July 2007 - Ifeffit - millenia.cars.aps.anl.gov

feff6 and mac intel os x
by Katy Evans 17 Jul '07

17 Jul '07

Yay it works. I got the address for Feff6 by doing 'Show package contents' and then typed it into the Feff6 executable box, with Feff6 included at the end. And its all good. Thankyou for the suggestions and quick responses. Cheers, Katy Katy Evans Dept. App. Geol. k.evans(a)curtin.edu.au Curtin University Tel: 0061 8 9266 4682 Bentley Fax: 0061 8 9266 3153 GPO Box U 1987, WA6845

1 0

Re: [Ifeffit] Problems with EXAFS Analysis software for MAC
by Ravel, Bruce D. 16 Jul '07

16 Jul '07

Ross, The Ifeffit mailing list is a superb resource for all your ifeffit+friends questions. http://cars9.uchicago.edu/mailman/listinfo/ifeffit/ Among the many nice things about the mailing list is that there are a number of people who, unlike me, use the Mac and will know the answer to your question. I have taken the liberty of forwarding this along to the mailing list. You should join the list so that when someone answers, you will get the mail. Good luck, B -----Original Message----- From: Ross Williams [mailto:Ross.Williams@curtin.edu.au] Sent: Mon 7/16/2007 9:47 AM To: Ravel, Bruce D. Subject: Problems with EXAFS Analysis software for MAC Hi I am having problems running ATHENA, ARTEMIS, and HEPHAESTUS, well actually an of the programs in the package. I have a new Intel MacBook with OS X version 10.4.10. I installed the X11 SDK from the OS X dvd, after I install it I could install your package. However when I open on of the programs (by opening them in Applications/Ifeffit) I am prompted to pick a output device, "X11 graphics" or "aquaterm". Either choice the program icon appears briefly in the dock then dissappears, this happens for all the programs. Any advice would be appreciated. Thanks, Ross +++++++++++++++++++++++++ Ross Williams Centre for Materials Research Curtin University of Technology GPO Box U1987 Perth WA 6845 Western Australia ross.williams(a)curtin.edu.au

2 1

Mac intel OSX - Feff6 whereabouts
by Katy Evans 16 Jul '07

16 Jul '07

Hi, Apologies if this question has a very simple answer but I can't work it out. I installed the iXAFS package onto my new Mac (OSX 10.4.8) and almost everything works very well and it is very pleasant to use so thankyou. BUT Feff6 won't run. I can fit to existing Feff calculations but I can't make new ones, from .inp files that used to work on my other computer, or from quick first shell calculations. The message from Artemis starts 'This error is probably due to having Artemis configured incorrectly and so it does not know how to run Feff on your computer...' and goes on to say that I should check the value of the Feff executable in Preferences, and set it to Feff6. So I checked it and it was indeed Feff6. I looked for Feff6 on my computer and could only find a Feff6.atp file in the Perl directory (/Library/Perl/5.8.6/darwin-thread- multi-2level/Xray/atp) - should there be anything else? I tried typing this address into the box for the Feff executable option but this didn't help. I tried to remove everything and reinstall from the disk image but I am not sure if that was successful since I still only got the option to 'upgrade' when I clicked on the installer package. Where are all the things I need to remove if I want to get rid of the old version? Thankyou, Katy Katy Evans Dept. App. Geol. k.evans(a)curtin.edu.au Curtin University Tel: 0061 8 9266 4682 Bentley Fax: 0061 8 9266 3153 GPO Box U 1987, WA6845

3 2

Basic questions on XANES
by Ashley Harvey 14 Jul '07

14 Jul '07

Dear ifeffit users, This posting is with quite basic questions on XANES data processing. I am a somewhat new XANES experimentalist, in a group that does not typically use XANES, so I am lacking some basic knowledge. For normalization of XANES, my impression is that people generally normalize the spectra from ca. 50 eV up to 100 eV or more after the edge onset. Is there a standard acceptable normalization range for K edges? I have noticed that when I change the start of the normalization window by even a few eV, this can make substantial differences in the XANES when comparing two similar spectra (for example, change in peak and pre-edge peak intensities between XANES of one sample at two temperatures). I keep second-guessing my choice of normalization range. Second, I am also looking at the effect of the various ways to set E0. When I start with ifeffit's default (how is this determined?) and then proceed to set E0 to the zero-crossing of 2nd derivative, I'll get value X. When I change it to a set fraction of the edge step (is this legitimate?) I typically get a lower value, and then when I proceed again to set it to the 2nd derivative zero-crossing, I get a value different from the first time it was set to the zero- crossing. For example, the E0 at an Fe K edge: ifeffit default = 7128.9 eV 2nd derivative zero = 7128.8 set fraction = 7125.1 2nd derivative zero = 7125.5 The value given by the 2nd derivative zero-crossing is dependent on the previous E0 setting. I am having a hard time to move on to the actual interpretation of the data while I am still uncertain about such details. Thanks for your patience with some simple questions. Best, Ashley

2 1

xanes pyrite
by s440697＠stud.uni-goettingen.de 10 Jul '07

10 Jul '07

Hello, i have problems with feff-xanes calculations related to pyrite. I try to get the k-edge of sulfur (as absorber) in FeS2. I get the edge at ~2472 eV and i think this is wrong because i get the same energy with gypsum and i think there should be an energyshift related to 2472 eV. My proceeding is as follows: calculate the atomic positions with the asymetric unit from the http://rruff.geo.arizona.edu/AMS/amcsd.php database (Pyrite spacegroup Pa3) respectively http://rruff.geo.arizona.edu/AMS/xtal_data/CIFfiles/00596.cif with "powdercell 2.4" feffrun with the feff.inp-file like in the attachment (thanks to Josh Kas for his feff-hints) I started the feff-run on the one hand with 12 atoms (unitcell) and on the other hand with 22 atoms (14x Fe and 8x S in the cube) After this i plotted from xmu.dat the absorbtion mu (column 4) as a function of the energy (column 1). The result is in the attachment too. I don't know why i get everytime the Sulfur-k-edge at the same position (for pyrite or gypsum) respectively without energyshift related to 2472 eV. many thanks for your help :-) Ciao, Eckhard

1 0

Re: [Ifeffit] Ifeffit Digest, Vol 53, Issue 3
by Emiliano Fonda 04 Jul '07

04 Jul '07

Thanks for the help, I did a mess using the pgplot package from the distro instead using that compiled with the Ifeffit distribution. I removed that of the distro, cleaned up the installation and started again with the pgplot_install script. Everything is fine now. It took just a few minutes. The fact athena was working (I got a graphic window), while the python wrapper not, that puzzled me. Thanks again, Emiliano. > Message: 2 > Date: Tue, 3 Jul 2007 09:43:56 -0500 > From: "Matt Newville" <newville(a)cars.uchicago.edu> > Subject: Re: [Ifeffit] RE : Ifeffit Digest, Vol 53, Issue 1 > To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: > <b8522e3d0707030743q76eb78bdkd7ce7186a31c75b(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Emilano, > > I use the python wrapper for Ifeffit on linux all the time, and also > use python "for several things on the beamline". And just for the > record, I do not use debian packages. >

2 1

Re: [Ifeffit] RE : Ifeffit Digest, Vol 53, Issue 1
by Matt Newville 03 Jul '07

03 Jul '07

Hi Emilano, I use the python wrapper for Ifeffit on linux all the time, and also use python "for several things on the beamline". And just for the record, I do not use debian packages. Over the years, I've experienced many problems using a shared object version of PGPLOT with Ifeffit and its wrappers. These problems are why I wrote PGPLOT_Install, and why I strongly recommend following the instructions for installing Ifeffit, which includes first installing PGPLOT with the PGPLOT_Install script. They are also why I asked you to run 'ldd' on both /usr/local/bin/ifeffit and /usr/lib/python2.5/site-packages/Ifeffit/_ifeffit.so to see what libraries they load dynamically. Is there a problem with doing these steps? If so, try to find someone who can help you follow the build instructions. For 1.2.10, I will make the following changes: a) PGPLOT_Install will be altered to create libpgplot_iff.a instead of libpgplot.a, and this will be installed to /usr/local/share/ifeffit/pgplot. b) The configuration and makefiles will be altered to link against this libpgplot_iff.a, and not with libpgplot that might be installed by some other package. This will avoid the sorts of conflicts you're seeing an also eliminate the possibility of assuming that using the debian/whatever PGPLOT package will work, as it will not work for anything. It will cause some headaches for everyone using the source installations will be forced to do a COMPLETE re-install (including PGPLOT_Install). But, if someone decides to build and support a package for Ifeffit it will then have no chance of conflicting with or depending on any PGPLOT package. Cheers, --Matt

1 0

RE : Ifeffit Digest, Vol 53, Issue 1
by FONDA Emiliano 03 Jul '07

03 Jul '07

Well, I was attracted by the possibility of importing ifeffit in python, since I started using python for several things on beamline. I am not interested in the gifeffit itself, but in the python wrapper. I will test C. Segre packages if they fix the issue. Thanks, Emiliano. > Is there some feature of gifeffit that you cannot live without? > B.

4 4

Re: [Ifeffit] Meaning of sigma^2 and real space resolution in XAFS
by Scott Calvin 02 Jul '07

02 Jul '07

Hi all, This got marked spam and rejected when I sent it from home this weekend... :) At 12:48 AM 6/30/2007, you wrote: >Hello, > >Thanks Bruce and Matt for the previous comments© >I have the following questions and I would appreciate comments about them: > >My Questions are: >1- Can we consider sigma^2 of a single >scattering path to be a measure of Debey Waller factor? If you mean the Debye-Waller factor from x-ray diffraction, the answer is no. The EXAFS sigma^2 is the variance in the absorber scatterer distance, the XRD sigma^2 is the variance in the position of an atom relative to its lattice point in the crystal. Thus, IF the motion of the absorber and scatterer were uncorrelated, it would be reasonable to think that the EXAFS sigma^2 would be twice the XRD Debye-Waller factor. For nearest-neighbors, though, this is a terrible assumption, as the atoms will tend to move in a correlated fashion (put another way, acoustic phonons dominate over optical ones). Thus the EXAFS sigma^2 for nearest-neighbors will usually be much less than the XRD Debye-Waller factor. Further confusing matters is terminology. In EXAFS, sigma^2 is sometimes called the Debye-Waller factor...but this Debye-Waller factor is not the same as that from XRD! I've also seen "Debye-Waller factor" used to include all information about the shape of the distribution of the absorber-scatterer distance, so that sigma^2 is "the harmonic part of the Debye-Waller factor," but that seems to be an older usage. >2- Is sigma^2 a measure of ¥or directly proportional to¤ strain in a bond? Hmm...I'd say no, although I think I know what you're getting at. One major contributor to sigma^2 is thermal vibrations, which of course increase with temperature. I don't think that's generally categorized as "strain" (although I'm wary of the differing definitions that terms such as this can have in different specialties!). Another contributor to sigma^2 is variations in absorber-scatterer distance due to local defects, surface effects, etc., generally lumped together under the term "static disorder." This term itself can be a little misleading, as, e.g., a nanoparticle can have a sigma^2 that varies in a perfectly regular way with distance from the surface--we call that static disorder, even though it is not particularly disorderly. :) At any rate, what material scientists call "strain" can show up as static disorder. But even in that case, note that if all the bonds in a sample were strained, sigma^2 would not reflect it--it's only when some are strained and some are not that it shows up. So yes, I've seen (knowledgeable) people point at a sigma^2 and say "I think that's high because of strain." But that's a kind of short-hand for what's going on. >3- When doing first shell fitting in Artemis, >The actual bond length is: r_eff + dr +- delta ¥dr¤© >Are the error bars associated with dr values >¥delta¥dr¤ of about 0©001 A¤ realistic? ¥i©e© >0©001 A is too small to detect by XAFS¤© Your formatting didn't come through very well, but I'll give it a shot. Ifeffit (and thus Artemis) do a pretty good job of putting a lower bound on delta dr, in my opinion. Why a lower bound? Because there are all sorts of systematic errors that could be coming in, e.g. an iffy model--such as a first-shell only fit for a crystalline material, since there's often a bit of spectral leakage from more distant shells. I'd be very surprised if Artemis ever gave a 0.001 A delta dr, though, and absolutely shocked if it did so on a first-shell only model. Are you saying that it did do that for you? >4- What determines the real space resolution in >XAFS measurements other than K_max? k_min, of course. To answer the gist of your question more fully, though, I have to get on my soapbox. :) "Resolution" is often taken to mean something other than it does. Resolution criteria literally mean the point at which you could be expected to distinguish between two peaks. It is NOT the limit to the precision of information that can be retrieved by a clever person. Huh? Let's take an example of, oh, a proposal that there are two slightly different (but consistent) nearest-neighbor distances in some material. If those distances differ by less than the resolution implied by the k-space range, then they will not show up as two peaks in the Fourier transform. Instead, they'll show up as one broad peak; i.e. a peak with an anomalously large sigma^2. If a multiple-shell fit was performed and splitting was known to be a possibility, this anomalously large sigma^2 could be taken as indirect evidence for the splitting. In fact, if there were some way to estimate sigma2's a priori (I'll grant you that's a big if!), then the broad peak could be modeled as two scattering paths, with the splitting as a free parameter. In that case, EXAFS could give information about splitting to a greater precision than the resolution of the measurement. A lot of the lore about the capabilities of EXAFS suffers from a similar lack of subtlety. Joe Woicik recently gave a very interesting talk at the NSLS Users' Meeting. It is generally bandied about that EXAFS cannot distinguish scatterers that differ in atomic number by less than 5. This is kind of true--in a mindless first-shell fit--because in those cases del_r and sigma^2 will usually just slop up the differences in phase and amplitude due to the different atomic number of the scatterer. But if you really really knew del_r and sigma^2 a priori, even a difference of one atomic number stands out like a sore thumb! The upshot is that if you model, say, zinc scatterers as if they were iron, the fit will probably "work," but you'll be introducing substantial systematic errors into your fitted variables. A corollary is that in the case of a highly-constrained fit, you may be able to do considerably better than the usual +/- 5 rule. The bottom line of this little speech is that the oft-quoted limits of EXAFS analysis are usually referring to a fit in which no a priori information is used. If you know (or suspect) anything about the system and incorporate that into your model, greater precision is sometimes possible. Of course, the results are then only as good as the a priori information; the whole thing could be a house of cards ready to collapse. But in favorable cases, multiple lines of evidence can be used to construct a convincing scenario... Hope that helped! --Scott Calvin Sarah Lawrence College

1 0

gifeffit installation issue on ubuntu feisty fawn
by Emiliano Fonda 02 Jul '07

02 Jul '07

Hi, I would like to use gifeffit on the beamline where I work for fast extraction of EXAFS data during scans and so on. But I have a problem even before starting to code: horae and ifeffit works well, I compiled and installed the python wrapper, but gifeffit refuse to work and I cannot import the Ifeffit module in python. The error message is: fonda@nemotele:~$ gifeffit Traceback (most recent call last): File "/usr/local/bin/gifeffit", line 2, in <module> import GIFeffit, sys File "/usr/lib/python2.5/site-packages/Ifeffit/GIFeffit.py", line 27, in <module> from Ifeffit import Ifeffit File "/usr/lib/python2.5/site-packages/Ifeffit/Ifeffit.py", line 46, in <module> import _ifeffit, types, cmd, os, sys ImportError: /usr/lib/python2.5/site-packages/Ifeffit/_ifeffit.so: undefined symbol: pgclos_ The linux distro is ubuntu feisty fawn and I got the libpgplot5 package installed... ... may anyone help me, please? Thanks, E. Fonda SAMBA beamline SOLEIL synchrotron

3 2