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

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 04 Sep '10

04 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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XANES calculation
by JeongEunSuk 03 Sep '10

03 Sep '10

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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iXAFS for Mac OS X
by Matt Newville 03 Sep '10

03 Sep '10

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://cars9.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

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Re: [Ifeffit] Fwd: Methods to break correlations
by Bruce Ravel 01 Sep '10

01 Sep '10

On Tuesday 31 August 2010 06:49:36 pm you wrote: > I just noticed my reply to your message with a little more detail on my > error with the SSRL plugin did not post to the mailing list, so here is a > little more detail (with a few pictures). Thanks again (to you and all the > other users on the mailing list) for all of the tips for updating iXAfS, it > looks like I started a spark that got a bunch of folks pounding away at > their command lines. > Brandon, The most useful thing you sent me was a copy of the data that triggered the problem. With it, I was able to figure out what was going on. It turns out that version 2.0 of the SSRL XAS Data Collector stores its binary data differently from earlier versions. Who knew? Certainly not me! This difference was such that the data, as interpreted by the Athena plugin, were severely corrupted in a way that lead to Athena feeding very strange data to Ifeffit. Fortunately, Sam Webb once again came to the rescue. Suspecting that the problem would be something like this, I downloaded Sam's latest source code for SixPack and found the place where he imports SSRL binary data. Armed with Sam's knowledge, I was able to fix the SSRLB plugin. Sam, it seems that I owe you yet another beer the next time I see you. At this rate, it's going to be quite a bar tab. So .... grab the version of the plugin that I just committed to the svn repository: http://cars9.uchicago.edu/svn/horae/trunk/lib/Ifeffit/Plugins/Filetype/Athe… Drop this new version in place on top of the old one wherever it sits on your computer. Try again and let me know if this fixes the problem. It worked for me on the data file you sent. B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

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Manual update to iXAFS
by Paul Fons 31 Aug '10

31 Aug '10

Hi Bruce, Regards from a far too hot Japan, Thanks for the update suggestions for iXAFS Bruce. I managed to get it to work, but I found a couple of problems. 1. There is another intermediate directory in your steps (3,4,5), e.g. " /Applications/iXAFS/Contents/Resources/bin" should read " /Applications/iXAFS/Contents/Resources/Horae/bin" The intermediate directory Horae is missing in each case. 2. SVN is installed by default on the Mac. When I tried to run the mkartemis.pl and friends after downloading the latest svn release, however, I found that the rc.pl files were missing. How does one generate these from the svn files? I used a rc.pl from a horae-70 release I had around and it apparently worked. 3. The version numbers in the SVN release conflict within the files from the SVN (at least when following the procedure you mentioned above). Some of the files from the SVN release have (ArtemisLog) $VERSION set to 0.8.014 while others (e.g. Group.pm had $VERSION = "0.0.8.061"). This triggers an error in the athena and artemis of a version mismatch. I "fixed" this by disabling the check, as the logic of the versioning is not very clear from a simple examination of the files. What should the "$VERSION" string (and any other version related strings) be set to in each of the files? In any case it work, but it sure would be nice to have a nice new official release! paul

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Re: [Ifeffit] Methods to break correlations
by Brandon Reese 30 Aug '10

30 Aug '10

Hi Bruce, Thanks for the tip on updating iXAFS, I will give that a try. As to the plugin not working on Athena, apologies about the vagueness. I have tried to open the file using iXAFS (ifeffit v.1.2.10, Athena v.0.8.054) and received the attached error message. After clicking 'ok' Athena remains open. I have also tried to open the same data file on Parallels running WinXP SP3 using the standard *.exe installer (ifeffit v.1.2.11c, Athena v.0.8.061) and received the attached error message. After clicking 'ok' for the windows error, Athena quits (leaving the plot window open). According to the header of the file it was collected using "SSRL - EXAFS Data Collector 2.0". I have tried several combination's which plug-ins are selected and it didn't seem to make a difference. Thanks for the tips Brandon On Mon, Aug 30, 2010 at 11:00 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. Re: Methods to break correlations (Bruce Ravel) > 2. Re: Methods to break correlations (Bruce Ravel) > 3. Re: Residual EXAFS spectra (Bruce Ravel) > 4. Re: Methods to break correlations (Jeff Terry) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 30 Aug 2010 10:08:13 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Methods to break correlations > Message-ID: <201008301008.13700.bravel(a)bnl.gov> > Content-Type: Text/Plain; charset="iso-8859-15" > > On Saturday 28 August 2010 02:47:11 pm Brandon Reese wrote: > > Does anyone have an Athena plugin for the SSRL data Collector > > v2.0? The SSRL plugins available make the program crash when I try and > use > > them. (moderators, let me know if these questions should have been in a > > separate posting) > > > > Here is the SSRL binary plugin from the svn repository > > > http://cars9.uchicago.edu/svn/horae/trunk/lib/Ifeffit/Plugins/Filetype/Athe… > > And here is the one for data files that have been converted to ascii > > > http://cars9.uchicago.edu/svn/horae/trunk/lib/Ifeffit/Plugins/Filetype/Athe… > > They should be placed in $HOME/.horae/Ifeffit/Plugins/Filetype/Athena/ > > > > I am willing to take a look at the problem you are seeing, but "it > crashes" doesn't give me much to work with. Obviously the plugins > worked for me otherwise I would not have considered them ready for > release. You need to provide some clue as to what the problem is. > Either supply a data file that triggers the problem or by cut and > paste what gets written after starting Athena in a terminal window or > (preferably) both. > > B > > -- > > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 > Building 535A > Upton NY, 11973 > > My homepage: http://xafs.org/BruceRavel > EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/<http://cars9.uchicago.edu/%7Eravel/software/exafs/> > > > ------------------------------ > > Message: 2 > Date: Mon, 30 Aug 2010 10:11:06 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Cc: Jeff Terry <terryj(a)iit.edu> > Subject: Re: [Ifeffit] Methods to break correlations > Message-ID: <201008301011.06685.bravel(a)bnl.gov> > Content-Type: Text/Plain; charset="iso-8859-15" > > On Saturday 28 August 2010 02:47:11 pm Brandon Reese wrote: > > I am running iXAFS 2.1 b1, is there any way to update the > > Athena/Artemis versions, or would I have to an source install? > > That is actually a question I need to know the answer to as well. In > fact, our group's post-doc has the same question, so I plan to look > into it this week. (Since I did not make the iXAFS package, I am not > 100% clear on how it works -- which is actually true of most things on > a Mac!) > > I believe the answer is yes, but I'll let you know what I know more. > > B > > > -- > > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 > Building 535A > Upton NY, 11973 > > My homepage: http://xafs.org/BruceRavel > EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/<http://cars9.uchicago.edu/%7Eravel/software/exafs/> > > > ------------------------------ > > Message: 3 > Date: Mon, 30 Aug 2010 10:20:02 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Residual EXAFS spectra > Message-ID: <201008301020.02497.bravel(a)bnl.gov> > Content-Type: Text/Plain; charset="iso-8859-1" > > On Monday 30 August 2010 09:57:09 am Bruce Ravel wrote: > > > Hi all, > > > I am doing an EXAFS spectra analysis of Eu(III) sorbed on mineral > oxides. > > > In course of this, I came across a lierature article(Geochimica et > > > cosmochimica Acta 64(16),2737,2000.) where a residual spectra (denoting > a > > > particular shell) was generated after subtracting four other different > > > paths contribution from the EXAFS spectra(k3.chi(k)). This procedure > was > > > adopted to identify and isolate different paths/shells informations > > > available in the EXAFS spectra. As the paper doesnot explain about the > > > procedure, I am little confused whether the author has adopted just the > > > linear subtraction methodology(i.e, sum of few selected paths minus the > > > original spectra) in creating the residual spectra or some other > > > mathematical approach. > > > > The caption to figure 5 in the article you cite says: > > > > "Residual EXAFS (produced by subtraction of U=Oax, U-Oeq, U-C, and > > U-U shells) ..." > > > > Seems pretty clear to me that what they show is the Fourier transform of > > > > data_chi(k) - sum_of_specified_paths(k) > > > > B > > > > Ummm... of course, I meant to say that the subtraction is done after > performing some kind of a fit to determine values of the parameters > affecting the paths included in the sum. > > Now I'll editorialize a bit ... the advantage of analyzing a > difference spectrum of this sort is that a small part of the data that > might get "lost" in the full fit gets emphasized. The disadvantage -- > and a big one at that -- is that you loose the ability to evaluate > correlations between the parameters of the fit to the residual and the > parameters that were used to determine the sum of paths used to make > the residual. Consequently, doing an analysis of the residual > spectrum requires a high level of confidence in the parameters used > for the subtracted paths. In my experience, that level of confidence > is rarely defensible. > > B > > -- > > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 > Building 535A > Upton NY, 11973 > > My homepage: http://xafs.org/BruceRavel > EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/<http://cars9.uchicago.edu/%7Eravel/software/exafs/> > > > ------------------------------ > > Message: 4 > Date: Mon, 30 Aug 2010 09:47:58 -0500 > From: Jeff Terry <terryj(a)iit.edu> > To: Bruce Ravel <bravel(a)bnl.gov> > Cc: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Methods to break correlations > Message-ID: <FA839956-699F-4DB8-88FE-3B5E17E3AAAA(a)iit.edu> > Content-Type: text/plain; charset=us-ascii > > iXAFS originally started out as a wrapper to launch the individual > programs. At that time, it was a simple matter to replace any of the > individual programs. Ken McIvor has improved iXAFS so that it now builds > universal projects but has perl code embedded. This makes it more difficult > to update. > > That said there is a directory structure within iXAFS and I would guess > that replacing the individual programs would work. I make no guarantees > though as I am not sure of all the changes that Ken has made since I > initially wrote the cocoa wrapper. > > Jeff > > Sent from my iPhone > > On Aug 30, 2010, at 9:11 AM, Bruce Ravel <bravel(a)bnl.gov> wrote: > > > On Saturday 28 August 2010 02:47:11 pm Brandon Reese wrote: > >> I am running iXAFS 2.1 b1, is there any way to update the > >> Athena/Artemis versions, or would I have to an source install? > > > > That is actually a question I need to know the answer to as well. In > > fact, our group's post-doc has the same question, so I plan to look > > into it this week. (Since I did not make the iXAFS package, I am not > > 100% clear on how it works -- which is actually true of most things on > > a Mac!) > > > > I believe the answer is yes, but I'll let you know what I know more. > > > > B > > > > > > -- > > > > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > > > National Institute of Standards and Technology > > Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 > > Building 535A > > Upton NY, 11973 > > > > My homepage: http://xafs.org/BruceRavel > > EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/<http://cars9.uchicago.edu/%7Eravel/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 90, Issue 24 > *************************************** >

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