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

Larch: problems importing feff paths
by Johan Nilsson 09 Apr '14

09 Apr '14

Hello, I'm experimenting a bit with exafs fitting in Larch but I've come across a problem when I try to import my feff paths. Basically what happens is: $ larch Larch 0.9.22 (12-Dec-2013) M. Newville, T. Trainor using python 2.7.5, numpy 1.7.1, wx-enabled, wx version 2.8.12.1 larch> path = feffpath('feff0001.dat') file <stdin>, line 0 IndexError: list index out of range path = feffpath('feff0001.dat') ^^^ larch> I don't know if this is an issue with my input file to feff or if this is some sort of bug in Larch. I wrote the feff.inp from scratch using a template and the structure is supposed to be bulk PdO. I've attached my feff.inp and feff0001.dat if someone wants to try and reproduce the problem. I tried another set of paths that was calculated for FeO using an input file from webatoms and those appear to import without issues. I've attached those as well in a zip if someone wants to compare the two sets. I'm running Ubuntu 13.10 on my PC. Best regards, Johan

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D-Atoms program, common positions and occupancies
by Moneeb Shatnawi 09 Apr '14

09 Apr '14

Dear Robert Gordon, Hello, Thank you so much for the reply. Yes, it turned out that I was using a relaxed model of CdSe where I should have changed the space group accordingly. When I replaced the input file with the correct one, everything went fine with no error messages, I appreciate your help, Moneeb

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my backlog of Demeter chores
by Bruce Ravel 08 Apr '14

08 Apr '14

Hi everyone, For the last couple of weeks, I have been having trouble finding time to address the bugs that have been reported. Moneed Shatnawi, Alexander Britz, Matt Frith, Mengling Stuckman, Alison Tebo, and Thomas Huthwelker have all asked reasonable questions about actual issues with the software. I am writing today to assure them that they are on my mind, but there haven't been enough hours in the day or days in the week recently for me to address the problems. But I will! Soon, I hope. Cheers, B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel

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D-Atoms program, common positions and occupancies
by Moneeb Shatnawi 07 Apr '14

07 Apr '14

Dear Bruce Ravel, Hello, I am Moneeb Shatnawi from the University of Jordan. I have a question and I appreciate your help in advance. I have installed the Demeter program (version 0.9.18) and I tried to use your (D)Atoms program using the attached input files. When I try to run atoms, I get a warning message stating that two sites generate one or more common positions and their occupancies sum to more than 1. (attached also the warning message that I got). If I ignore this warning message and try to run FEFF, the program crashes. When I change the space group to P 1 (as indicated by the message) , the program runs well. My question is, could you please figure out the problem with these input files, so that I can run them with the correct space group? Thank you so much in advance, Moneeb

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Re: [Ifeffit] Problem with importing projects from ATHENA into ARTEMIS
by Matt Newville 07 Apr '14

07 Apr '14

Hi Alexander, I think you may not alone in having this issue. You should be using normalized chi(k) in Artemis, but I don't think Artemis would be reading chi(k) from the project file incorrectly.... Perhaps there is something strange about how you're doing the normalization? Or perhaps it is just a question of what k-weighting is being used for the plot. Unfortunately, the PNGs I see have been cropped and don't show the labels of the axes. I'm sending this to the Ifeffit mailing list, where you'll probably get a more complete answer. On Mon, Apr 7, 2014 at 9:57 AM, Britz, Alexander <alexander.britz(a)xfel.eu> wrote: > Dear Mr. Newville, > > I came across a problem when I import an ATHENA project after normalization into ARTEMIS. Maybe you could tell me who to contact about this problem. Let me try to explain it in few words: > > I normalize my EXAFS data in ATHENA and safe it a s a .prj file. When I open the .prj file in ARTEMIS I noticed, that the amplitude of some oscillations have changed. When I save the chi(k) as .txt, this problem does not occur. When I open the chi(k) text file in ARTEMIS, the normalization and the amplitude of the oscillations are exactly the same as in ATHEN. > > I have attached a .png file for the EXAFS in k-space. It is the same .prj file, one time opened in ARTEMIS, one time in ATHENA. To be more specific, the amplitude of the oscillation at k=3 is -1.4 and -1.6, respectively. > > Thank you very much for your help in advance! > > Best regards from Hamburg, > Alexander > > ________________________________________ > Alexander Britz > European XFEL GmbH > alexander.britz(a)xfel.eu > Tel. +49 (0)40 8998-6986 > Fax +49 (0)40 8998-1905 > www.xfel.eu/de > > Postadresse: Notkestraße 85, 22607 Hamburg > Sitz: Albert-Einstein-Ring 19, 22761 Hamburg > > Geschäftsführer: Prof. Dr. Massimo Altarelli, Dr. Claudia Burger > Registriert als European X-Ray Free-Electron Laser Facility GmbH > beim Amtsgericht Hamburg, HRB 111165 > > > > -- --Matt Newville <newville at cars.uchicago.edu> 630-252-0431

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Peaks in MCA spectra
by George Sterbinsky 02 Apr '14

02 Apr '14

Hello, I am writing with a general XAS question. It does not necessarily pertain to Ifeffit, however, I think the topic is something some, maybe most, list members will be knowledgeable about. So it seems like this list is a good place to post this question. On to the question. I have attached a plot of a MCA spectrum collected with a vortex silicon drift detector. The spectrum is actually the average of several spectra, all collected in the post edge region of the Co L-edge. The spectra were averaged to reduce noise. The three peaks result from fluorescence from carbon, oxygen, and cobalt. Low-energy shoulders on the Co and O peaks are also observed. These can be seen as the regions of the spectrum that are not well reproduced by the fit. The main reason I included the fit in the plot is to illustrate the presence of these shoulders, particularly in the oxygen florescence, where the additional intensity is not so obvious. I am writing to see if anyone has any suggestion as to what the origins of these peaks might be. They are not due to additional elements, as they appear at the same incident energies as the main florescence peaks, i.e. the Co shoulder appears at the same incident energies as the main Co peak, and the O shoulder appears at the same incident energies as the main O peak. It is possible that the peaks result form other transitions. Considering Co, the main peak is due to L3/L2-M4 transitions, and the shoulder is in a position that could be consistent with L3/L2-M1 transitions. However, by fitting the peaks with Gaussians, one finds an area for the shoulder that is about 25% of the area of the main peak. This is significantly larger than what one might expect from tabulated transition strengths like those given in Hephaestus. To summarize, does anyone know what these shoulders might result from if not lower energy transitions? If they are low energy transitions, why would the relative transition strengths differ from tabulated values? Thank you, George

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Vacancy
by Khalid, Syed 31 Mar '14

31 Mar '14

The Laboratory of Excellence Plasmas in Paris LABEX PLAS@PAR, University Pierre et Marie CURIE 4 place Jussieu, 75005 Paris, FRANCE Vacancy at LABEX PLAS@PAR Three years fixed term vacancy, from May 2014 Conception and experimental techniques engineer. PLAS@PAR is a laboratory of excellence that federates leading plasma scientists in the Paris area, working in different scientific sectors. PLAS@PAR stimulates fundamental research in plasma physics and promotes innovation in domains ranging from nanotechnology to environment, aeronautics and security as also in the areas of environmental protection and medicine. Context and mission : The engineer will work directly with teams whose activities are centered on fundamental processes that occur in hot plasmas. They belong to the Laboratoire de Chimie Physique-Matière et Rayonnement (LCPMR), the Institut des NanoSciences de Paris (INSP) and the Laboratoire pour l'Utilisation des Lasers Intenses (LULI). The engineer will be based in the LCPMR. The engineer will take care of the conception and the development of an innovative experimental setup on X-ray photon detection in the energy range from 2 to 5 keV. This instrumentation will include a multi-crystal spectrometer combined to a fast position sensitive detector leading to high detection efficiency allowing for coincidence measurements with other particles and high resolving power. Core Activities : The engineer will have to analyze the scientific needs of the different teams involved, to conceive the instrument, and to evaluate and propose the techniques that should be used. He will develop the methods of measurements, write the specifications, to organize the progress in the achievement, manage the measurements, and organize the installation, the dismantling and the travel of the setup between the different laboratories as well as at the large facilities where test experiments will be performed (particle accelerators, synchrotron radiation facilities, free electron lasers). Skills : The engineer should have a good knowledge in physics (Atomic and Molecular Physics), in science and techniques for engineer, more specifically in the domain of X-ray photon detection. Skills in ultra high vacuum technologies, experimentation and measurement are required. The engineer should have a good level in english (spoken and written), should know how to work in a team and will have to adapt himself to the constraints of experimental research. Contacts Marc Simon, tel.+33 1 44 27 66 20 marc.simon(a)upmc.fr Dominique Vernhet, tel. +33 1 44 27 45 18 dominique.vernhet(a)insp.jussieu.fr Syed Khalid Beamline Scientist and Spokesperson X18B and X19A NSLS-NSLS-II, Photon Sciences Division, 98, Rochester Street, Bldg. 743, 3L146 Brookhaven National Laboratory, Upton, NY 11973 khalid(a)bnl.gov<mailto:khalid@bnl.gov> Phone: 631-344-7496 Fax:631-344-7039

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Interest in more accurate theoretical standards
by Samuel T. Chill 25 Mar '14

25 Mar '14

Dear List, I have noticed that EXAFS fits to Au foils at 298 K underestimate the known equilibrium bond length. According to the CRC Handbook the lattice constant at 298 K is 4.0782 +/- 0.0002 Å. This is a bond length of 2.884 Å. However, in published EXAFS work[1] as well as fits that I have performed the bond length is about 2.867 Å. The error is small -- about half a percent too short -- but I am interested in using EXAFS to study relatively small changes in bond length and I am curious about the resolution that can be achieved. I want to understand the source of this error. I think the two biggest sources of error would be correlation between variables in the fitting model and errors in the theoretical standard (FEFF6 in this case). The random experimental error for a foil should be negligible. I would like to know if it is possible to create a better theoretical standard using a more ab initio approach. Is anyone aware of any other software for performing more accurate EXAFS calculations? It is okay if it is a very expensive calculation as I have plenty of computer time. I have seen that some DFT packages can perform XANES calculations, but I have seen no mention of EXAFS. Thanks, Sam Chill 1. http://journals.aps.org/prb/abstract/10.1103/PhysRevB.85.195419

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Bug report: Artemis cannot re-open saved projects
by Mengling Yi Stuckman 25 Mar '14

25 Mar '14

Dear all, I'm using Demeter version 0.9.18.2 in Windows 7 Enterprise. Starting from yesterday, I could not re-open what I saved as ***.fpj any more. I tried to re-open my previous projects as well created new projects and then re-opened them. Artemis program would close after spending 1 or 2 seconds in trying to load what I asked it to load. Mainly, the following two error messages were showing in the log file in the %APPDATA%\demeter when I tried to open different project files: Can't call method "workspace" without a package or object reference at C:/strawberry/perl/site/lib/Demeter/Fit.pm line 1550. Can't call method "group" on an undefined value at C:/strawberry/perl/site/lib/Demeter/UI/Artemis/Project.pm line 466. I only had problems with loading ***.fpj files. Athena projects and feff input files can be imported in Artemis as normal. Thank you very much if you can help to fix the problem! Mengling -- Mengling Yi Stuckman Graduate Research Assistant Civil and Environmental Engineering and Geodetic Science Ohio State University 2070 Neil Ave., Columbus, OH, 43210

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questions about ifeffit
by Artillery 24 Mar '14

24 Mar '14

Hi, I am a student from Shanghai. Now I am using IFEFFIT to do my thesis. Athena is useful to process the raw data and provides figures after background removal or E-k space transformation. I want to know whether I can obtain the processed data. For example, the data after the spectrum has been normalized. How can I get these data? I am looking forward to your reply. Best regards, Jingyuan

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