January 2005 - Ifeffit - millenia.cars.aps.anl.gov

installation of horae in fedora2
by ynliu＠eps.mcgill.ca 22 Mar '05

22 Mar '05

Hello,all We finally succeeded in installing horae-048 in Fedora 2! It took us a long time to figure out why Tk could not be detected, but it turned out that the right version of Tk is the key. We found Tk-804.027 working in our Fedora2 system. The right order of installation is also important. We had to restart everything in installing horae after we set up Tk.If you are using this Tk-804.027, you don't need to look for unix folder as said on some web,just simply gunzip tar -xvf finename.tar (enter the new folder Tk-804.027) make make install(after this,you can make test if you want) And then the installation of horae will jsut go fluently following the instructions! To use athena or artemis, you need to enter the fold where athena.pl and artemis.pl are,and then "perl athena.pl". cheers Yanan ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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RE: [Ifeffit] Two edge problem (in the same scan)
by Kelly, Shelly D. 26 Jan '05

26 Jan '05

> -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit- > bounces(a)millenia.cars.aps.anl.gov] On Behalf Of Bruce Ravel > Sent: Wednesday, January 26, 2005 1:30 PM > To: asg2(a)lehigh.edu; XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] Two edge problem (in the same scan) > > > Hello everybody, > > I have a question/problem. Last year during the EXAFS course at NSLS, I > > had requested Bruce if it is possible to analyze the data with two > > edges. For example, I have the data for As and Se K-edges, which I > > collect in the same scan. In WinXAS program, I can section the edges and > > analyze them separately. At that time, the program was not able to > > perform these edges or the sectioning. Have we reached this possibility. > > I tried again using the latest updated Athena, but it seems not to be > > working. Can you please tell me whether the sectioning or dealing with > > two edges in the same spectra can be done > > I don't unfderstand why "sectioning" is necessary. What precludes you > from reading the data set a second time and setting e0 to be appropriate > for the second edge? Then your pre- and post-edge lines will be made > using the second e0 and everything else should just follow normally. > > I understand that Athena does not have a way to specify the second edge in > the column selection dialog, but that seems to me like an inconvenience > more than a real limitation. It is an inconvenience because you then have > to specify the second e0 by hand rather than have Athena's magic find it > for you, but is that really so hard? > > B > [Kelly, Shelly D.] Another feature that I have found useful for data with multiple edges is the truncate function. Once you read the data set into Arthena. Make a copy of the data set. Choose your e-zero for each data set. And then truncate the data sets to the "normal" range. This will help with some of the automatic presets, which use the full data range by default, and can give you a very scary initial background function. SK

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Two edge problem (in the same scan)
by Ashtosh Ganjoo 26 Jan '05

26 Jan '05

Hello everybody, I have a question/problem. Last year during the EXAFS course at NSLS, I had requested Bruce if it is possible to analyze the data with two edges. For example, I have the data for As and Se K-edges, which I collect in the same scan. In WinXAS program, I can section the edges and analyze them separately. At that time, the program was not able to perform these edges or the sectioning. Have we reached this possibility. I tried again using the latest updated Athena, but it seems not to be working. Can you please tell me whether the sectioning or dealing with two edges in the same spectra can be done Ashtosh

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[DATA-REQUEST] Platinum standards
by MauRo 24 Jan '05

24 Jan '05

Hi to all, I'm looking forward for some EXAFS (transmission or fluorescence) spectra of Platinum oxide and Platinum carbide at L_III and/or L_I edge. Is there anyone who has taken this data and is so kind to send them to me? Thanks, Mauro

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Increase NOVP error message meaning
by Paul Fons 23 Jan '05

23 Jan '05

I am trying to run feff on some chalcogenide structures that have rather nearest-neighbor long bond lengths, e.g. > Bond search from target site: Te1 > ...found 6 atoms within 0.00 - 3.20 A of this site > > ------------------------ > dist [Å] atoms > ------------------------ > 1. 3.0488 6 > ------------------------ > Bond search complete When I use this structure in feff82, I get the rather mysterious error INCREASE NOVP: > > Calculating potentials ... > free atom potential and density for atom type 0 > free atom potential and density for atom type 1 > free atom potential and density for atom type 2 > free atom potential and density for atom type 3 > initial state energy > overlapped potential and density for unique potential 0 > overlapped potential and density for unique potential 1 > overlapped potential and density for unique potential 2 > overlapped potential and density for unique potential 3 > muffin tin radii and interstitial parameters > tell authors to INCREASE NOVP Being an experimentalist, I did increase novp until the previous error message stopped, however this resulted in a core dump: > Calculating potentials ... > free atom potential and density for atom type 0 > free atom potential and density for atom type 1 > free atom potential and density for atom type 2 > free atom potential and density for atom type 3 > initial state energy > overlapped potential and density for unique potential 0 > overlapped potential and density for unique potential 1 > overlapped potential and density for unique potential 2 > overlapped potential and density for unique potential 3 > muffin tin radii and interstitial parameters > iph, rnrm(iph)*bohr, rmt(iph)*bohr, folp(iph) > 0 1.76126E+00 1.74898E+00 1.01667E+00 > 1 1.71891E+00 1.63874E+00 1.12886E+00 > 2 1.35785E+00 8.69242E-01 1.15000E+00 > 3 1.78418E+00 1.76792E+00 1.02193E+00 > mu_old= nan > Done with module 1: potentials. > Calculating LDOS ... > LDOS calculation for specified grid > Calculating energy and space dependent l-DOS. > It takes time ... > potential type 0 > Segmentation fault (core dumped) When running the equivalent file in feff6, I get the > Calculating potentials and phases... > free atom potential and density for atom type 0 > free atom potential and density for atom type 1 > free atom potential and density for atom type 2 > free atom potential and density for atom type 3 > overlapped potential and density for unique potential 0 > overlapped potential and density for unique potential 1 > overlapped potential and density for unique potential 2 > overlapped potential and density for unique potential 3 > muffin tin radii and interstitial parameters > phase shifts for unique potential 0 > Hard tests failed in fovrg. > Muffin-tin radius may be too large; coordination number too small. > phase shifts for unique potential 1 > Hard tests failed in fovrg. > Muffin-tin radius may be too large; coordination number too small. > phase shifts for unique potential 2 > Hard tests failed in fovrg. > Muffin-tin radius may be too large; coordination number too small. > phase shifts for unique potential 3 > Hard tests failed in fovrg. > Muffin-tin radius may be too large; coordination number too small. > Preparing plane wave scattering amplitudes... > nncrit in prcrit 9 This message seems similar to the troubleshooting section in feff8 for which it states: • Non-physical, widely spaced distributions of atoms. Symptoms of this common problem are very large muffin-tin radii (see the header of any ‘.dat’ file) and possibly a failure of the phase-shift program to converge. This gives error message hard test fails in fovrg. How to I avoid this problem (obviously the crystal structure is a given!). I tried the INTERSTITIAL card, but to no avail. Any suggestions are welcome. Dr. Paul Fons Senior Researcher National Institute for Advanced Industrial Science & Technology METI Center for Applied Near-Field Optics Research (CANFOR) AIST Central 4, Higashi 1-1-1 Tsukuba, Ibaraki JAPAN 305-8568 tel. +81-298-61-5636 fax. +81-298-61-2939 email: paul-fons(a)aist.go.jp The lines below are in a Japanese font 〒３０５−８５６８茨城県つくば市東１−１−1 つくば中央第４近接場光応用工学センターポール・フォンス主任研究官

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Windows update for athena/artemis
by Matt Newville 18 Jan '05

18 Jan '05

Hi, I've built a Windows update file to upgrade to the latest versions of Athena and Artemis. Since Bruce is off-line for a while and since there is no easy way for us to make these executables, there is not much we'll be able to do if there is a problem with this version. Because of this, I am NOT releasing this as a normal update yet, but would like the braver of you to download and install this update by hand and give the new versions of Athena and Artemis a test drive. The update file is at http://cars9.uchicago.edu/ifeffit/updates/ifup_013.zip which is just a simple zip file that can be unpacked in your Ifeffit folder. (Probably C:/Program Files/Ifeffit). If you're willing to try these versions, please let me know how it goes. I'll wait until I hear some positive responses before I make a general update release that would automatically update everyone to these versions. Thanks, --Matt

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RE: [Ifeffit] Some questions about ATOMS and FEFF
by Barton, David (DG) 16 Jan '05

16 Jan '05

Patrick, Welcome to the mailing list! This list is an excellent forum for newcomers and veterans alike. > 2) Running the FEFF6 software directly or through the Artemis > bundle, I never get any "chi.dat" output file as a weighted sum of the > individual This feature is built into Artemis. After you run the FEFF calculation with Artemis and choose which paths to import, just highlight the paths in the DATA & PATHS window that you would like to sum and then choose DATA-->SUM OF PATHS-->SELECTED DATA PATHS from the menu. This will produce the chi(k) sum which can be plotted along with your data set. A shortcut to this menu item can also be found by right-clicking on the selected paths and choosing DATA-->SUM OF PATHS-->SELECTED DATA PATHS. I often use this feature to get a rough feeling for the relative contributions of each path in the calculation by plotting the SUM along with all of the individual paths. Have Fun, Dave _________________________________ David Barton, PhD. The Dow Chemical Company Catalysis R&D 1776 Building Midland, MI 48674 USA Ph: (989) 636-4753 Fax: (989) 638-6225 Email: dgbarton_remove_me(a)dow.com > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov > [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Patoo > Sent: Sunday, January 16, 2005 9:07 AM > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Some questions about ATOMS and FEFF > > > Hi, > > I am just starting to work with the ARTEMIS/ATHENA software suite for > EXAFS data processing and analysis and a newcomer in this > mailing list. This project is really very nice and useful for > the EXAFS community and > I really enjoy to learn how to use it. > I read most of the documents which are available on the website and > around, but I have already two questions : > 1) in the "feff.inp" command file, what are the options of the cards > CONTROL and PRINTS > 2) Running the FEFF6 software directly or through the Artemis > bundle, I > never get any "chi.dat" output file as a weighted sum of the > individual > "feffNNNN.dat" individual path contribution. Is there any forgotten > option to get it ? > > Thanks in advance for your help > > Patrick > > -- > *********************************************************** > Dr. Patrick Judeinstein > R.M.N. en Milieu Orienté, (UMR 8074), Bâtiment 410 > I C M M O (Institut de Chimie Moléculaire et des Matériaux d'Orsay) > Université Paris-Sud, 91405 Orsay Cedex - France > Tel : +33 (0)1 69 15 70 17 ou ++ 33 (0)1 69 15 47 68 ; Fax + > 33 (0)1 69 15 81 05 > > e-mail : pjudeins(a)icmo.u-psud.fr > web site : http://patoo.hope.free.fr > > *********************************************************** > > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listi> nfo/ifeffit >

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Some questions about ATOMS and FEFF
by Patoo 16 Jan '05

16 Jan '05

Hi, I am just starting to work with the ARTEMIS/ATHENA software suite for EXAFS data processing and analysis and a newcomer in this mailing list. This project is really very nice and useful for the EXAFS community and I really enjoy to learn how to use it. I read most of the documents which are available on the website and around, but I have already two questions : 1) in the "feff.inp" command file, what are the options of the cards CONTROL and PRINTS 2) Running the FEFF6 software directly or through the Artemis bundle, I never get any "chi.dat" output file as a weighted sum of the individual "feffNNNN.dat" individual path contribution. Is there any forgotten option to get it ? Thanks in advance for your help Patrick -- *********************************************************** Dr. Patrick Judeinstein R.M.N. en Milieu Orienté, (UMR 8074), Bâtiment 410 I C M M O (Institut de Chimie Moléculaire et des Matériaux d'Orsay) Université Paris-Sud, 91405 Orsay Cedex - France Tel : +33 (0)1 69 15 70 17 ou ++ 33 (0)1 69 15 47 68 ; Fax + 33 (0)1 69 15 81 05 e-mail : pjudeins(a)icmo.u-psud.fr web site : http://patoo.hope.free.fr ***********************************************************

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re:fits
by k-kupiecki＠northwestern.edu 15 Jan '05

15 Jan '05

Thank you Bruce and Shelley! I just wanted to thank Matt, Bruce and everyone involved with IFEFFIT/Artemis/Athena... it has been a Godsend.... I couldn't have stumbled on it at a better time (I'm frantically trying to analyze about 4 beamtimes worth of SEXAFS data for papers and my thesis and WINXAS wasn't really working out for me)!!!!! Does anyone have any suggestions for additional literature in regards to better understanding the quality of fits and the parameters involved?.... or perhaps know when we might be able to expect a updated version of the Artemis literature? (What is currently there has helped me sooo much that I've been checking for an update every couple of weeks hoping to get see sections 2.2-3.2..... ) Also.... I guess I've realized that only knowing IFEFFIT with Artemis I kinda take things for granted (like I didn't know that IFEFFIT was having problems, in certain cases since I had only been checking the "Results" and the error messages on the bottom of the window....) which meant I missed errors like this in the IFEFFIT (since I didn't notice anything unusual in the "Results"): ............ # Do the fit! ## fitting difference of Cov_0_06ML_bl1435_111703.chi and one or more paths ... ## === data set #1 of 1 feffit(1-8, group=data0_fit, chi=data0.chi, k=data0.k, kweight=2.00, rmin=1, rmax=4, kmin=2.5, kmax=15, dk=2, kwindow=kaiser-bessel, fit_space=R, do_bkg=no, data_set=1, data_total=1) feffit fitting 1 data sets fitting ... fitting ... fitting ... fitting ... fitting ... fitting ... fitting ... fitting ... no uncertainties estimated! fit gave a warning message: too many fit iterations. try again with better guesses or a simpler problem. ............................................... I guess my question is.... is there anything else I should be looking for in the IFEFFIT printout that I might not otherwise notice by just using Artemis and looking at the error messages and "Results"? Thanks for the input! Sincerely, Kristine Witkowski Northwestern University

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another bug
by Norbert Weiher 13 Jan '05

13 Jan '05

Hi Bruce, sorry to bother again - here's the issue: I fit a given spectrum say in kw=2, choose as plotting option "kw". If I plot the fit and the data, only the data gets the correct kw, the fit is displayed with kw=1. If I select kw=1,2 or 3, everything is fine. The problem exists also when exporting the fits to a file... I noticed this in diana and artemis... Cheers, Norbert -- Dr. rer. nat. Norbert Weiher (norbert.weiher(a)manchester.ac.uk) School of Chemical Engineering and Analytical Science Sackville Street, Manchester, M60 1QD - Phone: +44 161 306 4468

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