May 2007 - Ifeffit - millenia.cars.aps.anl.gov

Re: [Ifeffit] An Ifeffit question.
by Bruce Ravel 21 May '07

21 May '07

On Friday 18 May 2007, Christian Lange wrote: > I am using "your" Athena and so on-software package for the evaluation > of my XAS-measurements. So far everything is working fine, but i have > one problem. The plots of this "graphics window" are a bit inconvenient > if it comes to a publication, because I cannot change line styles, > colors and so on. Or at least I don't know how to do this. > > That's why I want to ask you, whether it is possible to get the data for > the fourier transform plots in some sort of ASCII-format to import it in > Origin. Maybe with some file jiggling at the DOS prompt level? Hi Christian, This is a good question for the Ifeffit mailing list, so I am taking the liberty of CCing my answer there. This should be answered in the FAQ -- it certainly is frequently asked in my email! I completely agree that the plots made by pgplot are not pretty enough for publication and I suspect that Matt would not argue either. We use pgplot because it works well within the context of Ifeffit, because it is free and redistributable, and because it works equivalently on Windows, Unix, and the Mac. Matt and I both prefer to spend our limited time making good XAS software -- neither of us really felt particularly inclined to make and maintain publication quality plotting software. There are, after all, plenty of excellent packages out there for making beautiful plots. The trick, then, is the link between Athena and your favorite plotting package. In the File menu, there are a number of option for exporting data into plain-text, column-data files. These can then be imported easily into your favorite plotting program. The File menu options from "Save mu(E)" through "Save chi(q)" will save the current data group (i.e. the one highlighted in the groups list and the one whose parameters are currently on display in the main window). The mu(E) file, for instance, contains columns for energy data, background, I0, pre-edge line, and post-edge polynomial. You can import these columns into your favorite plotting program and have your way with them. The chi(R) file, as another example, has columns of R, real part, imaginary part, magnitude, phase, and back-transform window in R. Below those options is a submenu labeled "Save marked groups as data". The idea there is to save column data file where each column contains the data from a marked group (i.e. the ones with the little purple button in the groups list clicked). There are options for saving data in this way in each of the plotting spaces. Finally, it is possible to have some control over how the plots are made. In the Settings menu, select "Edit preferences". Then open up the Plot branch by clicking on its little plus sign. The options c0 through c9 and the linetypes option might be of interest to your. Nothing among the preferences will magically make pgplot prettier, but it may help you visualize your data. HTH, B P.S. You can join the Ifeffit mailing list at http://cars9.uchicago.edu/mailman/listinfo/ifeffit/ It tends to be high quality conversation (except the parts written by me, of course) and high signal-to-noise. -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advanced Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

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Open post-doctoral position - please, advertise
by Michel Meyer 16 May '07

16 May '07

Dear colleagues, Bruce Ravel has suggested me to contact you in order to post the following announcement on the IFEFFIT website. Thank you very much for considering this offer. The position will stay open until the end of the year 2007. With all my best regards, Michel Meyer Post-doctoral fellowship The Institut de Chimie Moléculaire de l'Université de Bourgogne (Dijon, France) is seeking a motivated candidate for a one-year funded postdoctoral position with a strong background in X-ray Absorption Spectroscopy (XAS). In collaboration with the Rossendorf Beamline scientists at ESRF, the successful candidate will be involved both in the acquisition and interpretation of XANES and EXAFS data in order to unravel the coordination scheme of U(VI), Pu(IV) and Eu(III) on surface-modified mesoporous hybrid materials obtained by covalent grafting of functionalized macrocyclic ligands onto silica gel. These materials have found applications as solid/liquid extracting agents of actinides in an ultrapufication process of radioactive wastewaters. The following points are considered mandatory: * The applicant should have a well-established experience in X-ray absorption spectroscopy. * The applicant should hold a Ph.D. for less than 5 years. ....* Only candidates that have never been employed in France are eligible. Additional Information can be found at http://www.icmub.fr/ Please send your application including a CV, list of publications and at least 3 references to: Dr Michel MEYER LIMRES Institut de Chimie Moléculaire de l'Université de Bourgogne UMR 5260 du CNRS 9, Avenue Alain Savary BP 47870 21078 DIJON Cedex - FRANCE Tel : (33) 03 80 39 37 16 Fax : (33) 03 80 39 61 17 e-mail : Michel.Meyer(a)u-bourgogne.fr ****************************************************************** Michel MEYER Chargé de Recherche LIMRES Institut de Chimie Moléculaire de l'Université de Bourgogne UMR 5260 du CNRS 9, Avenue Alain Savary BP 47870 21078 DIJON Cedex - FRANCE Tel : (33) 03 80 39 37 16 Fax : (33) 03 80 39 61 17 e-mail : Michel.Meyer(a)u-bourgogne.fr site web http://www.u-bourgogne.fr/LIMSAG/ ******************************************************************

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How to select important MS paths in wurtzite?
by Mauro Rovezzi 16 May '07

16 May '07

Dear all, Do you know if in literature there are studies on the important multiple scattering (MS) paths in fitting wurtzite XAFS spectra? I mean which are the important paths to properly fit a wurtzite structure up to 6 A in a elegant way (<20 paths)? I'm asking this question thinking at old works by Filipponi et al. on the fcc and bcc structures explaining very well the importance of some specific triangular and collinear paths to fit the EXAFS spectrum... Well, this was my coffee-break question :) Mauro -- Mauro Rovezzi <rovezzi(a)esrf.fr> PhD student - GILDA BM08 c/o ESRF (Grenoble, FR)

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Re: [Ifeffit] how to recognize element with a difference of Z<2?
by Bruce Ravel 15 May '07

15 May '07

Sebastiano, You are correct that EXAFS is relatively insensitive to atoms that are nearby on the periodic table. This is because the backscattering amplitudes and phase shifts are functions of, in part, Z number. In the case of stochastic replacement of a host atom by a dopant on the exact position of the lattice site, it can be difficult or impossible to distinguish nearby atoms. However, if the introduction of the dopant is accompanied by a distortion to the lattice, the situation might be a lot friendlier. In that case, you may be able to notice two (or more) distances in the neighboring shells, one of which can be explained by the host atom and the other(s) by the dopant. Even better, you can measure data at the edges of both host and dopant and corefine the data. That additional information might be enough to figure out what's going on. I also think that your case -- an alloy -- might be a good candidate for high energy diffraction using PDF analysis methods. PDF, or PDF combined with EXAFS, might help for your problem. Good luck, B On Tuesday 15 May 2007, Cammelli Sebastiano wrote: > Dear > > I am Sebastiano and I am working on some metallic alloy composed by > several diluted elements in a Fe matrix. The main elements are: Cu, Cr < > 0.5at%; Mn, Ni < 1.5at%, I collected some spectra at different K edge > (Mn, Ni, Cu). Submitting this alloy by annealing treatment (775K) and > neutron irradiation, some clusters are expected mainly composed by Cu; > Ni and Mn play an important role but it is not so clear. Some problems > rise when I try to analyze these data: > > "It is known" that it is not so easy to recognize by EXAFS the > difference from near elements as Fe and Mn (Z=26,25) and Cu, Ni (29,28) > because these elements has a similar electronic distribution. Performing > the analysis by Artemis I found some 'realistic' value of Mn Fe and Ni > in the first and second shell (Cu K edge), have these values any > physical meaning since I cannot distinguish element as Fe and Mn? > > Do you know any tricks that could help me? Maybe the right answer is > that EXAFS is not enough to investigate these alloys, but if I cannot > distinguish the different atoms, which kind of quantitative information > could I get? The interatomic distances are important but which is the > meaning of distance between the absorber (Cu) and an unknown atom (Fe or > Mn, Cr or Mn, Cu or Ni?)? > > Thank you help and for your time. > > Sebastiano > > > > Sebastiano.cammelli(a)psi.ch > > Paul Scherrer Institute, Villigen 5232 (CH) -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advanced Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/

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Document Bug?
by Annette.Koo＠csiro.au 15 May '07

15 May '07

Not sure if this is the right place to report bugs, but upon opening either Artemis or Athena, and clicking 'Help - Document' I get the following error message, along with an empty 'pod'. Tk::Error: image "fileopen16" doesn't exist at /Per1App/Tk.pm line 228. Tk callback for image5 [\&main::_ANON_] <menu invoke> main::_ANON_<'Tk::Error: image "fileopen16" doesn\'t exist at /Per1App...... and so on for several more lines. It was working alright last month so not sure what happened. Do I need to re-install? Thanks for your help, Annette

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care and feeding of Athena
by Bruce Ravel 09 May '07

09 May '07

Hi, This week I received a bug report from an Athena user here at the APS. The problem is a bit complicated to explain, but the executive summary is that two different ways of moving chi(k) data from an Athena project file into Artemis resulted in two different spectra even though they should have been identical. I spent a bit of time trying to track down the exact nature of the bug, but it has proven a bit elusive. I can say this, the Athena project file which demonstrates the problem has 148 groups in the group list. This problem cannot be replicated in a project file with a few (or even a couple dozen) groups in the group list. Many of you will recognize the nature of the problem. 148 is more groups than Athena can comfortably handle. I'll explain this issue in some detail below. Before I do, I'll give a good rule of thumb that will help keep Athena happy with you and you happy with her: =*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*= Don't import too much data into your Athena project! About 50 or 60 data groups in the group list is a good upper limit. With fewer groups, Athena should work reliably. With more, Athena will eventually become unstable. If you need more than 60 data groups, you need to split your ensemble of data into two or more subsets and process each subset individually. =*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*= Why is that? Well, to answer, I need to explain a bit about how Athena works. All of the hard work (Fourier transforms, background removal, normalization, and so on) is done by a library of numerical and exafs-related functions called Ifeffit, which is the thing written by Matt. Athena is really just a glorified bookkeeper. She keeps track of your data and of the values of all your parameters. When it comes time to do any of the actual numerical work, she organizes the problem, then asks the Ifeffit library to take care of it. When it comes time to make a plot, Athena organizes how the plot should be made, then asks Ifeffit to take care of it. In the case of plotting, Ifeffit, in turn, asks another library called Pgplot to actually make the plot on the screen. This stack of software tools is actually quite more complicated than that. Ifeffit and Pgplot are written in a programming language called Fortran. Athena is written in a different language called Perl. There is a small piece of code written in C which allows the Perl program to talk to the Fortran libraries. Additionally, Athena uses a graphical toolkit called Tk, which is written in C, to draw buttons and sliders and text boxes and such on the screen. The point here is that Athena is something of a house of cards. Lots of different software components need to be working together correctly in order for you to do your data analysis. (One might be astonished that Athena works in the first place. Ssshhhh!!! If you lose faith, everything will come tumbling down!) Because Athena requires so many concurrently functioning pieces, it has some weak spots. One of these weak spots is quite serious. The Fortran programming language (the one used to write Ifeffit) is quite old -- early versions of Fortran date back to the mid 60s, a time when RAM was measured in kilobytes rather than gigabytes. One feature of modern programming languages that Fortran lacks is the ability to claim and release memory. Consequently, a Fortran program has to allocate enough memory to run at the moment that it starts running. If, during the course of operation, the Fortran program moves to a state in which it needs more memory -- it's out of luck. What's worse, Fortran does not even provide particularly good tools for failing gracefully when it attempts to exceed its memory limit. Ifeffit, then, allocates some large amount of memory up front and then uses some clever heap management techniques written by Matt himself to make the most effective use of the available memory. It works well, up to a point. If you attempt to import too much data into Athena, Ifeffit will run into its memory limit and begin to behave erratically. Obviously, when Ifeffit behaves erratically, so does Athena. It would seem that having 148 data groups triggers a bug in the heap management scheme. Drat! And that is why you should not have too many data groups in your Athena project file. So, should Ifeffit be rewritten in some language that does dynamic memory allocation? Probably, but that would be a lot of work and Matt has both a daughter and a day job. B -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advanced Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/

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Coordination of ball-milled alloys
by Alejandro Fernandez-Martinez 09 May '07

09 May '07

Dear all, I am quite new to XAS data analysis, maybe you can help me with a little problem I have. I am trying to fit EXAFS data at Cr K-edge of a bcc Fe30Cr70 alloy synthesized by ball-milling. For those who don't know it, this technique is very effective in alloying metals but introduces a lot of structural defects in the structure. This is clearly seen in neutron diffraction data (with DW 2 times larger than DWs of a Cr reference and larger FWHMs). When fitting the EXAFS data without any specific constrain (only for distances) I get DWs on the same order of magnitude for the Cr-foil than for the alloy, and a very reduced coordination of N1=2.3 (compare with N1=8 for the Cr-foil) for the first neighbour (without physical sense?). In order to take into account the larger DWs for the alloyed sample (as found in diffraction data) I have constrained the minimum value of the DWs to a value double than the DWs of the Cr-foil. This gives me an increase of the N for the first shell, but at the same time, I have to refine lambda (photoelectron mean free path) in order to correct the excesive decay introduced by the DW exponential in the EXAFS formula, and to get a good fit. Then I get a more physically understandable N1=5.5. - The 1st question is: do you think the logical discourse that I have followed until now is correct? I don't have idea on how much some quantities as lambda should or not be refined. - 2nd question: what dou you think about the use of diffraction data as constraint for EXAFS data analysis? Many thanks in advance! cheers, Alex -- Alejandro Fernandez-Martinez Institut Laue-Langevin 6, rue Jules Horowitz - B.P. 156 38042 Grenoble Cedex 9, France Tel: +33 (0)4.76.20.75.71 Fax: +33 (0)4 76.20.76.48 fernande(a)ill.fr -- Geochimie de l'Environnement LGIT - UJF BP 53 38041 Grenoble Cedex France

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How to use "OVERLAP" card?
by Jun Lin 09 May '07

09 May '07

I have read some references of Kelly Shelly, and I have got some idea of how to construct a structure without difinite crystalline structure. But when I try to apply to my own question, meet some difficulties. In my case, four nitrogen atoms is surrounding a iron atom. So I use OVERLAP and SS card as to define such system as described in the FEFF manual: -------------------------------------------------- POTENTIALS * ipot Z element 0 26 Fe 1 7 N * Determine approximate overlap for central and 1st nn in Cu OVERLAP 0 *determine overlap for central atom of Fe *iphovr novr rovr * ipot, number in shell, distance 1 4 2.15 OVERLAP 1 *determine approximate overlap for 1st shell N *iphovr novr rovr * ipot, number in shell, distance 0 1 2.15 *SS index ipot deg rss SS 1 1 4 2.15 -------------------------------------------------- but feff8 stopped and said: Absorbing atom coords not specified. Cannot find multiple scattering paths. since the OVERLAP does't need ATOMES card, where can I define the coordination of absorbing atom? Is there any other CARD needed for such situation? ========================================= Hi Jun, That keyword is explained here: http://feff.phys.washington.edu/feff/wiki/index.php?title=OVERLAP I think the problem is that you have not specified the SS keyword: http://feff.phys.washington.edu/feff/wiki/index.php?title=SS I use the overlap/ss thing in feff very infrequently. My preference is to start from a known structure that is somehow similar to the material I am investigating. For example, if I were to look at amorphous germanium, I would use crystalline germanium as my starting point. I would then construct the model in such a way that I parameterize the differences between the starting structure and what I expect to find in the data. I'd recommend reading papers by Scott Calvin or Anatoly Frenkel on nanoparticles or by Shelly Kelly on uranium in biogeochemical systems for excellent examples of how that sort of analysis is done. Hope that helps, B -- Shanghai Institute of Applied Physics, Chinese Academy of Sciences No. 2019, Baojia Road, Jiading District, Shanghai,China 201800

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How to use "OVERLAP" card?
by Jun Lin 08 May '07

08 May '07

Hi everybody: It is the first time I send mail to this list. I wanna use OVERLAP of Feff8.4 to design a structure for my analysis, but the program give error message as followed: > Feff 8.40 > OVERLAP: > Expert option, please read documentation carefully and check your results. > OVERLAP: > Expert option, please read documentation carefully and check your results. > My test for OVERLAP > Absorbing atom coords not specified. > Cannot find multiple scattering paths. > RDINP > STOP statement executed in my feff.inp, I wrote like this: TITLE My test for OVERLAP * pot xsph fms paths genfmt ff2chi CONTROL 1 1 1 1 1 1 PRINT 0 0 0 0 0 0 POTENTIALS * ipot Z element * l_scmt l_fms stoichiometry 0 26 Fe 1 7 N OVERLAP 0 0 1 0.00 1 4 1.15 END Is there anyone give me some suggestion? Thanks! Lin Jun -- Shanghai Institute of Applied Physics, Chinese Academy of Sciences No. 2019, Baojia Road, Jiading District, Shanghai,China 201800

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Ru input file - a question and a problem
by Vivek Murthi 02 May '07

02 May '07

Hi Bruce/Matt/Scott I am trying to fit some Ru based catalysts using Ifeffit - 0.8.007. 1. Does anyone have an atoms input file for Ruthenium that they can share with me? _ The problem:_ 1. I got the crystallographic data for Ru from "database.iem.ac.ru/*mincryst*/" which I used inside atoms to generate FEFF a input file. However, FEFF returns an error saying that my atoms list might be wrong and that two atoms are separated by less than an 0.93 angstroms. I also checked the 5 digit precision in the input file to make sure that wasn't creating the problem. The FEFF input file generated by atoms definitely has atoms bizarrely close to each other. I do not understand why a standard crystallographic data would give such results. I have attached the "Ru.inp" input file I used and the error buffer from FEFF below for your convenience. 2. So I tried playing around with the atoms input file. I set all the xyz co-ordinates to 0, then the FEFF runs without any error but that however gives me 2 Ru paths with two separate R eff ( 2.14 and 2.70 A) but very close to each other in the first shell. Is this a possible scenario? Thank you for your time/comments/solutions. Vivek # Artemis version 0.8.007 # This file created at 16:41:31 on 2 May, 2007 # using Windows XP, perl 5.006001, Tk 800.024, and Ifeffit 1.2.9 # IFEFFIT_DIR is C:\Program Files\Ifeffit # Workspace: C:\Program Files\Ifeffit\horae\stash\artemis.project.1\ Feff 6L.02 WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 1 2 1 0.00000 0.00000 0.00000 2 0.00000 0.00018 0.00000 Run continues... WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 3 9 3 -1.56108 0.00014 2.14100 9 -1.56116 0.00009 2.14100 Run continues... WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 4 5 4 0.78066 -1.35186 2.14100 5 0.78058 -1.35191 2.14100 Run continues... WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 6 10 6 -1.56108 0.00014 -2.14100 10 -1.56116 0.00009 -2.14100 Run continues... WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 7 8 7 0.78066 -1.35186 -2.14100 8 0.78058 -1.35191 -2.14100 Run continues... WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 11 13 11 0.78058 1.35209 2.14100 13 0.78066 1.35214 2.14100 Run continues... WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 12 14 12 0.78058 1.35209 -2.14100 14 0.78066 1.35214 -2.14100 Run continues... WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 15 23 15 0.00000 -2.70382 0.00000 23 0.00000 -2.70400 0.00000 Run continues... WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 16 21 16 2.34173 -1.35182 0.00000 21 2.34173 -1.35200 0.00000 Run continues... WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 17 22 17 -2.34173 -1.35182 0.00000 22 -2.34173 -1.35200 0.00000 Run continues... WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 18 24 18 2.34173 1.35200 0.00000 24 2.34173 1.35218 0.00000 Run continues... WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 19 25 19 -2.34173 1.35200 0.00000 25 -2.34173 1.35218 0.00000 Run continues... WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 20 26 20 0.00000 2.70400 0.00000 26 0.00000 2.70418 0.00000 Run continues... ... Calculating potentials and phases... free atom potential and density for atom type 0 free atom potential and density for atom type 1 overlapped potential and density for unique potential 0 overlapped potential and density for unique potential 1 muffin tin radii and interstitial parameters phase shifts for unique potential 0 This warning indicates a problem in the Atoms list. For some reason you have atoms that are separated by than 0.93 Angstroms (or 1.75 Rydberg). This may be due to the presence of hydrogen atoms in your feff.inp file, in which case this is an innocuous warning and may be ignored. However, this may indicate a problem constructing the Atoms list. The most common cause of this problem is a mistake in the crystallographic data used on the Atoms page. You may have incorrect values for lattice constants or angles or incorrect values for site coordinates. You may need a shift vector to move the lattice into its standard setting. Please be aware that Atoms works with 5 digits of precision. Thus, if you have a site with a coordinate of 1/3, you should use either "1/3" or "0.33333" on the Atoms page. Using insufficient precision, say "0.333" is a common cause of this error message. Artemis has continued on the possibility that the warning is caused by hydrogen atoms, but be warned that the feff.inp may require your attention. ! This atoms input file was generated by Artemis 0.8.007 ! Atoms written by and copyright (c) Bruce Ravel, 1998-2001 title = ... space = P63/MMC a = 2.7040 b = 2.7040 c = 4.2820 alpha = 90.0 beta = 90.0 gamma = 120.0 core = Ru edge = K rmax = 3.0 shift 0.00000 0.00000 0.00000 atoms ! elem x y z tag occ. Ru 0.33330 0.66670 0.25000 Ru 1.00000

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