July 2011 - Ifeffit - millenia.cars.aps.anl.gov

Portable Ifeffit packet + portable python
by jack song 01 Aug '11

01 Aug '11

Dear all, I made a portable version of Ifeffit, which is updated to the latest version. To run a program x, please double click RunXxx.bat file. There are also 3 portable python (2.5, 2.6, 2.7) with Ifeffit module. Please extract it to the same folder. (extract here as folderA\IfeffitPortable, folderA\PythonPortablexxx) Download below, IfeffitPortable: http://dl.dropbox.com/u/2776935/IfeffitPortable.zip<http://dl.dropbox.com/u/2776935/IfeffitPortable.zip> Python 2.5 portable: http://dl.dropbox.com/u/2776935/PythonPortable_1.1_py2.5.4.zip Python 2.6 portable: http://dl.dropbox.com/u/2776935/PythonPortable_1.1_py2.6.1.zip Python 2.7 portable: http://dl.dropbox.com/u/2776935/PythonPortable2.7.2.1.zip If there is a problem, please let me know. I will make more information available later. PS, if you need a dropbox, which I highly recommend. Please click my refer link http://db.tt/WRHqYkA, which will increase my box 250MB. Best, Jack Song

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FEFF6L.02 - missing path?
by Pawel Zajdel 29 Jul '11

29 Jul '11

Hi Matt, OK, I got the point and it is clear now. Thanks Pawel > As you've probably read in the Feff documentation, Feff has a couple > of filters that it uses: one fast and less accurate to eliminate > really unimportant scattering paths to make the path-finding mechanism > more efficient, and one slightly more accurate one to decide later > which paths to calculate the EXAFS for. At this point, both of these > optimizations seems less-than-critical, and just turning them off > completely (CRITERIA 0 0) is not so bad, especially for moderately > ordered systems like your crystal structure.

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Re: [Ifeffit] problems in installing PGPLOT in UBUNTU
by Enyuan Hu 29 Jul '11

29 Jul '11

Dear Matt, I checked the log file but didn't see any error message. I don't know if it's because I succeeded in installing Athena and Artemis following Carlo's suggestion and the log file is thereby updated. Here's the content of the log file: "#!/bin/sh # PGPLOT install log # system = linux == linux g77_gcc # prefix = /usr/local/ # fortran compiler = gfortran gzip -dc pgplot5.2.tar.gz | tar xf - mkdir -p /usr/local//share/ifeffit/pgplot/ # driver.list written to /usr/local//share/ifeffit/pgplot//drivers.list # starting build cd /usr/local//share/ifeffit/pgplot// rm -f grfont.dat pgplot.doc pgxwin_server lib*pgplot* pgdemo* /home/enyuan/ifeffit-1.2.11d/pgplot/makemake /home/enyuan/ifeffit-1.2.11d/pgplot linux g77_gcc # customizing grgil.f for ifeffit sed 's|/usr/local/pgplot/|/usr/local//share/ifeffit/pgplot/|g' /home/enyuan/ifeffit-1.2.11d/pgplot/src/grgfil.f > /home/enyuan/ifeffit-1.2.11d/pgplot/src/grgfil_iff.f mv makefile Tmp sed 's|grgfil|grgfil_iff|g' Tmp > makefile sed 's|libpgplot|libpgplot_iff|g' makefile > Tmp sed 's|-lpgplot|-lpgplot_iff|g' Tmp > makefile # customizing xwdriv.c for ifeffit sed 's|getenv("PGPLOT_DIR")|'"/usr/local//share/ifeffit/pgplot/"'|g' /home/enyuan/ifeffit-1.2.11d/pgplot/drivers/xwdriv.c > /home/enyuan/ifeffit-1.2.11d/pgplot/drivers/xwdriv_iff.c mv makefile Tmp sed 's|xwdriv|xwdriv_iff|g' Tmp > makefile # fix png driver mv makefile Tmp sed 's|pndriv.o : ./png.h|#### pndriv.o : ./png.h|g' Tmp > makefile make FCOMPL= gfortran FFLAGC=-O1 libpgplot_iff.a make FCOMPL= gfortran grfont.dat prog pgplot.doc pgxwin_server cpg make clean " I hope the length is not too bothering and thank you very much for the help! -- Enyuan

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Re: [Ifeffit] FEFF6L.02 - missing path?
by Pawel Zajdel 29 Jul '11

29 Jul '11

Matt, Thanks for the explanation. In this case, next two questions. 1. Is there a way to say it was rejected other than re-running feff with CRITERIA 0 0? I expected it to show in Feff.run file with "neglected" flag. My "default" Feff.run file says " Curved wave chi amplitude ratio 4.00% Discard feff.dat for paths with cw ratio < 2.67%" and the "neglected" flag is present for those with <2.67%. 2. Also there is still one path left (all paths No# 10 Se-Zn-Se) with cw ratio 2.83, which passes the <2.67 criterion but is weaker than the two paths that are rejected before it with amps 3.952 and 3.999. In other words - when using "default" generated feff.inp, which paths in Feff.run are reported as neglected and which are not reported at all? Best Pawel >> Message: 1 > Date: Thu, 28 Jul 2011 18:25:56 -0400 > From: Pawe? Zajdel <pawel.zajdel(a)us.edu.pl> > To: <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] FEFF6L.02 - missing path? > Message-ID: <5EB6FA326A714E6BAD00215CBFB556AE@NewLapek> > Content-Type: text/plain; charset="iso-8859-2"; Format="flowed" > > Dear All, > > I am facing a strange issue while playing with EXAFS for a spinel type > structure. I tried two typical examples: MgAl2O4 and ZnCr2Se4 with > octahedral site K edge of Al or Cr. > The MgAl2O4 is fine but for ZnCr2Se4, FEFF seems to omit one scattering > path. It is not reported as being rejected by <2.6% amp criterion, so I > wonder, while it is not shown. > This is path 3 (as seen in MgAl2O4), which goes from Cr/Al to anion, then > over the "octahedron" edge to another anion and back to Cr/Al. > For oxide Reff=3.2251 > <cut from feff.run> > path cw ratio deg nleg reff > 1 100.000 6.000 2 1.9371 > 2 37.913 6.000 2 2.8853 > 3 10.687 12.000 3 3.2251 <-- It's here > 4 9.664 2.000 2 3.3444 > </cut> > For selenide Reff=4.2354 > <cut from feff.run> > path cw ratio deg nleg reff > 1 100.000 6.000 2 2.5248 > 2 47.173 6.000 2 3.7084 <-- should be after this > one. > 3 25.382 6.000 2 4.3485 > </cut> > I am attaching two atoms.inp files, which may help. It is space grup 227, > standard setting (2), atom list is correct. > I am using Ifeffit 1.2.11c with Feff 6L.02. It s present under WinVista > and > Linux on two different machines. > Am I missing something? > I would appreciate any suggestions. > > Best > Pawel > Message: 2 > Date: Thu, 28 Jul 2011 21:27:57 -0500 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] FEFF6L.02 - missing path? > Message-ID: > <CA+7ESbpzXoP+OkH2Nq14DY-W4SP-cgCnh_0=+b7OhSvLMG80xA(a)mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Pawel, > > For these two structures, the location of the anions (Se for ZnCr2Se4 > and O for MgAl2O4) are not in in exactly the same location in the unit > cell. The nearly identical double scattering paths: > Al->O->O->Al > and > Cr->Se->Se->Cr > each have small estimated scattering amplitudes ("Zabinsky Curved Wave > Importance Factors"). The Cr->Se->Se->Cr path is filtered out with > the default settings, and so not included in the path list, while the > Al->O->O->Al path is not filtered out. > > You can guarantee to see all the paths if you put > CRITERIA 0 0 > > in the feff.inp file. > > For a more detailed reason of why Al->O->O->Al has an estimated > amplitude of 10.7 (and so not filtered out) while the Cr->Se->Se->Cr > has an estimated amplitude of 3.9 (and so is filtered out), there are > a few points to consider: > > 1. The amplitude reported is relative to the strongest scattering > path, which always has amplitude 100. In both cases, this is the > first shell Al->O->Al and Cr->Se->Cr. Se is a stronger back-scatterer > than O. > > 2. Both absorber and scatterer are heavier in the Zn-Cr-Se case > than the Mg-Al-O case, and the the heavier atoms are more point-like > in their electron density. > > 3. The Se atoms are closer to 0.25, 0.25, 0.25 in the unit cell > than the O atoms. This makes the Cr->Se->Se->Cr path have a > scattering angle beta a little closer to 90 degrees, which gives less > scattering amplitude. > > I think all three of these conspire to give the Cr->Se->Se->Cr path > less amplitude than the Al->O->O->Al path. > > Hope that helps, > > --Matt > -- dr Pawel Zajdel Division of Physics of Crystals Institute of Physics University of Silesia Uniwersytecka 4 40-007 Katowice Poland [48]323591978

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problems in installing PGPLOT in UBUNTU
by Enyuan Hu 29 Jul '11

29 Jul '11

Dear all, Has anyone met a problem when installing PGPLOT in UBUNTU? I fellowed the prescribed recipe in http://cars9.uchicago.edu/~ifeffit/src/INSTALL but always encounter problem when trying to get PGPLOT installed. The message is like this: "= Uh-oh. PGPLOT is missing some important files! = It looks like PGPLOT failed during building or = is only partially installed. = = Please consult the PGPLOT installation instructions = in the subdirectory pgplot/, and the log file: = /home/enyuan/ifeffit-1.2.11d/PGPLOT_install.log = which contains a full list of commands run. = = You may want to repeat these steps by hand or = consult the PGPLOT installations instructions = in install-unix.txt " I'm a newbie to UBUNTU so I would really appreciate it if the answer can consider my ignorance and be as simple as possible :) BTW, the motivation I'm switching to UBUNTU is the video of doctor Bruce lecturing on vimeo.comwhich were done in the environment of Demeter...juicy!! -- Enyuan

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Peak fitting analysis
by Abhijeet Gaur 29 Jul '11

29 Jul '11

Hi all, I am doing XAFS analysis of some Cu(II) samples. As well known Cu(II) samples shows a pre-edge feature at around 8976 eV, characterstic of Cu(II) spectra. I am trying to perform peak fitting analysis of this pre-edge feature to determine its intensity as it is related to the coordination. I am trying Peak fitting analysis with Athena, but unable to get some results. May be I am doing something wrong. The Athena project is attached herewith. With thanks Abhijeet Gaur

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FEFF6L.02 - missing path?
by Paweł Zajdel 28 Jul '11

28 Jul '11

Dear All, I am facing a strange issue while playing with EXAFS for a spinel type structure. I tried two typical examples: MgAl2O4 and ZnCr2Se4 with octahedral site K edge of Al or Cr. The MgAl2O4 is fine but for ZnCr2Se4, FEFF seems to omit one scattering path. It is not reported as being rejected by <2.6% amp criterion, so I wonder, while it is not shown. This is path 3 (as seen in MgAl2O4), which goes from Cr/Al to anion, then over the "octahedron" edge to another anion and back to Cr/Al. For oxide Reff=3.2251 <cut from feff.run> path cw ratio deg nleg reff 1 100.000 6.000 2 1.9371 2 37.913 6.000 2 2.8853 3 10.687 12.000 3 3.2251 <-- It's here 4 9.664 2.000 2 3.3444 </cut> For selenide Reff=4.2354 <cut from feff.run> path cw ratio deg nleg reff 1 100.000 6.000 2 2.5248 2 47.173 6.000 2 3.7084 <-- should be after this one. 3 25.382 6.000 2 4.3485 </cut> I am attaching two atoms.inp files, which may help. It is space grup 227, standard setting (2), atom list is correct. I am using Ifeffit 1.2.11c with Feff 6L.02. It s present under WinVista and Linux on two different machines. Am I missing something? I would appreciate any suggestions. Best Pawel -- dr Pawel Zajdel Division of Physics of Crystals Institute of Physics University of Silesia Uniwersytecka 4 40-007 Katowice Poland [48]323591978

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Re : EXAFS analysis of a sample having two metal centres with different coordination geometry
by Abhijeet Gaur 22 Jul '11

22 Jul '11

<Abhijeet, <This seems like a system which might require more information before using EXAFS analysis. How did you come to the conclusion that there are <two metal centers? You begin by asking how to model two metal centers with different coordination and then in question 3, you lead the list to <believe that there might not be two metal centers? I assume you have found structural data for the sample? You have different geometry as <well as different ligands (atoms). Do the metal centers only contain the absorbing metal or is it mixed? If you had a bit more information <about the material through other methods, I am sure several people could suggest helpful ideas for your analysis. <Chris -- Christopher J. Patridge PhD. 405 NSC - Dept of Chemistry University at Buffalo State University of New York Buffalo, NY 14260 Office:(716)645-4137 Contact:(315)529-0501 <E-mail: patridge at buffalo.edu<http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> Dear Chris, I am sorry for making my problem a bit difficult to understand. Let me clarify the problem: 1. Yes, I have the crystal strcuture of the sample with me, from which I know that there are two metal centers. With this crystal strcuture data, I have generated the theoretical model for the two metal sites. 2. Yes, the metal centers only contain the absorbing metal, i.e., copper but with with different coordination. And my question is whether by using EXAFS analysis of experimetal data, the contribution of two metal center present in sample can be confirmed? Also, is it possible to calculate that how much one metal center contribute to the experimetal data? If, one of the theoretical model does not fit to the experimetal EXAFS data, what does it signify about the corresponding metal center? I hope this will make my problem clear to the members of the mailing list. With thanks Abhijeet Gaur

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EXAFS analysis of a sample having two metal centres with different coordination geometry
by Abhijeet Gaur 21 Jul '11

21 Jul '11

Hi all, I am doing EXAFS analysis of a sample having two metal centres with different coordination geometry. In my sample two (Cu) metal centres are present and these metal centres are surrounded by different ligands (atoms) in different coordination geometry. As I understand the EXAFS data of such sample will have contributions from both the metal centres. So, in order to analyse the EXAFS data, I have generated theoretical model (using Artemis) for both the metal centres. Then, I have fitted these theoretical models to the experimetal data. But, I have some questions regarding this type of analysis as I am not sure whether I going in right direction or not: 1. I have to fit these theoretical models one by one or simultaneously to the experimetal data. 2. How can I confirm that whether the EXAFS data of the sample has contributions from both the metal centres. 3. If one of the model does not fit well to the exp data, does this mean that the corresponding metal centre is not present or the metal centre is present but not contributing. 4. Is it possible to calculate the percentage of contributions from different metal centres to the experimetal data. If someone can suggest some available literature on this problem, it will be really helpful to me. With thanks Abhijeet Gaur Research Scholar School of Studies in Physics Vikram University, Ujjain, India

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Re: [Ifeffit] Scripting - Python
by Andrew Korinda 21 Jul '11

21 Jul '11

Thanks for the help. Sorry it took so long to report back but I can only do must of my work on this on weekends. The corrected code worked great and I'm moving forward again. No message was given when the code wasn't working. Andy Korinda On Nov 1, 2010 1:55 PM, "Matt Newville" <newville(a)cars.uchicago.edu> wrote: Hi Andrew, On Mon, Nov 1, 2010 at 12:01 PM, Andrew Korinda <a-korinda(a)northwestern.edu> wrote: > I'm looking t... This is almost certainly due to space in the filename, and is really more of a problem with the fortran than python (or perl for that matter). That is, with a space in the file name, you should explicitly use read_data(file=...., group=...) This should work better:: import Ifeffit iff = Ifeffit.Ifeffit() ret = iff.ifeffit("read_data(file=C:\Program Files\Ifeffit\examples\Ifeffit\data\cu.xmu, group=c)") If it doesn't, let use know. > >From this experience I have some questions: > > ~First does anyone have some debugging tips for ... There should have been a printed message that might have altered you that the file hadn't been read in correctly: *** read_data: no file name given! was that message not given? > ~Secondly, Does anyone have any example Python scripts for Ifeffit > that they would like to shar... I sort of deliberately have left the base Ifeffit python module bare-bones. It would certainly be possible to add more functionality to that, or distribute add-on packages. It sort of depends what people would find desirable. I have many example scripts using Ifeffit + Python, mostly scripts, not documented, reliable code. Of course, there is also sixpack. I had some older GUIs as well. Would it be helpful to add some small examples on a wiki page? > ~Finally, would I be better off coding in Perl and using Demeter? That's a difficult question. The relative merits of Perl v Python are sort of a topic all on their own. For what it's worth, I believe (far) more people have used Python than Perl, but several very notable Ifeffit programs are written in Perl ;). --Matt PS: The next version of Ifeffit will be in python. Progress is slow, and when it will start to look like an EXAFS analysis program is a fair question. It probably shouldn't sway your decision much. _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.g...

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