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

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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RE: [Ifeffit] regarding Lytle detector
by Bare, Simon 08 May '06

08 May '06

This is an interesting topic - shouldn't someone at the APS (XOR staff member) be trained in repairing Lytle detectors? It would be a great service to APS XAFS users. Simon R. Bare Senior R&D Associate UOP LLC 25 East Algonquin Road Des Plaines, IL 60017-5017 Phone - 847.391.3171 Fax - 847.391.3719 simon.bare(a)uop.com www.uop.com -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Barton, David (DG) Sent: Monday, May 01, 2006 4:27 PM To: 'XAFS Analysis using Ifeffit' Subject: RE: [Ifeffit] regarding Lytle detector Soma, I believe the person that they were referring to was John Kulpin who was employed at DND-CAT. He left APS and Argonne a couple of years ago and I don't know where he is at now. Dave Barton > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov > [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf > Of soma(a)agni.phys.iit.edu > Sent: Monday, May 01, 2006 11:03 AM > To: XAFS Analysis using Ifeffit > Subject: [Ifeffit] regarding Lytle detector > > > > Hi MAtt > > Carlo told me to ask you about this one: > > Is there somebody in APS who has been trained by Farrel > Lytle's company to repair Lytle detectors for APS beamlines? > Jeff Terry said that Lytle did train somebody but we do not > know the person's name. > > IF you know the name of this person, could you please drop me > a line so that we can contact him regarding repair of few of > our lytle detectors? > > Thanks a lot > Soma > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Re: atoms.inp
by Bruce Ravel 05 May '06

05 May '06

On Friday 05 May 2006 09:19, you wrote: > Dear Bruce > I try to write the Atoms.inp file of a apatite which has been > published by suetsugu. the space group is P6 bar (please find the > publication attached [Journal of Solid State Chemistry 155, 292 } 297 > (2000)]). How can i write this space group in the atoms.inp file? > Thanks in advance > Take care Hi Dominique, This should work: space = p -6 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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Re: problems with artemis help
by Bruce Ravel 04 May '06

04 May '06

On Thursday 04 May 2006 09:32, M Ceolin wrote: > Hi Bruce. > > I am a user of the ifeffit. I use the programs running under Windows 2000 > and I experienced problems trying to use any of the help buttons associated > to artemis. The echo I received was > > ------------------------------------------------------------------ > Tk::Error: image "fileopen16" doesn´t exist at /PerlApp/Tk.pm line 228. > Tk callback for image8 > [\&main::__ANON__] > (menu invoke) > main::__ANON__(´Tk::Error: image "fileopen16" doesn´t exist at > /PerlApp /Tk.pm l...´) called at blib\lib\Tk.pm (autosplit into > blib\lib\auto\Tk\Error.al ) line 402 > Tk::Error(´MainWindow=HASH(0x21471c30)´, ´image "fileopen16" > doesn\´t ex ist at /PerlApp/Tk.pm line 228.^J´, ´Tk callback for image8´, > ´[\&main::__ANON__ ]´, ´(menu invoke)´) called at /PerlApp/Tk.pm line 340 > eval {...} called at /PerlApp/Tk.pm line 340 > Tk::MainLoop() called at artemis line 2107 > ------------------------------------------------------------ > > Is it possible to fix the problem ?. Hi Marcelo, I am aware of this problem and intend to fix it in the next release. This: http://cars9.uchicago.edu/~ravel/software/doc/Athena/athena.html and the pages it links to are generated from the help pages built into the program, and so have the same content. Here is the same content as an ugly, all-in-one PDF file: http://cars9.uchicago.edu/~ravel/software/doc/Athena/athena.pdf Unfortunately, the way I currently build executables for windows to make it easy to install and update on windows also precludes simple, user-servicable fixes for problems like this one. That means that when a problem like this crops up, everyone ha to wait for me to find the time to make a new release. Hopefully, the next one will be in the next couple of weeks. 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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odd behaviour in the lDOS of GeO2
by Andreas Schacht 03 May '06

03 May '06

Dear helper team, i was trying to calculate the XANES spectra for alpha-quartz GeO2. The principle problem seems to be, that the fermi energy in the lDOS-calculations seems to be completetly wrong. If i look at the xanes-spectra with this fermi-energy the spectra does not fit with any experiment. In my opinion the fermi level should be shifted approximately by -18ev or so. If I try to fix the problem by simply adding an exchange energy in the feff.inp that does not give any better results so it would be very helpfull if someone can help me, perhaps having the same problems with totally wrong fermi-levels. additionally I give you my feff.inp file for the GeO2. And of course the atoms list consists of about 160 atoms but I omit them here. Thanks for any help * This feff8 input file was generated by WebAtoms 1.8 (Atoms 3.0beta10) * Atoms written by and copyright (c) Bruce Ravel, 1998-2001 TITLE GeO2 alpha * This feff8 input file was generated by WebAtoms 1.8 (Atoms 3.0beta10) * Atoms written by and copyright (c) Bruce Ravel, 1998-2001 TITLE GeO2 alpha * Ge K edge energy = 11103.0 eV EDGE K S02 1.0 * pot xsph fms paths genfmt ff2chi CONTROL 1 1 1 1 1 1 PRINT 1 0 0 0 0 0 *** ixc=0 means to use Hedin-Lundqvist * ixc [ Vr Vi ] EXCHANGE 0 *** Radius of small cluster for *** self-consistency calculation *** A sphere including 2 shells is *** a good choice *** l_scf = 0 for a solid, 1 for a molecule * r_scf [ l_scf n_scf ca ] SCF 5.0 *** Upper limit of XANES calculation. *** This *must* be uncommented to *** make Feff calculate full multiple *** scattering rather than a path expansion * kmax [ delta_k delta_e ] XANES 4.0 *** Radius of cluster for Full Multiple *** Scattering calculation *** l_fms = 0 for a solid, 1 for a molecule * r_fms l_fms FMS 8.0 0 *** Energy grid over which to calculate *** DOS functions * emin emax eimag LDOS -30 20 0.1 *** for EXAFS: RMAX 8.0 and uncomment *** the EXAFS card RPATH 0.1 *EXAFS 20 POTENTIALS * ipot Z element l_scmt l_fms stoichiometry 0 32 Ge 2 2 0.001 1 32 Ge 2 2 3 2 8 O 1 1 6 ATOMS * this list contains 163 atoms * x y z ipot tag distance 0.00000 0.00000 0.00000 0 Ge1 0.00000 0 1.53968 -0.61764 0.51379 2 O1 1.73668 1 0.23495 1.64222 -0.51379 2 O1 1.73668 2 -1.06503 -0.14213 1.37021 2 O1 1.74125 3 ...

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