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

problem install horae ubuntu 12.04 Precise
by denis.testemale 12 Jun '12

12 Jun '12

Dear members of the list, dear Carlo, I'm currently trying to install horae on a colleague's computer. He recently switched to Linux (ubuntu) so I'm in charge of the installs until he's used to the new OS. We are facing a problem to install horae. The linux and (incomplete) horae install are: ###### ## lsb_release -a LSB Version: core-2.0-amd64:core-2.0-noarch:core-3.0-amd64:core-3.0-noarch:core-3.1-amd64:core-3.1-noarch:core-3.2-amd64:core-3.2-noarch:core-4.0-amd64:core-4.0-noarch Distributor ID: Ubuntu Description: Ubuntu 12.04 LTS Release: 12.04 Codename: precise ## dpkg -l | grep horae rc horae 071~svn536-1 interactive graphical processing and analysis of EXAFS data ## dpkg -l | grep pgplot5 ii pgplot5 5.2.2-18 large subroutine library for plotting scientific data ## dpkg -l | grep perl-tk ii perl-tk 1:804.029-1.1ubuntu2 Perl module providing the Tk graphics library ## dpkg -l | grep ifeffit ii ifeffit 2:1.2.11d-8~oneiric0 Interactive XAFS analysis program ###### As you see, we lack the libifeffit-perl library wich is confirmed by the error messages we get when trying to install horae (it's in french, but you'll get the idea): ##### sudo apt-get install horae Lecture des listes de paquets... Fait Construction de l'arbre des dépendances Lecture des informations d'état... Fait Certains paquets ne peuvent être installés. Ceci peut signifier que vous avez demandé l'impossible, ou bien, si vous utilisez la distribution unstable, que certains paquets n'ont pas encore été créés ou ne sont pas sortis d'Incoming. L'information suivante devrait vous aider à résoudre la situation : Les paquets suivants contiennent des dépendances non satisfaites : horae : Dépend: libifeffit-perl mais ne sera pas installé E: Impossible de corriger les problèmes, des paquets défectueux sont en mode « garder en l'état ». sudo apt-get install libifeffit-perl Lecture des listes de paquets... Fait Construction de l'arbre des dépendances Lecture des informations d'état... Fait Certains paquets ne peuvent être installés. Ceci peut signifier que vous avez demandé l'impossible, ou bien, si vous utilisez la distribution unstable, que certains paquets n'ont pas encore été créés ou ne sont pas sortis d'Incoming. L'information suivante devrait vous aider à résoudre la situation : Les paquets suivants contiennent des dépendances non satisfaites : libifeffit-perl : Dépend: perlapi-5.12.4 mais il n'est pas installable E: Impossible de corriger les problèmes, des paquets défectueux sont en mode « garder en l'état ». ##### So perlapi seems to be one problem. Any idea? Thanks for your help. Denis Denis Testemale Institut Néel - Département MCMF 25 avenue des Martyrs BP166 38042 Grenoble, France ph: +33 476 881 045 email: denis.testemale at grenoble.cnrs.fr

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Postdoctoral position at the Synchrotron Catalysis Consortium
by Anatoly I Frenkel 12 Jun '12

12 Jun '12

Physics Department of Yeshiva University in New York City will have an opening for a postdoctoral research associate position, beginning September 2012. The postdoc will develop new experimental methods of investigations of thermal, structural and electronic properties of supported metal clusters. He or she will contribute to the ongoing research in heterogeneous catalysis in Anatoly Frenkel's group and will be stationed at Brookhaven National Laboratory. Required qualifications: expert knowledge of XAFS and its applications to nanomaterials, hands-on experience with vibrational spectroscopies, experience with in situ experiments. The research will be performed under the direction of Prof. Anatoly Frenkel primarily at the Synchrotron Catalysis Consortium at the NSLS but also at other synchrotrons as needed: APS, ESRF, SLS and, eventually, NSLS-II. Applicants should forward cover letter and CV to Prof. Frenkel at anatoly.frenkel(a)yu.edu. Yeshiva University is an Equal Opportunity Employer. Anatoly Frenkel, Ph.D., 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, Email: anatoly.frenkel(a)yu.edu

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Fitting pre-edge feature in Fe XANES
by shbone＠berkeley.edu 11 Jun '12

11 Jun '12

Dear All: I would like to attempt fits to the pre-edge features of a set of Fe K-edge XANES spectra for Fe(II) samples that show partial oxidation with the goal of determining whether Fe(III) exists in octahedral or tetrahedral coordination (e.g. Wilke et al., American Mineralogist, 2001). Broadly, the fitting procedure involves extracting the pre-edge feature from the edge using a spline function and then deconvoluting this feature using a set of pseudo-voigt functions. I believe that I can use the LCF module in Sixpack to fit the feature using the pseudo-voigt functions, but I'm having trouble extracting the pre-edge feature. I've tried using the spline function in Sixpack (and Athena), but I don't have enough options to modify the spline. It seems to me that I need to use a very rigid spline (for instance, one with only 3 or so knots), and that the options in Sixpack and Athena don't allow for this. I heard the program exafspak would allow me more freedom to control the spline function, but I haven't been able to successfully download the program, let alone use it. So, my questions are the following: (1) Is there a program other than exafspak that I could use to fit a spline to my data where I would have more control over the spline options? I would prefer not to use exafspak since my knowledge of unix is nil. (2) Has anyone used exafspak on a mac? I'm using OS 10.5.8 and I'd appreciate any tips you might be able to give me on installing the program. I followed the directions for installation provided on the website, but the command to install the program (i.e. "add_exafs") wasn't recognized. Thanks for your help! Sharon

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Ni spectra
by Cserháti Csaba 06 Jun '12

06 Jun '12

Hello, we are studying the kinetic of Ni/Si solid state reaction. To analyze the data, we need the EXAFS spectra of pure Ni. We would appreciate if anyone could send us this spectrum. Thanks a lot in advance, Regards, Csaba Cserháti

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Feff 9.0 CFAVERAGE
by Dreher Marian 05 Jun '12

05 Jun '12

Dear feff community, I'm aware that the issue of CFAVERAGE not creating a xmu.dat output file has already been discussed some years ago for feff 8.2; back then it was suggested to make some changes in the source code and recompile or wait for a newer version of feff in which this bug would be fixed. However, I'm running feff 9.0 and I still seem to have this issue. When using the CFAVERAGE card, no xmu.dat or chi.dat output is being created. Do I still need to manipulate the source code do fix that? Many thanks, Marian. Marian Dreher, Dipl. Chem. PhD Student, Catalytic Process Engineering Group Paul Scherrer Institut General Energy Research (ENE) Laboratory for Bioenergy and Catalysis Office: OLGA/221 CH-5232 Villigen PSI Switzerland Phone: +41 (0)56 310 2937 email: marian.dreher(a)psi.ch

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how to obtain average vacancy files?
by María Elena Montero Cabrera 01 Jun '12

01 Jun '12

Dear friends, I am trying to fit with Artemis, not very successfully, a maghemite structure. The main difficulty seems to be the vacancies in the structure. My idea, following a recently given Bruce’s advice to a person in this list, is to obtain “average vacancies” FEFF files and to work with the fully occupied magnetite structure. I wanted to obtain each file for a given vacancy configuration in the first coordination sphere and then to multiply the obtained functions by the weight of each configuration and summ them all. I had the hope of doing this by using the feff00nn.dat files that I have used when working with SixPack, some years ago. Surprisingly, I couldn’t find the Artemis’ corresponding feff00nn.dat files at any folder. What can I do? -- María Elena Dra. María Elena Montero Cabrera Centro de Investigación en Materiales Avanzados (CIMAV) Miguel de Cervantes 120, Compl. Ind. Chihuahua Chihuahua CP 31109, Chih. México Tel (614) 4391123

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atoms file of Zr-foil
by JeongEunSuk 26 May '12

26 May '12

Hello everyone Does anybody know atoms file of Zr-foil? I checked it in atoms.inp archive but it is no there. so I made it as following: title name: Zirconium title formula: Zr title sites: Zr1 title refer1: title refer2: title schoen: title notes1: metal, hexagonal close packed space p 63/ m m c a = 3.232 b = 3.232 c = 514.7 alpha= 90 rmax = 6.00 core = Zr1 atom Zr 0.33333 0.66667 0.25000 Zr1 ------ is it right?

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problem with Demeter- Artemis/Atoms
by Matt Frith 24 May '12

24 May '12

I was attempting to import a .cif file into Artemis to use for a FEFF calculation and I am getting the following error message: "Atoms is currently unable to use crystal data which has sites of partial occupancy. Sorry." These .cif files work fine with the old version of Artemis/Atoms. Is there currently a way around this problem, or is this something that will be addresses in later version. Thank you for your help. Sincerely, Matt Frith

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Question: About using polarization and ellipticity cards in FEFF
by xu dongbin 13 May '12

13 May '12

Hi, I would like to ask a question which has confused me for a few days. In my current case, I'm dealing with samples with c texture in the film normal. The sample was measured with linear polarized x-ray in both directions with the surface of sample parallel/perpendicular to the electrical field of x-ray. During measurement, the sample was always rotated around the film normal. Therefore, I think the parallel direction data can be treated with random orientated grains in the film plane. In order to describe this, I need use POLARIZATION and ELLIPTICITY cards in FEFF calculation. However, I'm not sure which case below is the correct one I should include in FEFF calculation for my case: a. POLARIZATION 1 1 0 ELLIPTICITY 1 0 0 1 b. ELLIPTICITY 1 0 0 1 I think these two cases should give the same calculation results, however, when I sum the paths in these two cases respectively using the same parameters(S02, E0, delR, sigma^2). The results give substantial difference. Can anyone help me to figure out this? Thanks&Regards!

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Debye function model, Math expression
by NIRAWAT THAMMAJAK 11 May '12

11 May '12

Hello, May I add more questions to this. I do a research on magnetic materials. Bond lenghts and geometries are really important to understand the magnetic interactions and I think EXAFS is the promising tool for this. I have measured the EXAFS spectra for quite a complex material system. There are 3 sites of absorbing atom (Fe) in the crystal structure, therefore I created 3 FEFF models to fit the data with different amplitudes. Closest neighbours are oxygen atoms, and then Li. The strongest scatterers are La atoms sitting ~4.26 angtrom away from the absorbing atom, which contribute a significant 3rd shell. Yes, there are many paths to include. Math expressions together with bulk structure details obtained from neutron diffraction help to minimise the parameters somewhat. However, there are thermal factorss, very small but too many of them. I measured my sample at 1.5 K, then sigma^2 are quite small. Could you please suggest any papers, models, or math expressions constraining these factors at low temperature. Would it be sensible to constrain them as 0, or a range of small numbers obtained from the significant shells? Thank you very much, Nirawat. On 24 August 2010 18:25, Frenkel, Anatoly <frenkel(a)bnl.gov> wrote: > Just to add: > These procedures, described in that article, can be easily implemented in > Mathematica. > Anatoly > > > ------------------------------ > *From:* ifeffit-bounces(a)millenia.cars.aps.anl.gov on behalf of Ravel, > Bruce > *Sent:* Tue 8/24/2010 1:23 PM > *To:* XAFS Analysis using Ifeffit > *Subject:* Re: [Ifeffit] debye function > > On Tuesday 24 August 2010 12:23:18 pm Kleber Daum Machado wrote: > > Hi, > > > > I'd like to know the explicit mathematical expressions that are > > represented by the functions debye(temp,thetad) and eins(temp,thetae). > > Are they given in some documentation file or article? > > See > > "Extended x-ray absorption fine structure Debye-Waller > factors. I. Monatomic crystals" > E. Sevillano, H. Meuth, J. J. Rehr > Phys. Rev. B 20, 4908–4911 (1979) > http://link.aps.org/doi/10.1103/PhysRevB.20.4908 > > B > > > -- > > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 > Building 535A > Upton NY, 11973 > > My homepage: http://xafs.org/BruceRavel > EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/ > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > >

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