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

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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Re: atoms.inp
by Bruce Ravel 15 May '06

15 May '06

On Monday 15 May 2006 03:40, you wrote: > Dear Bruce, > I have some problems with the occupation probability which it is in > the publication. To take into account of this factor, A solution is > to remove manually the atoms (the half for an occupation of 1/2) but > is there such possiblity in the Atoms program? Dominique, This is perhaps the most frequent of the frequently asked questions. See FAQ #14 at this page: http://cars9.uchicago.edu/iffwiki/FAQ/FeffitModeling 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: about atoms.inp data of As2O3 (arsenious oxide)
by Bruce Ravel 09 May '06

09 May '06

On Monday 08 May 2006 08:47, you wrote: > I am a Ph.D. student in Gwangju Institute Science and Technology, South > Korea. I have been tried to analyze my EXAFS sample with reference of As2O3 > (arsenious oxide) obtained from "The Atoms.inp Archive > (http://cars9.uchicago.edu/~newville/adb/search.html) But I could not run > the feff in the Artemis (version 0.8.006) successfully with the As2O3 atoms > file. Could you let me know how to solve the problem? It would be very > honor to me if you let suggest a clue for the problem, sir. Ji-Hoon, This is the sort of question that should be asked on the Ifeffit mailing list, so I am taking the liberty of CCing my answer there. I agree that the input file for As2O3 from the database is wrong. It generates an obviously incorrect list of coordinates. You need to go to the crystallography literature and find the correct data for that structure. There is nothing wrong (at least with respect to this question!) with Artemis. It seems likely that the problem is with the reliability of the data for As2O3 in the database. 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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Problems with fitting in ATHENA for XANES
by Pushan Shah 08 May '06

08 May '06

Hello Everyone! I am the new user of XAFS method. Recently I obtained some data with XANES method. I have just started using ATHENA for my data analysis. I am using "Using ATHENA" document to learn the software. I have two questions 1.For XANES, Which method is better for knowing unknown data with known standards: Peak fitting analysis or Linear combination analysis. I would like to get some comments from your experiences so far which works better if tried both for same type of data. 2. In the peak fit analysis, in literature related to my work it was mentioned that peak modelled by 50%-50% combination of Gaussian and Lorentzian functions works better. Is it possible to do in ATHENA.? Hope to recieve some useful reply. Regards, Pushan ********************************************* Pushan Shah PhD Candidate CRC for Coal in Sustainable Development Graduate School of The Environment Macquarie University Australia Phone : +61 2 9850 7950 Fax: +61 2 9850 7972 **********************************************

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