September 2010 - Ifeffit - millenia.cars.aps.anl.gov

Bkg fit in Artemis
by hemantha aranwela 10 Sep '10

10 Sep '10

Hi All, I like to understand the way how the background fitting is done in Artemis. How the background functions are obtained (or defined)? How do we use the bkg fit in analyzing the data? I have a good idea about how Athena does the bkg reduction. But have no clue in case of Artemis. I would appreciate if somebody can direct me to an article written on this or can give a brief introduction about it. Thanks. Aranwela

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iXAFS & python scripting
by Brugger, Joel (SAM) 09 Sep '10

09 Sep '10

Hi Matt, Actually we did run . /Applications/iXAFS.app/Contents/Resources/local/bin/iff_init.sh (I was just wondering if it was still required). Hopefully the following output will be clearer than my prose. Line 5 in "iff = Ifeffit.Ifeffit()". The problem seems to be access to "/Users/Newville/Codes/ifeffit/local/share/ifeffit" while running Ifeffit.Ifeffit(). Thanks! Joel + Barb Last login: Fri Sep 10 08:14:26 on ttys004 JoelMacBook-Silver:~ joelb$ echo $PATH /opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin JoelMacBook-Silver:~ joelb$ . /Applications/iXAFS.app/Contents/Resources/local/bin/iff_init.sh JoelMacBook-Silver:~ joelb$ echo $PATH /Applications/iXAFS.app/Contents/Resources/local/bin:/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin JoelMacBook-Silver:~ joelb$ cd /Users/joelb/data_ifeffit/APS-April08-Pascal/python JoelMacBook-Silver:python joelb$ python aps-12p9mLiCl.py failed to load ifeffit library libifeffit.dylib /Users/Newville/Codes/ifeffit/local/share/ifeffit:/Applications/iXAFS.app/Contents/Resources/local/bin:/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin Traceback (most recent call last): File "aps-12p9mLiCl.py", line 5, in <module> iff = Ifeffit.Ifeffit() File "/Library/Python/2.6/site-packages/Ifeffit/Ifeffit.py", line 79, in __init__ raise ImportError('Cannot load ifeffit library') ImportError: Cannot load ifeffit library JoelMacBook-Silver:python joelb$ echo $PATH /Applications/iXAFS.app/Contents/Resources/local/bin:/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin ________________________________________ ------------------------------ Message: 4 Date: Thu, 9 Sep 2010 10:12:09 -0500 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Cc: "barbara.etschmann(a)adelaide.edu.au" <barbara.etschmann(a)adelaide.edu.au> Subject: Re: [Ifeffit] IXAFS3.0.2 and python scripting Message-ID: <AANLkTikYLAwnRcwZWNK+yBL0Byp7NgxNJ=Zrn_v3V56M(a)mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Hi Joel and Barb, Ah, sorry. I believe you need to do . /Applications/iXAFS.app/Contents/Resources/local/bin/iff_init.sh in the shell prior to running python, or add this to your bash .profile file. It would be better if the setup procedure detected that it was on a Mac and set the environment up automatically. I'll work on that (and on the build for10.5). --Matt > Works great on 10.6 for us too. Thanks a million times, and fingers crossed for finding the error in 10.5 ! > > We tried the python scripting, but apparently a /Users/Newville still lurks in there. > > Running the aps-12p9mLiCl.py ?script > > 1. #!/usr/bin/python > 2. > 3. import math > 4. import Ifeffit > 5. iff = Ifeffit.Ifeffit() > > gives the following error: > > bash-3.2$ python aps-12p9mLiCl.py > ?failed to load ifeffit library ?libifeffit.dylib > /Users/Newville/Codes/ifeffit/local/share/ifeffit:/opt/local/bin:/opt/local/sbin:/opt/pgi/osx86/10.4/bin:/Users/joelb/Public/XDS/XDS-OSX_Intel:/Applications/iXAFS.app/Contents/Resources/local/bin:/opt/local/bin:/opt/local/sbin:/sw/bin:/sw/sbin:/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:/usr/X11R6/bin:/usr/local/lib:/Users/joelb/Desktop/FitYK/:/usr/local/lib/:/sw/lib/:/sw/include/readline/:/unix/Molecular Dynamics/moldy-2.16e:/Users/joelb/Public/XDS/XDS-OSX_Intel:/Users/joelb/Desktop/fdmnes:/usr/local/lib:/Users/joelb/Desktop/FitYK/:/usr/local/lib/:/sw/lib/:/sw/include/readline/:/unix/Molecular Dynamics/moldy-2.16e:/Users/joelb/Public/XDS/XDS-OSX_Intel:/Users/joelb/Desktop/fdmnes:/Applications/iXAFS.app/Contents/Resources/local/bin > Traceback (most recent call last): > ?File "aps-12p9mLiCl.py", line 5, in <module> > ? ?iff = Ifeffit.Ifeffit() > ?File "/Library/Python/2.6/site-packages/Ifeffit/Ifeffit.py", line 79, in __init__ > ? ?raise ImportError('Cannot load ifeffit library') > ImportError: Cannot load ifeffit library > > > I tried to add /Applications/iXAFS.app/Contents/Resources/local/lib to PATH (there's a libifeffit.dylib there), but that did not help. > > Also notice that my PATH variables have been duplicated. This happens because I still have '. /Applications/iXAFS.app/Contents/Resources/local/bin/iff_init.sh' in my '.profile'. Do I need to keep this? If so, it would be nice to fix iff_init.sh too :-) > > Thanks, > > Joel + Barb >

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atoms input file
by mohamed sobhy 09 Sep '10

09 Sep '10

Dear I would like to fit the signal from (U0.8Ce0.2)O2, so I tried to put Ce in the same position of U but all atoms generated files give no Ce in the scattering paths and some fitting give negative amplitude values. Could you help me with the Atoms input file? Mohamed

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IXAFS3.0.2 and python scripting
by Brugger, Joel (SAM) 09 Sep '10

09 Sep '10

Dear Matt, Works great on 10.6 for us too. Thanks a million times, and fingers crossed for finding the error in 10.5 ! We tried the python scripting, but apparently a /Users/Newville still lurks in there. Running the aps-12p9mLiCl.py script 1. #!/usr/bin/python 2. 3. import math 4. import Ifeffit 5. iff = Ifeffit.Ifeffit() gives the following error: bash-3.2$ python aps-12p9mLiCl.py failed to load ifeffit library libifeffit.dylib /Users/Newville/Codes/ifeffit/local/share/ifeffit:/opt/local/bin:/opt/local/sbin:/opt/pgi/osx86/10.4/bin:/Users/joelb/Public/XDS/XDS-OSX_Intel:/Applications/iXAFS.app/Contents/Resources/local/bin:/opt/local/bin:/opt/local/sbin:/sw/bin:/sw/sbin:/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:/usr/X11R6/bin:/usr/local/lib:/Users/joelb/Desktop/FitYK/:/usr/local/lib/:/sw/lib/:/sw/include/readline/:/unix/Molecular Dynamics/moldy-2.16e:/Users/joelb/Public/XDS/XDS-OSX_Intel:/Users/joelb/Desktop/fdmnes:/usr/local/lib:/Users/joelb/Desktop/FitYK/:/usr/local/lib/:/sw/lib/:/sw/include/readline/:/unix/Molecular Dynamics/moldy-2.16e:/Users/joelb/Public/XDS/XDS-OSX_Intel:/Users/joelb/Desktop/fdmnes:/Applications/iXAFS.app/Contents/Resources/local/bin Traceback (most recent call last): File "aps-12p9mLiCl.py", line 5, in <module> iff = Ifeffit.Ifeffit() File "/Library/Python/2.6/site-packages/Ifeffit/Ifeffit.py", line 79, in __init__ raise ImportError('Cannot load ifeffit library') ImportError: Cannot load ifeffit library I tried to add /Applications/iXAFS.app/Contents/Resources/local/lib to PATH (there's a libifeffit.dylib there), but that did not help. Also notice that my PATH variables have been duplicated. This happens because I still have '. /Applications/iXAFS.app/Contents/Resources/local/bin/iff_init.sh' in my '.profile'. Do I need to keep this? If so, it would be nice to fix iff_init.sh too :-) Thanks, Joel + Barb ________________________________________ Today's Topics: 1. Re: iXAFS3.0.2 (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Wed, 8 Sep 2010 11:36:06 -0500 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] iXAFS3.0.2 Message-ID: <AANLkTinmG5RGjBwj5eX5yui2JQo_nEP+1JJuMMdWPndh(a)mail.gmail.com> Content-Type: text/plain; charset=windows-1252 Hi Brandon, Thanks for the report. I've seen the same errors on the only system I have access to running 10.5.something: All the executable programs (perl, ifeffit) report the same dyld error. I thought these messages were perhaps because I had built a "universal binary" that included x86_64 and i386, so I rebuilt for i386 but not x86_64, hoping that would solve the problem. But it didn't. I've looked into a little bit more (if anyone knows more, please let me know!!), and believe the issue may be solved by adding compiler flags of -mmacosx-version-min=10.5 -isysroot /Developer/SDKs/MacOSX10.5u.sdk I have not tried this yet, but will try to get this rebuilt in the next day or two. Sorry for the trouble. FWIW, I still get results I don't understand on PPC, where ifeffit and artemis run but hephaestus are artemis do not.... isn't that amazing? --Matt

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iXAFS3.0.2
by Matt Newville 08 Sep '10

08 Sep '10

Hi All, OK, I put a next attempt for a Mac distribution at http://cars9.uchicago.edu/~ifeffit/src/iXAFS3.0.2.dmg which should have some improvements. I believe this should work on 10.6 without issue -- I tested it on one other system at work, and everything launched without trouble. The Python module should now install well. With earlier attempts, I still had problems with a 10.5 machine, and suspected something wrong with i386 v x86_64. So I rebuilt everything (including perl) to be for i386 and ppc architectures, but not x86_64. In fact, I noticed some Aquaterm-related issues that also seemed x86_64 v i386, and went back to using (and including in the distribution) the standard issue Aquaterm1.0.1 that has i386 and ppc binaries, but not x86_64. Thus, iXAFS3.0.2 has no x86_64 binaries. For one thing, this makes the image "only" 60Mb. I could not find suitable 10.5 or PowerPC machines at work, but will test later today. For PPC, the iXAFS launcher application is now universal, and runs on PPC (G4) machine. With an earlier incarnation (when x86_64 was still included) I could run the Ifeffit shell and Athena. Unfortunately, both Artemis and Hephaestus failed to load with dyld: lazy symbol binding failed: Symbol not found: ___gcc_gmul Referenced from: ....local/bin/perl Expected in: /usr/lib/libSystem.B.dylib Hephaestus showed a splash screen, Artemis did not. I grepped out all the 'use' statements from Hephaestus, and these can all be loaded. In addition, all '*.bundle" files (Perl's binaries) claim to be universal binaries (including ppc). I don't really know what to make of this, but will try again with the latest build. Any feedback on what works and what doesn't would be greatly appreciated. Cheers, --Matt On Mon, Sep 6, 2010 at 11:06 AM, Jeff Terry <terryj(a)iit.edu> wrote: > Hi All, > > Looks like it works now on intel machines.. > I can run ifeffit from the iXAFS shell. > > The iXAFS app is not universal though, it is Intel only. > > Nice job Matt. > > Jeff > > > On Sep 6, 2010, at 10:17 AM, Matt Newville wrote: > >> Hi Joel, All, >> >> Yes, sorry for that. I'm still learning how to do this. Here's the >> latest news (some progress, incomplete): >> >> With Jeff's earlier message I looked into and solved at least one of >> the problems: that /Users/Newville/Codes/ifeffit/local/bin/perl >> was all over the place and expected. Of course, this worked when I >> tested it on my own machine!! I also found an issue with png >> support. >> >> I put a 3.0.1 dmg with these changes at >> http://cars9.uchicago.edu/~ifeffit/src/iXAFS3.0.1.dmg >> >> I believe this may work on 10.6 systems. >> >> I tried this on a 10.5.7, i386 system (Julie's). The main iXAFS app >> runs, but I unfortunately get 'dyld' loading errors for all >> executables (including perl and ifeffit). I do not understand this, >> as thhe executables are definitely listed as "universal", ut I suspect >> it is a x86_64 v i386 issue. If anyone does understand this, please >> let me know. FWIW, the machine I'm building on is less than 3 months >> old, so I think it's x86_64, but 'arch' and 'uname -p' report i386. >> On the build machine, running >> arch -x86_64 ifeffit >> runs fine. >> arch -i386 ifeffit >> runs, but Aquaterm does not generate a plot (using PGPLOT_DEV=/XS does >> generate a plot with both settings). So my sense is that my box is >> really x86_64, but reports i386 and this may be causing trouble on >> real i386 machines. >> >> What's stranger is that I also tried this on a very old G4 powerpc, >> running 10.5. Here the iXAFS.app does not run, and indeed >> the iXAFS executable (iXAFS.app/Contents/MacOS/iXAFS) is indeed i386 >> only. But, the ifeffit application DOES RUN(!!!) on this machine. >> Perl runs too, but it appears I forgot to rebuild Ifeffit.pm for perl >> after some change for png support because >> perl -e 'use Ifeffit' still complains about png support. This is >> fixable. I'll look into making the iXAFS launcher application be >> universal. >> >> The python problem is definitely fixable too -- sorry for such poor testing! >> >> If you or Jeff or someone else wants to try this v3.0.1 out, that >> would be fine, but there are definitely "known problems". I'll make >> a v3.0.2 with the perl and python fixes today. I'll look into the >> i386 v x86_64 issues too, but that will take some research... >> >> Cheers, >> >> --Matt >> >> On Mon, Sep 6, 2010 at 7:34 AM, Brugger, Joel (SAM) >> <Joel.Brugger(a)samuseum.sa.gov.au> wrote: >>> Hi Matt, >>> >>> Not much luck with iXAFS3.0 so far. >>> >>> Under 10.5.8 (two macbooks), iXAFS crashes at startup. >>> >>> Under 10.6.4 (macbook pro), IXAFS opens, but clicking on athena/Artemis/Hephaestus only opens an X11 terminal. >>> >>> I think that somehow the installer expects perl to live in /Users/Newville/: >>> >>> $ pwd >>> /Applications/iXAFS.app/Contents/Resources/local/bin >>> b$ artemis >>> -bash: /Applications/iXAFS.app/Contents/Resources/local/bin/artemis: /Users/Newville/Codes/ifeffit/local//bin/perl: bad interpreter: No such file or directory >>> $ >>> >>> >>> >>> I also tried to install python, but something must be wrong with setup.py since files are copied to /Users/Newville. I now have such an inhabitant on my HD thanks to sudo, but even then the install failed. See details below. >>> >>> Hope it’s nothing traumatic! >>> >>> Thanks, JOEL >>> >>> >>> >>> JoelMacBook-Silver:IfeffitPython-2.0.0 joelb$ python setup.py install >>> running install >>> running build >>> running build_py >>> creating build >>> creating build/lib >>> creating build/lib/Ifeffit >>> copying lib/__init__.py -> build/lib/Ifeffit >>> copying lib/Ifeffit.py -> build/lib/Ifeffit >>> copying lib/ifeffit_config.py -> build/lib/Ifeffit >>> copying lib/shell.py -> build/lib/Ifeffit >>> running install_lib >>> creating /Library/Python/2.6/site-packages/Ifeffit >>> copying build/lib/Ifeffit/__init__.py -> /Library/Python/2.6/site-packages/Ifeffit >>> copying build/lib/Ifeffit/Ifeffit.py -> /Library/Python/2.6/site-packages/Ifeffit >>> copying build/lib/Ifeffit/ifeffit_config.py -> /Library/Python/2.6/site-packages/Ifeffit >>> copying build/lib/Ifeffit/shell.py -> /Library/Python/2.6/site-packages/Ifeffit >>> byte-compiling /Library/Python/2.6/site-packages/Ifeffit/__init__.py to __init__.pyc >>> byte-compiling /Library/Python/2.6/site-packages/Ifeffit/Ifeffit.py to Ifeffit.pyc >>> byte-compiling /Library/Python/2.6/site-packages/Ifeffit/ifeffit_config.py to ifeffit_config.pyc >>> byte-compiling /Library/Python/2.6/site-packages/Ifeffit/shell.py to shell.pyc >>> running install_data >>> creating /Users/Newville >>> error: could not create '/Users/Newville': Permission denied >>> >>> >>> Running as SUDO: >>> >>> JoelMacBook-Silver:IfeffitPython-2.0.0 joelb$ sudo python setup.py install >>> Password: >>> running install >>> running build >>> running build_py >>> running install_lib >>> running install_data >>> creating /Users/Newville >>> creating /Users/Newville/Codes >>> creating /Users/Newville/Codes/ifeffit >>> creating /Users/Newville/Codes/ifeffit/local >>> creating /Users/Newville/Codes/ifeffit/local/bin >>> error: can't copy 'ifeffit_shell.py': doesn't exist or not a regular file >>> >>> >>> >>> >>> >>> _______________________________________________ >>> Ifeffit mailing list >>> Ifeffit(a)millenia.cars.aps.anl.gov >>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >>> >>> >> >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > >

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PhD Positions in Spectroscopy and Microscopy
by Matthias Bauer 07 Sep '10

07 Sep '10

Dear ifeffit mailing list users, the group of Prof. Grunwaldt at the Institute for Chemical Technology and Polymer Chemistry of the Karlsruher Insitute of Technology and myself are seeking for PhD Positions in Spectroscopy and Microscopy Karlsruhe Institute of Technology (KIT) is the result of the merger of the University of Karlsruhe and the Research Center, Karlsruhe. It is a unique institution in Germany, which combines the mission of a university with that of a large-scale research center of the Helmholtz Association. With 8000 employees and an annual budget of EUR 650 million, KIT is one of the largest research and edu-cation institutions worldwide. We are a establishing a new research group at the Institute for Technical Chemistry and Polymer Chemistry (ICTP) of the Karlsruhe Institute of Technology (KIT) in Southern Germany with focus on in situ spectroscopy, exhaust gas catalysis, biomass conversion and fine chemical processes. We combine effective catalyst preparation with profound spectroscopic knowledge of the catalysts and are therefore a highly interdisciplinary group. Presently, we have a number of open positions for enthusiastic Ph.D. students at the interface of physical, technical and solid state chemistry as well as in the field of chemical engineering and materials science. The work typically lasts over a period of 3 years. The salary will be according to E13/2, also depending on your professional and personal qualification. Open positions are presently available with focus on In situ spectroscopy of catalysts X-ray microscopy of heterogeneous catalysts Enthusiastic applicants with good English and/or German language knowledge should contact Prof. Dr. Jan-Dierk Grunwaldt (grunwaldt(a)kit.edu) or Dr. Matthias Bauer (matthias.bauer(a)kit.edu) for further information or visit the homepage http://www.itcp.uni-karlsruhe.de and www.grunwaldt.eu. KIT is pursuing a gender equality policy. Women are therefore particularly encouraged to apply. If qualified, handicapped applicants will be preferred. Please send your application including a CV, reference letters and publication list until 30.09.2010 to the Karlsruhe Institute of Technologie (KIT), Institute for Chemical Technology and Polymer Chemistry, Prof. Dr. Jan-Dierk Grunwaldt, Kaiserstr. 12, D-76131 Karlsruhe. Thanks for your attention and best regards, matthias bauer

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opening: Postdoctoral Fellow in Operando Spectroscopy
by Matthias Bauer 07 Sep '10

07 Sep '10

Dear ifeffit mailing list users, the group of Prof. Grunwaldt at the Institute for Chemical Technology and Polymer Chemistry of the Karlsruher Insitute of Technology is seeking for a Postdoctoral Fellow in Operando Spectroscopy Karlsruhe Institute of Technology (KIT) is the result of the merger of the University of Karlsruhe and the Research Center, Karlsruhe. It is a unique institution in Germany, which combines the mission of a university with that of a large-scale research center of the Helmholtz Association. With 8000 employees and an annual budget of EUR 650 million, KIT is one of the largest research and education institutions worldwide. The Institute for Technical Chemistry and Polymer Chemistry (ICTP) of the Karlsruhe Institute of Technology (KIT) in Southern Germany has an exciting opportunity for a Postdoctoral Fellow in Operando Spectroscopy for in situ characterization of heterogeneous catalysts in our catalysis laboratories at synchrotron radiation sources. Are you interested to work at the interface of physical chemistry and questions relevant to catalysis? The position is focused on the physico-chemical characterization of catalysts, mainly the identification and characterization of the active catalytic sites by means of X-ray absorption spectroscopy in combination with other spectroscopic methods like UV/Vis, FTIR and Raman techniques. The development of spectroscopic measurement cells as well as the realization of the according infrastructure are highly relevant for this work, which will be conducted in close cooperation with synchrotron radiation facilities such as ANKA (Karlsruhe), DESY (Hamburg), ESRF (Grenoble), and SLS (Switzerland). A PhD in chemistry, physics, chemical engineering or a related scientific field is a prerequisite for this position. Knowledge and experience with spectroscopic methods, mainly X-ray absorption in combination with other techniques, in catalysis is mandatory. Enthusiastic applicants with good English language knowledge should contact Prof. Dr. Jan-Dierk Grunwaldt (grunwaldt(a)kit.edu) for further information or visit the homepage http://www.itcp.uni-karlsruhe.de. KIT is pursuing a gender equality policy. Women are therefore particularly encouraged to apply. If qualified, handicapped applicants will be preferred. Please send your application including a CV, reference letters and publication list until 30.09.2010 to the Karlsruhe Institute of Technologie (KIT), Institute for Chemical Technology and Polymer Chemistry, Prof. Dr. Jan-Dierk Grunwaldt, Kaiserstr. 12, D-76131 Karlsruhe. On behalf of Prof. Grunwaldt, Matthias Bauer

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Re: [Ifeffit] XANES calculations
by Joshua Kas 06 Sep '10

06 Sep '10

Hi Jeong Eun Suk, FEFF doesn't come with any fitting program, but there is a program called FitIt developed by G. Smolentsev which is available for fitting XANES and can be used with FEFF or FDMNES. You can find FitIt at http://www.nano.sfedu.ru/fitit.html Cheers, Josh Kas > > > Thank Josha > > I already read the letter which you introduced but I misunderstood. > > can I ask a question? > > Other progrems like FDMNES are possibe to fit to experiment data. > > can I fit theory obtained from FEFF to experiment data like EXAFS? > > I couldn't have heard that from other users and I also didn't find fitting > parameters in FEFF. > > > > > > Date: Sat, 4 Sep 2010 10:36:48 -0700 > From: joshua.j.kas(a)gmail.com > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] XANES calculation > > Hi Jeong Eun Suk, > FEFF doesn't use basis functions. There is a truncation in angular > momentum, but the XANES is calculated by first calculating the Green's > function using multiple scattering theory. The Green's function is expanded > in terms of an angular momentum basis about each atom, and radial solutions > are numerical. Muffin tin potentials are used in FEFF8 and there is no > option for full potential calculations at present. For more information on > multiple scattering theory, > see for example > > Multiple scattering in solids By Antonios Gonis, > > > or > > > Theoretical approaches to x-ray absorption fine structure > J. J. Rehr and R. C. Albers > Rev. Mod. Phys. 72, 621 (2000) > > > Cheers, > Josh > On Sat, Sep 4, 2010 at 10:00 AM, < > ifeffit-request(a)millenia.cars.aps.anl.gov> wrote: > > 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. iXAFS for Mac OS X (Matt Newville) > 2. Re: iXAFS for Mac OS X (Matt Newville) > 3. Re: iXAFS for Mac OS X (Jeff Terry) > 4. XANES calculation (JeongEunSuk) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 3 Sep 2010 22:08:57 -0500 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] iXAFS for Mac OS X > Message-ID: > <AANLkTinSvabP-Z5ARvxYO4Gh6xMTrF_sErC=ykxUFdcR(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi Folks, > > With help from Ken McIvor and Jeff Terry, I've built a new version of > iXAFS for Mac OS X. This version should be considered experimental, > but for the brave and/or foolhardy please try it out and let us know > how it works. This version offers the latest versions of Athena, > Artemis, and Hephaestus, and the latest version of Ifeffit. It is > meant to be universal (for x86_64, i386, and ppc), though I have not > fully tested this. > > The download is fairly large (~74Mb), mostly because it includes a > full distribution of Perl built right in (so it doesn't interfere with > the system Perl). It also provides a "complete" Unix shell-like > environment that can be used for those who need it. For example, a > python module is included that can be installed. > > The disk image is at > http://car9.uchicago.edu/~ifeffit/src/iXAFS3.0.dmg This should be > able to be installed by dragging the iXAFS application to any folder. > > To use the Unix shell, you'd put > . /Applications/iXAFS.app/Contents/Resources/local/bin/iff_init.sh > > in your .profile or from a bash Terminal command prompt (assuming you > installed to /Applications/). To install the Python module, first > run iff_init.sh above, then > copy and unpack > > /Applications/iXAFS.app/Contents/Resources/local/extras/IfeffitPython-2.0.0.tar.gz > and run 'python setup.py install'. > > Again, this should be considered a beta release. Please be willing to > look for and report problems. > > Cheers, > > --Matt > > > ------------------------------ > > Message: 2 > Date: Fri, 3 Sep 2010 22:11:36 -0500 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] iXAFS for Mac OS X > Message-ID: > <AANLkTiku48seVpa5HTaW30_hiB7-Lap7u79zt0yFVQ3v(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Sorry for the typo. The download is at > http://cars9.uchicago.edu/~ifeffit/src/iXAFS3.0.dmg > > --Matt > > On Fri, Sep 3, 2010 at 10:08 PM, Matt Newville > <newville(a)cars.uchicago.edu> wrote: > > Hi Folks, > > > > With help from Ken McIvor and Jeff Terry, ?I've built a new version of > > iXAFS for Mac OS X. ?This version should be considered experimental, > > but for the brave and/or foolhardy please try it out and let us know > > how it works. This version offers the latest versions of Athena, > > Artemis, and Hephaestus, and the latest version of Ifeffit. ? ?It is > > meant to be universal (for x86_64, i386, and ppc), though I have not > > fully tested this. > > > > The download is fairly large (~74Mb), mostly because it includes a > > full distribution of Perl built right in (so it doesn't interfere with > > the system Perl). ?It also provides a "complete" Unix shell-like > > environment that can be used for those who need it. ?For example, a > > python module is included that can be installed. > > > > The disk image is at > > http://car9.uchicago.edu/~ifeffit/src/iXAFS3.0.dmg ? This should be > > able to be installed by dragging the iXAFS application to any folder. > > > > To use the Unix shell, you'd put > > ? . /Applications/iXAFS.app/Contents/Resources/local/bin/iff_init.sh > > > > in your .profile or from a bash Terminal command prompt (assuming you > > installed to /Applications/). ?To ?install the Python module, ?first > > run iff_init.sh above, then > > copy and unpack > > > /Applications/iXAFS.app/Contents/Resources/local/extras/IfeffitPython-2.0.0.tar.gz > > and run 'python setup.py install'. > > > > Again, this should be considered a beta release. ?Please be willing to > > look for and report problems. > > > > Cheers, > > > > --Matt > > > > > > ------------------------------ > > Message: 3 > Date: Fri, 3 Sep 2010 22:38:23 -0500 > From: Jeff Terry <terryj(a)iit.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] iXAFS for Mac OS X > Message-ID: <06727371-5AD2-401E-9EEF-0D981144D0E8(a)iit.edu> > Content-Type: text/plain; charset=us-ascii > > Hi All, > > If you have been using the iXAFS Shell for command line access, note that > it is currently not working in this version. > > Jeff > > On Sep 3, 2010, at 10:08 PM, Matt Newville wrote: > > > Hi Folks, > > > > With help from Ken McIvor and Jeff Terry, I've built a new version of > > iXAFS for Mac OS X. This version should be considered experimental, > > but for the brave and/or foolhardy please try it out and let us know > > how it works. This version offers the latest versions of Athena, > > Artemis, and Hephaestus, and the latest version of Ifeffit. It is > > meant to be universal (for x86_64, i386, and ppc), though I have not > > fully tested this. > > > > The download is fairly large (~74Mb), mostly because it includes a > > full distribution of Perl built right in (so it doesn't interfere with > > the system Perl). It also provides a "complete" Unix shell-like > > environment that can be used for those who need it. For example, a > > python module is included that can be installed. > > > > The disk image is at > > http://car9.uchicago.edu/~ifeffit/src/iXAFS3.0.dmg This should be > > able to be installed by dragging the iXAFS application to any folder. > > > > To use the Unix shell, you'd put > > . /Applications/iXAFS.app/Contents/Resources/local/bin/iff_init.sh > > > > in your .profile or from a bash Terminal command prompt (assuming you > > installed to /Applications/). To install the Python module, first > > run iff_init.sh above, then > > copy and unpack > > > /Applications/iXAFS.app/Contents/Resources/local/extras/IfeffitPython-2.0.0.tar.gz > > and run 'python setup.py install'. > > > > Again, this should be considered a beta release. Please be willing to > > look for and report problems. > > > > Cheers, > > > > --Matt > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > ------------------------------ > > Message: 4 > Date: Sat, 4 Sep 2010 13:03:21 +0900 > From: JeongEunSuk <eunsuk1986(a)hotmail.com> > To: ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] XANES calculation > Message-ID: <BLU151-w31DB451074575B1BBF5E5EDA8E0(a)phx.gbl> > Content-Type: text/plain; charset="ks_c_5601-1987" > > > Hi all > > I calculated XANES by using FEFF8.0. > > The manuel of FEFF8.0 demonstrates that basis functions of angular momentum > in each atom is used to calculate SCF potential and FMS. > > I know some codes use special basis functions of angular momentum like the > set of Slater-Type Orbital, contracted Gaussian-type function to describe > molecule or solid . > > Does anybody know what kinds of basis function is used in FEFF8.0 to > calculate SCF and FMS? > > and how can I know the contribution of each basis function? > > Finally, I read FEFF8.0 uses overlapped sherical muffin-tin(MT) to > calculate XANES. > > Is the non-muffin tin calculation impossible In FEFF8.0? > >

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iXAFS3.0 - not much luck so far
by Brugger, Joel (SAM) 06 Sep '10

06 Sep '10

Hi Matt, Not much luck with iXAFS3.0 so far. Under 10.5.8 (two macbooks), iXAFS crashes at startup. Under 10.6.4 (macbook pro), IXAFS opens, but clicking on athena/Artemis/Hephaestus only opens an X11 terminal. I think that somehow the installer expects perl to live in /Users/Newville/: $ pwd /Applications/iXAFS.app/Contents/Resources/local/bin b$ artemis -bash: /Applications/iXAFS.app/Contents/Resources/local/bin/artemis: /Users/Newville/Codes/ifeffit/local//bin/perl: bad interpreter: No such file or directory $ I also tried to install python, but something must be wrong with setup.py since files are copied to /Users/Newville. I now have such an inhabitant on my HD thanks to sudo, but even then the install failed. See details below. Hope it’s nothing traumatic! Thanks, JOEL JoelMacBook-Silver:IfeffitPython-2.0.0 joelb$ python setup.py install running install running build running build_py creating build creating build/lib creating build/lib/Ifeffit copying lib/__init__.py -> build/lib/Ifeffit copying lib/Ifeffit.py -> build/lib/Ifeffit copying lib/ifeffit_config.py -> build/lib/Ifeffit copying lib/shell.py -> build/lib/Ifeffit running install_lib creating /Library/Python/2.6/site-packages/Ifeffit copying build/lib/Ifeffit/__init__.py -> /Library/Python/2.6/site-packages/Ifeffit copying build/lib/Ifeffit/Ifeffit.py -> /Library/Python/2.6/site-packages/Ifeffit copying build/lib/Ifeffit/ifeffit_config.py -> /Library/Python/2.6/site-packages/Ifeffit copying build/lib/Ifeffit/shell.py -> /Library/Python/2.6/site-packages/Ifeffit byte-compiling /Library/Python/2.6/site-packages/Ifeffit/__init__.py to __init__.pyc byte-compiling /Library/Python/2.6/site-packages/Ifeffit/Ifeffit.py to Ifeffit.pyc byte-compiling /Library/Python/2.6/site-packages/Ifeffit/ifeffit_config.py to ifeffit_config.pyc byte-compiling /Library/Python/2.6/site-packages/Ifeffit/shell.py to shell.pyc running install_data creating /Users/Newville error: could not create '/Users/Newville': Permission denied Running as SUDO: JoelMacBook-Silver:IfeffitPython-2.0.0 joelb$ sudo python setup.py install Password: running install running build running build_py running install_lib running install_data creating /Users/Newville creating /Users/Newville/Codes creating /Users/Newville/Codes/ifeffit creating /Users/Newville/Codes/ifeffit/local creating /Users/Newville/Codes/ifeffit/local/bin error: can't copy 'ifeffit_shell.py': doesn't exist or not a regular file

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Re: [Ifeffit] XANES calculation
by Joshua Kas 05 Sep '10

05 Sep '10

Hi Jeong Eun Suk, FEFF doesn't use basis functions. There is a truncation in angular momentum, but the XANES is calculated by first calculating the Green's function using multiple scattering theory. The Green's function is expanded in terms of an angular momentum basis about each atom, and radial solutions are numerical. Muffin tin potentials are used in FEFF8 and there is no option for full potential calculations at present. For more information on multiple scattering theory, see for example Multiple scattering in solids By Antonios Gonis, or Theoretical approaches to x-ray absorption fine structure<http://rmp.aps.org/abstract/RMP/v72/i3/p621_1> J. J. Rehr and R. C. Albers Rev. Mod. Phys. 72, 621 (2000) Cheers, Josh On Sat, Sep 4, 2010 at 10:00 AM, <ifeffit-request(a)millenia.cars.aps.anl.gov>wrote: > 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. iXAFS for Mac OS X (Matt Newville) > 2. Re: iXAFS for Mac OS X (Matt Newville) > 3. Re: iXAFS for Mac OS X (Jeff Terry) > 4. XANES calculation (JeongEunSuk) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 3 Sep 2010 22:08:57 -0500 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] iXAFS for Mac OS X > Message-ID: > <AANLkTinSvabP-Z5ARvxYO4Gh6xMTrF_sErC=ykxUFdcR(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi Folks, > > With help from Ken McIvor and Jeff Terry, I've built a new version of > iXAFS for Mac OS X. This version should be considered experimental, > but for the brave and/or foolhardy please try it out and let us know > how it works. This version offers the latest versions of Athena, > Artemis, and Hephaestus, and the latest version of Ifeffit. It is > meant to be universal (for x86_64, i386, and ppc), though I have not > fully tested this. > > The download is fairly large (~74Mb), mostly because it includes a > full distribution of Perl built right in (so it doesn't interfere with > the system Perl). It also provides a "complete" Unix shell-like > environment that can be used for those who need it. For example, a > python module is included that can be installed. > > The disk image is at > http://car9.uchicago.edu/~ifeffit/src/iXAFS3.0.dmg This should be > able to be installed by dragging the iXAFS application to any folder. > > To use the Unix shell, you'd put > . /Applications/iXAFS.app/Contents/Resources/local/bin/iff_init.sh > > in your .profile or from a bash Terminal command prompt (assuming you > installed to /Applications/). To install the Python module, first > run iff_init.sh above, then > copy and unpack > > /Applications/iXAFS.app/Contents/Resources/local/extras/IfeffitPython-2.0.0.tar.gz > and run 'python setup.py install'. > > Again, this should be considered a beta release. Please be willing to > look for and report problems. > > Cheers, > > --Matt > > > ------------------------------ > > Message: 2 > Date: Fri, 3 Sep 2010 22:11:36 -0500 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] iXAFS for Mac OS X > Message-ID: > <AANLkTiku48seVpa5HTaW30_hiB7-Lap7u79zt0yFVQ3v(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Sorry for the typo. The download is at > http://cars9.uchicago.edu/~ifeffit/src/iXAFS3.0.dmg > > --Matt > > On Fri, Sep 3, 2010 at 10:08 PM, Matt Newville > <newville(a)cars.uchicago.edu> wrote: > > Hi Folks, > > > > With help from Ken McIvor and Jeff Terry, ?I've built a new version of > > iXAFS for Mac OS X. ?This version should be considered experimental, > > but for the brave and/or foolhardy please try it out and let us know > > how it works. This version offers the latest versions of Athena, > > Artemis, and Hephaestus, and the latest version of Ifeffit. ? ?It is > > meant to be universal (for x86_64, i386, and ppc), though I have not > > fully tested this. > > > > The download is fairly large (~74Mb), mostly because it includes a > > full distribution of Perl built right in (so it doesn't interfere with > > the system Perl). ?It also provides a "complete" Unix shell-like > > environment that can be used for those who need it. ?For example, a > > python module is included that can be installed. > > > > The disk image is at > > http://car9.uchicago.edu/~ifeffit/src/iXAFS3.0.dmg ? This should be > > able to be installed by dragging the iXAFS application to any folder. > > > > To use the Unix shell, you'd put > > ? . /Applications/iXAFS.app/Contents/Resources/local/bin/iff_init.sh > > > > in your .profile or from a bash Terminal command prompt (assuming you > > installed to /Applications/). ?To ?install the Python module, ?first > > run iff_init.sh above, then > > copy and unpack > > > /Applications/iXAFS.app/Contents/Resources/local/extras/IfeffitPython-2.0.0.tar.gz > > and run 'python setup.py install'. > > > > Again, this should be considered a beta release. ?Please be willing to > > look for and report problems. > > > > Cheers, > > > > --Matt > > > > > > ------------------------------ > > Message: 3 > Date: Fri, 3 Sep 2010 22:38:23 -0500 > From: Jeff Terry <terryj(a)iit.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] iXAFS for Mac OS X > Message-ID: <06727371-5AD2-401E-9EEF-0D981144D0E8(a)iit.edu> > Content-Type: text/plain; charset=us-ascii > > Hi All, > > If you have been using the iXAFS Shell for command line access, note that > it is currently not working in this version. > > Jeff > > On Sep 3, 2010, at 10:08 PM, Matt Newville wrote: > > > Hi Folks, > > > > With help from Ken McIvor and Jeff Terry, I've built a new version of > > iXAFS for Mac OS X. This version should be considered experimental, > > but for the brave and/or foolhardy please try it out and let us know > > how it works. This version offers the latest versions of Athena, > > Artemis, and Hephaestus, and the latest version of Ifeffit. It is > > meant to be universal (for x86_64, i386, and ppc), though I have not > > fully tested this. > > > > The download is fairly large (~74Mb), mostly because it includes a > > full distribution of Perl built right in (so it doesn't interfere with > > the system Perl). It also provides a "complete" Unix shell-like > > environment that can be used for those who need it. For example, a > > python module is included that can be installed. > > > > The disk image is at > > http://car9.uchicago.edu/~ifeffit/src/iXAFS3.0.dmg This should be > > able to be installed by dragging the iXAFS application to any folder. > > > > To use the Unix shell, you'd put > > . /Applications/iXAFS.app/Contents/Resources/local/bin/iff_init.sh > > > > in your .profile or from a bash Terminal command prompt (assuming you > > installed to /Applications/). To install the Python module, first > > run iff_init.sh above, then > > copy and unpack > > > /Applications/iXAFS.app/Contents/Resources/local/extras/IfeffitPython-2.0.0.tar.gz > > and run 'python setup.py install'. > > > > Again, this should be considered a beta release. Please be willing to > > look for and report problems. > > > > Cheers, > > > > --Matt > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > ------------------------------ > > Message: 4 > Date: Sat, 4 Sep 2010 13:03:21 +0900 > From: JeongEunSuk <eunsuk1986(a)hotmail.com> > To: ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] XANES calculation > Message-ID: <BLU151-w31DB451074575B1BBF5E5EDA8E0(a)phx.gbl> > Content-Type: text/plain; charset="ks_c_5601-1987" > > > Hi all > > I calculated XANES by using FEFF8.0. > > The manuel of FEFF8.0 demonstrates that basis functions of angular momentum > in each atom is used to calculate SCF potential and FMS. > > I know some codes use special basis functions of angular momentum like the > set of Slater-Type Orbital, contracted Gaussian-type function to describe > molecule or solid . > > Does anybody know what kinds of basis function is used in FEFF8.0 to > calculate SCF and FMS? > > and how can I know the contribution of each basis function? > > Finally, I read FEFF8.0 uses overlapped sherical muffin-tin(MT) to > calculate XANES. > > Is the non-muffin tin calculation impossible In FEFF8.0? > >

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