April 2006 - Ifeffit - millenia.cars.aps.anl.gov

Log-ratio method
by lisandro＠fisica.unlp.edu.ar 11 Apr '06

11 Apr '06

Hi, I recently realized that Athena implement the ratio method as an analysis tool. I have look in the ifeffit web page and Athena manual and can not find any manual or user guide. Does anyone know any kind of instructive or manual for this type of analysis with Athena? Thanks Lisandro Giovanetti

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Ifeffit files
by Matt Newville 11 Apr '06

11 Apr '06

Hi Todd, Todd Luxton wrote (and the mail somehow got bounced): > > I am new to the use of the Ifettit, but I am currently trying to model XAFS > data for arsenate adsorbed onto a ruthenium oxide. If anyone has any ideas > on how to construct the problem, or could recommend a good source to review > I would be very grateful. Additionally, if anyone could recommend a decent > text on analyzing XAS data I would greatly appreciate it. > > > Thanks > > Todd Luxton I think the best bet is to go through the tutorials and examples from the workshops at http://cars.uchicago.edu/xafs/workshops.html Hopefully others will have more to say.... --Matt

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Re: my problem
by Matt Newville 11 Apr '06

11 Apr '06

Hi Stefano, On 4/8/06, Stefano Ciurli <stefano.ciurli(a)unibo.it> wrote: > OK. Now the latest horae061 package works. Artemis works. The only > "strange" thing is that when I expand the 061 disk image, I get 060 > as the label. Maybe it is meaningless, but anyway. Glad to hear it finally worked!! My guess is that a leftover Receipt was preventing the installation of some of the components. Does that seem right to you? If not, can you give us an idea of what might have been the problem before (for example, was there stale stuff left under /usr/local/)? I will add the notes I sent you (also below) to the Mac section of the Wiki: http://cars9.uchicago.edu/iffwiki/IfeffitOnMacintosh If you (or Paul, or anyone else) find errors in this, or would like to add information to the wiki, please do!! --Matt PS: for the record, a more complete transaction of off-line email: > > > >I'd recommend deleting (or moving to somewhere else) all of > >/Applications/Ifeffit and > >/Library/Perl (not /System/Library/Perl!! and note that this is > >assuming that you are using perl only for horae -- more below). You > >should also delete/move the 'Ifeffit installation receipts': In > >/Library/Receipts/Ifeffit-*. > > > >Then look in /usr/local/bin and /usr/local/lib (which depending on > >your system may have many things or very few things in them) for > >anything with the name "pgplot" -- delete/move these. > > > >Then install Ifeffit using the Installer. > > OK. Now the latest horae061 package works. Artemis works. ....

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Re: [Ifeffit] New release (061) of my codes -- Macintosh 10.4 binary installer
by Matt Newville 07 Apr '06

07 Apr '06

Stefano, You don't need a a file named libpglot.a. The application ifeffit statically includes the pgplot library. If you were to build a new Ifeffit application (including building the base perl module, which horae's build does), it would look in the file /Applications/Ifeffit/share/ifeffit/config/Config.mak and see that it should build with 'libpgplot_iff.a' in the directory '/Applications/Ifeffit/pgplot'. And it should work. The result you sent from otool definitely makes it look like your installation is broken. It also seems to use Aquaterm, which is strange. Paul, is there any chance that Aquaterm is looking for a dynamic pgplot library? Stefano, you did delete all the Ifeffit installation receipts in '/Library/Receipts' and installed the binary package, right? > > Can anyone else confirm / deny if the installer works on OS X 10.4? > > maybe I am the only one using it? :-) I sort of doubt that, but it would be more convenient if we didn't have to support it. --Matt

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Re: [Ifeffit] xafs on wikipedia
by Bruce Ravel 07 Apr '06

07 Apr '06

On Friday 07 April 2006 14:04, you wrote: > Does it seem reasonable to you (and Bruce?) to use the 'CC > share-alike' license for all web / wiki content on xafs.org (and > perhaps the ifeffit wiki?), and make it clear to anyone posting that > what they post uses that license unless explicitly different? I think > we'd all agree on this, but it would be best to be clear. For the last couple years I have been using the CC Attribution-ShareAlike license for many things that I write. http://creativecommons.org/licenses/by-sa/2.5/ The attribution clause is consistent with how scientific attribution is typically done in the literature and the share-alike clause is consistent with how Matt and I license our codes. 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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new release (061) of my codes
by Bruce Ravel 07 Apr '06

07 Apr '06

Hi folks, I just made a new release of Athena (0.8.049) and Artemis (0.8.006). A new source tarball is at SourceForge and at my website. An updater for Windows is on Matt's server. There is nothing big in this release, just some bug fixes and a few small usability improvements. See the release notes http://cars9.uchicago.edu/iffwiki/HoraeVersion061 for details. Enjoy, 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/exafs/

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Ifeffit on 10.4
by Emmanuelle Montarges 06 Apr '06

06 Apr '06

Hi everyone Working on MacOs10.4 computer, after several unsuccessful installations of ifeffit package....I have the following message when I try to run Athena from the Terminal window. I downloaded Tk-804.027.tar and installed it in "temp" directory, but I still have the same message...have you ever had this error? ************ Can't load '/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Tk/Tk.bundle' for module Tk: dlopen(/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Tk/Tk.bundle, 1): Library not loaded: /usr/X11R6/lib/libX11.6.dylib Referenced from: /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Tk/Tk.bundle Reason: image not found at /System/Library/Perl/5.8.6/darwin-thread-multi-2level/DynaLoader.pm line 230. at /Applications/Ifeffit/bin/athena line 52 Compilation failed in require at /Applications/Ifeffit/bin/athena line 52. BEGIN failed--compilation aborted at /Applications/Ifeffit/bin/athena line 52. ********** thanks in advance for your help Emmanuelle MONTARGES-PELLETIER

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Re: latest version
by Bruce Ravel 06 Apr '06

06 Apr '06

On Tuesday 04 April 2006 11:09, you wrote: > Hi, Bruce, > > Could you please direct me to get the latest version of Athena and > Artemis? I am not sure if other windows users have the same > problem as I have but I don't think the download from Matt's webpage > been updated. And somehow the switch for the software to update > automatically in my computer was turned off and I can not get it turn > back on. Ning Download the most recent version of the installer then let the updater handle the chore of getting your computer up to date. Here are the details of how the updater works, including some troubleshooting tips: http://cars9.uchicago.edu/iffwiki/IfeffitOnWindows/WinUpdater If there are any other problems/questions -- ask on the mailing list. HTH, 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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tungsten spectra
by Renato Canha Ambrosio 06 Apr '06

06 Apr '06

Dear colleagues, I woulk like to know if anyone ha the XANES spectra at LI, II and III from a W foil obtained at a conventional XAFS beamline. I need it in order to calibrate DXAS data. Thank you very much Renato Canha rcanha(a)ccet.ufrn.br -- Open WebMail Project (http://openwebmail.org) ---------- Original Message ----------- From: ifeffit-request(a)millenia.cars.aps.anl.gov To: ifeffit(a)millenia.cars.aps.anl.gov Sent: Sun, 2 Apr 2006 12:00:11 -0500 Subject: Ifeffit Digest, Vol 38, Issue 2 > 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. xafs on wikipedia (Francesco Giannici) > 2. Re: xafs on wikipedia (Stefano Ciurli) > 3. Re: xafs on wikipedia (Carlo Segre) > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 2 Apr 2006 09:00:56 +0200 > From: "Francesco Giannici" <zenarcade(a)libero.it> > Subject: [Ifeffit] xafs on wikipedia > To: "ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <IX325K$B150A1BE546B51869BD525DBC482B4F4(a)libero.it> > Content-Type: text/plain; charset=iso-8859-1 > > Hi all. > I'd like to let you know that the Italian version of Wikipedia now > contains an article on X-ray absorption, at > http://it.wikipedia.org/wiki/EXAFS . > (Wikipedia is a free encyclopedia that anyone can edit). I used some > images by Bruce, who asked me to make this announcement. Although > the article is written in Italian, maybe it could motivate the > readers of this list to do the same on their local wikipedia. > > Bye > -- > Francesco Giannici > Dept. of Inorganic Chemistry > University of Palermo > giannici at pa dot ismn dot cnr dot it > > ------------------------------ > > Message: 2 > Date: Sun, 2 Apr 2006 10:32:24 +0200 > From: Stefano Ciurli <stefano.ciurli(a)unibo.it> > Subject: Re: [Ifeffit] xafs on wikipedia > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <a06230903c0553c88e83b(a)[192.168.1.3]> > Content-Type: text/plain; charset="us-ascii" ; format="flowed" > > Dear Francesco, > very well done! Thanks! > Stefano > -- > ____________________________________________ > > Stefano Ciurli > Professor of Chemistry > Laboratory of Bioinorganic Chemistry > Department of Agro-Environmental Science and Technology > University of Bologna > Viale Giuseppe Fanin, 40 > I-40127 Bologna > Italy > Phone: +39-051-209-6204 > Fax: +39-051-209-6203 > > "Fatti non foste a viver come bruti, > ma per seguir virtute e canoscenza" > Dante Alighieri - Inferno - Canto XXVI > > "Ihr seid bestimmt, nicht Tieren gleich zu leben, > Nein, Tugend zu erringen und Erkenntnis" > "Ye were not form'd to live the life of brutes, > But virtue to pursue and knowledge high" > > ------------------------------ > > Message: 3 > Date: Sun, 2 Apr 2006 10:39:50 -0500 (CDT) > From: Carlo Segre <segre(a)iit.edu> > Subject: Re: [Ifeffit] xafs on wikipedia > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <Pine.LNX.4.64.0604021039290.4587(a)localhost.localdomain> > Content-Type: text/plain; charset=us-ascii; format=flowed > > Dear Francesco: > > Excellent! > > Carlo > > On Sun, 2 Apr 2006, Francesco Giannici wrote: > > > Hi all. I'd like to let you know that the Italian version of Wikipedia > > now contains an article on X-ray absorption, at > > http://it.wikipedia.org/wiki/EXAFS . (Wikipedia is a free encyclopedia > > that anyone can edit). I used some images by Bruce, who asked me to make > > this announcement. Although the article is written in Italian, maybe it > > could motivate the readers of this list to do the same on their local > > wikipedia. > > > > Bye > > > > -- > Carlo U. Segre -- Professor of Physics > Associate Dean for Special Projects, Graduate College > Illinois Institute of Technology > Voice: 312.567.3498 Fax: 312.567.3494 > Carlo.Segre(a)iit.edu http://www.iit.edu/~segre > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > End of Ifeffit Digest, Vol 38, Issue 2 > ************************************** ------- End of Original Message -------

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Re: latest version
by Bruce Ravel 05 Apr '06

05 Apr '06

On Tuesday 04 April 2006 11:09, you wrote: > Hi, Bruce, > > Could you please direct me to get the latest version of Athena and > Artemis? I am not sure if other windows users have the same > problem as I have but I don't think the download from Matt's webpage > been updated. And somehow the switch for the software to update > automatically in my computer was turned off and I can not get it turn > back on. Ning Download the most recent version of the installer then let the updater handle the chore of getting your computer up to date. Here are the details of how the updater works, including some troubleshooting tips: http://cars9.uchicago.edu/iffwiki/IfeffitOnWindows/WinUpdater If there are any other problems/questions -- ask on the mailing list. HTH, 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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