Re: [Ifeffit] XAS viewer unit detection during data reading
Dear Siebe, did you try to change the data type from "raw" to XAS. If you click on the small arrow on the right you should have the choice between xas and raw. On my computer that works and after that I can choose the unit for the X-axis. For some reason "raw" seems to be the preset choice. Maybe Matt could change that, I fell into this trap several times. Cheers, Edmund From: "van der Veer, Siebe" To: "XAFS Analysis using Ifeffit" Sent: Tuesday, 28 February, 2023 13:16:18 Subject: [Ifeffit] XAS viewer unit detection during data reading Dear all, I am not sure if this mailing list is the correct medium for this question. Apologies, if not. I am looking to import files in XAS viewer, which worked fine in ATHENA, but in XAS viewer the correct units of the data are not detected and I cannot manually change them. I can get a plot of the data, but the data is not recognized by the software as XAS data, i.e. a lot of plotting/conversion options do not show. I hope the following screenshots provide sufficient information to illustrate my issue. Reading in a .dat file of fluorescence data. I can't change the units in the marked area. The data can be read into the XAS viewer, but I don't have the regular plotting options in these dropdown menus. Any advice would be much appreciated. Kind regards, -- Siebe van der Veer | PhD student Nanostructures of Functional Oxides | Zernike Institute for Advanced Materials University of Groningen | Nijenborgh 4, 9747 AG Groningen | The Netherlands Email: [ mailto:s.van.der.v...@rug.nl | s.van.der.v...@rug.nl ] | ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
Re: [Ifeffit] Installation of Athena on Linux Ubuntu
Dear Mohamed, you will find instructions how to install the software under Linus on Bruce's webpages: [ https://bruceravel.github.io/demeter/ | https://bruceravel.github.io/demeter/ ] Look out for "David Hughes' guide to Demeter Installation on Ubuntu" Don't use the version from the Ubuntu repositories, it is very old. You have to compile the software on your computer. If you follow the instructions you will (finally) be able to do so. Please be aware, that the instructions are for older Linux/Ubuntu versions and that some libraries are meanwhile updated. Well, you have to read all the stuff that is written in the terminal when you install the dependencies, some will not be installed with the version numbers in the instructions, you must identify the correct version numbers and install these newer versions. Best of luck, Edmund From: "MOHAMED NAJI" To: Ifeffit@millenia.cars.aps.anl.gov Sent: Thursday, 7 March, 2019 14:05:45 Subject: [Ifeffit] Installation of Athena on Linux Ubuntu Dear All, I would like to install Athena in my Linux Ubuntu 16.04 OS. Any idea on how to and if there is already a software develloped for Linux OS. I searched but didn't find it and I'm wondering if someone has already developed it. Thank you Mohamed Naji -- ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
Re: [Ifeffit] Transmission EXAFS sample
Dear Jatin, the optimum mued of 2.x is not just derived by simple photon counting statistics. As Matt pointed out, for transmission measurements at a synchrotron beamline in conventional scanning mode this is seldom a matter. Nevertheless, one should avoid to measure subtle changes of absorption at the extreme ends, that is, transmission near 0 % or 100 %. In optical photometry this is described by the more or less famous Ringbom plots which describe the dependency of the accuracy of quantitative analysis by absorption measurements (usually but not necessarily in the UV/Vis) from the total absorption of the sample. This time the number is only near to 42, the optimum transmission is 36.8 % (mue = 1). So, to achieve the highest accuracy in the determination of small Delta c (c = concentration) you should try to measure samples with transmissions near to this value (actually the minimum is broad and transmissions between 0.2 and 0.7 are ok). In our case, we are not interested in the concentration of the absorber, but we are also interested in (very) small changes of the transmission resp. absorption in our samples. Or, using Bouger, Lambert Beer's law, in our case mue (-ln(I1/I0) is a function of the absorption coefficient (mue0). The concentration of the absorber and the thickness (d) of the sample are constant. -ln(I1/I0) = mue0 * c * d But then: If the optimum is a mue between 0.35 and 1.6 why are we all measuring successfully (ok, more or less ;-) using samples having a mue between 2 and 3? ...and 0.35 seems desperately small to me! Maybe sample homogeneity is an issue? Cheers, Edmund Welter ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] consultation
Dear Mingliang, Thanks for your explain. But I am still puzzled. Following your instruction, I performed *Self-Absorption *for the samples, choosing *XANES(Fluo) *from *algorithm*, but I did not know the real meaning of *Formula*. Does it mean the species formula which I wish to detect? Or the whole composition of the sample? The composition of the whole sample. You do not need to know the species, you only need to know thew elemental composition of your sample. A hairy task if you don't digest your sample completely and put it into an ICP-MS or anything like that. I don't know which precision is necessary to yield usable results. Maybe someone else tested or calculated it. In principle the matrix produces just a smooth background absorption and knowing the composition it is easy to calculate the amount of this absorption using tabulated scattering factors. But it should also be possible to determine this background experimentally, for instance extrapolating the background before the edge. But for this you would need a blank spectrum to calibrate the mued value. If you follow the link to the document section in Athena a very instructive webpage will open and among other things you will find citations of the original papers underlying the four different algorithms used for the self absorption correction. I used natural mineral to interact with selenite, then I wish to check the speciation of the selenium reaction product. For my case, should I fill the blank with Se or FeSe or both of them (because currently I do not know the exactly containing speciation)? As said before, the chemical Formula of the entire sample. Chemical formula here does not mean you have any kind of chemical bond, it just means molar ratio. For the angles, normally are they 45? Becuase I measured the samples in fluorescence mode, and didnot measure the angles between sample, incoming beam and detector. I tried to input *Se *in the *Formula* entry, and select 45 for the angles, then I got a corrected spectra which was higher than the original one. 45 degrees is the usually used geometry. However, the program asks for the geometry which you used not for the usually used geometry! If it was 45 degrees than its fine. Obviously the algorithm does what it is supposed to do, it amplifies the oscillations. But this does not mean that the result is correct! It will only be correct if the input parameters were correct. But when I using this spectra for LCF analysis, I still could not got overlapping line for the fitted spectra with the sample spectra... Using pure Se in the self absorption correction is definitely wrong, it overestimates the effect dramatically. Actually the effect more or less disappears for diluted samples. But even if the spectra were properly corrected I can not see any reason why the used set of reference spectra MUST fit the spectrum of your sample. There are many possible reasons for this, the most likely is that you are missing one or more important reference spectrum (Or you are not using enough references/free parameters in your fit...;-) Best regards, Edmund Welter ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] consultation
Dear Mingliang, simply because Athena is not normalising the height of the highest peak (the white line) but the EXAFS region, that is it starts some 10 eV above the edge. You choose the normalisation region in Athenas settings. You can see in your plots that it does this job quite well, the spectra oscillate around 1 (at E E0+40 eV). Anyway, take care what you do when you try to fit a fluorescence yield XAFS spectrum with references which were measured in transmission mode. You must at least be sure that you considered the self absorption effect which dampens the oscillations (most notably the large oscillations in the XANES region). The importance of this effect depends on your sample's composition. Athena contains functions to correct the self absorption. In order to do this you need the elemental composition of your sample and the angles between sample, incoming beam and detector. Best regards, Edmund Welter ?? wrote: Dear, I want to to ask a question about using Linear Combination Fitting in Athena. I normalized all the references(measured in transmission mode) and samples (fuorescence mode) with Athena, and then wish to use LCF to quantify each unique component in the samples. But I noted that the normalized samples spectra had lower height at the white line peak than any references(shown pic-1.emf in annex), thus the fitted spectra were also higher than the original sample spectra (shown pic-2 and -3.emf in annex). I do not know why? I also attached all the original data(before normalization). Wish to obtain guidance from you. Thanks! Best wishes Mingliang ?? http://www.yeah.net/?from=o1 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
[Ifeffit] Open position at HASYLAB
Dear XAFS users, if you are interested or know someone who might be interested in a postdoc position in the field of spectroscopy with X-rays, please have a look at our recent job advertisement: http://www.desy.de/v2/docs/1257511440-e.pdf Regards, Edmund Welter ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Pellet sample preparation
Hi Dominik, you can use cellulose powder (Aldrich) it forms very stable pellets and does not stick to your pressing tool like BN. Chemically it is definitely less inert than PE but I never saw that it reacted with samples. An advantage of the cellulose powder over the Uvasol PE is that the grain size distribution is much more homogeneous and the particles are smaller enabling much more homogeneous samples than the PE (That is you must not sieve it before use). If you use BN be sure to have some vaseline at hand, otherwise you will not be able to remove the pellet from the pressing tool. Some people used PTFE powder, don't know if it works but at least F is a heavy element compared to H. When Merck ceased to sell the Uvasol PE we tested a all PE powders we could lay our hands on but couldn't find one that formed stable pellets. Regards, Edmund Dominik Samuelis wrote: Dear list, for many years, I have used Merck Uvasol Polyethylene for spectroscopy PE powder as a diluent and binder for pressing self-supporting pellets especially of air-sensitive substances. When I today wanted to order a new bottle, I had to learn that it's not available anymore (actually, since 2002... :-)). Does anyone of you know about any other supplier of spectroscopy-grade polyethylene powder? And more general, which binder/diluent do you use for preparing pellets of sensitive substances ? Best regards, Dominik ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] negative amplitude
Dear Wojciech, I presume you mean the amp_x value, this topic was discussed in January 07 on this list and Scott Calvin and Kelly Shelly gave useful hints (The subject was is there a physical meaning to a negative S02) It all boils down to the question what happens if you multiply sin(x) with -1. So it seems that the model you use in your FEFF calculation is off by a half an oscillation. regards, Edmund Welter Wojciech Starosta wrote: Sorry if it is FAQ. But I spent some time on fitting without success and have not found answer to this. Does anybody could explain me if negative value of amplitude has any sense. I can get beautiful plot after fit, but unfortunately the message appear concerning negative value of amplitude (amplitudes). How to avoid it. Any written material will be very helpful. I know that I can define amplitude as squared value of new variable. But sometimes it does not work. Ifeffit stops with message that value of this variable cannot be determined With the best regards Wojtek Starosta Institute of Nuclear Chemistry and Technology 03-195 Warsaw, Dorodna 16 Institute of Nuclear Chemistry and Technology --- avast! Antivirus: Outbound message clean. Virus Database (VPS): 0649-1, 2006-11-18 Tested on: 2007-11-30 13:45:41 avast! - copyright (c) 1988-2007 ALWIL Software. http://www.avast.com ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
[Ifeffit] XAFS postdoc position at HASYLAB
Dear colleagues, at the Hamburger Synchrotron Strahlungslabor (HASYLAB) a postdoc position in the XAFS business is available. If you or one of your colleagues is interested please contact me by e-mail or phone (address at the bottom of this mail). The main task will be the operation of our new XAFS-beamline (beamline C). As a postdoc you will have the opportunity to use HASYLAB's facilities for your own research. Moreover, you will be a live witness of the construction and commissioning of the new high brilliance source PETRA III (user operation at PETRA III will start in 2009) and of the start phase of the XFEL project. If you have questions about this mail or the available position please do not reply to the mailing list, but contact me directly instead. Best regards, Edmund Welter ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
