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

Right way of choosing E0 in Athena
by Vadim G Palshin 03 Jul '06

03 Jul '06

>Since you know the spectra are well calibrated relative >to one another, I would use a single E0 for all >background subtractions. In such a situation, I tend to >play with the background parameters for one of the >spectra and then apply these background >parameters to all other spectra. Thanks, Matt! Yes, that’s pretty much what I have been doing, just had some trouble getting reasonable fit values for E0’s in my last set of samples. Aligning chi(k) of the standard to theory – great guide, Shelly! – and then applying the same parameters to the other spectra helped solve this. Now, more questions: 1. Many experts advise to do multiple k-weight fitting to deal with correlated variables. Should one always use multiple k-weights, or is it better to switch to one kw value once the correlations are taken care of – to refine the remaining variables? Does it make any difference? 2. When modeling the Debye-Waller factors for multiple-scattering paths, is it possible to express them in terms of the sigma^2’s of single-scattering paths that correspond to the atoms involved in the multiple scattering events; i.e. for a core—atomA—atomB—core path, can sigma^2 be obtained by some combination of core—atomA and core—atomB sigmas? It seems intuitively that they should be related, and also that the amplitudes of multiple scattering paths should be more sensitive to disorder. Does this make any sense? Thanks again for your replies! Vadim.

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E0 and background subtraction
by Vadim G Palshin 29 Jun '06

29 Jun '06

Hi everyone, I have the following question: I have a set of spectra collected in transmission with 3 ionization chambers and a standard between 2nd and 3rd ion chambers for calibration, so I know my spectra are nicely calibrated relative to each other. Should I then force Athena(/autobk) to use the same E0 for all of them (e.g. use the atomic value) or let it find E0 independently for each sample? Thanks! Vadim.

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Fwd: Re: r-factor
by Bruce Ravel 23 Jun '06

23 Jun '06

On Friday 23 June 2006 05:01, you wrote: > I have a question about Artemis log file. I noticed that two r-factors are > reported in the log file. One is in the fifth line and it is called > 'R-factor' and the other one is under the data set fitting conditions and > it is called 'r-factor for this data set'. They have in general different > values. What does it mean? Which is the difference between the two? It probably means that I am calculating something wrongly. Here's the concept. If you do a multiple data set fit and you have some value of R-factor, you would like to know how that misfit is partitioned among the data sets. That is, you'd like to know if one set is contributing to the misfit for significantly than the others. When Ifeffit computes the R-factor, it is for the entire fit. My idea in Artemis was to use the formula for R factor from page 18 of http://cars9.uchicago.edu/~newville/feffit/feffit.ps on each data set in a multiple data set fit and report that in the log file. At some point, I must have convinced myself that I was doing the calulcation in Artemis identically to how it is done in Ifeffit. If you are seeing different values, it would seem I was mistaken. I'll make an entry in my to do list to look into that. 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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data file format
by emmanuelle montarges-pelletier 22 Jun '06

22 Jun '06

Hello I have some problems with data file format as I try to import exafs files in Artemis or in Athena. I am working on a powerbook G4, with OSX 10.4.6. I installed the ifeffit package, including Athena and Artemis. Athena could open any XAS "raw" file from fluorescence or transmission measurements. However, if I perform any modifications on these raw files with exterior programs (Michalowicz programs, Kaleidagraph) and try to import the new files , saved as text files, Athena or Arthemis can not open them. I guess it may come from the encoding of the text file. Do you have any clue on this encoding issue? Do you know any program which would allow me to transform these text files in readable files for Artemis? Thank you for your answer sincerely Emmanuelle ********************************************* Emmanuelle Montargés-Pelletier CR CNRS LEM UMR7569 CNRS-INPL-ENSG 15 avenue du charmois BP40 54501 Vandoeuvre les Nancy cedex France Tel 33 (0)3 83 59 62 52 fax 33 (0)3 83 59 62 55 emmanuelle.montarges(a)ensg.inpl-nancy.fr http://www.ensg.inpl-nancy.fr/lem/ **************************************************

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The most important fitting parameters
by Bridget Ingham 21 Jun '06

21 Jun '06

Hi Bruce and Shelly, thanks for your replies. The problem I am encountering is that we know virtually nothing about the crystallography, only the elements that are present. We expect the structure to be quite different to CuWO4, even though this is the stoichiometry obtained. Addressing some of your questions/comments: Shelly: 1) I will try this. In other systems I've tried the second oxygen shells don't contribute significantly, so maybe they are unnecessary and only adding to the uncertainty in the other shells. 2) & 3) As mentioned above, we don't even know this about the structure. But it is worth me having a go at restricting the delr's to relate to CuWO4. I am loathe to do the same with the amplitudes however, as I expect the co-ordination numbers to be completely different. 4) Yes, I ran a CuWO4 standard at the same time. It looks completely different ;) 5) & 6) Thanks for these tips! Bruce: I have kept E0 the same for all shells, hence 13 parameters (4 shells x amp, delr, ss; plus E0). Sorry for not making that clear enough. The data stops at 9 Ang-1 because there seems to be some Zn edge impurity :( I will play around with the constraints a bit more (starting with the CuWO4 standard) and let you know how I get on. Thanks again for your help! Bridget This electronic transmission and any documents accompanying this electronic transmission contain confidential information belonging to the sender. This information may be legally privileged. The information is intended only for the use of the individual or entity named above. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution or the taking of any action in reliance on or regarding the contents of this electronically transmitted information is strictly prohibited. This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

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Debian packages of ifeffit and horae
by Carlo Segre 20 Jun '06

20 Jun '06

It has taken a bit of time but the Debian packages of ifeffit and horae are now uploaded to my apt repository. Note that horae requires a new Perl module to be installed (libtext-glob-per) and so will have to be upgraded expplicitly. Also note that if you are using the "etch" or "sid" versions of the packages, that a new version of pgplot5 will be also installed. This is to correct a serious bug that exists in the Debian version at this time. Thanks to Ken McIvor for fixing this. hopefully a new official Debian version will be coming out soon to fix this officially. The repositories for the various distributions are, as always: # For the stable (sarge) distribution deb http://fermi.phys.iit.edu/debian/sarge binary/ deb-src http://fermi.phys.iit.edu/debian/sarge source/ # For the testing (etch) distribution deb http://fermi.phys.iit.edu/debian/etch binary/ deb-src http://fermi.phys.iit.edu/debian/etch source/ # For the unstable (sid) distribution deb http://fermi.phys.iit.edu/debian/sid binary/ deb-src http://fermi.phys.iit.edu/debian/sid source/ 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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how to creat a chi.dat
by tony vitova 19 Jun '06

19 Jun '06

Hi, I will be very thankful, if you tell me how to create a chi.dat file with Artemis. My PRINT and CONTROL cards in feff.inp are: CONTROL 1 1 1 1 PRINT 5 1 1 1 I am expecting it to be in D:\Program Files\Ifeffit\horae\stash\artemis.project.3\data0.feff1 but it is not there? Is there another way ...? Thank you very much for the help! Tonya Vitova --------------------------------- Yahoo! Messenger with Voice. PC-to-Phone calls for ridiculously low rates.

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The most important fitting parameters
by Bridget Ingham 16 Jun '06

16 Jun '06

Dear all, I am trying to use EXAFS, along with other techniques, to attempt to find information about an unknown structure. It is an organic-inorganic hybrid material, EDX reveals Cu1-W1-O4 as the stoichiometry of the inorganic component, which we are most interested in structurally. We have not been able to solve the structure from XRD, although not for want of trying. I started off with CuWO4 as the model compound and constrained the fitting parameters: - take all 1st oxygen shells (x6 at slightly different distances) and give them all amp1, dr1*reff, enot and ss1 - take all 1st copper shells (x2) and give them both amp2, dr2*reff, enot and ss2 - take all 2nd oxygen shells (x6), amp3, dr3*reff, enot, ss3 - take all 1st tungsten shells (x6), amp4, dr4*reff, enot, ss4 This gave me 13 parameters with 14.8 independent points. (Other factors: fitted in kw=2&3, k-range 2-9, used Athena with default background subtraction parameters as the chi(k) from that seemed sensible. The data were collected at SSRL, beamline 11-2, in transmission.) I was happy with the final result (R-factor 0.014), but am just wondering if this is a sensible way to go about doing things - bearing in mind I am not sure of the structure in the first place. Any hints or advice would be much appreciated. I should have collected data at the tungsten edge as well, as it is not that much higher in energy from Cu, but this didn't occur to me until later. Regards, Bridget This electronic transmission and any documents accompanying this electronic transmission contain confidential information belonging to the sender. This information may be legally privileged. The information is intended only for the use of the individual or entity named above. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution or the taking of any action in reliance on or regarding the contents of this electronically transmitted information is strictly prohibited. This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

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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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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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