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

ifeffit 1.2.9 and horae 062
by Bruce Ravel 16 Jun '06

16 Jun '06

Hi everyone, Matt and I are pleased to announce new releases of Ifeffit and horae today. You can find source code for ifeffit 1.2.9 and horae 062 on SourceForge and on the Ifeffit wiki: http://sourceforge.net/project/showfiles.php?group_id=80919 http://cars9.uchicago.edu/iffwiki/Downloads You can also find a new Windows installer at both places. This weighs in a chunky 27 MB, but includes the latest versions of Ifeffit, Athena, Artemis, Hephaestus, and SixPack all installable with a point and a click. OSX and debian users: be patient -- packages for those systems should be following shortly. We do not, at this time, have an updater package to bring a Windows installation of 1.2.8 up to date with the current release. If someone wanted to volunteer to make one, that would be great! We also do not have OSX disk images for Intel hardware. That would be another excellent volunteer effort. As always, report any bugs or other problems to the mailing list AFTER checking in with the FAQ (http://cars9.uchicago.edu/iffwiki/FAQ) Regards, Bruce and Matt -- 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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RE: [Ifeffit] bromate XAFS example
by Barton, David (DG) 16 Jun '06

16 Jun '06

Katy, Katy Evans wrote: > Does anyone know of a paper that shows what aqueous bromate XAFS > looks like? Solid would also be useful, though less so. Matsuo, S.; Nachimuthu, P.; Lindle, D. W.; Perera, R. C. C.; Wakita, H. The electronic structures of crystalline and aqueous solutions of NaBr and NaBrO3 using in-situ Na K and Br L edge X-ray absorption spectroscopy. Physica Scripta, T (2005), T115(12th X-Ray Absorption Fine Structure International Conference (XAFS12), 2003), 966-969. Levason, William; Ogden, J. Steven; Spicer, Mark D.; Young, Nigel A. Characterization of the oxoanions of bromine BrOx- (x = 1-4) by infrared, Raman, nuclear magnetic resonance, and bromine K-edge extended x-ray absorption fine structure techniques. Journal of the Chemical Society, Dalton Transactions: Inorganic Chemistry (1972-1999) (1990), (1), 349-53. Have fun, Dave > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov > [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf > Of Katy Evans > Sent: Thursday, June 15, 2006 1:00 AM > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] bromate XAFS example > > > 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 > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

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Fwd: help please
by Bruce Ravel 16 Jun '06

16 Jun '06

Hi folks, Does anyone recognize this problem that Sergio is having? B ---------- Forwarded Message ---------- Subject: help please Date: Thursday 15 June 2006 14:51 From: "Sergio Moreno" <meketo(a)gmail.com> To: bravel(a)anl.gov Hi Bruce, I have downloaded to whole ifeffit package for windows XP because I want to use Atoms. Once installed I tried to run the programs but I received this error message: "The procedure entry point _FIIfexp_ could not be located in the dynamic link library DFORRT.dll" I understand this is a problem with my notebook but I send you this comment just in case you have found it previously and knows how to fix it. Many thanks in advance for any help you can give me!. Sincerely, Sergio -- M. Sergio Moreno Centro Atómico Bariloche 8400 - S. C. de Bariloche Argentina FAX: 54-2944-445299 Te. 54-2944-445100 ext.5389 ------------------------------------------------------- -- 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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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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