August 2007 - Ifeffit - millenia.cars.aps.anl.gov

Debye-Waller factors for metal oxides ?
by Ian James Drake 16 Apr '09

16 Apr '09

Hi, There is little discussion over the significance of fitted Debye-Waller factors (ss2) found for metal centers in metal oxides of heterogeneous catalysts. I am searching for a better way of determining how reasonable these values are in the fits I get. 1. Are phenomenological models like the correlated Debye model and Einstein model appropriate? It seems that Debye temperatures are hard to find for oxides. 2. Is there an equivalent value for ss2 in x-ray crystallography data that I can refer to for comparison in these materials? What should I look for in reviewing published x-ray crystallographic data? 3. Is the temperature dependence reported for the ss2 for some metals (like Cu and Al) similar to their respective oxides? For example, in Debye-Waller factor calculations reported for Al metal by R.C.G Killean (in J.Phys.F: Metal Phys., v. 4, pg. 1908, 1974), the ss2 changes by a factor of three between 25C and 300C. Would I expect a factor of three increase in crystalline zeolites (AlO4 structural units). 4. Specific to my work: I have studied Al containing oxides at temperatures between 25 and 300 C. I would like to quantify coordination changes by doing EXAFS fitting of the Al K-edge data. The EXAFS was taken at temperature and I observe no change in the broadening of the data. Likewise, the fitting shows no sensitivity in the Debye-Waller factor. It is nearly constant at 0.001 A over the temperatures of interest. Since ss2 and the coordination number (CN) are correlated, I would like a way to bind the error on the fitted CN by modeling real physical changes in the Debye-Waller factors. Do you have any suggestions? Looking forward to your thoughts. Ian Drake Graduate Student UC Berkeley

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New Method for Normalization?
by Barton, David (DG) 30 Mar '09

30 Mar '09

XANES Aficionados, I know most users on this list are hard-core EXAFS analysts, but some of us use XANES analysis to decipher mixed phases or use it to get structural clues when data quality isn't sufficient for EXAFS analysis. Anyway, I have a question for those interested in quantitative analysis of XANES or those that are willing to offer an opinion on methods to normalize raw spectra to get reliable, repeatable comparisons of near-edge features. Has anyone considered using the methods of Penner-Hahn to normalize their data to get reliable intensities of near-edge features? The reference to their method of normalization is below: J. Synchrotron Rad. (2005). 12, 506-510 [doi:10.1107/S0909049504034193] "A method for normalization of X-ray absorption spectra" T.-C. Weng, G. S. Waldo and J. E. Penner-Hahn It is my understanding the Ifeffit uses a linear function to remove the pre-edge and a quadratic for the post-edge and that the Athena's flatten is a subtraction of these functions. This is an excellent method under most scenarios since the background is usually fairly smooth and can be well approximated by a quadratic equation. Personally, I have had only a few rare cases where the quadratic function on the post-edge was not sufficient to reliably normalize the data and in those cases a third-order polynomial was sufficient. Does anyone else have an opinion on using alternative normalization routines? Dave _________________________________ David Barton The Dow Chemical Company

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Ifeffit Ok on BlueWhite64, ...
by Chachi Rojas 03 Feb '09

03 Feb '09

Hi Matt Ifeffit run perfectely (thanks Matt) after installed by your scripts on RC1. Now, a question for Bruce try to install horae-065, but, error message is below: ---------- === The Ifeffit wrapper, Athena, Artemis, and Hephaestus === This is linux. Checking dependencies ... Tk is not installed. Download the latest from http://search.cpan.org/search?module=Tk Failed dependencies. Not installing athena and artemis. ------ Tk modules (version 8.4.15) were installed on /usr, but perl Makefile.PL it does not recognize Some idea Ch. > Date: Wed, 22 Aug 2007 15:56:26 -0500 > From: "Matt Newville" <newville(a)cars.uchicago.edu> > Subject: [Ifeffit] Ifeffit and gfortran (was: iffefit compile on > BlueWhite64) > To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: > <b8522e3d0708221356y37280877v86ac576fe9b6b96c(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi Chachi, all > > I believe I have a source kit that will build correctly for you using > gfortran. I've tested on three different generations of Fedora/Redhat > linux systems, one with only g77, one with only gfortran, and one with > both, and the installation now works on all of them. > > Please try > http://cars9.uchicago.edu/~ifeffit/src/ifeffit-1.2.10_rc1.tar.gz > > With this tar ball, you will need to install pgplot: > tar xvzf ifeffit-1.2.10_rc1.tar.gz > cd ifeffit-1.2.10 > sh PGPLOT_install > ./configure > make > make install > > (doing the two 'install steps' with sufficient privilege). Again, you > need to install PGPLOT with the provided script. Both the PGPLOT and > Ifeffit installations will use gfortran if available, and g77 if > gfortran is not available. I think it would not be too difficult to > attempt to use Intel's ifort compiler or g95, though I do not know > that it's needed-- all linux distribution come with gcc so have > easy-to-use packages for gfortran (and, for "legacy", g77). > > I did get horae-065 and the python wrappers to build with no trouble > (once the Tk modules were installed) on all systems, though I haven't > done much more than trivial testing. > > Since I tested only on a few linux boxes, I'd be interested in hearing > reports for other systems. > > I'll wait a few days (or more) to hear reports before uploading this > as ifeffit-1.2.10. > > --Matt >

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2007 APS XAFS School
by Julie Olmsted Cross 04 Apr '08

04 Apr '08

The on-line application for the 2007 APS XAFS School is now available at xafs.org http://www.xafs.org/Workshops/APS2007 ~^^~^~^~~^~^~^~^~^~^~^~^~~^~^~ Julie O. Cross Advanced Photon Source Argonne National Lab 9700 South Cass Ave., Bldg. 401/B4204 Argonne IL 60439 tel: 630 327 7825 fax: 630 252 0580 ~^^~^~^~~^~^~^~^~^~^~^~^~~^~^~

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Can't change values in Athena and Artemis on Ubuntu(Feisty)
by Jun Lin 06 Sep '07

06 Sep '07

Hi Carlo Segre, I install Athena and Artemis from your compiled deb package for feisty. When I try to change values in Athena and Artemis, it doesn't work. The only way change the value is click on the plot canvas. I have tried to execute program as root user, but it also doesn't work. Looking forward for you help. Sincerely, Lin Jun -- Shanghai Institute of Applied Physics, Chinese Academy of Sciences No. 2019, Baojia Road, Jiading District, Shanghai,China 201800

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Re: [Ifeffit] Ifeffit Digest, Vol 54, Issue 21
by Jun Lin 31 Aug '07

31 Aug '07

Dear Caro, Thank you for your reply :) I followed your suggestion to double click or choose all text in the boxes, but still doesn't work. I installed the software in my two computers(both Ubuntu 7.04), but the symptoms are the same. Would you please tell me how to build deb package from source? Jun On 8/31/07, ifeffit-request(a)millenia.cars.aps.anl.gov < ifeffit-request(a)millenia.cars.aps.anl.gov> wrote: > > > > Message: 2 > Date: Wed, 29 Aug 2007 23:16:07 -0500 (CDT) > From: Carlo Segre <segre(a)iit.edu> > Subject: Re: [Ifeffit] Can't change values in Athena and Artemis on > Ubuntu(Feisty) > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <Pine.LNX.4.64.0708292306530.2507(a)localhost.localdomain> > Content-Type: text/plain; charset=us-ascii; format=flowed > > > Hi Jun: > > Do you mean changing the values in the text boxes? Sometimes, I have > noticed that you have to double click on the box or select all of the text > in order to be able to change values using the keyboard. I haven't > figured out when this happens though, it seems sort of random to me. > > Carlo > > -- Shanghai Institute of Applied Physics, Chinese Academy of Sciences No. 2019, Baojia Road, Jiading District, Shanghai,China 201800

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Ifeffit and gfortran (was: iffefit compile on BlueWhite64)
by Matt Newville 27 Aug '07

27 Aug '07

Hi Chachi, all I believe I have a source kit that will build correctly for you using gfortran. I've tested on three different generations of Fedora/Redhat linux systems, one with only g77, one with only gfortran, and one with both, and the installation now works on all of them. Please try http://cars9.uchicago.edu/~ifeffit/src/ifeffit-1.2.10_rc1.tar.gz With this tar ball, you will need to install pgplot: tar xvzf ifeffit-1.2.10_rc1.tar.gz cd ifeffit-1.2.10 sh PGPLOT_install ./configure make make install (doing the two 'install steps' with sufficient privilege). Again, you need to install PGPLOT with the provided script. Both the PGPLOT and Ifeffit installations will use gfortran if available, and g77 if gfortran is not available. I think it would not be too difficult to attempt to use Intel's ifort compiler or g95, though I do not know that it's needed-- all linux distribution come with gcc so have easy-to-use packages for gfortran (and, for "legacy", g77). I did get horae-065 and the python wrappers to build with no trouble (once the Tk modules were installed) on all systems, though I haven't done much more than trivial testing. Since I tested only on a few linux boxes, I'd be interested in hearing reports for other systems. I'll wait a few days (or more) to hear reports before uploading this as ifeffit-1.2.10. --Matt

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[Fwd: Ifeffit Ok on BlueWhite64, ...]
by Chachi Rojas 25 Aug '07

25 Aug '07

Hello list again Tk module run ok. Now, my problem is compling horae-065, error message: ... make[1]: Entering directory `/usr/local/src/ifeffit-1.2.10/horae-065/Absorption' /usr/bin/perl5.8.8 chantler2st.PL chantler.db Can't locate Chemistry/Elements.pm in @INC (@INC contains: /usr/lib/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 /usr/lib/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl .) at chantler2st.PL line 40. BEGIN failed--compilation aborted at chantler2st.PL line 40. make[1]: *** [chantler.db] Error 2 make[1]: Leaving directory `/usr/local/src/ifeffit-1.2.10/horae-065/Absorption' make: *** [subdirs] Error 2 ch@pcbox:/usr/local/src/ifeffit-1.2.10/horae-065$ ...... it seems not to find Chemistry/Elements.pm file (module) Ch --------------------------------- Original Message --------------------------------- Subject: Ifeffit Ok on BlueWhite64, ... From: "Chachi Rojas" <crojasa(a)unmsm.edu.pe> Date: Fri, August 24, 2007 5:12 pm To: ifeffit(a)millenia.cars.aps.anl.gov ------------------------------------------------------------------------------------ Hi Matt Ifeffit run perfectely (thanks Matt) after installed by your scripts on RC1. Now, a question for Bruce try to install horae-065, but, error message is below: ---------- === The Ifeffit wrapper, Athena, Artemis, and Hephaestus === This is linux. Checking dependencies ... Tk is not installed. Download the latest from http://search.cpan.org/search?module=Tk Failed dependencies. Not installing athena and artemis. ------ Tk modules (version 8.4.15) were installed on /usr, but perl Makefile.PL it does not recognize Some idea Ch. > Date: Wed, 22 Aug 2007 15:56:26 -0500 > From: "Matt Newville" <newville(a)cars.uchicago.edu> > Subject: [Ifeffit] Ifeffit and gfortran (was: iffefit compile on > BlueWhite64) > To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: > <b8522e3d0708221356y37280877v86ac576fe9b6b96c(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi Chachi, all > > I believe I have a source kit that will build correctly for you using > gfortran. I've tested on three different generations of Fedora/Redhat > linux systems, one with only g77, one with only gfortran, and one with > both, and the installation now works on all of them. > > Please try > http://cars9.uchicago.edu/~ifeffit/src/ifeffit-1.2.10_rc1.tar.gz > > With this tar ball, you will need to install pgplot: > tar xvzf ifeffit-1.2.10_rc1.tar.gz > cd ifeffit-1.2.10 > sh PGPLOT_install > ./configure > make > make install > > (doing the two 'install steps' with sufficient privilege). Again, you > need to install PGPLOT with the provided script. Both the PGPLOT and > Ifeffit installations will use gfortran if available, and g77 if > gfortran is not available. I think it would not be too difficult to > attempt to use Intel's ifort compiler or g95, though I do not know > that it's needed-- all linux distribution come with gcc so have > easy-to-use packages for gfortran (and, for "legacy", g77). > > I did get horae-065 and the python wrappers to build with no trouble > (once the Tk modules were installed) on all systems, though I haven't > done much more than trivial testing. > > Since I tested only on a few linux boxes, I'd be interested in hearing > reports for other systems. > > I'll wait a few days (or more) to hear reports before uploading this > as ifeffit-1.2.10. > > --Matt > -- Chachi Rojas Ayala GMC FCF UNMSM Claro:01-97489347 email:crojasa@unmsm.edu.pe chachi.rojas(a)gmail.com

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Re: [Ifeffit] Ifeffit Digest, Vol 54, Issue 15
by joshua jason kas 23 Aug '07

23 Aug '07

Hi Eckhard, Add the following card to your feff.inp file. FOLP 2 0.8 Our default overlap is not so good for hydrogen, and 0.8 is the recommended value given in the documentation. There is some instability in the calculation of the densities near the nucleus, which in hydrogen, turns out to be comparable to the total density, and gives negative densities. I don't know why folp 0.8 helps, but it does. Cheers, Josh > > Message: 1 > Date: Wed, 22 Aug 2007 14:21:14 +0200 (CEST) > From: s440697(a)stud.uni-goettingen.de > Subject: Re: [Ifeffit] log1.dat & program break > To: "Bruce Ravel" <bravel(a)anl.gov>, "XAFS Analysis using Ifeffit" > <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: > <54988.134.76.41.165.1187785274.squirrel(a)webmail.stud.uni-goettingen.de> > > Content-Type: text/plain;charset=iso-8859-1 > > Hi Bruce, > > maybe my mail was a little bit confusing. The log1.dat from the attachment > belongs to the first problem ("negative dens "). I found this message in > the log1.dat file. > > sincerely yours, > Eckhard > >> I don't know what the lines from the log file mean. As to the program >> crashing -- Josh addressed this in his email yesterday. >> > > > --------------------------------- > Eckhard Bosman > e.bosman(a)stud.uni-goettingen.de > +49 (0)551-39-14441 > Raum: E0.104 > Institut f?r R?ntgenphysik > Friedrich-Hund-Platz 1 > 37077 G?ttingen > Germany >

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iffefit compile on BlueWhite64
by Chachi Rojas 22 Aug '07

22 Aug '07

Hello list I try to install ifeffit 1.2.9 on Linux Bluewhite64 12.0 (slackware 12.0 based) PGPLOt run perfectely, ./configure ifeffit ok but when compile, error message: ... /usr/local/src/ifeffit-1.2.9/src/lib/iff_cursor.f:68: undefined reference to `_gfortran_concat_string' /usr/X11R6/lib/libgfortranbegin.a(fmain.o): In function `main': (.text+0x5): undefined reference to `_gfortran_set_args' /usr/local/pgplot//libpgplot.so: undefined reference to `_gfortran_pow_i4_i4' /usr/local/pgplot//libpgplot.so: undefined reference to `_gfortran_transfer_array' /usr/local/pgplot//libpgplot.so: undefined reference to `_gfortran_pow_r4_i4' collect2: ld returned 1 exit status make[3]: *** [ifftest1] Error 1 make[3]: Leaving directory `/usr/local/src/ifeffit-1.2.9/src/test' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/usr/local/src/ifeffit-1.2.9/src' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/usr/local/src/ifeffit-1.2.9' make: *** [all-recursive-am] Error 2 My computer: Linux chy 2.6.21.5 #1 SMP Fri Jun 15 08:49:16 EEST 2007 x86_64 Intel(R) Core(TM)2 CPU 6400 @ 2.13GHz GenuineIntel GNU/Linux Same idea about this error message, Thanks Ch -- Chachi Rojas Ayala GMC FCF UNMSM Claro:01-97489347 email:crojasa@unmsm.edu.pe chachi.rojas(a)gmail.com

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