April 2013 - Ifeffit - millenia.cars.aps.anl.gov

Re: [Ifeffit] Launching Athena on Mountain Lion (Mac OS 10.8)
by Kyler Carroll 05 Dec '14

05 Dec '14

Hello, I had posted a comment/question a few months back when I had initially installed Mountain Lion on my mac regarding iXAFS compatibility with XQuartz and the new OS not supporting X11 anymore. Since then I have received a few comments back and I found one solution to be the best. This was originally sent by Tsu-Chien Weng from SSRL (tsuchien(a)slac.stanford.edu) Please find the following solution below. Once you install XQuartz the rest will be done in the Terminal.app. This is a one time solution and I havent had any trouble thus far with the program. Hope this works as well for everyone else as it did for me. 1. Install XQuartz from <http://xquartz.macosforge.org/landing/> 2. open Terminal.app 3. cd /Applications/Utilities 4. sudo mkdir X11.app 5. cd X11.app 6. sudo ln -s ../XQuartz.app/Contents Thank you, Kyler J. Carroll, Ph.D. Assistant Project Scientist Department of NanoEngineering University of California, San Diego

3 2

problem with importing data between version of artemis
by Georges Siddiqi 14 May '13

14 May '13

Hi All, I've done a fit in the old version of Artemis (0.8.014), and wanted to import this fit into the new version of artemis (demeter 0.9.15) that I have to play around with it a bit more. The problem is, when I import the the "old-style artemis project", and do the same fit, the values, and fit itself are nowhere near similar to what i got with the old version of Artemis. what is the cause of this discrepancy? As far as I can tell from double checking all the fitting parameters, windows, variables, etc, they are all exactly the same. Even if I try to just do a summation in the new version with my best-fit values from the old version, the fit is completely different. Previously when I was importing fits between versions I had no issues whatsoever. I've attached the artemis project file (W EXAFS.apj) that gives me a good fit in the old version, and a poor fit in the new version. thanks, georges

6 9

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

4 3

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

2 1

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

3 4

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

6 5

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>

3 2

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>

1 0

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

1 0