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

WG: [Ifeffit] hephaestus
by Peter Leinweber 02 Nov '05

02 Nov '05

hello bruce, i am a new user of your software. when i load the programm the following shows up lower right: Emin -200 and Emax 800. when i load data they are plotted with proper x-axis. but when i did any modification the scaling of x-axis changes to invalid or in-comfortable values. i can fix it by modifying Emin and Emax but to get an axis of 395 to 410 eV i have to type Emin -400 and Emax 18000. is that o.k. ? another question: will you or will someone of your group attend the CLS user meeting here in saskatoon in november. there is interest of other newcomers like me to get introduced into ATHENA. perhaps some arrangement such as coverage of additional hotel costst for staying a day longer or so could be made. kind greetings, peter Prof. Dr. Peter Leinweber Institute for Land Use Universitaet Rostock D-18051 Rostock Present address: Department of Soil Science University of Saskatchewan 51 Campus Drive SK S7N 5A8 Canada phone: 001-306-966-6866 fax: 001-306-966-6881 ----- Originalnachricht ----- Von: Bruce Ravel <bravel(a)anl.gov> Datum: Mittwoch, November 2, 2005 5:31 pm Betreff: [Ifeffit] hephaestus > > > Hi all, > > Today, in a conversation that Carlo, Matt, and I have been having, > Matt said the following: > > > I know some beamlines (PNC-CAT, for example) don't install > > Ifeffit/hephaestus on data collection machines because it uses too > > much memory (~40Mb+ on Win32). > > In fact, the only thing for which hephaestus uses Ifeffit is the f'/f" > utility. None of the other tools in hephaestus make use of ifeffit in > any way. > > Would there be some interest in a "hephaestus-lite"? That is, a > version of hephaestus that does not include the f'/f" utility. > Such a > thing would have a much smaller footprint on the computer -- just > whatever the perl interpreter requires, maybe 4 or 5 meg. > > If enough people express inetrest, I can inlcude thas in the > distribution. I can even make a stand-alone distribution that > installs only hephaestus-lite and the external files it needs to do > its thing. That would be a much smaller beast (both in disk space and > memory footprints) than the full ifeffit install. > > B > > > -- > Bruce Ravel ---------------------------------------------- > bravel(a)anl.gov > Molecular Environmental Science Group, Building 203, Room E-165 > MRCAT, Sector 10, Advance Photon Source, Building 433, Room B007 > > Argonne National Laboratory phone and voice mail: (1) 630 > 252 5033 > Argonne IL 60439, USA fax: (1) 630 > 252 9793 > > My homepage: http://cars9.uchicago.edu/~ravel > EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

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hephaestus
by Bruce Ravel 02 Nov '05

02 Nov '05

Hi all, Today, in a conversation that Carlo, Matt, and I have been having, Matt said the following: > I know some beamlines (PNC-CAT, for example) don't install > Ifeffit/hephaestus on data collection machines because it uses too > much memory (~40Mb+ on Win32). In fact, the only thing for which hephaestus uses Ifeffit is the f'/f" utility. None of the other tools in hephaestus make use of ifeffit in any way. Would there be some interest in a "hephaestus-lite"? That is, a version of hephaestus that does not include the f'/f" utility. Such a thing would have a much smaller footprint on the computer -- just whatever the perl interpreter requires, maybe 4 or 5 meg. If enough people express inetrest, I can inlcude thas in the distribution. I can even make a stand-alone distribution that installs only hephaestus-lite and the external files it needs to do its thing. That would be a much smaller beast (both in disk space and memory footprints) than the full ifeffit install. B -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advance Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

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SPAM score=5.6*** Troubles in Running Iffeffit
by Adiraj Srinivas (Dr) 31 Oct '05

31 Oct '05

-------------------- Start SpamAssassin results ---------------------- Content analysis details: (score=5.6,required=5.3) 8.0 SOFTWARE_APS BODY: Words and phrases for selling software 0.1 HTML_IMAGE_RATIO_06 BODY: HTML has a low ratio of text to image area 0.0 HTML_90_100 BODY: Message is 90% to 100% HTML -2.6 BAYES_00 BODY: Bayesian spam probability is 0 to 1% [score: 0.0033] 0.0 HTML_MESSAGE BODY: HTML included in message -------------------- End of SpamAssassin results --------------------- The original message was not completely plain text, and may be unsafe to open with some email clients; in particular, it may contain a virus, or confirm that your address can receive spam. If you wish to view it, it may be safer to save it to a file and open it with an editor.

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S02
by Juan Antonio Maciá Agulló 31 Oct '05

31 Oct '05

Hi people, I fitted several supported platinum based catalysts by Artemis. I obtained good R-factors < 0.02 but stranges values of SO2 (<0.30) and I do not know if these low values of SO2 are related with a low coordination number for Pt. I know that particle sizes of these catalysts are very small and then the coordination number is smaller than 12. Thank you very much. JA

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RE: [Ifeffit] Problems with Windows XP Installation.
by Brewer, Luke N 21 Oct '05

21 Oct '05

Bruce, thank you for the solutions. Solution 2 seems to have fixed the problem. I now look forward to learning to run the software. Thanks again, Luke. -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Bruce Ravel Sent: Friday, October 21, 2005 12:36 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Problems with Windows XP Installation. On Friday 21 October 2005 13:14, Brewer, Luke N wrote: > Hello All- > > I have just downloaded and installed the ifeffit.1.2.8.exe package > for Windows XP from a mirror to sourceforge. The installation > appeared to run just fine. I read the note on website about using the > runner.exe instead of the individual executable files. > > When I click on the runner.exe, a window asks me what application I > would like to run (Athena, Artemis, etc.). The window disappears, and > nothing happens for about a minute after which an error window appears > asking me to check the runner.exe.log. The last line of each log > entry reads "timeoutsocket.Timeout: Attempted connect to > ('164.54.160.111', 80) timed out." > > I get the same error each time I try to run the software, regardless > of which application I select. > > Any advice? I would be happy to forward the runner.exe.log to anyone > who can/is willing to help. I think I know the problem -- Matt may have more wisodm. The first version of the runner did not play well without a reliable internet connection. It would seem you have been bitten by this problem. Possible solution #1: If, in fact, you were on a computer with out an internet connection (either by design or because it was temporarily down), make sure the computer is connected and try again. Possible solution #2: Grab this file: http://cars9.uchicago.edu/ifeffit/updates/iff_001.zip and unpack it by hand in C:\Program File\Ifeffit\ (or wherever you installed the whole ifeffit package). That file is the first updater package. It updates the runner as well as Athena, Artemis, and a bunch of documents and example. For more info on how the runner works and how updates happen, see the wiki: http://cars9.uchicago.edu/iffwiki/IfeffitOnWindows/RunnerProgram HTH, B -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advance Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/ _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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new Tip of the Week
by Bruce Ravel 21 Oct '05

21 Oct '05

Hi! I just posted a new Tip of the Week at http://cars9.uchicago.edu/iffwiki/HoraeTipOfTheWeek This week's bit of magic is Artemis: Quickly plotting paths from the Feff interpretation page Enjoy, B -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advance Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

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Problems with Windows XP Installation.
by Brewer, Luke N 21 Oct '05

21 Oct '05

Hello All- I have just downloaded and installed the ifeffit.1.2.8.exe package for Windows XP from a mirror to sourceforge. The installation appeared to run just fine. I read the note on website about using the runner.exe instead of the individual executable files. When I click on the runner.exe, a window asks me what application I would like to run (Athena, Artemis, etc.). The window disappears, and nothing happens for about a minute after which an error window appears asking me to check the runner.exe.log. The last line of each log entry reads "timeoutsocket.Timeout: Attempted connect to ('164.54.160.111', 80) timed out." I get the same error each time I try to run the software, regardless of which application I select. Any advice? I would be happy to forward the runner.exe.log to anyone who can/is willing to help. Thanks. Luke. Luke N. Brewer, Ph.D. Sandia National Laboratory Materials Characterization Dept.

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L2 vs. L3 edge comparisons
by McCready, Alistair 20 Oct '05

20 Oct '05

OK, a theoretical question whose answer may be straight-forward (and I will probably ridiculed for such a simple question)!! If you analyse, for example, the Pb L3 edge of 2 minerals and you then analyse the Pb L2 edge of the same 2 minerals, will the difference between the edges of 2 minerals be the same, irrespective of the edge you use? Cheers Alistair ------------------------------------------ Dr. Alistair J. McCready Mining & Minerals Saskatchewan Research Council 125-15 Innovation Blvd. Saskatoon, SK, S7N 2X8 Canada Tel: 306 933-7103 Fax: 306 933-7446 email: mccready(a)src.sk.ca "SRC provides Smart Science Solutions" This e-mail and any files transmitted with it are intended only for the named recipients and may contain legally privileged and/or confidential information. If you are not the intended recipient please do not disseminate, distribute or copy this e-mail without the consent of the sender.

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horae Debian package
by Carlo Segre 18 Oct '05

18 Oct '05

Hello All: Because of the new dependency on libmath-round-perl. The Debian package of horae 056 will have to be installed manually. It can be found at the deb http://fermi.phys.iit.edu/debian/woody binary/ deb http://fermi.phys.iit.edu/debian/sarge binary/ deb http://fermi.phys.iit.edu/debian/sid binary/ depending on the distribution you are using. Cheers, 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 Carlo.Segre(a)iit.edu http://www.iit.edu/~segre

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new windows updater
by Bruce Ravel 14 Oct '05

14 Oct '05

Hi again, The windows updater containing an update to the runner as well as all the new stuff from today's Athena&Artemis source code release is now available. The runner should find it the next time you start one of the programs. Let us know if you have any troubles with the update or with the new runner. Bruce & Matt -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advance Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/

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tarball 056 released & new tip of the week
by Bruce Ravel 14 Oct '05

14 Oct '05

Hi folks! The new Tip of the Week is about automated replotting in Athena. http://cars9.uchicago.edu/iffwiki/HoraeTipOfTheWeek I have also released version 056 of the source code tarball, which is available at my web site and at SourceForge. A description of what's new in Athena and Artemis is at http://cars9.uchicago.edu/iffwiki/HoraeVersion056 The major new features are both in Athena: session defaults and improvements to linear combination fitting. Please read the release notes for a complete description of these new features. An updater for windows users should be available within a few days. Unix and Mac OSX users should download and install the new source tarball. Enjoy, B -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advance Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

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Small clusters in Feff
by Kelly, Shelly D. 07 Oct '05

07 Oct '05

Hi EXAFS friends, I was reading a paper this morning where the authors used a small hydrated cluster in Feff8.2. The cluster has a metal center surrounded by one shell of oxygen atoms. All feff paths in the calculation were used in the model fits. No mention was made in the manuscript of the muffin tin radii used in the Feff8.2 calculation based on this small cluster, hence I assume that these authors were unaware of the potential pit falls in doing so. Using feff7, I have run a comparison of the calculated signal from a bounded and unbounded shell of atoms at the same distance. I found that the unbounded shell of atoms has a muffin tin radii that is really big because it is not bounded by any other atoms giving rise to an error in the calculated signal from these atoms. Has anyone run this experiment with Feff8.2? I have always used the metal-oxide crystal structure in my modeling of hydrated metal ions and have found reasonable agreement with chemical speciation calculations. I believe that the non-expert users of Feff, find it difficult to remember not to use the exact model within Feff because of this "feature". Is there any discussion of adding a hydration sphere option into Feff? I look forward to your comments. Shelly Shelly Kelly Bldg 203 RM E113 Skelly(a)anl.gov Argonne National Laboratory 630-252-7376 9700 S Cass Ave www.mesg.anl.gov Argonne, IL 60440

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new tip of the week
by Bruce Ravel 07 Oct '05

07 Oct '05

Hi, The Tip Of The Week took last week off to go visit my mom ;-) This week's is about "Selecting paths to plot automatically after a fit" in Artemis. http://cars9.uchicago.edu/iffwiki/HoraeTipOfTheWeek Enjoy! B -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advance Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

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delR versus thermal expansion A and first cumulant C1*
by Leandro Langie Araujo 05 Oct '05

05 Oct '05

Dear all, I’m writing because I’ve been trying to analyze some thermal dependent EXAFS data for the first shell of a c-Ge sample and ended up in a conceptual confusion. If any of you could give me some help on this I’d be very grateful. Whenever we fit an EXAFS spectrum with Artemis/IFEFFIT, we get a /delR/ value. As far as my (very) limited comprehension goes, /delR/ is the difference between the theoretical (FEFF8) bond length, /R0/, and the result of the best fit to my data, /R/, which gives the experimental bond length. So, this should be the /first cumulant/ of my distance distribution, right? The net linear thermal expansion /A/ (as defined by Anatoly Frenkel and John Rehr in [PRB48, 585, 1993]) from an one-dimensional model seems to have been considered as equal to the temperature variation of the /delR/ values by several people, including Matt Newville (on his thesis). Following this approach, it is possible to relate the EXAFS cumulants (/delR/, /ss/, /C3/ and /C4/) of the distance distribution with the constants of an one-dimensional anharmonic effective potential, following a correlated Einstein model. I was going through this path... … when I came across some papers (P. Fornasini and G. Dalba in [PRL82, 4240, 1999; PRB70, 174301, 2004] and E. A. Stern in [J.Phys.IV 7, C2-137,1997]) where an issue is raised; it is said that the thermal evolution of the first cumulant /C1/* of the real distance distribution in a crystal (which was said to be equivalent to /delR/) is NOT equal to /A/, because in a crystal there are vibrations perpendicular to the bond direction which are not considered in the one-dimensional model. It is argued that the temperature dependence of these vibrations perpendicular to the bond direction give raise to a positive shift of the minimum of the effective pair potential, while the net thermal expansion /A/ accounts only for changes due to the asymmetry of the potential. So, the main questions hammering my head are: - does /delR/ include any contribution from vibrations perpendicular to the bond direction? Can really /delR/ and /C1/* be the same quantity? - is the thermal evolution of /delR/ equal to the net thermal expansion /A/? Or should some correction for perpendicular vibrations be added to relate both quantities? Sorry if I made it too long, but it was something hard to express in a few words… Any help will be greatly appreciated. Cheers, Leandro

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R-factor and reduced chi square
by OWEN N LI 05 Oct '05

05 Oct '05

Hi, I understand R-factor and reduced chi square are statistical ways to see if the model is reasonable (R-factor) and if one model is better than the others (reduced chi square). But how much should I read into it? I have model A and B, I believe A is more theoretical sound than B. but when I fit them using IFEFFIT, the R-factor and reduced chi square of B is slightly better than A (B: 0.03, 28; A: 0.04, 33). What does that tell me? Is my assumption incorrect? Or are they more or less the same? Owen

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RE: [Ifeffit] New Method for Normalization?
by Barton, David (DG) 04 Oct '05

04 Oct '05

Bruce, You mentioned: > Isn't Ifeffit's Cromer-Liberman normalization scheme > substantially similar to the method presented in that paper? > When I use the Cromer-Liberman background subtraction routine in Athena the Normalized data is not flattened. Normalized, but not *flattened* data results in a skewed XANES region which is affected by the amount of curvature in the background. If I choose "Flatten" in Athena, it is my understanding that it applies a linear pre-edge and 2nd order polynomial post-edge regardless of which background was chosen (Autobk or CLNorm). The Clnorm background does appear to "flatten" the chi(k) data which can be useful for EXAFS analysis, but it doesn't flatten the mu(E) data. When one attempts to analyze XANES data it is preferred to have the entire post-edge "flattened" in mu(E) space so that the background curvature is eliminated from the dataset. Ultimately, as Matt stated, it would be nice to be able to combine a Victoreen and CLNorm background to get a reasonably "flattened" mu(E) function. I would also suggest adding the ability to independently set the pre-edge and post-edge functions (n'th order polynomial, Victoreen, CLNorm, or MBACK??) for Normalization and Flattening. These choices would be separate from the choice of background removal method to get chi(k) (Autobk or CLNorm). Dave > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov > [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf > Of Bruce Ravel > Sent: Thursday, September 29, 2005 5:20 PM > To: XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] New Method for Normalization? > > > On Thursday 29 September 2005 15:48, Barton, David (DG) wrote: > > 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? > > Isn't Ifeffit's Cromer-Liberman normalization scheme > substantially similar to the method presented in that paper? > > B > > > -- > Bruce Ravel ---------------------------------------------- > bravel(a)anl.gov > > Molecular Environmental Science Group, Building 203, Room > E-165 MRCAT, Sector 10, Advance Photon Source, Building 433, > Room B007 > > Argonne National Laboratory phone and voice mail: > (1) 630 252 5033 > Argonne IL 60439, USA fax: > (1) 630 252 9793 > > My homepage: http://cars9.uchicago.edu/~ravel > EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/ > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

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RE: [Ifeffit] R-factor and reduced chi square
by Kelly, Shelly D. 04 Oct '05

04 Oct '05

Hi Owen, A test for a significant change in the reduced chi square (RCS). [(RCS1)^2/(RCS2)^2] - 1 greater than 2 * sqrt ( 2 / degrees of freedom) If you can not read that, I have this published in J. Phys Chem B, V105 no27 year (2001). You can down load that paper from my web page www.mesg.anl.gov. I guess it is a reasonable test:). For most model fits a change by a factor of 2 is needed to be statistically significant. Good luck Shelly Shelly Kelly Bldg 203 RM E113 Skelly(a)anl.gov Argonne National Laboratory 630-252-7376 9700 S Cass Ave www.mesg.anl.gov Argonne, IL 60440 > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit- > bounces(a)millenia.cars.aps.anl.gov] On Behalf Of OWEN N LI > Sent: Tuesday, October 04, 2005 1:08 PM > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] R-factor and reduced chi square > > Hi, > I understand R-factor and reduced chi square are statistical ways to > see if the model is reasonable (R-factor) and if one model is better > than the others (reduced chi square). But how much should I read into it? > > I have model A and B, I believe A is more theoretical sound than B. > but when I fit them using IFEFFIT, the R-factor and reduced chi square > of B is slightly better than A (B: 0.03, 28; A: 0.04, 33). What does > that tell me? Is my assumption incorrect? Or are they more or less the > same? > > Owen > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Muffin tin radius adjustment?
by Paul Fons 03 Oct '05

03 Oct '05

I am trying to analyze some XAFS data on a Sb-Te compound and when I run feff(6) I get errors regarding the coordination number being too small implying the muffin tin radius is too big. In this material the first nearest neighbor bond length is about 3 angstroms (slightly more or less depending on the site). I assume this is related to the cause of the problem. Any suggestions as to how to fix/avoid this sort of problem? feff6 output is pasted below. Interestingly enough, feff8 does not output any error messages and the sum of the paths looks identical (at least at first glance). Is this a false error message or (more likely) has feff8 become more intelligent with regards to defining the muffin tin radius? Feff6 output Calculating potentials and phases... free atom potential and density for atom type 0 free atom potential and density for atom type 1 free atom potential and density for atom type 2 overlapped potential and density for unique potential 0 overlapped potential and density for unique potential 1 overlapped potential and density for unique potential 2 muffin tin radii and interstitial parameters phase shifts for unique potential 0 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. phase shifts for unique potential 1 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. phase shifts for unique potential 2 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. Preparing plane wave scattering amplitudes... nncrit in prcrit 9 Searching for paths... WARNING in PATHS Module: rmax > distance to most distant atom. Some paths may be missing. rmax, ratx 15.50000 15.40291 Rmax 15.5000 keep and heap limits 0.0000000 0.0000000 Preparing neighbor table Feff8 output Calculating potentials ... free atom potential and density for atom type 0 free atom potential and density for atom type 1 free atom potential and density for atom type 2 initial state energy overlapped potential and density for unique potential 0 overlapped potential and density for unique potential 1 overlapped potential and density for unique potential 2 muffin tin radii and interstitial parameters iph, rnrm(iph)*bohr, rmt(iph)*bohr, folp(iph) 0 1.79879E+00 1.71274E+00 1.13279E+00 1 1.81342E+00 1.72495E+00 1.13595E+00 2 1.83703E+00 1.74437E+00 1.14149E+00 mu_old= -0.508 Done with module 1: potentials. Calculating LDOS ... LDOS calculation for specified grid Calculating energy and space dependent l-DOS. It takes time ... potential type 0 potential type 1 potential type 2 Calculating chi and rho... 0 Calculating chi and rho... 1 Calculating chi and rho... 2 Done with LDOS. Calculating cross-section and phases... absorption cross section phase shifts for unique potential 0 phase shifts for unique potential 1 phase shifts for unique potential 2 Done with module 2: cross-section and phases... Done with module 3: FMS. Preparing plane wave scattering amplitudes... Searching for paths... WARNING: rmax > distance to most distant atom. Some paths may be missing. rmax, ratx 1.55000E+01 0.00000E+00 Rmax 15.5000 keep and heap limits 0.0000000 0.0000000 Preparing neighbor table Dr. Paul Fons Senior Researcher National Institute for Advanced Industrial Science & Technology METI Center for Applied Near-Field Optics Research (CANFOR) AIST Central 4, Higashi 1-1-1 Tsukuba, Ibaraki JAPAN 305-8568 tel. +81-298-61-5636 fax. +81-298-61-2939 email: paul-fons(a)aist.go.jp The lines below are in a Japanese font 〒３０５−８５６８茨城県つくば市東１−１−1 つくば中央第４近接場光応用工学センターポール・フォンス主任研究官

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Runner.exe Network Error
by Barton, David (DG) 28 Sep '05

28 Sep '05

Bruce and Matt, I am running the Ifeffit 1.2.8 on a Win2000 box and I having several issues with the startup of Athena/Artemis when I am not connected to a network. First thing is that all programs run fine when I am connected to the internet. So the obvious workaround for me is to just make sure that I have an open network connection before running Athena/Artemis. However, it would be nice if the auto-update feature in "Runner.exe" would still let me run Athena/Artemis when I wasn't connected to the network, basically just ignore looking for an update when I don't have a network connection. The errors that I get in the Runner.exe.log are below. There are two different cases shown. The first set of errors are when I have a connection to my local network, but have not yet logged onto the firewall that lets me out onto the internet. The second set of errors comes up when I unplug the network connection completely. Hope these help. NETWORK CONNECTION NO INTERNET CONNECTION ----------------------------------------- Traceback (most recent call last): File "runner.py", line 753, in ? File "runner.py", line 184, in __init__ File "runner.py", line 275, in LookForUpdates File "runner.py", line 299, in read_web_version File "urllib.pyc", line 76, in urlopen File "urllib.pyc", line 181, in open File "urllib.pyc", line 306, in open_http File "urllib.pyc", line 319, in http_error File "urllib.pyc", line 565, in http_error_302 File "urllib.pyc", line 580, in redirect_internal File "urllib.pyc", line 181, in open File "urllib.pyc", line 306, in open_http File "urllib.pyc", line 319, in http_error File "urllib.pyc", line 616, in http_error_401 File "urllib.pyc", line 624, in retry_http_basic_auth File "urllib.pyc", line 650, in get_user_passwd File "urllib.pyc", line 658, in prompt_user_passwd NO NETWORK CONNECTION -------------------------------------- File "runner.py", line 753, in ? File "runner.py", line 184, in __init__ File "runner.py", line 275, in LookForUpdates File "runner.py", line 302, in read_web_version Dave _________________________________ David Barton The Dow Chemical Company

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getting chi(r) information out of command line IFEFFIT
by Sean X. Luo 28 Sep '05

28 Sep '05

Hello all. It's been a while since I've written on the mailing list about this project, but it's come up that I need everyone's general input. Just a brief overview of the project: I am working with Scott Calvin to simultaneously fit 12 data sets in the command line of IFEFFIT, and I need to somehow get the chi(r) information for the fit out of the command line. I've tried around with the "show" command and the different permutations possible with that, but whenever I type in "show(fit.r, fit.chir_real)" (which is our guess right now on how to get the information I need out of the command line), it gives me the error that the arrays fit.r and fit.chir_real does not exist, or something along those lines. Does anyone else have any idea on how to run this? Thanks in advance, - Sean.

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RE: [Ifeffit] Fe oxide
by Kelly, Shelly D. 26 Sep '05

26 Sep '05

Hi Juro, I had some fun playing with this project file. I hope you don't mind. Here is a list of suggestions. 1st: Don't use the paths that are less than 0.1 Angstroms apart. 1st-b: If you don't know the CN set it to ONE and then vary just the amplitude. There is a degen box multiplied by a amp box. Degen should be one. 2st: set the values for CN, and s2, while letting delr vary 3rd. Let the CN and delr vary. You will find that the Fe path around 3 Ansgroms isn't needed. 4th. Make sure your fit range and data ranges are appropriate. 5th. Add as much constraints as you think is reasonable. First Oxygen coordination number should be 6 or 4 total. I thought 6 worked well. 6th. Fit the data with k-weight of 1,2, and 3, to get the uncertainties smaller. Take a look at the project file. I think that this model or one like it might work. You need a separate S02 value from the Amp value. Amp should be S02*Amp. I didn't add a S02 part. You should get that from a known standard measured on the same beamline. S02 should be between 0.70 and 1.0. So the CN reported are likely a bit too big. Good luck, Shelly Shelly Kelly Bldg 203 RM E113 Skelly(a)anl.gov Argonne National Laboratory 630-252-7376 9700 S Cass Ave www.mesg.anl.gov Argonne, IL 60440 > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit- > bounces(a)millenia.cars.aps.anl.gov] On Behalf Of Juraj Majzlan > Sent: Monday, September 26, 2005 8:46 AM > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Fe oxide > > Hello, > > I am trying to fit an EXAFS spectrum of an X-ray amorphous > Fe precipitate. In a model (goethite), there are Fe atoms > at 3.02, 3.29, and 3.45 A. Fitting the two most distant > shells of iron gives strange results. Fitting them > simultaneously gives very high amplitudes (32, -66) which > cancel each other (fig. 1) and produce a beautiful and > unreasonable fit (fig. 2). > > Fitting them separate gives small ('reasonable') > amplitudes, but the distance (dr) have very high > uncertainties, e.g., dr = 0.12 +- 20.3. > > Can I expect to resolve these three Fe shells or is it > asking too much? > > I am also attaching the Artemis file, but will appreciate > any comments and suggestions. > > Juro Majzlan > > > ---------------------------------- > Juraj Majzlan > Institute of Mineralogy and Petrology > Albert-Ludwig-University of Freiburg > Albertstrasse 23b > Freiburg, D-79104, Germany > telephone +49-761-203-6416 > fax +49-761-203-6407 > http://www.minpet.uni-freiburg.de/sites/personen/majzlan.html

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Fe oxide
by Juraj Majzlan 26 Sep '05

26 Sep '05

Hello, I am trying to fit an EXAFS spectrum of an X-ray amorphous Fe precipitate. In a model (goethite), there are Fe atoms at 3.02, 3.29, and 3.45 A. Fitting the two most distant shells of iron gives strange results. Fitting them simultaneously gives very high amplitudes (32, -66) which cancel each other (fig. 1) and produce a beautiful and unreasonable fit (fig. 2). Fitting them separate gives small ('reasonable') amplitudes, but the distance (dr) have very high uncertainties, e.g., dr = 0.12 +- 20.3. Can I expect to resolve these three Fe shells or is it asking too much? I am also attaching the Artemis file, but will appreciate any comments and suggestions. Juro Majzlan ---------------------------------- Juraj Majzlan Institute of Mineralogy and Petrology Albert-Ludwig-University of Freiburg Albertstrasse 23b Freiburg, D-79104, Germany telephone +49-761-203-6416 fax +49-761-203-6407 http://www.minpet.uni-freiburg.de/sites/personen/majzlan.html

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problems on running the windows 1.2.8 ifeffit version
by M Ceolin 23 Sep '05

23 Sep '05

Dear Bruce et al. I just installed the new 1.2.8 for windows version of ifeffit and I am experiencing problems to run any of the programs associated (arthemis, athena, etc.). I installed the programs in a Win98 machine where the previous versions of IFEFFIT were running. I took care of adding the suggested line to the config.sys file and installed the program in c:\ifeffit (as suggested). However, both, starting from the icons in the desktop, from the applications installed at c:\ifeffit\bin or from the menu at the start, the runner program (installed with the pakage) send an error message forcing to abort the run. The message says: (sorry, in spanish) Este programa ha efectuado una operacion no admitida y sera interrumpido (in the datails window says) RUNNER provoco un error de pagina no valida en el modulo MSVCRT.DLL de 017f:7801274b. etc. (registry numbers). Could you comment the point and, perhaps, suggest a solution ?. Yours. Marcelo Ceolin. *************************************** Dr. Marcelo Ceolin Centro Regional de Estudios Genomicos UNLP-AUGM Av. Calchaqui km 23,5 (4to piso) (1888) Florencio Varela Argentina Tel/Fax: +54-11-42758100 e-mail 1: mceolin(a)creg.org.ar e:mail 2: mrceolin(a)yahoo.com.ar WEB: www.creg.org.ar *************************************** PLEASE NOTE THAT THE E-MAIL ADDESSS mceolin(a)gwdg.de IS NO LONGER AVAILABLE. USE ONE OF THE ADDRESSES ABOVE. --------------------------------- 1GB gratis, Antivirus y Antispam Correo Yahoo!, el mejor correo web del mundo Abrí tu cuenta aquí

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RE: [Ifeffit] writing beam time proposals
by Frenkel, Anatoly 23 Sep '05

23 Sep '05

I rate proposals on the merit but it a former XAFS school student is a research group member it makes me happier. Anatoly -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov on behalf of Matt Newville Sent: Fri 9/23/2005 12:06 PM To: Carlo Segre; XAFS Analysis using Ifeffit Cc: Subject: Re: [Ifeffit] writing beam time proposals In my opinion, it is better for the student or post-doc to write the beamtime proposal and be listed as PI, with the advisor listed somewhere on the proposal Many proposal foms have a checkbox for 'is this work part of a thesis', and that is definitely monitored (at least at the APS, but I'd imagine it to be true at other facilities), even if it is not formalized. There is usually an eagerness for bringing new students (and new post-docs and new faculty members) to the syncrotrons. Also, in my experience reading beamtime proposals now and then, students and post-docs do a better job at writing them <wink>. Even f the professor is listed first (and many groups do this!), I would suggest that the student/post-doc actually write the proposal and have the advisor look it over before submitting. Other advice for writing proposals: - communicate with the beamline scientist to make sure the work is feasible and appropriate. - write it to convince someone in a *different field* why the experiment is important. - include references to previous work to show that you know the field. --Matt _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Tip of the Week: Constraining parameters between data groups in Athena
by Bruce Ravel 23 Sep '05

23 Sep '05

Hi, This week's tip of the week is "Constraining parameters between data groups in Athena": http://cars9.uchicago.edu/iffwiki/HoraeTipOfTheWeek?action=show B -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advance Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

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