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

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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spline fitting
by Matthias Filez 29 Aug '14

29 Aug '14

Dear mailing list users, I am trying to fit the spline background function in a proper way to a spectrum (Ga K edge, see attached). However, it doesn't seem to work out, but I don't see why. I already tried the following: * Vary the Rbkg value * Change spline k-weight * Change k-range of spline fitting * Alter the strength of spline clamps ... and the combination of these effects. Since there is a strong white line, I suspect this causes the spline misfit. The data quality is OK. If you have any idea, please post it. Thanks in advance, Matthias _____________________ Matthias Filez Laboratory for Chemical Technology Department of Chemical Engineering Ghent University Technologiepark 914, B-9052 Zwijnaarde, Belgium +32 (0)9 33 11721 www.lct.ugent.be<http://www.lct.ugent.be/> Disclaimer: http://helpdesk.UGent.be/e-maildisclaimer.php<http://helpdesk.ugent.be/e-maildisclaimer.php>

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Demeter OS X plot button colors in Athena
by Schima, Frank 27 Aug '14

27 Aug '14

Hi Bruce, We are seeing an issue in Athena where the plot buttons are not colored correctly. According to section 2.1 of the Athena Users’s Guide, the top row of plot buttons highlighted in the image should be the same color (purple) as the plotting option widgets below them. The 2nd row of plot buttons should be yellowish. However on OS X, all plot buttons appear uncolored. By far the best way to illustrate this is with a screenshot of the Athena UI. I hope the attached image is clear enough to show the issue. I am running Demeter version 0.9.20pre10 via Macports demeter-devel on OS X 10.9.4. BTW, I am happy to work with you on other OS X issues but I am not actually a demeter user and I don’t have much data myself. But if you send me some data, I can follow steps to try to reproduce issues. [cid:F140B9BC-1ABC-4ACE-B222-A833F804F78B] Cheers! Frank

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XAFS short course at Brookhaven
by Anatoly I Frenkel 26 Aug '14

26 Aug '14

Dear subscribers: An annual short course on Methods and Applications of XAFS Spectroscopy will be run at Brookhaven National Laboratory in Nov. 13-15, 2014. The application deadline is Sep. 1. The application form is available at the course web site: http://workshops.ps.bnl.gov/?w=XAFS2014 The application form should filled out first; the 45 participants accepted to the course will be later contacted with registration information. Best regards, Anatoly Anatoly Frenkel, Professor Department of Physics, Yeshiva University 245 Lexington Avenue, New York, NY 10016 https://yu.edu/faculty-bios/frenkel/ Spokesperson, Synchrotron Catalysis Consortium http://yu.edu/scc Office: (212) 340-7827, Lab: (631) 344-3013, Email: anatoly.frenkel(a)yu.edu<mailto:anatoly.frenkel@yu.edu>

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math functions on GDS page
by huyanyun＠physics.utoronto.ca 21 Aug '14

21 Aug '14

Hi there, When I input math expression in the GDS page, I wonder if Artemis recognizes some general math functions, such as 'sqrt', 'cos', 'sin'. Could anyone help me find a list of all math functions covered in Artemis? Best, Yanyun

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Re: [Ifeffit] Questions for Artemis fit
by 이국승 20 Aug '14

20 Aug '14

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Re: [Ifeffit] Artemis and FEFF interaction in fit process
by Nate Turner 19 Aug '14

19 Aug '14

In an instance of Artemis, the Feff executable is run as needed to make the feffNNNN.dat files. That is, the first time you make a plot or a fit (there are a few other actions that will also trigger this), Artemis will run the Feff executable to make the path that is needed. Thus each path plotted or used in a fit requires a system call. I see, so to be clear if I run FEFF9 and make the feffNNNN.dat paths through it, outside of Artemis, then import the feffNNNN.dat files into Artemis, FEFF6L is still called to when I want to plot or use a path in a fit? Thanks for the quick response. Nate Turner

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Artemis and FEFF interaction in fit process
by Nate Turner 19 Aug '14

19 Aug '14

Hello All, I have a question about Artemis' interaction with FEFF. I know you can either run FEFF6L in Artemis to populate a paths list or externally create the FEFFnnnn.dat files in FEFF and import them into Artemis. We currently do the later using FEFF9, the use of the SCF card gives a better Eo initial guess and our compound has fractional occupancy/disorder that requires us to do some altering of the atoms list after its populated in ATOMS, which we find best to do outside of Artemis. My question is once these external FEFF9 paths are brought in does Artemis use FEFF6L in the fit process or is FEFF in Artemis only to populate the paths list? If Artemis doesn't use FEFF in the fit process then there's no issue but while I've read the mailing list and seen that many do not believe there is any improvement in the EXAFS results from FEFF6L to FEFF9, I'd rather be consistent in which version of FEFF we use throughout the analysis. I would have Artemis calling to FEFF9 instead of FEFF6L if in fact Artemis does use FEFF in the fit. The reason I haven't gone ahead with having Artemis call to FEFF9 making this a non issue is I'm not sure how. I know you can direct Artemis to whatever version of FEFF you want under preferences, but then I'm not sure what file I need to direct to specifically for FEFF9. So to summarize, Does Artemis use FEFF in the fitting process or is its only function in Artemis to create the paths for the fit? If it does use FEFF in the fitting, how do you/is it possible to have Artemis call to FEFF9 instead of FEFF6L? Thanks all for your time, Nate Turner

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