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

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

3 2

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

1 0

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

2 2

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

4 6

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

3 2

Re: [Ifeffit] SRS data
by Michael Stockenhuber 18 Nov '11

18 Nov '11

Hi Matt, Thank you very much. I will have a look at the script and maybe I can modify it. I am not really good in coding but you certainly gave me an idea where to start. Thank you for looking at the files. If I get anywhere I will certainly post. I am sure I am not the only one having to do that :) Cheers Michael >>> Matt Newville <newville(a)cars.uchicago.edu> 18/11/11 3:13 AM >>> Hi Michael, On Thu, Nov 17, 2011 at 5:17 AM, Michael Stockenhuber <Michael.Stockenhuber(a)newcastle.edu.au> wrote: > 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 OK, there are a few separate formatting issues here. First, these files end with a line reading "END OF DATA", which ifeffit doesn't like, but which it can ignore. Second, two of the files (r94731.dat and r66946.dat) do not have data arranged so that one line is one energy point, and they have an inconsistent number of columns per line. Ifeffit usually considers line breaks to be significant. Third, one of the files (r48683.dat) has two lines with '----' starting after a comment character -- ifeffit takes such a line to signify the end of the header. Athena allows file-reading plugins to be written in perl -- I think you'll probably want to consult with Bruce about writing (or having one of these written for these files). Alternatively, you could write a program to convert these files to ones that make ifeffit's limited read_ascii() routine happy. Perhaps DUBBLE.py (I'm not familiar with that) can be made to do this conversion? Hope that helps, --Matt _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

1 0

Re: [Ifeffit] Ifeffit Digest, Vol 105, Issue 8
by Carmelo Prestipino 17 Nov '11

17 Nov '11

Hi Thanks to all About the GUI, it is a quick and dirty job so I was a little ashamed to public show it. It is aimed to analyze sequentially big set of data coming from dispersive and qexafs beamlines. Source code and installer for windows are available at the link http://code.google.com/p/prestopronto/ The code is in a very beta stage, so big part of documentation is missing and is not tested extensively, I'm sure that it is still full of bugs. However If someone is interested to tests, modifies, give a look it is obviously welcomed. Thanks again Carmelo > 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. feff6l licence (Carmelo Prestipino) > 2. Re: feff6l licence (John J. Rehr) > 3. Re: feff6l licence (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 16 Nov 2011 17:23:36 +0100 > From: Carmelo Prestipino <carmelo.prestipino(a)univ-rennes1.fr> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] feff6l licence > Message-ID: > <CAHPDQqzXQ3+3+Ej4KhfV_1HSwkUep4ZwRwAMTKn0rTBxcyVnig(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi to everybody > I'm currently working to an another GUI to Ifeffit, aimed to large > dataset , it is still in beta version and full of bug but some > collaborators start to use it . > In the installer that I send to them is present the "feff6l.exe" > file, to generates phase and amplitudes , but now I have a doubt. > Does the feff6l licence allows a generic redistribution? , or have > the Horae and the Sixpack packages a special agreement? > Thanks in advance > Carmelo > > -- > Carmelo Prestipino > Sciences Chimiques de Rennes UMR 6226 > Campus de Beaulieu, B?t 10B > F-35042 RENNES > France > Tel: (+33) 22323 6531 > FAX: (+33) 22323 5959 > > > > ------------------------------ > > Message: 2 > Date: Wed, 16 Nov 2011 08:36:45 -0800 (PST) > From: "John J. Rehr" <jjr(a)uw.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > > Hi Carmelo et al., > > Short answer: FEFF6L may be freely distributed; there is no special > agreement restricting the code to IFEFFIT or other codes. Let me know > if you have other questions about this. > > Sincerely, > J. Rehr > PI FEFF Project > > From the FEFF6L license header: > > c/////////////////////////////////////////////////////////////////////// > c Distribution: FEFF6L > c Copyright (c) [2002] University of Washington > c > c This software was prepared in part with US Government Funding under > c DOE contract DE-FG03-97ER45623. > > c Redistribution and use of this Distribution in source and binary > c formats, with or without modification is permitted, provided the > c following conditions are met: > c > c Redistributions must retain the above notices and the following list > c of conditions and disclaimer; > c > c Modified versions carry the marking > c "Based on or developed using Distribution: FEFF6L > c Copyright (c) [2002] University of Washington" > c > c Recipient acknowledges the right of the University of Washington to > c prepare uses of this Distribution and its modifications that may be > c substantially similar or functionally equivalent to > c Recipient-prepared modifications. > c Recipient and anyone obtaining access to the Distribution through > c recipient's actions accept all risk associated with possession and > c use of the Distribution. > c > c THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESS OR IMPLIED > c WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF > c MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. > c IN NO EVENT SHALL THE UNIVERSITY OF WASHINGTON OR CONTRIBUTORS TO THE > c DISTRIBUTION BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, > c EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, > c PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR > c REVENUE; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF > c LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING > c NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS > c SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. > c/////////////////////////////////////////////////////////////////////// > > > > > > On Wed, 16 Nov 2011, Carmelo Prestipino wrote: > >> Hi to everybody >> I'm currently working to an another GUI to Ifeffit, aimed to large >> dataset , it is still in beta version and full of bug but some >> collaborators start to use it . >> In the installer that I send to them is present the "feff6l.exe" >> file, to generates phase and amplitudes , but now I have a doubt. >> Does the feff6l licence allows a generic redistribution? , or have >> the Horae and the Sixpack packages a special agreement? >> Thanks in advance >> Carmelo >> >> -- >> Carmelo Prestipino >> Sciences Chimiques de Rennes UMR 6226 >> Campus de Beaulieu, B?t 10B >> F-35042 RENNES >> France >> Tel: (+33) 22323 6531 >> FAX: (+33) 22323 5959 >> >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> > > > ------------------------------ > > Message: 3 > Date: Wed, 16 Nov 2011 11:32:23 -0600 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] feff6l licence > Message-ID: > <CA+7ESbrX1WAkUPXPCZph27foRtwy2f7LD176WtB7oRU_3Qp3eA(a)mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Hi Carmelo, > > As John said, Feff6L is NOT tied to ifeffit, and is distributed with a > very liberal license. Using the ifeffit source kit might be the > easiest way to get the source code, but this code (and ifeffit's code) > can be pulled out if you'd like. For windows, you can just copy the > feff6l.exe executable and include it with your GUI. > > Of course, I think many of us would be interested in hearing more > about your GUI. > > --Matt > > -- Carmelo Prestipino Sciences Chimiques de Rennes UMR 6226 Campus de Beaulieu, Bât 10B F-35042 RENNES France Tel: (+33) 22323 6531 FAX: (+33) 22323 5959

1 0

feff6l licence
by Carmelo Prestipino 16 Nov '11

16 Nov '11

Hi to everybody I'm currently working to an another GUI to Ifeffit, aimed to large dataset , it is still in beta version and full of bug but some collaborators start to use it . In the installer that I send to them is present the "feff6l.exe" file, to generates phase and amplitudes , but now I have a doubt. Does the feff6l licence allows a generic redistribution? , or have the Horae and the Sixpack packages a special agreement? Thanks in advance Carmelo -- Carmelo Prestipino Sciences Chimiques de Rennes UMR 6226 Campus de Beaulieu, Bât 10B F-35042 RENNES France Tel: (+33) 22323 6531 FAX: (+33) 22323 5959

3 2

Re: [Ifeffit] software issues on a 10.1" netbook (Coppage, Ryan H)
by denis testemale 08 Nov '11

08 Nov '11

Hello Ryan. As Chris suggested, you may want to change the fonts to allow the window to show everything (even if gaining 1/3rd of the screen seems a lot, you might need very small fonts). I don't know about Windows, but in case the file names are similar I can tell you where to do this under linux: in the .horae folder, you want to edit the athenarc and artemisrc config files. This is the only way to change the font sizes (if you go to the Edit/preferences menu in a running athena or artemis session, the message will be that it is the only parameter that you have to change through the config files). Hope it helps. Cheers denis Le Samedi 05 Novembre 2011 12:00:01 ifeffit-request(a)millenia.cars.aps.anl.gov a écrit : > software issues on a 10.1" netbook (Coppage, Ryan H) I'm a grad student at the University of Miami. I purchased a dual-core netbook for travel purposes and intended to use IFEFFIT on it. It runs windows 7. When attempting to run athena, the window text will not resize on my screen, to show me the rest of the software window. The bottom half is cut off, and it won't let me move the window out of the screen to see the bottom 1/3 or so. There are no scroll bars to move up or down the athena window, so i cannot even open data to manage. Has anyone else had issues with this or knows a solution to the issue? Any help would be greatly appreciated. Ryan Coppage Graduate Student University of Miami ------------------------------ _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit End of Ifeffit Digest, Vol 105, Issue 4 *************************************** -- denis testemale Institut Néel-Département MCMF BP166 38042 Grenoble Cedex 9 (tel) +33 476 88 10 45 (fax) +33 476 88 10 38 http://neel.cnrs.fr/spip.php?rubrique264

1 0

Re: [Ifeffit] Ifeffit Digest, Vol 105, Issue 4
by Lisa Van Loon 07 Nov '11

07 Nov '11

Hi Ryan, I have the same problem when I use my netbook. The only solution I've come up with is to change the display settings to "Portrait" to open a project file or import data. Then I switch back to "Landscape" view when I'm working with the data. It's not an ideal solution, but it works. Lisa Lisa Van Loon, Ph.D. Industrial Research Scientist Canadian Light Source Inc. (306)657-3585 lisa.vanloon(a)lightsource.ca www.lightsource.ca -------------------------------------------------------------------- Message: 1 Date: Fri, 4 Nov 2011 19:36:30 +0000 Hi. I'm a grad student at the University of Miami. I purchased a dual-core netbook for travel purposes and intended to use IFEFFIT on it. It runs windows 7. When attempting to run athena, the window text will not resize on my screen, to show me the rest of the software window. The bottom half is cut off, and it won't let me move the window out of the screen to see the bottom 1/3 or so. There are no scroll bars to move up or down the athena window, so i cannot even open data to manage. Has anyone else had issues with this or knows a solution to the issue? Any help would be greatly appreciated. Ryan Coppage Graduate Student University of Miami

2 1