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

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 31 Aug '06

31 Aug '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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Re: problem with normalization
by Bernd Griesebock 31 Aug '06

31 Aug '06

Dear Bruce, thank you very much for the answer. I forgot to say that I load this macro which athena uses for the step function at the very beginning of using ifeffit. Your advise make me looking at my macro file, where I found a little typing error. That was it! Thank you so much! Regards Bernd > Message: 2 > Date: Thu, 31 Aug 2006 09:33:26 -0500 > From: Bruce Ravel <bravel(a)anl.gov> > Subject: Re: [Ifeffit] problem with normalization > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <200608310933.27010.bravel(a)anl.gov> > Content-Type: text/plain; charset="iso-8859-6" > > On Thursday 31 August 2006 02:57, Bernd Griesebock wrote: > >> Hi there, >> >> I have a litte question about normalizing data using the commands that >> athena uses. >> >> I used the following commands (in an ifeffit shell), which I copied from >> the ifeffit buffer from athena, but I replaced most of the values with >> the corresponding variables (see at the "set" commands): >> > > I have taken the liberty of numbering and slightly rearranging the lines of > your script. > > > 1 > read_data(file="Rh_sample_11.dat.spektrum.00040", group=rh, no_sort) > 2 > set ___n = npts(rh.1) > 3 > set rh.energy = 1000*rh.1 > 4 > set rh.xmu = (rh.2) / (rh.3) > 5 > pre_edge("rh.energy+0", rh.xmu) > 6 > erase rh.4 > 7 > show e0 > 8 > pre_edge("rh.energy+0", rh.xmu, e0=23228.9989104549, pre1=-150, > 9 > pre2=-30, norm_order=3, norm1=150, norm2=514.053) > 10 > spline("rh.energy+0", rh.xmu, e0=23228.9989104549, rbkg=1.0, kmin=0.5, > 11 > kmax=12.695, kweight=1, dk=0, kwindow=kaiser-bessel, pre1=-150, > 12 > pre2=-30, norm_order=3, norm1=150, norm2=514.053, clamp2=24, > 13 > nclamp=5, interp=quad) > 14 > set rh.preline = pre_offset+pre_slope*(rh.energy + 0) > 15 > set rh.postline = > 16 > norm_c0+norm_c1*(rh.energy+0.000000)+norm_c2*(rh.energy+0.000000)**2 > 17 > step rh.energy e0 rh.theta > 18 > set flat_c0 =norm_c0 - pre_offset > 19 > set flat_c1 =norm_c1 - pre_slope > 20 > set flat_c2 =norm_c2 > 21 > set rh.line = (flat_c0 + flat_c1*(rh.energy+0) + > 22 > flat_c2*(rh.energy+0)**2) > 23 > set rh.flat = (rh.pre + (edge_step - rh.line)*rh.theta) / edge_step > 24 > set rh.fbkg = (rh.bkg-rh.preline+(edge_step-rh.line)*rh.theta)/edge_step > 25 > newplot(rh.energy+0, "1*rh.fbkg+0", xlabel="E (eV)", ylabel="norm > 26 > x\gm(E)", fg=black, bg=white, grid, gridcolor="grey82", > 27 > xmin=23028.99891, xmax=24028.99891, style=lines, color="red", > 28 > key=bkg, title="rh_sample_11") > >> At this point athena plots the normalized background function with all >> data points in the post edge region at arround 1. This is exactly what I >> want, but in the ifeffit shell I get an error message: >> ** plot error: no data in y array >> >> Ifeffit> show rh.fbkg >> rh.fbkg = 399 pts [-0.2709E-01: 1.205 ] >> >> So there is data in that array! Using the following plot command: >> >> newplot(rh.energy+0, rh.fbkg, xlabel="E (eV)", ylabel="norm x\gm(E)", >> fg=black, bg=white, grid, gridcolor="grey82", xmin=23028.99891, >> xmax=24028.99891, style=lines, color="red", key=bkg, >> title="rh_sample_11") >> >> plots the background function but not normalized in the sense, that the >> data points in post edge region are at arround 1. >> >> Where is my mistake??? If you need some plot examples please feel free >> to ask for them. >> > > > I suspect that the problem is in line 17 of the ifeffit script. "step" is not > a built-in Ifeffit command. Instead it is a macro that Athena defines when > you start the program. Fire up Athena and look near the beginning of the > ifeffit buffer -- you'll see where the macro is defined. > > The purpose of the macro is to define a step function centered at a given > energy and placed on a particular energy grid. If you don't define this macro > the .theta array is undefined, leading to trouble with the .flat and .fbkg > arrays. > > Hope that helps, > B > > >

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problem with normalization
by Bernd Griesebock 31 Aug '06

31 Aug '06

Hi there, I have a litte question about normalizing data using the commands that athena uses. I used the following commands (in an ifeffit shell), which I copied from the ifeffit buffer from athena, but I replaced most of the values with the corresponding variables (see at the "set" commands): read_data(file="Rh_sample_11.dat.spektrum.00040", group=rh, no_sort) set ___n = npts(rh.1) set rh.energy = 1000*rh.1 set rh.xmu = (rh.2) / (rh.3) pre_edge("rh.energy+0", rh.xmu) erase rh.4 show e0 pre_edge("rh.energy+0", rh.xmu, e0=23228.9989104549, pre1=-150, pre2=-30, norm_order=3, norm1=150, norm2=514.053) spline("rh.energy+0", rh.xmu, e0=23228.9989104549, rbkg=1.0, kmin=0.5, kmax=12.695, kweight=1, dk=0, kwindow=kaiser-bessel, pre1=-150, pre2=-30, norm_order=3, norm1=150, norm2=514.053, clamp2=24, nclamp=5, interp=quad) set rh.preline = pre_offset+pre_slope*(rh.energy + 0) set rh.postline = norm_c0+norm_c1*(rh.energy+0.000000)+norm_c2*(rh.energy+0.000000)**2 step rh.energy e0 rh.theta set flat_c0 =norm_c0 - pre_offset set flat_c1 =norm_c1 - pre_slope set flat_c2 =norm_c2 set rh.line = (flat_c0 + flat_c1*(rh.energy+0) + flat_c2*(rh.energy+0)**2) set rh.flat = (rh.pre + (edge_step - rh.line)*rh.theta) / edge_step set rh.fbkg = (rh.bkg-rh.preline+(edge_step-rh.line)*rh.theta)/edge_step newplot(rh.energy+0, "1*rh.fbkg+0", xlabel="E (eV)", ylabel="norm x\gm(E)", fg=black, bg=white, grid, gridcolor="grey82", xmin=23028.99891, xmax=24028.99891, style=lines, color="red", key=bkg, title="rh_sample_11") At this point athena plots the normalized background function with all data points in the post edge region at arround 1. This is exactly what I want, but in the ifeffit shell I get an error message: ** plot error: no data in y array Ifeffit> show rh.fbkg rh.fbkg = 399 pts [-0.2709E-01: 1.205 ] So there is data in that array! Using the following plot command: newplot(rh.energy+0, rh.fbkg, xlabel="E (eV)", ylabel="norm x\gm(E)", fg=black, bg=white, grid, gridcolor="grey82", xmin=23028.99891, xmax=24028.99891, style=lines, color="red", key=bkg, title="rh_sample_11") plots the background function but not normalized in the sense, that the data points in post edge region are at arround 1. Where is my mistake??? If you need some plot examples please feel free to ask for them. Thank you for your help in advance. Best regards Bernd

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Contributions from 2 paths
by McPheeters, Matthew 25 Aug '06

25 Aug '06

Dear All, I am analyzing Neodymium Oxide with G.I.Feffit. I have two paths and I'm having trouble showing the contributions (chi data, Forward and back Fouirer Transform) to the fit from each path. I ran into a problem with the Sigma2 for the second path, sigma2_2. When I guess sigma2_2 I can print out the individual path contributions to the fit with the fitted parameters factored in. If I define, def ( ), sigma2_2 = sigma2_1 then the path contributions that I try to print out do not have the debye-waller parameters factored in. I have tried the analysis with feffit245 and the path contributions it shows seem be consistent with the fit. So, I figure I must be writing something wrong in my command file. I have attached the fit command files, log files, and contribution graphs for when I guess sigma2_2 and define sigma2_2 = sigma2_1. In the graphs black = data, red = fit, green= contribution from path 2, blue= contribution from path 1. Thanks, Matt McPheeters Dr. Mayanovic's Lab Assistant Missouri State University

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Problem loading application on Mac OSX 10.4.7
by chessel＠ualberta.ca 22 Aug '06

22 Aug '06

Hello, I just downloaded ifeffit version - ifeffit-1-1.2.9-Mac10.4_horae62_pkg.dmg - to my Mac - Version 10.4.7 - and am having some trouble running the programs. When I double click on the application file I am prompted to "Please pick an output device;" my choices are either "X11 graphics" or "Aquaterm." When I choose either of them, the application fails and the icon disappears from the dock. Has anyone else encountered this problem? Is there a different version available for Mac OSX 10.4.7? Thanks, Colin

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Mehmet Alper Sahiner/FAC/SHU is out of the office.
by Mehmet Sahiner 22 Aug '06

22 Aug '06

I will be out of the office starting 08/21/2006 and will not return until 09/05/2006. I will be out of the office betwen 8/21/06-9/05/06. Alper

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hafnium oxide
by m.bauer 17 Aug '06

17 Aug '06

hi everybody, does anyone have a literature reference explaining the shoulder in the XANES spectrum of HfO2 after the white line at about 9.58 keV. I think it is related to the number of oxygens coordinating, but i could not find any note about it by browsing the journals.... thanks very much! matthias -- Matthias Bauer Universität Stuttgart Institut für Physikalische Chemie Arbeitskreis Prof. Dr. H. Bertagnolli Pfaffenwaldring 55 70569 Stuttgart (Vaihingen) Telefon: (+49) 0711-685-4472 Fax: (+49) 0711-685-4443 E-Mail: m.bauer(a)ipc.uni-stuttgart.de homepage: http://www.ipc.uni-stuttgart.de/~matthias/index.htm

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