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

bromate XAFS example
by Katy Evans 15 Jun '06

15 Jun '06

Hi, Does anyone know of a paper that shows what aqueous bromate XAFS looks like? Solid would also be useful, though less so. Regards, Katy katy.evans(a)anu.edu.au RSES, ANU, Mills Rd, ACT 0200 Ph: 02 61254228 Fx: 02 61250738

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Re: Ifeffit Digest, Vol 40, Issue 5
by Bradley Roberts 14 Jun '06

14 Jun '06

I get the same error upon quitting, will try playing with the ownership a bit. Aquaterm appears to work well - images are clearer too. > >Message: 1 >Date: Wed, 14 Jun 2006 10:08:20 +0900 >From: Paul Fons <paul-fons(a)aist.go.jp> >Subject: Re: [Ifeffit] Mac binary installer for ifeffit 1.2.9 and > horae 062 >To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >Message-ID: <64666EBC-C496-4F78-A213-70F8B71318C2(a)aist.go.jp> >Content-Type: text/plain; charset="us-ascii" > >I will take a look into this I suspect it is a cosmetic problem >only. The applescript doesn't save anything (it just invokes the >perl scripts via a sh script) so I don't understand what the cause is >at first glance. The error message would seem to be from the >applescript though. For safety I always change all of the ownerships >to root and wheel for all of the files so that an ordinary user has >only read/execute permissions whereas on my own machine I typically >leave myself as the owner (as I have to modify the scripts >sometimes). To save yourself from seeing the message one quick >thing you could try would be to make yourself the owner of the >Athena.app script. In the meantime, I will try and install it on >another mac and see if I can reproduce the problem. Does the >aquaterm stuff work OK? > > > Paul >On Jun 12, 2006, at 10:49 PM, Stefano Ciurli wrote: > >> Hi Paul, >> I downloaded and run the installer. I opened Athena using Aquaterm >> as graphic terminal and opened a project. NO problems so far. I did >> nothing else and just quit. The following message appeared: >> <P4036C8F4> >> I am logged in with my username. The same thing happens if I close >> the project before quitting. >> ANy clues on why this happens? >> 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" >> <P4036C8F4> >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > -- Bradley Roberts (br2(a)u.washington.edu) Graduate Student, Department of Materials Science & Engineering Roberts Hall 302 Box 352120 University of Washington Seattle, WA 98195 206-616-7485 lab 206-543-3100 fax

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XAS School at the APS
by Bruce Ravel 02 Jun '06

02 Jun '06

Hi folks, We are almost at the application deadline for this summer's XAS school at the APS. Here is the URL: http://cars9.uchicago.edu/xafs_school/ This year's course is July 26-28. This will be an "advanced topics" class. The material covered will be geared toward people who have some background already in XAS and XAS data analysis and wish to sharpen their skills, expand their knowledge, and learn some of the tricks of the trade that the experts use in their own research. If you are interested -- please apply, but do so soon because time is running out! Regards, 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 Debian package of SixPack
by Carlo Segre 26 May '06

26 May '06

I have uploaded a Debian package of the new version of Sam Webb's SixPack. It should also look for Ubuntu variants (use the "sid" version) Use the following apt lines for the different releases. deb http://fermi.phys.iit.edu/debian/sarge binary/ deb http://fermi.phys.iit.edu/debian/etch binary/ deb http://fermi.phys.iit.edu/debian/sid binary/ P.S. - will also produce Ifeffit 1.2.9 packages after Memorial Day. There are some unexpected changes in the Debian version of pgplot5 which I have to work through... Cheers, Carlo -- 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

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Can ifeffit be run in MAC OS X based on Intel Processor?
by Jingen Xiang 25 May '06

25 May '06

Hi, guys I tried to install the ifeffit to my macbook (intel processor). But it's failed to run the athena which is software based on ifeffit. The version of ifeffit is "ifeffit-1.2.8-Mac10.4_horae61a_pkg.dmg". This version software works well in iBook (PowerPC). Who knows whether ifeffit can be run in MAC OS X based on Intel Processor? Thank you very much! Jingen

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residual in non-equally spaced data
by Francesco Giannici 21 May '06

21 May '06

Hope it'n not a known bug. Anyway, I have to report a strange behavior in Artemis 0.8.006 & Ifeffit 1.2.8 (everything updated today). I have extracted a chi(k) with EDA, which returns non-equally spaced data (equally-spaced in energy, I think), but the fix_chik macro in Artemis fixes everything (or so it seems) interpolating the data over an equally-spaced grid. Next, when I try to plot the residual functions, both in k and R-space, very weird things appear. Anyway, as expected, if I do myself the interpolation and I use the clean data, everything is ok. Bye, -- Francesco Giannici Dept. of Inorganic Chemistry University of Palermo giannici at pa dot ismn dot cnr dot it

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Re: from I.Demchenko - Institute of Physics PAS (question about FEFF6, 8)
by Bruce Ravel 17 May '06

17 May '06

Hi Iraida, I am sending my answer to the mailing list -- in part because it is an interesting and relevant question and in part because I am not sure I know the correct answer to your question. On Wednesday 17 May 2006 08:02, you wrote: > Dear Bruce, > > After reading on site http://millenia.cars.aps.anl.gov/pipermail/ifeffit/ > about possible differences in calculations by FEFF6 and FEFF8 I've tested > my models by both FEFF programs. And now, perhaps I'm making a stupid > mistake in atom.inp file and next in feff.inp files.or I have a problem. I > need to examine GaxMn1-xAs samples with the concentration of Mn about 1-2% > (for example). The measurements were done for K edge of Mn. Within the > initial model Ga atoms are replaced by Mn. My atom.inp file is present > below: > > title = GaAs:Mn (Mn_Ga model) > space = F -4 3 M > a = 5.65330 > core = Ga > edge = K > rmax = 6.0 > out = feff.inp > atoms > ! elem x y z tag > Ga 0.00000 0.00000 0.00000 > As 0.25000 0.25000 0.25000 > > Then in the feff.inp file in "potentials" card I change the central Ga atom > to Mn (in connection with the small concentration of Mn (1-2%) I didn't add > any Mn atoms in the second and third coordination shells). For this model > in the elementary cell we have: 48.4372% of Ga atoms; 50% of As atoms and > 1.56% of Mn atoms. Our cluster is limited to 6 Å (rmax = 6.0). > > POTENTIALS > * ipot z [ label l_scmt l_fms stoichiometry ] > 0 25 Mn -1 -1 0 > 1 33 As -1 -1 1 > 2 31 Ga -1 -1 1 > > ATOMS > 0.00000 0.00000 0.00000 0 Mn 0.00000 > -1.41332 -1.41332 1.41332 1 As 2.44795 > -1.41332 1.41332 -1.41332 1 As 2.44795 > 1.41332 -1.41332 -1.41332 1 As 2.44795 > 1.41332 1.41332 1.41332 1 As 2.44795 > -2.82665 0.00000 -2.82665 2 Ga 3.99749 > 2.82665 -2.82665 0.00000 2 Ga 3.99749 > 0.00000 -2.82665 2.82665 2 Ga 3.99749 > -2.82665 -2.82665 0.00000 2 Ga 3.99749 > 0.00000 2.82665 2.82665 2 Ga 3.99749 > 0.00000 2.82665 -2.82665 2 Ga 3.99749 > 2.82665 0.00000 2.82665 2 Ga 3.99749 > -2.82665 0.00000 2.82665 2 Ga 3.99749 > 0.00000 -2.82665 -2.82665 2 Ga 3.99749 > -2.82665 2.82665 0.00000 2 Ga 3.99749 > 2.82665 0.00000 -2.82665 2 Ga 3.99749 > 2.82665 2.82665 0.00000 2 Ga 3.99749 > .......... > .......... > > Then I do the calculations by FEFF6 and FEFF8 programs, respectively. > > In the table you'll find the differences in Amp for calculations done by > FEFF6 and FEFF8 programs (there are values only for the first three single > scat.). > > # degen reff Amp Scat. path > 1 4 2.448 100 feff6 Mn-As > 100 feff8 > 2 12 3.998 88.07 feff6 Mn-Ga > 101.44 feff8 > 5 12 4.688 64.42 feff6 Mn-As > 67.22 feff8 > > > > My question is: why do we have such big differences in Amp? Should I prefer > the calculations done by FEFF6 program? Asimilar question to this came up recently on the mailing list: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2006-March/002368.html And here is my response, explaining my best memory of how that amplitude term is computed http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2006-March/002405.html Jeremy and Feng also give useful responses to the original question in that thread. The bottom line is, I think, that the amplitude term is a very imprecise measure of the actual size and importance of a path. What's more, the exact details of how it is inaccurately calculated may be different in Feff6 and Feff8 (although I do not know that for a fact). What seems like a much more relevant comparison between the two is how they actually compare when plotted. So, import both the feff6 and feff8 calculations into Artemis and compare the two calculations path by path in k-space AND in R-space. When you do that, how different are they? And where in k- and R-space are the differences most pronounced? That will, I think, be a much more accurate comparison of the two calculations. Hope that helps, 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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Re: Athena won't read my NSLS x10c data
by Bruce Ravel 15 May '06

15 May '06

On Monday 15 May 2006 12:58, you wrote: > Dear Bruce, > > I downloaded the ifeffit-1.2.8.exe installer from > cars.uchicago.edu/ifeffit/download.html to my PC running Windows XP version > 2002, SP1. I can launch Athena (version 0.8.046 obtained through the > download) using either the desktop icon or the runner.exe, but when I try > to open one of my data files from NSLS beamline X10c, I get the message: > "filename could not be read by ifeffit as data file" My understanding from > reading on your website is that Athena should pre-process my data file so > it can be read by ifeffit. The version of Athena at the light source had no > problem reading my data files. Is there something I can do with this new > version to allow it to read my files or do I need to get the old version > from my colleagues at NSLS? I've attached one of my data files that could > not be opened by this version of Athena. Thanks for any suggestions you can > offer! Hi Nancy, This is a good mailing list question, so I am taking the liberty of CCing my response to the list. Not so long, I changed (hopefully improved) how Athena interacts with strangely formatted data. (NSLS X10C most certainly falls in the category of beamlines with strangely formatted data.) Now, Athena uses a plugin architecture to recognize and process strange data. This feature was implemented in Athena 0.8.045 and is described in some detail here http://cars9.uchicago.edu/iffwiki/HoraeVersion057 and in excruciating detail here http://cars9.uchicago.edu/iffwiki/AthenaFiletypePlugins The bottom line is that you need to enable the X10C plugin by going to the Setting menu, selecting "Plugin Registry", then enabling the X10C plugin by clicking its button on. The plugin registry is persistent -- that is, it remembers which plugins are enabled between sessions. You should only need to enable the X10C plugin once. It would seem that the version of Athena at the beamline either had this feature enabled or was older than version 0.8.045. I certainly had no trouble reading that data file once I had enabled the X10C plugin on my computer. B P.S. The current version of Athena 0.8.049. It is a bit of mystery to me why so many people tell the runner never to update their software. It's your computer and your choice, obviously, but it's a mystery to me nonetheless. To change your runner setting my hand, see: http://cars9.uchicago.edu/iffwiki/IfeffitOnWindows/WinUpdater If the value of "next_checktime" in updater.ini is set to something like "never" or "next year", then it's guaranteed that you'll soon be using an out-of-date version of Athena. -- 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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Wurtzite interstitial sites
by Mauro Rovezzi 15 May '06

15 May '06

Dear all, Do you know the coordinates of the octahedral interstitial site in wurtzite? I mean, in a way that I can use Atoms to simulate a dopant in this site? Thanks, Mauro -- Mauro Rovezzi <rovezzi(a)esrf.fr> PhD student - GILDA BM08 c/o ESRF (Grenoble, FR)

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lambda in parameter Ei
by Arkadiusz Onyszko 15 May '06

15 May '06

Dear All, I found in manual, that lamda ~ 1/sqrt(Ei) I want calculate lambda with fitting parameter Ei. How do it ? What is the exact dependence Ei and lambda ? During fitting I have example Ei=7,5, so I want calculate lambda. This dependence: lamda ~ 1/sqrt(Ei) is not a complitly. Yours faithfully Arkadisz Onyszko

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