July 2016 - Ifeffit - millenia.cars.aps.anl.gov

No Reference Foil... Continued
by Neil M Schweitzer 14 Jul '16

14 Jul '16

Thanks for the responses. When I had originally tried fitting the CeO2 data, the fit was awful, but I think it was because the Eo was really far off. I set it close to where it should be and was able to find a common feature in Io to calibrate the rest of the samples to. That being said, fitting CeO2 is still quite difficult. I found a reference online (EXAFS analysis of the L3 edge of Ce in CeO2: effects of multielectron excitations and final-state mixed valence: J. Synchrotron Rad. (1999). 6, 34-42) that, from my understanding, essentially suggests duplicating all the paths and using a second delta_Eo value for the duplicated paths while also weighing the SO2 of each set of paths based on the degeneracy of the excitations. This does tend to make the fit better (as one would expect from doubling the number of paths!), but does anyone know if this is a generally accepted correction for fitting ceria materials? Does anyone have a different reference that might help me? Thanks for all the help! Neil

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No Reference Foil
by fred.mosselmans＠diamond.ac.uk 13 Jul '16

13 Jul '16

Dear Neil, Sorry this may be too exact an interpretation of your English, but if you are looking at the exafs then calibration is normally pretty irrelevant as long as it is not wildly out, as you refine E0 anyway in the fitting. The bond distances will be very little altered by this. If you are looking at XANES and it is 3/4 then CeL3 as I am sure you know has two "white lines" for four and one for three and the ratio of the two peaks can be used to Look at oxidation state mixtures, I think you should be able to align the peaks and fit the area e.g. Burnham AD, Berry AJ, 2014, The effect of oxygen fugacity, melt composition, temperature and pressure on the oxidation state of cerium in silicate melts, Chemical Geology, Vol:366, ISSN:0009-2541, Pages:52-60 Best wishes Fred -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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No Reference Foil
by Neil M Schweitzer 12 Jul '16

12 Jul '16

Hello, Long time follower/user and first time subscriber! I work at Northwestern University, and one of the services I provide is analyzing XAS data for users who collect data at APS. Generally, I am not at APS to help them collect spectra, I help analyze the data afterwards. A user came to me recently with some Ce L3 data that does not have reference foil data. If I am trying to compare the EXAFS of several different samples (all which should be similar oxidation state, and of which I have other references of similar oxidation state). Does anyone have a suggestion how to work up the data if I can't calibrate it? ------ Neil M. Schweitzer, Ph.D Operations Director, CleanCat Core Facility Research Assistant Professor Chemical and Biological Engineering Northwestern University 2137 Sheridan Road Evanston, IL 60208-3000 Office: 847-491-2955 http://cleancat.northwestern.edu

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Artemis (FEFF) question
by Louis Forto 12 Jul '16

12 Jul '16

Dear All, I am trying to run a FEFF calculations on a quaternary glass , when I import crystalline data obtained from ICSD website and try to run FEFF to calculate the scattering paths of nearest neighbour atoms relative to absorbing atom, I get an error message that says " generate one or more common positions and their occupancies sum to more than 1". I don't know how to go about this, any help , I will appreciate. Thanks.

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Athena crash on mac on import
by George Sterbinsky 08 Jul '16

08 Jul '16

Hello, Athena crashes upon import of the attached project file. I am using the latest release of Athena for mac (0.9.22) on OSX 10.10.5. I am able to open the file on windows. The message that is printed to the terminal when Athena crashes is pasted below. Please let me know if any further information would be helpful. Thank you, George [!!!] bkg_funnorm is not an attribute to set for Demeter::Data=HASH(0x7fe2e57967c8) at /opt/local/lib/perl5/site_perl/5.22/darwin-thread-multi-2level/MooseX/SetGet.pm line 9. MooseX::SetGet::set(Demeter::Data=HASH(0x7fe2e57967c8), "bkg_spl2e", 110.195726042215, "y_offset", 0, "bft_rwindow", "hanning", "fft_kwindow", "hanning", ...) called at /opt/local/lib/perl5/site_perl/5.22/darwin-thread-multi-2level/Demeter/Data/Prj.pm line 411 Demeter::Data::Prj::_record(Demeter::Data::Prj=HASH(0x7fe2e5785c70), 5, "psmtj") called at /opt/local/lib/perl5/site_perl/5.22/darwin-thread-multi-2level/Demeter/Data/Prj.pm line 197 Demeter::Data::Prj::record(Demeter::Data::Prj=HASH(0x7fe2e5785c70), 1) called at /opt/local/lib/perl5/site_perl/5.22/darwin-thread-multi-2level/Demeter/UI/Athena/IO.pm line 802 Demeter::UI::Athena::IO::_prj(Demeter::UI::Athena=HASH(0x7fe2dc0226a8), "/Users...sta"..., "/Users...sta"..., 1, "") called at /opt/local/lib/perl5/site_perl/5.22/darwin-thread-multi-2level/Demeter/UI/Athena/IO.pm line 164 Demeter::UI::Athena::IO::Import(Demeter::UI::Athena=HASH(0x7fe2dc0226a8)) called at /opt/local/lib/perl5/site_perl/5.22/darwin-thread-multi-2level/Demeter/UI/Athena.pm line 859 Demeter::UI::Athena::OnMenuClick(Wx::Frame=HASH(0x7fe2e28ff570), Wx::CommandEvent=SCALAR(0x7fe2e5781840), Demeter::UI::Athena=HASH(0x7fe2dc0226a8)) called at /opt/local/lib/perl5/site_perl/5.22/darwin-thread-multi-2level/Demeter/UI/Athena.pm line 782 Demeter::UI::Athena::__ANON__(Wx::Frame=HASH(0x7fe2e28ff570), Wx::CommandEvent=SCALAR(0x7fe2e5781840)) called at /opt/local/bin/athena line 44 eval {...} called at /opt/local/bin/athena line 44

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Re: [Ifeffit] How to change the data file in Dartemis?
by Isabelle Kieffer 08 Jul '16

08 Jul '16

Dear Bruce, dear all, Just to add some input and precise my question. The problem I encounter with "replace this chi(k)" did not appear to me until I tried to fit a spectrum twice with two different normalisations. In this case, after a fit on the first spectrum, I "replace this chi" with another that is normalised differently, and when I try to fit, it stops with the following error message: This data came from the the same source as another data group. You seem to be trying to increase your number of independent points by fitting the same data more than once in a multiple data set fit. Seeing that, I wondered whether "replace this chi" was doing what I thought. The upgrade did not change anything. I just tried with a colleague working under windows and the result is also the same. Shall I do differently to fit those two really similar spectra? Thank you for your help, Isabelle On 01/07/2016 21:08, Bruce Ravel wrote: > On 07/01/2016 01:57 PM, Isabelle Kieffer wrote: >> You mean that when you "Replace this chi(k)", it asks what to do, or it >> supposes that you want to fit new data with the same model? > > What I mean is: upgrade. Many of the problems you are reporting have > been fixed already. If you upgrade and still see these problems, make > a bug report and I will look into it. > > B > > -- Isabelle KIEFFER, Ingénieur de Recherche CNRS, Ligne CRG FAME (BM30B) ESRF - The European Synchrotron CS 40220 - 38043 Grenoble Cedex 9 - France Tel : +33 (0)4 76 88 25 47 - Bureau : LOB 2-50

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Athena and Artemis on the Mac
by Bruce Ravel 08 Jul '16

08 Jul '16

A few minutes ago, I made a post suggesting a work-around to a problem reported by a Mac user. My suggestion was an inherently horrible solution. That sort of line-by-line hackery is completely unsustainable. The real solution is that that fellow and his colleague should both be using the most recent version of Athena. If Athena and Artemis are to be supported on the Mac, then someone is going to have to find the time and willingness to maintain the Mac packaging. Joe Fowler did an amazingly generous thing when he made the MacPorts package, but Joe does not (to my knowledge) use Athena and Artemis for his own work. Someone who is invested in the use of the software simply has to step up. I myself have neither the resources nor the interest in doing so. If no one steps up, then there simply won't be support for my software on the Mac. B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

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Breaking off spec files within Athena
by Katharine Elizabeth Silberstein 07 Jul '16

07 Jul '16

Hi, The Cornell High Energy Synchrotron Source (CHESS) primarily uses SPEC software for XAS data collection. The data output is one continuous file containing individual scans. We are able to break off scans to import into Athena. For the convenience of CHESS users, is there any way for Athena to recognize a continuous file besides manually setting data ranges during import? Thanks, Katie Silberstein CHESS Postdoctoral Associate

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How to change the data file in Dartemis?
by Isabelle Kieffer 01 Jul '16

01 Jul '16

Dear all, I am using artemis from Demeter and I am unable to "change the current data file (that is, to apply this fitting model to a different data set)" as it was possible with the "open file" function of the old artemis. This function openned a popup window asking to choose between "read a new data file" or "change the current data file". If I use the "open project or data" function of Dartemis (or the "Add" button of the "Data sets" frame), it opens the data set in a new window. Then, I am unable to use the paths and parameters used for the previous fit. Any attemp to export, transfer or drag/drop paths or parameters has either no effect or crashes the program. If I use the "Replace this chi(k)" function, it automatically chooses to "read a new data file (that is, to do multiple data set fitting)" without opening any popup window asking my choice. I suppose I did not find the good way to apply my fitting model to a new data set. Thank you for advice. Isabelle -- Isabelle KIEFFER, Ingénieur de Recherche CNRS, Ligne CRG FAME (BM30B) ESRF - The European Synchrotron CS 40220 - 38043 Grenoble Cedex 9 - France Tel : +33 (0)4 76 88 25 47 - Bureau : LOB 2-50

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