March 2014 - Ifeffit - millenia.cars.aps.anl.gov

Re: [Ifeffit] Launching Athena on Mountain Lion (Mac OS 10.8)
by Kyler Carroll 05 Dec '14

05 Dec '14

Hello, I had posted a comment/question a few months back when I had initially installed Mountain Lion on my mac regarding iXAFS compatibility with XQuartz and the new OS not supporting X11 anymore. Since then I have received a few comments back and I found one solution to be the best. This was originally sent by Tsu-Chien Weng from SSRL (tsuchien(a)slac.stanford.edu) Please find the following solution below. Once you install XQuartz the rest will be done in the Terminal.app. This is a one time solution and I havent had any trouble thus far with the program. Hope this works as well for everyone else as it did for me. 1. Install XQuartz from <http://xquartz.macosforge.org/landing/> 2. open Terminal.app 3. cd /Applications/Utilities 4. sudo mkdir X11.app 5. cd X11.app 6. sudo ln -s ../XQuartz.app/Contents Thank you, Kyler J. Carroll, Ph.D. Assistant Project Scientist Department of NanoEngineering University of California, San Diego

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Rendering of windows in Artemis and transferring paths from feff calculation
by Alison Tebo 23 Apr '14

23 Apr '14

Hi All, I am running Demeter 0.9.18 installed on a Mac 10.6.8 via the (very helpful!) Macports port. I've had nearly no problems with processing my data, but Artemis appears very strange. Most of the button can't be seen and are black instead (I've attached a screenshot). The bigger problem is that once I run a Feff calculation, I can't seem to transfer the paths from the Feff Window into the Data Window (see second screenshot). The program seems to think it's doing it--there are no error messages in the log and it even makes the little graphic as it 'grabs' the path--but it never transfers it over to the Data Window. I have attached a project file where I get this error, the feff input file that I run the calculation on, and two screenshots of what Artemis looks like for me. I don't think the input and project file matter much since this happens for me even with examples from the various courses Bruce has given. Any advice would be greatly appreciated. Sincerely, Alison

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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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Re: [Ifeffit] Bug report: Artemis cannot re-open saved projects
by Mengling Yi Stuckman 20 Mar '14

20 Mar '14

Sorry I think my attachment didn't go through. Maybe the zip file will work. Mengling On Thu, Mar 20, 2014 at 9:22 AM, Mengling Stuckman <menglingyi1023(a)gmail.com > wrote: > Thanks, Bruce, > > I'm sending a couple. One is new that I didn't do any fit. The other is > old that contained my fitting. Both of them can't open in my Artemis. > > Mengling > > > On Wed, Mar 19, 2014 at 5:47 PM, Bruce Ravel <bravel(a)bnl.gov> wrote: > >> >> Can you humor me and send me one of your .fpj files? I would like to >> examine its contents. >> >> B >> >> >> On 03/19/2014 05:36 PM, Mengling Stuckman wrote: >> >>> Thank you, Bruce, >>> >>> This is the complete log file: >>> >>> "Started at 2014-03-19T14:26:09 >>> Win7Enterprise (64-bit) Service Pack 1Service Pack 16176012102561 >>> >>> >>> PATH: >>> C:\windows\system32;C:\windows;C:\windows\System32\ >>> Wbem;C:\windows\System32\WindowsPowerShell\v1.0\;C:\ >>> strawberry\perl\bin;C:\strawberry\perl\site\bin;C:\strawberry\c\bin;C:\ >>> strawberry1\perl\bin;C:\strawberry1\perl\site\bin;C:\ >>> strawberry1\c\bin;\\admin.netl.doe.gov >>> <http://admin.netl.doe.gov>\it\Oracle11g\product\11.2.0\client_1\bin; >>> >>> >>> perl version: v5.12.3 >>> >>> @INC: >>> C:/strawberry/perl/site/lib >>> C:/strawberry/perl/vendor/lib >>> C:/strawberry/perl/lib >>> . >>> >>> Can't call method "workspace" without a package or object reference at >>> C:/strawberry/perl/site/lib/Demeter/Fit.pm line 1550." >>> >>> or this very last sentence will change to >>> >>> "Can't call method "group" on an undefined value at >>> C:/strawberry/perl/site/lib/Demeter/UI/Artemis/Project.pm line 466." >>> if I open a different .fpj file. >>> >>> Because the first few lines were similar to what I saw in Athena log >>> file when Athena is working, I didn't cite these. >>> >>> Thank you very much for double-checking it! >>> >>> I did try to check the permission of that folder by adding a file into >>> that folder and extracting a zip file into that folder. Neither had any >>> problem. I do have permission of that folder. >>> >>> I also tried to open my files in Artemis installed on several other >>> computers in my workplace. Other computers didn't work as well. I guess >>> it might be a problem with the operating system/software conflict in my >>> workplace? I didn't install any other software by myself. All the other >>> updates for antivirus or Windows 7 are automatic through workplace >>> system management that I don't have control. I might be able to call IT >>> support tomorrow to see if they know anything about the system that >>> might have conflict with Demeter. >>> >>> "Without being able to watch this on one of my computers, I can only >>> guess what the problem might be by examining the two lines of code you >>> cite." >>> >>> I am wondering how to examine the two lines of code I cited. Maybe I >>> could talk to IT support about the code and see if there is anything >>> they or we can do to fix that. >>> >>> Really appreciated for your replies! I know this is a very personalized >>> computer problem, not related to your software, which might be beyond >>> your duty to fix. So really thankful for your help! >>> >>> Mengling >>> >>> >>> On Wed, Mar 19, 2014 at 4:44 PM, Bruce Ravel <bravel(a)bnl.gov >>> <mailto:bravel@bnl.gov>> wrote: >>> >>> On 03/19/2014 04:19 PM, Mengling Stuckman wrote: >>> >>> >>> Again, the message showing in the log file is: >>> "Can't call method "workspace" without a package or object >>> reference at >>> C:/strawberry/perl/site/lib/__Demeter/Fit.pm line 1550." >>> >>> >>> or sometimes: >>> >>> "Can't call method "group" on an undefined value at >>> C:/strawberry/perl/site/lib/__Demeter/UI/Artemis/Project.pm line >>> >>> 466." >>> >>> >>> Are you quite sure that is the only text in the log file? >>> >>> Demeter first writes several lines about the environment in which >>> Demeter is operating. The error message is almost always followed by >>> several lines of backtrace. All of that provides context for me to >>> understand the proximal cause of the problem. If you extract a part >>> of the log file, then that context is lost to me. >>> >>> >>> Demeter also seemed to work fine last week and only stopped >>> working >>> yesterday. I didn't update anything on my work computer, so I >>> don't >>> know what is causing the problem. >>> >>> >>> Artemis worked on that computer last week and does not work this >>> week? >>> And you did nothing to change the computer? Something doesn't add >>> up. >>> >>> Did your anti virus software update? Did your institution's system >>> administrators perform an update? Did you install any new software? >>> Anything? It's hard for me to understand how the behavior of the >>> program can change simply by walking away for a few days. >>> >>> Without being able to watch this on one of my computers, I can only >>> guess what the problem might be by examining the two lines of code >>> you >>> cite. >>> >>> My best guess is that something is preventing you from unpacking the >>> project file. An .fpj file is nothing more than a zip file with a >>> different file extension. It gets unpacked in %APPDATA%\stash (where >>> %APPDATA% is the location of the log file). That means that you have >>> to have permission to write files to that location. So, my best >>> guess >>> is that something is preventing you from writing to that space. I >>> have no guess for what the cause of that is. >>> >>> So, check the permission of that folder. Try making a file in that >>> folder by hand. Try extracting a zip file buy hand into that folder. >>> >>> If not that, then I'm afraid I'm out of ideas. >>> >>> >>> B >>> >>> >>> -- >>> Bruce Ravel ------------------------------__------ bravel(a)bnl.gov >>> <mailto:bravel@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 >>> _________________________________________________ >>> Ifeffit mailing list >>> Ifeffit(a)millenia.cars.aps.anl.__gov >>> <mailto:Ifeffit@millenia.cars.aps.anl.gov> >>> http://millenia.cars.aps.anl.__gov/mailman/listinfo/ifeffit >>> >>> <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> >>> >>> >>> >>> >>> >>> -- >>> Mengling Stuckman >>> ORISE Research Fellow >>> National Energy Technology Laboratory >>> U.S. Department of Energy >>> Pittsburgh, PA >>> STUCKMAN.MENGLING(a)CONTR.NETL.DOE.GOV >>> <mailto:STUCKMAN.MENGLING@CONTR.NETL.DOE.GOV> >>> Office: 412-386-7387 >>> >>> >>> >>> _______________________________________________ >>> Ifeffit mailing list >>> Ifeffit(a)millenia.cars.aps.anl.gov >>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >>> >>> >> >> -- >> 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 >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> >> >> > > > -- > Mengling Stuckman > ORISE Research Fellow > National Energy Technology Laboratory > U.S. Department of Energy > Pittsburgh, PA > STUCKMAN.MENGLING(a)CONTR.NETL.DOE.GOV > Office: 412-386-7387 > -- 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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Inequivalent atomic positions (V2O5 xerogel)
by Douglas Langie da Silva 18 Mar '14

18 Mar '14

Dear all, I am working with EXAFS data of V2O5 xerogel. In this form, the V2O5 present a monoclinic structure formed by bi-layers of VO5 pyramids intercalated with water molecules. Fig 1 attached presents a view of the V2O5 xerogel structure. There are two Vanadium atoms per unit cell, each one surrounded by oxygen atoms at distinct distances, characterizing two inequivalent sites. My question is how to fit the data in dartemis considering the two inequivalent positions? My first approach was run Feff two times. Then I get two theoretical models, one for V1 atoms and the other for the V2 atoms. Each of Feff runs are present attached as model V1 and model V2. After that I transfer the paths of the first shell of each model to dartesmis data windows (fig 2) and proceed with the fit. We pay attention in the site fraction of each vanadium atom in order to setup the S02 parameter for each model. Without attempting at this point with the numbers, the final results are present in Fig. 3 e 4. Fig 4 presents the log file and the results for the each patch. My question is: this procedure is valid? Since now thak you. -- Douglas Langie da Silva Instituto de Física e Matemática Departamento de Física Universidade Federal de Pelotas Campus Universiário s/n CP 354 Pelotas/RS CEP 96010-900 55 53 32757477 55 53 32757345 Douglas Langie da Silva Physics Department Federal University of Pelotas POBox 354 Pelotas/RS ZCode 96010-900 55 53 32757477 55 53 32757345

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EXAFS Fitting for Ni sorb to bacterial biomass and Mn oxides
by Sathish Mayanna 18 Mar '14

18 Mar '14

Dear all So far, this forum has been very helpful for me to learn and understand how to fit EXAFS spectra of Mn oxides, thanks everyone for your suggestions. Recently, I am working with Ni k-edge EXAFS and I have kind of similar question as Abhijeet Gaur (Ifeffit Digest, Vol 133, Issue 1), in my case, I am trying to fit EXAFS spectra of Ni(II) sorbed to bacterial biomass and Mn oxides (attached). I followed the Matt suggestions by replacing Ni in place of Mn after running Atoms (birnessite model) to generate feff.inp. I have two questions regarding this: 1) Ni(II) can be surface sorbed and or incorporated into Mn oxide structures. But, I cannot generate paths for this particular r-space. What and how can I edit the feff calculations? (attached). 2) Ni(II) sorp to bacterial biomass via some organic ligands (humic or carboxylic acids): The first shell mainly associates with Ni-O distances, there might be also Ni-C distances in later shells. I am wondering, how can I input the C in atoms or feff calculations? I would be happy to receive your comments. Regards Sathish

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