October 2006 - Ifeffit - millenia.cars.aps.anl.gov

still the spike
by Silvio Levy 19 Oct '06

19 Oct '06

Dear Shelly, Dear Bruce Thanks for both your answers. Going through Shelly's slides was a nice refresher course. Bruce, ok, I see why normalization is not affected. However.... The data were already correctly aligned. I've now explicitly tied the data to the standard, using the Data menu, and the auto-align shift was only 0.02 eV. So this had no effect on the spike. Setting the lower bound of the spline range to 0 mainly shifts the position of the spike to near k=0, and so hides it somewhat when we multiply chi by a power of k. But it's still visible in E space (a large negative peak in the spline). Setting a spine clamp at the low end changes things slightly but not qualitatively. Changing E0 would seem to be a reasonable step. After all, there is no reason why k=0 should coincide exactly with the first inflection point on the edge!! But again, all attempts, for Eshift varying from -5 to 10eV, make no qualitative difference. All other tweaks I've tried also maintain the spike, or else distort the spline so much as to introduce other errors. For comparison, I took the first curve (labeled 0.12) in project AuChloride_LCF_example.prj from Scott's talk. There is something of a sharp departure between the spline and the data visible in E space, as in my case. But the plot in k space -- even of chi itself without multiplying a power of k -- is nice and smooth. All this is in http://www.msri.org/~levy/files/example.prj which contains only one group from me and one from Scott. Would you be willing to take a closer look? I'd not be asking except that I'm completely stumped. My data seem perfectly normal. Thanks again, Silvio

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Athena bug and a question
by Silvio Levy 18 Oct '06

18 Oct '06

Bruce - thanks a lot for your post. I've encountered this bug a few times, but I thought it might be a problem with my machine; in any case I could never replicate the problem and file a bug report. I have another question to the list - how do I get rid of a spike at low k? See for instance http://www.msri.org/~levy/files/Cinnabar/cinnabar.prj If you open this file with Athena and plot in k-space, there is a big spike at low k; I haven't worried about this too much, but now that I'm starting to show other people my work, I'd like to get rid of it. Presumably my background subtraction is at fault, but how to fix it? The spike also messes the normalization. Thanks, Silvio

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possibly Athena bug and a work-around
by Bruce Ravel 18 Oct '06

18 Oct '06

Hi, Yesterday I observed a very serious bug in Athena that will, I think, only effect certain linux users. The bug is a race condition that makes Athena unresponsive and indefinately consumes 100% of the CPU. That's a bad thing, indeed! The bug is triggered by passing the mouse over an item in the groups list, causing it to redisplay in a larger blue font. On a machine where the larger font does not exist, perl/Tk enters into the race condition. I have documented this and a work-around as question 8 of this FAQ page: http://cars9.uchicago.edu/iffwiki/FAQ/HoraeQuestions I believe that Windows and Mac users will not be effected. If you install Athena onto a linux machine and see this behavior, please see the FAQ. A permanent fix will be included in the next 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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Problems with Feff calculation in Artemis
by SCOTT, Abby 16 Oct '06

16 Oct '06

Hi guys, I'm warning you now, I am only a mere undergrad student who has been using the Ifeffit programs for a few weeks now, so my problem may have already been addressed, but here goes; I entered the following data for crystalline Ag2S into the feff.inp section in Artemis 0.8.003 using Windows XP: TITLE Crystal Ag2S T=25C HOLE 1 1 * mphase,mpath,mfeff,mchi CONTROL 1 1 1 1 PRINT 1 0 0 0 RMAX 7 NLEG 2 POTENTIALS * ipot Z element 0 47 Ag absorbing atom 1 16 S scattering sulphurs 1 47 Ag scattering silvers ATOMS * x y z ipot 0 0 0 0 Ag absorber 1.767 1.767 0 1 S scatterer shell 1 1.767 0 1.767 1 S scatterer 0 1.767 1.767 1 S scatterer -1.838 1.838 0 1 S scatterer shell 2 -1.838 -1.838 0 1 S scatterer 2.078 -2.078 0 1 Ag scatterer shell 3 0 -2.078 -2.078 1 Ag scatterer 2.093 0 -2.093 1 S scatterer shell 4 -2.093 0 -2.093 1 S scatterer 1 2.0449 2.0449 1 Ag scatterer shell 5 2.0449 1 2.0449 1 Ag scatterer 2.0449 2.0449 1 1 Ag scatterer -1 2.0449 2.0449 1 Ag scatterer 2.0449 -1 2.0449 1 Ag scatterer 2.0449 2.0449 -1 1 Ag scatterer -1 -2.0449 2.0449 1 Ag scatterer 0 0 3.23 1 Ag scatterer shell 6 0 3.23 0 1 Ag scatterer 3.23 0 0 1 Ag scatterer 0 0 -3.23 1 Ag scatterer When I clicked 'Run Feff' it came back with this message in the 'Messages' tab in the window labelled 'Artemis palettes'; Feff 6L.02 Crystal Ag2S T=25C Calculating potentials and phases... free atom potential and density for atom type 0 free atom potential and density for atom type 1 overlapped potential and density for unique potential 0 overlapped potential and density for unique potential 1 muffin tin radii and interstitial parameters Also, the following text was in the 'Echo' tab, also in the window labelled 'Artemis palettes'; Preparing to run FEFF ... Performing autosave ... Saving feff.inp file Performing autosave ... done! Running feff (this could take a few minutes, please be patient) ... Running feff ... done! There are no feffNNNN.dat files! Something has gone wrong with your Feff calculation! What is the meaning of this error and is it fixable by a novice undergraduate? I apologise if this is extremely basic, or if I've been a little excessive with the detail in this message. Hope you can help, Thanks, Abby Scott

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I am looking for a volunteer
by Bruce Ravel 12 Oct '06

12 Oct '06

Hi, There is a chore that needs to be done that would have an impact far beyond Ifeffit and friends, but which I don't have time to devote to right now. Consequently, I am looking for a volunteer to take this on. OpenBabel (http://openbabel.sourceforge.net/wiki/Main_Page) is a very cool molecular and chemistry package. It is a library which allows programs to easily convert between different file formats for describing molecules and clusters of atoms -- a chore in what you might call chemoinformatics. As an example, a program using OpenBabel can import a file from the Protein Data bank and export an input cartesian file for Gaussian. OpenBabel supports 70+ file formats for this conversion process (http://openbabel.sourceforge.net/wiki/Category:Formats) One format OpenBabel does not support is feff.inp. I trust it is not hard to imagine how useful it would be to be able to easily convert cartesian data in some other format into valid input to Feff. Any program using OpenBabel (http://openbabel.sourceforge.net/wiki/Related_Projects) would immediately be able to generate feff.inp files. And because there is a perl wrapper for OpenBabel, Artemis would be able to import virtually any kind of cartesian data. Super cool! OpenBabel is written in C++ and comes with very clear instructions (http://openbabel.sourceforge.net/wiki/HowTo:Add_A_New_File_Format) on how to add file formats. I would like someone to volunteer to write, test, and document format code for feff.inp files. I am happy to give advice in the design phase and to help with testing. I think this is a highly rewarding project in the sense that the ratio between the impact on the Feff-using community and the time required for taking on this chore will be quite high. 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: Novice FEFF question--feel free to post
by Bruce Ravel 10 Oct '06

10 Oct '06

Hi Ryan, I am taking the liberty of CCing this to the Ifeffit mailing list. > I have a novice FEFF question for you guys. > > > > Assuming one has a good idea of the SO^2 value for a specific element > either from published literature or analysis of a relevant standard > reference phase (e.g. 0.85 for Co in Co(OH)2), what is the consensus on > fixing the SO^2 value for the FEFF simulation and if one does fix the value > in the feff.inp file (@ 0.85 for this thought experiment) would one still > fix SO^2 at the same value during the fit (or fix at one)? I'll assume that you are famliar with the normal caveats of the assumption of the "chemical transferability" of S02 and that you are aware that you introduce a source of systematic uncertainty into your analysis when you make that assumption. If that's not clear, please ask so that I or someone else on the list can talk about that. I can only answer you question by explaining what I prefer. I cannot presume to speak for the consensus -- different practitioners reasonably come to their own conclusions. I prefer to run feff with S02=1 and all sigma^2 values set to zero. I then prefer to use Ieffit (or Artemis or WinXAS or EXAFSPAK or whatever) to change the parameters of the EXAFS equation from their nominal values. Of course, setting S02 to 0.85 in Feff and then setting it to 1 in Ifeffit is equivalent to setting it to 1 in Feff and 0.85 in Ifeffit. While multiplication is unambigously commutative, human brains are usually notoriously poor at disentangling a sequence of arithmatic. If you: (1) set S02 to something other than 1 in Feff, (2) need to modify the value when doing analysis in Ifeffit, (3) go on vacation for two weeks, and finally (4) return home to write a paper on your analysis --- are you going to remember that you need to multiply your two values of S02 together when you report on your analysis in the paper? Hmmmm..... Another way of looking at this is to remember what Feff (that is, Feff6 -- Feff8 adds a few steps) does: 1. computes potentials and phases 2. determines the path list 3. constructs chi(k) for each path in the path list using the potentials and phases from part 1 4. sums up all the paths to make the theoretical chi(k) If you consider Ifeffit to be a much more interesting version of the fourth part of Feff, then it should be clear that the better approach is to use Ifeffit to deal with S02. 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/exafs/

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Postdoc search
by Frenkel, Anatoly 10 Oct '06

10 Oct '06

Dear IFEFFIT users: please announce it to those who may be interested in this position. Thank you, Anatoly Postdoctoral position at Yeshiva University and the National Synchrotron Light Source Physics Department of Yeshiva University in New York City has immediate opening for a postdoctoral research associate position. PhD in physics, chemistry, or materials science and experience with synchrotron x-ray absorption fine-structure techniques are required. The postdoc will support the ongoing nanomaterials research projects which will include multi-technique characterization of nanoparticles, Quick XAFS experiments, design of reactor cells for nanocatalysis science. He or she will be stationed in Brookhaven National Laboratory (BNL) and work closely with BNL departments (Chemistry and the Center for Functional Nanomaterials) as well as the outside collaborators which include University of Illinois at Urbana-Champaign and University of Pittsburgh. The research will be performed at the Synchrotron Catalysis Consortium (http://www.yu.edu/scc <http://www.yu.edu/scc> ) at the National Synchrotron Light Source (BNL) under the direction of Dr. Anatoly Frenkel. Applicants should forward cover letter and CV, and arrange for three letters of recommendation to be sent to Dr. Frenkel at anatoly.frenkel(a)yu.edu <mailto:anatoly.fenkel@yu.edu> .

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Artemis: sum path NAN NAN NAN NAN
by Mauro Rovezzi 06 Oct '06

06 Oct '06

Hi guys, I've found a weird behavior in Artemis: during the fit procedure in the shell normally appears "sum path # # # #" where # = real number, but sometimes the minimization process fall in an infinite loop saying: "sum path NAN NAN NAN NAN". The only solution is to kill Artemis and restart. I've also observed that saving the project and/or removing all files in the .horae directory and/or changing the fit model temporary solve the problem. Well, it's not a problem to manage this "divergence"... Mauro PS: My environment: Artemis 0.8.006 using linux, perl 5.008008, Tk 804.027, and Ifeffit 1.3.0 -- Mauro Rovezzi <rovezzi(a)esrf.fr> PhD student - GILDA BM08 c/o ESRF (Grenoble, FR)

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IFEFFIT with Intel Macs
by Dustin Collier 02 Oct '06

02 Oct '06

Hi everyone, Since there has been a demand for running IFEFFIT on a new Intel-based Macintosh product, I thought I would send this link along. I'm not sure if anyone else has attempted this, but I recently installed Windows XP on my MacBook using Apple's Boot Camp software. All you need is an Intel Mac, a blank CD used to burn drivers for Windows XP (Boot Camp does this for you), and a copy of Windows XP SP2. IFEFFIT runs perfectly on my MacBook running Windows XP, and you can partition your hard drive as low as 5GB if you are only going to use this for this software. It is very easy to switch between OSX and XP, and the user's guide on the website is very helpful. Until someone can develop a working version for the Intel Macs, this might be an useful option for some of you and I thought I would pass it along. The link can be found below: http://www.apple.com/macosx/bootcamp/ If anyone has any questions on running Boot Camp, feel free to let me know. DCC -- Dustin C. Collier Graduate Teaching Assistant Department of Chemistry University of Tennessee Buehler Hall

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