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

Re: [Ifeffit] space group C-1
by Ravel, Bruce 10 Oct '07

10 Oct '07

Nan, You haven't quite given me enough information to actually help. In this case, I'd need to see the crystallographic reference, or at least the input data, for the problem at hand. This is point #5 at http://cars9.uchicago.edu/~ravel/software/bugs.html. B -- Bruce Ravel ----------------------------------- bravel(a)bnl.gov My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/ -----Original Message----- From: Nan Jiang [mailto:Nan.Jiang@asu.edu] Sent: Tue 10/9/2007 5:59 PM To: bravel(a)anl.gov Subject: space group C-1 Dear Dr Ravel I use Atoms to generate clusters for FEFF calculations. My space group is C-1, which is not included in your table. I tried to use P-1 instead, but it does not work properly. There are four symmetries in C-4, but only 2 in P-1. Could you advise me on this? Thanks for your time. Nan Jiang

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Intel Mac release of latest horae package 066
by Paul Fons 04 Oct '07

04 Oct '07

I know Jeff Terry is busy and I wanted the latest release for the Intel Mac my own purposes so I built a release using the traditional (/Applications/Ifeffit) file structure (I said I needed quickly, right?) using gfortran. The new installer is on the sourceforge site under the ifeffit project (http://downloads.sourceforge.net/ifeffit/ Ifeffit-1.2.10-Mac10.4_Intel_horae66.dmg?use_mirror=osdn). I will update the Wiki as well to the new release. As I said, I made the release for myself and am sharing it -- meaning I have only tested it on the system I built it on (Mac Pro) and my Mac Book Pro laptop (for which I used the installer). It works on both of these systems just fine, but they are of course setup in a similar way. If anyone has any problems let me know (although I have an extended series of synchrotron runs coming up and my focus will be on my (day and night) job. Note that you *must* have installed the X11 environment (an optional install located on the restore disks that come with new Macs) for this to work (it runs under X11). Paul Dr. Paul Fons Nano-Optics Reseach Team Team Leader National Institute for Advanced Industrial Science & Technology METI Center for Applied Near-Field Optics Research (CANFOR) AIST Central 4, Higashi 1-1-1 Tsukuba, Ibaraki JAPAN 305-8568 tel. +81-298-61-5636 fax. +81-298-61-2939 email: paul-fons(a)aist.go.jp The following lines are in a Japanese font 〒305-8562 茨城県つくば市つくば中央東 1-1-1 産業技術総合研究所近接場光応用工学研究センター近接場光基礎研究チーム　チーム長ポール・フォンス

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SCC Mailing List
by Anatoly Frenkel 04 Oct '07

04 Oct '07

Hello all: Our group, Synchrotron Catalysis Consortium, or SCC, at the NSLS has started a mailing list (SCC-Forum) to provide our users with an opportunity to discuss problems that are specific to nanocatalysis science. Most of our users come to SCC to perform in situ XAFS in catalysis reactors, collect time-resolved data, analyze low dimensional systems (e.g., nanoparticles, monolayers, nanorods, and their real time reactivity, as just a few examples) and thus may benefit from a specialized forum where these issues are addressed in depth. Postings by our list members would facilitate discussions of experimental setups needed to study a specific catalysis problem, experimental regimes, typical experimental pitfalls in these type of measurements and how to avoid them, data modeling tricks and know-how, etc. The purpose of the list is to help each other and the SCC group here at the NSLS by sharing your experience and stimulate further development of catalysis science done by XAFS and other synchrotron techniques. For those who are not familiar with SCC, a good starting point describing our activities is: http://www.yu.edu/scc. To subscribe to the SCC mailing list, and start receiving and sending postings, use as the entry point the main SCC web page: http://www.yu.edu/scc and click at the SCC Discussion Forum link in the bottom right. Note that you may choose to receive daily digests of the postings; regardless of your choice, you can access the message archives by logging in to the list using the main entry point above. The interface is the same as IFEFFIT; in fact, Matt kindly helped me to configure it to have the same settings as IFEFFIT, to make it easier for those who wants to subscribe to the both lists. Perhaps, such specialized lists could be set up in the future by other groups using XAFS, say, life sciences and environmental sciences, who will continue using IFEFFIT as a fantastic resource for general XAFS analysis advice but have their own list themes, as does SCC-Forum. Regardless of whether it may or may not be a good idea in general, I hope the SCC-Forum list will be a useful resource for you. Any comments, please let me know. Anatoly Anatoly Frenkel, Professor Department of Physics, Yeshiva University 245 Lexington Avenue, New York, NY 10016 http://www.yu.edu/faculty/afrenkel Spokesperson, Synchrotron Catalysis Consortium http://www.yu.edu/scc Office: (212) 340-7827, Lab: (631) 344-3013, Fax: (212) 340-7868 Email: anatoly.frenkel(a)yu.edu

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The common question!
by 沛昌蔡 02 Oct '07

02 Oct '07

To Dear Authors; We have accumulate some questions on attach ptt.file, that including theoretical and athena background removal file. In order to present our questions more clear and short, we make this way, Thanks for your time and help! Pei-chang Tsai 杜絕網路駭客，保障帳號安全 - 馬上設定 Yahoo!奇摩安全圖章！

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[FEFF8.4] Re(x) is .le. zero in besjn ?
by Mauro Rovezzi 02 Oct '07

02 Oct '07

Hi all, A little question about a FEFF8 error message I have and I cannot understand what it means : Re(x) is .le. zero in besjn This error is generated when I try to add the SCF to an EXAFS calculation on MnO (manganosite) and the SCF iteration is at step 9 of 30. Seen that the cards in the feff.inp file are properly used (I normally run SCF in EXAFS calculations) do you have any idea of what is going on? Thanks for your help, as usual! Mauro -- Mauro Rovezzi <rovezzi(a)esrf.fr> PhD student - GILDA BM08 c/o ESRF (Grenoble, FR)

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Ifeffit 1.2.10
by Matt Newville 02 Oct '07

02 Oct '07

Hi Folks, I've just uploaded Ifeffit 1.2.10 to the cars.uchicago.edu and sourceforge.net sites. I'm posting both source code (ifeffit-1.2.10.tar.gz) and a Windows installer (ifeffit-1.2.10.exe) which includes the latest versions of Hephaestus, Athena, and Artemis. Installers for Mac users shouldn't be too far behind. For now, the downloads page at http://cars9.uchicago.edu/ifeffit/Downloads links to both 1.2.10 and 1.2.9 versions. It may take a day or so for the files to show up on all the sourceforge.net mirrors. The new Windows Installer reflects a new build process for the underlying library. This took some time to work out (you may recall some emails about this over the summer) , but we think it is working as well as any previous version. There are quite a few changes to Bruce's codes, all for the better. And this version does install and work on Windows Vista. For the source code kit, this now uses a new install location for PGPLOT, so if you're installing you must run PGPLOT_Install before installing ifeffit. Also in this version is support for (and default use of) gfortran instead of g77. If you need to use a different fortran compiler from the one found by default, you can use ./PGPLOT_Install --with-fortran=g77 ./configure --with-fortran=g77 make install As always, let us know if there are any problems. Cheers, --Matt

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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 17 Sep '07

17 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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Double picks on Near Edge region.
by 沛昌蔡 12 Sep '07

12 Sep '07

To whom it may concern, Dear Prof.; Here have some questions about Zn doped LiNbO3 single crsystal EXAFS fitting problem, we did the similar EXAFS absorption spectra as you can see the attach reference paper Fig 7, that shows double picks on Near Edge region, and our questions are, (1) Base on your great knowledge, how comes about these two picks, and is it normal? (2) On Artemis program R-figure display, we can find a great pick appeared in 0~1 angstrom range (k range=1~12), but we find this pick disappeared under (k range=2~12) parameter choosing ,so is it relation to question (1)? (3) If we want to cut near edge contribution, how should we deal with these double picks? choose the rear EXAFS spectrum (aviod these two picks)? Or using Athena background removal it? Thanks for your time and helping. Pei-chang Tsai 2007/09/12 設定安全圖章，保護您的 Yahoo!奇摩帳號不被駭客盜用！

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Creating Athena Projects from Ifeffit command line
by Matthew Ginder-Vogel 11 Sep '07

11 Sep '07

Hi Bruce and list, Has anyone written an Ifeffit wrapper and/or script that can take a series of data files and create an Athena project without actually having to use Athena? If you have, would you be willing to share it? I'm sure it's possible, but I don't want to recreate the wheel if I don't have to. 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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Re: [Ifeffit] Atoms question
by Bruce Ravel 07 Sep '07

07 Sep '07

On Friday 07 September 2007, Saraiya, Neeraj M. wrote: > Hi Bruce, > I am somewhat of a first time user of the Ifeffit software package > and had a question regarding the Atoms package. I am trying to input > x,y,z coordinates for a crystal structure and I realized that the > coordinates are the same for two different elements - i.e. two elements > that can interchange with each other in the structure. How can I > account for the differing ratios of occupancy between the two elements? > Thanks in advance for addressing this question. > > Best, > Neeraj Neeraj, This is a common question, so I am taking the liberty of CCing my answer to the mailing list. Look at the last question ("How do I handle doped materials? Why doesn't Atoms handle doped materials?") on this FAQ page: http://cars9.uchicago.edu/iffwiki/FAQ/FeffitModeling If you still have questions after reading that, go ahead and post your questions on the mailing list and we'll see what we can do about answering them. B -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advanced 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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energy scale when averaging data
by Matthew Ginder-Vogel 07 Sep '07

07 Sep '07

Hello Everyone, I have a very large number of data files (>10,000) that I'm trying to average using Ifeffit. However, I'm having trouble coming up with the energy scale for the averaged file. The energy scale for each individual file is very similar, but not identical, so I'm not sure if it is the best idea to use the energy scale of a single file as the energy scale for the averaged file. I'm sure that I'm not the first person to deal with this problem, so I'm interested to hear how other people deal with this problem. I'm also sure that Bruce has already come up with a clever way of dealing with this problem in Athena, but unfortunately loading 50 files at a time into Athena to average is a too slow a process. So I'd rather do them 50 at a time from the command line. 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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Linear Combination Fitting in Athena
by Skya Fawcett 06 Sep '07

06 Sep '07

A couple questions about linear combination fitting in Athena: 1. There is the option of floating an E0 for the standards, is there any way to restrict how much it floats, ie. constrain it to +/-0.4eV shifts during fitting? 2. If I am fitting normalized u(E), and only care about the XANES region at this point, is perfecting background removal needed? (I have, of course, carefully checked the pre-edge and normalization range). Thank you! Skya Fawcett PhD Candidate Department of Geological Sciences and Geological Engineering Queen's University, Kingston, Canada

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Can't change values in Athena and Artemis on Ubuntu(Feisty)
by Jun Lin 06 Sep '07

06 Sep '07

Hi Carlo Segre, I install Athena and Artemis from your compiled deb package for feisty. When I try to change values in Athena and Artemis, it doesn't work. The only way change the value is click on the plot canvas. I have tried to execute program as root user, but it also doesn't work. Looking forward for you help. Sincerely, Lin Jun -- Shanghai Institute of Applied Physics, Chinese Academy of Sciences No. 2019, Baojia Road, Jiading District, Shanghai,China 201800

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Re: [Ifeffit] Ifeffit Digest, Vol 54, Issue 21
by Jun Lin 31 Aug '07

31 Aug '07

Dear Caro, Thank you for your reply :) I followed your suggestion to double click or choose all text in the boxes, but still doesn't work. I installed the software in my two computers(both Ubuntu 7.04), but the symptoms are the same. Would you please tell me how to build deb package from source? Jun On 8/31/07, ifeffit-request(a)millenia.cars.aps.anl.gov < ifeffit-request(a)millenia.cars.aps.anl.gov> wrote: > > > > Message: 2 > Date: Wed, 29 Aug 2007 23:16:07 -0500 (CDT) > From: Carlo Segre <segre(a)iit.edu> > Subject: Re: [Ifeffit] Can't change values in Athena and Artemis on > Ubuntu(Feisty) > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <Pine.LNX.4.64.0708292306530.2507(a)localhost.localdomain> > Content-Type: text/plain; charset=us-ascii; format=flowed > > > Hi Jun: > > Do you mean changing the values in the text boxes? Sometimes, I have > noticed that you have to double click on the box or select all of the text > in order to be able to change values using the keyboard. I haven't > figured out when this happens though, it seems sort of random to me. > > Carlo > > -- Shanghai Institute of Applied Physics, Chinese Academy of Sciences No. 2019, Baojia Road, Jiading District, Shanghai,China 201800

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Ifeffit and gfortran (was: iffefit compile on BlueWhite64)
by Matt Newville 27 Aug '07

27 Aug '07

Hi Chachi, all I believe I have a source kit that will build correctly for you using gfortran. I've tested on three different generations of Fedora/Redhat linux systems, one with only g77, one with only gfortran, and one with both, and the installation now works on all of them. Please try http://cars9.uchicago.edu/~ifeffit/src/ifeffit-1.2.10_rc1.tar.gz With this tar ball, you will need to install pgplot: tar xvzf ifeffit-1.2.10_rc1.tar.gz cd ifeffit-1.2.10 sh PGPLOT_install ./configure make make install (doing the two 'install steps' with sufficient privilege). Again, you need to install PGPLOT with the provided script. Both the PGPLOT and Ifeffit installations will use gfortran if available, and g77 if gfortran is not available. I think it would not be too difficult to attempt to use Intel's ifort compiler or g95, though I do not know that it's needed-- all linux distribution come with gcc so have easy-to-use packages for gfortran (and, for "legacy", g77). I did get horae-065 and the python wrappers to build with no trouble (once the Tk modules were installed) on all systems, though I haven't done much more than trivial testing. Since I tested only on a few linux boxes, I'd be interested in hearing reports for other systems. I'll wait a few days (or more) to hear reports before uploading this as ifeffit-1.2.10. --Matt

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[Fwd: Ifeffit Ok on BlueWhite64, ...]
by Chachi Rojas 25 Aug '07

25 Aug '07

Hello list again Tk module run ok. Now, my problem is compling horae-065, error message: ... make[1]: Entering directory `/usr/local/src/ifeffit-1.2.10/horae-065/Absorption' /usr/bin/perl5.8.8 chantler2st.PL chantler.db Can't locate Chemistry/Elements.pm in @INC (@INC contains: /usr/lib/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 /usr/lib/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl .) at chantler2st.PL line 40. BEGIN failed--compilation aborted at chantler2st.PL line 40. make[1]: *** [chantler.db] Error 2 make[1]: Leaving directory `/usr/local/src/ifeffit-1.2.10/horae-065/Absorption' make: *** [subdirs] Error 2 ch@pcbox:/usr/local/src/ifeffit-1.2.10/horae-065$ ...... it seems not to find Chemistry/Elements.pm file (module) Ch --------------------------------- Original Message --------------------------------- Subject: Ifeffit Ok on BlueWhite64, ... From: "Chachi Rojas" <crojasa(a)unmsm.edu.pe> Date: Fri, August 24, 2007 5:12 pm To: ifeffit(a)millenia.cars.aps.anl.gov ------------------------------------------------------------------------------------ Hi Matt Ifeffit run perfectely (thanks Matt) after installed by your scripts on RC1. Now, a question for Bruce try to install horae-065, but, error message is below: ---------- === The Ifeffit wrapper, Athena, Artemis, and Hephaestus === This is linux. Checking dependencies ... Tk is not installed. Download the latest from http://search.cpan.org/search?module=Tk Failed dependencies. Not installing athena and artemis. ------ Tk modules (version 8.4.15) were installed on /usr, but perl Makefile.PL it does not recognize Some idea Ch. > Date: Wed, 22 Aug 2007 15:56:26 -0500 > From: "Matt Newville" <newville(a)cars.uchicago.edu> > Subject: [Ifeffit] Ifeffit and gfortran (was: iffefit compile on > BlueWhite64) > To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: > <b8522e3d0708221356y37280877v86ac576fe9b6b96c(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi Chachi, all > > I believe I have a source kit that will build correctly for you using > gfortran. I've tested on three different generations of Fedora/Redhat > linux systems, one with only g77, one with only gfortran, and one with > both, and the installation now works on all of them. > > Please try > http://cars9.uchicago.edu/~ifeffit/src/ifeffit-1.2.10_rc1.tar.gz > > With this tar ball, you will need to install pgplot: > tar xvzf ifeffit-1.2.10_rc1.tar.gz > cd ifeffit-1.2.10 > sh PGPLOT_install > ./configure > make > make install > > (doing the two 'install steps' with sufficient privilege). Again, you > need to install PGPLOT with the provided script. Both the PGPLOT and > Ifeffit installations will use gfortran if available, and g77 if > gfortran is not available. I think it would not be too difficult to > attempt to use Intel's ifort compiler or g95, though I do not know > that it's needed-- all linux distribution come with gcc so have > easy-to-use packages for gfortran (and, for "legacy", g77). > > I did get horae-065 and the python wrappers to build with no trouble > (once the Tk modules were installed) on all systems, though I haven't > done much more than trivial testing. > > Since I tested only on a few linux boxes, I'd be interested in hearing > reports for other systems. > > I'll wait a few days (or more) to hear reports before uploading this > as ifeffit-1.2.10. > > --Matt > -- Chachi Rojas Ayala GMC FCF UNMSM Claro:01-97489347 email:crojasa@unmsm.edu.pe chachi.rojas(a)gmail.com

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