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

Can't open Athena project
by Antony Burnham 06 Apr '19

06 Apr '19

I'm having trouble opening my Athena project in Artemis. This contains two transmission spectra of zirconium phases. They plot just fine in Athena but when I try to import them in Artemis it doesn't recognise that there are any files at all in the project (except that one of the two spectra does display in the plot window). There's just a blank space in the left hand pane where the list of files usually appears. I don't have this problem with any of my fluorescence data from the same experiment. And when I have an Athena project with a mix of fluo and transmission spectra, only the former are listed in the import window. I attach the project and the two files that went into it, in the hope that someone can tell me what I (or the software) did wrong. Regards, Antony Burnham

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Demeter crashing on WIndows
by mauricio.maps 05 Apr '19

05 Apr '19

Dear sirs I experienced a problem already reported on previous discussions, such as in: https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg05069.html Following Bruce´s assumption that the antivirus must be the source of the crash of arthemis and athena, I disabled my free AVG antivirus and everything worked fine. With the antivirus on, it doesn´t work. Please, can anyone help me on how can I fix it? The log file is attached. Thank you for any help. <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_cam…> Virus-free. www.avg.com <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_cam…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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Data Import Bug (Athena 0.9.26)
by Clark Adam Hugh (PSI) 05 Apr '19

05 Apr '19

Dear Mailing List I have recently come across a data import error when using Athena version 0.9.26. When importing data there appears to be a resampling which significantly reduces the resolution of the data. Attached is an example dataset with an energy step of 0.5 eV on the Cu K edge. When importing with Athena 0.9.26 this data is significantly resampled resulting in an energy resolution on the edge of 1.5 eV which can either be seen by plotting or by exporting and inspecting the datafile. Using version 0.9.25 resolves this issue entirely. The data itself appears to actually be visible correctly during the import process (the import tab shows the data listed correctly when choosing which columns to import). Is there a setting somewhere within Athena 0.9.26 that sets the default behavior to resample the imported data? Thanks Adam Clark __________________________________________ Paul Scherrer Institut Adam Hugh Clark WLGA/129 Forschungsstrasse 111 5232 Villigen PSI Schweiz Telefon: +41 56 310 41 51 E-Mail: adam.clark(a)psi.ch

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Export measured difference integrated areas
by Patridge, Christopher 04 Apr '19

04 Apr '19

Hello everyone, Is there an export option for the integrated areas found in difference spectra from Athena? It appears the only option is exporting the picture of plotted values? I was hoping to save a little from transcribing each value inside Athena. Thanks everyone, Chris ********************************************** Dr Christopher Patridge Assistant Professor Department of Chemistry SASE 315 D’Youville College 320 Porter Ave. Buffalo, NY 14201 716-829-8096 / 315-529-0501 patridgc(a)dyc.edu<mailto:patridgc@dyc.edu>

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how to best implement fitting u (oxygen parameter) in an spinel
by Juan de la figuera 01 Apr '19

01 Apr '19

Dear all, I have a naive question. I have some mixed spinels, of which I want to fit among other parameters the oxygen parameter u which indicates the distortions around the oxygen anions, using only the single scattering paths. What would be the simplest way of fitting that? In the tests I did before using Artemis, I would start with the structure (usually with a cif file), using atoms/FEFF to calculate all the paths. But changing u changes the initial structure. One way I can think of is to apply a correction, obtained by hand, to deltaR on each O-M path. Of course, this is not a general solution but only good for a few paths. Am I missing something? Thanks in advance, Juan ---------------------------------------------------------------------------- Juan de la Figuera Instituto de Quimica Fisica "Rocasolano" c/ serrano, 119 Madrid, Spain 28006 Phone: +34 91 745 9517 http://surfmoss.iqfr.csic.es/ <http://surfmoss.iqfr.csic.es/surflab/people/juan-de-la-figuera> http://scholar.google.com/citations?user=GOiP624AAAAJ -----------------------------------------------------------------------------

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Amplitude ratios greater than 100%
by Raj kumar 01 Apr '19

01 Apr '19

Dear All, With the attached CIF file, i have generated chi and other files. In turn, for some paths, i have found amplitude ratios are greater than 100% (even it is reaching few thousands % for some paths - chi file also attached with this email). I know, it is meaningless. I would like to know, why am i getting these weird ratios? What is wrong with the CIF file? Thanks, Raj

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Demeter question and Larch
by Patridge, Christopher 27 Mar '19

27 Mar '19

Hi everyone, A Demeter question - Is the memory limit hard set in Athena? I know that I can change the 50 dataset limit, but can I increase the memory to handle more data as I have a relatively large set of spectra (~150)? I have installed and tested Larch, but I do not see an option to run difference spectra in Larch GUI unless I missed something? I am running windows virtualization (win 7 - 64 bit) Demeter if that affects the memory question. Thanks everyone, Chris ********************************************** Dr Christopher Patridge Assistant Professor Department of Chemistry SASE 315 D’Youville College 320 Porter Ave. Buffalo, NY 14201 716-829-8096 / 315-529-0501 patridgc(a)dyc.edu<mailto:patridgc@dyc.edu>

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demeter on Mac 10.14.3 Mojave
by Ping, Yuan 19 Mar '19

19 Mar '19

Hello, I have a new mac laptop with Mac 10.14.3 Mojave and would like to install demeter in it. Following the steps in the website, everything worked ok during the installation. However, when I finally typed “athena” in the terminal, the following warning showed up. If I clicked OK, the Athena will just quit and gave a message “perl5.26 quit unexpectedly”. The same thing for Artemis. Hephaestus showed the same warning, but still works after clicking OK. Any clue to fix this problem? [cid:image001.png@01D4DDCA.F5FB5AD0] Thanks a lot! Yuan

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Peaks in Background Subtraction in Athena
by Nathan Nakamura 18 Mar '19

18 Mar '19

Hello, I am working on some data processing of ZrO2 thin films collected in fluorescence mode, and had a question regarding the background subtraction in Athena. When I use the default values, I see a large negative spike in the background curve (shown in BGsubtract1.png). I can vary the spline clamps and other parameters to reduce this (BGsubtract1.copy), but it does not seem to have any significant effect on the final EXAFS (EXAFScompare.png). My question is, do large spikes/instabilities on the edge like this need to be accounted for, or are they ok as long as the background fit after the edge seems fine? My thought is that as long as the EXAFS is not significantly affected, it should be fine, but I do not have a good sense for how the presence of this peak may impact the background curve beyond the absorption edge. I have also attached the project file in Athena for reference. Thanks, -Nathan

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Question on XES in FEFF
by FonsPaul 18 Mar '19

18 Mar '19

I wrote a couple of days ago asking about XES calculations in FEFF9. But I didn't hear anything back so I am rephrasing the question with a little more detail. I am calculating XES for organic molecules and used the following input. CONTROL 1 1 1 1 1 1 EDGE K EXCHANGE 0 0 1.0 FMS 5.1 LDOS -30. 15. .1 PRINT 5 0 0 0 0 0 AFOLP 1.3 S02 1.0 SCF 4.5 0 30 .2 1 XES 8 0.05 0 The XES output is shown from what I understand in the xmu.dat file in the chi column, however plotting this data shows a curve that is not positive definite. As I don’t think there is such a thing as negative emission, this probably means that my understanding is less than complete. The FEFF manual is also not very helpful on this issue and says nothing about the XES emission output. On a related question, the Feff9 docs (http://monalisa.phys.washington.edu/feff/Docs/feff9/feff90/feff90_users_gui…) specify that the XES card has the following options: XES emin emax estep But the examples that come with JFEFF seem to show options that don’t make sense with this definition: BN crystal: XES -20 20 0.2 Cu: XES 8 0.07 0.0 GeCl4 (molecule): XES 8 0.05 0.0 It is hard to understand how an emax value of 0.05 or 0.07 makes any sense. Does anyone know that the correct definitions are? Perhaps the documentation should be updated as well.

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