November 2008 - 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

9 21

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

12 22

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 >

8 9

Re: [Ifeffit] about wolframite crystallographic file (Ravel, Bruce)
by Yordy Licea Fonseca 25 Nov '08

25 Nov '08

Hi all, In my case, Artemis version 0.8.012 (c), the error in Echo is just: "Artemis trapped one or more errors! Error message dumped to screen." Thank you very much, the problem is solved the way Dominik and Carl have suggested. Best regards, Yordy 2008/11/17 <ifeffit-request(a)millenia.cars.aps.anl.gov> > 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: about wolframite crystallographic file (Ravel, Bruce) > 2. Re: about wolframite crystallographic file (Dominik Samuelis) > 3. Re: about wolframite crystallographic file (Ponader, Carl W Dr) > 4. Re: [PGPLOT build problem] Upgrading to ifeffit-1.2.11b on > Ubuntu from source (Mauro Rovezzi) > 5. Re: [PGPLOT build problem] Upgrading to ifeffit-1.2.11b on > Ubuntu from source (Carlo Segre) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 17 Nov 2008 09:16:25 -0500 > From: "Ravel, Bruce" <bravel(a)bnl.gov> > Subject: Re: [Ifeffit] about wolframite crystallographic file > To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <8FA2653072F45348BC6E32FEB95CDC62D3D1(a)exchangemb5.bnl.gov> > Content-Type: text/plain; charset="iso-8859-1" > > > Yordy, > > I'll look into this when I get a chance, but that might not be until later > in the week (I am on travel at the moment). > > B > > -- > Bruce Ravel ----------------------------------- bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Methods Group at Brookhaven National Laboratory > Building 535A > Upton NY, 11973 > > My homepage: http://cars9.uchicago.edu/~ravel > EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/ > > > > > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov on behalf of Yordy Licea > Fonseca > Sent: Sat 11/15/2008 6:36 PM > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] about wolframite crystallographic file > > Hi all, > > As soon as I load this attached CIF crystallographic file from ISCD in > Artemis0.8.012 the software says: > "Artemis trapped one or more errors! Error message dumped to screen." > I can`t go on runnig Atoms as it seems to be a problem with the file. I > have > read the suggestion made in FAQ, but I can not manage to find the error. > Could you help me, please? > It would be nice once the problem been fixed to add this structure to > Matt's > atoms.inp database. > > Thanks you very much, Yordy > > -- > Yordy E. Licea Fonseca > Departamento de F?sico-Qu?mica > Instituto de Qu?mica-IQ/UFRJ > Laborat?rio de Cat?lise Heterog?nea > Rio de Janeiro, RJ, CEP 21.949-909 > Brasil > Email: yliceafonseca(a)gmail.com > >

1 0

Re: [Ifeffit] Hexagonal WO3 (Carlo Segre)
by Yordy Licea Fonseca 25 Nov '08

25 Nov '08

Hi Carlo and Ying, Does it means that if the sample is a random solid solution at experimental temperature, in principle, you would be able to simulate the EXAFS spectra whichever be the Mo/W ratio in the second shell coordination in the Feff.inp, am I right? Thanks, Yordy 2008/11/18 <ifeffit-request(a)millenia.cars.aps.anl.gov> > 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: [PGPLOT build problem] Upgrading to ifeffit-1.2.11b on > Ubuntu from source (Matt Newville) > 2. Ifeffit 1.2.11c (was Re: [PGPLOT build problem] Upgrading to > ifeffit-1.2.11b on Ubuntu from source) (Matt Newville) > 3. Re: Ifeffit 1.2.11c (was Re: [PGPLOT build problem] Upgrading > to ifeffit-1.2.11b on Ubuntu from source) (Carlo Segre) > 4. Re: Ifeffit 1.2.11c (was Re: [PGPLOT build problem] Upgrading > to ifeffit-1.2.11b on Ubuntu from source) (Matt Newville) > 5. Hexagonal WO3 (Ying Zhou, Anorganisch-Chemisches Inst.) > 6. Re: Hexagonal WO3 (Carlo Segre) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 17 Nov 2008 12:30:20 -0600 > From: "Matt Newville" <newville(a)cars.uchicago.edu> > Subject: Re: [Ifeffit] [PGPLOT build problem] Upgrading to > ifeffit-1.2.11b on Ubuntu from source > To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: > <b8522e3d0811171030o2db1e183va43b9dcb4d99705e(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi, > > This is my fault... and I apologize for the sloppiness and for being > late in fixing this. I've been mixing 'development/testing' and > 'production' versions, and haven't been very good at keeping them > cleanly separated. I think I have this mostly under control now, > but I will have to work on a decent "test suite". > > I think I found another reason to make a 1.2.11c version too, that the > mixing of "devel" and "production" > caused an experiment in how fitting was done to be the default, so > that the reported chi-square doesn't actually match the documentation > (instead of summing real and imaginary parts, it sums real and > magnitude components of the misfit, which is part of an experiment to > see how Feff8.5 worked for XAFS. Using Magnitude as well Phase for > another way to report chi-square and misfits is potentially a useful > approach, but it's not what is documented. Anyway, mixing devel and > production versions like this (for the past couple years, really) is > very sloppy on my part, and I apologize again. > > I actually have an ubuntu box now, though I built pgplot from source, > and have never made a .deb file. > There is a new source kit at > http://cars.uchicago.edu/~ifeffit/src/ifeffit-1.2.11c.tar.gz I'll > post this to sourceforge this afternoon, and I'll also make a new DLL > for Windows and post all of these on the download page. I'll also make > a new updater for Windows. > > --Matt > > > On Mon, Nov 17, 2008 at 10:07 AM, Mauro Rovezzi <rovezzi(a)esrf.fr> wrote: > > Carlo Segre wrote: > >> > >> Hi Mauro: > >> > >> I have now produced a package of ifeffit 1.2.11b. It is in Debian > >> unstable and available for Ubuntu intrepid and jaunty in my repository > >> > >> deb http://debian-xray.iit.edu intrepid main contrib non-free > > > > Carlo, > > > > Thank you very much for the package. > > > > Actually, I was able to build/install ifeffit 1.2.11b from source but > > not able to build than the Perl/Python wrappers and so no Horae&Friends > > from Bruce SVN. > > > > Well, now I have "pgplot5", "ifeffit", "perl-ifeffit" and > > "python-ifeffit" from binaries and "libperlxray" "horae" and "demeter" > > built from source (Bruce SVN). > > > > Everything seems fine but I still do not understand why ifeffit 1.2.11 > > has all these "IFF str = *" output as stated also by Gareth in his > > "Ifeffit 1.2.11b terminal output" post. Is it normal? > > > > Cheers, > > Mauro > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > > > ------------------------------ > > Message: 2 > Date: Mon, 17 Nov 2008 17:06:35 -0600 > From: "Matt Newville" <newville(a)cars.uchicago.edu> > Subject: [Ifeffit] Ifeffit 1.2.11c (was Re: [PGPLOT build problem] > Upgrading to ifeffit-1.2.11b on Ubuntu from source) > To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: > <b8522e3d0811171506h438ba6abke90121bbb1744818(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi Folks, > > I've uploaded source kits for Ifeffit 1.2.11c to the cars.uchicago.edu > and sourceforge.net download sites. > > I have a Windows dll made for this bug fix version. If anyone is > interested, this is currently at > http://cars.uchicago.edu/~ifeffit/updates/011/bin/ifeffit_12.dll > > This should be a drop-in replacement for the > IFEFFIT_DIR\bin\ifeffit_12.dll on your system. > Artemis.exe will not be updated from this dll, as it has this dlls > "compiled in". Bruce will have to make a new Artemis.exe, and then > we'll make a automatic update. > > Sorry for all the trouble, > > --Matt > > > On Mon, Nov 17, 2008 at 12:30 PM, Matt Newville > <newville(a)cars.uchicago.edu> wrote: > > Hi, > > > > This is my fault... and I apologize for the sloppiness and for being > > late in fixing this. I've been mixing 'development/testing' and > > 'production' versions, and haven't been very good at keeping them > > cleanly separated. I think I have this mostly under control now, > > but I will have to work on a decent "test suite". > > > > I think I found another reason to make a 1.2.11c version too, that the > > mixing of "devel" and "production" > > caused an experiment in how fitting was done to be the default, so > > that the reported chi-square doesn't actually match the documentation > > (instead of summing real and imaginary parts, it sums real and > > magnitude components of the misfit, which is part of an experiment to > > see how Feff8.5 worked for XAFS. Using Magnitude as well Phase for > > another way to report chi-square and misfits is potentially a useful > > approach, but it's not what is documented. Anyway, mixing devel and > > production versions like this (for the past couple years, really) is > > very sloppy on my part, and I apologize again. > > > > I actually have an ubuntu box now, though I built pgplot from source, > > and have never made a .deb file. > > There is a new source kit at > > http://cars.uchicago.edu/~ifeffit/src/ifeffit-1.2.11c.tar.gz I'll > > post this to sourceforge this afternoon, and I'll also make a new DLL > > for Windows and post all of these on the download page. I'll also make > > a new updater for Windows. > > > > --Matt > > > > > > On Mon, Nov 17, 2008 at 10:07 AM, Mauro Rovezzi <rovezzi(a)esrf.fr> wrote: > >> Carlo Segre wrote: > >>> > >>> Hi Mauro: > >>> > >>> I have now produced a package of ifeffit 1.2.11b. It is in Debian > >>> unstable and available for Ubuntu intrepid and jaunty in my repository > >>> > >>> deb http://debian-xray.iit.edu intrepid main contrib non-free > >> > >> Carlo, > >> > >> Thank you very much for the package. > >> > >> Actually, I was able to build/install ifeffit 1.2.11b from source but > >> not able to build than the Perl/Python wrappers and so no Horae&Friends > >> from Bruce SVN. > >> > >> Well, now I have "pgplot5", "ifeffit", "perl-ifeffit" and > >> "python-ifeffit" from binaries and "libperlxray" "horae" and "demeter" > >> built from source (Bruce SVN). > >> > >> Everything seems fine but I still do not understand why ifeffit 1.2.11 > >> has all these "IFF str = *" output as stated also by Gareth in his > >> "Ifeffit 1.2.11b terminal output" post. Is it normal? > >> > >> Cheers, > >> Mauro > >> _______________________________________________ > >> Ifeffit mailing list > >> Ifeffit(a)millenia.cars.aps.anl.gov > >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > >> > >> > > > > > ------------------------------ > > Message: 3 > Date: Mon, 17 Nov 2008 20:03:06 -0600 (CST) > From: Carlo Segre <segre(a)iit.edu> > Subject: Re: [Ifeffit] Ifeffit 1.2.11c (was Re: [PGPLOT build problem] > Upgrading to ifeffit-1.2.11b on Ubuntu from source) > To: Matt Newville <newville(a)cars.uchicago.edu> > Cc: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <alpine.DEB.2.00.0811172002240.3650(a)hydride.iit.edu> > Content-Type: text/plain; charset=us-ascii; format=flowed > > > Debian packages have been uploaded to unstable and I am in the process of > building Ubuntu packages for my repository. i expect that they will be up > tonight. > > carlo > > On Mon, 17 Nov 2008, Matt Newville wrote: > > > Hi Folks, > > > > I've uploaded source kits for Ifeffit 1.2.11c to the cars.uchicago.edu > > and sourceforge.net download sites. > > > > I have a Windows dll made for this bug fix version. If anyone is > > interested, this is currently at > > http://cars.uchicago.edu/~ifeffit/updates/011/bin/ifeffit_12.dll > > > > This should be a drop-in replacement for the > > IFEFFIT_DIR\bin\ifeffit_12.dll on your system. > > Artemis.exe will not be updated from this dll, as it has this dlls > > "compiled in". Bruce will have to make a new Artemis.exe, and then > > we'll make a automatic update. > > > > Sorry for all the trouble, > > > > --Matt > > > > > > On Mon, Nov 17, 2008 at 12:30 PM, Matt Newville > > <newville(a)cars.uchicago.edu> wrote: > >> Hi, > >> > >> This is my fault... and I apologize for the sloppiness and for being > >> late in fixing this. I've been mixing 'development/testing' and > >> 'production' versions, and haven't been very good at keeping them > >> cleanly separated. I think I have this mostly under control now, > >> but I will have to work on a decent "test suite". > >> > >> I think I found another reason to make a 1.2.11c version too, that the > >> mixing of "devel" and "production" > >> caused an experiment in how fitting was done to be the default, so > >> that the reported chi-square doesn't actually match the documentation > >> (instead of summing real and imaginary parts, it sums real and > >> magnitude components of the misfit, which is part of an experiment to > >> see how Feff8.5 worked for XAFS. Using Magnitude as well Phase for > >> another way to report chi-square and misfits is potentially a useful > >> approach, but it's not what is documented. Anyway, mixing devel and > >> production versions like this (for the past couple years, really) is > >> very sloppy on my part, and I apologize again. > >> > >> I actually have an ubuntu box now, though I built pgplot from source, > >> and have never made a .deb file. > >> There is a new source kit at > >> http://cars.uchicago.edu/~ifeffit/src/ifeffit-1.2.11c.tar.gz I'll > >> post this to sourceforge this afternoon, and I'll also make a new DLL > >> for Windows and post all of these on the download page. I'll also make > >> a new updater for Windows. > >> > >> --Matt > >> > >> > >> On Mon, Nov 17, 2008 at 10:07 AM, Mauro Rovezzi <rovezzi(a)esrf.fr> > wrote: > >>> Carlo Segre wrote: > >>>> > >>>> Hi Mauro: > >>>> > >>>> I have now produced a package of ifeffit 1.2.11b. It is in Debian > >>>> unstable and available for Ubuntu intrepid and jaunty in my repository > >>>> > >>>> deb http://debian-xray.iit.edu intrepid main contrib non-free > >>> > >>> Carlo, > >>> > >>> Thank you very much for the package. > >>> > >>> Actually, I was able to build/install ifeffit 1.2.11b from source but > >>> not able to build than the Perl/Python wrappers and so no Horae&Friends > >>> from Bruce SVN. > >>> > >>> Well, now I have "pgplot5", "ifeffit", "perl-ifeffit" and > >>> "python-ifeffit" from binaries and "libperlxray" "horae" and "demeter" > >>> built from source (Bruce SVN). > >>> > >>> Everything seems fine but I still do not understand why ifeffit 1.2.11 > >>> has all these "IFF str = *" output as stated also by Gareth in his > >>> "Ifeffit 1.2.11b terminal output" post. Is it normal? > >>> > >>> Cheers, > >>> Mauro > >>> _______________________________________________ > >>> 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 > > > > -- > Carlo U. Segre -- Professor of Physics > Associate Dean for Special Projects, Graduate College > Illinois Institute of Technology > Voice: 312.567.3498 Fax: 312.567.3494 > segre(a)iit.edu http://www.iit.edu/~segre segre(a)debian.org > > > ------------------------------ > > Message: 4 > Date: Mon, 17 Nov 2008 21:10:51 -0600 > From: "Matt Newville" <newville(a)cars.uchicago.edu> > Subject: Re: [Ifeffit] Ifeffit 1.2.11c (was Re: [PGPLOT build problem] > Upgrading to ifeffit-1.2.11b on Ubuntu from source) > To: segre(a)agni.phys.iit.edu > Cc: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: > <b8522e3d0811171910p4509bdacn3dc6ed65606d9580(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Thanks, Carlo! > > --Matt > > > > > On Mon, Nov 17, 2008 at 8:03 PM, Carlo Segre <segre(a)iit.edu> wrote: > > > > Debian packages have been uploaded to unstable and I am in the process of > > building Ubuntu packages for my repository. i expect that they will be > up > > tonight. > > > > carlo > > > > On Mon, 17 Nov 2008, Matt Newville wrote: > > > >> Hi Folks, > >> > >> I've uploaded source kits for Ifeffit 1.2.11c to the cars.uchicago.edu > >> and sourceforge.net download sites. > >> > >> I have a Windows dll made for this bug fix version. If anyone is > >> interested, this is currently at > >> http://cars.uchicago.edu/~ifeffit/updates/011/bin/ifeffit_12.dll > >> > >> This should be a drop-in replacement for the > >> IFEFFIT_DIR\bin\ifeffit_12.dll on your system. > >> Artemis.exe will not be updated from this dll, as it has this dlls > >> "compiled in". Bruce will have to make a new Artemis.exe, and then > >> we'll make a automatic update. > >> > >> Sorry for all the trouble, > >> > >> --Matt > >> > >> > >> On Mon, Nov 17, 2008 at 12:30 PM, Matt Newville > >> <newville(a)cars.uchicago.edu> wrote: > >>> > >>> Hi, > >>> > >>> This is my fault... and I apologize for the sloppiness and for being > >>> late in fixing this. I've been mixing 'development/testing' and > >>> 'production' versions, and haven't been very good at keeping them > >>> cleanly separated. I think I have this mostly under control now, > >>> but I will have to work on a decent "test suite". > >>> > >>> I think I found another reason to make a 1.2.11c version too, that the > >>> mixing of "devel" and "production" > >>> caused an experiment in how fitting was done to be the default, so > >>> that the reported chi-square doesn't actually match the documentation > >>> (instead of summing real and imaginary parts, it sums real and > >>> magnitude components of the misfit, which is part of an experiment to > >>> see how Feff8.5 worked for XAFS. Using Magnitude as well Phase for > >>> another way to report chi-square and misfits is potentially a useful > >>> approach, but it's not what is documented. Anyway, mixing devel and > >>> production versions like this (for the past couple years, really) is > >>> very sloppy on my part, and I apologize again. > >>> > >>> I actually have an ubuntu box now, though I built pgplot from source, > >>> and have never made a .deb file. > >>> There is a new source kit at > >>> http://cars.uchicago.edu/~ifeffit/src/ifeffit-1.2.11c.tar.gz I'll > >>> post this to sourceforge this afternoon, and I'll also make a new DLL > >>> for Windows and post all of these on the download page. I'll also make > >>> a new updater for Windows. > >>> > >>> --Matt > >>> > >>> > >>> On Mon, Nov 17, 2008 at 10:07 AM, Mauro Rovezzi <rovezzi(a)esrf.fr> > wrote: > >>>> > >>>> Carlo Segre wrote: > >>>>> > >>>>> Hi Mauro: > >>>>> > >>>>> I have now produced a package of ifeffit 1.2.11b. It is in Debian > >>>>> unstable and available for Ubuntu intrepid and jaunty in my > repository > >>>>> > >>>>> deb http://debian-xray.iit.edu intrepid main contrib non-free > >>>> > >>>> Carlo, > >>>> > >>>> Thank you very much for the package. > >>>> > >>>> Actually, I was able to build/install ifeffit 1.2.11b from source but > >>>> not able to build than the Perl/Python wrappers and so no > Horae&Friends > >>>> from Bruce SVN. > >>>> > >>>> Well, now I have "pgplot5", "ifeffit", "perl-ifeffit" and > >>>> "python-ifeffit" from binaries and "libperlxray" "horae" and "demeter" > >>>> built from source (Bruce SVN). > >>>> > >>>> Everything seems fine but I still do not understand why ifeffit 1.2.11 > >>>> has all these "IFF str = *" output as stated also by Gareth in his > >>>> "Ifeffit 1.2.11b terminal output" post. Is it normal? > >>>> > >>>> Cheers, > >>>> Mauro > >>>> _______________________________________________ > >>>> 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 > >> > > > > -- > > Carlo U. Segre -- Professor of Physics > > Associate Dean for Special Projects, Graduate College > > Illinois Institute of Technology > > Voice: 312.567.3498 Fax: 312.567.3494 > > segre(a)iit.edu http://www.iit.edu/~segre segre(a)debian.org > > > > > > > ------------------------------ > > Message: 5 > Date: Tue, 18 Nov 2008 17:20:24 +0100 > From: "Ying Zhou, Anorganisch-Chemisches Inst." <ying.zhou(a)aci.uzh.ch> > Subject: [Ifeffit] Hexagonal WO3 > To: ifeffit(a)millenia.cars.aps.anl.gov > Message-ID: <web-16292974(a)idmailbe2b.unizh.ch> > Content-Type: text/plain;charset=iso-8859-1;format="flowed" > > Dear All > > Recently, I got one compound, W/Mo oxide, which has the similar structure > with hexagonal WO3. We tested the EXAFS of W L3 edge and Mo K edge of this > compound. So, we use the hexagonal WO3 model to refine the structure of our > compounds. My question is that how can I get the FEFF file of this > compound. > Can I directly change some of W to Mo in FEFF file? or Do I need to add the > Mo in the atom file? I do appreciate your help. > > Best wishes > Ying > > > ------------------------------ > > Message: 6 > Date: Tue, 18 Nov 2008 10:33:35 -0600 (CST) > From: Carlo Segre <segre(a)iit.edu> > Subject: Re: [Ifeffit] Hexagonal WO3 > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <alpine.DEB.2.00.0811181023390.19806(a)oxide.phys.iit.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > > Hi Ying: > > On Tue, 18 Nov 2008, Ying Zhou, Anorganisch-Chemisches Inst. wrote: > > > Dear All > > > > Recently, I got one compound, W/Mo oxide, which has the similar structure > > with hexagonal WO3. We tested the EXAFS of W L3 edge and Mo K edge of > this > > compound. So, we use the hexagonal WO3 model to refine the structure of > our > > compounds. My question is that how can I get the FEFF file of this > compound. > > Can I directly change some of W to Mo in FEFF file? or Do I need to add > the > > Mo in the atom file? I do appreciate your help. > > > > There are several ways to do this, depending on what you are trying to > find out. If you change W to Mo in the atoms input file than you are > really making MoO3. What it seems like you need to do is to generate the > FEFF input file from the WO3 structure, then replace the central atom with > Mo. This will give you the first path which is likely oxygen. The second > longest set of paths are likely to be W/Mo and you can do two things, one > is to generate a FEFF calculation with W in this position and then make a > second calculation with Mo and use both paths to fit the Mo environment. > You will have to be careful about multiplicities though since by starting > with the WO3 structure, you are assuming some degeneracies in the paths. > The advantage is that you potentially have some multiple scatteing paths > available to use. > > Another approach is to generate the FEFF input file from WO3, look at the > near neighbors and then generate some "quick first shell" paths for the > nearest neighbor (oxygen) and then two fro the next near neighbor (one > with W and one with Mo). The difference here is that you now have > uncorrelated paths with no implied degeneracies. You cannot use this to > fit multiple scattering paths. > > I guess that my approach would be to start with the latter, more simple > approach first to try to understand the problem. If I see that the > environment looks like it is possible to fit with multiple scattering, I > would move to the first approach, being careful to realize that in a solid > sloution compound, the occupancy of the second shell of metal atoms is > probably random and not perfectly ordered like a FEFF input file with > substitutions would be. > > Hope this helps. > > Carlo > > -- > Carlo U. Segre -- Professor of Physics > Associate Dean for Special Projects, Graduate College > Illinois Institute of Technology > Voice: 312.567.3498 Fax: 312.567.3494 > segre(a)iit.edu http://www.iit.edu/~segre segre(a)debian.org > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 69, Issue 13 > *************************************** > -- Yordy E. Licea Fonseca Departamento de Físico-Química Instituto de Química-IQ/UFRJ Laboratório de Catálise Heterogênea Rio de Janeiro, RJ, CEP 21.949-909 Brasil Email: yliceafonseca(a)gmail.com

3 3

Athena problem with integration in Difference of Normalized Spectra (norm(E))
by Zajac, Dariusz 19 Nov '08

19 Nov '08

Hi All, first - I am using Athena 0.8.054 under Windows XP and Adam 0.8.057 under Linux We have checked this problem at 2 computers. I played a little bit with Analysis function - Difference Spectra - norm(E) It works fine when I work with one group - it plots spectrum, difference and program computes the difference and the integral. Now, I want to do the same for marked groups - it computes and makes as new groups the difference spectra. If I want to compute also integrals for marked groups program does not execute operation. Simply it does nothing, or tries to do something with the first marked group, but without result. the error message from shell window is like that: for Athena 0.8.057 Linux: Tk::Error: Can't upgrade that kind of scalar at /usr/bin/athena line 12950. main::diff_marked at /usr/bin/athena line 12950 main::__ANON__ at /usr/bin/athena line 12614 Tk callback for .frame1.frame1.frame2.button Tk::__ANON__ at /usr/lib/perl5/vendor_perl/5.8.8/i386-linux-thread-multi/Tk.pm line 250 Tk::Button::butUp at /usr/lib/perl5/vendor_perl/5.8.8/i386-linux-thread-multi/Tk/Button.pm line 175 <ButtonRelease-1> (command bound to event) and for Athena 0.8.054 Windows Tk::Error: Can't upgrade that kind of scalar at athena line 12863. main::diff_marked at athena line 12863 main::__ANON__ at athena line 12527 Tk callback for .frame1.frame2.frame2.button Tk::__ANON__ at /PerlApp/Tk.pm line 252 Tk::Button::butUp at /PerlApp/Tk/Button.pm line 111 <ButtonRelease-1> (command bound to event) cheers darek and adam ------------------------------------------------------------------------ dr. Zajac Dariusz A. Deutsches Elektronen-Synchrotron -Hasylab phone: +49-40-8998-2932 Notkestr. 85 fax: +49-40-8998-2787 22607 Hamburg e-mail: dariusz.zajac(a)desy.de Germany ------------------------------------------------------------------------

2 1

Hexagonal WO3
by Ying Zhou, Anorganisch-Chemisches Inst. 18 Nov '08

18 Nov '08

Dear All Recently, I got one compound, W/Mo oxide, which has the similar structure with hexagonal WO3. We tested the EXAFS of W L3 edge and Mo K edge of this compound. So, we use the hexagonal WO3 model to refine the structure of our compounds. My question is that how can I get the FEFF file of this compound. Can I directly change some of W to Mo in FEFF file? or Do I need to add the Mo in the atom file? I do appreciate your help. Best wishes Ying

2 1

Ifeffit 1.2.11c (was Re: [PGPLOT build problem] Upgrading to ifeffit-1.2.11b on Ubuntu from source)
by Matt Newville 17 Nov '08

17 Nov '08

Hi Folks, I've uploaded source kits for Ifeffit 1.2.11c to the cars.uchicago.edu and sourceforge.net download sites. I have a Windows dll made for this bug fix version. If anyone is interested, this is currently at http://cars.uchicago.edu/~ifeffit/updates/011/bin/ifeffit_12.dll This should be a drop-in replacement for the IFEFFIT_DIR\bin\ifeffit_12.dll on your system. Artemis.exe will not be updated from this dll, as it has this dlls "compiled in". Bruce will have to make a new Artemis.exe, and then we'll make a automatic update. Sorry for all the trouble, --Matt On Mon, Nov 17, 2008 at 12:30 PM, Matt Newville <newville(a)cars.uchicago.edu> wrote: > Hi, > > This is my fault... and I apologize for the sloppiness and for being > late in fixing this. I've been mixing 'development/testing' and > 'production' versions, and haven't been very good at keeping them > cleanly separated. I think I have this mostly under control now, > but I will have to work on a decent "test suite". > > I think I found another reason to make a 1.2.11c version too, that the > mixing of "devel" and "production" > caused an experiment in how fitting was done to be the default, so > that the reported chi-square doesn't actually match the documentation > (instead of summing real and imaginary parts, it sums real and > magnitude components of the misfit, which is part of an experiment to > see how Feff8.5 worked for XAFS. Using Magnitude as well Phase for > another way to report chi-square and misfits is potentially a useful > approach, but it's not what is documented. Anyway, mixing devel and > production versions like this (for the past couple years, really) is > very sloppy on my part, and I apologize again. > > I actually have an ubuntu box now, though I built pgplot from source, > and have never made a .deb file. > There is a new source kit at > http://cars.uchicago.edu/~ifeffit/src/ifeffit-1.2.11c.tar.gz I'll > post this to sourceforge this afternoon, and I'll also make a new DLL > for Windows and post all of these on the download page. I'll also make > a new updater for Windows. > > --Matt > > > On Mon, Nov 17, 2008 at 10:07 AM, Mauro Rovezzi <rovezzi(a)esrf.fr> wrote: >> Carlo Segre wrote: >>> >>> Hi Mauro: >>> >>> I have now produced a package of ifeffit 1.2.11b. It is in Debian >>> unstable and available for Ubuntu intrepid and jaunty in my repository >>> >>> deb http://debian-xray.iit.edu intrepid main contrib non-free >> >> Carlo, >> >> Thank you very much for the package. >> >> Actually, I was able to build/install ifeffit 1.2.11b from source but >> not able to build than the Perl/Python wrappers and so no Horae&Friends >> from Bruce SVN. >> >> Well, now I have "pgplot5", "ifeffit", "perl-ifeffit" and >> "python-ifeffit" from binaries and "libperlxray" "horae" and "demeter" >> built from source (Bruce SVN). >> >> Everything seems fine but I still do not understand why ifeffit 1.2.11 >> has all these "IFF str = *" output as stated also by Gareth in his >> "Ifeffit 1.2.11b terminal output" post. Is it normal? >> >> Cheers, >> Mauro >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> >> >

2 2

[PGPLOT build problem] Upgrading to ifeffit-1.2.11b on Ubuntu from source
by Mauro Rovezzi 17 Nov '08

17 Nov '08

Dear all, I decided to upgrade ifeffit-1.2.11 on my Ubuntu 8.10 (Intrepid Ibex) desktop machine. Well, up to now I have always worked with PGPLOT & Ifeffit binaries from Carlo that are just working fine but seen that they are still not ready for the new version I decided to build them by source. First of all let me say that Ifeffit builds fine if I use the "pgplot5" binary package, BUT, as stated by Matt in the README.PGPLOT, Ifeffit will compile without plotting support in this case. So the only way is to build also PGPLOT from source. Unfortunately the experience has failed both with the "PGPLOT_install" script and following steps in the "install-unix.txt". I have tried many possibilities but the make process interrupts on the drivers compilations. Seen that following "install-unix.txt" gives the same error (but on another driver!) of "PGPLOT_install", let's focus on this last procedure to try debugging the situation: $sudo ./PGPLOT_install ... [all fine until the PGPLOT make] [long list of errors + warnings like:] ... /home/mauro/local/ifeffit-1.2.11/pgplot/drivers/xwdriv_iff.c:4445: error: ‘XWdev’ has no member named ‘gc’ ... make: *** [xwdriv_iff.o] Error 1 ... [then the final error due to the bad compilation] collect2: ld returned 1 exit status make: *** [pgdemo1] Error 1 OK, I have described more or less the situation but I would not flood the list with technical mails, so if someone would help me with this issue we can continue in private and then send just the solution to the list. Anyway, the problem is not "urgent" seen that I can work with the 1.2.10 binary installation. Have a nice day! Mauro -- Mauro Rovezzi <rovezzi(a)esrf.fr> PhD student - GILDA BM08 c/o ESRF (Grenoble, FR)

4 7

about wolframite crystallographic file
by Yordy Licea Fonseca 17 Nov '08

17 Nov '08

Hi all, As soon as I load this attached CIF crystallographic file from ISCD in Artemis0.8.012 the software says: "Artemis trapped one or more errors! Error message dumped to screen." I can`t go on runnig Atoms as it seems to be a problem with the file. I have read the suggestion made in FAQ, but I can not manage to find the error. Could you help me, please? It would be nice once the problem been fixed to add this structure to Matt's atoms.inp database. Thanks you very much, Yordy -- Yordy E. Licea Fonseca Departamento de Físico-Química Instituto de Química-IQ/UFRJ Laboratório de Catálise Heterogênea Rio de Janeiro, RJ, CEP 21.949-909 Brasil Email: yliceafonseca(a)gmail.com

4 3