- 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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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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RE: [Ifeffit] regarding Lytle detector
by Barton, David (DG) 01 May '06

01 May '06

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 >

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RE: [Ifeffit] regarding Lytle detector
by Kelly, Shelly D. 01 May '06

01 May '06

I don't know... SK > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit- > bounces(a)millenia.cars.aps.anl.gov] On Behalf Of soma(a)agni.phys.iit.edu > Sent: Monday, May 01, 2006 10:03 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

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XAFS Summer School at APS
by Matt Newville 01 May '06

01 May '06

Hi Folks, There will be an XAFS Summer School at the Advanced Photon Source, Argonne July 26 to July 28, 2006. The school this year will be a little different from the XAFS Schools held over the past few years at the APS and NSLS. This year, we will cover "advanced analysis". The school will be 3 days, there will be no beam time involved, and students will be expected to be familiar with XAFS and data processing (at approximately the level of using Athena). Instructors will include Bruce Ravel, Scott Calvin, Shelly Kelly, and myself. For more details, and to apply for this years XAFS summer school, see http://cars.uchicago.edu/xafs_school/ The application deadline is June 1st. --Matt

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FEFF8
by Ivana Radisavljevic 26 Apr '06

26 Apr '06

Dear Mr. Ravel, I have read in one of the papers of the authors A.I. Lebedev and I.A. Sluchinskaya that Pb scattering form factors in FEFF6 were not precisely determined. As I am dealing with the similar systems, Pb1-xMnxTe(In, Ga) to be precise, could You please tell me if this is also true for the FEFF8 version (if it is true et all)? Another thing that bothers me is that all of the real part Furier transformed EXAFS spectra taken at the tellurium K edge, appear to have the first peak divided. Since there is no direct indication of the sub-shells' existence and having in mind the similar tellurium feature noticed in Your paper "Combined EXAFS and first-principles theory study of Pb1-xGexTe", I am wondering what this feature should represent? I thank You very much in advance, Ivana Radisavljevic Vinca Institute for Nuclear Sciences, Lab 011 P.O. Box. 522, 11001 Belgrade, Serbia and Montenegro Tel. +381 11 2458222/434 Fax. +381 11 3440100 E-mail: iva(a)vin.bg.ac.yu

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(no subject)
by tony vitova 25 Apr '06

25 Apr '06

Hi, I just started to do EXAFS analysis with Artemis and I am not sure if my fit is sufficiently good. It is an attempt to fit the first shell: the first two peaks of LiNbO3 (Nb absorber). Could somebody have a fast look at my Artemis project? I wanted to fix the amplitude and to vary the coordination numbers, thus the places of "N" and "SO2" are changed. Is there another way to do this? Thanks a lot! Tonya --------------------------------- How low will we go? Check out Yahoo! Messengers low PC-to-Phone call rates.

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RE: [Ifeffit] dk setting in Athena
by Kelly, Shelly D. 24 Apr '06

24 Apr '06

Hi Geoff, I don't think that I understand your definition of dk, so I am going to give you mine. A Fourier transform is a complex transformation that requires the data that is being transformed to be defined from -infinity to +infinity. Since our data does not cover this range, we pad the data set with zeros for most of the transformed data range. At the edges in between the actual data range and all the zeros there is a step function, as the data goes from zero to some non-zero number abruptly. A Fourier transform (FT) of a step function is a bunch of signals at all R-values called a FT ripple. This is not a good think to have in your FT. So we spread out the step function by applying a window. The length of the window is defined by dk. In general dk should not be zero. See this presentation for some more discussion of dk. http://www.mesg.anl.gov/Presentations/basics%20of%20exafs%20analysis%202 003.pdf HTH Shelly > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit- > bounces(a)millenia.cars.aps.anl.gov] On Behalf Of Geoff Eldridge > Sent: Monday, April 24, 2006 10:29 AM > To: Ifeffit List > Subject: [Ifeffit] dk setting in Athena > > Hello everyone, > > I've just started doing EXAFS in my research and I have found all your > posts to be very helpful. > > My question is about the dk setting in Athena. I know from earlier > reading that dk affects where the window for the FT is set in k-space > (i.e. a dk setting of one moves the window out further than the k-min > and k-max settings). I believe the purpose of this is to prevent > cutting the tops of peaks out of the FT window. If this is the case, > would a dk setting of 0 then be appropriate provided no parts of peaks > are clipped as shown in a k-space plot with the window shown? > > Thanks, > > Geoff > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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dk setting in Athena
by Geoff Eldridge 24 Apr '06

24 Apr '06

Hello everyone, I've just started doing EXAFS in my research and I have found all your posts to be very helpful. My question is about the dk setting in Athena. I know from earlier reading that dk affects where the window for the FT is set in k-space (i.e. a dk setting of one moves the window out further than the k-min and k-max settings). I believe the purpose of this is to prevent cutting the tops of peaks out of the FT window. If this is the case, would a dk setting of 0 then be appropriate provided no parts of peaks are clipped as shown in a k-space plot with the window shown? Thanks, Geoff

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Artemis- Loading up error
by Zohair Hussain 17 Apr '06

17 Apr '06

Hi! I recently had to install ifeffit software package on our network computer. The first time I ran Artemis I was asked to update which I did. However, Artemis did not start after that. The error message that I got is shown in the attached figures artemis-error1a and 1b. Please note that only Artemis doesn't work, all the other softwares (Athena, Hephaestus, TKAtoms etc.) work fine. I tried running the .bat file from the Ifeffit folder but that didn't work either. I also tried to run the artemis.exe file and received the error shown in figure "artemis-error2". Later I unisntalled and re-installed Ifeffit and chose not to do the updates and Artemis is now running fine. I was wondering if anyone has any idea why this is so or if there is a way around installing the updates and still being able to use Artemis??? Thanks, Zohair

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problem compiling ifeffit 1.2.8
by Igor Vasconcelos 12 Apr '06

12 Apr '06

Dear all, I came across the following error when trying to compile ifeffit-1.2.8 (uprading from version 1.2.6) in my Linux FC4 box: ifort -g -c ifftest1.f fortcom: Error: ifftest1.f, line 202: A RETURN statement is invalid in the main program. return -------^ compilation aborted for ifftest1.f (code 1) make[3]: *** [ifftest1.o] Error 1 Does anyone know what the problem might be? Thanks, Igor _________________________________________________________________ Dont just search. Find. Check out the new MSN Search! http://search.msn.click-url.com/go/onm00200636ave/direct/01/

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Log-ratio method
by lisandro＠fisica.unlp.edu.ar 11 Apr '06

11 Apr '06

Hi, I recently realized that Athena implement the ratio method as an analysis tool. I have look in the ifeffit web page and Athena manual and can not find any manual or user guide. Does anyone know any kind of instructive or manual for this type of analysis with Athena? Thanks Lisandro Giovanetti

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Ifeffit files
by Matt Newville 11 Apr '06

11 Apr '06

Hi Todd, Todd Luxton wrote (and the mail somehow got bounced): > > I am new to the use of the Ifettit, but I am currently trying to model XAFS > data for arsenate adsorbed onto a ruthenium oxide. If anyone has any ideas > on how to construct the problem, or could recommend a good source to review > I would be very grateful. Additionally, if anyone could recommend a decent > text on analyzing XAS data I would greatly appreciate it. > > > Thanks > > Todd Luxton I think the best bet is to go through the tutorials and examples from the workshops at http://cars.uchicago.edu/xafs/workshops.html Hopefully others will have more to say.... --Matt

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Re: my problem
by Matt Newville 11 Apr '06

11 Apr '06

Hi Stefano, On 4/8/06, Stefano Ciurli <stefano.ciurli(a)unibo.it> wrote: > OK. Now the latest horae061 package works. Artemis works. The only > "strange" thing is that when I expand the 061 disk image, I get 060 > as the label. Maybe it is meaningless, but anyway. Glad to hear it finally worked!! My guess is that a leftover Receipt was preventing the installation of some of the components. Does that seem right to you? If not, can you give us an idea of what might have been the problem before (for example, was there stale stuff left under /usr/local/)? I will add the notes I sent you (also below) to the Mac section of the Wiki: http://cars9.uchicago.edu/iffwiki/IfeffitOnMacintosh If you (or Paul, or anyone else) find errors in this, or would like to add information to the wiki, please do!! --Matt PS: for the record, a more complete transaction of off-line email: > > > >I'd recommend deleting (or moving to somewhere else) all of > >/Applications/Ifeffit and > >/Library/Perl (not /System/Library/Perl!! and note that this is > >assuming that you are using perl only for horae -- more below). You > >should also delete/move the 'Ifeffit installation receipts': In > >/Library/Receipts/Ifeffit-*. > > > >Then look in /usr/local/bin and /usr/local/lib (which depending on > >your system may have many things or very few things in them) for > >anything with the name "pgplot" -- delete/move these. > > > >Then install Ifeffit using the Installer. > > OK. Now the latest horae061 package works. Artemis works. ....

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Re: [Ifeffit] New release (061) of my codes -- Macintosh 10.4 binary installer
by Matt Newville 07 Apr '06

07 Apr '06

Stefano, You don't need a a file named libpglot.a. The application ifeffit statically includes the pgplot library. If you were to build a new Ifeffit application (including building the base perl module, which horae's build does), it would look in the file /Applications/Ifeffit/share/ifeffit/config/Config.mak and see that it should build with 'libpgplot_iff.a' in the directory '/Applications/Ifeffit/pgplot'. And it should work. The result you sent from otool definitely makes it look like your installation is broken. It also seems to use Aquaterm, which is strange. Paul, is there any chance that Aquaterm is looking for a dynamic pgplot library? Stefano, you did delete all the Ifeffit installation receipts in '/Library/Receipts' and installed the binary package, right? > > Can anyone else confirm / deny if the installer works on OS X 10.4? > > maybe I am the only one using it? :-) I sort of doubt that, but it would be more convenient if we didn't have to support it. --Matt

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Re: [Ifeffit] xafs on wikipedia
by Bruce Ravel 07 Apr '06

07 Apr '06

On Friday 07 April 2006 14:04, you wrote: > Does it seem reasonable to you (and Bruce?) to use the 'CC > share-alike' license for all web / wiki content on xafs.org (and > perhaps the ifeffit wiki?), and make it clear to anyone posting that > what they post uses that license unless explicitly different? I think > we'd all agree on this, but it would be best to be clear. For the last couple years I have been using the CC Attribution-ShareAlike license for many things that I write. http://creativecommons.org/licenses/by-sa/2.5/ The attribution clause is consistent with how scientific attribution is typically done in the literature and the share-alike clause is consistent with how Matt and I license our codes. 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 release (061) of my codes
by Bruce Ravel 07 Apr '06

07 Apr '06

Hi folks, I just made a new release of Athena (0.8.049) and Artemis (0.8.006). A new source tarball is at SourceForge and at my website. An updater for Windows is on Matt's server. There is nothing big in this release, just some bug fixes and a few small usability improvements. See the release notes http://cars9.uchicago.edu/iffwiki/HoraeVersion061 for details. Enjoy, 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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Ifeffit on 10.4
by Emmanuelle Montarges 06 Apr '06

06 Apr '06

Hi everyone Working on MacOs10.4 computer, after several unsuccessful installations of ifeffit package....I have the following message when I try to run Athena from the Terminal window. I downloaded Tk-804.027.tar and installed it in "temp" directory, but I still have the same message...have you ever had this error? ************ Can't load '/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Tk/Tk.bundle' for module Tk: dlopen(/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Tk/Tk.bundle, 1): Library not loaded: /usr/X11R6/lib/libX11.6.dylib Referenced from: /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Tk/Tk.bundle Reason: image not found at /System/Library/Perl/5.8.6/darwin-thread-multi-2level/DynaLoader.pm line 230. at /Applications/Ifeffit/bin/athena line 52 Compilation failed in require at /Applications/Ifeffit/bin/athena line 52. BEGIN failed--compilation aborted at /Applications/Ifeffit/bin/athena line 52. ********** thanks in advance for your help Emmanuelle MONTARGES-PELLETIER

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Re: latest version
by Bruce Ravel 06 Apr '06

06 Apr '06

On Tuesday 04 April 2006 11:09, you wrote: > Hi, Bruce, > > Could you please direct me to get the latest version of Athena and > Artemis? I am not sure if other windows users have the same > problem as I have but I don't think the download from Matt's webpage > been updated. And somehow the switch for the software to update > automatically in my computer was turned off and I can not get it turn > back on. Ning Download the most recent version of the installer then let the updater handle the chore of getting your computer up to date. Here are the details of how the updater works, including some troubleshooting tips: http://cars9.uchicago.edu/iffwiki/IfeffitOnWindows/WinUpdater If there are any other problems/questions -- ask on the mailing list. 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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tungsten spectra
by Renato Canha Ambrosio 06 Apr '06

06 Apr '06

Dear colleagues, I woulk like to know if anyone ha the XANES spectra at LI, II and III from a W foil obtained at a conventional XAFS beamline. I need it in order to calibrate DXAS data. Thank you very much Renato Canha rcanha(a)ccet.ufrn.br -- Open WebMail Project (http://openwebmail.org) ---------- Original Message ----------- From: ifeffit-request(a)millenia.cars.aps.anl.gov To: ifeffit(a)millenia.cars.aps.anl.gov Sent: Sun, 2 Apr 2006 12:00:11 -0500 Subject: Ifeffit Digest, Vol 38, Issue 2 > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > Today's Topics: > > 1. xafs on wikipedia (Francesco Giannici) > 2. Re: xafs on wikipedia (Stefano Ciurli) > 3. Re: xafs on wikipedia (Carlo Segre) > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 2 Apr 2006 09:00:56 +0200 > From: "Francesco Giannici" <zenarcade(a)libero.it> > Subject: [Ifeffit] xafs on wikipedia > To: "ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <IX325K$B150A1BE546B51869BD525DBC482B4F4(a)libero.it> > Content-Type: text/plain; charset=iso-8859-1 > > Hi all. > I'd like to let you know that the Italian version of Wikipedia now > contains an article on X-ray absorption, at > http://it.wikipedia.org/wiki/EXAFS . > (Wikipedia is a free encyclopedia that anyone can edit). I used some > images by Bruce, who asked me to make this announcement. Although > the article is written in Italian, maybe it could motivate the > readers of this list to do the same on their local wikipedia. > > Bye > -- > Francesco Giannici > Dept. of Inorganic Chemistry > University of Palermo > giannici at pa dot ismn dot cnr dot it > > ------------------------------ > > Message: 2 > Date: Sun, 2 Apr 2006 10:32:24 +0200 > From: Stefano Ciurli <stefano.ciurli(a)unibo.it> > Subject: Re: [Ifeffit] xafs on wikipedia > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <a06230903c0553c88e83b(a)[192.168.1.3]> > Content-Type: text/plain; charset="us-ascii" ; format="flowed" > > Dear Francesco, > very well done! Thanks! > 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" > > ------------------------------ > > Message: 3 > Date: Sun, 2 Apr 2006 10:39:50 -0500 (CDT) > From: Carlo Segre <segre(a)iit.edu> > Subject: Re: [Ifeffit] xafs on wikipedia > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <Pine.LNX.4.64.0604021039290.4587(a)localhost.localdomain> > Content-Type: text/plain; charset=us-ascii; format=flowed > > Dear Francesco: > > Excellent! > > Carlo > > On Sun, 2 Apr 2006, Francesco Giannici wrote: > > > Hi all. I'd like to let you know that the Italian version of Wikipedia > > now contains an article on X-ray absorption, at > > http://it.wikipedia.org/wiki/EXAFS . (Wikipedia is a free encyclopedia > > that anyone can edit). I used some images by Bruce, who asked me to make > > this announcement. Although the article is written in Italian, maybe it > > could motivate the readers of this list to do the same on their local > > wikipedia. > > > > Bye > > > > -- > 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 > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > End of Ifeffit Digest, Vol 38, Issue 2 > ************************************** ------- End of Original Message -------

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Re: latest version
by Bruce Ravel 05 Apr '06

05 Apr '06

On Tuesday 04 April 2006 11:09, you wrote: > Hi, Bruce, > > Could you please direct me to get the latest version of Athena and > Artemis? I am not sure if other windows users have the same > problem as I have but I don't think the download from Matt's webpage > been updated. And somehow the switch for the software to update > automatically in my computer was turned off and I can not get it turn > back on. Ning Download the most recent version of the installer then let the updater handle the chore of getting your computer up to date. Here are the details of how the updater works, including some troubleshooting tips: http://cars9.uchicago.edu/iffwiki/IfeffitOnWindows/WinUpdater If there are any other problems/questions -- ask on the mailing list. 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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xafs on wikipedia
by Francesco Giannici 02 Apr '06

02 Apr '06

Hi all. I'd like to let you know that the Italian version of Wikipedia now contains an article on X-ray absorption, at http://it.wikipedia.org/wiki/EXAFS . (Wikipedia is a free encyclopedia that anyone can edit). I used some images by Bruce, who asked me to make this announcement. Although the article is written in Italian, maybe it could motivate the readers of this list to do the same on their local wikipedia. Bye -- Francesco Giannici Dept. of Inorganic Chemistry University of Palermo giannici at pa dot ismn dot cnr dot it

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Re: [Ifeffit] new release (061) of my codes
by Matt Newville 31 Mar '06

31 Mar '06

Stefano, I'm very confused. Please help me understand what does and does not work for you. Today you said: > 2) If I just type 'ifeffit' from the command line I get the following: > > > stefano% ifeffit > > dyld: Library not loaded: /usr/local/lib/libpgplot.dylib > Referenced from: /Applications/Ifeffit/bin/ifeffit > Reason: image not found > > Trace/BPT trap > Emmanuelle seems to have similar behavior. Of course, you know that this means that no ifeffit applications will run correctly. The messages you sent yesterday implied very strange permission problems and was definitely different than this. What changed? Has the ifeffit command-line program EVER worked for you? Really, I hope this question illustrates my confusion about what does and does not work for you. But you also said today: > just to let people know that for me (OSX 10.4.5) Athena works fine > after installation from ifeffit-1.2.8-Mac10.4.1_pkg.dmg OK... so Ifeffit and athena work??? That is very confusing. It also seems to be very different from Emmanuelle's experience. Hmmm. Then again, if Ifeffit and athena do work, what is the problem you're having? --Matt

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Re: [Ifeffit] new release (061) of my codes
by Matt Newville 31 Mar '06

31 Mar '06

Stefano, I don't know why 'ifeffit i' reports a blank during perl's configuration. Can you verify these from a terminal: A. what does ~> /Applications/Ifeffit/bin/ifeffit -i report? B. Start the command-line ifeffit and type ifeffit> print $&install_dir what does this say? Then again, I don't understand why horae needs to do 'ifeffit -i' on a Mac. It will always be /Applications/Ifeffit/share/ifeffit. --Matt

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Re: [Ifeffit] new release (061) of my codes
by Matt Newville 30 Mar '06

30 Mar '06

HI Stefano, > stefano% ~> /Applications/Ifeffit/bin/ifeffit -i > tcsh: /Users/stefano: Permission denied. But that's implying that you can't even run ifeffit due to permission problems. That makes it seem much more about your system than about Ifeffit. > stefano# ifeffit > stefano# ifeffit> print $&install_dir Hmm, that's weird. The banner message didn't print and the prompt is wrong (it should be "Ifeffit>"). Any ideas why that might be? > stefano# ifeffit> print $&install_dir > su: Illegal variable name. > stefano# print $&install_dir > su: Illegal variable name. Hmm, that's weird too. I'm not sure what wrote "su: Illegal variable name." I'm pretty sure that is not from the ifeffit program. --Matt

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Number of independent points: Artemis & Feffit
by Mauro Rovezzi 30 Mar '06

30 Mar '06

Hi guys, I've noticed a strange behaviour in Artemis during the calculation of N_idp; the value differs from the Feffit one. In fact, with command line feffit (ver. 2.984) N_idp=(2*delta_k*delta_R/pi)+2 but with Artemis the "+2" value disappears. Seen that the procedure is: Artemis-->Ifeffit-->feffit(), why they differs? Mauro -- Mauro Rovezzi <rovezzi(a)esrf.fr> PhD student - GILDA BM08 c/o ESRF (Grenoble, FR)

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(no subject)
by Emmanuelle Montarges 30 Mar '06

30 Mar '06

Hi everyone Working on MacOs10.4 computer, after several unsuccessful installations of ifeffit package....I have the following message when I try to run Athena from the Terminal window. I downloaded Tk-804.027.tar and installed it in "temp" directory, but I still have the same message...have you ever had this error? ************ Can't load '/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Tk/Tk.bundle' for module Tk: dlopen(/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Tk/Tk.bundle, 1): Library not loaded: /usr/X11R6/lib/libX11.6.dylib Referenced from: /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Tk/Tk.bundle Reason: image not found at /System/Library/Perl/5.8.6/darwin-thread-multi-2level/DynaLoader.pm line 230. at /Applications/Ifeffit/bin/athena line 52 Compilation failed in require at /Applications/Ifeffit/bin/athena line 52. BEGIN failed--compilation aborted at /Applications/Ifeffit/bin/athena line 52. ********** thanks in advance for your help Emmanuelle MONTARGES-PELLETIER

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Re: [Ifeffit] Fe B standard
by Scott Calvin 30 Mar '06

30 Mar '06

Thanks, all! That info did the trick...I ended up using an Excel spreadsheet to do the processing, which may make some of you wince, but I found it easy enough. :) --Scott Calvin Sarah Lawrence College >

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Contour plot
by Mauro Rovezzi 29 Mar '06

29 Mar '06

Hi to all, Does someone has already written an Ifeffit script calculating a contour plot? In 2003 Norbert opened this thread on "Scanning of Potential Surfaces in EXAFS": http://cars9.uchicago.edu/pipermail/ifeffit/2003-July/000398.html Do you have any "wild code" to send me? :) Thanks, Mauro -- Mauro Rovezzi <rovezzi(a)esrf.fr> PhD student - GILDA BM08 c/o ESRF (Grenoble, FR)

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core hole lifetime in XANES calculation using FEFF82
by Qi Q Z 29 Mar '06

29 Mar '06

Dear all, Feff82 uses the data from K. Rahkonen and K. Krause (Atomic Data and Nuclear Data Tables, Vol 14, Number 2, 1974) to set core hole lifetime(gamach parameter). My question is if people can set gamach parameter in Feff82 by themselves? may I use a minus vi0 in EXCHANGE card to reduce broading caused by core hole lifetime? Thanks in advance. Qi

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Re: [Ifeffit] Odd feff result
by Bruce Ravel 25 Mar '06

25 Mar '06

On Friday 24 March 2006 13:01, Scott Calvin wrote: > So here's the question. These three paths are identical except for > the identity of one of the scattering atoms. The degeneracy of the > path with boron and the path with nickel is the same. Why is the feff > amplitude ratio for the boron-containing path higher than that of the > nickel-containing path? Shouldn't nickel scatter more strongly? And > yes, I double-checked...the potentials are defined correctly in the > feff.inp file. Scott, I am inclined to side with Jeremy and Feng. One might be surprised by how quick-n-dirty the amplitude calculation is. If memory serves (and who knows how likely *that* is), feff computes the complex chi(k) using plane waves, which is a very quick calculation. It then adds up the magnitude of the complex chi(k) at 4 points. That's it. The amplitude is never meant to be more than a guide to eye. As you well know, to know how each path contributes to the data, you actually need to plot them or -- better -- do a fit. 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: [Ifeffit] Odd feff result
by Feng Wang 24 Mar '06

24 Mar '06

Hi Scott and Jeremy It is interesting result, and I strongly agree with Jeremy's explanation. We also notices such a phonomenon before, a prominent postpeak, about 40 eV above iron L3 edge, even in very thin films of iron fluoride. The peak gradually disappears as fluorine is removed by electron irradiation, but appears when an iron film is oxidized.Oxygen and fluorine anions in transition-metal compounds are strong backscatters, as confirmed by the FEFF calculation, I believe boron is another strong scatter. Best regards, Feng > Scott, > > This doesn't seem like too unusual a result to me. The amp ratio from > feff is more of a qualitative than a quantitative prediction. Now I am > just making a guess; nevertheless, a boron scattering path will probably > have a significantly higher amplitude at low k compared to a Ni or Fe > scattering path. This could easily be the cause of the difference you > observe. > > Jeremy Kropf > > Chemical Engineering Division > Argonne National Laboratory > Argonne, IL 60439 > > Ph: 630.252.9398 > Fx: 630.252.9373 > kropf(a)cmt.anl.gov > > > > -----Original Message----- > > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov > > [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf > > Of Scott Calvin > > Sent: Friday, March 24, 2006 1:01 PM > > To: XAFS Analysis using Ifeffit > > Subject: [Ifeffit] Odd feff result > > > > Hi all, > > > > I just ran a feff calculation using feff6L and got a result > > that surprised me a little. I was modelling a ferrite with a > > nickel and boron substituted for iron in a small fraction of > > sites. Here's part of files.dat: > > > > file sig2 amp ratio deg nlegs r effective > > feff0010.dat 0.00000 2.706 2.000 3 3.7141 > > feff0011.dat 0.00000 26.472 20.000 3 3.7141 > > feff0012.dat 0.00000 4.038 2.000 3 3.7141 > > > > and the corresponding part of the paths.dat: > > > > 10 3 2.000 index, nleg, degeneracy, r= 3.7141 > > x y z ipot label rleg > > beta eta > > -3.126710 1.042240 1.042240 1 > > 'Ni ' 3.4567 150.5039 0.0000 > > -1.146460 1.146460 1.146460 3 > > 'O ' 1.9857 58.9923 0.0000 > > 0.000000 0.000000 0.000000 0 > > 'Fe ' 1.9857 150.5039 0.0000 > > 11 3 20.000 index, nleg, degeneracy, r= 3.7141 > > x y z ipot label rleg > > beta eta > > 1.042240 -3.126710 1.042240 2 > > 'Fe ' 3.4567 150.5039 0.0000 > > 1.146460 -1.146460 1.146460 3 > > 'O ' 1.9857 58.9923 0.0000 > > 0.000000 0.000000 0.000000 0 > > 'Fe ' 1.9857 150.5039 0.0000 > > 12 3 2.000 index, nleg, degeneracy, r= 3.7141 > > x y z ipot label rleg > > beta eta > > -1.042240 3.126710 1.042240 4 > > 'B ' 3.4567 150.5039 0.0000 > > -1.146460 1.146460 1.146460 3 > > 'O ' 1.9857 58.9923 0.0000 > > 0.000000 0.000000 0.000000 0 > > 'Fe ' 1.9857 150.5039 0.0000 > > > > So here's the question. These three paths are identical > > except for the identity of one of the scattering atoms. The > > degeneracy of the path with boron and the path with nickel is > > the same. Why is the feff amplitude ratio for the > > boron-containing path higher than that of the > > nickel-containing path? Shouldn't nickel scatter more > > strongly? And yes, I double-checked...the potentials are > > defined correctly in the feff.inp file. > > > > --Scott Calvin > > Sarah Lawrence College > > > > _______________________________________________ > > 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 ================================== Feng Wang fwang(a)phys.ualberta.ca Electron Microscopy Group Department of Physics University of Alberta =========================================================

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RE: [Ifeffit] Odd feff result
by Kropf, Arthur Jeremy 24 Mar '06

24 Mar '06

Scott, This doesn't seem like too unusual a result to me. The amp ratio from feff is more of a qualitative than a quantitative prediction. Now I am just making a guess; nevertheless, a boron scattering path will probably have a significantly higher amplitude at low k compared to a Ni or Fe scattering path. This could easily be the cause of the difference you observe. Jeremy Kropf Chemical Engineering Division Argonne National Laboratory Argonne, IL 60439 Ph: 630.252.9398 Fx: 630.252.9373 kropf(a)cmt.anl.gov > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov > [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf > Of Scott Calvin > Sent: Friday, March 24, 2006 1:01 PM > To: XAFS Analysis using Ifeffit > Subject: [Ifeffit] Odd feff result > > Hi all, > > I just ran a feff calculation using feff6L and got a result > that surprised me a little. I was modelling a ferrite with a > nickel and boron substituted for iron in a small fraction of > sites. Here's part of files.dat: > > file sig2 amp ratio deg nlegs r effective > feff0010.dat 0.00000 2.706 2.000 3 3.7141 > feff0011.dat 0.00000 26.472 20.000 3 3.7141 > feff0012.dat 0.00000 4.038 2.000 3 3.7141 > > and the corresponding part of the paths.dat: > > 10 3 2.000 index, nleg, degeneracy, r= 3.7141 > x y z ipot label rleg > beta eta > -3.126710 1.042240 1.042240 1 > 'Ni ' 3.4567 150.5039 0.0000 > -1.146460 1.146460 1.146460 3 > 'O ' 1.9857 58.9923 0.0000 > 0.000000 0.000000 0.000000 0 > 'Fe ' 1.9857 150.5039 0.0000 > 11 3 20.000 index, nleg, degeneracy, r= 3.7141 > x y z ipot label rleg > beta eta > 1.042240 -3.126710 1.042240 2 > 'Fe ' 3.4567 150.5039 0.0000 > 1.146460 -1.146460 1.146460 3 > 'O ' 1.9857 58.9923 0.0000 > 0.000000 0.000000 0.000000 0 > 'Fe ' 1.9857 150.5039 0.0000 > 12 3 2.000 index, nleg, degeneracy, r= 3.7141 > x y z ipot label rleg > beta eta > -1.042240 3.126710 1.042240 4 > 'B ' 3.4567 150.5039 0.0000 > -1.146460 1.146460 1.146460 3 > 'O ' 1.9857 58.9923 0.0000 > 0.000000 0.000000 0.000000 0 > 'Fe ' 1.9857 150.5039 0.0000 > > So here's the question. These three paths are identical > except for the identity of one of the scattering atoms. The > degeneracy of the path with boron and the path with nickel is > the same. Why is the feff amplitude ratio for the > boron-containing path higher than that of the > nickel-containing path? Shouldn't nickel scatter more > strongly? And yes, I double-checked...the potentials are > defined correctly in the feff.inp file. > > --Scott Calvin > Sarah Lawrence College > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

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cyber-security
by Khalid, Syed 24 Mar '06

24 Mar '06

I did download the latest version Ifeffit-1.2.8a for our computers > running Windows 2000 OS. The programs work great. > To start with, I increased the 'user' privilege to 'administrator', > downloaded the program and then executed to setup. All the program 'icons' > appear on the desktop and work fine, however, they do not work if I remove > the 'administrator' privilege and login as 'user'. When you click or double > click the icons, no response what so ever. > > I went back to 'administrator' privilege, but keeping this high privilege > for users does not make our cyber-security guys happy. Any solution to this problem? > > > Syed Khalid 725 D, National Synchrotron Light Source Brookhaven National Laboratory Upton, NY 11973 Phone: 631-344-7496 FAX: 631-344-3238 e-mail: khalid(a)bnl.gov

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CORRELATION MATRIX IN IFEFFIT
by Renato Canha Ambrosio 24 Mar '06

24 Mar '06

Hi folks I'm need to explore more the correlation matrix R(ij)given by ifeffit since my fit several variables are ajusted (the number is far bellow the number of independent data points). In my MACRO, the command correl (@all, @all, print) permit to obtain the correlation matrix. So I have some questions about the calculation of correlations (rij): 1) Is the correlations(rij) calculated in ifeffit the sample linear correlation which measures the linear dependence between two vectos (in this sense, I'm thinking the term vector as a nx1 matrix in which n corresponds to the sample size - perhaps the number of fit iteractions)? If so, can I use a conventional hypothesis test like t (t = rij*sqrt[(n-1)/(1-rij**rij)] and how many degress of fredon can I consider to fint the t score on the table of t student distribution? 2) As I need to explore more the correlation matriz I would like to know if someone uses principal component analysis on Rij or some other chemometric approach. Thank you very much Renato Canha Ambrosio -- Open WebMail Project (http://openwebmail.org) ---------- Original Message ----------- From: ifeffit-request(a)millenia.cars.aps.anl.gov To: ifeffit(a)millenia.cars.aps.anl.gov Sent: Wed, 22 Mar 2006 12:00:17 -0600 Subject: Ifeffit Digest, Vol 37, Issue 6 > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > Today's Topics: > > 1. GeO2 (Santiago J.A. Figueroa) > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 21 Mar 2006 17:06:45 -0300 > From: "Santiago J.A. Figueroa" <figueroa(a)inifta.unlp.edu.ar> > Subject: [Ifeffit] GeO2 > To: <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <004701c64d23$00f973a0$8c01010a@NEVERMIND> > Content-Type: text/plain; charset="iso-8859-1" > > Hi all, > > Anyone out there have spectra for a GeO2 standard? > > Thanks! > > Lic. Santiago J. A. Figueroa > Instituto de Investigaciones Fisicoquímicas > Teóricas y Aplicadas (INIFTA) > Fac. de Cs. Exactas. > Universidad Nacional de La Plata > Diag. 113 y 64 > C.C.16 suc.4 (1900) La Plata > TEL: (0221) 425 7430 interno: 144 > FAX: (0221) 425 4642 > WEB: www.inifta.unlp.edu.ar > >

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Re: Fw: Doped Crystal in Artemis
by Scott Calvin 24 Mar '06

24 Mar '06

1 0

GeO2
by Santiago J.A. Figueroa 21 Mar '06

21 Mar '06

Hi all, Anyone out there have spectra for a GeO2 standard? Thanks! Lic. Santiago J. A. Figueroa Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA) Fac. de Cs. Exactas. Universidad Nacional de La Plata Diag. 113 y 64 C.C.16 suc.4 (1900) La Plata TEL: (0221) 425 7430 interno: 144 FAX: (0221) 425 4642 WEB: www.inifta.unlp.edu.ar

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Re: Trying to create atoms.inp
by Bruce Ravel 10 Mar '06

10 Mar '06

Gerald, You are correct that the link you give does not provide you with enough information about the structure to use Atoms. Have you looked in the Crystal Structires series by Wyckoff? Or the Inorganic Crystal Structure Database (ICSD)? Have you tried to do a search through the crystallography literature? I am sending this to the Ifeffit Mailing List (which is probably the correct place for a question like this) in hopes that someone will have more information that I do. B On Friday 10 March 2006 04:33, Schmidt, Gerald wrote: > Dear Bruce, > > a colleague of mine attended the recent workshop at the SLS in Villigen, > Switzerland (Damdin, from Mongolia). Maybe he told you that we're currently > working on some Zr and As EXAFS data...? > > Well, the original substance used for the samples was zirconium dinitrate, > which was applied to activated charcoal. We want to find out how the > sorption of As alters the crystal structure. > > The problem seems to be that we can't find enough information about > zirconium dinitrate to create a feff model. In all the databases I have > heard of it could not be found. The only thing I found was the attached > file (from > http://www.chemexper.com/index.shtml?main=http://www.chemexper.com/search/c >as/14985-18-3.html). It contains, at least, some xyz coordinates. > But obviously the space group and the lattice constants are missing. > > Do you have any idea what we could do to find the missing parameters so we > can successfully run atoms? > > Thanks & best regards, > Gerald > > --------------------------------- > Gerald Schmidt (Dipl. Geoecologist) > Institute of Geosciences > Mineralogy Section > Johannes-Gutenberg-University Mainz > Becherweg 21 > D-55099 Mainz > Germany > Tel. +49-6131-39-24780 > Fax +49-6131-39-23070 > gschmidt(a)uni-mainz.de -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advance 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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k weight in Athena
by koppolu uma mahendra kumar 08 Mar '06

08 Mar '06

Dear All, I have a doubt about k-weights while extracting the signal in ATHENA. In athena Background removal panel conatins one button called k-weight. My question is how significant k weigths at the stage of background removal. Please explain Thanking You Mahendra -- Research Student Material Science Laboratory University of Hyderabad(india) X-ray Synchrotron Radiation Laboratory University of Trento(Italy)

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Re: Tkatoms
by Bruce Ravel 08 Mar '06

08 Mar '06

Linda, I am CCing this question and my (short) answer to the Ifeffit mailing list. > I am installing atoms for the first time on my Windows XP PC. When I > download the file ifeffit.1.2.8.exe I can run the atoms command line > version but I don't find how I can run the TK version on my PC. > Thanks for your answer. http://cars9.uchicago.edu/cgi-bin/ifeffit/faqwiz?req=all#7.3 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: [Ifeffit] Amplitude in Artemis
by Barton, David (DG) 03 Mar '06

03 Mar '06

Balwant, I have done a number of LCF using Athena and have found that this error message is typically associated with the rejection of one of your standards as a possible component in the fit. This error message may be avoided in most cases if you uncheck the options of --weights between 0 &1 and --Force weights to sum to 1 AND you put in an appropriate initial guess for the fit. When you rerun the fit with these options unchecked, it should be obvious what caused the error since one or more of your standard spectra will get a negative weight. When this occurs it is probably a good sign that the standard is not appropriate in the fit and some other standard should be used. Hope this helps, Dave > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov > [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf > Of bsin1033(a)mail.usyd.edu.au > Sent: Thursday, March 02, 2006 3:41 PM > To: XAFS Analysis using Ifeffit; Kelly, Shelly D. > Cc: XAFS Analysis using Ifeffit > Subject: RE: [Ifeffit] Amplitude in Artemis > > > Hi Ifeffitters, > > I was trying to use the linear combination fitting function > in Athena to quantifying Cr(VI) and Cr(III) species. I used > two endmembers of Cr species as the two standards but the > program fails and gives error message "The fit flagged a > warning--probably that error bars could not be calculated. > That is probably an indication that one or more of your > standards are inappropriate for this fit." It appears I am > either using the wrong settings or even wrong function to do > the job, any suggestions. We have additional 3 spectra with > variable combinations of Cr(VI) and > Cr(III) as well. > > Cheers, > > Balwant Singh > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging > Program. _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

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RE: [Ifeffit] Amplitude in Artemis
by Kelly, Shelly D. 02 Mar '06

02 Mar '06

Hi Paul, Here is an edited version of the Fe project file. I believe that the first shell signal is not isolated from the 2nd and third shells. One way for the fit to look better when not enough paths are present is for the s2 value to be large to spread the signal out with an outrageous coordination number. I added a C and a Zn path to model the region from r=1 to 3.5 Å. The fit is not that great, the background needs to be fixed and I'm not sure that the C and Zn paths are the best choice. If you look at the real or imaginary parts of the fit with kweights of 1 and 2 and 3 you will see that we have done a fair job at reproducing the data. Hopefully this little bit of help will get you going in the right direction. Shelly ________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Paul Sent: Tuesday, February 28, 2006 5:54 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Amplitude in Artemis Hi Shelly I've attached the artemis project files. Hopefully you get further with them than I have been able to. Cheers Paul ----- Original Message ----- From: Kelly, Shelly D. <mailto:SKelly@anl.gov> To: XAFS Analysis using Ifeffit <mailto:ifeffit@millenia.cars.aps.anl.gov> Sent: Wednesday, March 01, 2006 1:50 AM Subject: RE: [Ifeffit] Amplitude in Artemis Hi Paul, How close are the distances for the 6 ligands? It is usually not possible to fit a single peak in the EXAFS spectrum by 6 independent signals. It sound like the distribution of distances for these 6 ligands is incorrect. I suggest that you try to fit just the first peak with one and then with two different shells with unknown coordination numbers and distances. This will give you some more information about what the data indicate the structure is like. If you send me an artemis file, I'll take a peak at it. Shelly skelly(a)anl.gov ________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Paul Sent: Monday, February 27, 2006 6:31 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Amplitude in Artemis Hi Shelly Unfortunately the coordination number is 1 for all atoms present. I have the crystal structure of the complex, so I am currently including 6 ligating atoms all at distances defined by the structure in the input file. It seems to be the first shell that is causing the problems, with a quickfit first shell artemis fit giving nominally 13 ligating species (which is of course absurd). So I believe something else must be the problem. Cheers Paul ----- Original Message ----- From: Kelly, Shelly D. <mailto:SKelly@anl.gov> To: XAFS Analysis using Ifeffit <mailto:ifeffit@millenia.cars.aps.anl.gov> Sent: Tuesday, February 28, 2006 12:55 AM Subject: RE: [Ifeffit] Amplitude in Artemis Hi Paul, It seems possible that one of the other amplitude terms is also incorrect. Scott already mentioned the step height but what about the coordination number? The amplitude of the model is given by coordination number * S02. You mentioned that the S02 value was somewhere between 2 and 4. What is the value for coordination number * S02? If the coordination number is 1, then it is possible that the parameters are switched. Maybe the coordination number should be between 2 and 4 and S02 should be around 1. HTH, Shelly ________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Paul Sent: Sunday, February 26, 2006 6:52 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Amplitude in Artemis I have just started a PhD and have been given alot of EXAFS data to simulate but I don't know much about artemis. I have tried to fit the data for quite some time now, but can't get any kind of good fit unless the amplitude is above 1. Is there any way amp can be above 1 and rationally explained? Cheers, Paul ________________________________ _______________________________________________ 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: [Ifeffit] Amplitude in Artemis
by Kelly, Shelly D. 28 Feb '06

28 Feb '06

Hi Paul, How close are the distances for the 6 ligands? It is usually not possible to fit a single peak in the EXAFS spectrum by 6 independent signals. It sound like the distribution of distances for these 6 ligands is incorrect. I suggest that you try to fit just the first peak with one and then with two different shells with unknown coordination numbers and distances. This will give you some more information about what the data indicate the structure is like. If you send me an artemis file, I'll take a peak at it. Shelly skelly(a)anl.gov ________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Paul Sent: Monday, February 27, 2006 6:31 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Amplitude in Artemis Hi Shelly Unfortunately the coordination number is 1 for all atoms present. I have the crystal structure of the complex, so I am currently including 6 ligating atoms all at distances defined by the structure in the input file. It seems to be the first shell that is causing the problems, with a quickfit first shell artemis fit giving nominally 13 ligating species (which is of course absurd). So I believe something else must be the problem. Cheers Paul ----- Original Message ----- From: Kelly, Shelly D. <mailto:SKelly@anl.gov> To: XAFS Analysis using Ifeffit <mailto:ifeffit@millenia.cars.aps.anl.gov> Sent: Tuesday, February 28, 2006 12:55 AM Subject: RE: [Ifeffit] Amplitude in Artemis Hi Paul, It seems possible that one of the other amplitude terms is also incorrect. Scott already mentioned the step height but what about the coordination number? The amplitude of the model is given by coordination number * S02. You mentioned that the S02 value was somewhere between 2 and 4. What is the value for coordination number * S02? If the coordination number is 1, then it is possible that the parameters are switched. Maybe the coordination number should be between 2 and 4 and S02 should be around 1. HTH, Shelly ________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Paul Sent: Sunday, February 26, 2006 6:52 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Amplitude in Artemis I have just started a PhD and have been given alot of EXAFS data to simulate but I don't know much about artemis. I have tried to fit the data for quite some time now, but can't get any kind of good fit unless the amplitude is above 1. Is there any way amp can be above 1 and rationally explained? Cheers, Paul ________________________________ _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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RE: [Ifeffit] Amplitude in Artemis
by Kelly, Shelly D. 28 Feb '06

28 Feb '06

Hi Paul, It seems possible that one of the other amplitude terms is also incorrect. Scott already mentioned the step height but what about the coordination number? The amplitude of the model is given by coordination number * S02. You mentioned that the S02 value was somewhere between 2 and 4. What is the value for coordination number * S02? If the coordination number is 1, then it is possible that the parameters are switched. Maybe the coordination number should be between 2 and 4 and S02 should be around 1. HTH, Shelly ________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Paul Sent: Sunday, February 26, 2006 6:52 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Amplitude in Artemis I have just started a PhD and have been given alot of EXAFS data to simulate but I don't know much about artemis. I have tried to fit the data for quite some time now, but can't get any kind of good fit unless the amplitude is above 1. Is there any way amp can be above 1 and rationally explained? Cheers, Paul

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Amplitude in Artemis
by Paul 27 Feb '06

27 Feb '06

I have just started a PhD and have been given alot of EXAFS data to simulate but I don't know much about artemis. I have tried to fit the data for quite some time now, but can't get any kind of good fit unless the amplitude is above 1. Is there any way amp can be above 1 and rationally explained? Cheers, Paul

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SPAM score=47.4*** Fonts in document pods
by Dave Baker 22 Feb '06

22 Feb '06

-------------------- Start SpamAssassin results ---------------------- Content analysis details: (score=47.4,required=5.3) -2.6 BAYES_00 BODY: Bayesian spam probability is 0 to 1% [score: 0.0000] 50 STOCKS_APS FULL: Hot Stocks Spam -------------------- End of SpamAssassin results --------------------- The original message was not completely plain text, and may be unsafe to open with some email clients; in particular, it may contain a virus, or confirm that your address can receive spam. If you wish to view it, it may be safer to save it to a file and open it with an editor.

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Re: How to change the spline knots in Athena
by Bruce Ravel 21 Feb '06

21 Feb '06

On Tuesday 21 February 2006 03:08, you wrote: > I am using Athena (0.8.048) software for XAFS analysis. > It is greatly helpful to me for XAFS characterization. > > I have a question on the background estimation. > Spline knots is displayed by "About current group" menu. > Could you tell me how to change the spline knots, if possible. > Changing the knots is useful to suppress the long-range variation. This is the kind of question that is better sent to the mailing list, so I am CCing my answer there. The number of knots is determined by the values of the k-range of the spline fit and by the value of Rbkg. The number of knots is delta_k * Rbkg * 2 / pi and the knots are evenly spaced in k. Ifeffit (and so Athena) does not allow you to move the knots to different locations nor does it allow you add or remove knots. The AUTOBK algorithm works by making a distinction between data and background in terms of Fourier components. Consequently it *cannot* allow you to move the knots or use more knots, since doing so would change the Fourier components included in the background spline. 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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error message in help
by Bradley Roberts 21 Feb '06

21 Feb '06

With Ifeffit 1.2.8, Athena 0.8.047, Artemis 0.8.004 running on OS X and plotting correctly, I'm not able to pull up any of the help windows. In either of the GUI programs, when I click on the Help menu and choose Document (or any of the sub-menu items in Athena) X11 beeps in error, and a window opens with the title "pod" and nothing displayed within the window. I mentioned before that I could not get tk::pod to install correctly via CPAN (the response being) Installing tk::pod FAILED windows would pop up during the make test routine that said: Can't find Pod 'perl' with an OK button and that the Text::English and Tk::HistEntry modules were not installed (though they are installed, says CPAN) I recognize that this is probably more of a Perl/CPAN related question but perhaps someone has seen this problem before. -- 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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Re: [Ifeffit] pgplot+Kubuntu+/XWINDOW /XSERVE
by Bruce Ravel 21 Feb '06

21 Feb '06

On Monday 20 February 2006 23:48, Denis Testemale wrote: > I've been using Ifeffit+horae (VERY GOOD) stuff for a while on my > previous Mandrake linux distro. I've changed to Kubuntu now. I have > difficulties to install everything on this new laptop. [Please be > aware that I use Linux for quite some time now but still consider > myself as an "everyday beginner"] > > I'm stuck at the installation of PGPLOT. > I've tried then to install from Mat's PGPLOT_install script but ran > into the same kind of error. Here it is: Kubuntu is debian-based and, I think, can use any debian repository. So I think you should be able to use Carlo's debian repository to install the software. Just point kynoptic at the repositories mentioned here: http://cars9.uchicago.edu/~ravel/software/downloads.html#debian 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: How to change the spline knots in Athena
by Bruce Ravel 21 Feb '06

21 Feb '06

On Tuesday 21 February 2006 03:08, you wrote: > I am using Athena (0.8.048) software for XAFS analysis. > It is greatly helpful to me for XAFS characterization. > > I have a question on the background estimation. > Spline knots is displayed by "About current group" menu. > Could you tell me how to change the spline knots, if possible. > Changing the knots is useful to suppress the long-range variation. This is the kind of question that is better sent to the mailing list, so I am CCing my answer there. The number of knots is determined by the values of the k-range of the spline fit and by the value of Rbkg. The number of knots is delta_k * Rbkg * 2 / pi and the knots are evenly spaced in k. Ifeffit (and so Athena) does not allow you to move the knots to different locations nor does it allow you add or remove knots. The AUTOBK algorithm works by making a distinction between data and background in terms of Fourier components. Consequently it *cannot* allow you to move the knots or use more knots, since doing so would change the Fourier components included in the background spline. 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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pgplot+Kubuntu+/XWINDOW /XSERVE
by Denis Testemale 21 Feb '06

21 Feb '06

Hello. I've been using Ifeffit+horae (VERY GOOD) stuff for a while on my previous Mandrake linux distro. I've changed to Kubuntu now. I have difficulties to install everything on this new laptop. [Please be aware that I use Linux for quite some time now but still consider myself as an "everyday beginner"] I'm stuck at the installation of PGPLOT. I've tried then to install from Mat's PGPLOT_install script but ran into the same kind of error. Here it is: -if I try to install without any driver but the /NULL one, this what it tells: g77 -fno-backslash -o pgdemo1 /usr/local/src/pgplot/examples/pgdemo1.f -L`pwd` -lpgplot -L/usr/X11R6/lib -lX11 /usr/bin/ld: ne peut trouver -lX11 collect2: ld a retourné 1 code d'état d'exécution - if I try with the /XWINDOW and /XSERVE: gcc -c -Wall -fPIC -DPG_PPU -O -I. -I/usr/X11R6/include /usr/local/src/pgplot/drivers/xwdriv.c /usr/local/src/pgplot/drivers/xwdriv.c:127:21: erreur: X11/Xos.h : Aucun fichier ou répertoire de ce type /usr/local/src/pgplot/drivers/xwdriv.c:128:22: erreur: X11/Xlib.h : Aucun fichier ou répertoire de ce type /usr/local/src/pgplot/drivers/xwdriv.c:129:23: erreur: X11/Xutil.h : Aucun fichier ou répertoire de ce type /usr/local/src/pgplot/drivers/xwdriv.c:130:24: erreur: X11/keysym.h : Aucun fichier ou répertoire de ce type /usr/local/src/pgplot/drivers/xwdriv.c:131:23: erreur: X11/Xatom.h : Aucun fichier ou répertoire de ce type ... make: *** [xwdriv.o] Erreur 1 Let me add that my examples here are taken from an installation from the PGPLOT source, but I would have the same kind of error messages with Mat's script. In my long struggle I remember I had PGPLOT installed and working correctly (i.e. the demo would work) but without /XWINDOW neither /XSERVE. If I remember well, at that time my desperate attempt had been to delete "|X11" from a LIBS line in the make file. But of course, following up to the installation of horae, I could not have the plotting interface in athena/artemis. I read somewhere that Bruce had some Kubuntus running some where. Maybe somebody else? Did you face this kind of difficulties. Thanks for any kind of advice and please feel free to ask any additional information needed. Cheers denis ps: I'm not a 64 bit linux.

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Errors from Webatoms?
by Feng Wang 20 Feb '06

20 Feb '06

Hi everyone: I used WEBATOMS(version 1.8), to calculated the feff.inp for Si-K of alpha-SiO2 (quartz phase), using the crystal structure (as listed below) from Wyckoff's Crsytal Structures(P312-313), however, I could not get correct atomic configuration, such as, I did not get the tetrahedron (of 4 nearest neighboring oxygen atoms), I got two n.n. oxygen atoms only, please refer to the results on the bottom. As suggested by Dr. Ravel, I tried the atoms in Artemis, but still I could not get correct feff.inp.Would you please help me to check and suggest, thank you so much. Best regards, Feng alpha-SiO2 crystal structure (from Wyckoff's book): hexagonal, a=4.91304, c=5.40463, space group: p3121 (#152). Si (3a): (-u,- u,1/3), (u,u,0) (0,u,2/3); O: (6c): (x,y,z), (y-x, -x, z+1/3), (-y, x-y, z+2/3), (x-y, -y,-z), (y,x,2/3-z), (-x,y-x,1/3-z). In which, u(si)=0.465, x=0.415, y=0.272, z=0.120. According to it, I used the input for WEBATOMS: Space group: p3121 OUTPUT type: feff8.inp Edge: K shift: 0 0 0 A=4.91304, c=5.40463 Crystallographic Sites: Si (-0.465 -0.465, 1/3) O (0.415, 0.272, 0.12). And I got the atomic configuration in feff.inp as below: ATOMS * this list contains 449 atoms * x y z ipot tag distance 0.00000 0.00000 0.00000 0 Si 0.00000 0 -0.51058 -0.99735 -1.15297 2 O 1.60771 1 0.21274 1.45917 -0.64854 2 O 1.61091 2 0.00000 0.00000 1.80158 1 Si 1.80158 3 -2.27633 0.97033 0.00004 1 Si 2.47451 4 1.97849 -1.48619 0.00004 1 Si 2.47451 5 0.82118 -2.40002 0.64857 2 O 2.61822 6 -1.11902 0.05650 -2.45008 2 O 2.69412 7 0.82118 2.51302 0.64857 2 O 2.72218 8 -1.66789 1.91117 1.15301 2 O 2.78637 9 1.37005 -0.54535 2.45012 2 O 2.85964 10 2.58693 -0.54535 1.15301 2 O 2.88428 11 -2.27633 0.97033 -1.80153 1 Si 3.06084 12 -0.29784 2.45652 -1.80153 1 Si 3.06083 13 1.97849 -1.48619 -1.80153 1 Si 3.06083 14 -0.29784 -2.45652 -1.80153 1 Si 3.06083 15 -0.29784 2.45652 1.80154 1 Si 3.06084 16 -0.29784 -2.45652 1.80154 1 Si 3.06084 17 -1.11902 0.05650 2.95455 2 O 3.15987 18 1.37005 -0.54535 -2.95451 2 O 3.30206 19 -3.43364 0.05650 0.64857 2 O 3.49481 20 0.21274 -3.45387 -0.64854 2 O 3.52066 21 0.00000 0.00000 -3.60305 1 Si 3.60305 22 -1.66789 -3.00187 1.15301 2 O 3.62250 23 1.97849 3.42685 0.00004 1 Si 3.95698 24 -0.51058 3.91569 -1.15297 2 O 4.11372 25 3.74424 1.45917 -1.15297 2 O 4.18065 26 -4.04208 -0.99735 -0.64854 2 O 4.21352 27 -2.88477 1.91117 2.45012 2 O 4.23999 28 3.95698 0.00000 -1.80153 1 Si 4.34778 29 1.97849 3.42685 -1.80153 1 Si 4.34778 30 3.95698 0.00000 1.80154 1 Si 4.34779 31 -0.29784 2.45652 -3.60309 1 Si 4.37098 32 -0.29784 -2.45652 -3.60309 1 Si 4.37098 33 -2.27633 0.97033 3.60310 1 Si 4.37099 34 -0.29784 2.45652 3.60310 1 Si 4.37099 35 1.97849 -1.48619 3.60310 1 Si 4.37099 36 -0.29784 -2.45652 3.60310 1 Si 4.37099 37 -0.51058 -0.99735 4.25166 2 O 4.39682 38 -2.88477 1.91117 -2.95451 2 O 4.55012 39 -2.27633 -3.94271 0.00004 1 Si 4.55265 40 4.46756 -0.99735 -0.64854 2 O 4.62325 41 ================================== Feng Wang fwang(a)phys.ualberta.ca Electron Microscopy Group Department of Physics University of Alberta =========================================================

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RE: [Ifeffit] Errors from Webatoms?
by Barton, David (DG) 18 Feb '06

18 Feb '06

Feng, Attached is a CIF file for alpha-SiO2 with the same space group (P3121) that you are attempting to use. The major difference that I see in this file compared with your input file is the Si location (0.465 0 1/3) vs. (-.465 .465 1/3). I am no crystallographer so I cannot tell you if a shift vector would make these equal, but this CIF file imports directly into Artemis and does give a 4-coordinate Si-O. Dave > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov > [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf > Of Feng Wang > Sent: Saturday, February 18, 2006 2:28 AM > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Errors from Webatoms? > > > Hi everyone: > > I used WEBATOMS(version 1.8), to calculated the feff.inp for Si-K of > alpha-SiO2 (quartz phase), using the crystal structure (as > listed below) > from Wyckoff's Crsytal Structures(P312-313), however, I could not get > correct atomic configuration, such as, I did not get the > tetrahedron (of 4 > nearest neighboring oxygen atoms), I got two n.n. oxygen > atoms only, please > refer to the results on the bottom. > As suggested by Dr. Ravel, I tried the atoms in Artemis, but > still I could > not get correct feff.inp.Would you please help me to check > and suggest, > thank you so much. > > Best regards, > > Feng > > alpha-SiO2 crystal structure (from Wyckoff's book): > > hexagonal, a=4.91304, c=5.40463, space group: p3121 (#152). > Si (3a): (-u,- u,1/3), (u,u,0) (0,u,2/3); O: (6c): (x,y,z), > (y-x, -x, z+1/3), (-y, x-y, > z+2/3), (x-y, -y,-z), (y,x,2/3-z), (-x,y-x,1/3-z). In which, > z+u(si)=0.465, > x=0.415, y=0.272, z=0.120. > > According to it, I used the input for WEBATOMS: > Space group: p3121 > OUTPUT type: feff8.inp > Edge: K > shift: 0 0 0 > A=4.91304, c=5.40463 > Crystallographic Sites: Si (-0.465 -0.465, 1/3) O (0.415, > 0.272, 0.12). > > And I got the atomic configuration in feff.inp as below: > > ATOMS * this list contains 449 atoms > * x y z ipot tag distance > 0.00000 0.00000 0.00000 0 Si 0.00000 0 > -0.51058 -0.99735 -1.15297 2 O 1.60771 1 > 0.21274 1.45917 -0.64854 2 O 1.61091 2 > 0.00000 0.00000 1.80158 1 Si 1.80158 3 > -2.27633 0.97033 0.00004 1 Si 2.47451 4 > 1.97849 -1.48619 0.00004 1 Si 2.47451 5 > 0.82118 -2.40002 0.64857 2 O 2.61822 6 > -1.11902 0.05650 -2.45008 2 O 2.69412 7 > 0.82118 2.51302 0.64857 2 O 2.72218 8 > -1.66789 1.91117 1.15301 2 O 2.78637 9 > 1.37005 -0.54535 2.45012 2 O 2.85964 10 > 2.58693 -0.54535 1.15301 2 O 2.88428 11 > -2.27633 0.97033 -1.80153 1 Si 3.06084 12 > -0.29784 2.45652 -1.80153 1 Si 3.06083 13 > 1.97849 -1.48619 -1.80153 1 Si 3.06083 14 > -0.29784 -2.45652 -1.80153 1 Si 3.06083 15 > -0.29784 2.45652 1.80154 1 Si 3.06084 16 > -0.29784 -2.45652 1.80154 1 Si 3.06084 17 > -1.11902 0.05650 2.95455 2 O 3.15987 18 > 1.37005 -0.54535 -2.95451 2 O 3.30206 19 > -3.43364 0.05650 0.64857 2 O 3.49481 20 > 0.21274 -3.45387 -0.64854 2 O 3.52066 21 > 0.00000 0.00000 -3.60305 1 Si 3.60305 22 > -1.66789 -3.00187 1.15301 2 O 3.62250 23 > 1.97849 3.42685 0.00004 1 Si 3.95698 24 > -0.51058 3.91569 -1.15297 2 O 4.11372 25 > 3.74424 1.45917 -1.15297 2 O 4.18065 26 > -4.04208 -0.99735 -0.64854 2 O 4.21352 27 > -2.88477 1.91117 2.45012 2 O 4.23999 28 > 3.95698 0.00000 -1.80153 1 Si 4.34778 29 > 1.97849 3.42685 -1.80153 1 Si 4.34778 30 > 3.95698 0.00000 1.80154 1 Si 4.34779 31 > -0.29784 2.45652 -3.60309 1 Si 4.37098 32 > -0.29784 -2.45652 -3.60309 1 Si 4.37098 33 > -2.27633 0.97033 3.60310 1 Si 4.37099 34 > -0.29784 2.45652 3.60310 1 Si 4.37099 35 > 1.97849 -1.48619 3.60310 1 Si 4.37099 36 > -0.29784 -2.45652 3.60310 1 Si 4.37099 37 > -0.51058 -0.99735 4.25166 2 O 4.39682 38 > -2.88477 1.91117 -2.95451 2 O 4.55012 39 > -2.27633 -3.94271 0.00004 1 Si 4.55265 40 > 4.46756 -0.99735 -0.64854 2 O 4.62325 41 > > > > > ================================== > Feng Wang > fwang(a)phys.ualberta.ca > Electron Microscopy Group > Department of Physics > University of Alberta > ========================================================= > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

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R-space
by Marcos Eleoterio 12 Feb '06

12 Feb '06

Good morning, I have a question about the R-range in Artemis, i want to fit the first shell region only, but what are the criteria to select the R-range? if i select the first peak just a,little bit different to one fit from the other, the fit get very different. reagards Marcos Eleotério

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Athena 0.8.048, Artemis 0.8.005, Hephaestus 0.13
by Bruce Ravel 11 Feb '06

11 Feb '06

Hi, Today I have released version 060 of the source code tarball, which includes Athena 0.8.048, Artemis 0.8.005, Hephaestus 0.13. This is mostly a bug fix release, although both Athena and Hephaestus have minor new features. The problem with displaying documentation should be solved. Please read the release notes at http://cars9.uchicago.edu/iffwiki/HoraeVersion060 New versions of the tarball are at SourceForge and at my website. I built new Windows executables -- a new updater is available and should install the next time you fire up one of the programs. As always, let me know if you run into any problems or have any great new suggestions. 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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sample holders
by Silvio Levy 09 Feb '06

09 Feb '06

I beg the indulgence of the list owner to post a question not directly related to Ifeffit. Where can on purchase sample holders to be used in the SSRL beam (both for liquid samples and solid ones)? I've asked some researchers at SSRL and at UCB but they use ones milled at their respective institutions, and I don't have this option. Silvio Levy Cal State University East Bay Mathematical Sciences Research Institute

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Mac OS X installation
by Bradley Roberts 09 Feb '06

09 Feb '06

Bottom line - I was able to install - hopefully my comments below help someone in the future. > >I'm not sure I understand the full sequence of events, but I'd >definitely recommend re-installing from the binary installer. >Building from source is possible, of course, but once you run into a >problem it's a lot harder to guess what's wrong. I'm trying to avoid building from source, and was trying to re-install from binary. > > I am able to load ifeffit and execute commands, however when I >try to load any of >> the ancillary programs there are failures (see printout below). > >It looks like the core ifeffit is installed fine, but not the perl >libraries needed by athena, artemis, etc. Do you have any ideas why >that might be the case? What, if anything, is in /Library/Perl? /Library/Perl had (and has) a full installation of 5.8.6 although since starting this, there is now a 5.8.1 folder with the dir darwin-thread-multi-2level which I think I'll just leave alone for now. > > As per previous posts, I've installed and updated g77 via fink, >as well as tk and tk::pod via >> cpan. I also had to install LWP via cpan before I could get >>ifeffit to run. > >OK.... but none of this should be needed for athena to run. It did appear that LWP was necessary to get ifeffit to run. It also didn't start to work until g77 was installed, somewhat confirmed with this page: http://cars9.uchicago.edu/cgi-bin/ifeffit/faqwiz?req=show&file=faq02.010.htp tk, tk::pod did not appear to be necessary > > From the install notes I see that ifeffit's intall program >trashes the LWP directory in perl, > >Hmmm, where do you see this? (and I'd hope it doesn't trash >anything!!) The installer does write a bunch of perl modules to >/Library/Perl. "trash" was probably the wrong word. I can't find where I was concerned about LWP specifically, but this note is the closest: If you are using Perl on Mac OS X for other purposes, you may want to consult with Matt and/or Bruce before installing this package. > > so I'm curious if I've caused this problem myself (and if so, how >do I fix it?). Secifically, the >> ifeffit.pm and Tk/Pod.pm files cannot be found anywhere in the >>@INC directories. Also, >>running the locate command I cannot find the files on the drive >>anywhere else. > >They should be in /Library/Perl. still not seen by the locate command, however as I note below, the programs run. > > Additionally, I tried to download and re-install ifeffit from the > > disk image and it cannot install - the error says "you cannot >> continue. there is nothing to install." > >You probably need to delete the "installation receipt" by removing >the /Library/Receipt/Ifeffit-1.2.*****.pkg folder(s). Then you should >be able to do a full re-install. >After that happens, check the contents of /Library/Perl. I re-downloaded the 1.2.8 binary package from sourceforge and removed the previous receipt. Upon re-installation, athena/artemis/etc appear as applications (with icons, etc) and are properly launched either via double click or command line. I can't say what, specifically, caused it to install correctly this time, or what steps I went through that were unnecessary, but hopefully these notes will help someone else next time. Thanks for your help - now I've got to learn how to use the program. >Hope that helps. Let us know how it works out. > >Cheers, > >--Matt > -- 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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Athena
by lkh＠ensm-douai.fr 09 Feb '06

09 Feb '06

Hi, I'm working with Athena (00.8.046 version). I have two questions about xanes treatment : 1- When I open a file as xanes(E) the self absorption correction is not accessible. I must open it as mu(E). Why? 2- About Peak fit, It's possible to introduce new functions? Thank you very much. L. Khouchaf Analyse Physique Centre de Recherche de l'Ecole des Mines de Douai. Douai France. khouchaf(a)ensm-douai.fr

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Re: using FEFF8 to calculate the xanes spectra of solid solutions
by Bruce Ravel 09 Feb '06

09 Feb '06

On Thursday 09 February 2006 09:24, Valmor Mastelaro wrote: > >Hello Bruce, > > could you please help me with the following question: > > I truing to calculate the xanes spectra of Pb1-xLaxTiO3 solid solutions. I > calculated the PbTiO3 xanes spectra and is quite similar to published one. > When I substitute some Pb atoms by La atoms, even for x=15%, I only > observed few changes on the calculated spectra compared with the undoped > one. > > Please, could you verify if I´m using a correct feff imput file (in > attach)... > > thanks for your help > > Regards Hi Valmor, I hope you don't mind that I am CCing my response to the Ifeffit mailing list. Your question is one that I see often, so I think that others would benefit by seeing this discussion. In a solid solution, one expects the dopant to substitute stochastically into the lattice. That is, in the absence of some kind of structural phase transition that leads to a different crystal symmetry, we expect the dopant to enter randomly into the crystal. In your case, each Pb site in the crystal has a 15% chance of being replaced by a La atom. If we ignore La-La correlations, the probability of a Pb site being replaced by La is unaffected by the occupancy of the adjacent Pb sites. Here are the first several lines of the feff.inp file you sent me, with several lines not related to this discussion deleted: TITLE PLT10 Com lantânio,a=3.885,c=4.139 HOLE 1 1.0 POTENTIALS * ipot z label 0 22 Ti 2 3 0.01 1 8 O 2 3 3.00 2 82 Pb 3 3 0.90 3 22 Ti 2 3 0.99 4 57 La 3 3 0.10 ATOMS .00000 .00000 .00000 0 Ti .00000 .00000 .00000 -1.87041 1 axial 1.87041 -1.95921 .00000 .33980 1 Planar 1.98846 .00000 -1.95921 .33980 1 Planar 1.98846 1.95921 .00000 .33980 1 Planar 1.98846 .00000 1.95921 .33980 1 Planar 1.98846 .00000 .00000 2.15145 1 axial 2.15145 1.95921 -1.95921 1.91754 4 La 3.36956 1.95921 1.95921 1.91754 2 Pb 3.36956 -1.95921 -1.95921 1.91754 2 Pb 3.36956 -1.95921 1.95921 1.91754 2 Pb 3.36956 1.95921 -1.95921 -2.10432 2 Pb 3.47925 -1.95921 -1.95921 -2.10432 2 Pb 3.47925 1.95921 1.95921 -2.10432 2 Pb 3.47925 -1.95921 1.95921 -2.10432 2 Pb 3.47925 .00000 -3.91842 .00000 3 Ti 3.91842 .00000 3.91842 .00000 3 Ti 3.91842 3.91842 .00000 .00000 3 Ti 3.91842 -3.91842 .00000 .00000 3 Ti 3.91842 .00000 .00000 4.02186 3 Ti 4.02186 .00000 .00000 -4.02186 3 Ti 4.02186 This feff.inp file does NOT adequately represent a solid solution. The Pb sites here are NOT occupied by La 15% of the time. In this example, there is one Pb site that is occupied by La 100% of the time and all the rest are never occupied by La. That's NOT a solid solution -- that's a different crystal. Thus, this feff.inp file might be some kind of approximation of a solid solution, but probably not a very good one. Unfortunately, Feff does not allow you to put 15% of an atom at a site. Each site is either all or nothing. That doesn't mean that Feff is not helpful in the case of a solid solution -- it just means that you have to do more work. One way of better approximating a solid solution is to use a random number generator and to run Feff many times. Each time you run feff, pre-process the feff.inp file, using a random number generator to decide for *every* lead site whether it should be replaced with a La atom. If you run enough feff calculations with Pb randomly substituted in this way, the ensemble will be a good representation of a solid solution. You can add up the subsequent calculations until the sum of spectra converges. There is at least one person out there in Ifeffit-land who has done some work on approximating solid solutions in this way. He might be inspired to comment further on this topic. There is an additional issue that you are not considering in the feff.inp file that you sent me. It is quite unlikely that the La atoms rests exactly on the Pb site. Much more likely is that the La atom introduces some kind of local disorder, moving off-site, pushing surrounding atoms away or drawing them closer. Those distortions might be large enough to be significantly effect the local environment about the Ti atom. If so, ignoring them in the feff.inp file is obviously incorrect. One last thing: take a look at the PDF file of a talk I have been giving recently on multiple scattering theory: http://cars9.uchicago.edu/~ravel/talks/pimst.pdf. In section 3, I show a simple sequence of calculations on PbTiO3. One rule of thumb that I try to get across in that part of the talk is that light atoms tend to effect the XANES more than heavy atoms. I don't want to overstate this issue, but it is quite possible that the difference between Pb and La in the XANES of an oxide is pretty subtle. That is, the XANES is probably more sensitive to where the oxygen atoms are than to whether a Pb site is occupied by Pb or La. If that is the case, then, of the two issues I discuss above, the more serious is the possibility that La introduces distortions to the oxygen octahedra. Although your feff.inp file certainly does not do a complete job at modelling a solid solution, the more serious issue is probably that it does not introduce new distortions. And that is my best guess for why your feff.inp file does not seem to replicate the changes you see in your Ti-edge spectra. 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/exafs/

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Re: [Feffusers] Fwd: Some question about FMS calculation with FEFF
by Bruce Ravel 09 Feb '06

09 Feb '06

On Thursday 09 February 2006 01:57, Michel Jaouen wrote: > Now a question about Hephaestus: for f' and f" one has rodio buttons > allowing to select among various set (Crmer Liberman, Henke, ..). I > have try to select several and it always return CL! Why and how to > fix this (not sure it is a bug but?). To quote from the Hephaestus document about the f'/f" utility: This utility plots the complex corrections to the scattering factors for the elements. i.e. the energy dependent f'(E) and f"(E) terms. These functions are tabulated from the Cromer-Liberman calculations for the isolated, neutral atom. The selection in the Resource menu is ignored. That's by design. The reason is that I have never been able to figure out how to do the interpolation off of Chantler's ffast tables near the absorption edges such that the f' function is well behaved near the absorption edge. The dteails are at http://physics.nist.gov/PhysRefData/FFast/Text/cover.html. The last time I looked at this in detail, my implementation gave very poor results in the region of f' that was changing quickly. 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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Re: [Ifeffit] Installation troubles on OS X
by Matt Newville 08 Feb '06

08 Feb '06

Hi Brad, I'm not sure I understand the full sequence of events, but I'd definitely recommend re-installing from the binary installer. Building from source is possible, of course, but once you run into a problem it's a lot harder to guess what's wrong. > I am able to load ifeffit and execute commands, however when I try to load any of > the ancillary programs there are failures (see printout below). It looks like the core ifeffit is installed fine, but not the perl libraries needed by athena, artemis, etc. Do you have any ideas why that might be the case? What, if anything, is in /Library/Perl? > As per previous posts, I've installed and updated g77 via fink, as well as tk and tk::pod via > cpan. I also had to install LWP via cpan before I could get ifeffit to run. OK.... but none of this should be needed for athena to run. > From the install notes I see that ifeffit's intall program trashes the LWP directory in perl, Hmmm, where do you see this? (and I'd hope it doesn't trash anything!!) The installer does write a bunch of perl modules to /Library/Perl. > so I'm curious if I've caused this problem myself (and if so, how do I fix it?). Secifically, the > ifeffit.pm and Tk/Pod.pm files cannot be found anywhere in the @INC directories. Also, >running the locate command I cannot find the files on the drive anywhere else. They should be in /Library/Perl. > Additionally, I tried to download and re-install ifeffit from the > disk image and it cannot install - the error says "you cannot > continue. there is nothing to install." You probably need to delete the "installation receipt" by removing the /Library/Receipt/Ifeffit-1.2.*****.pkg folder(s). Then you should be able to do a full re-install. After that happens, check the contents of /Library/Perl. Hope that helps. Let us know how it works out. Cheers, --Matt

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secondary notes
by Bradley Roberts 08 Feb '06

08 Feb '06

My previous post was incomplete, after looking at last night's late late late notes: Installing tk::pod FAILED windows would pop up during the make test routine that said: Can't find Pod 'perl' with an OK button and that the Text::English and Tk::HistEntry modules were not installed (I thought they'd be autoinstalled if they're needed?) Other error messages at the beginning indicate that Test::More and Test::Without::Moderate were not installed. Hopefully this additional information will be helpful? -- 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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Installation troubles on OS X
by Bradley Roberts 08 Feb '06

08 Feb '06

I've spent the past few days going through the backlogs of this list and have been able to solve many problems so far. However, I've hit a point where I don't see a record of this problem/solution and am hoping someone can help. I am able to load ifeffit and execute commands, however when I try to load any of the ancillary programs there are failures (see printout below). As per previous posts, I've installed and updated g77 via fink, as well as tk and tk::pod via cpan. I also had to install LWP via cpan before I could get ifeffit to run. From the install notes I see that ifeffit's intall program trashes the LWP directory in perl, so I'm curious if I've caused this problem myself (and if so, how do I fix it?). Secifically, the ifeffit.pm and Tk/Pod.pm files cannot be found anywhere in the @INC directories. Also, running the locate command I cannot find the files on the drive anywhere else. Additionally, I tried to download and re-install ifeffit from the disk image and it cannot install - the error says "you cannot continue. there is nothing to install." My setup is: PB 15" G4 OS X 10.4.4 ifeffit 1.2.8 perl 5.8.6 fink and cpan selfupdated to the latest via cvs epic-glory:~ apple$ athena Can't locate Ifeffit.pm in @INC (@INC contains: /sw/lib/perl5 /sw/lib/perl5/darwin /System/Library/Perl/5.8.6/darwin-thread-multi-2level /System/Library/Perl/5.8.6 /Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 /Library/Perl /Network/Library/Perl/5.8.6/darwin-thread-multi-2level /Network/Library/Perl/5.8.6 /Network/Library/Perl /System/Library/Perl/Extras/5.8.6/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at /Applications/Ifeffit/bin/athena line 54. BEGIN failed--compilation aborted at /Applications/Ifeffit/bin/athena line 58. epic-glory:~ apple$ artemis Can't locate Ifeffit.pm in @INC (@INC contains: /sw/lib/perl5 /sw/lib/perl5/darwin /System/Library/Perl/5.8.6/darwin-thread-multi-2level /System/Library/Perl/5.8.6 /Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 /Library/Perl /Network/Library/Perl/5.8.6/darwin-thread-multi-2level /Network/Library/Perl/5.8.6 /Network/Library/Perl /System/Library/Perl/Extras/5.8.6/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at /Applications/Ifeffit/bin/artemis line 49. BEGIN failed--compilation aborted at /Applications/Ifeffit/bin/artemis line 53. epic-glory:~ apple$ hephaestus Can't locate Tk/Pod.pm in @INC (@INC contains: /sw/lib/perl5 /sw/lib/perl5/darwin /System/Library/Perl/5.8.6/darwin-thread-multi-2level /System/Library/Perl/5.8.6 /Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 /Library/Perl /Network/Library/Perl/5.8.6/darwin-thread-multi-2level /Network/Library/Perl/5.8.6 /Network/Library/Perl /System/Library/Perl/Extras/5.8.6/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at /Library/Perl/5.8.6/darwin-thread-multi-2level/Tk/widgets.pm line 14. at /Applications/Ifeffit/bin/hephaestus line 66 BEGIN failed--compilation aborted at /Applications/Ifeffit/bin/hephaestus line 66. -- 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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FEFF8 vrs FEFF6
by Kelly, Shelly D. 06 Feb '06

06 Feb '06

Hello Ifeffit friends, It is my understanding that FEFF6 or equivalently FEFF7 are considered the standard for Extended X-ray Absorption Fine Structure Analysis. In my experience, FEFF8 is a dangerous tool for EXAFS analysis as it has the ability to produce results that differ significantly from FEFF6 or FEFF7. In the review of EXAFS manuscripts where FEFF8 is the tool of choice, what parameters should be reported to give the reader some confidence that the authors have not tweaked the code to cover-up some errors in the model(s). A Big Thanks Shelly Shelly Kelly Bldg 203 RM E113 Skelly(a)anl.gov Argonne National Laboratory 630-252-7376 9700 S Cass Ave www.mesg.anl.gov Argonne, IL 60439

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Again _ for help with Webatoms input_sorry for incomplete information
by Feng Wang 03 Feb '06

03 Feb '06

Hi Everyone, I had a trouble with the input for webatoms in trying to get feff.inp from it. I got the crystal structure information from papers, as attached below, would you please suggest what should I input for the items listed below: Shift: Alpha= Beta= Gamma= The table of Crystallgraphic sites: Would Dr. Ravel or some of you can help with that? Thank you so much in advance. Best regards, Feng Crystal structure information: Iron trifluorine has a ReO3 type structure (hexagonal), with spac group of R- 3C, with two Fe atoms at (0 0 0) and (0.5 0.5 0.5)and 6 fluorines at (x, 0.5- x, 0.25), -(x, 0.5-x, 0.25), (0.5-x,0.25 x),-(0.5-x,0.25 x), (0.25 x, 0.5- x), -(0.25 x, 0.5-x), and with x=-0.164. ================================== Feng Wang fwang(a)phys.ualberta.ca Electron Microscopy Group Department of Physics University of Alberta =========================================================

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for help with Webatoms input
by Feng Wang 03 Feb '06

03 Feb '06

Hi Everyone, I had a trouble with the input for webatoms in trying to get feff.inp from it. I got the crystal structure information from papers, as attached below, would you please suggest what should I input for the items listed below: Shift: Alpha= Beta= Gamma= The table of Crystallgraphic sites: Thank you so much in advance. Best regards, Feng Crystal structure information: Iron trifluorine has a ReO3 type structure (hexagonal), with spac group of R- 3C, with two Fe atoms at (0 0 0) and (0.5 0.5 0.5)and 6 fluorines at (x, 0.5- x, 0.25), -(x, 0.5-x, 0.25), (0.5-x,0.25 x),-(0.5-x,0.25 x), ( ================================== Feng Wang fwang(a)phys.ualberta.ca Electron Microscopy Group Department of Physics University of Alberta =========================================================

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correlated Einstein model and Debye model
by Renato Canha Ambrosio 02 Feb '06

02 Feb '06

Good afternoon everybody I have questions about the Einstein and Debye correlated models in IFEFFIT. As described in page 80 of the EXAFS ANALYSIS WITH FEFF AND FEFFIT - PART 2: COMMENTARY by Bruce Ravel the eins function is a function evaluated in the context of the current path. So the reduced mass is calculated with the mass of the atoms in the path. Its ok but I have several scans at different temperatures so I would like to refine not only the Theta (Einstein temperature) but also the reduced mass and perhaps the static disorder. Can I do it in the context of the path or I have to perform a non - xafs refinement with the file containing the temperatures and sigma^2. I make the same question for the Debye correlated model. Thank you very much for your kind attention Renato Canha Universidade Federal do Rio Grande do Norte Natal - RN - BRASIL Open WebMail Project (http://openwebmail.org) ---------- Original Message ----------- From: ifeffit-request(a)millenia.cars.aps.anl.gov To: ifeffit(a)millenia.cars.aps.anl.gov Sent: Wed, 1 Feb 2006 12:00:12 -0600 Subject: Ifeffit Digest, Vol 36, Issue 1 > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > Today's Topics: > > 1. Re: FEFF8 vrs FEFF6 (Matt Newville) > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 1 Feb 2006 08:54:22 -0600 > From: Matt Newville <newville(a)cars.uchicago.edu> > Subject: Re: [Ifeffit] FEFF8 vrs FEFF6 > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: > <b8522e3d0602010654j195cf712hf30b878a67bac08e(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > HI Shelly, > > I wouldn't say it's wrong to use Feff8 for EXAFS analysis, just > rarely necessary. > > Feff8 was definitely designed for XANES, and improvements for EXAFS > were not the main goal. But there are a few cases where Feff8 _is_ > known to be better for EXAFS than Feff6. (I'll leave out Feff7 as it > seems no one is using this much). Clusters with H is one, and > transuranic elements is another. I've heard a few people claim that > Feff8 gives "better E0's", which I think means that E0 refines to a > value closer to 0 (that is, to where the it's arbitrarily assigned in > the data processing). Since E0 has to be refined and has little > physical significance, I don't find this to be a compelling advantage > for Feff8. > > Early versions of Feff8 (pre-release? Including 8.00?? I'm not sure) > were much worse for EXAFS.This did get fixed, but I'm not sure when > (I have a hard time understanding Feff8 version numbers and can never > really tell which get released and widely used: I've given up > complaining and live wih the fact that "Feff8" means one snapshot of > 8 years worth of work.). By Feff8.1 for sure, and maybe eralier, there > were essentially no difference between Feff6, 7, and 8 for EXAFS. > That was based on analysis of data on metal foils (Cu, Ag, Au), and > could hardly be called thorough and possibly not even 'highly > relevent to real-world problems', as it doesn't even test changes in > exchange or overlap of metal-oxygen potentials. Better testing and > comparisons would be very good. > > Anyway, I think it's fine to use Feff6, 7, or 8 for EXAFS. > > I don't think anything should change for these versions in the > reporting of how a Feff calculation was done for EXAFS. Most EXAFS > work using Feff give no details about the calculation, and I think > that's mostly OK, as the Feff/Atoms/Artemis default parameters are > generally quite reasonable. If the work discusses comparing > different Feff calculations, then obviously more detail on what was > changing would be needed. > > That's my opinion, anyway. > > --Matt > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > End of Ifeffit Digest, Vol 36, Issue 1 > ************************************** ------- End of Original Message -------

3 2

RESTRAINTS IN IFEFFIT
by Renato Canha Ambrosio 25 Jan '06

25 Jan '06

Hi Folks, this is my first message on the list. Perhaps someone could help me. The subject is how to include restraints on exafs refinement. There is just scanty information about this on the ifeffit reference manual. I'm trying to refine the exafs data of a rhombohedral perovskite. The main MS contributions to the signal at about 3.5 A (non phase correct) arise from M O M interactions being M the absorber . We have a significant SS path, a two-legged and a three-legged path. The structural parameters of these three terms are correlated since all refers to the same A-B-C triangle and the A-B and B-C distances must be that found for M-O1 nearest-neighbor configurations. For these reasons we constrained the photo electron path length for three-legged to the M-O nearest-neighbor distance:R(three-leg = 2*RM-O). I'm trying to intoroduce the quantity defined as delta = R(three-legged)-R(two-legged) and thus define the SS half path length as a function of delta R(SS) = R (three-legged) - 2*delta. I think it is a restraint not a constraint. So I defined (def) the delta function on the line above the command FEFFIT also delr for the SS path. I introduced the restraint in the line FEFFIT as restraint = delrSS). The fit produce the same results as obtainde without the definition of delta and delrSS (function of delta). So I need to know how to introduce this restraint in the fit in order to calculate de M - O - M bond angle (this angle should be calculated using simple geometric relationships) - perhaps introduce the bond angle as a restraint. Someone can say me where I introduce the definitions of restraint parameters? Thank you very much for your kind attention Renato Canha Universidade Federal do Rio Grande doNorte Departamento de Quimica Natal - RN - BRAZIL Open WebMail Project (http://openwebmail.org) ---------- Original Message ----------- From: ifeffit-request(a)millenia.cars.aps.anl.gov To: ifeffit(a)millenia.cars.aps.anl.gov Sent: Mon, 23 Jan 2006 12:00:13 -0600 Subject: Ifeffit Digest, Vol 35, Issue 14 > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > Today's Topics: > > 1. Re: Re: I should be able to find this somewhere... (Bruce Ravel) > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 22 Jan 2006 16:58:07 -0600 > From: Bruce Ravel <bravel(a)anl.gov> > Subject: Re: [Ifeffit] Re: I should be able to find this somewhere... > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <200601221658.07513.bravel(a)anl.gov> > Content-Type: text/plain; charset="iso-8859-1" > > Hi, > > In fact, Artemis and Athena both attempt to deal correctly with input > chi(k) data that is not on the expected grid. Both codes perform a > test to see if the data is on the standard grid and, if not, > front-loads the data with zeros and uses Ifeffit's boxcar rebinning > function to put the data on the expected grid. > > Alas, there was a bug in the rebinning macro used by A&A which caused > it to fail in a particular situation met by the data in Matthew's > example. This bug will be fixed in the next release. > > If you import mu(E) data into Athena and then import data from the > Athena project file into Artemis, you will never see the problem that > Matthew reported. > > B > > On Tuesday 17 January 2006 16:09, Matt Newville wrote: > > Hi Matthew, Bruce, > > > > OK, I think it's a bug. Well, maybe it's just a consequence of a > > "known but not well advertised" problem. > > > > The chi(k) data you have doesn't start at k=0. By itself, this should > > be OK, and the fit seems to be mostly fine. There seems to be a bug > > in Ifeffit that the output fit chi(k) has the same number of data > > points as the input chi(k) data. In this case is incorrect -- it > > should go to the last data point in k. From looking at the code, I'm > > pretty sure this has no effect on the fit and is only an error in the > > output array. But the shortened chi_fit(k) will have an impact on the > > way Bruce is calculating the residual. Even if that were fixed, the > > residual would still be wrong, as the residual in Artemis is > > calculated as > > set(data0_res.k = data0.k) > > set(data0_res.chi = data0.chi - data0_fit.chi) > > > > and then Fourier transforming to R-space. Since the data and fit > > aren't aligned in k-space, the residual is incorrect. It should be > > > > set(data0_res.chi = data0.chi - interp(data0_fit.k, data0_fit.chi, > > data0.k)) > > > > or some variation on that. > > > > Sorry for the trouble. It's definitely a result of narrow-mindedly > > expecting that all chi(k) data comes from Ifeffit/Athena and will > > always start at k=0. We should get this fixed (it's mostly there!) so > > that data from other sources can be used. Right now, the easiest > > work-around is to pre-pack the chi(k) data with zeros (starting from > > k=0.00) > > > > --Matt > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > -- > Bruce Ravel ---------------------------------------------- bravel(a)anl.gov > > Molecular Environmental Science Group, Building 203, Room E-165 > MRCAT, Sector 10, Advance 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/ > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > End of Ifeffit Digest, Vol 35, Issue 14 > *************************************** ------- End of Original Message -------

2 1

RE: [Ifeffit] RESTRAINTS IN IFEFFIT
by Kelly, Shelly D. 25 Jan '06

25 Jan '06

Hi Renato, See below for some comments: > > Hi Folks, this is my first message on the list. Perhaps someone could help > me. The subject is how to include restraints on exafs refinement. There is > just scanty information about this on the ifeffit reference manual. > > I'm trying to refine the exafs data of a rhombohedral perovskite. > > The main MS contributions to the signal at about 3.5 A (non phase correct) > arise from M - O - M interactions being M the absorber . We have a > significant SS path, a two-legged and a three-legged path. The structural > parameters of these three terms are correlated since all refers to the > same > A-B-C triangle and the A-B and B-C distances must be that found for > M-O1 nearest-neighbor configurations. For these reasons > we constrained the photo electron path length for three-legged to the > M-O nearest-neighbor distance:R(three-leg = 2*RM-O). [Kelly, Shelly D.] The three-leg path length is given by half the total path length. Calculated as R = (distance_AB + distance_BC + distance_AC) * 0.5 You know the distance from A-B and the distance from B-C but the distance from A-C is dependent on the angle of the triangle path. You can write an equation to determine the angle A. a^2 = b^2 + c^2 -2bc cos(A) where a=distance_AC, b=distance_AB, c=distance_BC and A is the angle opposite of the AC side of the triangle. Then the four leg path has a path length defined as R = (2*distance_AB + 2*distance_BC)*0.5 The single path from A to B has the distance R = (2*distance_AB)*0.5 The single path from A to C has the distance R = (2*distance_AC)*0.5 Which also depends on the angle A and distance_AB as defined above. So for your case you have one unknown length and one unknown bond angle to describe these path lengths. i.e. distance_AB=distance_BC is unknown and angle A is unknown. HTH Shelly I'm trying to > intoroduce the quantity defined as delta = R(three-legged)-R(two-legged) > and thus define the SS half path length as a function of delta R(SS) = R > (three-legged) - 2*delta. I think it is a restraint not a constraint. > So I defined (def) the delta function on the line above the command FEFFIT > also delr for the SS path. I introduced the restraint in the line FEFFIT > as > restraint = delrSS). The fit produce the same results as obtainde without > the definition of delta and delrSS (function of delta). > So I need to know how to introduce this restraint in the fit in order to > calculate de M - O - M bond angle (this angle should be calculated using > simple geometric relationships) - perhaps introduce the bond angle as a > restraint. > Someone can say me where I introduce the definitions of restraint > parameters? > > Thank you very much for your kind attention > > Renato Canha > > Universidade Federal do Rio Grande doNorte > Departamento de Quimica > Natal - RN - BRAZIL > Open WebMail Project (http://openwebmail.org) > > > ---------- Original Message ----------- > From: ifeffit-request(a)millenia.cars.aps.anl.gov > To: ifeffit(a)millenia.cars.aps.anl.gov > Sent: Mon, 23 Jan 2006 12:00:13 -0600 > Subject: Ifeffit Digest, Vol 35, Issue 14 > > > Send Ifeffit mailing list submissions to > > ifeffit(a)millenia.cars.aps.anl.gov > > > > To subscribe or unsubscribe via the World Wide Web, visit > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > or, via email, send a message with subject or body 'help' to > > ifeffit-request(a)millenia.cars.aps.anl.gov > > > > You can reach the person managing the list at > > ifeffit-owner(a)millenia.cars.aps.anl.gov > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of Ifeffit digest..." > > > > Today's Topics: > > > > 1. Re: Re: I should be able to find this somewhere... (Bruce Ravel) > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Sun, 22 Jan 2006 16:58:07 -0600 > > From: Bruce Ravel <bravel(a)anl.gov> > > Subject: Re: [Ifeffit] Re: I should be able to find this somewhere... > > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > > Message-ID: <200601221658.07513.bravel(a)anl.gov> > > Content-Type: text/plain; charset="iso-8859-1" > > > > Hi, > > > > In fact, Artemis and Athena both attempt to deal correctly with input > > chi(k) data that is not on the expected grid. Both codes perform a > > test to see if the data is on the standard grid and, if not, > > front-loads the data with zeros and uses Ifeffit's boxcar rebinning > > function to put the data on the expected grid. > > > > Alas, there was a bug in the rebinning macro used by A&A which caused > > it to fail in a particular situation met by the data in Matthew's > > example. This bug will be fixed in the next release. > > > > If you import mu(E) data into Athena and then import data from the > > Athena project file into Artemis, you will never see the problem that > > Matthew reported. > > > > B > > > > On Tuesday 17 January 2006 16:09, Matt Newville wrote: > > > Hi Matthew, Bruce, > > > > > > OK, I think it's a bug. Well, maybe it's just a consequence of a > > > "known but not well advertised" problem. > > > > > > The chi(k) data you have doesn't start at k=0. By itself, this should > > > be OK, and the fit seems to be mostly fine. There seems to be a bug > > > in Ifeffit that the output fit chi(k) has the same number of data > > > points as the input chi(k) data. In this case is incorrect -- it > > > should go to the last data point in k. From looking at the code, I'm > > > pretty sure this has no effect on the fit and is only an error in the > > > output array. But the shortened chi_fit(k) will have an impact on the > > > way Bruce is calculating the residual. Even if that were fixed, the > > > residual would still be wrong, as the residual in Artemis is > > > calculated as > > > set(data0_res.k = data0.k) > > > set(data0_res.chi = data0.chi - data0_fit.chi) > > > > > > and then Fourier transforming to R-space. Since the data and fit > > > aren't aligned in k-space, the residual is incorrect. It should be > > > > > > set(data0_res.chi = data0.chi - interp(data0_fit.k, data0_fit.chi, > > > data0.k)) > > > > > > or some variation on that. > > > > > > Sorry for the trouble. It's definitely a result of narrow-mindedly > > > expecting that all chi(k) data comes from Ifeffit/Athena and will > > > always start at k=0. We should get this fixed (it's mostly there!) so > > > that data from other sources can be used. Right now, the easiest > > > work-around is to pre-pack the chi(k) data with zeros (starting from > > > k=0.00) > > > > > > --Matt > > > > > > _______________________________________________ > > > Ifeffit mailing list > > > Ifeffit(a)millenia.cars.aps.anl.gov > > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > -- > > Bruce Ravel ---------------------------------------------- > bravel(a)anl.gov > > > > Molecular Environmental Science Group, Building 203, Room E-165 > > MRCAT, Sector 10, Advance 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/ > > > > ------------------------------ > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > End of Ifeffit Digest, Vol 35, Issue 14 > > *************************************** > ------- End of Original Message ------- > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

1 0

Re: Possible bug in Artemis. (Bruce Ravel)
by joshua jason kas 25 Jan '06

25 Jan '06

Hi Bruce, Thanks for the tips. I fooled around with the feff.inp and found that artemis somehow has a problem when feff is run with the RMULTIPLIER card. This card is purely for convenience, so I took it out and things work fine. This card was used in feff6 although the code runs very slowly with it for some reason. Anyway, here is the feff.inp file that I was using for feff6 or feff8 (they both have the problem). Thanks, Josh TITLE GeCl4 HOLE 1 1.0 CONTROL 1 1 1 1 1 1 (feff8) CONTROL 1 1 1 1 (feff6) PRINT 1 0 0 0 0 3 EXCHANGE 0 1 1 CORRECTIONS 1.2427845974 0.0041969513 RMAX 10.0 RMULTIPLIER 1.01 POTENTIALS 0 32 Ge -1 -1 1 1 17 Cl -1 -1 4 ATOMS 0.0000000000 0.0000000000 0.0000000000 0 1.1568027 1.1568027 1.1568027 1 Cl 1.1568027 -1.1568027 -1.1568027 1 Cl -1.1568027 1.1568027 -1.1568027 1 Cl -1.1568027 -1.1568027 1.1568027 1 Cl END > From: Bruce Ravel <bravel(a)anl.gov> > Subject: Re: [Ifeffit] Possible bug in Artemis. > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <200601231845.59426.bravel(a)anl.gov> > Content-Type: text/plain; charset="iso-8859-1" > > On Monday 23 January 2006 17:47, joshua jason kas wrote: >> Hi, >> When I import a feff calculation, or run feff, the paths show up in >> artemis, but the description is garbled. What I mean is that the path >> description under Scattering Path which normally looks like >> >> [+] Cl [+] O ... >> >> looks like >> >> [+] <?> [+] <?> ... > > This looks like another version of a bug that has cropped up here and there. > The algorithm for generating the interpretation page parses the feff.inp file > and a couple of feff's output files. Every so often, someone throws a > hand-made feff.inp file at Artemis that works in feff but breaks the rather > crufty parser I wrote. > > If you can send me the feff.inp file that would help. The artemis project > file might help also, so send that along. Even if it is one that makes > Artemis do bad things when you try to read, I can still peak on the inside and > figure out what's going on. > > 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/ > > > > ------------------------------ > > Message: 2 > Date: Mon, 23 Jan 2006 20:18:42 -0500 > From: "TAO, Ye" <yetao(a)chem.uga.edu> > Subject: Re: [Ifeffit] Possible bug in Artemis. > To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <00f001c62084$1d8d28c0$3b05c080@RASD800> > Content-Type: text/plain; format=flowed; charset="iso-8859-1"; > reply-type=original > > Josh, > > Have a try to set the absorber coordinate as origin (0 0 0) in feff.inp, > then it should work. > > Ye > ----- Original Message ----- > From: "joshua jason kas" <hebhop(a)u.washington.edu> > To: <ifeffit(a)millenia.cars.aps.anl.gov> > Sent: Monday, January 23, 2006 6:47 PM > Subject: [Ifeffit] Possible bug in Artemis. > > >> Hi, >> When I import a feff calculation, or run feff, the paths show up in >> artemis, but the description is garbled. What I mean is that the path >> description under Scattering Path which normally looks like >> >> [+] Cl [+] O ... >> >> looks like >> >> [+] <?> [+] <?> ... >> >> and if I save the project file and reopen it, it can't >> I have attached a screenshot. >> Here is some info on my software >> 1) artemis 0.8.004 >> 2) ifeffit 1.2.8 >> 3) perl -e 'use Tk; print $Tk::VERSION,$/' gives 804.027 >> 4) perl v5.8.7 >> >> I tried updating Tk, and that works about as well as it always has on my >> system. Most of the tests passed, a few failed. >> This may be a problem with my version of Linux, or my version of perl/Tk. >> Anyway, any help would be much appreciated. >> Thank you very much, >> Josh Kas > > > -------------------------------------------------------------------------------- > > >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> > > > > ------------------------------ > > Message: 3 > Date: Tue, 24 Jan 2006 11:43:30 -0300 > From: "Renato Canha Ambrosio" <rcanha(a)ccet.ufrn.br> > Subject: [Ifeffit] RESTRAINTS IN IFEFFIT > To: ifeffit(a)millenia.cars.aps.anl.gov > Message-ID: <20060124142316.M21887(a)ccet.ufrn.br> > Content-Type: text/plain; charset=iso-8859-1 > > Hi Folks, this is my first message on the list. Perhaps someone could help > me. The subject is how to include restraints on exafs refinement. There is > just scanty information about this on the ifeffit reference manual. > > I'm trying to refine the exafs data of a rhombohedral perovskite. > > The main MS contributions to the signal at about 3.5 A (non phase correct) > arise from M � O � M interactions being M the absorber . We have a > significant SS path, a two-legged and a three-legged path. The structural > parameters of these three terms are correlated since all refers to the same > A-B-C triangle and the A-B and B-C distances must be that found for > M-O1 nearest-neighbor configurations. For these reasons > we constrained the photo electron path length for three-legged to the > M-O nearest-neighbor distance:R(three-leg = 2*RM-O). I'm trying to > intoroduce the quantity defined as delta = R(three-legged)-R(two-legged) > and thus define the SS half path length as a function of delta R(SS) = R > (three-legged) - 2*delta. I think it is a restraint not a constraint. > So I defined (def) the delta function on the line above the command FEFFIT > also delr for the SS path. I introduced the restraint in the line FEFFIT as > restraint = delrSS). The fit produce the same results as obtainde without > the definition of delta and delrSS (function of delta). > So I need to know how to introduce this restraint in the fit in order to > calculate de M - O - M bond angle (this angle should be calculated using > simple geometric relationships) - perhaps introduce the bond angle as a > restraint. > Someone can say me where I introduce the definitions of restraint parameters? > > Thank you very much for your kind attention > > Renato Canha > > Universidade Federal do Rio Grande doNorte > Departamento de Quimica > Natal - RN - BRAZIL > Open WebMail Project (http://openwebmail.org) > > > ---------- Original Message ----------- > From: ifeffit-request(a)millenia.cars.aps.anl.gov > To: ifeffit(a)millenia.cars.aps.anl.gov > Sent: Mon, 23 Jan 2006 12:00:13 -0600 > Subject: Ifeffit Digest, Vol 35, Issue 14 > >> Send Ifeffit mailing list submissions to >> ifeffit(a)millenia.cars.aps.anl.gov >> >> To subscribe or unsubscribe via the World Wide Web, visit >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> or, via email, send a message with subject or body 'help' to >> ifeffit-request(a)millenia.cars.aps.anl.gov >> >> You can reach the person managing the list at >> ifeffit-owner(a)millenia.cars.aps.anl.gov >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of Ifeffit digest..." >> >> Today's Topics: >> >> 1. Re: Re: I should be able to find this somewhere... (Bruce Ravel) >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Sun, 22 Jan 2006 16:58:07 -0600 >> From: Bruce Ravel <bravel(a)anl.gov> >> Subject: Re: [Ifeffit] Re: I should be able to find this somewhere... >> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >> Message-ID: <200601221658.07513.bravel(a)anl.gov> >> Content-Type: text/plain; charset="iso-8859-1" >> >> Hi, >> >> In fact, Artemis and Athena both attempt to deal correctly with input >> chi(k) data that is not on the expected grid. Both codes perform a >> test to see if the data is on the standard grid and, if not, >> front-loads the data with zeros and uses Ifeffit's boxcar rebinning >> function to put the data on the expected grid. >> >> Alas, there was a bug in the rebinning macro used by A&A which caused >> it to fail in a particular situation met by the data in Matthew's >> example. This bug will be fixed in the next release. >> >> If you import mu(E) data into Athena and then import data from the >> Athena project file into Artemis, you will never see the problem that >> Matthew reported. >> >> B >> >> On Tuesday 17 January 2006 16:09, Matt Newville wrote: >>> Hi Matthew, Bruce, >>> >>> OK, I think it's a bug. Well, maybe it's just a consequence of a >>> "known but not well advertised" problem. >>> >>> The chi(k) data you have doesn't start at k=0. By itself, this should >>> be OK, and the fit seems to be mostly fine. There seems to be a bug >>> in Ifeffit that the output fit chi(k) has the same number of data >>> points as the input chi(k) data. In this case is incorrect -- it >>> should go to the last data point in k. From looking at the code, I'm >>> pretty sure this has no effect on the fit and is only an error in the >>> output array. But the shortened chi_fit(k) will have an impact on the >>> way Bruce is calculating the residual. Even if that were fixed, the >>> residual would still be wrong, as the residual in Artemis is >>> calculated as >>> set(data0_res.k = data0.k) >>> set(data0_res.chi = data0.chi - data0_fit.chi) >>> >>> and then Fourier transforming to R-space. Since the data and fit >>> aren't aligned in k-space, the residual is incorrect. It should be >>> >>> set(data0_res.chi = data0.chi - interp(data0_fit.k, data0_fit.chi, >>> data0.k)) >>> >>> or some variation on that. >>> >>> Sorry for the trouble. It's definitely a result of narrow-mindedly >>> expecting that all chi(k) data comes from Ifeffit/Athena and will >>> always start at k=0. We should get this fixed (it's mostly there!) so >>> that data from other sources can be used. Right now, the easiest >>> work-around is to pre-pack the chi(k) data with zeros (starting from >>> k=0.00) >>> >>> --Matt >>> >>> _______________________________________________ >>> Ifeffit mailing list >>> Ifeffit(a)millenia.cars.aps.anl.gov >>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> >> -- >> Bruce Ravel ---------------------------------------------- bravel(a)anl.gov >> >> Molecular Environmental Science Group, Building 203, Room E-165 >> MRCAT, Sector 10, Advance 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/ >> >> ------------------------------ >> >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> >> End of Ifeffit Digest, Vol 35, Issue 14 >> *************************************** > ------- End of Original Message ------- > > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 35, Issue 16 > *************************************** >

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Possible bug in Artemis.
by joshua jason kas 24 Jan '06

24 Jan '06

Hi, When I import a feff calculation, or run feff, the paths show up in artemis, but the description is garbled. What I mean is that the path description under Scattering Path which normally looks like [+] Cl [+] O ... looks like [+] <?> [+] <?> ... and if I save the project file and reopen it, it can't I have attached a screenshot. Here is some info on my software 1) artemis 0.8.004 2) ifeffit 1.2.8 3) perl -e 'use Tk; print $Tk::VERSION,$/' gives 804.027 4) perl v5.8.7 I tried updating Tk, and that works about as well as it always has on my system. Most of the tests passed, a few failed. This may be a problem with my version of Linux, or my version of perl/Tk. Anyway, any help would be much appreciated. Thank you very much, Josh Kas

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Re: I should be able to find this somewhere...
by Bruce Ravel 22 Jan '06

22 Jan '06

On Friday 13 January 2006 20:25, you wrote: > By what factor is the residual multiplied when plotted in Artemis? I can't > find that figure quoted. > mam The residual is saved in k-space and Fourier transformed. 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: moving the legend in Athena
by Bruce Ravel 20 Jan '06

20 Jan '06

On Thursday 19 January 2006 14:05, Carlo Segre wrote: > When I plot data using athena, I would like to move the legend. How can I > do this? Go to the preferences, then to the plot branch. key_x and key_y are the xy coordinates of the upper left corner of the legend box. key_dy is the spacing between lines. The answer is the same for Artemis. 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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Enabling auto-updater for Artemis etc on startup (Windows)
by Simon Granville 19 Jan '06

19 Jan '06

Hello and Happy New Year all, my first of possibly many questions to this list (so please be gentle!) should hopefully be an easy one. When at Matt's iFEFFIT session in Melbourne at the start of December, I changed something in the updater.inifile (in the config directory of ifeffit) so that Artemis and Athena didn't attempt to look for updates when those programs are started. Of course I did this from a hint by Matt - now I'd quite like to reenable that auo-update and I don't know what to change. I know there's a newer version or two out there (my Artemis version is 0.8.002). Here's what my updater.ini file looks like [updater] next_checktime = tomorrow update_site = http://cars9.uchicago.edu/ifeffit/updates/ timestamp = 1137635213.22 http_proxy = timeout_connect = 60.0 timeout_download = 2400.0 Cheers, Simon. Simon Granville PhD student MacDiarmid Institute for Advanced Materials and Nanotechnology Victoria University of Wellington Wellington New Zealand

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Re: XANES calculations
by John J. Rehr 17 Jan '06

17 Jan '06

Dear Antonio, It appears that you've just experienced a common problem with hexagonal space groups that one often needs a shift of the origin to get the "correct" crystal structure. According to the atoms documentation (click on SHIFT in Webatoms) there should be a note about this when you try to run, but I didn't see it anywhere when I tried WEBATOMS today. Anyway the fix is to introduce a MS shift vector of (0 0 .25), as in the atoms.inp file I sent you. I think it might be useful if an appropriate shift were introduced by default into the atoms database for very common lattice structures like graphite, or otherwise to detail more precisely the coordinates of the shift that one has to introduce by hand into atoms.inp (which is less desirable). Maybe Bruce Ravel can consider these friendly suggestions in future releases of atoms. I hope you don't mind, but I've forwarded this msg to the ifeffit list. Cheers, John ---------- Forwarded message ---------- Date: Mon, 16 Jan 2006 09:20:39 +0100 From: Antonio Politano <politano(a)fis.unical.it> To: 'John J. Rehr' <jjr(a)leonardo.phys.washington.edu> Subject: R: R: XANES calculations Yes, I understand about stoichiometry. But I don't have understood why using an atoms.inp file taken from the Atoms.inp archive I have six nearest neighbours of the central assorber at 1,42 A. In your feff.inp file under the ATOMS card there are only three nearest neighbours at 1,42 A (this is correct!!!). Thank you very much!!! Antonio Politano

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Re: possible bugs in Artemis
by Bruce Ravel 15 Jan '06

15 Jan '06

On Sunday 15 January 2006 03:22, you wrote: > When I push any of the 'Document' buttons, I get a blank window, a 'clunk' > and a bunch of error messages including a 'fileopen' error, suggesting that > the documentation pages aren't in the right places. Also, what determines > the k-range over which Artemis fits? If I ask for a longer k-range than > what it does by default, nothing seems to happen. Marcus is the second person to report this problem, which exists in the current versions of both Athena and Artemis. The problem exists in the tool that I use to display the document and falls into the category of obvious problems that I failed to test for before the last release. D'oh! The next release will fix this issue. Sadly, I might not have time to make a release in the next two weeks -- we'll see. In any case, the same documentation is available in a number of other places. On a Windows machine, there should be a Start menu entry labeled Ifeffit documentation that will lead you to html versions of the docs. Also, the html versions can be found at http://cars9.uchicago.edu/~ravel/software/docs.html B -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advance 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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[HOWTO] Ifeffit f1f2() function
by Mauro Rovezzi 09 Jan '06

09 Jan '06

Hi to all, Is it correct to use as energy convolution width (in the f1f2 Ifeffit function) the natural widths of atomic levels tabulated by Krause & Oliver (J. Phys. Chem. Ref. Data, Vol. 8, No. 2, 1979)? My problem is to smooth (arctg-like) Cromer-Liberman f"(E) at the edge region [NOTE: I don't use feff8 because is too slow]. Thanks, Mauro -- Mauro Rovezzi <mauro.rovezzi(a)esrf.fr> PhD student - GILDA BM08 c/o ESRF (Grenoble, FR)

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new versions for the new year!
by Bruce Ravel 07 Jan '06

07 Jan '06

Happy New Year everyone! I have just released Athena 0.8.047, Artemis 0.8.004 and Hephaestus 0.12. You can read all about them at http://cars9.uchicago.edu/iffwiki/HoraeVersion059 New source code tarballs are at SourceForge and at my website. A Windows updater package has been made available and should be offered to the Windows users the next time you fire up one of the codes. Debian users can check Carlo's repository in the next few days -- he is usually quite punctual in making debian packages. The horae_update script has been fixed (I think). Those that want to use it can grab its newest version at http://cars9.uchicago.edu/~ravel/software/packages/horae_update and use it to install the software. As always, let me know about any problems or suggestions. 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/exafs/

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RE: [Ifeffit] my problem
by Scott Calvin 19 Dec '05

19 Dec '05

Hi Tadej, I agree with the general drift of Anatoly's comment--this is what Shelly meant by saying it sounds like a tough problem! But I think it came off sounding a little more harsh than I suspect Anatoly meant it to be, particularly considering some of the systems he himself has examined! Anatoly's description is fair IF only a nearest-neighbor fit is performed. But it's possible that inequivalent sites have very different environments at greater Reff, particularly since niobium is so much heavier than oxygen! For example, there's been a lot of work done that shows that there is a screamingly large difference in the EXAFS spectra of A and B sites in the spinel structure (Vince Harris did a lot of this, for example). In such a case, Artemis is able to find the site occupancy without too much trouble, using a strategy such as Shelly explained. Of course, =seven= freely-floating sites sounds likely to yield nonsense fits. It would help if you could use some physical intuition to try to simplify the problem, at least at first. Consider also using the "restraint" feature in Artemis/Ifeffit liberally in your early fits to keep the fit from wandering off into nonsensical territory. --Scott Calvin Sarah Lawrence College At 12:14 PM 12/15/2005, Anatoly wrote: >boundary="----_=_NextPart_001_01C6019A.F6711239" > >You cannot resolve these sites from EXAFS analysis. Even if you had >only 2 inequivalent sites of the same central atom with occupancies >N1 and N2, you would not be able to resolve N1 and N2 in the fit >because different Nb atoms would have similar environments (e.g., 4 >and 6 oxygens), and they will have similar Nb-O distances around >each site. The best you can do is to try to fit the first nearest >neighbor peak as an average Nb-O contribution (if it is a well >isolated peak) and try to make use of sigma2 that may turn out to be >larger than in some well known Nb oxide reference that you should >analyze first. > >Anatoly > >Dear collegues, > >my name is Tadej Rojac and I'm writing from the Institute Jozef >Stefan in Ljubljana, Slovenia. I work in the Department of >electronic ceramics. Actually, I'm working on a EXAFS spectra with >Artemis. What I am trying to do is mainly to describe an EXAFS >spectrum with a model concerning the structure of Nb2O5. I'm working >togheter with prof. Iztok Arcon, who is a specialist in the field. >My main problem is that I have to do some suppositions. In fact >Nb2O5 structure is quite complicated. It is composed of seven >different Nb positions which I took into account using 7 feffs in >Artemis. I don't know the exact occupancies of the seven positions. >In order to make the search easier I did at first a supposition >that all the occupancies must be positive, which is realistic. I set >this with the command "abs" in each feff file. Secondly, I need to >supose that the sum of all occupancies is 1. In that way the search >for the result is much easier, otherwise I get the sum greater than >one, which, for sure, is not the case. My question is how can I do >that? For example, if the occupancies are O1, O2, O3, O4, O5, O6 and >O7 and I define them with a starting value (let use say the same, so >1/7) than I can do O = O1+O2+O3+O4+O5+O6+O7. Finally I need to do O >=1, but here Artemis doesn't want to define the same parameter (O in >this case) twice. So, how can I insert the conditions, that the sum >of all the occupancies is 1, into Artemis? I hope you can help me.

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(no subject)
by Victor Krayzman 19 Dec '05

19 Dec '05

Hi Bruce, This is Victor Krayzman. I haven't seen you for ten years. Currently I am at NIST as a guest scientist. Besides other codes I work with Athena and Artemis and I have some troubles with Artemis. (It runs under Windows 2000) Last time I read a data file, made two FEFF calculations, read one more data file and made three FEFF calculations for it. Then I saved project, quit Artemis, open it again and tried to read the saved project. I found only data files and two FEFF calculations for the first data set. FEFF calculations for the second set disappeared. I met the same situation some time ago. To fix the problem I had to reinstall the Artemis. But now I have got the same thing. Could you help me? I attached the saved project and the message in a window. Thank you. Best regards to Ed. Sincerely. Victor

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RE: [Ifeffit] Pd data
by Barton, David (DG) 19 Dec '05

19 Dec '05

Sorry I meant to include that. The file at DND-CAT is a bit unwieldy. The key is: Col 4=energy, Col 25=Io, Col 26=It. Dave > -----Original Message----- > From: Kelly, Shelly D. [mailto:SKelly@anl.gov] > Sent: Monday, December 19, 2005 12:13 PM > To: XAFS Analysis using Ifeffit > Subject: RE: [Ifeffit] Pd data > > > Hi Dave, > > Thanks a bunch for the data file. Could I trouble you for a > key for the columns within the file? > > Shelly > > Shelly Kelly Bldg 203 RM E113 > Skelly(a)anl.gov Argonne National Laboratory > 630-252-7376 9700 S Cass Ave > www.mesg.anl.gov Argonne, IL 60439 > > > > > > -----Original Message----- > > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit- > > bounces(a)millenia.cars.aps.anl.gov] On Behalf Of Barton, David (DG) > > Sent: Monday, December 19, 2005 10:11 AM > > To: 'XAFS Analysis using Ifeffit' > > Subject: RE: [Ifeffit] Pd data > > > > Shelly, > > > > Attached is a Pd foil data set. It was only collected out > to k=16A-1, > > otherwise the data looks great. Data was collected with > Si111 mono at > > DND-CAT (APS-ANL). > > > > Dave > > > > -----Original Message----- > > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit- > > bounces(a)millenia.cars.aps.anl.gov] On Behalf Of Kelly, Shelly D. > > Sent: Monday, December 19, 2005 10:38 AM > > To: XAFS Analysis using Ifeffit > > Subject: [Ifeffit] Pd data > > > > > > Hello friends, > > > > Does anyone have Pd foil data or know of an EXAFS study that models > the > > data beyond the first shell? I have some data but it > doesn't seem to > > correspond to the crystallographic structure of Pd. I'm suspicious > that > > something about the foil sample caused the structure to become > non-ideal. > > > > Thanks > > Shelly > > > > > > > > > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

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RE: [Ifeffit] Pd data
by Kelly, Shelly D. 19 Dec '05

19 Dec '05

Hi Dave, Thanks a bunch for the data file. Could I trouble you for a key for the columns within the file? Shelly Shelly Kelly Bldg 203 RM E113 Skelly(a)anl.gov Argonne National Laboratory 630-252-7376 9700 S Cass Ave www.mesg.anl.gov Argonne, IL 60439 > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit- > bounces(a)millenia.cars.aps.anl.gov] On Behalf Of Barton, David (DG) > Sent: Monday, December 19, 2005 10:11 AM > To: 'XAFS Analysis using Ifeffit' > Subject: RE: [Ifeffit] Pd data > > Shelly, > > Attached is a Pd foil data set. It was only collected out to k=16A-1, > otherwise the data looks great. Data was collected with Si111 mono at > DND-CAT (APS-ANL). > > Dave > > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit- > bounces(a)millenia.cars.aps.anl.gov] On Behalf Of Kelly, Shelly D. > Sent: Monday, December 19, 2005 10:38 AM > To: XAFS Analysis using Ifeffit > Subject: [Ifeffit] Pd data > > > Hello friends, > > Does anyone have Pd foil data or know of an EXAFS study that models the > data beyond the first shell? I have some data but it doesn't seem to > correspond to the crystallographic structure of Pd. I'm suspicious that > something about the foil sample caused the structure to become non-ideal. > > Thanks > Shelly > > > >

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RE: Ifeffit Digest, Vol 34, Issue 18
by Vivek Srinivasamurthi 19 Dec '05

19 Dec '05

Shelly, Sorry, forgot to attach the file before.. vivek -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Monday, December 19, 2005 11:12 AM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 34, Issue 18 Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)millenia.cars.aps.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Ifeffit digest..." Today's Topics: 1. Pd data (Kelly, Shelly D.) 2. RE: Pd data (Barton, David (DG)) ---------------------------------------------------------------------- Message: 1 Date: Mon, 19 Dec 2005 09:37:47 -0600 From: "Kelly, Shelly D." <SKelly(a)anl.gov> Subject: [Ifeffit] Pd data To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <A7B9B5614B54BE48B378DAE209FECC30ABE841(a)ROCKY.anl.gov> Content-Type: text/plain; charset="us-ascii" Hello friends, Does anyone have Pd foil data or know of an EXAFS study that models the data beyond the first shell? I have some data but it doesn't seem to correspond to the crystallographic structure of Pd. I'm suspicious that something about the foil sample caused the structure to become non-ideal. Thanks Shelly

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RE: Ifeffit Digest, Vol 34, Issue 18
by Vivek Srinivasamurthi 19 Dec '05

19 Dec '05

Shelly, Attached is a Pd nanoparticle sample on a carbon support. The data was taken upto 18 k-space. It also has a Pd foil in the reference channel. The data was collected with a Si(111) monochromator at BNL-NSLS -X18B. Vivek -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Monday, December 19, 2005 11:12 AM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 34, Issue 18 Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)millenia.cars.aps.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Ifeffit digest..." Today's Topics: 1. Pd data (Kelly, Shelly D.) 2. RE: Pd data (Barton, David (DG)) ---------------------------------------------------------------------- Message: 1 Date: Mon, 19 Dec 2005 09:37:47 -0600 From: "Kelly, Shelly D." <SKelly(a)anl.gov> Subject: [Ifeffit] Pd data To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <A7B9B5614B54BE48B378DAE209FECC30ABE841(a)ROCKY.anl.gov> Content-Type: text/plain; charset="us-ascii" Hello friends, Does anyone have Pd foil data or know of an EXAFS study that models the data beyond the first shell? I have some data but it doesn't seem to correspond to the crystallographic structure of Pd. I'm suspicious that something about the foil sample caused the structure to become non-ideal. Thanks Shelly

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RE: [Ifeffit] Pd data
by Barton, David (DG) 19 Dec '05

19 Dec '05

Shelly, Attached is a Pd foil data set. It was only collected out to k=16A-1, otherwise the data looks great. Data was collected with Si111 mono at DND-CAT (APS-ANL). Dave -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Kelly, Shelly D. Sent: Monday, December 19, 2005 10:38 AM To: XAFS Analysis using Ifeffit Subject: [Ifeffit] Pd data Hello friends, Does anyone have Pd foil data or know of an EXAFS study that models the data beyond the first shell? I have some data but it doesn't seem to correspond to the crystallographic structure of Pd. I'm suspicious that something about the foil sample caused the structure to become non-ideal. Thanks Shelly

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Pd data
by Kelly, Shelly D. 19 Dec '05

19 Dec '05

Hello friends, Does anyone have Pd foil data or know of an EXAFS study that models the data beyond the first shell? I have some data but it doesn't seem to correspond to the crystallographic structure of Pd. I'm suspicious that something about the foil sample caused the structure to become non-ideal. Thanks Shelly

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Re: [Ifeffit] Mac installer for 10.4 with horae-048
by Matt Newville 15 Dec '05

15 Dec '05

Stefano, Paul, I just tried this on a fairly fresh OS 10.4 machine (Ifeffit had been installed over a year ago, when it was a 10.3 machine, and I wiped /Library/Perl/5.8.1 and /Applications/Ifeffit, and cleared the /Library/Receipt for Ifeffit....). I got the same behaviour as Stefano. It looks like everything did get installed this time, but that the resulting version of Ifeffit depends on Aquaterm. Downloading and installing Aquaterm from the disk-image package from sourceforge.net was simple (though it requires a privileged password) and made Athena and Artemis run fine. So my immediate recommendation is to install Aquaterm from Sourceforge. http://sourceforge.net/projects/aquaterm/ --Matt PS: We should probably also figure out how to not depend on Aquaterm, but telling people they need Aquaterm as well as X11.app seems simple enough.

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IFEFFIT installation problem
by Frenkel, Anatoly 15 Dec '05

15 Dec '05

On behalf of Joe Woicik (please reply to: woicik(a)bnl.gov) I downloaded version 1.2.8. Runner. exe gives me the following error and Athena does not run. Please let me know if anyone on the list has experienced similar problem. Joe Woicik Traceback (most recent call last): File "runner.py", line 753, in ? File "runner.py", line 184, in __init__ File "runner.py", line 275, in LookForUpdates File "runner.py", line 299, in read_web_version File "urllib.pyc", line 76, in urlopen File "urllib.pyc", line 181, in open File "urllib.pyc", line 297, in open_http File "httplib.pyc", line 712, in endheaders File "httplib.pyc", line 597, in _send_output File "httplib.pyc", line 564, in send File "httplib.pyc", line 538, in connect File "timeoutsocket.pyc", line 237, in connect timeoutsocket.Timeout: Attempted connect to ('164.54.160.111', 80) timed out. Traceback (most recent call last): File "runner.py", line 753, in ? File "runner.py", line 184, in __init__ File "runner.py", line 275, in LookForUpdates File "runner.py", line 299, in read_web_version File "urllib.pyc", line 76, in urlopen File "urllib.pyc", line 181, in open File "urllib.pyc", line 297, in open_http File "httplib.pyc", line 712, in endheaders File "httplib.pyc", line 597, in _send_output File "httplib.pyc", line 564, in send File "httplib.pyc", line 538, in connect File "timeoutsocket.pyc", line 237, in connect timeoutsocket.Timeout: Attempted connect to ('164.54.160.111', 80) timed out. Traceback (most recent call last): File "runner.py", line 753, in ? File "runner.py", line 184, in __init__ File "runner.py", line 275, in LookForUpdates File "runner.py", line 299, in read_web_version File "urllib.pyc", line 76, in urlopen File "urllib.pyc", line 181, in open File "urllib.pyc", line 297, in open_http File "httplib.pyc", line 712, in endheaders File "httplib.pyc", line 597, in _send_output File "httplib.pyc", line 564, in send File "httplib.pyc", line 538, in connect File "timeoutsocket.pyc", line 237, in connect timeoutsocket.Timeout: Attempted connect to ('164.54.160.111', 80) timed out.

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RE: [Ifeffit] my problem
by Frenkel, Anatoly 15 Dec '05

15 Dec '05

You cannot resolve these sites from EXAFS analysis. Even if you had only 2 inequivalent sites of the same central atom with occupancies N1 and N2, you would not be able to resolve N1 and N2 in the fit because different Nb atoms would have similar environments (e.g., 4 and 6 oxygens), and they will have similar Nb-O distances around each site. The best you can do is to try to fit the first nearest neighbor peak as an average Nb-O contribution (if it is a well isolated peak) and try to make use of sigma2 that may turn out to be larger than in some well known Nb oxide reference that you should analyze first. Anatoly -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov]On Behalf Of Tadej Rojac Sent: Thursday, December 15, 2005 7:44 AM To: Ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] my problem Dear collegues, my name is Tadej Rojac and I'm writing from the Institute Jozef Stefan in Ljubljana, Slovenia. I work in the Department of electronic ceramics. Actually, I'm working on a EXAFS spectra with Artemis. What I am trying to do is mainly to describe an EXAFS spectrum with a model concerning the structure of Nb2O5. I'm working togheter with prof. Iztok Arcon, who is a specialist in the field. My main problem is that I have to do some suppositions. In fact Nb2O5 structure is quite complicated. It is composed of seven different Nb positions which I took into account using 7 feffs in Artemis. I don't know the exact occupancies of the seven positions. In order to make the search easier I did at first a supposition that all the occupancies must be positive, which is realistic. I set this with the command "abs" in each feff file. Secondly, I need to supose that the sum of all occupancies is 1. In that way the search for the result is much easier, otherwise I get the sum greater than one, which, for sure, is not the case. My question is how can I do that? For example, if the occupancies are O1, O2, O3, O4, O5, O6 and O7 and I define them with a starting value (let use say the same, so 1/7) than I can do O = O1+O2+O3+O4+O5+O6+O7. Finally I need to do O =1, but here Artemis doesn't want to define the same parameter (O in this case) twice. So, how can I insert the conditions, that the sum of all the occupancies is 1, into Artemis? I hope you can help me. I'm looking forward t hearing from you...thank you... Tadej Rojac Jozef Stefan Institute Jamova 39 1000 Ljubljana Slovenia Tel.: +386 1 477 38 34 Fax: +386 1 477 38 87 E-mail: tadej.rojac(a)ijs.si

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RE: [Ifeffit] my problem
by Kelly, Shelly D. 15 Dec '05

15 Dec '05

Hi Tadej, ________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Tadej Rojac Sent: Thursday, December 15, 2005 6:44 AM To: Ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] my problem Dear collegues, my name is Tadej Rojac and I'm writing from the Institute Jozef Stefan in Ljubljana, Slovenia. I work in the Department of electronic ceramics. Actually, I'm working on a EXAFS spectra with Artemis. What I am trying to do is mainly to describe an EXAFS spectrum with a model concerning the structure of Nb2O5. I'm working togheter with prof. Iztok Arcon, who is a specialist in the field. My main problem is that I have to do some suppositions. In fact Nb2O5 structure is quite complicated. It is composed of seven different Nb positions which I took into account using 7 feffs in Artemis. I don't know the exact occupancies of the seven positions. In order to make the search easier I did at first a supposition that all the occupancies must be positive, which is realistic. I set this with the command "abs" in each feff file. Secondly, I need to supose that the sum of all occupancies is 1. In that way the search for the result is much easier, otherwise I get the sum greater than one, which, for sure, is not the case. My question is how can I do that? For example, if the occupancies are O1, O2, O3, O4, O5, O6 and O7 and I define them with a starting value (let use say the same, so 1/7) than I can do O = O1+O2+O3+O4+O5+O6+O7. Finally I need to do O =1, but here Artemis doesn't want to define the same parameter (O in this case) twice. So, how can I insert the conditions, that the sum of all the occupancies is 1, into Artemis? I hope you can help me. [Kelly, Shelly D.] In the path page for each path of each feff calculation you need to have a variable that represents the occupancy. S02xN = abs(S02 * O1) ..... Then in the variable page (guess set def) Guess O1 = 0.15 Guess O2 = 0.15 Guess O3 = 0.15 .... Def O7 = 1 - abs(O1) -abs(O2) -abs(O3) - abs(O4) - abs(O5) -abs(O6) Hence you get one occupancy for free for knowing one more piece of information. Sounds like a tough problem. I'm looking forward t hearing from you...thank you... Tadej Rojac Jozef Stefan Institute Jamova 39 1000 Ljubljana Slovenia Tel.: +386 1 477 38 34 Fax: +386 1 477 38 87 E-mail: tadej.rojac(a)ijs.si

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my problem
by Tadej Rojac 15 Dec '05

15 Dec '05

Dear collegues, my name is Tadej Rojac and I'm writing from the Institute Jozef Stefan in Ljubljana, Slovenia. I work in the Department of electronic ceramics. Actually, I'm working on a EXAFS spectra with Artemis. What I am trying to do is mainly to describe an EXAFS spectrum with a model concerning the structure of Nb2O5. I'm working togheter with prof. Iztok Arcon, who is a specialist in the field. My main problem is that I have to do some suppositions. In fact Nb2O5 structure is quite complicated. It is composed of seven different Nb positions which I took into account using 7 feffs in Artemis. I don't know the exact occupancies of the seven positions. In order to make the search easier I did at first a supposition that all the occupancies must be positive, which is realistic. I set this with the command "abs" in each feff file. Secondly, I need to supose that the sum of all occupancies is 1. In that way the search for the result is much easier, otherwise I get the sum greater than one, which, for sure, is not the case. My question is how can I do that? For example, if the occupancies are O1, O2, O3, O4, O5, O6 and O7 and I define them with a starting value (let use say the same, so 1/7) than I can do O = O1+O2+O3+O4+O5+O6+O7. Finally I need to do O =1, but here Artemis doesn't want to define the same parameter (O in this case) twice. So, how can I insert the conditions, that the sum of all the occupancies is 1, into Artemis? I hope you can help me. I'm looking forward t hearing from you...thank you... Tadej Rojac Jozef Stefan Institute Jamova 39 1000 Ljubljana Slovenia Tel.: +386 1 477 38 34 Fax: +386 1 477 38 87 E-mail: tadej.rojac(a)ijs.si

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Re: [Ifeffit] statistical parameters
by Matt Newville 15 Dec '05

15 Dec '05

Hi Stefano, all, > same old question that emerges again: > > What formula is used by IFEFFIT to calculate the number of > independent points? Does it use the formula 2DkDR/pi? or 2DkDR/pi +1? > or 2DkDR/pi +2? And how does it approximate the resulting number to > integer? Ifeffit uses an approximation of 2*delta_k * delta_R / pi. Well, it could use a better approximation -- see below. But Ifeffit does not use 2dKdR/pi + 2. The Stern paper considers "independent points" to be discrete, counts the endpoints of this discrete array of "independent points", and neglects the rather significant problem of the limit dk->0. I find each of these to be problematic. The dk->0 limit problem makes it especially hard to implement in a meaningful way. Ifeffit uses n_idp = 2*delta_k * delta_R / pi, but is cautious (and probably overly so) in determining delta_k and delta_R. First, it puts these on the k- and R- grids (0.05 Ang^-1 and ~0.03067Ang). It is also works to avoid rounding incorrectly. Thus, currently your ranges: kmin=2.0, kmax=12, rmin=1.0, rmax=6.0 get mapped to kmin = 2.05, kmax=12.00 , rmin=1.012427, rmax=5.98525 Thus you should have n_idp = 31.4824. You can confirm that with 'print n_idp' from the command line. It sounds like that's what you're getting. And yes, I do think that having "kmin=2.00" map to "kmin=2.05" for this part of the calculation is overly cautious, and I will fix that in the next release (and n_idp will equal ~31.64). I could be persuaded to just use the user-supplied values, but the round-off errors shouldn't matter much. In general, I agree with most of the answers to not take N_idp too seriously. I would say to report it to 1 decimal place, just to emphasize that it is understood to be an estimate and not a discrete number. Saying "n_idp=12" implies "I could fit up to 12 parameters with confidence". It's easy enough to show this is usually NOT the case, but some people sure like a hard and fast rule. And, sadly, n_idp does influence the error bars some, so it seems wise to get it as close as we can. That's sort of rambly, but hope that helps --Matt PS: For autobk/spline(), the number of knots is actually chosen as n = 2 * int( rbkg * (kmax-kmin)/pi ) + 1 It turns out that for the b-spline algorithm used, the number of knots used needs to be an odd number greater than 4. So, the formula is convenient. Is it right? Well, it seems to work pretty well. As fitting variables, the spline y-values are somewhat correlated, so you might argue that you could have a few more variables. That's easy enough to try with spline(data.chi, rbkg=1, nknots=17) In my experience, this rarely helps but it might be worth re-visiting.

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RE: [Ifeffit] statistical parameters
by Kelly, Shelly D. 15 Dec '05

15 Dec '05

Hi Stephano > >Since 2dkdr/pi is not always an integer number, the degrees of freedom > >which is the NIP (number of independent points) - number of variables is > >not always an integer number. > > but I notice that in all papers this is reported as an integer > number, which makes sense. DOes it mean I have to round it up to the > closest integer? Plus, in the conversion from chi^2 to reduced-chi^2, > does IFEFFIT consider it as an integer number or not? [Kelly, Shelly D.] Well, In my opinion that depends on where you are publishing the data. If you are publishing the data in PRB then you should use the XX.X number. If you are publishing in Science Magazine then you should use the rounded number. If the answer depends on weather or not you round the number then I'd be suspicious. Often we round the number so that we don't have to explain why we have a non-integer numbers. You need ~ a factor of 2 for there to be a statistically significant difference in the reduced chi squared. So 33.5, 30, and 40 are all about the same number. Therefore I would round them all off to the nearest whole number that works. I like to show changes in the reduced chi square rather than the absolute value. Instead of showing a reduced-chi-square of 100 and 350, I show them as 1 and 3.5. Then you can say that 3.5 is much bigger than 1 so the model that gave 1 is the best. It is the relative change in the reduced chi square that matters. We get the absolute value wrong for a number of reasons. By showing the change you can side step all that explanation. > > > Plus, I have found a > >> few documents in which Matt reports Nidp as 2dkdr/pi, some others in > >> which he reports 2dkdr/pi+1. In SK's thesis, which is available on > >> the net (thanks Shelly :-)) she says +2. I was simply wondering which > >> is the right formula used in IFEFFIT, and if it is different from > >> what reported in Stern, Phys. Rev. B, 1993, 48, 9825-9827, why it is > >> so. > > > >Most importantly, all of these expressions for the number of independent > >points are similar. > > I know, but since I am reporting in a paper we are writing a table in > which we show chi^2, reduced chi^2, Nidp and Npar (and therefore the > degress of freedom) I was trying to be tidy and rigorous. But I am > facing numbers which I cannot make much sense of. [Kelly, Shelly D.] [Kelly, Shelly D.] That seems to be a problem. Are you processing the data with more than one k-weight in IFEFFIT? Try a test case were you use only one k-weight and see if you like the answers better. If you use more than one k-weight then the answers should be averages for all three data sets. > > >The most important part is that the number of > >independent points goes like 2dkdr/pi. When fitting EXAFS data you > >really need to have a lot more independent points than the number of > >fitted variables. In that case the +0, +1, or +2 doesn't really matter > >as long as you are consistent. > > of course, but see above. > > >The +1 and +2 come from the information at the beginning of the data > >set. I think of the raw chi(k) data as being chopped up into pieces > >with the length of each piece about dk ~ pi/dr. For every multiple of > >this length you get two data points representing an amplitude and phase, > >hence the 2dkdr/pi part. If this length is -- then a data set like this > >.--.--.--.--.- Has 4.5 independent points, plus the one at the > >beginning hence +1 (count the "."). Now often Fourier transforms are > >done from r=0 to some other bigger r value. At the special value of r=0 > >you only need one variable, the amplitude, since the phase is known, > >hence 2dkdr/pi + 1. For EXAFS analysis we never start at r=0 so we get > >two parameters for each length, hence 2drdk/pi + 2. > > OK. This is the sense of the paper by Stern, which now I understand > better, thanks! > 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" > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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RE: [Ifeffit] statistical parameters
by Kelly, Shelly D. 14 Dec '05

14 Dec '05

Hi Stephano, > Not sure I fully follow, as I am not talking about background > removal, but in any case, shouldn't the ratio between chi^2 and > reduced-chi^2 be an integer number, whichever? Since 2dkdr/pi is not always an integer number, the degrees of freedom which is the NIP (number of independent points) - number of variables is not always an integer number. > Plus, I have found a > few documents in which Matt reports Nidp as 2dkdr/pi, some others in > which he reports 2dkdr/pi+1. In SK's thesis, which is available on > the net (thanks Shelly :-)) she says +2. I was simply wondering which > is the right formula used in IFEFFIT, and if it is different from > what reported in Stern, Phys. Rev. B, 1993, 48, 9825-9827, why it is > so. Most importantly, all of these expressions for the number of independent points are similar. The most important part is that the number of independent points goes like 2dkdr/pi. When fitting EXAFS data you really need to have a lot more independent points than the number of fitted variables. In that case the +0, +1, or +2 doesn't really matter as long as you are consistent. The +1 and +2 come from the information at the beginning of the data set. I think of the raw chi(k) data as being chopped up into pieces with the length of each piece about dk ~ pi/dr. For every multiple of this length you get two data points representing an amplitude and phase, hence the 2dkdr/pi part. If this length is -- then a data set like this .--.--.--.--.- Has 4.5 independent points, plus the one at the beginning hence +1 (count the "."). Now often Fourier transforms are done from r=0 to some other bigger r value. At the special value of r=0 you only need one variable, the amplitude, since the phase is known, hence 2dkdr/pi + 1. For EXAFS analysis we never start at r=0 so we get two parameters for each length, hence 2drdk/pi + 2. HTH Shelly Shelly Kelly Bldg 203 RM E113 Skelly(a)anl.gov Argonne National Laboratory 630-252-7376 9700 S Cass Ave www.mesg.anl.gov Argonne, IL 60439 > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit- > bounces(a)millenia.cars.aps.anl.gov] On Behalf Of Stefano Ciurli > Sent: Wednesday, December 14, 2005 11:16 AM > To: Ravel, Bruce D.; XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] statistical parameters > > Bruce, > > >According to what you said above, Nvar = 7, so nu=24.83, which is much > >closer to 23.54. > > of course. My mistake. But still... > > >That still seems bigger than rounding errors, though. > > that's what I am saying... > > >Here is my understanding of Ifeffit, but I am sure Matt can elaborate. > >Background removal uses the integer part of dk*dr*2/pi+1 to determine > >the number of knots. Fitting uses dk*dr*2/pi as a real number to > >determine Nidp. In any case, that's what Artemis reports when you ask > >it how many independent points in a project. My memory is that I > >checked it against Ifeffit's report of Nidp. > > > 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" > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Re: statistical parameters (Josh Kas)
by joshua jason kas 14 Dec '05

14 Dec '05

Hi, I don't know what ifeffit does, but here is a nice paper by Ed Stern which goes through the theory Number of relevant independent points in x-ray-absorption fine-structure spectra. PRB V. 48 Number 13 The conlcusion is that if you are using r-space data that includes r=0 then Nidp = 2dkdR/pi + 1 otherwise, when r=0 is not included in the fit Nidp = 2dkdR/pi + 2 Hope this helps. Josh Kas

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phase shifts
by Stefano Ciurli 14 Dec '05

14 Dec '05

Hello, yet another one... sorry today is my day... With Athena it appears that I can simply (maybe too simply) click on a button and plot the phase shifted spectrum in R-space. How can I try to do the same using IFEFFIT from the command line? In practice, using IFEFFIT we can plot the fitted spectrum and the FT'ed experimental spectrum, but the plot does not consider the phase shift. We need to extract the phase shift in oder to translate the plot to show the phase shifted spectrum. How can we do that? What is the parameter in IFEFFIT that allows one - as in Athena - to add a constant number and shift the plot? Stefano PS: needless to say that we are learning... -- ____________________________________________ 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"

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statistical parameters
by Stefano Ciurli 14 Dec '05

14 Dec '05

Hello, same old question that emerges again: What formula is used by IFEFFIT to calculate the number of independent points? Does it use the formula 2DkDR/pi? or 2DkDR/pi +1? or 2DkDR/pi +2? And how does it approximate the resulting number to integer? Next: as far as I understand, the conversion from chi^2 to reduced-chi^2 involves dividing the first by the number of degrees of freedom. The latter is obtained by subtracting the number or floating parameters from the number of independent point right?. What if one fixes the value of one parameter, let's say S0^2 to unity? Does the number of parameters includes S0^2 in that case? We consider that it does not. Here is an example. We find with IFEFFIT (we use Dk= 10 (from 2 to 12), DR=5 (from 1 to 6). chi^2 = 87.1 reduced chi^2 = 3.7 parameters: E0, three distances and three sigma^2 we set S0^2 fixed to 1 R-factor: 1.15% The ratio between chi^2 and reduced chi^2 is 23.54, which is not an integer number as we would expect. Plus, this number does not correspond to Ninp -Nvar (31.83 - 5 = 26.83) What are we missing? Sorry if the question sounds silly to most of you. 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"

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Athena 0.8.046 and the "%" character
by Mauro Rovezzi 14 Dec '05

14 Dec '05

Hi folks, I've just noticed a strange behaviour in Athena. Please, let me know if you can reproduce this "error": - Open a project with two mu(E) - Merge them in chi(k) [noise weighted] - Rename the "merge" group in "something%something_else" - Save the new group as chi(k) - Save the project Well: 1. The generated .chi file contains nothing 2. Artemis fails to open the chi(k) from the Athena project (trapping an error and showing nothing). 3. Re-doing everything *without the "%" character, works!* Cheers, Mauro

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wiggly lines
by Stefano Ciurli 14 Dec '05

14 Dec '05

Hello all, I found this funny dialog on the web. I think it is worth a smile :-) Stefano "What is feff," You ask? "Well, I am glad that you asked that," I say. Then I continue, "Feff is a computer program that makes wiggly lines appear on your computer screen." "Not my computer screen," you say. "Yes, I suppose not YOUR computer screen- MY computer screen... Anyways, sometimes the lines are long and really very wiggly, and sometimes the lines are hardly very wiggly at all. But, there are always at least a few wiggles; you can count on that." "And another thing about the wiggly lines," I exclaim. "Sometimes those wiggly lines are pretty good wiggly lines, but then again, sometimes they are pretty bad." "How can you tell the difference," you ask? "Well, that's really very simple. Just go show the wiggly lines to your boss, and if he looks HAPPY then you have just shown him GOOD wiggly lines... If he looks SAD then you have just shown him BAD wiggly lines. And if he says, 'What the hell are all these wiggly lines?' then you probably just went into the wrong office; try down the hall a bit... ...just a little further... ...now on your left... ... next one... that's it! Good luck with those wiggly lines!" -- ____________________________________________ 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"

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Re: [Ifeffit] Mac installer for 10.4 with horae-048
by Matt Newville 14 Dec '05

14 Dec '05

Paul, Is Perl/Tk for 5.8.6 included in the 10.4 installer? Do you have any suggestions for Stefano? Stefano: the Ifeffit apps from the 10.3 installer won't work directly with 10.4. With the 10.3 package installed, several people were able to build horae from source -- see the mailing list archives for directions on how this was done. But I sure hope you don't need to do this. The installer should work. I sort of don't understand what happened to break these apps. It was working for you once, right??? I sort of don't understand what happened. --Matt

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problem with ifeffit 1.2.8 at ESRF
by Carmelo PRESTIPINO 13 Dec '05

13 Dec '05

Hi to all I'm Carmelo (Lello) and I'm working on Bm29 in ESRF. Recently I have updated IFEFFIT to version 1.2.8 a computer in the beamline (OS winXP profesional edition), but I unfortunatly noticed that the applications didn't start. Makinig some test and looking the previus posted newsmail I concluded that this behavior is probably due to the firewall of ESRF. In order to obtain a more susessfull help from the computter service, anyone could explein me wich is exacly the problem Here below there is the runner.exe.log Traceback (most recent call last): File "runner.py", line 753, in ? File "runner.py", line 184, in __init__ File "runner.py", line 275, in LookForUpdates File "runner.py", line 299, in read_web_version File "urllib.pyc", line 76, in urlopen File "urllib.pyc", line 181, in open File "urllib.pyc", line 297, in open_http File "httplib.pyc", line 712, in endheaders File "httplib.pyc", line 597, in _send_output File "httplib.pyc", line 564, in send File "httplib.pyc", line 538, in connect File "timeoutsocket.pyc", line 237, in connect timeoutsocket.Timeout: Attempted connect to ('164.54.160.111', 80) timed out. Best Regards Lello

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Re: [Ifeffit] Mac installer for 10.4 with horae-048
by Matt Newville 12 Dec '05

12 Dec '05

Stefano, You should NOT need to compile perl/Tk -- it should be included in the installer. You had a working system that somehow got corrupted (though I do not understand how that happened, as a horae_update should have done absolutely nothing). How did you originally get Ifeffit installed on your OSX system? Bruce wrote: > On a similar topic, I see that IfeffitOnMacintosh on the wiki points to a page that hasn't > been written yet. Maybe Stefano or Paul will fill this in. The discussion of how to install Ifeffit+horae on OSX10.4 has been discussed several times on this mailing list in 2005. Several people were able to use the 10.3 installer, fink installed g77, and compile all the perl modules themselves. The installer is supposed to avoid all that. I don't know what's in the 10.4 installer. We should wait to hear from Paul. --Matt

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Ifeffit installer for Mac 10.4 (Tiger)
by Tonio Buonassisi 12 Dec '05

12 Dec '05

Hi Matt, I've just tried installing IFEFFIT (using "install Ifeffit on Tiger") on a new Mac running 10.4. The installer apparently runs to completion, but when I go to the application folder and double-click on the apps themselves (e.g., Artemis), they appear to open up but then immediately close down to the Finder again in less than a second. At the XAFS Summer School I remember this problem on newly-installed machines: we had to download a program from the Apple website (X-server?), although I can't recall what this is... Conscious that this is an old problem, I tried looking in the archives, but without search capabilities I didn't find the right thread... Any assistance would be appreciated, Best, Tonio

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writing beam time proposals
by Bruce Ravel 08 Dec '05

08 Dec '05

Hi folks, Yesterday I received an interesting question about writing beam time proposals. I know that proposal review panel members at least from APS and NSLS are readers of this mailing list (perhaps other synchrotrons as well), so I thought it would be interesting to start a thread on proposal writing strategies. The fellow who sent me mail asked: My question is, since I am a student, should my advisor be the official PI applying for time or should I be the PI? Is there any advantage one way or the other? In principle, I think it should not matter. Beam time should be awarded to a quality proposal. What advice do you all have for this proposal writer? What has your experience in applying for beam time? BTW, this fellow had been a student in a recent XAS summer school. I suggested he mention that in his proposal. Regards, B -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advance 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] Mac installer for 10.4 with horae-048
by Stefano Ciurli 02 Dec '05

02 Dec '05

Hello Ifeffitters on MAC OSX. Just to finish this thread, I inform you that I have solved my problem. The issue was with the /Library/Perl directory. Once I replaced it with a backup I diligently keep almost weekly, everything works fine with horae-056. Thanks a lot to those who tried to help me out (and also for those who silently sympathyzed about this problem I had created to myself :-)) Stefano

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Re: [Ifeffit] Mac installer for 10.4 with horae-048
by Matt Newville 01 Dec '05

01 Dec '05

Stefano, Hmmmm. What I would do next is to trash /Library/Perl. This is where much of where horae goes, though it should be overwritten on installation too. Trashing /Library/Perl is a little riskier than trashing /Applications/Ifeffit because it's possible that some other perl application is using that folder too. If you think you're not using any other perl programs, you probably are not. In any case, you could do sudo mv /Library/Perl /Library/Perl_SAVE You can also look at the list of Perl files installed (at least as of horae-0.48 on Mac 10.3) at http://cars9.uchicago.edu/ifeffit/src/MacOSX/PerlFiles This says 'Perl/5.8.1' everywhere and I believe 10.4 uses a more recent version of perl, but this list be helpful in looking for folders not installed by Ifeffit. After doing this, you can retry the installation. If that's too scary (or doesn't work ;>) I hope Paul has some insight! --Matt

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Re: [Ifeffit] Mac installer for 10.4 with horae-048
by Matt Newville 30 Nov '05

30 Nov '05

Stefano, Can you completely delete /Application/Ifeffit and reinstall? I know it sounds brutal, but it;s not going to do anything bad to your System.... --Matt

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Mac installer for 10.4 with horae-048
by Paul Fons 30 Nov '05

30 Nov '05

As the unix auto-update script has been broken due to changes by sourceforge, I have updated the ifeffit installer on sourceforge for Mac OS 10.4 to include the latest revisions (bug fixes to athena). Paul

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Re: Horae-058
by Bruce Ravel 23 Nov '05

23 Nov '05

On Wednesday 23 November 2005 07:35, you wrote: > Greetings from SPring-8 (getting chilly here, but no snow yet). We've got you beat here at the APS. There is snow on the ground right now! The Australian and Brazilian synchrotrons are looking awfully good right now.... > I tried downloading the latest tarball using your horae-update > script. It download a file with the right name, but that only > contains what appear to be sourceforge related web links. In other > words horae_update is broken (much like what happened before). SourceForge redesigned their web site. The screen scraper in horae_update no longer works. I am hesitant to just fix the current code -- it was a hand-built solution and, obviously, much too fragile. A better solution would require either using better html parsing tools from CPAN or figuring out how to gather information from SourceForge without needing to scrape their web pages. I am open to any suggestions or offers of coding help. 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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that didn't take long...
by Bruce Ravel 23 Nov '05

23 Nov '05

Hi folks, I just discovered a fairly serious bug in the version of Athena I just released yesterday. The auto-alignment function is broken. Fortunately, alignment can still be done by hand using the +/- buttons in the alignment dialog. The fix is simple, but I won't be able to post updates until next week. (It's a holiday tomorrow here in the States and I am leaving for the airport soon.) My apologies to anyone who needs that feature in the next few days and especially to Paul who just did a bnch of work to make and post a new OSX installer. 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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new tarball and windows updater
by Bruce Ravel 22 Nov '05

22 Nov '05

Hi folks, Today I made a release that is mostly for maintenence purposes on Athena. Most of the changes have to do with various bug fixes and small UI improvements. Artemis and Hephaestus are unchanged. The new tarball, version 58, is at my site and at SourceForge. I also built a new windows executable and an updater. See http://cars9.uchicago.edu/iffwiki/HoraeVersion058 for details about the release. Thanks to Shelly, Adam, and Norbert for their feedback on this release. 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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graphics help
by crojasa＠unmsm.edu.pe 21 Nov '05

21 Nov '05

Hello help in: why in my graphics the fit curve is more differents that data curve?. If that fit is ok, but the fit curve(red) is very underneath that data curve(blue). Some idea Chachi P.D my graphis is in attachment -- Chachi Rojas GMC FCF UNMSM Tel.Mo.:97499347 email:crojasa@unmsm.edu.pe

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RE: [Ifeffit] NiO data
by Kelly, Shelly D. 15 Nov '05

15 Nov '05

Hey Scott, Well, I botched the MRCAT part of the acknowledgement. Please use this one instead. Use of the APS was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, under Contract No. W-31-109-ENG-38. MRCAT operations are supported by the Department of Energy and the MRCAT member institutions. Thanks Shelly Shelly Kelly Bldg 203 RM E113 Skelly(a)anl.gov Argonne National Laboratory 630-252-7376 9700 S Cass Ave www.mesg.anl.gov Argonne, IL 60439 > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit- > bounces(a)millenia.cars.aps.anl.gov] On Behalf Of Scott Calvin > Sent: Monday, November 14, 2005 10:03 PM > To: XAFS Analysis using Ifeffit > Cc: SCalvin(a)slc.edu > Subject: RE: [Ifeffit] NiO data > > Thanks Shelly, Matt, and Jeremy! > > I'm using Shelly's data, since I need EXAFS. I've instructed the lead > author to include in the caption, > > "NiO data collected by S. Kelly at the MRCAT beamline of the APS." > > Good? > > --Scott Calvin > Sarah Lawrence College > > >Hi Scott, > > > >Here is some NiO data. > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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RE: [Ifeffit] NiO data
by Kelly, Shelly D. 15 Nov '05

15 Nov '05

Hi Scott, I'm glad to help. Did any of the other data come from the APS? I would be great to add an acknowledgement to the APS/MRCAT funding, if you can swing it. Something like: Use of the APS was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, under Contract No. W-31-109-ENG-38. The Materials Research Collaborative Access Team is supported under grant number DE-FG02-04ER46106. Thanks Shelly Shelly Kelly Bldg 203 RM E113 Skelly(a)anl.gov Argonne National Laboratory 630-252-7376 9700 S Cass Ave www.mesg.anl.gov Argonne, IL 60439 > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit- > bounces(a)millenia.cars.aps.anl.gov] On Behalf Of Scott Calvin > Sent: Monday, November 14, 2005 10:03 PM > To: XAFS Analysis using Ifeffit > Cc: SCalvin(a)slc.edu > Subject: RE: [Ifeffit] NiO data > > Thanks Shelly, Matt, and Jeremy! > > I'm using Shelly's data, since I need EXAFS. I've instructed the lead > author to include in the caption, > > "NiO data collected by S. Kelly at the MRCAT beamline of the APS." > > Good? > > --Scott Calvin > Sarah Lawrence College > > >Hi Scott, > > > >Here is some NiO data. > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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RE: [Ifeffit] NiO data
by Kelly, Shelly D. 15 Nov '05

15 Nov '05

Hi Scott, Here is some NiO data. There are several columns in the data files. They represent energy, I0, It, If, Iref. They were collected from MRCAT at the APS. Here are some beamline parameters. ID tapered 4 mm to decrease the change in x-ray energy over the scanned range. 1st harmonic of ID line used. double crystal Si(111) mono. Ph mirror to remove harmonics 0.7x0.7 mm slits to define x-ray cross-section 20/80 N2/H3 in Io, 100% N2 for It. quick scanning mode Ni filter of 6 absorption lengths was used in reference pin diode detector infront of I0. Reference signal is taken by log(Io/Iref). Cross and Frenkel have the reference for this. As far as I can tell, we haven't published this reference before. The log book mentions that the NiO particle size is less than 10 microns. I don't think that we ran XRD on it. The sample came from Aldrich (99% purity). Shelly -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov on behalf of Scott Calvin Sent: Sun 11/13/2005 5:50 PM To: XAFS Analysis using Ifeffit Cc: SCalvin(a)slc.edu Subject: [Ifeffit] NiO data Hi all, Anyone out there have spectra for a NiO standard? I bet one of you does, since there was a request for a NiO atoms.inp file a few months ago. I have a referee who wants to see that our data that matches Ni metal very well doesn't also match NiO well (I'm presuming this referee is not someone too familiar with EXAFS!). So anyway, also let me know how you'd like me to credit the data (e.g. a footnote listing you and the beamline it was collected on). Thanks! --Scott Calvin Sarah Lawrence College P.S. And no, Matt's database doesn't have NiO, and yes, the Lytle database does...but the Lytle data is not thoroughly documented and so I avoid it when possible. _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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RE: [Ifeffit] N K-edge XANES, normalization parameters
by Barton, David (DG) 14 Nov '05

14 Nov '05

Peter, ATHENA is mainly written for EXAFS analysis, however...it is still quite useful for XANES analysis as well. I opened your project that you sent and there were a couple of obvious challenges with this dataset. First of all, you should read the section regarding Normalization in the ATHENA help POD if you haven't already. One useful feature in ATHENA is the ability to turn ON the Pre-edge and Post-edge plots. After looking at your two Plots in the file you sent it is obvious that the choice of the Post-edge region is quite poor for the dataset "merge21to27". The "Flattening" Normalization routine in Athena uses a Linear function for the pre-edge (Pre-edge Region) and a quadratic for the post-edge (Normalization Region). Flattening is the process of subtracting these two functions from your experimental dataset (subtracting pre-edge function at energies below Eo and subtracting the post-edge function above Eo) and then scaling the dataset to unity over the normalization range. Your dataset is a bit challenging because the pre-edge region has a limited range so that a when you fit a linear function to it, it crosses over your data set indicating that it is not a good representation of the sample background. I can't think of a quick workaround for this, but you may want to consider manually subtracting a linear function with a smaller slope from your raw dataset prior to opening in ATHENA and then adding a couple of points to the begin of the dataset that could be used for the pre-edge region in ATHENA to force a zero slope. Then you could look closer at your post-edge region (Normalization Range) to ensure the shape of the quadratic is reasonably fitting your dataset. At this point ATHENA only allows a linear pre-edge and a quadratic post-edge, however it does looks like Matt and Bruce are working on adding additional fitting functions to IFEFFIT and ATHENA. So if you cannot get a sufficient background normalization fitting with these functions! you will have to try some other tool. Finally, ATHENA likes to work in eV so you should adjust your energy scale, especially if you want to attempt to use CLNORM background subtraction. Hope this helps, Dave > -----Original Message----- > From: Peter Leinweber [mailto:peter.leinweber@uni-rostock.de] > Sent: Monday, November 14, 2005 3:25 PM > To: ATHENA Userlist > Cc: fan.walley(a)usask.ca > Subject: [Ifeffit] N K-edge XANES, normalization parameters > > > dear all, > i am a new XANES and ATHENA user. i didi N K-edge XANES of > soil samples. while feeling very good with data import, > deglitching, truncation, merging etc. i am insecure about > parameters for normalization. > in the attached project i did truncation of data before > 395900 (it is milli-eV), because these seem to be invalid, > and i set an E-shift of -900 sinc the beamline had -9.9 eV > off compared to the N K-edge of N2 gas. in this way i should > be right back on scale ? the i did set the pre-edge > parameters manually at start of the curve, and around 397000 > since non of the previously measured N standard substances > had edge steps below this value. > however, then i am insecure how to set the other parameters > for normalization properly. depending on how i play with the > parameters sometimes i get normalized spectra which look > pretty reasonable, sometimes the curves disappear completely > from the graphics window, and sometimes i get curves of a > shape never senn in the literature. is there easily > understandable advice for the setting of the normalization > parameters available; or can anybody more experienced check > my project and give me recommendations. thanks, peter > > Prof. Dr. Peter Leinweber > Institute for Land Use > Universitaet Rostock > D-18051 Rostock > > Present address: > Department of Soil Science > University of Saskatchewan > 51 Campus Drive > SK S7N 5A8 > Canada > > phone: 001-306-966-6866 > fax: 001-306-966-6881 >

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N K-edge XANES, normalization parameters
by Peter Leinweber 14 Nov '05

14 Nov '05

dear all, i am a new XANES and ATHENA user. i didi N K-edge XANES of soil samples. while feeling very good with data import, deglitching, truncation, merging etc. i am insecure about parameters for normalization. in the attached project i did truncation of data before 395900 (it is milli-eV), because these seem to be invalid, and i set an E-shift of -900 sinc the beamline had -9.9 eV off compared to the N K-edge of N2 gas. in this way i should be right back on scale ? the i did set the pre-edge parameters manually at start of the curve, and around 397000 since non of the previously measured N standard substances had edge steps below this value. however, then i am insecure how to set the other parameters for normalization properly. depending on how i play with the parameters sometimes i get normalized spectra which look pretty reasonable, sometimes the curves disappear completely from the graphics window, and sometimes i get curves of a shape never senn in the literature. is there easily understandable advice for the setting of the normalization parameters available; or can anybody more experienced check my project and give me recommendations. thanks, peter Prof. Dr. Peter Leinweber Institute for Land Use Universitaet Rostock D-18051 Rostock Present address: Department of Soil Science University of Saskatchewan 51 Campus Drive SK S7N 5A8 Canada phone: 001-306-966-6866 fax: 001-306-966-6881

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atoms and the alloys
by Mauro Rovezzi 13 Nov '05

13 Nov '05

Hi to all, I have noticed that Atoms fails to generate a correct "feff.inp" file in the case of alloys. For example, let's take the Ni_xCu_{1-x}, x=0.5, an fcc substitutional. If I put Ni as central atom and give 0.5 occupancy on the shared Cu-Ni site (0,0,0.5) the result is a normal Ni fcc without Cu. At the moment I modify my feff.inp by hand to simulate alloys, but maybe I'm just not using Atoms properly. If this is the case, it could be useful to insert your answer in the FAQ. Cheers, Mauro

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Re: [Ifeffit] doubts
by Feng Wang 12 Nov '05

12 Nov '05

Dear Bruce and Scott, I am a beginner of IFEFFIT, trying to follow Scott's example. In the ZnO DEMO PART 1, everything went well before doing the fit, however when I click the green button "Fit", I was told by the message: This parameter uses a name which has special meaning in Ifeffit: dr You must change this parameter name before attempting to fit. One common example of this sort is a variable named "dr1", which should be changed to something like "dr_1" or "drone". Could you or anyone direct me? I would appreciate that. Best regards, Feng > > I could write on and on about this topic, but I think it would be > fruitful for you to follow the example that Scott Calvin wrote up. > Look at: > > http://cars9.uchicago.edu/~ravel/software/contrib.html > > And download the ZnO example. This consists of a series of Artemis > project files. Scott wrote comments in the journals of each project > to walk you through the process of using Artemis to fit real data. I > think that it would be helpful to you to work through this example > carefully. I suspect that doing so will help to clear up some of your > confusion. > > If, after working through Scott's example, you still have questions -- > we on the mailing list will be glad to help you out. > > B >

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Re: [Ifeffit] doubts
by Feng Wang 10 Nov '05

10 Nov '05

Hi Carlo. Thanks a lot for the solution, it works. Best regards, Feng > On Wed, 9 Nov 2005, Feng Wang wrote: > > > Dear Bruce and Scott, > > > > I am a beginner of IFEFFIT, trying to follow Scott's example. In the ZnO DEMO > > PART 1, everything went well before doing the fit, however when I click the > > green button "Fit", I was told by the message: > > > > This parameter uses a name which has special meaning in Ifeffit: > > dr > > You must change this parameter name before attempting to fit. > > One common example of this sort is a variable named "dr1", which > > should be changed to something like "dr_1" or "drone". > > > > Could you or anyone direct me? I would appreciate that. > > > Dear Feng: > > Click to the Interpretation tab and select "Guess, Def, Set" in the > middle pane. YOu should see all the variables that are defined. My guess > is that you have "dr" instead of something like "delr". Change the name > to "delr" and then click on the individual paths and change any occurence > of "dr" to "delr". > > If you are working on Scott's example for ZnO, I am not sure how you got > "dr" as he uses "delr" in evrything as far as I recall. In fact, I just > looked at the tutorial myself and if I follow all the instructions, I get > the following variables in the "Guess, Def, Set" > amp > enot > delr > ss > > note that Scott's instructions are for an older version of Artemis and > there is not menu entry for loading a FEFF calculation, instead you need > to Open File, go into the FEFF subdirectory and select "feff.inp". > Artemis is smart enough to know that this is a calculation and asks how > many paths to import. > > hope this helps, > > 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 ================================== Feng Wang fwang(a)phys.ualberta.ca CW182 (Tel 492-5599) Electron Microscopy Group Department of Physics =========================================================

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doubts
by Marcos Eleoterio 09 Nov '05

09 Nov '05

good afternooon, My name is Marcos Eleotério, i am undergraduate in physics and i have a scholarship at Brazilian Synchroton Light Laboratory, nearly one month ago i start using the software Athena and Artemis, to analyse some X-ray absorption data that i have, to make my problem more easy to you understand i list below the steps that i use in those programs: 1) After a normalization of the data, i put the data in "Athena" turn on the options: "pre-edge line", "post-edge line" and then "normalized" (in fact i usually turn the option "flatten" on, in dispite of the fact that i don´t know what that means, what that means?), i save using the option "Save chi(k)" in "file". 2)Then i open the program "Artemis" and insert the data saved in the step "1)" in the column of the middle i click with the right button of the mouse and select the option "theory", "atoms" and insert the spatial group, unit cell parameter, and atomic location (here its important to say that the compound that i'm studying is LaCaMnRuO6 the measure of x-ray absorption was performed in the K-edge of the Mn, we are interested in Mn-O ligands so in "Artemis" i only put the data of the Mn and O, right?) 3)I click in the option "run atoms" for each atoms that i inserted the information, choosing 10 paths in each step, i click the in the option "run feff" for each atom that i inserted the information (again), after that, i click in "Fit" then appears in the screem the advise: "there is something wrong with your math expressions" (or something like that) i ignore that advise and go on, but the big problem is that the fit appears very poor! I have to say that the information that i use to insert the atomic position, unit cell parameters, was obtained from a Riteveld refinament, that i performed with the data from a cooper x-ray tube, do i need a data from a beam line, at synchroton? Do you have some idea of my problem? Have i make the correct steps? I'm sorry for my english, i will be very thankful if you answer my e-mail or give to me someone who can do it! REGARDS

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Re: [Ifeffit] Question with FL Database
by Marco Alsina 08 Nov '05

08 Nov '05

El Martes, 8 de Noviembre de 2005 13:14, Matt Newville escribió: > Yes, there are a few different formats of data in the Lytle > database. As far as I can tell, the files with > 'CUEDGE START STOP BEG FSCTS: ...' > do not include a "known" d-spacing or steps-per-degree, but > tend to use Si(111) (dspace = 1.9202). You didn't include the > rest of the file or say which file you're trying to use, so it's > impossible to tell what problem you're having. Well actually what I was trying to do was to obtain a meanigful value for motor step 168620 (CUEDGE, which I included in the header), and with d-space set to 1.92017 and step-per-degree equal to 8000 you get CUEDGE =8977 eV, so set(dspace=1.92017, stpdeg=8000) fixed my problem For further files what I needed was possible values for stpdeg, which you already give me. Thanks Matt and the community,and also thanks for the macro too! Regards, Marco

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new release of my codes (horae-057)
by Bruce Ravel 08 Nov '05

08 Nov '05

Hi folks, This morning I made a new release of the source code tarball for my codes as well as a new Windows updater. Matt and I finally have the update system organized well enough that I can actually release the source and the windows update on the same day. Yay! New tarballs are at SourceForge and on my web site. The Windows updater should run the next time you fire up one of the programs. Artemis and Hephaestus are unchanged. All the new stuff is in Athena (new version is 0.8.045). See http://cars9.uchicago.edu/iffwiki/HoraeVersion057 for details. Most of the work was on the linear combination fitting tool and some improvements to the scheme for importing data in unusual file formats. There are a few other new tidbits and several bug fixes as well. One change which will be immediately obvious is that I split the controls for background removal parameters into two groups. The division is more or less between the more and less often used parameters. There are buttons for switching the display between the two groups of parameters. You'll see what I mean when you fire up Athena. The linear combination fitting has several fixes for bugs that people mentioned after the last release as well as a few new features. The scheme for importing data in unusual formats merits its own page on the wiki, which I'll post soon. Enjoy, B -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advance 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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ATHENA: Encoder option missing?
by Norbert Weiher 05 Nov '05

05 Nov '05

Bruce, I just updated to the latest version of A&A. When I open a file it seems that the "encoder" option in the energy units is missing... Regards, Norbert -- Dr. rer. nat. Norbert Weiher (norbert.weiher(a)manchester.ac.uk) School of Chemical Engineering and Analytical Science Sackville Street, Manchester, M60 1QD - Phone: +44 161 306 4468

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WG: [Ifeffit] hephaestus
by Peter Leinweber 02 Nov '05

02 Nov '05

hello bruce, i am a new user of your software. when i load the programm the following shows up lower right: Emin -200 and Emax 800. when i load data they are plotted with proper x-axis. but when i did any modification the scaling of x-axis changes to invalid or in-comfortable values. i can fix it by modifying Emin and Emax but to get an axis of 395 to 410 eV i have to type Emin -400 and Emax 18000. is that o.k. ? another question: will you or will someone of your group attend the CLS user meeting here in saskatoon in november. there is interest of other newcomers like me to get introduced into ATHENA. perhaps some arrangement such as coverage of additional hotel costst for staying a day longer or so could be made. kind greetings, peter Prof. Dr. Peter Leinweber Institute for Land Use Universitaet Rostock D-18051 Rostock Present address: Department of Soil Science University of Saskatchewan 51 Campus Drive SK S7N 5A8 Canada phone: 001-306-966-6866 fax: 001-306-966-6881 ----- Originalnachricht ----- Von: Bruce Ravel <bravel(a)anl.gov> Datum: Mittwoch, November 2, 2005 5:31 pm Betreff: [Ifeffit] hephaestus > > > Hi all, > > Today, in a conversation that Carlo, Matt, and I have been having, > Matt said the following: > > > I know some beamlines (PNC-CAT, for example) don't install > > Ifeffit/hephaestus on data collection machines because it uses too > > much memory (~40Mb+ on Win32). > > In fact, the only thing for which hephaestus uses Ifeffit is the f'/f" > utility. None of the other tools in hephaestus make use of ifeffit in > any way. > > Would there be some interest in a "hephaestus-lite"? That is, a > version of hephaestus that does not include the f'/f" utility. > Such a > thing would have a much smaller footprint on the computer -- just > whatever the perl interpreter requires, maybe 4 or 5 meg. > > If enough people express inetrest, I can inlcude thas in the > distribution. I can even make a stand-alone distribution that > installs only hephaestus-lite and the external files it needs to do > its thing. That would be a much smaller beast (both in disk space and > memory footprints) than the full ifeffit install. > > B > > > -- > Bruce Ravel ---------------------------------------------- > bravel(a)anl.gov > Molecular Environmental Science Group, Building 203, Room E-165 > MRCAT, Sector 10, Advance 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/ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

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hephaestus
by Bruce Ravel 02 Nov '05

02 Nov '05

Hi all, Today, in a conversation that Carlo, Matt, and I have been having, Matt said the following: > I know some beamlines (PNC-CAT, for example) don't install > Ifeffit/hephaestus on data collection machines because it uses too > much memory (~40Mb+ on Win32). In fact, the only thing for which hephaestus uses Ifeffit is the f'/f" utility. None of the other tools in hephaestus make use of ifeffit in any way. Would there be some interest in a "hephaestus-lite"? That is, a version of hephaestus that does not include the f'/f" utility. Such a thing would have a much smaller footprint on the computer -- just whatever the perl interpreter requires, maybe 4 or 5 meg. If enough people express inetrest, I can inlcude thas in the distribution. I can even make a stand-alone distribution that installs only hephaestus-lite and the external files it needs to do its thing. That would be a much smaller beast (both in disk space and memory footprints) than the full ifeffit install. B -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advance 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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SPAM score=5.6*** Troubles in Running Iffeffit
by Adiraj Srinivas (Dr) 31 Oct '05

31 Oct '05

-------------------- Start SpamAssassin results ---------------------- Content analysis details: (score=5.6,required=5.3) 8.0 SOFTWARE_APS BODY: Words and phrases for selling software 0.1 HTML_IMAGE_RATIO_06 BODY: HTML has a low ratio of text to image area 0.0 HTML_90_100 BODY: Message is 90% to 100% HTML -2.6 BAYES_00 BODY: Bayesian spam probability is 0 to 1% [score: 0.0033] 0.0 HTML_MESSAGE BODY: HTML included in message -------------------- End of SpamAssassin results --------------------- The original message was not completely plain text, and may be unsafe to open with some email clients; in particular, it may contain a virus, or confirm that your address can receive spam. If you wish to view it, it may be safer to save it to a file and open it with an editor.

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S02
by Juan Antonio Maciá Agulló 31 Oct '05

31 Oct '05

Hi people, I fitted several supported platinum based catalysts by Artemis. I obtained good R-factors < 0.02 but stranges values of SO2 (<0.30) and I do not know if these low values of SO2 are related with a low coordination number for Pt. I know that particle sizes of these catalysts are very small and then the coordination number is smaller than 12. Thank you very much. JA

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RE: [Ifeffit] Problems with Windows XP Installation.
by Brewer, Luke N 21 Oct '05

21 Oct '05

Bruce, thank you for the solutions. Solution 2 seems to have fixed the problem. I now look forward to learning to run the software. Thanks again, Luke. -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Bruce Ravel Sent: Friday, October 21, 2005 12:36 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Problems with Windows XP Installation. On Friday 21 October 2005 13:14, Brewer, Luke N wrote: > Hello All- > > I have just downloaded and installed the ifeffit.1.2.8.exe package > for Windows XP from a mirror to sourceforge. The installation > appeared to run just fine. I read the note on website about using the > runner.exe instead of the individual executable files. > > When I click on the runner.exe, a window asks me what application I > would like to run (Athena, Artemis, etc.). The window disappears, and > nothing happens for about a minute after which an error window appears > asking me to check the runner.exe.log. The last line of each log > entry reads "timeoutsocket.Timeout: Attempted connect to > ('164.54.160.111', 80) timed out." > > I get the same error each time I try to run the software, regardless > of which application I select. > > Any advice? I would be happy to forward the runner.exe.log to anyone > who can/is willing to help. I think I know the problem -- Matt may have more wisodm. The first version of the runner did not play well without a reliable internet connection. It would seem you have been bitten by this problem. Possible solution #1: If, in fact, you were on a computer with out an internet connection (either by design or because it was temporarily down), make sure the computer is connected and try again. Possible solution #2: Grab this file: http://cars9.uchicago.edu/ifeffit/updates/iff_001.zip and unpack it by hand in C:\Program File\Ifeffit\ (or wherever you installed the whole ifeffit package). That file is the first updater package. It updates the runner as well as Athena, Artemis, and a bunch of documents and example. For more info on how the runner works and how updates happen, see the wiki: http://cars9.uchicago.edu/iffwiki/IfeffitOnWindows/RunnerProgram HTH, B -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advance 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/ _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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new Tip of the Week
by Bruce Ravel 21 Oct '05

21 Oct '05

Hi! I just posted a new Tip of the Week at http://cars9.uchicago.edu/iffwiki/HoraeTipOfTheWeek This week's bit of magic is Artemis: Quickly plotting paths from the Feff interpretation page Enjoy, B -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advance 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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Problems with Windows XP Installation.
by Brewer, Luke N 21 Oct '05

21 Oct '05

Hello All- I have just downloaded and installed the ifeffit.1.2.8.exe package for Windows XP from a mirror to sourceforge. The installation appeared to run just fine. I read the note on website about using the runner.exe instead of the individual executable files. When I click on the runner.exe, a window asks me what application I would like to run (Athena, Artemis, etc.). The window disappears, and nothing happens for about a minute after which an error window appears asking me to check the runner.exe.log. The last line of each log entry reads "timeoutsocket.Timeout: Attempted connect to ('164.54.160.111', 80) timed out." I get the same error each time I try to run the software, regardless of which application I select. Any advice? I would be happy to forward the runner.exe.log to anyone who can/is willing to help. Thanks. Luke. Luke N. Brewer, Ph.D. Sandia National Laboratory Materials Characterization Dept.

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L2 vs. L3 edge comparisons
by McCready, Alistair 20 Oct '05

20 Oct '05

OK, a theoretical question whose answer may be straight-forward (and I will probably ridiculed for such a simple question)!! If you analyse, for example, the Pb L3 edge of 2 minerals and you then analyse the Pb L2 edge of the same 2 minerals, will the difference between the edges of 2 minerals be the same, irrespective of the edge you use? Cheers Alistair ------------------------------------------ Dr. Alistair J. McCready Mining & Minerals Saskatchewan Research Council 125-15 Innovation Blvd. Saskatoon, SK, S7N 2X8 Canada Tel: 306 933-7103 Fax: 306 933-7446 email: mccready(a)src.sk.ca "SRC provides Smart Science Solutions" This e-mail and any files transmitted with it are intended only for the named recipients and may contain legally privileged and/or confidential information. If you are not the intended recipient please do not disseminate, distribute or copy this e-mail without the consent of the sender.

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horae Debian package
by Carlo Segre 19 Oct '05

19 Oct '05

Hello All: Because of the new dependency on libmath-round-perl. The Debian package of horae 056 will have to be installed manually. It can be found at the deb http://fermi.phys.iit.edu/debian/woody binary/ deb http://fermi.phys.iit.edu/debian/sarge binary/ deb http://fermi.phys.iit.edu/debian/sid binary/ depending on the distribution you are using. 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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new windows updater
by Bruce Ravel 14 Oct '05

14 Oct '05

Hi again, The windows updater containing an update to the runner as well as all the new stuff from today's Athena&Artemis source code release is now available. The runner should find it the next time you start one of the programs. Let us know if you have any troubles with the update or with the new runner. Bruce & Matt -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advance 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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tarball 056 released & new tip of the week
by Bruce Ravel 14 Oct '05

14 Oct '05

Hi folks! The new Tip of the Week is about automated replotting in Athena. http://cars9.uchicago.edu/iffwiki/HoraeTipOfTheWeek I have also released version 056 of the source code tarball, which is available at my web site and at SourceForge. A description of what's new in Athena and Artemis is at http://cars9.uchicago.edu/iffwiki/HoraeVersion056 The major new features are both in Athena: session defaults and improvements to linear combination fitting. Please read the release notes for a complete description of these new features. An updater for windows users should be available within a few days. Unix and Mac OSX users should download and install the new source tarball. Enjoy, B -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advance 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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Small clusters in Feff
by Kelly, Shelly D. 07 Oct '05

07 Oct '05

Hi EXAFS friends, I was reading a paper this morning where the authors used a small hydrated cluster in Feff8.2. The cluster has a metal center surrounded by one shell of oxygen atoms. All feff paths in the calculation were used in the model fits. No mention was made in the manuscript of the muffin tin radii used in the Feff8.2 calculation based on this small cluster, hence I assume that these authors were unaware of the potential pit falls in doing so. Using feff7, I have run a comparison of the calculated signal from a bounded and unbounded shell of atoms at the same distance. I found that the unbounded shell of atoms has a muffin tin radii that is really big because it is not bounded by any other atoms giving rise to an error in the calculated signal from these atoms. Has anyone run this experiment with Feff8.2? I have always used the metal-oxide crystal structure in my modeling of hydrated metal ions and have found reasonable agreement with chemical speciation calculations. I believe that the non-expert users of Feff, find it difficult to remember not to use the exact model within Feff because of this "feature". Is there any discussion of adding a hydration sphere option into Feff? I look forward to your comments. Shelly Shelly Kelly Bldg 203 RM E113 Skelly(a)anl.gov Argonne National Laboratory 630-252-7376 9700 S Cass Ave www.mesg.anl.gov Argonne, IL 60440

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new tip of the week
by Bruce Ravel 07 Oct '05

07 Oct '05

Hi, The Tip Of The Week took last week off to go visit my mom ;-) This week's is about "Selecting paths to plot automatically after a fit" in Artemis. http://cars9.uchicago.edu/iffwiki/HoraeTipOfTheWeek Enjoy! B -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advance 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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delR versus thermal expansion A and first cumulant C1*
by Leandro Langie Araujo 06 Oct '05

06 Oct '05

Dear all, I’m writing because I’ve been trying to analyze some thermal dependent EXAFS data for the first shell of a c-Ge sample and ended up in a conceptual confusion. If any of you could give me some help on this I’d be very grateful. Whenever we fit an EXAFS spectrum with Artemis/IFEFFIT, we get a /delR/ value. As far as my (very) limited comprehension goes, /delR/ is the difference between the theoretical (FEFF8) bond length, /R0/, and the result of the best fit to my data, /R/, which gives the experimental bond length. So, this should be the /first cumulant/ of my distance distribution, right? The net linear thermal expansion /A/ (as defined by Anatoly Frenkel and John Rehr in [PRB48, 585, 1993]) from an one-dimensional model seems to have been considered as equal to the temperature variation of the /delR/ values by several people, including Matt Newville (on his thesis). Following this approach, it is possible to relate the EXAFS cumulants (/delR/, /ss/, /C3/ and /C4/) of the distance distribution with the constants of an one-dimensional anharmonic effective potential, following a correlated Einstein model. I was going through this path... … when I came across some papers (P. Fornasini and G. Dalba in [PRL82, 4240, 1999; PRB70, 174301, 2004] and E. A. Stern in [J.Phys.IV 7, C2-137,1997]) where an issue is raised; it is said that the thermal evolution of the first cumulant /C1/* of the real distance distribution in a crystal (which was said to be equivalent to /delR/) is NOT equal to /A/, because in a crystal there are vibrations perpendicular to the bond direction which are not considered in the one-dimensional model. It is argued that the temperature dependence of these vibrations perpendicular to the bond direction give raise to a positive shift of the minimum of the effective pair potential, while the net thermal expansion /A/ accounts only for changes due to the asymmetry of the potential. So, the main questions hammering my head are: - does /delR/ include any contribution from vibrations perpendicular to the bond direction? Can really /delR/ and /C1/* be the same quantity? - is the thermal evolution of /delR/ equal to the net thermal expansion /A/? Or should some correction for perpendicular vibrations be added to relate both quantities? Sorry if I made it too long, but it was something hard to express in a few words… Any help will be greatly appreciated. Cheers, Leandro

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R-factor and reduced chi square
by OWEN N LI 05 Oct '05

05 Oct '05

Hi, I understand R-factor and reduced chi square are statistical ways to see if the model is reasonable (R-factor) and if one model is better than the others (reduced chi square). But how much should I read into it? I have model A and B, I believe A is more theoretical sound than B. but when I fit them using IFEFFIT, the R-factor and reduced chi square of B is slightly better than A (B: 0.03, 28; A: 0.04, 33). What does that tell me? Is my assumption incorrect? Or are they more or less the same? Owen

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RE: [Ifeffit] New Method for Normalization?
by Barton, David (DG) 04 Oct '05

04 Oct '05

Bruce, You mentioned: > Isn't Ifeffit's Cromer-Liberman normalization scheme > substantially similar to the method presented in that paper? > When I use the Cromer-Liberman background subtraction routine in Athena the Normalized data is not flattened. Normalized, but not *flattened* data results in a skewed XANES region which is affected by the amount of curvature in the background. If I choose "Flatten" in Athena, it is my understanding that it applies a linear pre-edge and 2nd order polynomial post-edge regardless of which background was chosen (Autobk or CLNorm). The Clnorm background does appear to "flatten" the chi(k) data which can be useful for EXAFS analysis, but it doesn't flatten the mu(E) data. When one attempts to analyze XANES data it is preferred to have the entire post-edge "flattened" in mu(E) space so that the background curvature is eliminated from the dataset. Ultimately, as Matt stated, it would be nice to be able to combine a Victoreen and CLNorm background to get a reasonably "flattened" mu(E) function. I would also suggest adding the ability to independently set the pre-edge and post-edge functions (n'th order polynomial, Victoreen, CLNorm, or MBACK??) for Normalization and Flattening. These choices would be separate from the choice of background removal method to get chi(k) (Autobk or CLNorm). Dave > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov > [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf > Of Bruce Ravel > Sent: Thursday, September 29, 2005 5:20 PM > To: XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] New Method for Normalization? > > > On Thursday 29 September 2005 15:48, Barton, David (DG) wrote: > > Has anyone considered using the methods of Penner-Hahn to normalize > > their data to get reliable intensities of near-edge features? The > > reference to their method of normalization is below: > > > > J. Synchrotron Rad. (2005). 12, 506-510 > [doi:10.1107/S0909049504034193] > > "A method for normalization of X-ray absorption spectra" > T.-C. Weng, > > G. S. Waldo and J. E. Penner-Hahn > > > > It is my understanding the Ifeffit uses a linear function to remove > > the pre-edge and a quadratic for the post-edge and that the > Athena's > > flatten is a subtraction of these functions. This is an excellent > > method under most scenarios since the background is usually fairly > > smooth and can be well approximated by a quadratic equation. > > Personally, I have had only a few rare cases where the quadratic > > function on the post-edge was not sufficient to reliably > normalize the > > data and in those cases a third-order polynomial was > sufficient. Does > > anyone else have an opinion on using alternative normalization > > routines? > > Isn't Ifeffit's Cromer-Liberman normalization scheme > substantially similar to the method presented in that paper? > > B > > > -- > Bruce Ravel ---------------------------------------------- > bravel(a)anl.gov > > Molecular Environmental Science Group, Building 203, Room > E-165 MRCAT, Sector 10, Advance 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/ > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

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RE: [Ifeffit] R-factor and reduced chi square
by Kelly, Shelly D. 04 Oct '05

04 Oct '05

Hi Owen, A test for a significant change in the reduced chi square (RCS). [(RCS1)^2/(RCS2)^2] - 1 greater than 2 * sqrt ( 2 / degrees of freedom) If you can not read that, I have this published in J. Phys Chem B, V105 no27 year (2001). You can down load that paper from my web page www.mesg.anl.gov. I guess it is a reasonable test:). For most model fits a change by a factor of 2 is needed to be statistically significant. Good luck Shelly Shelly Kelly Bldg 203 RM E113 Skelly(a)anl.gov Argonne National Laboratory 630-252-7376 9700 S Cass Ave www.mesg.anl.gov Argonne, IL 60440 > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit- > bounces(a)millenia.cars.aps.anl.gov] On Behalf Of OWEN N LI > Sent: Tuesday, October 04, 2005 1:08 PM > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] R-factor and reduced chi square > > Hi, > I understand R-factor and reduced chi square are statistical ways to > see if the model is reasonable (R-factor) and if one model is better > than the others (reduced chi square). But how much should I read into it? > > I have model A and B, I believe A is more theoretical sound than B. > but when I fit them using IFEFFIT, the R-factor and reduced chi square > of B is slightly better than A (B: 0.03, 28; A: 0.04, 33). What does > that tell me? Is my assumption incorrect? Or are they more or less the > same? > > Owen > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Muffin tin radius adjustment?
by Paul Fons 04 Oct '05

04 Oct '05

I am trying to analyze some XAFS data on a Sb-Te compound and when I run feff(6) I get errors regarding the coordination number being too small implying the muffin tin radius is too big. In this material the first nearest neighbor bond length is about 3 angstroms (slightly more or less depending on the site). I assume this is related to the cause of the problem. Any suggestions as to how to fix/avoid this sort of problem? feff6 output is pasted below. Interestingly enough, feff8 does not output any error messages and the sum of the paths looks identical (at least at first glance). Is this a false error message or (more likely) has feff8 become more intelligent with regards to defining the muffin tin radius? Feff6 output Calculating potentials and phases... free atom potential and density for atom type 0 free atom potential and density for atom type 1 free atom potential and density for atom type 2 overlapped potential and density for unique potential 0 overlapped potential and density for unique potential 1 overlapped potential and density for unique potential 2 muffin tin radii and interstitial parameters phase shifts for unique potential 0 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. phase shifts for unique potential 1 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. phase shifts for unique potential 2 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. Preparing plane wave scattering amplitudes... nncrit in prcrit 9 Searching for paths... WARNING in PATHS Module: rmax > distance to most distant atom. Some paths may be missing. rmax, ratx 15.50000 15.40291 Rmax 15.5000 keep and heap limits 0.0000000 0.0000000 Preparing neighbor table Feff8 output Calculating potentials ... free atom potential and density for atom type 0 free atom potential and density for atom type 1 free atom potential and density for atom type 2 initial state energy overlapped potential and density for unique potential 0 overlapped potential and density for unique potential 1 overlapped potential and density for unique potential 2 muffin tin radii and interstitial parameters iph, rnrm(iph)*bohr, rmt(iph)*bohr, folp(iph) 0 1.79879E+00 1.71274E+00 1.13279E+00 1 1.81342E+00 1.72495E+00 1.13595E+00 2 1.83703E+00 1.74437E+00 1.14149E+00 mu_old= -0.508 Done with module 1: potentials. Calculating LDOS ... LDOS calculation for specified grid Calculating energy and space dependent l-DOS. It takes time ... potential type 0 potential type 1 potential type 2 Calculating chi and rho... 0 Calculating chi and rho... 1 Calculating chi and rho... 2 Done with LDOS. Calculating cross-section and phases... absorption cross section phase shifts for unique potential 0 phase shifts for unique potential 1 phase shifts for unique potential 2 Done with module 2: cross-section and phases... Done with module 3: FMS. Preparing plane wave scattering amplitudes... Searching for paths... WARNING: rmax > distance to most distant atom. Some paths may be missing. rmax, ratx 1.55000E+01 0.00000E+00 Rmax 15.5000 keep and heap limits 0.0000000 0.0000000 Preparing neighbor table Dr. Paul Fons Senior Researcher National Institute for Advanced Industrial Science & Technology METI Center for Applied Near-Field Optics Research (CANFOR) AIST Central 4, Higashi 1-1-1 Tsukuba, Ibaraki JAPAN 305-8568 tel. +81-298-61-5636 fax. +81-298-61-2939 email: paul-fons(a)aist.go.jp The lines below are in a Japanese font 〒３０５−８５６８茨城県つくば市東１−１−1 つくば中央第４近接場光応用工学センターポール・フォンス主任研究官

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Runner.exe Network Error
by Barton, David (DG) 28 Sep '05

28 Sep '05

Bruce and Matt, I am running the Ifeffit 1.2.8 on a Win2000 box and I having several issues with the startup of Athena/Artemis when I am not connected to a network. First thing is that all programs run fine when I am connected to the internet. So the obvious workaround for me is to just make sure that I have an open network connection before running Athena/Artemis. However, it would be nice if the auto-update feature in "Runner.exe" would still let me run Athena/Artemis when I wasn't connected to the network, basically just ignore looking for an update when I don't have a network connection. The errors that I get in the Runner.exe.log are below. There are two different cases shown. The first set of errors are when I have a connection to my local network, but have not yet logged onto the firewall that lets me out onto the internet. The second set of errors comes up when I unplug the network connection completely. Hope these help. NETWORK CONNECTION NO INTERNET CONNECTION ----------------------------------------- Traceback (most recent call last): File "runner.py", line 753, in ? File "runner.py", line 184, in __init__ File "runner.py", line 275, in LookForUpdates File "runner.py", line 299, in read_web_version File "urllib.pyc", line 76, in urlopen File "urllib.pyc", line 181, in open File "urllib.pyc", line 306, in open_http File "urllib.pyc", line 319, in http_error File "urllib.pyc", line 565, in http_error_302 File "urllib.pyc", line 580, in redirect_internal File "urllib.pyc", line 181, in open File "urllib.pyc", line 306, in open_http File "urllib.pyc", line 319, in http_error File "urllib.pyc", line 616, in http_error_401 File "urllib.pyc", line 624, in retry_http_basic_auth File "urllib.pyc", line 650, in get_user_passwd File "urllib.pyc", line 658, in prompt_user_passwd NO NETWORK CONNECTION -------------------------------------- File "runner.py", line 753, in ? File "runner.py", line 184, in __init__ File "runner.py", line 275, in LookForUpdates File "runner.py", line 302, in read_web_version Dave _________________________________ David Barton The Dow Chemical Company

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getting chi(r) information out of command line IFEFFIT
by Sean X. Luo 28 Sep '05

28 Sep '05

Hello all. It's been a while since I've written on the mailing list about this project, but it's come up that I need everyone's general input. Just a brief overview of the project: I am working with Scott Calvin to simultaneously fit 12 data sets in the command line of IFEFFIT, and I need to somehow get the chi(r) information for the fit out of the command line. I've tried around with the "show" command and the different permutations possible with that, but whenever I type in "show(fit.r, fit.chir_real)" (which is our guess right now on how to get the information I need out of the command line), it gives me the error that the arrays fit.r and fit.chir_real does not exist, or something along those lines. Does anyone else have any idea on how to run this? Thanks in advance, - Sean.

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RE: [Ifeffit] Fe oxide
by Kelly, Shelly D. 26 Sep '05

26 Sep '05

Hi Juro, I had some fun playing with this project file. I hope you don't mind. Here is a list of suggestions. 1st: Don't use the paths that are less than 0.1 Angstroms apart. 1st-b: If you don't know the CN set it to ONE and then vary just the amplitude. There is a degen box multiplied by a amp box. Degen should be one. 2st: set the values for CN, and s2, while letting delr vary 3rd. Let the CN and delr vary. You will find that the Fe path around 3 Ansgroms isn't needed. 4th. Make sure your fit range and data ranges are appropriate. 5th. Add as much constraints as you think is reasonable. First Oxygen coordination number should be 6 or 4 total. I thought 6 worked well. 6th. Fit the data with k-weight of 1,2, and 3, to get the uncertainties smaller. Take a look at the project file. I think that this model or one like it might work. You need a separate S02 value from the Amp value. Amp should be S02*Amp. I didn't add a S02 part. You should get that from a known standard measured on the same beamline. S02 should be between 0.70 and 1.0. So the CN reported are likely a bit too big. Good luck, Shelly Shelly Kelly Bldg 203 RM E113 Skelly(a)anl.gov Argonne National Laboratory 630-252-7376 9700 S Cass Ave www.mesg.anl.gov Argonne, IL 60440 > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit- > bounces(a)millenia.cars.aps.anl.gov] On Behalf Of Juraj Majzlan > Sent: Monday, September 26, 2005 8:46 AM > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Fe oxide > > Hello, > > I am trying to fit an EXAFS spectrum of an X-ray amorphous > Fe precipitate. In a model (goethite), there are Fe atoms > at 3.02, 3.29, and 3.45 A. Fitting the two most distant > shells of iron gives strange results. Fitting them > simultaneously gives very high amplitudes (32, -66) which > cancel each other (fig. 1) and produce a beautiful and > unreasonable fit (fig. 2). > > Fitting them separate gives small ('reasonable') > amplitudes, but the distance (dr) have very high > uncertainties, e.g., dr = 0.12 +- 20.3. > > Can I expect to resolve these three Fe shells or is it > asking too much? > > I am also attaching the Artemis file, but will appreciate > any comments and suggestions. > > Juro Majzlan > > > ---------------------------------- > Juraj Majzlan > Institute of Mineralogy and Petrology > Albert-Ludwig-University of Freiburg > Albertstrasse 23b > Freiburg, D-79104, Germany > telephone +49-761-203-6416 > fax +49-761-203-6407 > http://www.minpet.uni-freiburg.de/sites/personen/majzlan.html

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Fe oxide
by Juraj Majzlan 26 Sep '05

26 Sep '05

Hello, I am trying to fit an EXAFS spectrum of an X-ray amorphous Fe precipitate. In a model (goethite), there are Fe atoms at 3.02, 3.29, and 3.45 A. Fitting the two most distant shells of iron gives strange results. Fitting them simultaneously gives very high amplitudes (32, -66) which cancel each other (fig. 1) and produce a beautiful and unreasonable fit (fig. 2). Fitting them separate gives small ('reasonable') amplitudes, but the distance (dr) have very high uncertainties, e.g., dr = 0.12 +- 20.3. Can I expect to resolve these three Fe shells or is it asking too much? I am also attaching the Artemis file, but will appreciate any comments and suggestions. Juro Majzlan ---------------------------------- Juraj Majzlan Institute of Mineralogy and Petrology Albert-Ludwig-University of Freiburg Albertstrasse 23b Freiburg, D-79104, Germany telephone +49-761-203-6416 fax +49-761-203-6407 http://www.minpet.uni-freiburg.de/sites/personen/majzlan.html

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problems on running the windows 1.2.8 ifeffit version
by M Ceolin 23 Sep '05

23 Sep '05

Dear Bruce et al. I just installed the new 1.2.8 for windows version of ifeffit and I am experiencing problems to run any of the programs associated (arthemis, athena, etc.). I installed the programs in a Win98 machine where the previous versions of IFEFFIT were running. I took care of adding the suggested line to the config.sys file and installed the program in c:\ifeffit (as suggested). However, both, starting from the icons in the desktop, from the applications installed at c:\ifeffit\bin or from the menu at the start, the runner program (installed with the pakage) send an error message forcing to abort the run. The message says: (sorry, in spanish) Este programa ha efectuado una operacion no admitida y sera interrumpido (in the datails window says) RUNNER provoco un error de pagina no valida en el modulo MSVCRT.DLL de 017f:7801274b. etc. (registry numbers). Could you comment the point and, perhaps, suggest a solution ?. Yours. Marcelo Ceolin. *************************************** Dr. Marcelo Ceolin Centro Regional de Estudios Genomicos UNLP-AUGM Av. Calchaqui km 23,5 (4to piso) (1888) Florencio Varela Argentina Tel/Fax: +54-11-42758100 e-mail 1: mceolin(a)creg.org.ar e:mail 2: mrceolin(a)yahoo.com.ar WEB: www.creg.org.ar *************************************** PLEASE NOTE THAT THE E-MAIL ADDESSS mceolin(a)gwdg.de IS NO LONGER AVAILABLE. USE ONE OF THE ADDRESSES ABOVE. --------------------------------- 1GB gratis, Antivirus y Antispam Correo Yahoo!, el mejor correo web del mundo Abrí tu cuenta aquí

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RE: [Ifeffit] writing beam time proposals
by Frenkel, Anatoly 23 Sep '05

23 Sep '05

I rate proposals on the merit but it a former XAFS school student is a research group member it makes me happier. Anatoly -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov on behalf of Matt Newville Sent: Fri 9/23/2005 12:06 PM To: Carlo Segre; XAFS Analysis using Ifeffit Cc: Subject: Re: [Ifeffit] writing beam time proposals In my opinion, it is better for the student or post-doc to write the beamtime proposal and be listed as PI, with the advisor listed somewhere on the proposal Many proposal foms have a checkbox for 'is this work part of a thesis', and that is definitely monitored (at least at the APS, but I'd imagine it to be true at other facilities), even if it is not formalized. There is usually an eagerness for bringing new students (and new post-docs and new faculty members) to the syncrotrons. Also, in my experience reading beamtime proposals now and then, students and post-docs do a better job at writing them <wink>. Even f the professor is listed first (and many groups do this!), I would suggest that the student/post-doc actually write the proposal and have the advisor look it over before submitting. Other advice for writing proposals: - communicate with the beamline scientist to make sure the work is feasible and appropriate. - write it to convince someone in a *different field* why the experiment is important. - include references to previous work to show that you know the field. --Matt _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Tip of the Week: Constraining parameters between data groups in Athena
by Bruce Ravel 23 Sep '05

23 Sep '05

Hi, This week's tip of the week is "Constraining parameters between data groups in Athena": http://cars9.uchicago.edu/iffwiki/HoraeTipOfTheWeek?action=show B -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advance 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] Ifeffit 1.2.8
by Matt Newville 20 Sep '05

20 Sep '05

Hi Stefano, If you have Ifeffit 1.2.7 working on Tiger, I'd suggest just doing horae_update. The changes to the Ifeffit library are very small, so you could just wait until an installer for Mac OS X 10.4 is available. If you really want to be using 1.2.8, you could try installing from source. --Matt On 9/18/05, Stefano Ciurli <stefano.ciurli(a)unibo.it> wrote: > Hi Matt, > > >Ifeffit 1.2.8 is now available. There are minor changes to the core > >library and new versions of horae (055: athena 0.8.043, and artemis > >0.8.002) in the Windows and Mac installers. A few version notes are below, > >and I will be putting more information at > >http://cars9.uchicago.edu/iffwiki/ReleaseNotes128/ > > Thanks a lot! I am running OSX Tiger on a G4 and I am currently > working with Athena 0.8.039 and Artemis 0.7.015 > > What should I do ot update my environment to Ifeffit 1.2.8? > Thanks > 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". > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > >

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RE: [Ifeffit] Fit in R and k space
by Frenkel, Anatoly 20 Sep '05

20 Sep '05

I personally like this argument in favor of r-space fitting over k-space fitting. I am pretty sure it was made by Ed Stern: R-space allows to think of EXAFS in terms of radial distribution of atomic positions relative to the central atom. Peaks in r-space usually correspond to atomic positions and the regions between the peaks - to the interstitial regions in the structure (of course, there are 1000 counter-examples, but we are talking about some 'average, well behaving' system where a peak is NOT an atomic AXAFS, nor it is caused by a Ramsauer-Townsend resonance, etc., and a valley is NOT a destructive interference between neighboring shells' - AF). We know, on another hand, that FEFF approximation electron charge density as spherical and the potential as muffin tin. This approximation is not as accurate in the interstitial region between the atoms (where potential profile in real systems may be anything but flat) as it is near the atoms. Thus, intuitively, FEFF should do better job fitting 'peaks' in r-space rather than fitting the interstitial. However, the r-factor and chi square do not really care. Technically, if two models give similar r-factors and chi-square, the one that has better fit in the peak region, the other - in the interstitial, one will examine the r-space fit and choose the one that fits peaks better over the one that fits interstititial region better. However, this information, localized in r-space, is distributed in k-space. Thus, if you look at the graph where data and fit are shown together, either in raw unfiltered k-space or in q-space, the misfit is difficult to interpret. It is, however, possible to interpret the misfit in r-space, and that what often helps to refine the model or choose the better one. Anatoly Anatoly Frenkel Department of Physics Yeshiva University -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov]On Behalf Of Michel Schlegel Sent: Tuesday, September 20, 2005 9:07 AM To: Ravel, Bruce; XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Fit in R and k space Hello Bruce, >Although I prefer to think about the EXAFS problem in R space, I don't think >this is the reason to do the fit in R space. Regardless of which fitting >space you use, you are relying on Feff to supply some fraction of all the >Fourier components in the data. We could also used reference-derived phase and amplitude function, as in the good ol'time ;) > The first-shell feff path only has Fourier >components (or frequencies, if you prefer) corresponding to the first-shell >portion of chi(R). Thus that feff path can only fit those frequencies. >That's true in k-space as well as in R-space True in R-space, and that's why Athena-Ifeffit are doing such a wonderful job at providing windows to fit only selected area of the fourier transform. Almost true also in q-space. In k-space... hmmm, well, I would love to see the mathematical demonstration of it for a limited k-range and a Feff(k) (eventhoug I agree that many people have performed tha fit in k- and R-spaces, and found about the same paramters, so it must be verified somehow). >What's more, I think the problem of non-modelled shells affecting the >modelled >portion of the data exists in R-space just as much as in k-space. Because of >sigma^2 and the finite data range, peaks have width. In R-space, a given >path is centered at a particular R-value (or, in other words, its >contribution to the spectrum is dominated by a particular frequency). >However, the peak has width (it contains frequencies below and above the >dominant frequency). Thus longer paths always interfere with shorter paths >to some extent. I think the effect of interfering contributions in the Konigsberger and Prins. What I noticed, though, is that the fit of closer shells can affect that of the furthest shell because of the "spillof" from the first peak. The recciprocal I was not aware of. But I do agree with you on the whole. However, I think that in the FT case, these interences are limited to the nearest shells, whereas in k-space, nothing protects you from shells at, say, 2R and 3R (so to speak. Best regards, Michel -- Michel Schlegel Commissariat à l'énergie atomique CEN de Saclay, DEN/DANS/DPC/SCP/LRSI Bat 391 - Piece 205B F91 191 Gif-sur-Yvette Cedex, France Ph: +33 (0)1 69 08 93 84 Fax: +33 (0)1 69 08 54 11 _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Re: [Ifeffit] Ifeffit installer for Mac 10.4 (Tiger)
by Matt Newville 20 Sep '05

20 Sep '05

Hi Stefano, If you've already done 'sudo horae_update' (and thanks for the correction!!) and have the latest versions of Athena and Artemis installed, I would say that you don't need to use the binary installer. The changes in the binary installer are tiny. --Matt

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Ifeffit installer for Mac 10.4 (Tiger)
by Matt Newville 20 Sep '05

20 Sep '05

Hi Everyone, Paul Fons has generously made a binary package installer for Ifeffit 1.2.8 for Mac 10.4 (Tiger). This is now available from both cars.uchicago.edu and sourceforge.net, from the Ifeffit download page: http://cars9.uchicago.edu/ifeffit/download.html If you try this out, please send positive and/or negative reports to me. Thanks again Paul!! --Matt

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RE: [Ifeffit] R-factor
by Scott Calvin 20 Sep '05

20 Sep '05

Hi Alison, I agree entirely with Victor and Anatoly. In addition, I'd say that in my work an R-factor of above 0.1 is pretty sketchy. How sketchy depends on the complexity of the fit, of course; you're going over a big r-range, so if it takes you only two or three parameters to get an R-factor of 0.11, I guess that's not too bad. But if you have more parameters than that and it's still not fitting so well, I'd be concerned. As a referee, for example, that would be a much larger warning flag to me than the little discrepancy between the R-factors for the k- and q-space fits. Just to echo Victor and Anatoly again: it's quite easy for me to believe that the fitting algorithm just happened to find a somewhat different minimum in the fitting space in the two cases. They both suggested ways to test if that is the case. Although I've never fit in q-space, I've seen something that on the face of it is equally baffling: sometimes I've added an additional fitting parameter, changing nothing else, and seen the R-factor <italic>increase </italic>slightly. In some ideal sense, that shouldn't be--the fitting routine (this one happened to be Ifeffit) "should" at worst get the identical fit as to when the new parameter was constrained. But it is impossible to write a fitting routine that is guaranteed to find the closest possible fit, so all routines will occasionally generate those kinds of results. --Scott Calvin Sarah Lawrence College >-------------- Original message -------------- > >> Bruce, >> >> I've looked, and my R-factors for the back-transformed >> space are not necessarily twice the value of the R-factors >> for the k-space fits. In fact, they are often quite >> close. For example, just recently I had a k-space >> R-factor of 0.102 and a q-space R-factor of 0.113. Now, I >> realize those numbers are very close, but I'm afraid if I >> try to publish this, then I will get criticism for the >> q-space R-factors being larger. If I can explain it, then >> maybe it won't be a problem. >

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RE: [Ifeffit] Fit in R and k space
by Kelly, Shelly D. 20 Sep '05

20 Sep '05

Hi Michel, Michel wrote: Finally, another issue - for which I would not lay out my neck, though - is the noise. In EXAFS, the signal to noise increases with k, and of course fitting in the raw k space is another way of dealing conveniently with the noise -or relative uncertainty, as we may name it. However, the FT is a way of filtering out some of this noise, and so maximise the signal from a shell. Likewise, fitting in filtered q-space may yield more accurate results, because some of the noise is filtered out. However, I concur that somehow the fact that the uncertainty on the high-q part of the filtered contribution os greater than in the low q-part should be implemented somehow. It is true that the signal to noise ratio becomes smaller at high k values. It does seem magical that the Fourier transform can pull a signal out of the high k-range where the noise is large and that this signal seems to be well defined. I find it helpful to remember that each signal in the EXAFS chi(k) spectra is given by ONE frequency. That frequency is well defined at low k were the signal to noise ratio is large. Extending this frequency into the high k-region is trivial as long as that frequency co-exists with all the noise at high k. In fact I don't need data at all to extend a well defined frequency to infinity. The part of the signal that is not so well defined at high k is the amplitude. A lot of noise often masks itself by a large variation in amplitude for a given signal at high k, this effect will result in poor values for CN and 2. But the amplitude of the signal has a well known k-dependence so with enough low k information about the amplitude even the amplitude does not become affected by the noise at high k. The point to remember is that the signals are defined from k=0 to k=something bigger than zero. As long as the signal to noise ratio is reasonable from k=0 to some k~10? Then the signal including frequency and amplitude is well described all the way to k=infinity. It is often helpful to look at the fit and the data in k-space all the way out to 16 1/angstroms even if you are only using the k-range to 12 1/angstroms. If the model continues to follow the data to 16 then it is a good model. Shelly Shelly Kelly Bldg 203 RM E113 Skelly(a)anl.gov Argonne National Laboratory 630-252-7376 9700 S Cass Ave www.mesg.anl.gov Argonne, IL 60440

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Ifeffit 1.2.8 installer for WinXP
by Leandro Langie Araujo 19 Sep '05

19 Sep '05

Greetings everybody, I'm another newcomer to the EXAFS world whose life was made much easier thanks to this wonderful software package. My sincere thanks to Matt, Bruce and everyone else involved in the "Ifeffit family" project. But, although the software is very nice, I'm having some trouble installing the newest version (1.2.8). I've been trying to install the Ifeffit 1.2.8 package on my WinXP, but there seems to be a problem with the files. I've downloaded the installers from both sourceforge and cars.uchicago.edu, but whenever I try to run any of them I get the following message: "The setup files are corrupted. Please obtain a new copy of the program." So, I'd like to ask if anyone from the mailing list managed to install Ifeffit 1.2.8 on WinXP or if anyone got the same kind of error message when trying to install. Thanks, Leandro

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Ifeffit 1.2.8
by Matt Newville 18 Sep '05

18 Sep '05

Hi Folks, Ifeffit 1.2.8 is now available. There are minor changes to the core library and new versions of horae (055: athena 0.8.043, and artemis 0.8.002) in the Windows and Mac installers. A few version notes are below, and I will be putting more information at http://cars9.uchicago.edu/iffwiki/ReleaseNotes128/ == Windows == For Windows, there is a new installer, but no update. The new installer has the latest versions of the programs and also has dramatic changes to how the programs are organized and run. The batch files and the old automatic updater are gone, replaced by a single program 'runner' that checks for updates and runs all of the applications. There is also a completely new layout of C:\Program Files\Ifeffit. Bruce and I have been working on this for a while, and we believe it will be a lot easier for us to maintain. We expect that the changes will be mostly invisible to users, except when you install it. A result of the new layout is that *** *** *** you must uninstall any previous version of *** *** Ifeffit before installing the new version. *** *** *** Really, we're not kidding. There is a potential problem with this, as you may have your own projects under C:\Program Files\Ifeffit, say in \horae\ or in \examples\. You probably don't want to delete these!!! We recommend that you either move C:\Program Files\Ifeffit\horae and any other folders you may have file in to somewhere safe *before* you remove Ifeffit, or simply rename C:\Program Files\Ifeffit to Ifeffit_OLD and leave it there for a few weeks. And of course, we recommend that you save your data somewhere outside of C:\Program Files and make regular backups ("Gee, thanks, Mom!"). Then use the Control Panel 'add/remove programs' to remove Ifeffit. This will try to delete everything that originally got installed (and so *should* leave your data, but I wouldn't bet on it!!), including the shortcuts in the Start Menu. Once the C:\Program Files\Ifeffit folder is gone or cleaned out, you can then safely install the new Windows installer. The older Windows version (1.2.7) will see one more update, which will simply remind you to install the new version of the full installer. All further updates will be available only to the new version. == Mac OS X == For Mac OS X (10.3), the binary installer includes the codes from horae-055. The previous attempt to support Aquaterm is now dropped -- plotting is done with the X Windows plotting terminal. Since Athena/Artemis require X, and since X11 now comes from Apple, the Aquaterm support was more trouble than it was worth. == Unix == For Linux/Unix users using the source kit, the 'where is termcap?' problems should be gone. In addition, building on 64-bit linux machines should be much easier. PGPLOT_install now has a '--with-64bit' option which is needed for 64bit linux. Ifeffit's normal './configure' should then work fine. It now warns if the termcap library cannot be found. Let us know if there are any questions or troubles with these new versions. --Matt

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Athena Bug in Peak Fitting
by Barton, David (DG) 16 Sep '05

16 Sep '05

Bruce, FYI: I recently installed Ifeffit v1.2.8 using the new Windows installer and it worked perfectly on a couple Win XP machines. After using the latest version of Athena 0.8.043 I noticed a bug in the Peak Fitting Routine and also have a couple of other minor suggestions. Description of Peak Fitting Bug: --The centroids that are reported on the screen and in the results file are not updating after a peak-fit is done. When the checkbox is marked to fit the centroid the fit appears to be changing the centroid because the resulting plot looks like a better fit, however the value of the centroid on the screen is not updating and the results file does not reflect any changes in centroid. Then if you push the "Plot Lineshapes" button it uses the centroid on the screen and the fit changes dramatically using the original value of the centroid. This bug can be reproduced by pulling up any spectra, setting the centroid of the arctan to something that results in a poor initial fit, check the box to fit centroid, run the fit....you should see that the fit moves the centroid however the value on the screen does not update and then if you "Plot Lineshapes" you will see the fit change to value of the original centroid. Other Suggestions for minor improvements to Athena: --In Compute Difference window it would be nice to have a checkbox that allows the user invert the difference (do spectra-ref instead of ref-spectra). This would be helpful for doing the difference of Marked spectra where we would like to do the spectra-ref. --in Compute Difference window it would be nice to have a checkbox to plot the components of the difference along with difference (similar to LCF window). Helpful for diagnostic checks of difference. --in your new Plot Style functionality it would be nice if Athena would automatically replot the last plot choice after a new Plot Style is chosen. This would save a few clicks as I click back and forth between two different plot ranges. --the link to the Plot Style POD documentation is broken. Let me know if you need any further clarification. Dave _________________________________ David Barton The Dow Chemical Company Catalysis R&D 1776 Building Midland, MI 48674 USA _________________________________ David Barton, PhD. The Dow Chemical Company Catalysis R&D 1776 Building Midland, MI 48674 USA

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Tip of the Week: Features of the Guess, Def, Set page in Artemis
by Bruce Ravel 16 Sep '05

16 Sep '05

Hi, This week's tip of the week is "Features of the Guess, Def, Set page in Artemis" http://cars9.uchicago.edu/iffwiki/HoraeTipOfTheWeek Enjoy, B -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advance 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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compiling Ifeffit and friends on a 64 bit linux machine
by Bruce Ravel 15 Sep '05

15 Sep '05

Hi, Some months ago -- see the thread that starts here: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2004-December/001550.html Jake from U. Calgary posted a message about trouble getting Ifeffit et al to compile on his 64 bit machine. Over the last few days I have been upgrading to SUSE 9.3 on my home computer, which has an Intel 64 bit processor. (2 of them actually, lucky me!) 9.3 is much better for a 64 bit machine than 9.2 was. (It's also the first OpenSUSE release, which is a development I am very happy about.) Initially I ran into the exact same problem that Jake described in his original post. At the time, Carlo suggested that the -fPIC flag ("Position Independent Code", whatever that is) would be important. That turned out to be the trick. When installing Ifeffit, it was necessary to do the configure step like this: ./configure CC="cc -fPIC" FFLAGS="-g -O2 -fPIC" After that, the rest of installing Ifeffit and all of installing the horae tarball proceded normally. BUT, there is one other caveat. I had to make a small change to the pgplot makefile to get it compiled for my 64 bit machine. Everyplace in the makefile where it said "/usr/X11R6/lib", I had to change that to "/usr/X11R6/lib64". Compiling pgplot requires a bit of voodoo. I have always relied on Matt's PGPLOT_install script, which comes with the ifeffit tarball. In this case, I ran the script. It did some stuff, the failed. I cd-ed to /usr/local/pgplot, which is where it gets installed, and edited the makefile in that directory as I indicated in the last paragraph. Then in that directory I did a "make" and the pgplot compilation went to completion. Of course, I had to be root run the PGPLOT_install script and to do the compilation in /usr/local/pgplot. Hope that helps! (I'd be interested to hear how it goes with your opteron, should you try this, Carlo.) Bruce -- Bruce Ravel ----------------------------------- bravel(a)anl.gov -or- ravel(a)phys.washington.edu Environmental Research Division, Building 203, Room E-165 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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Bug report for Artemis 0.8.000
by schmithals＠hmi.de 12 Sep '05

12 Sep '05

Hello Bruce, After a break I just started to use Artemis again and I am delighted about the new features, especially the ability to store and compare subsequent fits in one file. Below I want to submit the bugs that I came accross so far (on Win2000): - If one opens by mistake an input file that is unknown to Artemis (or Athena) this file will be destroyed and cut to about 4kB. Workaround: Just DON'T do this (or keep regular backups). - Funny things happen when one studies an atoms/feff calculation without having loaded an experiment file: I imported an atoms.inp, ran atoms and feff and did two summations (Sum | All included paths ..). For the first summation I included only the first path, for the second summation only the second path. The first summation seems fine, for the second summation Artemis obviously includes both paths. In subsequent summations this effect will continue: all paths used in the past are considered plus the paths currently included. Workaround: Load a 'dummy'-chi file even for just making summations. I was teaching the use of Artemis to a few colleagues. I recommend them to keep a copy of their atoms.inp-files at a separate place for re-use in later projects. If time permits maybe you could account for these issues: - If saving an atoms.inp file via Theory | Write special output | atoms the name 'artemis.stuff' will be provided. Is it possible to change that to 'atoms.inp'? - The link to TKAtoms is missing for newly installed systems. Cheers, Gerrit Schmithals

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new tip of the week
by Bruce Ravel 09 Sep '05

09 Sep '05

Hi! I just posted this week's Tip of the Week at http://cars9.uchicago.edu/iffwiki/HoraeTipOfTheWeek This weeks topic: Easily marking arbitrary groups in Athena Enjoy, B -- Bruce Ravel ----------------------------------- bravel(a)anl.gov -or- ravel(a)phys.washington.edu Environmental Research Division, Building 203, Room E-165 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] Re: ifeffit installation on Linux
by Matt Newville 09 Sep '05

09 Sep '05

Hi Peter, > Here's the output: > > src/cmdline/Makefile:TERMCAP_LIB = -ltermcap > src/cmdline/Makefile:# readline_LIB = -L$(top_srcdir)/readline > -lreadline $(TERMCAP_LIB) > src/cmdline/Makefile:readline_LIB = > $(top_srcdir)/readline/libreadline.a $(TERMCAP_LIB) > readline/Makefile:TERMCAP_LIB = -ltermcap > readline/Makefile: $(CC) $(CCFLAGS) -o $@ ./examples/rl.c > ../libreadline.a ${TERMCAP_LIB} > # locate termcap: > /usr/lib/libtermcap.so.2 > /usr/lib/libtermcap.so.2.0.8 > /usr/lib/termcap/libtermcap.a > /usr/lib/termcap/libtermcap.so > # locate curses: > /usr/lib/curses/libcurses.a > /usr/lib/curses/libcurses.so > /usr/lib/libcurses.so.1 > /usr/lib/libcurses.so.1.0.0 > Thanks for the report. That looks like the change to configure did what it was supposed to do: instead of having './lib/termcap/libtermcap.a', it now has '-ltermcap'. The odd things to me are that a) libtermcap.a seems to be in an odd location (/usr/lib/termcap), which makes me wonder how any readline applications work. b) you still end up with a './lib/termcap/libtermcap.a' somewhere in your Makefile, but *not* as TERMCAP_LIB=./lib/termcap/libtermcap.a I have no idea where that would be coming from. I don't think that an extra '-L./lib/termcap' is causing a problem (it's ok to have '-L' arguments that point nowhere) but that the linking can't find the right libtermcap.a with '-ltermcap' alone. If the Makefiles said TERMCAP_LIB= '-L/usr/lib/termcap -ltermcap' that would work for sure. I've been relying on a 'BASH_CHECK_LIB_TERMCAP' macro in autoconf, which apparantly doesn't know to look in /usr/lib/termcap. At this point, it may be easier to just write a function to look for the right termcap library. I think readline can use termcap, curses, or ncurses, and to be honest, I find the differences confusing. Anyway, thanks for the help! --Matt

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ifeffit installation on Linux
by marco antoni alsina corvalan 08 Sep '05

08 Sep '05

Hi everyone, I'm currently making my way into Linux, so I decided to change most of my programs to this plattform, which obviously include ifeffit ;) I downloaded the ".tar" file, ran with success the PGPlot script for the graphics library installation (at least the demos run!!), and executed the "configure" script, getting the message "ready for the next step"...however I also get the following info: .... checking termcap.h usability... no checking termcap.h presence... no checking for termcap.h... no .... checking for tgetent... no checking for tgetent in -ltermcap... no .... Anyway then I executed the "run" command, getting the following error: .... cc: ./lib/termcap/libtermcap.a: No such file or directory make[3]: *** [ifeffit] Error 1 make[3]: Leaving directory `/home/user/Programas/ifeffit-1.2.7/src/cmdline' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/user/Programas/ifeffit-1.2.7/src' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/user/Programas/ifeffit-1.2.7' make: *** [all-recursive-am] Error 2 If anyone can help me overcoming this impasse I would be very greatful. Also if you need more info please let me know Regards, Marco ______________ Marco A. Alsina Estudiante de Magíster Departamento de Ingeniería Hidráulica y Ambiental Pontificia Universidad Católica de Chile Vicuña Mackenna 4860, Santiago, Chile (56 2) 3544873

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Questions and answers
by Bruce Ravel 06 Sep '05

06 Sep '05

Good morning, Every week I receive a large amount of email regarding my software and XAS in general. I am sure that's no surprise to anyone reading this. While I certainly want to encourage people to feel free to contact me about XAS, the software, and any other topic, the time I have to address the needs and concerns of all the people contacting me is limited. In recent weeks I have received an unusual number of emails containing vague, ill-posed questions or requests for inordinate amounts of help. The other day I was frustrated by one such correspondent, so today I am indulging myself by ranting in a public forum ;-) Consider this message that I received the other day: > I have a sample with lead adsorbed onto manganese oxide and I have > its EXAFS. I want to study the Pb-Mn shell (including r(Pb-Mn) and > the number of Mn atom around Pb atom). How should I proceed? > > Awaiting your reply. Contrast that with an email I received from a user who had some questions along with a bug report regarding how e0 is determined by Athena: > I'm attaching an Athena project with a sample labeled Libethenite > and a Cu standard, along with an step by step explanation included > in the project journal. I trust the difference between these two is clear. I do not know either of these individuals except by their emails. Both are from places far away from Chicago. The first received a 5-line response while I spent two hours on a plane flight two weeks ago addressing the second one. I encourage people to contact me at any time with any question about XAS or my software. Indeed, if Athena and Artemis are useful data analysis tools today it is only because of the kind and generous feedback I have received from its users. But if a genie were to grant me a wish, it would be that more folks were like the second correspondent than the first. Thanks, B -- Bruce Ravel ----------------------------------- bravel(a)anl.gov -or- ravel(a)phys.washington.edu Environmental Research Division, Building 203, Room E-165 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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RE: [Ifeffit] Ifeffit Wiki
by Barton, David (DG) 06 Sep '05

06 Sep '05

Bruce, >It makes me kind of sad to think that some of these neat-o features > are not widely used. If it makes you feel any better, I just used your linear combination module in Athena to fit 165 XANES spectra. Dave > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov > [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf > Of Bruce Ravel > Sent: Friday, September 02, 2005 4:10 PM > To: XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] Ifeffit Wiki > > > On Wednesday 31 August 2005 17:22, Matt Newville wrote: > > Hi Folks, > > > > I've created and started a wiki for Ifeffit and related topics. > > Currently, this is at > > http://cars9.uchicago.edu/iffwiki > > I, for one, think the new Wiki is quite cool. Yet another > thing that we have to thank Matt for. > > My first use of the Wiki is to start a "Tip of the Week" web > page. Athena and Artemis have become sufficiently robust and > feature-full that there are a lot of interesting aspects of > the codes that are not widely known about or used. It makes > me kind of sad to think that some of these neat-o features > are not widely used. To keep a smile on my face, I've > decided to use the wiki to highlight some cool tidbit every > Friday afternoon. The first one is up at > > http://cars9.uchicago.edu/iffwiki/HoraeTipOfTheWeek > > Check it out. Feel free to send me suggestions for features > of A&A that you think would make a good Tip of the Week. My > plan is more or less to alternate between Athena and Artemis > and occassionally to throw in a Hephaestus tip as well. > > B > > -- > Bruce Ravel ----------------------------------- bravel(a)anl.gov -or- > ravel(a)phys.washington.edu > Environmental Research Division, Building 203, Room E-165 > Argonne National Laboratory phone and voice mail: > (1) 630 252 5033 > Argonne IL 60439, USA fax: > (1) 630 252 9793 > > My homepage: http://feff.phys.washington.edu/~ravel > EXAFS software: > http://feff.phys.washington.edu/~ravel/software/exafs/ > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

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RE: [Ifeffit] Ifeffit Wiki
by Barton, David (DG) 06 Sep '05

06 Sep '05

Bruce, > So would it be useful to have some more automation in the LCF > utility. Automation is always appreciated, not required, but much appreciated. The data set that I was fitting was indeed the result of multiple fast scans performed during an in-situ catalysis experiment, similar to what Anatoly is planning for NSLS. My biggest challenge with the current Athena code. 0.8.041 in fitting many XANES spectra was not having a single report where all fitting results could be exported to. I would imagine if you automated the fitting routine you would produce some report that lists all fitting results including fitting statistics in a single file. In addition, in the current fitting utility there was a few wasted clicks and edits because the fitting range kept reverting back to -15 to 45 eV... My fitting range was different than the default and every time I choose another data set to fit the fitting range reverted back to the default which meant I had to choose each box and make the appropriate changes for each new data set. Regardless of these issues, the LCF module is fantastic. I truly appreciate the ease of use, the ability to view the fit along with components of the fit, and the ability to plot the residual. Thanks for another useful tool to make my life easier. Regards, Dave > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov > [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf > Of Bruce Ravel > Sent: Friday, September 02, 2005 6:02 PM > To: XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] Ifeffit Wiki > > > On Friday 02 September 2005 16:12, Barton, David (DG) wrote: > > >It makes me kind of sad to think that some of these neat-o > features > > >are not widely used. > > > > If it makes you feel any better, I just used your linear > combination > > module in Athena to fit 165 XANES spectra. > > Spectacularly so! Thanks for the big smiley at the end of the week. > > So would it be useful to have some more automation in the LCF > utility. What occured to me as I read this was to have a way > to fit a fixed set of standards to all the marked groups and > right a big report at the end. That is, play around with > spectrum #1 until you have decided which standards to use and > how to do the fit. Then mark spectra 2-165, press the > button, and go get a cup of coffee. That seems like a good > idea to me. > > B > > -- > Bruce Ravel ----------------------------------- bravel(a)anl.gov -or- > > ravel(a)phys.washington.edu > > Environmental Research Division, Building 203, Room E-165 > Argonne National Laboratory phone and voice mail: > (1) 630 252 5033 > Argonne IL 60439, USA fax: > (1) 630 252 9793 > > My homepage: http://feff.phys.washington.edu/~ravel > EXAFS software: > http://feff.phys.washington.edu/~ravel/software/exafs/ > > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

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new source code release
by Bruce Ravel 04 Sep '05

04 Sep '05

Hi folks, I have released the latest source code tarball for my codes. Tarball 054 is now available on my web site and at Source Forge. I am continuing Matt's experiment providing an Ifeffit Wiki by posting the change log on my wiki page: http://cars9.uchicago.edu/iffwiki/BruceRavel Scroll to bottom of the page (after smiling at the photo of me and my adorable niece) to find the page documenting the new features and bug fixes in this release. Matt and I are getting close to having a completely new Windows installer prepared. The new package has a more sensible file structure, a much improved launching tool for the programs, and new executables of my codes made with PerlApp. This version of my codes will be in the first release of the new Windows installer. Hopefully that will be ready soon. Regards, B -- Bruce Ravel ----------------------------------- bravel(a)anl.gov -or- ravel(a)phys.washington.edu Environmental Research Division, Building 203, Room E-165 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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Ifeffit Wiki
by Matt Newville 02 Sep '05

02 Sep '05

Hi Folks, I've created and started a wiki for Ifeffit and related topics. Currently, this is at http://cars9.uchicago.edu/iffwiki At this point, this should be considered experimental. I'm still ambivalent about the whole thing, but we definitely need *something* to allow outside people to add content. Please feel free to play with this wiki, and let me know what you think. If this is something we decide we want to keep, I'll have this become part of the main set of Ifeffit and XAFS pages. I'd like to give it a trial run first, and hear some feedback. For those who aren't familar with wikis, these are set of web pages that are editable and expandable by users. There are all sorts of features for adding content -- too many to explain here. The basic idea is that you log onto the system, and edit the web pages using a web browser in a simplified structured text -- NOT directly editing HTML. Anyway, it's pretty easy to use, and there's plenty of documentation on how to use it. --Matt

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compilation problem under MacOSX 10.4 - again
by Hugh Harris 02 Sep '05

02 Sep '05

Hi all, I'm new to the list and ifeffit. I've tried to get ifeffit 1.2.7 installed (for the first time) under tiger (on a system upgraded from panther) according to the instructions posted in the FAQ and the following modification on the list; > Thanks Matt - installing g77 and then recompiling perl/Tk and horae > did the > trick! > > Bruce - sorry, I meant Perl/Tk... > > Paul, you may want to upgrade the installation notes to mention > that g77 has > to be installed first. Installion with Fink was a pleasure. > > Thanks again guys! > > JOEL I have Xcode installed, g77 via fink, and ran the ifeffit binary installer. Perl/Tk seemingly builds and installs ok but when I try to build horae 0.5.3 I get the following error; [harris:~/Desktop/horae-053] hugh% perl Makefile.PL === The Ifeffit wrapper, Athena, Artemis, and Hephaestus === This is Mac OSX. Checking dependencies ... Dependencies ok. Cool! Reading configuration file: Ifeffit/lib/athena/athena.config Wrote Ifeffit/lib/athena/athenarc Ifeffit/lib/athena/athenarcw Ifeffit/lib/athena/athena.ini athena_parts/rc.pl Reading configuration file: Ifeffit/lib/artemis/artemis.config Wrote Ifeffit/lib/artemis/artemisrc Ifeffit/lib/artemis/artemisrcw Ifeffit/lib/artemis/artemis.ini diana_parts/rc.pl Assembled athena.pl from its parts (athena_parts/). Assembled artemis.pl from its parts (diana_parts/). Assembled hephaestus.pl from its parts (hephaestus_parts/). Fixing execution path in the Athena, Artemis, and Hephaestus executables... Changing athena.pl to /usr/bin/perl Changing artemis.pl to /usr/bin/perl Can't process diana.pl: No such file or directory Changing hephaestus.pl to /usr/bin/perl Changing ifeffit_shell.pl to /usr/bin/perl Changing horae_update to /usr/bin/perl Changing rdaj.pl to /usr/bin/perl Changing atoms.pl to /usr/bin/perl Ifeffit's installations directory is (found by capturing `ifeffit -i`) Could not open /config/Config.mak file for reading [harris:~/Desktop/horae-053] hugh% Trying to run athena from the xterm gives; Can't locate Ifeffit.pm in @INC (@INC contains: /sw/lib/perl5 /sw/lib/ perl5/darwin /System/Library/Perl/5.8.6/darwin-thread-multi-2level / System/Library/Perl/5.8.6 /Library/Perl/5.8.6/darwin-thread- multi-2level /Library/Perl/5.8.6 /Library/Perl /Network/Library/Perl/ 5.8.6/darwin-thread-multi-2level /Network/Library/Perl/5.8.6 /Network/ Library/Perl /System/Library/Perl/Extras/5.8.6/darwin-thread- multi-2level /System/Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at /Applications/Ifeffit/bin/athena line 54. BEGIN failed--compilation aborted at /Applications/Ifeffit/bin/athena line 58. Any ideas? Am I missing something obvious? Cheers, Hugh -- ------------------------------------------------------------------ Hugh Harris ASRP Postdoctoral Fellow School of Chemistry, Building F11 University of Sydney, NSW, 2006, Australia Office: +612-9351-2745 -------------------------------------------------------------------

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Re: Fitting an Extended R-range
by Michel Jaouen 31 Aug '05

31 Aug '05

>Shelly wrote: > >I was hoping that you could help me put together a list of EXAFS papers >that fit the R-space data out to at least 5 Angstroms. Hi Shelly, You can add to Scott's list the following entry: Mutiple-scattering EXAFS and EXELFS of titanium alloys T. Sikora, G. Hug, M. Jaouen, and J.J. Rehr, PRB 32, n°3, 1723 (2000) Best regards, M. Jaouen -- __________________________________________ Michel Jaouen Universite de Poitiers - UFR Sciences - SP2MI LMP UMR 6630-CNRS Boulevard Pierre et Marie Curie - Teleport 2 BP 30179 86962 Futuroscope - Chasseneuil Cedex France Tel : (33) 5 49 49 67 37 Fax : (33) 5 49 49 66 92 e-mail : Michel.Jaouen(a)univ-poitiers.fr __________________________________________

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RE: [Ifeffit] Fitting an Extended R-range
by Kelly, Shelly D. 30 Aug '05

30 Aug '05

Hi Scott, Thank you for the help. Have a good one. Shelly -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Scott Calvin Sent: Monday, August 29, 2005 10:10 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Fitting an Extended R-range Sorry, the first one should have been: > >"Estimating crystallite size in polydispersed samples using EXAFS," S. >Calvin, C. J. Riedel, E. E. Carpenter, S. A. Morrison, R. M. Stroud, & V. >G. Harris, Physica Scripta, T115, 744 (2005). >> --Scott Calvin Sarah Lawrence College _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Fitting an Extended R-range
by Kelly, Shelly D. 30 Aug '05

30 Aug '05

Hello Friends, I was hoping that you could help me put together a list of EXAFS papers that fit the R-space data out to at least 5 Angstroms. Thank you Shelly

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RE: [Ifeffit] Fitting an Extended R-range
by Kelly, Shelly D. 29 Aug '05

29 Aug '05

Hi Michel, Since I'm not getting a huge list of papers from anyone, I will take all that you think might be appropriate. SK -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Michel Schlegel Sent: Monday, August 29, 2005 2:24 AM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Fitting an Extended R-range Hello Shelly, >Hello Friends, > >I was hoping that you could help me put together a list of EXAFS papers >that fit the R-space data out to at least 5 Angstroms. > >Thank you >Shelly Does comparison of fourier transforms count as well ? (or are you just interested in the accuracy/uncertainty on the fitting parameters?) Best regards, Michel -- Michel Schlegel Commissariat à l'énergie atomique CEN de Saclay, DEN/DPC/SCP/LRSI Bat 391 - Piece 205B F91 191 Gif-sur-Yvette Cedex, France Ph: +33 (0)1 69 08 93 84 Fax: +33 (0)1 69 08 54 11 _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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