doesn't actually match the documentation > > (instead of summing real and imaginary parts, it sums real and > > magnitude components of the misfit, which is part of an experiment to > > see how Feff8.5 worked for XAFS. Using Magnitude as well Phase for > > another way to report chi-square and misfits is potentially a useful > > approach, but it's not what is documented. Anyway, mixing devel and > > production versions like this (for the past couple years, really) is > > very sloppy on my part, and I apologize again. > > > > I actually have an ubuntu box now, though I built pgplot from source, > > and have never made a .deb file. > > There is a new source kit at > > http://cars.uchicago.edu/~ifeffit/src/ifeffit-1.2.11c.tar.gz I'll > > post this to sourceforge this afternoon, and I'll also make a new DLL > > for Windows and post all of these on the download page. I'll also make > > a new updater for Windows. > > > > --Matt > > > > > > On Mon, Nov 17, 2008 at 10:07 AM, Mauro Rovezzi <rovezzi(a)esrf.fr> wrote: > >> Carlo Segre wrote: > >>> > >>> Hi Mauro: > >>> > >>> I have now produced a package of ifeffit 1.2.11b. It is in Debian > >>> unstable and available for Ubuntu intrepid and jaunty in my repository > >>> > >>> deb http://debian-xray.iit.edu intrepid main contrib non-free > >> > >> Carlo, > >> > >> Thank you very much for the package. > >> > >> Actually, I was able to build/install ifeffit 1.2.11b from source but > >> not able to build than the Perl/Python wrappers and so no Horae&Friends > >> from Bruce SVN. > >> > >> Well, now I have "pgplot5", "ifeffit", "perl-ifeffit" and > >> "python-ifeffit" from binaries and "libperlxray" "horae" and "demeter" > >> built from source (Bruce SVN). > >> > >> Everything seems fine but I still do not understand why ifeffit 1.2.11 > >> has all these "IFF str = *" output as stated also by Gareth in his > >> "Ifeffit 1.2.11b terminal output" post. Is it normal? > >> > >> Cheers, > >> Mauro > >> _______________________________________________ > >> Ifeffit mailing list > >> Ifeffit(a)millenia.cars.aps.anl.gov > >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > >> > >> > > > > > ------------------------------ > > Message: 3 > Date: Mon, 17 Nov 2008 20:03:06 -0600 (CST) > From: Carlo Segre <segre(a)iit.edu> > Subject: Re: [Ifeffit] Ifeffit 1.2.11c (was Re: [PGPLOT build problem] > Upgrading to ifeffit-1.2.11b on Ubuntu from source) > To: Matt Newville <newville(a)cars.uchicago.edu> > Cc: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <alpine.DEB.2.00.0811172002240.3650(a)hydride.iit.edu> > Content-Type: text/plain; charset=us-ascii; format=flowed > > > Debian packages have been uploaded to unstable and I am in the process of > building Ubuntu packages for my repository. i expect that they will be up > tonight. > > carlo > > On Mon, 17 Nov 2008, Matt Newville wrote: > > > Hi Folks, > > > > I've uploaded source kits for Ifeffit 1.2.11c to the cars.uchicago.edu > > and sourceforge.net download sites. > > > > I have a Windows dll made for this bug fix version. If anyone is > > interested, this is currently at > > http://cars.uchicago.edu/~ifeffit/updates/011/bin/ifeffit_12.dll > > > > This should be a drop-in replacement for the > > IFEFFIT_DIR\bin\ifeffit_12.dll on your system. > > Artemis.exe will not be updated from this dll, as it has this dlls > > "compiled in". Bruce will have to make a new Artemis.exe, and then > > we'll make a automatic update. > > > > Sorry for all the trouble, > > > > --Matt > > > > > > On Mon, Nov 17, 2008 at 12:30 PM, Matt Newville > > <newville(a)cars.uchicago.edu> wrote: > >> Hi, > >> > >> This is my fault... and I apologize for the sloppiness and for being > >> late in fixing this. I've been mixing 'development/testing' and > >> 'production' versions, and haven't been very good at keeping them > >> cleanly separated. I think I have this mostly under control now, > >> but I will have to work on a decent "test suite". > >> > >> I think I found another reason to make a 1.2.11c version too, that the > >> mixing of "devel" and "production" > >> caused an experiment in how fitting was done to be the default, so > >> that the reported chi-square doesn't actually match the documentation > >> (instead of summing real and imaginary parts, it sums real and > >> magnitude components of the misfit, which is part of an experiment to > >> see how Feff8.5 worked for XAFS. Using Magnitude as well Phase for > >> another way to report chi-square and misfits is potentially a useful > >> approach, but it's not what is documented. Anyway, mixing devel and > >> production versions like this (for the past couple years, really) is > >> very sloppy on my part, and I apologize again. > >> > >> I actually have an ubuntu box now, though I built pgplot from source, > >> and have never made a .deb file. > >> There is a new source kit at > >> http://cars.uchicago.edu/~ifeffit/src/ifeffit-1.2.11c.tar.gz I'll > >> post this to sourceforge this afternoon, and I'll also make a new DLL > >> for Windows and post all of these on the download page. I'll also make > >> a new updater for Windows. > >> > >> --Matt > >> > >> > >> On Mon, Nov 17, 2008 at 10:07 AM, Mauro Rovezzi <rovezzi(a)esrf.fr> > wrote: > >>> Carlo Segre wrote: > >>>> > >>>> Hi Mauro: > >>>> > >>>> I have now produced a package of ifeffit 1.2.11b. It is in Debian > >>>> unstable and available for Ubuntu intrepid and jaunty in my repository > >>>> > >>>> deb http://debian-xray.iit.edu intrepid main contrib non-free > >>> > >>> Carlo, > >>> > >>> Thank you very much for the package. > >>> > >>> Actually, I was able to build/install ifeffit 1.2.11b from source but > >>> not able to build than the Perl/Python wrappers and so no Horae&Friends > >>> from Bruce SVN. > >>> > >>> Well, now I have "pgplot5", "ifeffit", "perl-ifeffit" and > >>> "python-ifeffit" from binaries and "libperlxray" "horae" and "demeter" > >>> built from source (Bruce SVN). > >>> > >>> Everything seems fine but I still do not understand why ifeffit 1.2.11 > >>> has all these "IFF str = *" output as stated also by Gareth in his > >>> "Ifeffit 1.2.11b terminal output" post. Is it normal? > >>> > >>> Cheers, > >>> Mauro > >>> _______________________________________________ > >>> 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 > > > > -- > 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 > > > ------------------------------ > > Message: 4 > Date: Mon, 17 Nov 2008 21:10:51 -0600 > From: "Matt Newville" <newville(a)cars.uchicago.edu> > Subject: Re: [Ifeffit] Ifeffit 1.2.11c (was Re: [PGPLOT build problem] > Upgrading to ifeffit-1.2.11b on Ubuntu from source) > To: segre(a)agni.phys.iit.edu > Cc: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: > <b8522e3d0811171910p4509bdacn3dc6ed65606d9580(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Thanks, Carlo! > > --Matt > > > > > On Mon, Nov 17, 2008 at 8:03 PM, Carlo Segre <segre(a)iit.edu> wrote: > > > > Debian packages have been uploaded to unstable and I am in the process of > > building Ubuntu packages for my repository. i expect that they will be > up > > tonight. > > > > carlo > > > > On Mon, 17 Nov 2008, Matt Newville wrote: > > > >> Hi Folks, > >> > >> I've uploaded source kits for Ifeffit 1.2.11c to the cars.uchicago.edu > >> and sourceforge.net download sites. > >> > >> I have a Windows dll made for this bug fix version. If anyone is > >> interested, this is currently at > >> http://cars.uchicago.edu/~ifeffit/updates/011/bin/ifeffit_12.dll > >> > >> This should be a drop-in replacement for the > >> IFEFFIT_DIR\bin\ifeffit_12.dll on your system. > >> Artemis.exe will not be updated from this dll, as it has this dlls > >> "compiled in". Bruce will have to make a new Artemis.exe, and then > >> we'll make a automatic update. > >> > >> Sorry for all the trouble, > >> > >> --Matt > >> > >> > >> On Mon, Nov 17, 2008 at 12:30 PM, Matt Newville > >> <newville(a)cars.uchicago.edu> wrote: > >>> > >>> Hi, > >>> > >>> This is my fault... and I apologize for the sloppiness and for being > >>> late in fixing this. I've been mixing 'development/testing' and > >>> 'production' versions, and haven't been very good at keeping them > >>> cleanly separated. I think I have this mostly under control now, > >>> but I will have to work on a decent "test suite". > >>> > >>> I think I found another reason to make a 1.2.11c version too, that the > >>> mixing of "devel" and "production" > >>> caused an experiment in how fitting was done to be the default, so > >>> that the reported chi-square doesn't actually match the documentation > >>> (instead of summing real and imaginary parts, it sums real and > >>> magnitude components of the misfit, which is part of an experiment to > >>> see how Feff8.5 worked for XAFS. Using Magnitude as well Phase for > >>> another way to report chi-square and misfits is potentially a useful > >>> approach, but it's not what is documented. Anyway, mixing devel and > >>> production versions like this (for the past couple years, really) is > >>> very sloppy on my part, and I apologize again. > >>> > >>> I actually have an ubuntu box now, though I built pgplot from source, > >>> and have never made a .deb file. > >>> There is a new source kit at > >>> http://cars.uchicago.edu/~ifeffit/src/ifeffit-1.2.11c.tar.gz I'll > >>> post this to sourceforge this afternoon, and I'll also make a new DLL > >>> for Windows and post all of these on the download page. I'll also make > >>> a new updater for Windows. > >>> > >>> --Matt > >>> > >>> > >>> On Mon, Nov 17, 2008 at 10:07 AM, Mauro Rovezzi <rovezzi(a)esrf.fr> > wrote: > >>>> > >>>> Carlo Segre wrote: > >>>>> > >>>>> Hi Mauro: > >>>>> > >>>>> I have now produced a package of ifeffit 1.2.11b. It is in Debian > >>>>> unstable and available for Ubuntu intrepid and jaunty in my > repository > >>>>> > >>>>> deb http://debian-xray.iit.edu intrepid main contrib non-free > >>>> > >>>> Carlo, > >>>> > >>>> Thank you very much for the package. > >>>> > >>>> Actually, I was able to build/install ifeffit 1.2.11b from source but > >>>> not able to build than the Perl/Python wrappers and so no > Horae&Friends > >>>> from Bruce SVN. > >>>> > >>>> Well, now I have "pgplot5", "ifeffit", "perl-ifeffit" and > >>>> "python-ifeffit" from binaries and "libperlxray" "horae" and "demeter" > >>>> built from source (Bruce SVN). > >>>> > >>>> Everything seems fine but I still do not understand why ifeffit 1.2.11 > >>>> has all these "IFF str = *" output as stated also by Gareth in his > >>>> "Ifeffit 1.2.11b terminal output" post. Is it normal? > >>>> > >>>> Cheers, > >>>> Mauro > >>>> _______________________________________________ > >>>> 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 > >> > > > > -- > > 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 > > > > > > > ------------------------------ > > Message: 5 > Date: Tue, 18 Nov 2008 17:20:24 +0100 > From: "Ying Zhou, Anorganisch-Chemisches Inst." <ying.zhou(a)aci.uzh.ch> > Subject: [Ifeffit] Hexagonal WO3 > To: ifeffit(a)millenia.cars.aps.anl.gov > Message-ID: <web-16292974(a)idmailbe2b.unizh.ch> > Content-Type: text/plain;charset=iso-8859-1;format="flowed" > > Dear All > > Recently, I got one compound, W/Mo oxide, which has the similar structure > with hexagonal WO3. We tested the EXAFS of W L3 edge and Mo K edge of this > compound. So, we use the hexagonal WO3 model to refine the structure of our > compounds. My question is that how can I get the FEFF file of this > compound. > Can I directly change some of W to Mo in FEFF file? or Do I need to add the > Mo in the atom file? I do appreciate your help. > > Best wishes > Ying > > > ------------------------------ > > Message: 6 > Date: Tue, 18 Nov 2008 10:33:35 -0600 (CST) > From: Carlo Segre <segre(a)iit.edu> > Subject: Re: [Ifeffit] Hexagonal WO3 > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <alpine.DEB.2.00.0811181023390.19806(a)oxide.phys.iit.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > > Hi Ying: > > On Tue, 18 Nov 2008, Ying Zhou, Anorganisch-Chemisches Inst. wrote: > > > Dear All > > > > Recently, I got one compound, W/Mo oxide, which has the similar structure > > with hexagonal WO3. We tested the EXAFS of W L3 edge and Mo K edge of > this > > compound. So, we use the hexagonal WO3 model to refine the structure of > our > > compounds. My question is that how can I get the FEFF file of this > compound. > > Can I directly change some of W to Mo in FEFF file? or Do I need to add > the > > Mo in the atom file? I do appreciate your help. > > > > There are several ways to do this, depending on what you are trying to > find out. If you change W to Mo in the atoms input file than you are > really making MoO3. What it seems like you need to do is to generate the > FEFF input file from the WO3 structure, then replace the central atom with > Mo. This will give you the first path which is likely oxygen. The second > longest set of paths are likely to be W/Mo and you can do two things, one > is to generate a FEFF calculation with W in this position and then make a > second calculation with Mo and use both paths to fit the Mo environment. > You will have to be careful about multiplicities though since by starting > with the WO3 structure, you are assuming some degeneracies in the paths. > The advantage is that you potentially have some multiple scatteing paths > available to use. > > Another approach is to generate the FEFF input file from WO3, look at the > near neighbors and then generate some "quick first shell" paths for the > nearest neighbor (oxygen) and then two fro the next near neighbor (one > with W and one with Mo). The difference here is that you now have > uncorrelated paths with no implied degeneracies. You cannot use this to > fit multiple scattering paths. > > I guess that my approach would be to start with the latter, more simple > approach first to try to understand the problem. If I see that the > environment looks like it is possible to fit with multiple scattering, I > would move to the first approach, being careful to realize that in a solid > sloution compound, the occupancy of the second shell of metal atoms is > probably random and not perfectly ordered like a FEFF input file with > substitutions would be. > > Hope this helps. > > 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 > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 69, Issue 13 > *************************************** > -- Yordy E. Licea Fonseca Departamento de Físico-Química Instituto de Química-IQ/UFRJ Laboratório de Catálise Heterogênea Rio de Janeiro, RJ, CEP 21.949-909 Brasil Email: yliceafonseca(a)gmail.com

3 3

Athena problem with integration in Difference of Normalized Spectra (norm(E))
by Zajac, Dariusz 19 Nov '08

19 Nov '08

Hi All, first - I am using Athena 0.8.054 under Windows XP and Adam 0.8.057 under Linux We have checked this problem at 2 computers. I played a little bit with Analysis function - Difference Spectra - norm(E) It works fine when I work with one group - it plots spectrum, difference and program computes the difference and the integral. Now, I want to do the same for marked groups - it computes and makes as new groups the difference spectra. If I want to compute also integrals for marked groups program does not execute operation. Simply it does nothing, or tries to do something with the first marked group, but without result. the error message from shell window is like that: for Athena 0.8.057 Linux: Tk::Error: Can't upgrade that kind of scalar at /usr/bin/athena line 12950. main::diff_marked at /usr/bin/athena line 12950 main::__ANON__ at /usr/bin/athena line 12614 Tk callback for .frame1.frame1.frame2.button Tk::__ANON__ at /usr/lib/perl5/vendor_perl/5.8.8/i386-linux-thread-multi/Tk.pm line 250 Tk::Button::butUp at /usr/lib/perl5/vendor_perl/5.8.8/i386-linux-thread-multi/Tk/Button.pm line 175 <ButtonRelease-1> (command bound to event) and for Athena 0.8.054 Windows Tk::Error: Can't upgrade that kind of scalar at athena line 12863. main::diff_marked at athena line 12863 main::__ANON__ at athena line 12527 Tk callback for .frame1.frame2.frame2.button Tk::__ANON__ at /PerlApp/Tk.pm line 252 Tk::Button::butUp at /PerlApp/Tk/Button.pm line 111 <ButtonRelease-1> (command bound to event) cheers darek and adam ------------------------------------------------------------------------ dr. Zajac Dariusz A. Deutsches Elektronen-Synchrotron -Hasylab phone: +49-40-8998-2932 Notkestr. 85 fax: +49-40-8998-2787 22607 Hamburg e-mail: dariusz.zajac(a)desy.de Germany ------------------------------------------------------------------------

2 1

Hexagonal WO3
by Ying Zhou, Anorganisch-Chemisches Inst. 18 Nov '08

18 Nov '08

Dear All Recently, I got one compound, W/Mo oxide, which has the similar structure with hexagonal WO3. We tested the EXAFS of W L3 edge and Mo K edge of this compound. So, we use the hexagonal WO3 model to refine the structure of our compounds. My question is that how can I get the FEFF file of this compound. Can I directly change some of W to Mo in FEFF file? or Do I need to add the Mo in the atom file? I do appreciate your help. Best wishes Ying

2 1

Ifeffit 1.2.11c (was Re: [PGPLOT build problem] Upgrading to ifeffit-1.2.11b on Ubuntu from source)
by Matt Newville 18 Nov '08

18 Nov '08

Hi Folks, I've uploaded source kits for Ifeffit 1.2.11c to the cars.uchicago.edu and sourceforge.net download sites. I have a Windows dll made for this bug fix version. If anyone is interested, this is currently at http://cars.uchicago.edu/~ifeffit/updates/011/bin/ifeffit_12.dll This should be a drop-in replacement for the IFEFFIT_DIR\bin\ifeffit_12.dll on your system. Artemis.exe will not be updated from this dll, as it has this dlls "compiled in". Bruce will have to make a new Artemis.exe, and then we'll make a automatic update. Sorry for all the trouble, --Matt On Mon, Nov 17, 2008 at 12:30 PM, Matt Newville <newville(a)cars.uchicago.edu> wrote: > Hi, > > This is my fault... and I apologize for the sloppiness and for being > late in fixing this. I've been mixing 'development/testing' and > 'production' versions, and haven't been very good at keeping them > cleanly separated. I think I have this mostly under control now, > but I will have to work on a decent "test suite". > > I think I found another reason to make a 1.2.11c version too, that the > mixing of "devel" and "production" > caused an experiment in how fitting was done to be the default, so > that the reported chi-square doesn't actually match the documentation > (instead of summing real and imaginary parts, it sums real and > magnitude components of the misfit, which is part of an experiment to > see how Feff8.5 worked for XAFS. Using Magnitude as well Phase for > another way to report chi-square and misfits is potentially a useful > approach, but it's not what is documented. Anyway, mixing devel and > production versions like this (for the past couple years, really) is > very sloppy on my part, and I apologize again. > > I actually have an ubuntu box now, though I built pgplot from source, > and have never made a .deb file. > There is a new source kit at > http://cars.uchicago.edu/~ifeffit/src/ifeffit-1.2.11c.tar.gz I'll > post this to sourceforge this afternoon, and I'll also make a new DLL > for Windows and post all of these on the download page. I'll also make > a new updater for Windows. > > --Matt > > > On Mon, Nov 17, 2008 at 10:07 AM, Mauro Rovezzi <rovezzi(a)esrf.fr> wrote: >> Carlo Segre wrote: >>> >>> Hi Mauro: >>> >>> I have now produced a package of ifeffit 1.2.11b. It is in Debian >>> unstable and available for Ubuntu intrepid and jaunty in my repository >>> >>> deb http://debian-xray.iit.edu intrepid main contrib non-free >> >> Carlo, >> >> Thank you very much for the package. >> >> Actually, I was able to build/install ifeffit 1.2.11b from source but >> not able to build than the Perl/Python wrappers and so no Horae&Friends >> from Bruce SVN. >> >> Well, now I have "pgplot5", "ifeffit", "perl-ifeffit" and >> "python-ifeffit" from binaries and "libperlxray" "horae" and "demeter" >> built from source (Bruce SVN). >> >> Everything seems fine but I still do not understand why ifeffit 1.2.11 >> has all these "IFF str = *" output as stated also by Gareth in his >> "Ifeffit 1.2.11b terminal output" post. Is it normal? >> >> Cheers, >> Mauro >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> >> >

2 2

[PGPLOT build problem] Upgrading to ifeffit-1.2.11b on Ubuntu from source
by Mauro Rovezzi 17 Nov '08

17 Nov '08

Dear all, I decided to upgrade ifeffit-1.2.11 on my Ubuntu 8.10 (Intrepid Ibex) desktop machine. Well, up to now I have always worked with PGPLOT & Ifeffit binaries from Carlo that are just working fine but seen that they are still not ready for the new version I decided to build them by source. First of all let me say that Ifeffit builds fine if I use the "pgplot5" binary package, BUT, as stated by Matt in the README.PGPLOT, Ifeffit will compile without plotting support in this case. So the only way is to build also PGPLOT from source. Unfortunately the experience has failed both with the "PGPLOT_install" script and following steps in the "install-unix.txt". I have tried many possibilities but the make process interrupts on the drivers compilations. Seen that following "install-unix.txt" gives the same error (but on another driver!) of "PGPLOT_install", let's focus on this last procedure to try debugging the situation: $sudo ./PGPLOT_install ... [all fine until the PGPLOT make] [long list of errors + warnings like:] ... /home/mauro/local/ifeffit-1.2.11/pgplot/drivers/xwdriv_iff.c:4445: error: ‘XWdev’ has no member named ‘gc’ ... make: *** [xwdriv_iff.o] Error 1 ... [then the final error due to the bad compilation] collect2: ld returned 1 exit status make: *** [pgdemo1] Error 1 OK, I have described more or less the situation but I would not flood the list with technical mails, so if someone would help me with this issue we can continue in private and then send just the solution to the list. Anyway, the problem is not "urgent" seen that I can work with the 1.2.10 binary installation. Have a nice day! Mauro -- Mauro Rovezzi <rovezzi(a)esrf.fr> PhD student - GILDA BM08 c/o ESRF (Grenoble, FR)

4 7

about wolframite crystallographic file
by Yordy Licea Fonseca 17 Nov '08

17 Nov '08

Hi all, As soon as I load this attached CIF crystallographic file from ISCD in Artemis0.8.012 the software says: "Artemis trapped one or more errors! Error message dumped to screen." I can`t go on runnig Atoms as it seems to be a problem with the file. I have read the suggestion made in FAQ, but I can not manage to find the error. Could you help me, please? It would be nice once the problem been fixed to add this structure to Matt's atoms.inp database. Thanks you very much, Yordy -- Yordy E. Licea Fonseca Departamento de Físico-Química Instituto de Química-IQ/UFRJ Laboratório de Catálise Heterogênea Rio de Janeiro, RJ, CEP 21.949-909 Brasil Email: yliceafonseca(a)gmail.com

4 3

Co doped ZnO
by Guvenc Akgul (gakgul) 16 Nov '08

16 Nov '08

dear all, I have 10%Co doped ZnO EXAFS data and I would like to figure out :Co-Co distance in the 10%Co doped ZnO.what will i do for this?if you can help to me about this i will be very glad. thanks all guvenc

2 1

Sealed Sample Cell
by Bhoopesh Mishra 12 Nov '08

12 Nov '08

Dear All, I am planning to conduct an EXAFS experiment which involves dealing with methyl mercury. Obviously, I want to be as cautious as I can in sealing the sample. In that connection, I am wondering if anyone on this forum can advise me regarding the best way to have a completely sealed (air tight) sample holder. My requirements are given below. Third requirement is not as important as the first two. 1. Sample cell (or the front and rear exit) should be made of low scattering material that would not attenuate photons too much at ~ 10-12 keV. 2. The sample cell should be a perfectly sealed, as gaseous phase methyl mercury or even di-methyl mercury could be produced in the cell. 3. I would like to inject solution using syringe in the sealed sample holder (if possible, this requirement is not necessary). Among several possibilities, I am thinking of designing a cuvette shaped rectangular box with a thin bottom section, and probably using some sort of polypropylene such that scattering is as low as possible. It should be easy to put two silicon rubber septa on the top. Other possibility could be using a thick Beryllium window (and please forgive my naivete' here - isn't there some restriction in using Be) on both the front and back of a rectangular or cylindrical box with rubber stopper at the top. The easiest and probably the best would be to have a commercially available sample cell that can serve my purpose. I don't know any commercially available product like that. But I suspect, people who work with volatile material and/or radioactive material might know a lot about it. If you know anything, please write me back. Any comments, suggestions, or criticism would be highly appreciated. PS: Sealing with kapton tape (or any other thin film) might not be enough in this case as gaseous phase methyl mercury might diffuse through kapton, and also air might diffuse through kapton making the inside of the cell environment aerobic while I need to do this experiment anaerobically. Thanks for your help! Bhoopesh

3 2

problem on opening data file
by Ruoshuang Huang 11 Nov '08

11 Nov '08

Hello All, Recently I found that I could not open my EXAFS data files using Athena any more. Previously I had no problem using Athena to do data analysis (the last time was in last year). Now when I try to open a data file, a small window appears saying this file 'could not be read by ifeffit as a data file'. This happened to both the old data files that could be opened previously and new ones that were obtained recently. All the raw data were taken on beamline X10C at NSLS in the format of .xfs. I appreciate it if someone could help and give me some suggestions. I've attached one of my data files as an example. Thank you so much, Ruoshuang

5 4

Athena's application
by abhijeet gaur 06 Nov '08

06 Nov '08

> I am doing my research work on EXAFS . For > that I am using the software ATHENA for analyzing my data > which my guide had brought from SSRL ( USA ) . But there is > some problem in that , Athena is taking the data and > plotting it but is not giving the required parameters. I am > sending you the copy of that data . So if you can go through > it and suggest me what is the problem , I wil be very > thankfull . > > > > > > > Did you know? You can CHAT without downloading > messenger. Go to http://in.webmessenger.yahoo.com/ Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/

2 1

Synchrotron Environmental Science meeting, Dec 11-13th, 2008 San Francisco CA
by Peter Nico 06 Nov '08

06 Nov '08

Hello All, I thought some readers of this list might be interested in the Synchrotron Environmental Science meeting described below and at the following link. http://esd.lbl.gov/sesIV08/index.html Even if I do say so myself, I think its going to be a very interesting conference form both a synchrotron science and environmental science point of view. Plus, its always nice to go to California in the winter. :) Thanks. --Peter *Synchrotron Environmental Science IV (SES-IV) Meeting, December 11 -- 13, 2008* <http://esd.lbl.gov/sesIV08/> * PREREGISTRATION DEADLINE IS NOV 14!* After Nov. 14, registration fees will increase. Please register at: http://www.regonline.com/Checkin.asp?EventId=649848 *PROGRAM HIGHLIGHTS INCLUDE:* * Key note perspective talks on CO2 sequestration, atmospheric chemistry, environmental remediation science, and marine sciences from world-leading scientists, with emphasis on the potential roles of synchrotron techniques. * Talks on new and emerging synchrotron techniques * Talks on developments in data acquisition hardware and software * Hands-on sessions at SSRL and ALS beam lines for prospective and new users * Introductory-level talks for prospective and new users * Facility reports from North American synchrotron sources * Poster session * * *CONFERENCE HOTEL INFORMATION -- Lodging Deadline is NOVEMBER 14* The lodging deadline for the Conference Hotel is also November 14th, however space is limited and is not guaranteed. The $152.00/per night rate at the Westin is actually less than the Government allowable in San Francisco of $164.00. Also, our rate is even lower than that offered through AGU of $164/night. You may extend your stay through the entire AGU session. You can make your lodging reservations for the Conference hotel by visiting: http://esd.lbl.gov/sesIV08/accomodations.html * ** KEY DATES:* *Early Discount Registration Closes November 14, 2008 Discount Lodging Registration Closes November 14, 2008* SES IV Conference Dates December 11 -- 13, 2008 Hands on Sessions December 11, 2008 Poster Session Evening, December 12, 2008 *COMPLETE MEETING PROGRAM* The complete Synchrotron Environmental Science IV (SES-IV) 2008 Meeting agenda is available at: http://esd.lbl.gov/sesIV08/program.html As you will see, the conference has a very exciting program! *HANDS ON SESSION:* On Thursday, December 11, there will be a tour and hands on training at beam lines at ALS or SSRL See web for more details and to enroll: http://esd.lbl.gov/sesIV08/session.html *QUESTIONS?* Please direct all questions or comments to CAValladao(a)lbl.gov. Best Regards, SES-IV 2008 Organizing Committee

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