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

ifeffit on Mac OSX 10.7 (Lion)?
by Peggy O'Day 08 Jan '12

08 Jan '12

Hi, Does anyone know if there is a version of ifeffit that works on the new Mac OSX 10.7 (Lion)? iXAFS on Snow Leopard was great… but doesn't work on Lion (at least not obviously). thanks, Peggy ********************************************************* Peggy O'Day Professor & Founding Faculty School of Natural Sciences University of California, Merced 5200 North Lake Road Merced, CA 95343 (209) 228-4338 poday(a)ucmerced.edu

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star parser to be installed for Horae
by denis testemale 05 Jan '12

05 Jan '12

Dear Carlo, dear members of the list, I just wanted to share something about a problem with horae I just solved. I don't know if it is related to the debian and debian-like builds of horae or something else. Here is the context: - I run ubuntu - I use the last versions of horae package, but I had the same problem for years... - I could not import a .cif file in Artemis (error trapped) and had to enter the data manually. I decided to take the time to solve this small but annoying problem and it appeared to be easily done: the error message said that I could not import a cif file because the STAR::Parser was not installed. By installing libstar-parser-perl I solved the problem. In an old message, Carlo you said that you had built the packages which included (among other things) this libstar-parser-perl package: http://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg00256.html but for some reasons it did not install even if I used your horae packages on your repositories. If that helps someone... Cheers denis

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Extracting "raw values" from ATHENA and ARTEMIS plots
by Tony Kelly 04 Jan '12

04 Jan '12

Hello All, I am attempting to essentially extract the numbers behind the graphical outputs of ARTEMIS and ATHENA. Currently, the only way I have been able to do this is to save a plot, then use third party software to click points on the graph and extract the information, which I can then analyze further and plot in ROOT. I suppose I could try to abandon the GUI interface and write command line scripts, writing out the arrays into text files as I go along... but I'd rather not have to go that far under the hood if possible. Does anyone know how I might extra this information from the GUI? An ATHENA example, say I plot the background subtracted signal in k-space, is there a way of then finding the numbers that went into forming this plot? Thanks much, Tony Kelly -- Tony Kelly, M.Sc. DTRA PhD Student Air Force Institute of Technology Nuclear Physics and Engineering

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Re: [Ifeffit] Deconvolution of K-edge of lanthanides
by Eugenio Otal 04 Jan '12

04 Jan '12

Hi Bruce, thanks for the help. Looks not so straightforward like L edges. The information has a price. I also found this software: http://www.cells.es/Beamlines/CLAESS/software/xanda.html Kind Regards, euG 2012/1/3 <ifeffit-request(a)millenia.cars.aps.anl.gov> > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. tutorial + data athena and sixpack (Pieter-Jan Sabbe) > 2. Re: tutorial + data athena and sixpack (Scott Calvin) > 3. Re: tutorial + data athena and sixpack (Bruce Ravel) > 4. Deconvolution of K-edge of lanthanides (Eugenio Otal) > 5. Re: Deconvolution of K-edge of lanthanides (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 02 Jan 2012 22:54:12 +0100 > From: "Pieter-Jan Sabbe" <PieterJan.Sabbe(a)ugent.be> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] tutorial + data athena and sixpack > Message-ID: <20120102225412.20801zllz36q8zgk(a)webmail.ugent.be> > Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; > format="flowed" > > Dear all, > > This spring I need to supervise some undergraduate students during a > 4-week project in my research group. I would like to introduce them > into the world of data processing with athena and sixpack. I would > like to find a tutorial for sixpack and some test data on principal > component analysis and linear combination fitting before giving them > some of my own data. Can anybody help me ? Or anybody else had to > teach something similar, any idea would help! > > Thank you very much in advance, > > Have a great 2012 > > PJ Sabbe > > -- > Met Vriendelijke groeten, > Pieter-Jan Sabbe > > > Pieter-Jan Sabbe > Vakgroep Analytische Chemie > Universiteit Gent > Krijgslaan 281 S12 > B-9000 Gent > Tel +32 (0)9/264 48 20 > E-mail: pieterjan.sabbe(a)ugent.be > > > > > ------------------------------ > > Message: 2 > Date: Mon, 2 Jan 2012 17:05:24 -0500 > From: Scott Calvin <scalvin(a)sarahlawrence.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] tutorial + data athena and sixpack > Message-ID: <D9F45019-20AC-4D45-923B-261BBFEE1877(a)slc.edu> > Content-Type: text/plain; charset="us-ascii" > > Hi Pieter-Jan, > > The "EXAFS Divination Set" should work as test data, although I haven't > tried PCA on it: http://www.xafs.org/EXAFS_Divination_Set > > Feel free to contact me for follow-up if you'd like to know more about > that set, etc.. > > --Scott Calvin > Sarah Lawrence College > > On Jan 2, 2012, at 1:54 PM, Pieter-Jan Sabbe wrote: > > > Dear all, > > > > This spring I need to supervise some undergraduate students during a > > 4-week project in my research group. I would like to introduce them > > into the world of data processing with athena and sixpack. I would > > like to find a tutorial for sixpack and some test data on principal > > component analysis and linear combination fitting before giving them > > some of my own data. Can anybody help me ? Or anybody else had to > > teach something similar, any idea would help! > > > > Thank you very much in advance, > > > > Have a great 2012 > > > > PJ Sabbe > > > > > ------------------------------ > > Message: 3 > Date: Tue, 3 Jan 2012 10:48:45 -0500 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] tutorial + data athena and sixpack > Message-ID: <201201031048.46156.bravel(a)bnl.gov> > Content-Type: Text/Plain; charset="iso-8859-1" > > On Monday, January 02, 2012 04:54:12 pm Pieter-Jan Sabbe wrote: > > Dear all, > > > > This spring I need to supervise some undergraduate students during a > > 4-week project in my research group. I would like to introduce them > > into the world of data processing with athena and sixpack. I would > > like to find a tutorial for sixpack and some test data on principal > > component analysis and linear combination fitting before giving them > > some of my own data. Can anybody help me ? Or anybody else had to > > teach something similar, any idea would help! > > Pieter-Jan, > > There is a ton of useful stuff and useful links at > http://xafs.org/Tutorials, including much written by folks whose > names you'll recognize from this mailing list. > > B > > -- > > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 > Building 535A > Upton NY, 11973 > > My homepage: http://xafs.org/BruceRavel > EXAFS software: http://cars9.uchicago.edu/ifeffit/Demeter > > > ------------------------------ > > Message: 4 > Date: Tue, 3 Jan 2012 17:10:58 +0100 > From: Eugenio Otal <eugenioh(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Deconvolution of K-edge of lanthanides > Message-ID: > <CAKUU9GSiBC2sNz4ow9g_C3_X=07kTQFW9Kh77Aw4VfCH1JAJTA(a)mail.gmail.com > > > Content-Type: text/plain; charset="iso-8859-1" > > Hi all, > I am dealing with some spectra of Er and Yb in the K-edge. > Does somebody was doing the deconvolution of the spectra in these energies? > I will appreciate all the help to treat the spectra in this high energy > regions. > Kind regards, euG >

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Deconvolution of K-edge of lanthanides
by Eugenio Otal 03 Jan '12

03 Jan '12

Hi all, I am dealing with some spectra of Er and Yb in the K-edge. Does somebody was doing the deconvolution of the spectra in these energies? I will appreciate all the help to treat the spectra in this high energy regions. Kind regards, euG

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tutorial + data athena and sixpack
by Pieter-Jan Sabbe 03 Jan '12

03 Jan '12

Dear all, This spring I need to supervise some undergraduate students during a 4-week project in my research group. I would like to introduce them into the world of data processing with athena and sixpack. I would like to find a tutorial for sixpack and some test data on principal component analysis and linear combination fitting before giving them some of my own data. Can anybody help me ? Or anybody else had to teach something similar, any idea would help! Thank you very much in advance, Have a great 2012 PJ Sabbe -- Met Vriendelijke groeten, Pieter-Jan Sabbe Pieter-Jan Sabbe Vakgroep Analytische Chemie Universiteit Gent Krijgslaan 281 S12 B-9000 Gent Tel +32 (0)9/264 48 20 E-mail: pieterjan.sabbe(a)ugent.be

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As(0)
by Anatoly I Frenkel 01 Jan '12

01 Jan '12

Dear IFEFFIT subscribers: Has anyone here published As K-edge XANES data in As(0)? If yes, and if you can share the raw data, please let me know. I need As(0) spectrum taken together with As(III) or As(V) reference for energy calibration and alignment. Thank you very much, and Happy 2012 to everyone, Anatoly

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Trouble running Demeter 0.9.6 under Parallels
by Scott Calvin 26 Dec '11

26 Dec '11

Hi all, I'm having trouble running Demeter 0.9.6 under Parallels, and I'm wondering if anyone has had a similar problem, and/or a suggested solution. I have a MacBook Pro running Snow Leopard (10.6.8) and Windows XP SP2 under Parallels 6. Demeter 0.4 was running fine. I attempted to install Demeter 0.9.6, and it appeared to install normally, but when I launched Athena I noticed I was still in 0.4. Some poking around individual files seemed to confirm they had not been replaced. I then tried uninstalling Demeter--it said it was uninstalling 0.9.6, but got rid of 0.4, as I intended. I then installed 0.9.6, which again seemed to work. Upon trying to launch any of the components of Demeter (Athena, Artemis, Hephaestus, Atoms) the splash box appears, sticks around a few seconds, and then disappears, along with the black DOS window. No notice of a crash appears; the program just fails to launch. Any ideas? --Scott Calvin Sarah Lawrence College

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Looking for reviewers for first chapter of new XAFS book
by Scott Calvin 17 Dec '11

17 Dec '11

Hi all, I have finally written the opening chapter of the XAFS textbook I'm working on. This is an introduction and overview, about 30 pages in length. It is (hopefully!) suitable for beginners, although more expert opinions are also welcome. If you are interested in reviewing the chapter and can get feedback to me by 9 January, please contact me directly at SCalvin(a)slc.edu<mailto:SCalvin@slc.edu> . As always, repeat reviewers are welcome! --Scott Calvin Sarah Lawrence College

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SRS data
by Michael Stockenhuber 28 Nov '11

28 Nov '11

Dear all, Thank you very much to the developers for this great software. I have a problem with some old SRS station 3.4 data. I cannot read in original data with athena. I enclose a data file r48683.dat )( Al K- edge). I have installed DUBBLE, but still does not want to read it. I also would like to read in data from station 9.3. This is fluorescence data with a 13 element detector and also includes E0 and E1 and I think Em. I enclose a data file, r94731.dat ( Cu K-edge). Any help would be greatly appreciated. DUBBLE.py reads in station 7.1 data. I enclose a datafile (r66946.dat). All the best and thank you for the help Michael

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