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

EXAFS course at Brookhaven
by Anatoly Frenkel 17 Jun '05

17 Jun '05

Hello IFEFFIT subscribers: In September 28-30, 2005, National Synchrotron Light Source at Brookhaven National Laboratory will host a short course: "EXAFS Course: Theory, Experiment, and Advanced Applications" This hands-on course is aimed to help design, perform and analyze EXAFS experiments, and to learn about some of the potential pitfalls that must be avoided. The course will be self-contained, starting with the fundamentals and proceeding to the more advanced topics, including recent theoretical developments, data analysis techniques and specific applications of EXAFS. More information is available at the course web page: http://www.nsls.bnl.gov/newsroom/events/workshops/exafs/Default.htm Please pass it along to all who may be interested. Anatoly Anatoly Frenkel Yeshiva University

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Athena and Artemis reference
by Bruce Ravel 15 Jun '05

15 Jun '05

Hi folks, I just got word today that my and Matt's submission to Journal of Synchrotron Radiation has been published and is available on-line. Here is the citation: ATHENA, ARTEMIS, HEPHAESTUS: data analysis for X-ray absorption spectroscopy using IFEFFIT B. Ravel and M. Newville Journal of Synchrotron Radiation, Volume 12, Part 4, pages 537---541. Here's a link: http://www.iucr.org/cgi-bin/paper?ph5155 This reference is more up-to-date and reflective of the current state of the codes than the reference in Physica Scripta from the Malmo EXAFS conference, so it is my preference that you use it. B -- Bruce Ravel ----------------------------------- bravel(a)anl.gov -or- ravel(a)phys.washington.edu Environmental Research Division, Building 203, Room E-165 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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odd feff6 behavior
by Bruce Ravel 13 Jun '05

13 Jun '05

Hi, Here's a feff6 curiosity. Take this atoms.inp file: title = TiN space = 225 a = 4.24173 b = 4.24173 c = 4.24173 core = Ti edge = K rmax = 7.0 atoms ! elem x y z Ti 0.00000 0.00000 0.00000 N 0.50000 0.50000 0.50000 Run atoms, then run feff6l (the one that comes with Ifeffit, it's the only version I've tried this with). Feff ends with this error message: Eliminating path degeneracies... Plane wave chi amplitude filter 2.50% np, np1x= 12001 12000 Fatal Error: at PATHSD: np > np1x This message comes from pathsd.f, but I don't understand either the message or the part of the code it comes from. Does anyone else have a hint as to the problem? One more datum. If you reduce rmax to 6.7 in the atoms.inp file, the problme persists. If you make rmax 6.6, feff6l is happy. Thanks, B -- Bruce Ravel ----------------------------------- bravel(a)anl.gov -or- ravel(a)phys.washington.edu Environmental Research Division, Building 203, Room E-165 Argonne National Laboratory phone: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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IFEFFIT on Tiger - confusion between Perl 5.8.1 and 5.8.6
by Brugger, Joel (SAM) 11 Jun '05

11 Jun '05

I lost IFEFFIT after upgrading to MAC OS X 10.4 (Tiger). Apparently, this is due to the fact that the upgrade replaced Perl 5.8.1 by Perl 5.8.6. I redid the IFEFFIT installation (for 10.3), which created a Perl5.8.1 folder with all the goodies. However, as the following error message shows, the system is not happy and is looking for some stuff in the new PERL. And does not find it. I'm not sure how to revert to 5.8.1, or alternatively more everything to the new 5.8.6. Hopefully this is a trivial question :-) Thanks for any help, JOEL [JoelG5:/Applications/Ifeffit/bin] joelb% ./hephaestus Can't load '/Library/Perl/5.8.1/darwin-thread-multi-2level/auto/Tk/Event/Event.bundle' for module Tk::Event: dlopen(/Library/Perl/5.8.1/darwin-thread-multi-2level/auto/Tk/Event/Event.bu ndle, 1): Library not loaded: /System/Library/Perl/5.8.1/darwin-thread-multi-2level/CORE/libperl.dylib Referenced from: /Library/Perl/5.8.1/darwin-thread-multi-2level/auto/Tk/Event/Event.bundle Reason: image not found at /System/Library/Perl/5.8.6/darwin-thread-multi-2level/XSLoader.pm line 68. at /Library/Perl/5.8.1/darwin-thread-multi-2level/Tk/Event.pm line 10Compilation failed in require at /Library/Perl/5.8.1/darwin-thread-multi-2level/Tk.pm line 13.BEGIN failed--compilation aborted at /Library/Perl/5.8.1/darwin-thread-multi-2level/Tk.pm line 13.Compilation failed in require at ./hephaestus line 54.BEGIN failed--compilation aborted at ./hephaestus line 54.Undefined subroutine &Tk::Event::CleanupGlue called at /Library/Perl/5.8.1/darwin-thread-multi-2level/Tk/Event.pm line 3.END failed--call queue aborted at ./hephaestus line 54.

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Importance and Edge Step
by Barton, David (DG) 08 Jun '05

08 Jun '05

Hello, I noticed two new features in Athena 0.8.040 and am unsure of how to use them. The new features are "Importance" and "Edge Step". I attempted to use the Edge Step feature by checking "Fix Step" and then entering a value, but the Edge Step always reverts back to the automated value. However, when I use the Increase/Decrease buttons (Left/Right arrow in Edge Step window) the edge step does change, but it only changes in increments of 0.01 which is much too large for my datasets. Is there something I am missing here? Also, I couldn't locate Bruce's changelog for Athena so I am unsure of what the new "Importance" feature does. Anyone used this new feature yet? Dave _________________________________ David Barton, PhD. The Dow Chemical Company Catalysis R&D 1776 Building Midland, MI 48674 USA

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Re: Ifeffit Digest, Vol 28, Issue 6
by Satyender Goel 07 Jun '05

07 Jun '05

Hi Matt, I have managed to get everything up and running. Thank you so much for your patience and help without which it wouldn't have been possible. I appreciate your effort and the interest taken in helping me solve my problem. Sorry for the trouble. Regards, Satyender Goel Quoting ifeffit-request(a)millenia.cars.aps.anl.gov: > 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: Re: Ifeffit Digest, Vol 28, Issue 4 (Matt Newville) > 2. Re: Bug report (Scott Calvin) > 3. Re: Importance and Edge Step (Gerrit Schmithals) > 4. Re: Bug report (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 7 Jun 2005 10:18:24 -0500 (CDT) > From: Matt Newville <newville(a)cars.uchicago.edu> > Subject: Re: [Ifeffit] Re: Ifeffit Digest, Vol 28, Issue 4 > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: > <Pine.LNX.4.44.0506070933460.14613-100000(a)millenia.cars.aps.anl.gov> > Content-Type: TEXT/PLAIN; charset=US-ASCII > > Satyender, > >> Finally i got my Perl script running using, >> >> BEGIN { >> $ENV{IFEFFIT_DIR} = 'C:\Program Files\Ifeffit\'; >> } >> >> at the begining of my program.... > > If your perl scripts are running, you must have the Ifeffit > modules installed, no??? If it's working, then it's probably > not necessary to rebuild the perl module. But if you're going > to be using it heavily, it might be worth figuring out how to do > build it anyway. > >> I have added the environment variable IFEFFIT_DIR, but it does >> not seem to make a difference. > > Hmm, that's really strange, but maybe I'm not understanding? > It should definitely work to set IFEFFIT_DIR as an environmental > variable and run perl in that environment without having BEGIN { > $ENV{IFEFFIT_DIR}='...';} in the script. Well, the BEGIN {} > block in the script is really setting the environmental > variable, so if that works, setting it from the Control Panel > should work to. Are you should the command shell you're using > has this environmental variable set? Try typing > C:\> set > to see a list of environmental variables. > >> I have tried.......... >> >> "C:\Program Files\Ifeffit\wrappers\perl\build, and do >> perl Makefile.PL >> nmake install" >> >> after editing makefile.pl as per... >> >> "'LIBS' => [' -LC:\"Program Files"\Ifeffit ifeffit_10 ']," >> and also copied ifeffit.pm to C:\perl\site\lib... >> >> I have visual studio installed on my computer, however the nmake command >> does not seem to be working. >> >> SCREEN DISPLAY AFTER THE CHANGES: >> >> C:\Program Files\Ifeffit\wrappers\perl\build>perl makefile.pl >> Note (probably harmless): No library found for oldnames.lib >> Note (probably harmless): No library found for kernel32.lib >> <snip> > > This is probably because the VC/Visual Studio stuff isn't in > your path, and since perl is going to try to run 'cl' and > 'nmake' from the command line, the command shell needs to find > them from the environmental variables. The details of how to do > this depends on how your compiler was installed. You can > probably start with and edit the batch file below. > > Please give more details and a better sense of what does and > doesn't work. Like, what does > > C:\> perl -e "use Ifeffit;" > > report? If it reports "cant find Ifeffit.pm in @INC ....", you > don't have the Ifeffit module installed. If it reports nothing, > it is installed, and you're ready to go. If it reports messages > about PGPLOT, you'll be fine once the environmental variables > for PGPLOT_DIR and PGPLOT_DEV are set. > > Hope that helps, > > --Matt > > REM ---- > REM sample settings for VC,NMAKE, etc > REM probably have to reset BASE_DIR > set BASE_DIR=C:\Program Files\Microsoft Visual Studio > set CPU=i386 > set INCLUDE=%BASE_DIR%\VC98\INCLUDE > set LIB=%BASE_DIR%\VC98\LIB > set > PATH=%BASE_DIR%\Common\Msdev98\BIN;%BASE_DIR%\VC98\BIN;%BASE_DIR%\Common\Tools;%BASE_DIR%\Common\Tools\WINNT;%PATH% > > REM ---- > > > > > ------------------------------ > > Message: 2 > Date: Tue, 07 Jun 2005 12:13:59 -0400 > From: Scott Calvin <scalvin(a)slc.edu> > Subject: Re: [Ifeffit] Bug report > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <3.0.1.32.20050607121359.00b15540(a)mail.slc.edu> > Content-Type: text/plain; charset="us-ascii" > > Thanks, Matt. > > Yes, I've been working around it by just adding "+0" to path expressions > that end in a parentheses. I hadn't quite figured out that it required > starting with a non-matched parentheses to trigger the error; it's good to > know exactly what circumstances cause it to arise. > > A suggestion for Bruce--ifeffit flags these kinds of syntax errors pretty > well. Is it possible for Artemis to look at the ifeffit output and alert > the user to examine the iffefit output if there is an error? > > --Scott Calvin > Sarah Lawrence College > > At 09:33 AM 6/7/2005 -0500, you wrote: >> Hi Scott, >> >> Yep, that is an ifeffit error. It turns out to be specific to >> math expressions in path() commands, but it is definitely a bug. >> It seems that a math expression for a path parameter that starts >> with '(' and ends with ')' and for which these '(' and ')' are >> not a matched pair will incorrectly raise a syntax error. This >> doesn't happen for set() or def(). >>> > > > ------------------------------ > > Message: 3 > Date: Tue, 07 Jun 2005 18:57:01 +0200 > From: Gerrit Schmithals <schmithals(a)hmi.de> > Subject: Re: [Ifeffit] Importance and Edge Step > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <42A5D1DD.6090603(a)hmi.de> > Content-Type: text/plain; charset=ISO-8859-1 > > On Monday 06 June 2005 09:27, Gerrit Schmithals wrote: > >>> How do I implement more than 4 references? There is a box for entering >>> the number but it does not enlarge the reference-list as I expected it >>> to do. >>> >>> > Bruce Ravel schrieb: > >> All of this is explained in the doc page for the LCF dialog. (That >> is, I think I explained it all there. It may be [is?] poorly >> explained ....;-) >> >> The length of the standards list is set in the preferences dialog. >> The relevant parameter is linearcombo->maxspectra. >> >> >> > Thanks for that hint. I really should have found that setting by myself. > > I did not use the combinatorical fitting so far, but concerning the > normal linear fitting I observed two issues: > > I had an Athena project with some references loaded as chi(k)-data and > some unknown samples as chi(k) as well. Athena won't let me start the > Linear Fit-Dialog stating that it (she) needs at least three > xmu-spectra. Changing the preference to "standard fit in k-space" does > not help. Workaround: I just loaded some dummy xmu-Spektra and can now > work with the dialog. > > Also, only these xmu-spectra can be selected from the "standards pluck > boxes", the only way to insert the chi(k)-references is to use "use > marked groups". That is a bit of a problem when you have to move one of > the groups up because its value is negative. Workaround is to move up > the groups in in Data group section. > > Some other issues came into my mind while working with the dialog but > they are really of minor importance: > - Is there any possibility to plot the linear fit and the data in > R-space right away? (without first saving it as a datagroup) > - It would be nice to be able to store the relative weigths together > with the newly created dataset. > > Cheers, > Gerrit > > > > > ------------------------------ > > Message: 4 > Date: Tue, 7 Jun 2005 12:01:02 -0500 > From: Bruce Ravel <bravel(a)anl.gov> > Subject: Re: [Ifeffit] Bug report > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <200506071201.02798.bravel(a)anl.gov> > Content-Type: text/plain; charset="iso-8859-1" > > On Tuesday 07 June 2005 11:13, Scott Calvin wrote: >> A suggestion for Bruce--ifeffit flags these kinds of syntax errors pretty >> well. Is it possible for Artemis to look at the ifeffit output and alert >> the user to examine the iffefit output if there is an error? > > One of the features new to ifeffit 1.2.7 is a scalar flag, &status, that gets > set to something other than 0 when something bad happens. Matt added this so > there would be an easy way for A&A to know when an error was encountered. > > I have not yet implemented any functionality surrounding &status, but it's on > the list of things to do. > > B > > -- > Bruce Ravel ----------------------------------- bravel(a)anl.gov -or- > ravel(a)phys.washington.edu > Environmental Research Division, Building 203, Room E-165 > Argonne National Laboratory phone: (1) 630 252 5033 > Argonne IL 60439, USA fax: (1) 630 252 9793 > > My homepage: http://feff.phys.washington.edu/~ravel > EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/ > > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 28, Issue 6 > ************************************** >

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Athena Problems
by McCready, Alistair 07 Jun '05

07 Jun '05

Hi, I am having some problems with Athena. I reformatted my hard drive the other day (windows XP Pro), and downloaded Athena etc. After installing the programs, they work fine. However, once I download the updates, Athena refuses to work. I try to open the program and all I get a black command-style box filled with odd words/text. I do not have a virus (first thing I checked), and all the updated versions of the other programs all work fine (e.g. Artemis, Hephaestus). I just wanted to check if anyone else has ever had this problem? Alistair "SRC provides Smart Science Solutions" This e-mail and any files transmitted with it are intended only for the named recipients and may contain legally privileged and/or confidential information. If you are not the intended recipient please do not disseminate, distribute or copy this e-mail without the consent of the sender.

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Re: Ifeffit Digest, Vol 28, Issue 4
by Satyender Goel 07 Jun '05

07 Jun '05

Thanks a lot Dear Matt and Bruce, Finally i got my Perl script running using, BEGIN { $ENV{IFEFFIT_DIR} = 'C:\Program Files\Ifeffit\'; } at the begining of my program.... I have added the environment variable IFEFFIT_DIR, but it does not seem to make a difference. I have tried.......... "C:\Program Files\Ifeffit\wrappers\perl\build, and do perl Makefile.PL nmake install" after editing makefile.pl as per... "'LIBS' => [' -LC:\"Program Files"\Ifeffit ifeffit_10 ']," and also copied ifeffit.pm to C:\perl\site\lib... I have visual studio installed on my computer, however the nmake command does not seem to be working. SCREEN DISPLAY AFTER THE CHANGES: C:\Program Files\Ifeffit\wrappers\perl\build>perl makefile.pl Note (probably harmless): No library found for oldnames.lib Note (probably harmless): No library found for kernel32.lib Note (probably harmless): No library found for user32.lib Note (probably harmless): No library found for gdi32.lib Note (probably harmless): No library found for winspool.lib Note (probably harmless): No library found for comdlg32.lib Note (probably harmless): No library found for advapi32.lib Note (probably harmless): No library found for shell32.lib Note (probably harmless): No library found for ole32.lib Note (probably harmless): No library found for oleaut32.lib Note (probably harmless): No library found for netapi32.lib Note (probably harmless): No library found for uuid.lib Note (probably harmless): No library found for ws2_32.lib Note (probably harmless): No library found for mpr.lib Note (probably harmless): No library found for winmm.lib Note (probably harmless): No library found for version.lib Note (probably harmless): No library found for odbc32.lib Note (probably harmless): No library found for odbccp32.lib Note (probably harmless): No library found for msvcrt.lib Writing Makefile for Ifeffit C:\Program Files\Ifeffit\wrappers\perl\build>nmake 'nmake' is not recognized as an internal or external command, operable program or batch file. Regards, Satyender Goel

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ifeffit module for perl
by Satyender Goel 06 Jun '05

06 Jun '05

Hi, I am developing algorithms for Automation of "DATA MINING FOR HIGH THROUGHPUT SYNCROTRON SPECTROSCOPIES" with Dr. S L M Schroeder group. I have come across a problem in accessing IFEFFIT libraries through Perl on WINDOWS Platform. I have installed latest version of IFEFFIT as well as PERL. Evertime i try accessing IFEFFIT Through Perl it gives the error like: c:\work>perl -w trial.pl Can't locate loadable object for module ifeffitin @INC <@INC contains: C:/Perl/lib c:/Perl/site/lib .> at trial.pl line 2. Compilation failed in require at trial.pl line 2. BEGIN failed--conpliation aborted at trial.pl line 2. I have trying putting 'Perl folder from wrappers of IFEFFIT' to Perl/site/lib, but no success so far. I am stuck with my work. Any solution to get Access of IFEFFIT libraries through Perl? Cheers!!! Satyender Goel MSc 'Cheminformatics'

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E0 limit
by alita＠chemmail.chem.fsu.edu 03 Jun '05

03 Jun '05

When I fit some Cr compound in Artemis I obtain a e0 for each path around 6.68 . In " Using Artemis" by dr. Bruce Ravel page 49 there is a example where he is also obtaing a 6.59 value for e0. Is there a limit for this e0? I must restrain this value to be under 5? How can I calculate this value? Thanks, Adrian Lita

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