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

The first step involve in Bio-physics simulation
by 沛昌蔡 15 Aug '08

15 Aug '08

Dear Prof. and authors: We have involved Bio-physics experiment recently, but we have no idea about the simulation softwave (free is better), and our protein sample is rod figure, so do you have any idea about the simulation, such as vibration mode, absorption, molecular structure. We are so appreciate with your information. Thanks for your time and feedback! Tsai pei-chang _________________________________________________________________________________________________________ 知識+ 的電玩高手全都在這裡！ http://tw.knowledge.yahoo.com/dir/group_buzz?time=total&type=article&sid=39…

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Bug: Can't type into Athena on Linux
by Gregory Merchan 14 Aug '08

14 Aug '08

Hi everyone, We uncovered a bug that affects Athena and friends. When SCIM is running, Perl/Tk programs do not respond to keyboard events. These reports have more information: https://bugzilla.novell.com/show_bug.cgi?id=77424 https://bugzilla.novell.com/show_bug.cgi?id=309794 (Googled for those links. We were running an up-to-date Ubuntu.) This affected Horae 066 and I've not yet tested the latest release. Hope this helps, Greg P.S. - Now googling the symptoms should be useful. I don´t expect a fix, since the problem is upstream.

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Re: [Ifeffit] Athena can not open any file
by Gilberto Fernandes Lopes Fabbris 14 Aug '08

14 Aug '08

Hello, I made as you said and now everything is working! Thanks!! Gilberto

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update to ifeffit source kit
by Matt Newville 13 Aug '08

13 Aug '08

Hi Folks, I found a serious bug in the ifeffit-1.2.11 source code kit that was on the cars.uchicago.edu and sourceforge.net sites. This bug would become readily apparent, as many operations beyond the simplest tests will not work correctly, so like any actual use of Athena would be clearly wrong. Sorry for any trouble! I uploaded a fixed source code kit (ifeffit-1.2.11a.tar.gz) to both the cars.uchicago.edu and sourceforge.net sites. This bug does not affect the Windows binaries. --Matt

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Re: [Ifeffit] Athena can not open any file
by Gilberto Fernandes Lopes Fabbris 12 Aug '08

12 Aug '08

Hello again, I tried to install the new package of both ifeffit(1.2.11) and horae (0.67) but it also didn't work. I first removed any file related to ifeffit and horae that I could find. Pgplot, ifeffit, Xray-Absorption, Xray-Scattering and Chemistry-Formula installation runned without error and I could open ifeffit on command line. But the error mensage below appeared when I runned the "perl Build.PL" on horae. ... Checking whether your kit is complete... Looks good Checking prerequisites... Package 'Config::IniFiles' already declared with version '2.39', ignoring subsequent declaration. Looks good Deleting Build Removed previous script 'Build' Creating new 'Build' script for 'horae' version '067' ... Even though this error I runned ./Build and ./Build install and no error appeared. But when I tried to run athena (it also happens on artemis) the error appeared: ...... Can't locate Ifeffit.pm in @INC (@INC contains: /usr/lib/perl5/5.10.0/x86_64-linux-thread-multi /usr/lib/perl5/5.10.0 /usr/lib/perl5/site_perl/5.10.0/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.10.0 /usr/lib/perl5/vendor_perl/5.10.0/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.10.0 /usr/lib/perl5/vendor_perl .) at /usr/bin/athena line 67. BEGIN failed--compilation aborted at /usr/bin/athena line 67. ..... I looked for the Ifeffit.pm file on /usr/lib/perl5 and it doesnt exist. Thanks, Gilberto ps: I will write on the FAQ as soon as possible... :)

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new software releases
by Bruce Ravel 11 Aug '08

11 Aug '08

Hi folks, I just uploaded source code and a Windows installer for Ifeffit 1.2.11 to SourceForge. Both are also available for download from the Ifeffit web site. Source code packages for my programs (Athena, Artemis, Hephaestus) can be found at SourceForge or on my website. Macintosh installer packages will be available soon. For the windows users, the new installer package has a number of advantages, including: * New compilation of ifeffit, resulting in noticeably faster execution compared to the 1.2.10 release * Latest versions of SixPack, Athena, Artemis, and Hephaestus * Perl 5.8 and PerlApp 7.2 were used to build my programs, solving a number of performance issues reported in recent months * The Athena User's Guide is included in the package and the html version is now used as the internal documentation in Athena We recommend that all windows users upgrade to the new version. As always, let us know about any issues, comments, or suggestions that you might have. This version was used successfully at the APS XAFS Summer School last week. While not an exhaustive testing, it seems to be a good release so far. Regards, B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

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several FEFF-questions
by Bosman, Eckhard 11 Aug '08

11 Aug '08

Hello, i read in the FEFF 8.4 manual, that the 6 modules are executed in ascending order. But now i'm confused concerning the modules 3 till 5. In module 3 the full multiple scattering is calculated. But only after this module the path enumeration (module 4) and the scattering amplitudes (module 5) are computed. I thought the path enumeration and the scattering amplitudes are required for calculation of the full multiple scattering? Why are these quantities calculated after the fms module? In my opinion this doesn't make sense. Another question affects the paper (page 9 and 10) of Zabinsky et al (attached). In the section "path enumeration" (respectively one side bevor) he introduced the quantity r_tot = total path length and R = r_tot/2 = effective path length. My question is, what is the meaning of the effective path length? In my opinion r_tot is the way and the way back? And R < r_tot is the path length without negligible contributions (scattering amplitude,...), is this right? The next question concerns the XANES-Card. What is the meaning of k respectively xkmax? In my opinion k is the wavenumber (of the photo electron wave?) which occurs in the xmu.dat in the third column, isn't it? Many thanks for your help! best regards, Eckhard

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Athena can not open any file
by Gilberto Fernandes Lopes Fabbris 11 Aug '08

11 Aug '08

hello, I have a amd 64 bits computer running opensuse 11. I tried to install ifeffit on it and it was very complicated. After some modifications on the makefile of PGPlot (as showed here: http://proteus.pha.jhu.edu/~dks/Unixtips/index.html) and during the horae install (http://cars9.uchicago.edu/pipermail/ifeffit/2006-September/002621.html and http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2008-January/003481.html) After those changes the artemis is working well, but athena is not... the program opens but I can not open any file. When I opened athena on terminal and tried to open a file the error below appeares. Tk::Error: Failed to AUTOLOAD 'Tk::FBox::_get_select_Path' at /usr/bin/athena line 5212 Carp::croak at /usr/lib/perl5/5.10.0/Carp.pm line 44 Tk::Widget::__ANON__ at /usr/lib/perl5/vendor_perl/5.10.0/x86_64-linux-thread- multi/Tk/Widget.pm line 347 Tk::FBox::Done at /usr/lib/perl5/vendor_perl/5.10.0/x86_64-linux-thread-multi/Tk/FBox.pm line 909 Tk::FBox::VerifyFileName at /usr/lib/perl5/vendor_perl/5.10.0/x86_64-linux-thread- multi/Tk/FBox.pm line 678 Tk::FBox::ActivateEnt at /usr/lib/perl5/vendor_perl/5.10.0/x86_64-linux-thread- multi/Tk/FBox.pm line 647 Tk::FBox::OkCmd at /usr/lib/perl5/vendor_perl/5.10.0/x86_64-linux-thread-multi/Tk/FBox.pm line 815 Tk callback for .fbox.frame1.button Tk::__ANON__ at /usr/lib/perl5/vendor_perl/5.10.0/x86_64-linux-thread-multi/Tk.pm line 250 Tk::Button::butUp at /usr/lib/perl5/vendor_perl/5.10.0/x86_64-linux-thread- multi/Tk/Button.pm line 175 <ButtonRelease-1> (command bound to event) Thanks, Gilberto

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[OT] Ball&sticks open source Perl/Python libraries
by Mauro Rovezzi 31 Jul '08

31 Jul '08

Dear all, I'm sorry if I introduce an off-topic (OT) subject but I would like to ask if you have knowledge of a simple ball&stick open source library that could be called from Perl or Python in order to generate "on the fly" theoretical paths visualization (or any atomic structure). At the moment the simplest (and useful!) utility I have found is XBS (http://ihp02.ihp-ffo.de/~msm/) but it is not the best solution because it needs input files and the output quality is low. Thanks for your help, Mauro -- Mauro Rovezzi <rovezzi(a)esrf.fr> PhD student - GILDA BM08 c/o ESRF (Grenoble, FR)

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reference spectra for Cu(OH)2
by Zajac, Dariusz 30 Jul '08

30 Jul '08

Hi all, as now we have a time for XAS spectra requests, I would like to ask you also for one. I need spectra of Cu(OH)_{2}. If someone could help I would preciate. Thanks in advance darek ------------------------------------------------------------------------ dr. Zajac Dariusz A. Deutsches Elektronen-Synchrotron -Hasylab phone: +49-40-8998-2932 Notkestr. 85 fax: +49-40-8998-2787 22607 Hamburg e-mail: dariusz.zajac(a)desy.de Germany ------------------------------------------------------------------------

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Re: [Ifeffit] Ifeffit Digest, Vol 65, Issue 21
by sankaran anantharaman 30 Jul '08

30 Jul '08

Hi Darek, If you have not found the spectrum in the database, here you go... -Sankaran Uni Stuttgart ! ! Comments %c EXAFS-Scan started at 28-Nov-2006 00:54:18, ended 02:23:54 Name: cuoh2_00002 from 8689 to 10175.77 Cu 0.8mu, MOT8 at 62.2 Counter readings are offset corrected and normalized to 1s, the offsets are: C1 0 C2 0 C3 0 C5 0 C1 0.1 C2 0.1 C3 0.1 C5 0 ! ! Parameter %p ! ! The EXAFS Scan Regions ! ! Energy Delta Sample_Time Edge Power ! 8689 1 1 0 0 ! 8949 0.5 1 0 0 ! 9019 0.818 1 8979 1 ! 10179 0 0 0 0 ! ENERGY = 8979 THETA2 = 12.72019 THETA1 = 12.72019 MC2_Z = 33.63474 EXIT_SLIT_TOP = 0.5000014 EXIT_SLIT_BOTTOM = -0.5 EXIT_SLIT_LEFT = 4 EXIT_SLIT_RIGHT = -4 SAMPLE_HEIGHT = 62.2 REFERENCE_HEIGHT = 40.01077 MONO_ENTR_SLIT = -60 PLANE_MIRR_SLIT = 0.5000793 PLANE_MIRR_THETA = -0.1680022 PLANE_MIRR_TRANSL = -32 PLANE_MIRR_HEIGHT = 0 REFL_SLIT_TOP = 2 REFL_SLIT_BOTTOM = -2 REFL_SLIT_LEFT = 8.5 REFL_SLIT_RIGHT = -7.5 TORO_MIRR_THETA = 0.01400023 TORO_MIRR_TRANSL = 5.7 TORO_MIRR_RHO_OLD = -0.5101779 TORO_MIRR_HEIGHT = 2.6 WHITE_SLIT_TOP = 0.9 WHITE_SLIT_BOTTOM = -0.9 TORO_MIRR_RHO = -0.4290012 MOT26 = -73 SAMPLE_HEIGHT_OLD = 24.50071 SAMPLE_RHO = 93 DET_VER = 10.5 MOT30 = 0 HE_KRYO_HEIGHT = 78.89 SAMPLE_HORIZONTAL = 84 ! ! Data %d Col 1 CUOH2_00002 FLOAT Col 2 CUOH2_00002 FLOAT Col 3 CUOH2_00002_REF FLOAT Col 4 cuoh2_00002_C1_SCAN_C1 FLOAT Col 5 cuoh2_00002_C2_SCAN_C2 FLOAT Col 6 cuoh2_00002_C3_SCAN_C3 FLOAT Col 7 cuoh2_00002_C5_SCAN_C4 FLOAT Col 8 CUOH2_00002_IDORIS FLOAT Col 9 CUOH2_00002_DELTA FLOAT Col 10 CUOH2_00002_SAMPLE_TIME FLOAT 8688.999 -0.9160514 -1.616946 79421 198505 1000005 582 140.702 1 1 8690.005 -0.916195 -1.616891 79414 198516 1000005 582 140.6929 1 1 8690.995 -0.9167968 -1.616227 79419 198648 1000006 581 140.6842 1 1 8692.002 -0.9169251 -1.616085 79420 198676 1000005 581 140.674 1 1 8692.992 -0.9172173 -1.616071 79398 198679 1000006 581 140.6638 1 1 8694 -0.9173985 -1.61589 79398 198715 1000006 581 140.6554 1 1 8695.007 -0.9175774 -1.616 79375 198693 1000006 581 140.6465 1 1 8695.998 -0.9180022 -1.61531 79396 198830 1000005 582 140.637 1 1 8697.006 -0.9181758 -1.6152 79391 198852 1000006 581 140.6282 1 1 8697.998 -0.9184055 -1.615411 79356 198810 1000005 581 140.6196 1 1 8699.006 -0.9188882 -1.614879 79360 198916 1000006 581 140.6109 1 1 8699.998 -0.919215 -1.614577 79358 198976 1000006 582 140.6004 1 1 8701.006 -0.9190844 -1.614758 79354 198940 1000006 581 140.5925 1 1 8702 -0.9195341 -1.614271 79357 199037 1000006 581 140.5798 1 1 8703.009 -0.9196827 -1.614235 79348 199044 1000006 582 140.5725 1 1 8704.002 -0.9202557 -1.613763 79340 199138 1000006 581 140.5607 1 1 8704.995 -0.9202415 -1.614004 79322 199090 1000006 581 140.5531 1 1 8706.005 -0.9206479 -1.613522 79328 199186 1000006 581 140.5436 1 1 8706.998 -0.9208564 -1.613352 79325 199220 1000006 581 140.5332 1 1 8707.992 -0.9210504 -1.61332 79312 199226 1000005 580 140.524 1 1 8709.004 -0.9215401 -1.612919 79305 199306 1000005 581 140.5152 1 1 8709.998 -0.9218105 -1.612548 79313 199380 1000005 581 140.5069 1 1 8710.993 -0.9218587 -1.612589 79306 199372 1000006 581 140.4979 1 1 8712.004 -0.9224178 -1.612042 79305 199481 1000006 580 140.4869 1 1 8712.999 -0.9223476 -1.612111 79305 199467 1000005 581 140.4789 1 1 8713.994 -0.9228746 -1.611686 79297 199552 1000006 581 140.4701 1 1 8715.007 -0.9229347 -1.611626 79297 199564 1000006 581 140.4633 1 1 8716.003 -0.9232742 -1.611475 79282 199594 1000005 581 140.4522 1 1 8716.999 -0.9237504 -1.61105 79278 199679 1000006 581 140.4415 1 1 8717.995 -0.9235653 -1.611261 79276 199637 1000006 581 140.4301 1 1 8718.992 -0.9242787 -1.610533 79277 199782 1000005 580 140.4213 1 1 8720.005 -0.9240496 -1.610915 79265 199706 1000006 581 140.4116 1 1 8721.002 -0.9245644 -1.610298 79273 199829 1000005 581 140.4038 1 1 8722 -0.9251846 -1.609943 79252 199900 1000005 581 140.3925 1 1 8722.997 -0.9253718 -1.609719 79255 199945 1000006 581 140.3823 1 1 8723.995 -0.9256028 -1.609589 79247 199971 1000006 581 140.3733 1 1 8724.993 -0.9256823 -1.609458 79251 199997 1000005 581 140.364 1 1 8726.008 -0.925855 -1.609564 79229 199976 1000006 581 140.3555 1 1 8727.006 -0.9264488 -1.608869 79237 200115 1000006 581 140.344 1 1 8728.005 -0.9264717 -1.608884 79234 200112 1000006 580 140.338 1 1 8729.004 -0.927026 -1.608544 79217 200180 1000006 581 140.3279 1 1 8730.003 -0.9269611 -1.608609 79217 200167 1000006 581 140.3182 1 1 8731.003 -0.9277296 -1.60779 79221 200331 1000006 581 140.3119 1 1 8732.002 -0.9276711 -1.607974 79211 200294 1000005 581 140.3007 1 1 8733.002 -0.9277956 -1.607825 79213 200324 1000006 582 140.2908 1 1 8734.003 -0.9280737 -1.60785 79189 200319 1000006 582 140.2835 1 1 8735.003 -0.9282715 -1.607501 79201 200389 1000006 581 140.273 1 1 8736.004 -0.9286039 -1.607421 79181 200405 1000006 581 140.2634 1 1 8737.005 -0.9287407 -1.607246 79184 200440 1000006 581 140.2543 1 1 8738.006 -0.9291416 -1.606998 79172 200490 1000007 580 140.2447 1 1 8739.007 -0.9293418 -1.606847 79168 200520 1000006 581 140.236 1 1 8739.992 -0.929958 -1.606269 79165 200636 1000006 581 140.2262 1 1 8740.994 -0.9298488 -1.606593 79148 200571 1000006 581 140.2196 1 1 8741.996 -0.9302292 -1.606149 79153 200660 1000006 581 140.2088 1 1 8742.998 -0.9306677 -1.605712 79153 200748 1000007 581 140.1994 1 1 8744.001 -0.9305344 -1.605756 79160 200739 1000006 581 140.1887 1 1 8745.004 -0.9311802 -1.605502 79129 200790 1000006 581 140.1833 1 1 8746.006 -0.9314628 -1.605143 79135 200862 1000006 581 140.1717 1 1 8746.993 -0.9318132 -1.604919 79125 200907 1000006 581 140.1613 1 1 8747.997 -0.9318757 -1.605034 79111 200884 1000006 581 140.1561 1 1 8749 -0.9325858 -1.604387 79106 201014 1000006 581 140.1431 1 1 8750.005 -0.9325852 -1.604501 79097 200991 1000006 581 140.1333 1 1 8750.991 -0.932791 -1.604257 79100 201040 1000006 581 140.1257 1 1 8751.996 -0.9329993 -1.604162 79091 201059 1000005 580 140.1168 1 1 8753.001 -0.9332858 -1.604053 79077 201081 1000006 581 140.1051 1 1 8754.006 -0.9335842 -1.603615 79088 201169 1000005 581 140.0964 1 1 8754.994 -0.9340215 -1.603318 79077 201229 1000006 580 140.089 1 1 8756 -0.9343268 -1.603138 79067 201265 1000005 580 140.0784 1 1 8757.006 -0.933955 -1.603561 79063 201180 1000006 581 140.0686 1 1 8757.994 -0.9349874 -1.602478 79067 201398 1000006 581 140.0589 1 1 8759 -0.9348328 -1.602861 79049 201321 1000006 581 140.0515 1 1 8760.007 -0.9350347 -1.602836 79035 201326 1000006 581 140.0409 1 1 8760.997 -0.9354887 -1.60223 79047 201448 1000006 580 140.0314 1 1 8762.004 -0.9356693 -1.602151 79039 201464 1000006 581 140.0201 1 1 8762.994 -0.9357593 -1.602224 79026 201449 1000005 581 140.0117 1 1 8764.002 -0.9361541 -1.601843 79025 201526 1000006 581 140.0029 1 1 8764.993 -0.9364461 -1.601639 79018 201567 1000006 580 139.9928 1 1 8766 -0.9369649 -1.60102 79026 201692 1000006 580 139.9855 1 1 8766.992 -0.9367937 -1.60143 79007 201609 1000005 580 139.9747 1 1 8768 -0.9372631 -1.601 79004 201696 1000006 581 139.9644 1 1 8768.992 -0.9377688 -1.60038 79013 201821 1000006 580 139.9571 1 1 8770.001 -0.9377069 -1.600682 78994 201760 1000006 581 139.9463 1 1 8770.993 -0.9379404 -1.600473 78992 201802 1000005 581 139.9344 1 1 8772.002 -0.938574 -1.599815 78994 201935 1000006 581 139.9287 1 1 8772.995 -0.9387199 -1.599885 78977 201921 1000006 581 139.9177 1 1 8774.005 -0.9390368 -1.599568 78977 201985 1000006 581 139.908 1 1 8774.998 -0.9392062 -1.599449 78973 202009 1000006 581 139.8988 1 1 8776.009 -0.9393038 -1.599502 78961 201998 1000005 581 139.8904 1 1 8777.002 -0.9398196 -1.599038 78957 202092 1000006 580 139.8799 1 1 8777.996 -0.939939 -1.599261 78930 202047 1000006 581 139.873 1 1 8779.007 -0.9400718 -1.598988 78941 202102 1000005 581 139.8622 1 1 8780.002 -0.9404982 -1.598499 78946 202201 1000006 581 139.8542 1 1 8780.996 -0.9407615 -1.598285 78942 202244 1000005 581 139.846 1 1 8782.008 -0.9411249 -1.598024 78934 202297 1000006 580 139.8362 1 1 8783.003 -0.9412766 -1.598113 78915 202279 1000006 581 139.8263 1 1 8783.998 -0.9413125 -1.598127 78911 202276 1000005 581 139.8191 1 1 8784.993 -0.941655 -1.597748 78914 202353 1000006 581 139.8055 1 1 8786.006 -0.9417889 -1.597435 78928 202416 1000005 581 139.7979 1 1 8787.002 -0.942345 -1.597184 78904 202467 1000006 581 139.7871 1 1 8787.998 -0.9426057 -1.597075 78892 202489 1000005 582 139.7815 1 1 8788.995 -0.9430081 -1.596483 78907 202609 1000006 581 139.7697 1 1 8790.008 -0.9426519 -1.597283 78872 202447 1000006 581 139.7613 1 1 8791.005 -0.9436069 -1.596227 78880 202661 1000006 581 139.7515 1 1 8792.002 -0.9436469 -1.59639 78864 202628 1000006 581 139.7449 1 1 8793 -0.9438987 -1.595871 78885 202733 1000006 580 139.7354 1 1 8793.997 -0.9439424 -1.59598 78873 202711 1000006 581 139.7269 1 1 8794.995 -0.9440198 -1.596118 78856 202683 1000006 581 139.718 1 1 8795.994 -0.9443827 -1.595768 78855 202754 1000006 581 139.7064 1 1 8796.992 -0.9447399 -1.595486 78849 202811 1000005 581 139.699 1 1 8798.007 -0.9448519 -1.595413 78846 202826 1000006 581 139.6903 1 1 8799.006 -0.9452216 -1.595043 78846 202901 1000006 581 139.6779 1 1 8800.005 -0.9456637 -1.594639 78843 202983 1000006 581 139.6713 1 1 8801.005 -0.9456754 -1.594944 78818 202921 1000005 581 139.6606 1 1 8802.005 -0.9462643 -1.594278 78824 203056 1000005 582 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85453.33 163812.3 581.282 132.6019 3.204 3.9 9596.03 -0.1346313 -0.6542099 74786.23 85564.03 164592.9 581.3776 132.5792 3.212 3.92 9599.252 -0.1367566 -0.6549785 74764.28 85720.91 165021.4 581.3776 132.5565 3.221 3.92 9602.458 -0.1377459 -0.6598048 74758.38 85798.98 165970.8 580.9645 132.5379 3.229 3.94 9605.686 -0.13916 -0.6622153 74744.16 85904.06 166575.1 581.2183 132.513 3.237 3.94 9608.935 -0.1409 -0.6645078 74716.41 86021.72 167186.1 581.3131 132.489 3.246 3.96 9612.187 -0.1423868 -0.6654978 74716.66 86150 167601.3 581.5657 132.4684 3.254 3.96 9615.439 -0.1441378 -0.6666825 74706.03 86288.7 168070.1 581.6583 132.445 3.262 3.98 9618.695 -0.1453122 -0.6691434 74687.44 86368.59 168640.2 581.1558 132.4236 3.271 3.98 9621.975 -0.1472188 -0.6701577 74681.25 86526.25 169119.5 581.25 132.4026 3.279 4 9625.254 -0.1482114 -0.6754264 74653.5 86580 170118.5 581.25 132.3776 3.287 4 9628.538 -0.1497721 -0.6768902 74636.32 86695.27 170594.5 581.3433 132.3576 3.296 4.02 9631.822 -0.1511741 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188090.8 581.4554 131.8056 3.496 4.26 9713.459 -0.1824195 -0.7516828 74319.62 89192.29 189138.1 581.7757 131.783 3.505 4.28 9716.945 -0.183632 -0.7557339 74303.27 89280.84 190094.4 581.3084 131.757 3.513 4.28 9720.477 -0.1852446 -0.7564353 74277.91 89394.41 190469.8 581.6279 131.7345 3.521 4.3 9723.989 -0.18661 -0.7602264 74269.77 89506.74 191433.5 581.3953 131.71 3.53 4.3 9727.525 -0.1882126 -0.7622097 74262.03 89640.97 192101.2 581.4814 131.6872 3.538 4.32 9731.064 -0.1897114 -0.7663843 74245.6 89755.55 193151.4 581.4814 131.6647 3.546 4.32 9734.605 -0.1913879 -0.7673346 74223.96 89879.95 193603 581.106 131.6408 3.555 4.34 9738.149 -0.1924753 -0.7704337 74219.12 89971.88 194402.5 581.3364 131.6174 3.563 4.34 9741.717 -0.1941731 -0.7727069 74201.38 90103.21 195129.4 581.1926 131.5921 3.571 4.36 9745.286 -0.1954897 -0.7756405 74198.62 90218.58 195953.2 581.1926 131.5687 3.58 4.36 9748.879 -0.1972325 -0.7773853 74178.08 90350.91 196583.3 581.2785 131.5416 3.588 4.38 9752.454 -0.1983988 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131.2562 3.688 4.5 9796.188 -0.2153694 -0.8171718 73995.78 91778.45 207794.4 581.5555 131.2299 3.697 4.5 9799.882 -0.2169705 -0.8197341 73985.4 91912.61 208632.1 581.8584 131.2065 3.705 4.52 9803.579 -0.2188276 -0.8212922 73976.21 92072.02 209319.8 581.0573 131.1819 3.713 4.54 9807.299 -0.2202323 -0.8233477 73951.54 92170.7 209975.3 581.0573 131.1584 3.722 4.54 9811.022 -0.2214481 -0.8277655 73920.84 92244.52 211073.9 581.579 131.132 3.73 4.56 9814.748 -0.2229134 -0.8313667 73930.7 92392.11 212174.3 581.579 131.1076 3.739 4.56 9818.498 -0.2242077 -0.8357968 73902.62 92476.64 213311.4 581.441 131.0814 3.747 4.58 9822.229 -0.2259346 -0.8372965 73884.5 92613.76 213948.2 581.6594 131.0585 3.755 4.58 9825.985 -0.2275993 -0.8394876 73886.74 92770.88 214781.3 581.3044 131.0333 3.764 4.6 9829.764 -0.2289489 -0.8420216 73863.7 92867.18 215549.8 581.3044 131.0102 3.772 4.6 9833.525 -0.2301332 -0.8469578 73846.54 92955.63 216822.7 581.6017 130.9845 3.78 4.62 9837.311 -0.2316851 -0.8518745 73840.7 93092.64 218212.6 581.1688 130.9587 3.789 4.62 9841.1 -0.2331145 -0.8530397 73824.36 93205.17 218731 580.819 130.9328 3.797 4.64 9844.89 -0.2347148 -0.8559673 73814.88 93342.46 219695.5 580.6035 130.9058 3.805 4.64 9848.705 -0.2361134 -0.8592763 73788.84 93440.13 220654.3 581.1159 130.8839 3.814 4.66 9852.524 -0.2375821 -0.8624155 73785.62 93573.39 221663.7 581.1159 130.8582 3.822 4.66 9856.346 -0.2389406 -0.866123 73765.81 93675.43 222729.7 580.9829 130.8306 3.83 4.68 9860.17 -0.240465 -0.8694502 73750.22 93798.51 223765.6 580.9829 130.8087 3.839 4.68 9864.019 -0.2416302 -0.8724822 73746.38 93902.98 224695.1 581.4894 130.7789 3.847 4.7 9867.849 -0.2433288 -0.8744358 73720.64 94029.79 225438.5 581.2766 130.7556 3.856 4.7 9871.702 -0.2449749 -0.8757373 73718.86 94182.42 226098.5 581.1441 130.7328 3.864 4.72 9875.581 -0.2466001 -0.8782026 73696.83 94307.42 226957.4 581.1441 130.7064 3.872 4.72 9879.443 -0.2476443 -0.882942 73674.9 94377.85 228205.9 581.2236 130.6818 3.881 4.74 9883.327 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5.1 10024.44 -0.3009697 -0.9957541 73139.02 98823.14 267491 581.1765 129.7409 4.181 5.1 10028.62 -0.3022175 -1.000394 73134.38 98940.23 269053.3 581.4453 129.7136 4.19 5.12 10032.8 -0.3035528 -1.00374 73104.69 99032.23 270206.1 581.4453 129.6855 4.198 5.12 10037 -0.3049954 -1.004922 73079.96 99141.64 270824.7 580.7393 129.659 4.206 5.14 10041.21 -0.3067298 -1.005635 73069.84 99300 271450.8 580.9338 129.6328 4.215 5.14 10045.42 -0.3081777 -1.009801 73054.27 99422.68 272920.6 581.3954 129.605 4.223 5.16 10049.64 -0.309582 -1.012877 73037.21 99539.15 274082.2 581.3954 129.5743 4.232 5.16 10053.88 -0.3105683 -1.016986 73020.85 99615.06 275420.7 581.4672 129.5518 4.24 5.18 10058.12 -0.3121064 -1.019782 72999.62 99739.38 276536.5 581.2742 129.523 4.248 5.18 10062.38 -0.3135855 -1.021047 72995.2 99880.97 277279.4 580.9615 129.4976 4.257 5.2 10066.63 -0.3147411 -1.025627 72978.27 99973.27 278809.8 580.9615 129.4716 4.265 5.2 10070.88 -0.3162828 -1.028625 72959.2 100101.3 280005.2 581.4177 129.4412 4.273 5.22 10075.16 -0.3174573 -1.032887 72938.12 100190 281450.4 581.4177 129.4168 4.282 5.22 10079.45 -0.3187815 -1.037973 72934.73 100318.1 283247.2 581.6794 129.3876 4.29 5.24 10083.74 -0.3202578 -1.040198 72920.23 100446.4 284240.8 581.8702 129.3656 4.298 5.24 10088.03 -0.3216768 -1.043282 72895.81 100555.3 285427.9 581.749 129.3376 4.307 5.26 10092.35 -0.323152 -1.045373 72871.48 100670.1 286352.1 581.5589 129.3069 4.315 5.26 10096.65 -0.3248683 -1.046986 72874.43 100847.2 287318.8 581.6288 129.2836 4.323 5.28 10100.98 -0.3260214 -1.051646 72851.13 100931.2 288901.5 581.8182 129.2527 4.332 5.28 10105.31 -0.3278494 -1.052939 72827.16 101082.6 289709.2 580.9434 129.2268 4.34 5.3 10109.66 -0.3293603 -1.056046 72798.11 101195.1 290933.9 581.3207 129.1986 4.348 5.3 10114 -0.3306668 -1.060307 72789.09 101314.8 292522 581.3909 129.173 4.357 5.32 10118.36 -0.3323018 -1.063432 72773.87 101459.4 293856.2 581.5789 129.1455 4.365 5.32 10122.73 -0.333741 -1.065545 72758.23 101583.7 294838.8 581.4606 129.117 4.374 5.34 10127.1 -0.3353355 -1.070271 72740.07 101720.4 296634.1 581.6479 129.0906 4.382 5.34 10131.48 -0.3369642 -1.074219 72736.2 101880.8 298276.8 581.3433 129.0607 4.39 5.36 10135.88 -0.3385116 -1.077082 72719.21 102014.7 299525.4 581.3433 129.034 4.399 5.36 10140.28 -0.3399971 -1.081194 72695.91 102133.6 301110.2 581.2267 129.0084 4.407 5.38 10144.69 -0.3415332 -1.083918 72693.3 102287 302384.9 581.4126 128.9791 4.415 5.38 10149.1 -0.3433089 -1.086838 72674.07 102441.7 303727.8 581.2963 128.9538 4.424 5.4 10153.52 -0.3447922 -1.090293 72658.7 102572 305166.8 581.4814 128.9231 4.432 5.4 10157.97 -0.3461569 -1.094603 72633.95 102677.1 306798.7 581.9188 128.8965 4.44 5.42 10162.39 -0.3477357 -1.096089 72625.83 102827.9 307706.3 581.9188 128.8687 4.449 5.42 10166.84 -0.3492052 -1.100713 72596.51 102937.5 309461.9 581.6176 128.8397 4.457 5.44 10171.3 -0.3507942 -1.104715 72591.91 103094.7 311177.2 581.6176 128.8124 4.465 5.44 10175.78 -0.3524879 -1.107431 72563.19 103228.6 312428.8 581.685 128.7832 4.465 5.46

2 1

reference spetra fo CoSi
by Cserháti Csaba 30 Jul '08

30 Jul '08

Dear all, I would like to ask if anyone has a reference spectra of CoSi. I would appreciate if someone could help. Thanks in advance! Csaba Cserhati P.S. I have already checked the databases you offered to Darek.

1 0

Proper link for Lytle Database
by Carlo Segre 29 Jul '08

29 Jul '08

Hello All: I have reworked the database web site a bit and I would appreciate it if the following URL is used to access it in the future. It would make my life a lot easier if I knew where users entered the database. http://ixs.iit.edu/database/ I took the liberty of continuing the association with the IXAS. If there is an objection, please let me know. Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre(a)iit.edu http://www.iit.edu/~segre segre(a)debian.org

1 0

Zn xanes
by Michel Jaouen 25 Jul '08

25 Jul '08

Hi everybody, I wish to know if somedody can send me a reference xanes spectrum for pure Zn (ascii file)? That would be great.... Thank you everybody Michel -- __________________________________________ Michel Jaouen Universite de Poitiers - UFR Sciences - SP2MI Laboratoire de Physique des Matériaux (PhyMat) 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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Bond lengths
by Bindu R. 25 Jul '08

25 Jul '08

Hi, Could you please clarify me, up to what decimal place in the bond lengths obtained from EXAFS fitting is reliable? If there are changes in the bond lengths in the fourth decimal place around the region of phase transition, can one consider this as a genuine one even though the error bars obtained from the EXAFS fitting are more than the variation in the bond lengths? Regards Bindu Dr.Bindu R. Visiting Fellow BG-37 DCMP&MS Tata Institute of Fundamental Research Homi Bhabha Road Colaba Mumbai-400 005 India Contact Number Lab- 022-2278 2256, 022-2278 2671 Mobile-919892536830 Bring your gang together. Do your thing. Find your favourite Yahoo! group at http://in.promos.yahoo.com/groups/

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Fwd: Re: Athena/Artemis
by Bruce Ravel 24 Jul '08

24 Jul '08

Hi gang, I received an interesting question this afternoon about EXAFS parameters and I thought that Olivier would benefit by hearing what more people than just me would have to say about this topic. He asks: Can you point me to documentation about the third and fourth cumulants? Since I study glasses, which are highly disordered, I would like to measure the anharmonicity parameters. What are typical values for C3 and C4? Grant Bunker has a very useful paper on the cumulants in Nucl. Instrum, and Meth. (1983) v. 207, p 437-444. Anatoly's paper on cumulants Phys. Rev. B 48, 585 - 588 (1993) is also handy and should give you some sense of what size the C3 and C4 parameters should be. In my experience, C3 and C4 should be smaller than sigma^2 -- perhaps by about 1 and 2 orders of magnitude, respectively. When they get much bigger than that, one can reasonably ask whether a short cumulant expansion (that is, an expansion out to only the 4th cumulant) is really adequate for describing the distribution of atoms in such a disordered material. There are people who have been applying reverse monte carlo or molecular dynamics to come up with better descriptions of highly disordered materials. Hopefully others will contribute to answering your questions. B Olivier: Sorry for switching languages on you -- hopefully it will prove useful to hear from others on the list. Je m'excuse de changer de langue pour cette conversacion -- on espere que il y aura des autres response utils ici sur la liste. ---------- Forwarded Message ---------- Subject: Re: Athena/Artemis Date: Thursday 24 July 2008 From: Olivier Villain <olivier.villain(a)impmc.jussieu.fr> To: Bruce Ravel <bravel(a)bnl.gov> Pourrais-tu m'indiquer où est l'aide concernant les paramètres 3rd et 4th ? Comme j'étudie des verres, donc du désordre, j'aimerais essayer des paramètres d'anharmonicité. Quelles sont les valeurs typiques ? Quelle est l'unité ? Je n'ai pas réussi à trouver ça dans l'aide. J'espère que je ne suis pas trop lourd... A bientôt, Olivier ------------------------------------------------------- -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

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Installation of the last versions on XP
by shiryaev＠crys.ras.ru 23 Jul '08

23 Jul '08

Hi Matt, I have a message pretty similar to what Kleper sees (both problems he has located: "could not read bitmap...." and "can´t open \share\per1\Xray\space_groups.db:"). This is indeed sounds like non-ASCII names on my computer. Would be nice to find a way to overcome the problem without logging as another user. Thanks in advance, A.Shiryaev

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Installation of the last versions on XP
by shiryaev＠crys.ras.ru 22 Jul '08

22 Jul '08

Hi everybody, Perhaps you may hep to resolve the following problem: I have no problems in installing and working with Ifeffit-1.2.6 on my Windows XP laptops. The problem concerns working with later versions: 1.2.9 and 1.2.10. There are no error messages on installation, but neither Athena not Artemis work. What can I change in setup? Thanks in advance, A.Shiryaev

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Linear Combination Fitting - More Questions
by Gudrun Lisa Bovenkamp 17 Jul '08

17 Jul '08

Hi everyone, I just learned that before Athena there was no such program to check on all combinations, so it was not that confusing - or just more work? I think this feature of Athena is very good tool, but when I really do not know what is in my sample how can it help? I try to answer it myself and someone can correct me: Certainly not all of my, say 10 reference spektra, are that similar that I can get several LCFs with the same say R-factor. So, I will get some clue to narrow the components. But still there can be, for example: Standard-combi 1, 2, 3 equal to 1, 4, 6. So, my analysis gives two solutions and one must be wrong, but both can be wrong. How can I tell? Can a PCA help me in this case? The results change significantly when I change the normalization. How do I know what is the 'correct' adjustment? - Yes, I read the Athena turorials, but I got no answers from there. I searched quite a while to find a complete documentation of the LCF formula used in Athena, but I could not find it. Many thanks, Lisa

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Re: [Ifeffit] Ifeffit Digest, Vol 65, Issue 10
by sankaran anantharaman 17 Jul '08

17 Jul '08

Hi Richard, If I could intervene in your discussion, a suitable phrase is already in use to differentiate the EXAFS Debye-Waller factor from that obtained in X-Ray diffraction..."Debye-Waller-like factor". Reference : M. Bauer, H. Bertagnolli:X-ray absorption spectroscopy - The Method and its application, Bunsen-Magazin, 9. Jahrgang, 6/2007, p.216 Regards, Sankaran Anantharaman Universität Stuttgart Institute of Physical Chemistry Research group of Prof. Dr. H. Bertagnolli Pfaffenwaldring 55 70569 Stuttgart > Bruce, > > While you're on your soapbox, if we drop "Debye-Waller factor" to describe > the EXAFS disorder term, would you suggest using only "disorder" or do you > have a better phrase to use? > > Rich > > -- > Richard Mayes > > Barnes Group > 450/452 Buehler Hall > Department of Chemistry > University of Tennessee > Knoxville, TN 37996 > > > >

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quotation of figures
by s440697＠stud.uni-goettingen.de 17 Jul '08

17 Jul '08

Hi, i have a print out of a talk (about XANES, XAFS and multiple scattering...) and i want to cite some figures (attached). Can anybody tell me the author etc...? I searched everywhere on the web (on several sites of XAFS-Summer Schools...). Unfortunately i do not have the talk as pdf-file only the print out. Maybe the talk is from Matt Newville? Maybe anybody recalls on this talk/slides or recognizes them? Thanks for your help. Have a nice day, Eckhard --------------------------------- Eckhard Bosman e.bosman(a)stud.uni-goettingen.de +49 (0)551-39-14441 Raum: E0.104 Institut für Röntgenphysik Friedrich-Hund-Platz 1 37077 Göttingen Germany

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third cumulant
by grant bunker 16 Jul '08

16 Jul '08

Matthew - as you know, it's trivial to just let b=1/a and the write the distribution as (x-x)^s Exp[- (x-x0)/b] so that the gaussian limit is obtained as b->0. So infinite parameters are not a problem. Your suggestion and other observations are quite right. In fact, if convoluting distributions is ok, you can use whatever your favorites are, since cumulants just add under convolution. grant On Jul 16, 2008, at 11:08 AM, ifeffit- request(a)millenia.cars.aps.anl.gov wrote: > OK, here's my $0.02. I've used the convolution of an exponential > tail function > exp(-(r-r0)/w) (r-r0)*w >= 0 > 0 (r-r0)*r < 0 > > with a Gaussian. This avoids having to have parameters go to > infinity to approach a gaussian. This function > is a little unwieldy in real space but is simple in k-space. > mam

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FEFF-SCF and Enot in Artemis
by Frommer Jakob 16 Jul '08

16 Jul '08

Dear all! Recently I read the two inspiring XAFS13-contributions of Shelly and Bruce dealing with the energy-shift (p.132) and the use of SCF-calculations (p. 137). In this respect I have a question regarding the Enot parameter in Artemis: Plotting the mue (4th column in xmu.dat) of a FEFF8.4 SCF calculation (of a transition metal oxide; here: Fe or Cr) against the second column ("e") of xmu.dat, I end up with a fairly decent reconstruction of my experimental XANES: the onset of the pre-edge resonances is located at negative energies (if I am right this is referred to as E_0 (bottom of the conduction band)) and the energy zero (i.e. Fermi energy) is located somewhere in the rising part of the absorption edge. If I then use the same (SCF) potentials and let FEFF do a path-expansion run, the header of the feffnnnn.dat contains a (negative) quantity called "edge", which gives exactly the difference between E_0 and E_fermi (as also explained in Matt's article: J. Sync. Rad., 2001, pp. 96-100). In the xmu.dat, k seems to be calculated relative to E_0 (i.e. to a negative energy in the 2nd ("e") column). Plotting a path in Artemis (or the xmu calculated for a single path) I had the impression that again k is referenced to E_0 (onset of the pre-edge feature) rather than to E_fermi (somewhere in the rising part of the edge). Is this true? Assuming that I set the E0-parameter in Athena to the first inflection point of the main edge (so in the upper nomenclature to something like E_Fermi) and assuming further that I do a shell-fit in Artemis, wouldn't I expect to end up (in an ideal case) with an Enot similar to the quantity "edge" given in the feffnnnn.dat rather than a Enot of (close to) 0? I also found a mailing-list contribution (dating back to 2004) of Wojciech and Matt addressing a similar topic - still it is not clear to me what the effect on Artemis' Enot will be. I hope I did not confuse too many things. I will greatly appreciate any hint clarifying this situation. With many thanks and best regards Jakob ___________________________________________________ Jakob Frommer Soil Chemistry Group Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich Universitätstrasse 16, CHN F19 CH - 8092 Zürich Tel: +41 44 632 87 58 Fax: +41 44 633 11 18 web: http://www.ibp.ethz.ch/research/soilchemistry

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cumulant/rdf question
by grant bunker 15 Jul '08

15 Jul '08

re the cumulant <--> rdf connection This isn't a general solution, but it may work well for your system. A poisson distribution (x-x)^s Exp[-a (x-x0)] is a pretty flexible for moderately skewed distributions, permitting variable C2 and C3 by adjusting parameters s and a. For large s and small a the distribution approaches a gaussian. Expressions for cumulants etc are in Yang et al, JNCS Volume 210, Number 2, March 1997 have fun - gb > matt, > > I have a problem with an exafs analysis: > from the exafs analysis (with feffit2.98) of the first shell of a > disordered > system > I get the first three cumulants. > now, I wander how can reconstruct from them the radial distribution > function > which is the best solution? I have tried with the skew-normal > distribution, > but for the high skewness (ratio of third cumulant to sigma3) > values I get - that is around 2.5 - it is not well defined. > Do you have a suggestion? > Thanks,

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polarization
by Asma Tougerti 15 Jul '08

15 Jul '08

Hi, I study the sorption of Ni on single crystals of alumina by exafs . the angle made between the electric field and the sample is 90 and 0 . I read in “Exafs analysis using feff and feffit , matthew Newville, j.synchrotron rad (2201), 8,96-100” that we can use feff and feffit to calculate exafs spectra . I have three questions: In this reference authors uses a feff7 Can I use feff6 or I need a feef recent version ? There is a manual that explain how to write a feffit.inp file? How I can include the polarization dependence on my calculation? Asma

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