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

Re: still the spike
by Silvio Levy 19 Oct '06

19 Oct '06

Dear Bruce, OK, I hear you. I'll stop obsessing about the spike and only show chi*k^2 plots in my thesis :-) More seriously -- Your answer helps put things into perspective, and the comparison between the FFT with k-range starting at 0 and 1 is instructive. It's worth noting, however, that in R space there is a hump from R=1 to R=1.4 that (to my knowledge) has no physical explanation, and which is more pronounced when the FT is taken starting at k=0. Should I not worry about this either? Thanks Silvio

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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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Consistency criterion
by Juan Antonio Maciá Agulló 29 Sep '06

29 Sep '06

Hi all, Scott answered my question about consistency but now I have a new doubt. I have two fits (one in k1 and other in k3 weights) with fitted parameters that have uncertainty ranges overlaped, then... in principle, they are consitent, right? But the fit in k1 weight have a R-factor too high (0.06) and therefore is not a good fit. So I do not know if I can say that they are consistent even so. Thank you very much Best regards, JA >I read in Artemis manual that a good fit must be consistent for different >k-weights. When two fits (one with k1 and other with k3) are consistent? I >mean, which is maximum allowed difference, 1%, 5%...between these two fits? Ideally, the fitted parameters should have uncertainty ranges that overlap. For example, one bond length might be 2.03 +/- 0.04 angstroms, and the equivalent bond length using a different k-weight might be 2.09 +/- 0.03 angstroms.

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Incorporating FEFF8 into IFEFFIT
by Richard Mayes 28 Sep '06

28 Sep '06

Bruce, I have just recieved a copy of FEFF8. Is there a way to incorporate it into Artemis on the windows version of IFEFFIT? In theory, we should be able to play a "shell game" with the names of the executable files and get FEFF8 to work while IFEFFIT thinks it's running FEFF6l (by changing the FEFF6l.exe file to something else, and rename the FEFF8 file to FEFF6l.exe) and then replace the DAT files to those for FEFF8. Is this possible or is it just better to run FEFF8 independently and import the .inp files into Artemis? Rich Mayes Barnes Group Dept. of Chemistry Univ. of Tennessee Knoxville, TN 37996

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Phase corrected Fourier transforms
by Juan Antonio Maciá Agulló 27 Sep '06

27 Sep '06

Hi all, I have read Phase corrected Fourier transforms in Athena manual and now I have a big doubt, ¿phase correction or not in a publication? I have read also that this correction is different (more complete) in Artemis and I am not sure if I should correct also in Artemis and which path should I use and why. I saw many papers dealing with EXAFS fits and they showed a "calculated" bond distance, I think it is: d = Reff + deltaR, right? I also ask for a paper where I can find that deltaE is ok (even for high-Z backscatterers) if deltaE < 10eV. I have high correlations between ss and SO2, and deltaR and deltaE. I tried different fits but I can not eliminate them, then...is the fit wrong? Sorry for these easy questions but I am a novice in XAFS. Thank you very much. Best regards, JA

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Re: [Ifeffit] Artemis error message
by Matt Newville 20 Sep '06

20 Sep '06

Hi Stefano, Did you try using /Applications/Ifeffit/bin/feff6 as the preferred feff executable in Artemis? That's what the error message was suggesting you try. Can you verify that you have /Applications/Ifeffit/bin/feff6? --Matt

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Artemis import from the text file
by Victor.Streltsov＠csiro.au 19 Sep '06

19 Sep '06

Hi All, I have the following Artemis problem: when I export variables to text file and then read them back into new Artemis run/project (import variables from the text file), Artemis cuts parts of the expressions starting from multiplication sign '*'. I tried different text editors and character coding as well as different platforms (Windows XP, Linux FC4). It always does the same thing with imported math expressions. It doesn't like '*' character. I am puzzled. I would appreciate your help and any suggestions. Thanks Victor Dr Victor Streltsov CSIRO Molecular & Health Technologies 343 Royal Parade Parkville VIC 3052 Australia Phone: +61 3 96627311 Fax: +61 3 96627101 victor.streltsov(a)csiro.au

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Short questions
by Juan Antonio Maciá Agulló 15 Sep '06

15 Sep '06

Hi Ifeffit people, I have a couple of short questions for you. I used the "Scott Calvin's rule" (number of variables < 2/3*Nip) to calculate the maximum number of allowed free parameters but I read that some people use the Nyquist theorem, which are the differences between them? and, which one is more correct? And finally, how are errors calculated in Artemis for the parameters N (coordination number), deltaE0, S02, deltaR and sigma^2? Thanks a lot JA

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FW: PhD position@LWV/PSI
by Degueldre Claude A. 12 Sep '06

12 Sep '06

-----Original Message----- From: Bruce Ravel [mailto:bravel@anl.gov] Sent: Montag, 11. September 2006 17:22 To: Degueldre Claude A. Subject: Re: PhD position@LWV/PSI URGENT AND FOR INFORMATION COULD YOU PLEASE VENTILATE THE INFO... We have 1 position free for doctorant with main topic EXAFS. You find the job below: http://pa.web.psi.ch/pages/offenestellen/d/index_offenestellen.php?was=l iste&kategorie=doktoranden With the KS 4334 If you have any candidate, please let me know... We need to evaluate candidates on Sep. 25. All the best CLAUDE DEGUELDRE ----------------------------------------------------- On Monday 11 September 2006 10:07, you wrote: > Bruce > We have 1 position free for doctorant with main topic EXAFS. You find > the job below: > http://pa.web.psi.ch/pages/offenestellen/d/index_offenestellen.php?was > =l > iste&kategorie=doktoranden > With the KS 4334 > If you have any candidate, please let me know... > We need to evaluate candidates on Sep. 25. > All the best Hi Claude, I don't know anyone who can fill the spot in the next two weeks, unfortunately. I think you should post this job opening on the Ifeffit mailing list. Matt and I consider that an excellent use of the mailing list. 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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Installing Tk/Horae on Fedora Core 5
by Bhoopesh Mishra 12 Sep '06

12 Sep '06

Dear All, I am in the process of installing Ifeffit 1.2.9 with latest Horae package (-062) on my a new machine on which I have put Fedora core 5. I followed the instructions for installing the entire package, and had partial success in it. Ifeffit and PGPLOT seem to be working fine. I believe Tk-804.027 is also working fine, I just ran "widget" and it works. However when I tried to ./horae_update, I got error message and it aborted without compilation. To look into the problem, I manually downloaded a previous version of horae (horae-061) from another computer on which everything is working fine (Tk-800.024 with horae-061 on a Fedora Core 2). In the manual installation of horae_061, perl Makefile.PL works fine. But "make" does not complete. It terminates with the same error message as the one with which ./horae_update terminated. (attached as a screenshot) I have attached the screenshots of the error message for horae_update. I have also attached screenshots of "make install" and "make test" for Tk-804-027 just in case you would like to see that. Since Ifeffit and PGPLOT are working, I am inclined to believe that it has something to do with Fedora Core 5 and its compatibility with Tk-804.027 and horae-062. Funny part is that I tried to downgrade the Tk to Tk-800.024, but it failed to install, which indicates some issues of Tk with FC 5. I also tried the combination of Tk-804.027 with horae-060. Has anyone gone through this combination of installing Tk-804.027 with horae-062 on a Fedora Core 5? Any insight would be extremely helpful. Thanks a lot in advance. Please let me know what more information would you need if the given information is insufficient. PS: I have been successfully using all these programs on FC 2 and FC 3 for last few years but some very generous people always helped me with the installation and am now trying to be independent. Thanks again, Bhoopesh

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Re: X11 on 10.4.7
by Bruce Ravel 11 Sep '06

11 Sep '06

On Monday 11 September 2006 15:34, Kjell Bolmgren wrote: KB> KB> Bruce, KB> KB> Did you ever find out how to install X11 on 10.4.7. KB> KB> I have tried to install it from the cd and to download it but neither KB> works so far. Kjell, I am CCing this to response to the mailing list in hopes that someone will be able to lend you a helping hand. I'll restate now what I say every time I make a post about anything Apple: I don't own a Mac, I don't have a Mac at work, and my experience on the Mac in any other context is extremely limited. That Athena and Artemis work on the Mac is thanks to my choice to use cross-platform programming tools (like perl and Tk) and on the kind contributions of people like Paul, who went the final mile to make easy-to-install packages. 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] Artemis error message
by Matt Newville 11 Sep '06

11 Sep '06

Stefano, Feff6 is an executable. When it runs it needs a file named feff.inp to be in the current working directory, otherwise it will say: Feff 6L.02 Fatal Error: cannot open file "feff.inp" in module rdinp which is exactly what you got when you typed 'feff6' in a directory without a feff.inp file. That doesn't tell us a lot, but it does mean that this version of feff6 is at least not corrupted, so the Installer is probably fine. The first error message from Artemis that you sent: "The error is probably due to having Artemis configured...." and gave an "Uh-Oh" in the Echo Buffer is definitely what Artemis says when it cannot find feff6. You said you got this when the feff_executable was set to 'feff6'. Did you try setting feff_executable to '/Applications/Ifeffit/bin/feff6'? Note that spelling counts. You could open a Terminal, type 'which feff6' and paste that into the feff_executable field. Note to Bruce: How about having a "browse" button for selecting the feff_executable? > I interpret this message with the conclusion that I can just type 'feff6' in > the Artemis preferences, as the command is actually seen and of course it is > missing the feff.inp file if I run the command from the terminal. Well, it *should* work that way, but using /Applications/Ifeffit/bin/feff6 will definitely work. It does work for several of us. Hope that helps, --Matt

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Re: [Ifeffit] Demeter: my new software project
by Bruce Ravel 11 Sep '06

11 Sep '06

On Saturday 09 September 2006 11:02, Mauro Rovezzi wrote: > I really like your new project! I think it's a great idea because > Athena&Artemis are good softwares but clicking on them all the day it's > quite boring. Exactly. To my mind, the biggest problem is that it is difficult, time consuming, and error prone to encode a complex fitting model using Artemis' GUI. I forsee that one of my common uses of Demeter will be to encode a complex fitting model in a one-off script and have that script write out an Artemis project file. Then I'll get the good parts of the GUI while using something automated to deal with the tedious parts. > On the other hand, I find the Ifeffit wrapper too > low-level. In fairness, Ifeffit is great at doing its low-level thing. It's just that low-level tools tend not to scale up gracefully. > Well, Demeter seems to me the best solution as a middle-level > interface to Ifeffit, that permits to fork to user-oriented projects > written in Perl. I also appreciate the choice to move this project to a > version control system (Subversion), that is the future possibility for > users to directly contribute to the code. Thanks for all the kind words, Mauro. I am excited that you get the point of middleware and that you get the point of using Subversion. Even if you use and don't contribute, Subversion lets you always use up-to-the-minute code. 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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Demeter: my new software project
by Bruce Ravel 08 Sep '06

08 Sep '06

Hi! I think that some of you will be interested in my latest XAS software project, which I am calling Demeter. Demeter is an object-oriented programming interface to Ifeffit written in Perl. It is intended to encompass most of the current functionality of Athena and Artemis while at the same time being more generalized, lower-level, and much more robust. In short, Demeter is not a software product. Rather, it is the thing that software products can be made from. Demeter is targeted at a wide variety of XAS data analysis chores, such as * GUI's like Athena and Artemis. In fact, I intend to rewrite Artemis using Demeter once I have incorporated enough functionality into Demeter. * A parser for feffit.inp files allowing you to translate your old analysis using feffit into ifeffit scripts and Artemis projects. * The analytic component of a high-throughput system such as those presented at the XAFS13 conference by the groups of Wolfram Meyer-Klaucke and Sven Schroeder. * The backend to specialized XAS software, like Shelly Kelly's mkfit program (http://www.mesg.anl.gov/exafs.html) or for ideosyncratic analysis like that described in Physical Review B, 73, p. 184121 (2006) There is still A LOT to do, but even at this early stage Demeter is very useful. In fact, Demeter can already be used for real data processing and analysis. Demeter is available on an anonymous Subversion server, so anyone with an SVN client can check out a copy of Demeter at any time. Information about Demeter and the Subversion server is at http://cars9.uchicago.edu/~ravel/software/demeter.html You can browse the Demeter source code with your web browser at http://cars9.uchicago.edu/svn/demeter/ If this seems interesting to you, take a look at some of the short example programs demonstrating Demeter's capabilities and economy of language: http://cars9.uchicago.edu/svn/demeter/examples 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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silly me!
by Bruce Ravel 06 Sep '06

06 Sep '06

Hi folks, It just occured to me that I didn't mention the web page where I document all the changes to my codes in the most recent release. Athena especially has a number of interesting new features. You might want to take a look at this http://cars9.uchicago.edu/iffwiki/HoraeVersion062 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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Compiling horae/iffefit on Mac OS 10.4.7 Intel
by Todd Hufnagel 02 Sep '06

02 Sep '06

Greetings: I'm trying to get ifeffit and the horae packages running on an Intel-based Mac running OS 10.4.7. As someone else noted previously, the binary downloads don't work on Intel Macs. (As an aside to the person who asked about the console log, in my case the programs quit immediately after launching and no messages are generated in either console.log or system.log. I do have X11 installed; this behavior is the same with either X11 or Aquaterm chosen for output.) So I decided to compile from the source. Unfortunately, I ran into a problem when compiling horae-062a. Using the Makefile.PL for Mac OS (http://cars9.uchicago.edu/~ravel/misc/horae_on_mac/Makefile.PL ) seems to work fine, and after "make;make install" I get no errors and executables for Artemis et al. are produced. Unfortunately, attempting to run any of the executables produces an error similar to the following: >tchmac:/Applications/ifeffit/bin hufnagel$ ./artemis >dyld: lazy symbol binding failed: Symbol not found: _iff_exec > Referenced from: >/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Ifeffit/Ifeffit.bundle > Expected in: dynamic lookup > >dyld: Symbol not found: _iff_exec > Referenced from: >/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Ifeffit/Ifeffit.bundle > Expected in: dynamic lookup > >Trace/BPT trap A little digging around on the net suggested that this error comes from compiling with gcc-4.0 rather than gcc-3.3. Switching to that compiler, I can again run Makefile.PL successfully, but then when I run 'make' I get a new and exciting error: >[...much successful stuff deleted...] >cp Zlib.pm ../../blib/lib/Compress/Zlib.pm >AutoSplitting ../../blib/lib/Compress/Zlib.pm >(../../blib/lib/auto/Compress/Zlib) >/usr/bin/perl /System/Library/Perl/5.8.6/ExtUtils/xsubpp -typemap >/System/Library/Perl/5.8.6/ExtUtils/typemap -typemap typemap >Zlib.xs > Zlib.xsc && mv Zlib.xsc Zlib.c >cc -c -I./zlib-src -g -pipe -fno-common -DPERL_DARWIN >-no-cpp-precomp -fno-strict-aliasing -I/usr/local/include -O3 >-DVERSION=\"1.41\" -DXS_VERSION=\"1.41\" >"-I/System/Library/Perl/5.8.6/darwin-thread-multi-2level/CORE" >Zlib.c >cc: installation problem, cannot exec `cc1': No such file or directory >make[2]: *** [Zlib.o] Error 1 >make[1]: *** [subdirs] Error 2 >make: *** [subdirs] Error 2 and obviously no executables are produced. A little more digging on the web revealed that the cc1 stuff should be in the /usr/libexec/gcc tree. Unfortunately, while there is a subdirectory there for gcc-4.0 for Intel, the only files for gcc-3.3 are for PowerPC. That is, while there is a /usr/libexec/gcc/darwin/ppc/3.3/cc1, there is no corresponding subdirectory for Intel processors. The reason the compilation worked for gcc-4.0 is that there is, in fact, a /usr/libexec/gcc/i686-apple-darwin8/4.0.1/cc1. At this point, I am stuck. I can compile under gcc-4.0 but get executables which don't run, and I can't compile at all under gcc-3.3. I also ran into trouble compiling ifeffit, but I haven't exhausted my own abilities in chasing down those problems (yet). Any assistance/advice/condolences would be appreciated. Thanks, Todd Hufnagel -- Todd C. Hufnagel Professor Department of Materials Science and Engineering Johns Hopkins University 102 Maryland Hall 3400 North Charles Street Baltimore, MD 21218-2681 Voice: (410) 516-6277 Fax: (410) 516-5293 Email: hufnagel(a)jhu.edu http://www.jhu.edu/~matsci/people/faculty/hufnagel/hufnagel.html

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Alloy EXAFS data fitting
by XQ WANG 01 Sep '06

01 Sep '06

Dear all, I am trying to understand some EXAFS data collected on an alloy system (sorry I can't say it since these are not my data). It is a two-element alloy system, name AB. Their fitting results showed that A-B coordination number and A-A coordination number did not follow the similar trend with the temperature increase. I am just wondering if this case is possible? I had thought if A-A and A-B are from the same compound, they should follow the same trend. Maybe I am wrong. Another question is whether it is OK to combine coordination of A-A in A compound with CN of A-A in AB alloy if these two A-A bond distances are very close? If this case is OK, then combination of A-A CN and CN of A-B could follow differnt trend (I guess). But I thought we could not combine CN from different materials. Maybe I am wrong again?? Please let me know any suggestions concerning this situation. Thanks! Xianqin _________________________________________________________________ Check the weather nationwide with MSN Search: Try it now! http://search.msn.com/results.aspx?q=weather&FORM=WLMTAG

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