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

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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Attempted XANES calc using FEFF8.1 - what's wrong?
by Matthew Marcus 15 Aug '06

15 Aug '06

I tried the XANES calculation on FEFF8.10 with calcite at the Ca K-edge as the object. I had just taken some data on this compound, and I wanted to see how it compares. The attached shows that it doesn't compare all that well. I've also attached the feff.inp file I used, which was made by ATOMS using coordinates from the atoms.inp database. I used default parameters and read the result from the xmu.dat file. The energy cal on the experimental data was done using the Sb L3-edge assumed at 4132.2eV, since 3um foils of Ca metal are a little hard to handle :-). Next stop, I suppose, is FDMNES, which I recently downloaded. mam

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Re: Ifeffit Digest, Vol 40, Issue 10
by Michel Jaouen 07 Aug '06

07 Aug '06

>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. data file format (emmanuelle montarges-pelletier) > 2. Re: data file format (Matthew) > 3. Re: data file format (Bruce Ravel) > 4. The most important fitting parameters (Bridget Ingham) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Wed, 21 Jun 2006 10:25:47 +0200 >From: emmanuelle montarges-pelletier > <emmanuelle.montarges(a)ensg.inpl-nancy.fr> >Subject: [Ifeffit] data file format >To: ifeffit(a)millenia.cars.aps.anl.gov >Message-ID: <1F268809-6D80-4EE8-996D-209DFF3FEE07(a)ensg.inpl-nancy.fr> >Content-Type: text/plain; charset=ISO-8859-1; delsp=yes; format=flowed > >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 > > >There are two types of encodings which may differ among text files from >different countries and OSs. I >don't know how Athena&Co. handle either of them. One is that numbers and >decimals can differ per country. If >Kgraph is using a local encoding other than the American standard, say, >using commas instead of periods, it's possible >that Artemis won't understand it. I have the same problem with my analysis >programs. Every so often I get a panicky email >from a user whose files won't open. The other variation is in what >constitutes the end of a line, which is OS-dependent. It could >be carriage return, linefeed, or CR-LF. > mam > > >Salut Emmanuelle, > >Matthew's suggestion of floats with commas is a good suggestion. A&A >make no attempt at respecting localization. (That is, a number >between one and two might be written as 1,234 -- which would confuse >A&A -- rather than 1.234.) If that is the case, your best bet is to >go back to the exterior program and ask it nicely to write out points >instead of commas. Or you might need to edit the file by hand. > >I thought that the end-of-line issue (Matthew's other suggestion) was >one that was solved in A&A years ago. If that proves not to be the >case, please let me know. > >Another possibility is that the exterior program added other text to >the file that is confusing A&A. Here is my explanation of how Athena >reads ascii data files > > http://cars9.uchicago.edu/iffwiki/FAQ/HoraeQuestions > >and here is the explanation of the file-reading function in Ifeffit >which Athena uses: > > http://cars9.uchicago.edu/~ifeffit/refman/node24.html > >The situation in Artemis is similar, although restricted in the sense >that Artemis is expecting its data to be chi(k). > >If none of that clarifies the issue for you, I'll need to see an >example of the data file which is causing the problem. > >The easiest way to move data from Athena to Artemis is to have Artemis >import its data directly from the Athena project file. > >If there is some data processing feature that Athena does not do but >which you require before moving on to data analysis, you should >consider making a feature request here on the mailing list. Athena >will never get the features that you need if I am not aware that they >are needed! > >B > Just an additional point: take care to save the file as unix file and not standard Mac (use a free text editor as TextWrangler to do this kind of manipulation). Michel -- __________________________________________ 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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