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

Re: [Ifeffit] Ifeffit Digest, Vol 123, Issue 3
by Eric John Peterson 01 May '13

01 May '13

Here you go... the low angle traces are the alignment scans done using the Ge220 monochromator ________________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [ifeffit-bounces(a)millenia.cars.aps.anl.gov] on behalf of ifeffit-request(a)millenia.cars.aps.anl.gov [ifeffit-request(a)millenia.cars.aps.anl.gov] Sent: Wednesday, May 01, 2013 1:26 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 123, Issue 3 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: Problem running JFEFF/FEFF9 on Windows 7 (Linda Lim) 2. Re: Problem with running Demeter (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Wed, 1 May 2013 12:01:15 -0700 From: Linda Lim <ywllim(a)stanford.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Problem running JFEFF/FEFF9 on Windows 7 Message-ID: <CALPaxYDE_9rDMFTLiAiEaXArWyZaMPQMOx=drz5xtrfj2=tAQQ(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Hi Ross I had the same issue earlier as well, and it turns out that It is due to the latest Java update. It can be fixed by rolling back to the previous Java update. Cheers Linda On Wed, May 1, 2013 at 11:50 AM, Ross Devol <devol(a)wisc.edu> wrote: > I'm a new FEFF user, and I installed JFEFF and FEFF 9 on a computer with > Windows 7. I can load feff.inp files into JFEFF just fine, but when I click > "Save & Run," the Run window is blank and never shows any output. Has > anyone else had this problem? Does anyone know how to fix it? > > Thanks, > Ross DeVol > University of Wisconsin - Madison > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

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Problem with running Demeter
by Amitava D Roy 01 May '13

01 May '13

Dear Bruce, I am having this strange problem since I used CC Cleaner to clean up my computer. (This may be coincidental.) [cid:image001.jpg@01CE466F.10C0D470] The following is the output of the dartemis.log file: Can't load 'C:/strawberry/perl/site/lib/auto/Wx/Wx.dll' for module Wx: load_file:The specified procedure could not be found at C:/strawberry/perl/lib/DynaLoader.pm line 200. at C:/strawberry/perl/site/lib/Wx/Perl/SplashFast.pm line 60 Compilation failed in require at C:\strawberry\perl\site\bin\dartemis.bat line 23. BEGIN failed--compilation aborted at C:\strawberry\perl\site\bin\dartemis.bat line 23. I have uninstalled and installed Demeter several times but the problem remains the same. This happened just when I needed to use Demeter the most. Thanks in advance, Amitava Roy J. Bennett Johnston, Sr., Center for Advanced Microstructures and Devices (CAMD) Louisiana State University, Baton Rouge, LA 70806

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Problem running JFEFF/FEFF9 on Windows 7
by Ross Devol 01 May '13

01 May '13

I'm a new FEFF user, and I installed JFEFF and FEFF 9 on a computer with Windows 7. I can load feff.inp files into JFEFF just fine, but when I click "Save & Run," the Run window is blank and never shows any output. Has anyone else had this problem? Does anyone know how to fix it? Thanks, Ross DeVol University of Wisconsin - Madison

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ATOMS: Partial occupancies -how to edit .cif File
by Sanwald, Kai 24 Apr '13

24 Apr '13

Hi, I would like to fit the NiFe2O4 spinel structure to EXAFS data of mixed Ni/Fe-(hydro)xide films. However, ATOMS cannot deal with structures exhibiting crystal sites with partial occupancies. I know that this problem has been adressed to some extent on the mailing-list already in May 2012 (see http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2012-May/010544.html) and Bruce Ravel shortly outlined how to edit the .cif file in order to run ATOMS and FEFF6. Attached you find the NiFe2O4.cif file that I like to employ. I tried the following: 1. changed occupancy from 0.5 to 1 in line Ni1 Ni2+ 16 d 0.625 0.625 0.625 . 0.5 0 2. subsequently deleted line Fe2 Fe3+ 16 d 0.625 0.625 0.625 . 0.5 0 I got rid of the ATOMS warning concerning the partial occupancy but FEFF6 crashes due to atoms being postioned too closely to each other. I am pretty sure that my editing resulted in a change of the structure. I would be very glad if someone could explain to me in some detail how I need to edit the .cif. Thank you very much for your help. Best, Kai

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background removal - spline range kmin
by Reagen Lan 23 Apr '13

23 Apr '13

Dear all, For removing the background from a spec with sharp white-line, I understand it is often to put larger value for kmin of Spline range in Athena. However, in my current case, there is a intensive XANES peak at c.a. 16ev after the white-line peak. Thus, should I input kmin in between these two peaks (see attached figure test1.png)? or increase kmin to avoid the second strong peak(attached figure test2.png)? The two conditions do give different chi(R). Please could some body advise? Thanks a lot! Best regards, Zhipeng

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Re: [Ifeffit] ifeffit R-factor
by Matt Newville 18 Apr '13

18 Apr '13

Hi Sandra, On Sat, Apr 6, 2013 at 12:37 PM, Sandra Luber <s.luber(a)pci.uzh.ch> wrote: > Dear Matt Newville, > > I do some fitting with ifeffit using EXAFS data generated by feff. > I wonder how the R-factor is calculated. Unfortunately, > I have not found any definition yet. Would it be possible > that you write me how it is obtained? > This would be great. > > Thanks a lot. > > Best regards > Sandra Luber > The basic definition is R = Sum( |data - fit|^2 ) / Sum( |data|^2 ) The old Feffit document probably has the clearest definition, in its Chapter 5 (pages 16-20 of http://cars.uchicago.edu/~newville/feffit/feffit.pdf ). The definition and briefer explanations are also given in several of the tutorials on http://xafs.org/Tutorials. Thanks for reminding me to put this and related information into the Larch documentation! --Matt

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L-edge soft X-ray data in Artemis and Athena
by Shoaib Muhammad 11 Apr '13

11 Apr '13

Hi, I am a research student and relatively new to XAFS. I have soft X-Ray L-edge data of Mn and Ni. Is it possible to process this data in Athena and then fit in Artemis like usual K-edge data? Thanks -- Shoaib

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ifeffit on Mac OS X
by Frank Schima 04 Apr '13

04 Apr '13

Hello list, I have created a port of ifeffit [1] on Macports [2] so that you can easily install ifeffit on Mac OS X. I have only run this myself on Mountain Lion (10.8), but I believe it built successfully on the Lion and Snow Leopard buildbots - so it should work there too. If anyone is interested in trying it, it is a two step process. 1. Install Macports [3]. 2. From a terminal window type the following: sudo port install ifeffit Feedback about how it runs would be appreciated. Cheers! Frank [1] <http://www.macports.org/ports.php?by=name&substr=ifeffit> [2] <http://www.macports.org> [3] <http://www.macports.org/install.php>

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ifeffit on Mac OS X
by Frank Schima 04 Apr '13

04 Apr '13

Hello list, I have created a port of ifeffit [1] on Macports [2] so that you can easily install ifeffit on Mac OS X. I have only run this myself on Mountain Lion (10.8), but I believe it built successfully on the Lion and Snow Leopard buildbots - so it should work there too. If anyone is interested in trying it, it is a two step process. 1. Install Macports [3]. 2. From a terminal window type the following: sudo port install ifeffit Feedback about how it runs would be appreciated. Cheers! Frank [1] <http://www.macports.org/ports.php?by=name&substr=ifeffit> [2] <http://www.macports.org> [3] <http://www.macports.org/install.php>

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APS/IIT XAFS Summer School July 8 - 12, 2013
by Robert Gordon 01 Apr '13

01 Apr '13

Notice attached. "This XAFS summer school is a continuation of the week-long summer school offered annually at the Advanced Photon Source, and again the venue will be at IIT in Chicago. Course material will cover fundamental and practical aspects of X-ray Absorption Fine Structure Spectroscopy: sample preparation, experiment, theory, data analysis. One day of hands-on experiments will be carried out by participants at several APS beamlines, followed by a guided data analysis laboratory using Athena/iFEFFIT and other programs. Computers will be available for those participants attending without their own laptops. The target audience is graduate students, postdocs, and other scientists who are new to XAFS and want to use it in their own research. Space is available for up to 40 students. Instructors include: Dr. Steve Heald (ANL), Dr. Matt Newville (UChicago), Prof. Bruce Bunker (U Notre Dame), Prof. Carlo Segre (IIT), Prof. Grant Bunker (IIT), and a number of other experienced XAFS researchers also will participate. The cost of the course is $500 USD, which covers most meals. Students will be responsible for their own housing (available on and off IIT campus) and travel to/from their home institutions. IIT is readily accessible by car, cab, and CTA train from O’Hare and Midway airports. Free time will be available most evenings for participants to visit Chicago attractions such as Grant Park, the Loop, Millennium Park, Lake Michigan; music, architecture, art, theater; Chinatown, White Sox, Field Museum, Shedd Aquarium, Adler Planetarium, and Navy Pier, restaurants, and pubs. Please email bunker(a)iit.edu with subject line “2013 XAFS School” -- Dr. Robert Gordon Staff Scientist, PNCSRF APS Sector 20 (PNC/XSD) 9700 S Cass Ave. 435E Argonne, IL, USA 60439 630-252-0581 630-252-0580 fax

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