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

Elise Fox is out of the office.
by Elise.Fox＠srnl.doe.gov 01 Oct '07

01 Oct '07

I will be out of the office starting 10/01/2007 and will not return until 10/08/2007. I will respond to your message when I return.

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Position available within the Molecular Environmental Science Group at Argonne National Laboratory
by Kenneth Kemner 27 Sep '07

27 Sep '07

Job Advertisement 312365 BIO – Assistant Physicist The Molecular Environmental Science Group in the Biosciences Division at Argonne National Laboratory has an immediate opening for an Assistant Physicist. This position is responsible for conducting research in environmental science by using synchrotron-based X-ray techniques. Work includes construction and operation of the MRCAT/ EnviroCAT bending magnet and insertion device beam lines at sector 10 at the Advanced Photon Source (APS), X-ray absorption studies, X-ray scattering, and X-ray microprobe techniques to gain a microscopic understanding of the fundamental chemical and physical processes that govern the outcome of macroscopic processes in the environment. Assists Molecular Environmental Science general users of the APS during the experiments at the APS. Also assists Molecular Environmental Science Group Leader to develop a national users` group for applying synchrotron-based techniques to problems in environmental science. Considerable knowledge of experimental X-ray absorption spectroscopy, including extended X-ray absorption fine-structure spectroscopy (EXAFS), X-ray near-edge spectroscopy (XANES) is required. Considerable skill in the operation of experimental equipment necessary for these and analysis and interpretation of these experiments is required. Good knowledge of X-ray diffraction and imaging techniques and the associated instrumentation. Good knowledge of potential applications of X-ray techniques to the outstanding problems in environmental science. These levels of knowledge and skills are typically achieved by attainment of a Ph.D. in Physics or a related discipline and 2-4 years of Postdoctoral experience applying synchrotron-based X-ray techniques to problems in environmental science. Ph.D. and 0-1 year experience/equivalent Master's Degree and 2-3 years of experience/equivalent Bachelor's Degree and 6-8 years experience/equivalent. Although a staff level research scientist position is available, outstanding applicants at the postdoctoral level will also be considered. Interested candidates should send a detailed CV, along with a list of publications, and the names and addresses of three references through the Argonne web site at http://www.anl.gov/jobs for requisition number 312365 BIO. Argonne is a U.S. Department of Energy laboratory managed by UChicago Argonne, LLC. Argonne is an equal opportunity employer, and we value diversity in our workforce.

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Re: [Ifeffit] Artemis fitting using FEFF paths plus experimentalreferences
by Matthew 25 Sep '07

25 Sep '07

[Ifeffit] Artemis fitting using FEFF paths plus experimentalreferencesOf course I tried PCA! Over a certain range of temperatures, one component looks tolerably like magnetite. The other is sort of, but not exactly, maghemite. However, if I go below that restricted range, it's not pseudobinary anymore. Also, I still don't know what the "maghemite-like" end-member actually is. Still, for the purposes of the ALS user-meeting poster I have to hang in a week or so, I'll probably take the PCA analysis plus a FEFF fit to the one end-member, and try to do a more thorough job when I have time. No, it doesn't fit well to a combo of the references I have, which does include maghemite. To be fair, what I have is not an isothermal series but an isochronal series at different temperatures, so there's less reason for expecting simple kinetics than in an isothermal series. mam ----- Original Message ----- From: Anatoly Frenkel To: MAMarcus(a)lbl.gov Sent: Monday, September 24, 2007 6:59 PM Subject: RE: [Ifeffit] Artemis fitting using FEFF paths plus experimentalreferences Matthew - please forward my reply to the list if you consider it appropriate. I am spammed out. Anatoly ************************* Matthew, May be it is not relevant, since I do not know if you have a series of EXAFS data at different stages of the oxidation, or just the initial and the final stages. If you do have several stages, including the starting (unoxidized) and final (oxidized, or a sum of oxidized and unoxidized, depending where you stopped at) ones, the principal component analysis seems to match your needs well. I assume you also have access to EXAFS data in bulk magnetite and maghemite references. PCA analysis may tell you (if you are lucky and your system is similar to those where such information was previously obtained): 1) The volume fractions of intermediate species at each stage of the oxidation: 2) Identities of each intermediate species The first part is entirely model-independent. The second part is not, but a reasonable selection of standard compounds (e.g., magnetite or maghemite) may help you isolating the intermediates. The good thing is that you do not need to fit a Fe-Fe and Fe-O bonds to the spectrum of the entire heterogeneous sample, where these contributions may be present in different species, and you have a large number of fitting parameters that describe such a model. Instead, you may end up obtaining that your species are identical with their bulk reference compounds (and thus no fit is required since the only thing you need to know is the volume fraction of this species) or, you may have to fit a couple of FEFF paths to that unknown species, after you deconvolute it from the mixture knowing what the rest of the phases are (it is doable in the case of one intermediate, but can be done in the case of a larger number of intermediates as well). Anatoly -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov]On Behalf Of Matthew Sent: Monday, September 24, 2007 7:05 PM To: XAFS Analysis using Ifeffit Subject: [Ifeffit] Artemis fitting using FEFF paths plus experimentalreferences I have a system in which Fe:C alloy nanoparticles are being oxidized. I have the EXAFS of the unoxidized nanoparticles, and I'd like to use that as a reference for fitting as in: Fe_EXAFS(oxidation_stage) = x*(unox_particles)+(1-x)*(Fe->O paths + Fe->Fe paths +...) where the Fe->O and Fe->Fe are based on magnetite and maghemite, which seem to be products of the oxidation. It's not just a linear fit to unoxidized+magnetite+maghemite because the oxide is somewhat disordered. If I do Artemis fits to the shells from the two oxides alone, I find I lose some Fe atoms (sum of fractions < 1), a result which is echoed in linear-combo fits to the oxides alone. Thus, I really want to do a hybrid fit. The unoxidized particles are highly disordered to the point where they don't fit well with reasonable shells, so I'd rather not have to represent them as FEFF shells. How can I do this hybrid fit? mam _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Artemis fitting using FEFF paths plus experimental references
by Matthew 24 Sep '07

24 Sep '07

I have a system in which Fe:C alloy nanoparticles are being oxidized. I have the EXAFS of the unoxidized nanoparticles, and I'd like to use that as a reference for fitting as in: Fe_EXAFS(oxidation_stage) = x*(unox_particles)+(1-x)*(Fe->O paths + Fe->Fe paths +...) where the Fe->O and Fe->Fe are based on magnetite and maghemite, which seem to be products of the oxidation. It's not just a linear fit to unoxidized+magnetite+maghemite because the oxide is somewhat disordered. If I do Artemis fits to the shells from the two oxides alone, I find I lose some Fe atoms (sum of fractions < 1), a result which is echoed in linear-combo fits to the oxides alone. Thus, I really want to do a hybrid fit. The unoxidized particles are highly disordered to the point where they don't fit well with reasonable shells, so I'd rather not have to represent them as FEFF shells. How can I do this hybrid fit? mam

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new Debian/Ubuntu packages
by Carlo Segre 23 Sep '07

23 Sep '07

Hello All: I apologize in advance for the length of this message. if you just want to download the packages the magic lines are at the bottom of this message, so you can just skip down there. I just posted new packages of ifeffit (1.2.10a), horae (066) and sixpack (0.61) in the debian-xray archives. At this point, I am supporting the following distributions and architectures: Debian etch (stable) i386, amd64, powerpc lenny (testing) i386, amd64, powerpc Ubuntu edgy i386, amd64, powerpc feisty i386, amd64, powerpc gutsy i386, amd64 The newest version of ifeffit (1.2.10a) required a new version of pgplot5, with a specific bug fix. This is also in the archive for the above architectures and distributions. A couple of notes about the specific distributions: Debian - If you are running etch/stable, my archive is the way to get these new versions. For the lenny/testing, you can simply wait until the packages migrate from sid/unstable but I have provided them in my archive if you want them sooner. When the migration happens, these packages will be replaced by the official Debian ones. The reason I am doing this is that there are sometimes long delays in the unstable ---> testing migration for ifeffit since it requires the non-free pgplot5 to be built. It is not always present on the Debian build machines (I am trying to make this happen, honest!). Of course, the sid/unstable packages (if you are brave enough to run the bleeding edge Debian system ;-) are in the Debian archives and should come in automagically. Ubuntu - The versions for edgy and feisty are backports. For gutsy, the release being currently prepared, I have built all the packages because the Ubuntu versions seem to be slightly behind those I put in Debian. Again, once the official Ubuntu versions become available they should replace my versions. Anyway, while I have tested the packages, please don't hesitate to email me aobut your problems. Now for the _real_ information. If you want to use these packages, you need to add my repository to your /etc/apt/sources.list or add them through the synaptic package manager if you manage your system in this, more graphical, way. ---- Debian (choose your distribution) deb http://debian-xray.iit.edu etch main contrib non-free deb http://debian-xray.iit.edu lenny main contrib non-free ---- Ubuntu (choose your distribution) deb http://debian-xray.iit.edu edgy main contrib non-free deb http://debian-xray.iit.edu feisty main contrib non-free deb http://debian-xray.iit.edu gutsy main contrib non-free Note that when you upgrade your Ubuntu system, say from edgy to feisty, these sources will not be automatically updated as the Ubuntu lines will. You will have to change them manually. Cheers, 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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Athena merging question...
by Matthew Ginder-Vogel 18 Sep '07

18 Sep '07

Hi Bruce and list, I think I almost have a decent IFEFFIT script for my averaging problem. However, while looking at the IFEFFIT command that Athena uses to merge files I thought of a few questions. When merging the energy scales of the various files, why did you choose to use a quadratic interpolation rather than a linear or spline interpolation? Also, I notice that Athena sends a lot of commands that look like set vpkr.energy = vpkr.energy+0 or set yybe.merge = qinterp(yybe.energy+0, yybe.xmu, vpkr.energy) to IFEFFIT when merging files. What does the +0 do at the end of the array? I've been looking through the IFEFFIT documentation, but can't seem to find anything that clarifies that command. Also, if I try and issue the command at the IFEFFIT command line I get an error that reads "** cannot set scalar value to array **". So why can Athena issue the command and I can't? 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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Elise Fox is out of the office.
by Elise.Fox＠srnl.doe.gov 17 Sep '07

17 Sep '07

I will be out of the office starting 09/17/2007 and will not return until 09/24/2007. I will respond to your message when I return.

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Re: [Ifeffit] Linear Combination Fitting in Athena
by Barton, David (DG) 17 Sep '07

17 Sep '07

Skya, Seeing an example Athena file would help, but my guess is that one or more of your standards are being rejected by the fit (i.e. near zero), when this occurs the LCF routine can finish without the sum forced equal to zero. If this is the case you can just rerun the fit excluding the standard that is near zero and the sum should now equal 1. Dave _________________________________ David Barton, -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Skya Fawcett Sent: Monday, September 17, 2007 3:07 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Linear Combination Fitting in Athena I'm trying to do linear combination fitting on a number of samples, and its working well for the most part, with 4 exceptions. There are 4 samples, of 22, that I can't get to sum to 1, despite the fact that I have "sum to 1" checked off before fitting. I've tried reprocessing the data, and tried reinstalling Athena with no luck. Any ideas? Skya Fawcett PhD Candidate Department of Geological Sciences and Geological Engineering Queen's University, Kingston, Canada _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Linear Combination Fitting in Athena
by Skya Fawcett 17 Sep '07

17 Sep '07

I'm trying to do linear combination fitting on a number of samples, and its working well for the most part, with 4 exceptions. There are 4 samples, of 22, that I can't get to sum to 1, despite the fact that I have "sum to 1" checked off before fitting. I've tried reprocessing the data, and tried reinstalling Athena with no luck. Any ideas? Skya Fawcett PhD Candidate Department of Geological Sciences and Geological Engineering Queen's University, Kingston, Canada

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Re: [Ifeffit] Need your help
by Bruce Ravel 16 Sep '07

16 Sep '07

Hi Jin, I am CCing my response to the Ifeffit mailing list: http://cars9.uchicago.edu/mailman/listinfo/ifeffit/ If you are not already a member of the mailing list, I encourage you to join. It is a great place to ask questions and learn about XAFS and the Ifeffit-based software. On Sunday 16 September 2007, you wrote: > Dear Ravel: > > I am just a student of Shanghai Applied Physics Institute, CSA. And I > meet some problem by using FEFF process. > > When I know the coordination number and the coordination distance of known > structure macular, how to set the atom inp file or feff inp file? I'm afraid that I am little unsure what you exact question is. If you know the coordination number and distance because your material is a known crystal, then you can just use a CIF file or an atoms.inp file of the sort described here: http://cars9.uchicago.edu/~ravel/software/doc/Atoms/Atoms/node4.html or available for many materials at this database: http://cars9.uchicago.edu/~newville/adb/search.html If you know coordination and distances because you have structural information of the sort that you might find in a protein data bank file or some other molecular format, then you should skip the use of atoms and simply convert the molecular data to a feff.inp file as described on page 36 of this talk I recently gave: http://cars9.uchicago.edu/~ravel/talks/pimst2.pdf It is important to remember that Atoms is a tool for converting crystallographic data into a list of atomic coordinates. That's all it does. If you are doing XAFS on something that is not a crystal, Atoms is of no use. > And another question is how get the usefully muffin tin from the XRD data > in the protein data bank? Feff computes muffin tins. In 99% of all situations, you do not need to modify how Feff does tht nor do you need to specify muffin tin radii. Feff's algorithm for determining muffin tin radii given a list of atomic coordinates is relatively simple, but surprisingly effective and completely automated. > I have tried many time as the handbook shows, but I also don't know how to > do? So I need your help ? Thank you very much You may find it useful to ask explicit questions on the mailing list by posting examples of the problem you are having. For instance, if you are having trouble running Feff, asking a question about the exact thing that is confusing and posting an example of the feff.inp file that is giving you trouble will help the people on the mailing list help you. Good luck and I hope this was helpful, Bruce > Smiling everyday, > > Best wishes, > > Jin Chan -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advance Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/

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