September 2014 - Ifeffit - millenia.cars.aps.anl.gov

Open position in XAFS spectroscopy at MAX IV
by Katarina Norén 09 Sep '14

09 Sep '14

Hi, At the MAX IV Laboratory we are looking for a beamline scientist in XAFS spectroscopy with profile in Environmental science for the BALDER beamline at the new 3 GeV ring that will be taken in operation in 2016. Link to the position announcement: http://www.lu.se/lediga-anstallningar-available-jobs?x=0&Dnr=625478&Type=E Best regards, Katarina Norén __________________________________________________ [https://webmail.lu.se/owa/attachment.ashx?id=RgAAAABSBK%2b9jD%2fNQZCL0w%2bj…] Katarina Norén, PhD Manager Hard X-ray Group MAX IV Laboratory Lund University P.O. Box 118, SE-221 00 Lund, Sweden Visiting address: Ole Römers väg 1, 223 63 Lund Telephone +46 46 222 68 09 Mobile: +46 709 32 34 23 www.maxlab.lu.se<http://www.maxlab.lu.se/>

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Cursor Issue in Athena Data Import Window
by Godfrey, Ian 05 Sep '14

05 Sep '14

Dear All, This bug report is for a very minor cosmetic issue, but I'm reporting it as it fooled me into thinking Athena had hung and doing a lot of unnecessary troubleshooting - hopefully I can save someone else from the same fate! I experienced this issue with Demeter 0.9.20 on Windows 8 x64 and Windows 7 x64. I don't recall this issue on previous versions of Demeter, but I could be wrong. The bug is as follows. When you open the Athena "Import" window (file > import data) the cursor over the data import window changes to the Windows' busy cursor indefinitely (see screenshot) when it should be the normal cursor (it doesn't impair functionality in anyway - you're still fully able to interact with the window, create plots etc.). Like I said, not a big bug but it led to me wasting a bit of time so I thought I'd report it. Regards, Ian Godfrey (UCL)

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Implementing constraints in EXAFS analysis
by Badari Rao 05 Sep '14

05 Sep '14

Dear Dr. Bruce, I have collected EXAFS data on a ferroelectric perovskite Sodium Bismuth Titanate which has an average rhombohedral R3c structure and am trying to fit the data with R3c as the starting model. But I am having trouble in implementing constraints for the fit. I found a paper authored by you, titled "Local structrue and phase transitions of BaTiO3, Ferroelectrics, 1998, 206-207, pp 407-430". I want to do similar kind of analysis using Artemis on my data. However, I am finding difficulty in understanding how the constraints have been implemented for the refinement of the barium K edge EXAFS, especially those for the bond lengths (Page 416 in the above mentioned article in particular is unclear). Could you please explain how the GDS window and the variables for different paths in this case would look like. Also how do you decide what parameters to refine and what to keep fixed (table IV in the article)? Also can you please suggest some literature for beginners which can guide me in implementing such constraints? Thanking you, -- Yours Sincerely, Badari Narayana. A. R. Ph.D Student, Nanoscience and Nanotechnology, c/o Prof Rajeev Ranjan, Electroceramics Lab, Department of Materials Engineering, Indian Institute of Science.

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extract backscattering amplitude and phase shift files after feff calculation
by Matthias Filez 05 Sep '14

05 Sep '14

Dear mailing list user, I would like to obtain the backscattering amplitude and phase shift files, generated during feff calculations, for photo-electron paths used during modelling. These files (containing F(k), *(k)) should be located in some directory but I really cannot find them back. I know this question has been asked before, but no conclusive answer was provided. I use Windows 7, Intel(R) Core(TM) i5-2520M CPU @ 2.5 GHz, 64-bit OS, 4 GB RAM. Currently I employ Demeter 0.9.13. Please provide me your suggestions/solutions, Many thanks in advance, Matthias Filez

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Re: [Ifeffit] EXAFS calculation with large RMAX and NLEG - exceeding path finder limit
by van der Veen, Renske 04 Sep '14

04 Sep '14

Dear Bruce and Josh, Many thanks for your help! I have followed Josh's suggestion and increased the limits of the nx and npx parameters to very large values (nx=10^6, npx = 800.000 in path_tot.f90, npx = 100.000 in ff2x_tot.f90), and recompiled. The npatx parameter was set to 8 already, so I didn't change it. In addition, in order to get enough paths included in the fine structure, I had to increase the np1x parameter from 60.000 to 200.000. I am not quite sure what kind of parameter this is, but by checking the path listing in the xmu.dat file, I find that all important paths up to 8 A are included now. The fine structure looks much more like the experiment now – yay! Unfortunately there are so many paths, that a real EXAFS fitting analysis is impossible. Thanks again & best wishes, Renske -- Dr. Renske M. van der Veen Deutsches Elektronen Synchrotron (DESY) Notkestraße 85, 22607 Hamburg and Max Planck Institute for Biophysical Chemistry Am Faßberg 11, 37077 Göttingen Germany Tel (work): 0551 201 1265 Tel (mobile): 0176 315 05894 http://www.mpibpc.mpg.de/11851537/vanderveen

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Re: [Ifeffit] Athena data exporting
by Bruce Ravel 03 Sep '14

03 Sep '14

On 09/03/2014 03:21 PM, Dissanayake, Amila C wrote: > Dear Bruce, > > I am Amila Dissanayake, a Ph.D intern at Pacific Northwest National Lab. > I am analyzing XAS data using Athena. But when I am trying to save a > list of data group (about 6 data group) using “ Save marked group > as..” command, all the data groups are not saving into different > columns. When I try to load this file into Origin I could find only just > two columns of data. Could you help me to sort out this problem. I am CCing my answer to the Ifeffit Mailing List, which is the appropriate place to ask questions about the software. http://cars9.uchicago.edu/mailman/listinfo/ifeffit/ You should address any follow up questions to the list. You've not offered enough information that I can even venture a guess as to what is happening. You have not told me what version of the software you are using. You've not provided an example of a project file that triggers the problem. You have not provided a recipe that would allow me to reproduce the problem on my computer. Alas, there's nothing for me to comment on. The "Save marked groups" feature works for me -- I just tried it on both the linux and Windows machines here in my office. Works fine. No one else has ever raised this problem. The one thing that occurs to me is that you may not understand what is meant by the phrase "marked groups". Have you read this page from the document? http://bruceravel.github.io/demeter/aug/ui/mark.html B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

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Maghemite, hematite and magnetite XANES standards
by Javier Alonso 03 Sep '14

03 Sep '14

Dear all, Is there a place where I can download some good XANES standards for these samples? I know that this has been a problem for some time and I have found in the literature recent articles which show different XANES spectra for the "same" iron oxide, so I was wondering about this. The only one I have managed to find is hematite: http://cars9.uchicago.edu/~ravel/software/doc/Standards/fe.html Thanks in advance, Javier -- *Javier Alonso Masa* Research Associate *Basque center for materials, applications & nanostructures*

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Regarding installation of demeter on Mac Mavericks system
by pushkar shejwalkar 03 Sep '14

03 Sep '14

Dear All, I am new to the mac and mac apps as well as not a techie either. I am trying to install the latest version of demeter (artemis, athena and heph) on my macbook using Mavericks OS. For this I followed the steps given on the site with Macports installation, then its activation step. and then I used terminal to connect and download the athena. However there was error which I thought might because of not having the windowing environment ( I am using all the words from site and dont know anything what it means). So I clicked to download X11 from XQuartz site. After that I logged out from terminal and logged in again. to check if anything changes but the following message was observed (the complete message is attached as word document but some part essentially the last portion talking about the error is pasted below. ---> Activating xorg-libXau @1.0.8_0 Error: org.macports.activate for port xorg-libXau returned: Image error: /opt/local/lib/libXau.6.dylib already exists and does not belong to a registered port. Unable to activate port xorg-libXau. Use 'port -f activate xorg-libXau' to force the activation. Error: Failed to install xorg-libXau Please see the log file for port xorg-libXau for details: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_x11_xorg-libXau/xorg-libXau/main.log Error: The following dependencies were not installed: quartz-wm xorg-libAppleWM xorg-libXext xorg-libX11 xorg-libXau xorg-libXdmcp xorg-libxcb python27 bzip2 db46 db_select gettext expat libiconv ncurses libedit openssl zlib python_select sqlite3 xorg-libpthread-stubs xorg-xcb-proto libxml2 xz xorg-xextproto xorg-libXinerama xorg-xineramaproto xorg-libXrandr xorg-randrproto xrender xorg-renderproto xinit mkfontdir mkfontscale freetype libpng xorg-libfontenc xauth xorg-libXmu xorg-libXt xorg-libsm xorg-libice xrdb xset xorg-libXfontcache xorg-fontcacheproto xorg-libXp xorg-printproto xorg-libXxf86misc xorg-xf86miscproto xkeyboard-config xkbcomp xorg-libxkbfile xorg-fonts font-adobe-100dpi fontconfig font-adobe-75dpi font-adobe-utopia-100dpi font-adobe-utopia-75dpi font-adobe-utopia-type1 font-alias font-arabic-misc font-bh-100dpi font-bh-75dpi font-bh-lucidatypewriter-100dpi font-bh-lucidatypewriter-75dpi font-bh-ttf font-bh-type1 font-bitstream-100dpi font-bitstream-75dpi font-bitstream-speedo font-bitstream-type1 font-cronyx-cyrillic font-cursor-misc font-daewoo-misc font-dec-misc font-ibm-type1 font-isas-misc font-jis-misc font-micro-misc font-misc-cyrillic font-misc-ethiopic font-misc-meltho font-misc-misc font-mutt-misc font-schumacher-misc font-screen-cyrillic font-sony-misc font-sun-misc font-winitzki-cyrillic font-xfree86-type1 xorg-encodings xorg-libXfixes xorg-fixesproto xorg-libXfont xorg-fontsproto To report a bug, follow the instructions in the guide: http://guide.macports.org/#project.tickets Error: Processing of port xorg-server failed Pushkar-Shejwalkars-MacBook:~ Pushkar$ Please help me installing it properly. Really very sorry for the long email but I thought it will be more helpful this way. Waiting for the replies. Thank you very much -- Best Regards, Pushkar Shejwalkar. Post-doctoral -Researcher,JSPS Fellow Hokkaido University, Sapporo, Japan

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Re: [Ifeffit] EXAFS calculation with large RMAX and NLEG - exceeding path finder limit
by Joshua Kas 02 Sep '14

02 Sep '14

Hi Renske, Unfortunately, Bruce's idea will not work for exactly the reason he guessed, i.e., that both path and genfmt have hard coded limits. Luckily, it is not so hard to recompile the code with larger dimensions. If you have access to a fortran compiler, you can just use your favorite find and replace to change the variables in question, or we can do it for you if you send us the details of your operating system. What you will want to search for is parameter (npatx = parameter (nx = parameter (npx = The first parameter (npatx) is the maximum number of atoms in a path, not including the absorbing atom at the beginning and the end, so that the maximum number of legs is npatx + 1. For 8 legs, you will need npatx=7. The second parameter (nx) is the dimension for the heap sort of the paths (maximum number of paths kept). I don't know how large this will need to be for graphite, but I have it set to 60000 in my personal version. I think by default it is set to 10000. The third parameter is the internal path finder limit and can be set quite large. I have it set to 4000000 in my personal version. You will probably want to play with the values so that you can get all the paths you want. If you find at some point that the code fails to run altogether (doesn't even start) you may have exceeded the stack limit. In linux you can set the stack limit to unlimited by running ulimit -s unlimited. Cheers, Josh On Tue, Sep 2, 2014 at 10:00 AM, <ifeffit-request(a)millenia.cars.aps.anl.gov> wrote: > 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. Re: EXAFS calculation with large RMAX and NLEG - exceeding > path finder limit (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 02 Sep 2014 11:36:53 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] EXAFS calculation with large RMAX and NLEG - > exceeding path finder limit > Message-ID: <5405E415.4010301(a)bnl.gov> > Content-Type: text/plain; charset=windows-1252; format=flowed > > > Hi Renske, > > As you can tell from the lack of response, there is not a lot of depth > of understanding of the fine details of Feff's pathfinder out there. > My vague memory is that there is a hardwired limit of 7-legged paths > in the pathfinder and that increasing that number is tricky due to > some optimizations that were written in to the code to make it fast on > computers in the early 1990s. But that's a vague memory and could be > wrong. > > Matt and I are in the early stages of working on a version of feff 8.5 > which the folks at the Feff Project contributed under redistributable > licensing. https://github.com/xraypy/feff85exafs > > We have a lot of things we want to do, but the most important thing is > to turn genfmt from a free-standing program into a library that can be > wrapped and called from other software, thus allowing recalculation of > scattering paths as part of the fitting loop. That's cool, but not > really to the point of your question. > > I don't know how much effort you want to put into your problem, but if > you do put in the effort to change the pathfinder in Feff's source, I > hope that you'll contribute your effort to feff85exafs. > > In Artemis, I don't actually use Feff's path finder -- I wrote my own to > overcome some other limitations of the original. Unfortunately, my > implementation stops at 4-legged paths. That's not a technical limit -- > I simply stopped writing code once I got 4-legged paths working. As you > probably know, your sort of problem is something of an outlier. Not a > lot of folk work on problems that need more than 4 legs. > > It would be very nice to have a path finder written for Matt's Larch > project. In fact, it's something I am thinking of doing myself (but I > certainly don't need to!). It would be lovely to have a path finder > in Larch with the advantageous features of Artemis' implementation and > no limit of order of scattering. > > I know that wasn't exactly helpful -- just my musings on the scope of > the problem. > > To make a comment that actually is helpful, I can offer a somewhat > tedious solution that may just work. This is entirely untested -- > there could be some reason I don't know about for why it won't work. > > 1. Run the part of Feff that computes the potentials and write the > phase.bin > > 2. Using a paths.dat from a feff calculation you've already made as a > model, keep the header (everything up to and including the line of > dashes), take a "paragraph" like this: > > 11 4 12.000 index, nleg, degeneracy, r= 5.1053 > x y z ipot label rleg beta > eta > 0.000000 -1.805000 -1.805000 1 'Cu ' 2.5527 > 180.0000 0.0000 > 0.000000 0.000000 0.000000 0 'Cu ' 2.5527 > 0.0000 0.0000 > 0.000000 1.805000 1.805000 1 'Cu ' 2.5527 > 180.0000 0.0000 > 0.000000 0.000000 0.000000 0 'Cu ' 2.5527 > 0.0000 0.0000 > > and edit it to look like this: > > 9999 8 12.000 index, nleg, degeneracy, r= 10.2106 > x y z ipot label > 0.000000 -1.805000 -1.805000 1 'Cu ' > 0.000000 0.000000 0.000000 0 'Cu ' > 0.000000 1.805000 1.805000 1 'Cu ' > 0.000000 0.000000 0.000000 0 'Cu ' > 0.000000 1.805000 1.805000 1 'Cu ' > 0.000000 0.000000 0.000000 0 'Cu ' > 0.000000 1.805000 1.805000 1 'Cu ' > 0.000000 0.000000 0.000000 0 'Cu ' > > That's an 8-legged path. The lreg, beta, and eta columns are not > needed -- those were only written for the human reader, anyway. > > 3. Rename your new file with the header and this one path to > "paths.dat" (preserving the old "paths.dat", of course). > > 4. Run the last part of Feff, the part that reads phase.bin and > paths.dat and writes out the feffNNNN.dat. Doing so will make a > file called "feff9999.dat" (the first integer on the first line > of the paragraph is the NNNN number -- it can be anything from 1 > to 9999). > > I am assuming that you have a sense of which paths you want to > consider and can make these paragarphs by hand without too much > difficulty and that you can figure out what the degeneracy is supposed > to be. (in this example, I think 12 is still correct.) > > Obviously, this a lot of work. And it may be that the nleg limit is > hardwired into genfmt as well. But it's something to try. > > B > > > On 08/22/2014 09:32 AM, van der Veen, Renske wrote: > > Dear FEFF users, > > > > Using FEFF8.4, I am trying to perform EXAFS calculations with rather > > large RMAX and NLEG values. The system of interest is graphite. It has > > been shown by Castrucci et al (J. Phys. Chem. C 2009, 113, 4848?4855), > > that convergence of the EXAFS modulations in the region 4-6 A-1 is only > > achieved for a cluster size of RMAX = 8 and including up to 8-body MS > > paths (NLEG = 8). I have tried to reproduce these calculations and > > noticed that the path finder runs into a limit when I use these > > parameters. I can maximally use RMAX = 7.5 and NLEG = 5. With larger > > RMAX or NLEG values I get the message: > > > > "Internal path finder limit exceeded -- path list may be incomplete.", > > > > and the cluster size subsequently truncated at 6-6.5 A (depending on > > NLEG), instead of the desired 8 A. > > > > My path filter criteria are 3% (plane-wave) and 4% (curved-wave). > > However, these values do not affect the appearance of the above message, > > which occurs before the path filter is applied. Consequently, altering > > the 'npx' parameter, as suggested here > > > http://leonardo.phys.washington.edu/feff/wiki/static/c/o/d/Code_Variables_a… > , > > does not help. > > > > Is there a way to increase this internal path limit so I can work with > > RMAX = 8 and NLEG = 8? > > > > P.S.1 I guess graphite is a special case for which MS can be very > > efficient within the graphite planes. In addition, the C-C bond length > > is quite short, which makes higher n-body paths more important. > > P.S.2 I have tried merging XANES and EXAFS using the cards: XANES, FMS > > 6, RPATH 8 and NLEG 8, but the same problem occurs and the agreement > > with experiment in the low-k region 3-6 A-1 does not become better using > > FMS (compared to the path expansion). > > > > Thanks in advance, > > Best wishes, > > Renske > > > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > -- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2 > Building 535A > Upton NY, 11973 > > Homepage: http://bruceravel.github.io/home/ > Software: https://github.com/bruceravel > Demeter: http://bruceravel.github.io/demeter/ > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 139, Issue 5 > *************************************** >

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EXAFS calculation with large RMAX and NLEG - exceeding path finder limit
by van der Veen, Renske 02 Sep '14

02 Sep '14

Dear FEFF users, Using FEFF8.4, I am trying to perform EXAFS calculations with rather large RMAX and NLEG values. The system of interest is graphite. It has been shown by Castrucci et al (J. Phys. Chem. C 2009, 113, 4848–4855), that convergence of the EXAFS modulations in the region 4-6 A-1 is only achieved for a cluster size of RMAX = 8 and including up to 8-body MS paths (NLEG = 8). I have tried to reproduce these calculations and noticed that the path finder runs into a limit when I use these parameters. I can maximally use RMAX = 7.5 and NLEG = 5. With larger RMAX or NLEG values I get the message: "Internal path finder limit exceeded -- path list may be incomplete.", and the cluster size subsequently truncated at 6-6.5 A (depending on NLEG), instead of the desired 8 A. My path filter criteria are 3% (plane-wave) and 4% (curved-wave). However, these values do not affect the appearance of the above message, which occurs before the path filter is applied. Consequently, altering the 'npx' parameter, as suggested here http://leonardo.phys.washington.edu/feff/wiki/static/c/o/d/Code_Variables_a…, does not help. Is there a way to increase this internal path limit so I can work with RMAX = 8 and NLEG = 8? P.S.1 I guess graphite is a special case for which MS can be very efficient within the graphite planes. In addition, the C-C bond length is quite short, which makes higher n-body paths more important. P.S.2 I have tried merging XANES and EXAFS using the cards: XANES, FMS 6, RPATH 8 and NLEG 8, but the same problem occurs and the agreement with experiment in the low-k region 3-6 A-1 does not become better using FMS (compared to the path expansion). Thanks in advance, Best wishes, Renske

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