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

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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Re: [Ifeffit] Ifeffit 1.2.8
by Matt Newville 20 Sep '05

20 Sep '05

Hi Stefano, If you have Ifeffit 1.2.7 working on Tiger, I'd suggest just doing horae_update. The changes to the Ifeffit library are very small, so you could just wait until an installer for Mac OS X 10.4 is available. If you really want to be using 1.2.8, you could try installing from source. --Matt On 9/18/05, Stefano Ciurli <stefano.ciurli(a)unibo.it> wrote: > Hi Matt, > > >Ifeffit 1.2.8 is now available. There are minor changes to the core > >library and new versions of horae (055: athena 0.8.043, and artemis > >0.8.002) in the Windows and Mac installers. A few version notes are below, > >and I will be putting more information at > >http://cars9.uchicago.edu/iffwiki/ReleaseNotes128/ > > Thanks a lot! I am running OSX Tiger on a G4 and I am currently > working with Athena 0.8.039 and Artemis 0.7.015 > > What should I do ot update my environment to Ifeffit 1.2.8? > Thanks > Stefano > -- > ____________________________________________ > > Stefano Ciurli > Professor of Chemistry > Laboratory of Bioinorganic Chemistry > Department of Agro-Environmental Science and Technology > University of Bologna > Viale Giuseppe Fanin, 40 > I-40127 Bologna > Italy > Phone: +39-051-209-6204 > Fax: +39-051-209-6203 > > "Fatti non foste a viver come bruti, > ma per seguir virtute e canoscenza" > Dante Alighieri - Inferno - Canto XXVI > > "Ihr seid bestimmt, nicht Tieren gleich zu leben, > Nein, Tugend zu erringen und Erkenntnis" > "Ye were not form'd to live the life of brutes, > But virtue to pursue and knowledge high". > _______________________________________________ > 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] Fit in R and k space
by Frenkel, Anatoly 20 Sep '05

20 Sep '05

I personally like this argument in favor of r-space fitting over k-space fitting. I am pretty sure it was made by Ed Stern: R-space allows to think of EXAFS in terms of radial distribution of atomic positions relative to the central atom. Peaks in r-space usually correspond to atomic positions and the regions between the peaks - to the interstitial regions in the structure (of course, there are 1000 counter-examples, but we are talking about some 'average, well behaving' system where a peak is NOT an atomic AXAFS, nor it is caused by a Ramsauer-Townsend resonance, etc., and a valley is NOT a destructive interference between neighboring shells' - AF). We know, on another hand, that FEFF approximation electron charge density as spherical and the potential as muffin tin. This approximation is not as accurate in the interstitial region between the atoms (where potential profile in real systems may be anything but flat) as it is near the atoms. Thus, intuitively, FEFF should do better job fitting 'peaks' in r-space rather than fitting the interstitial. However, the r-factor and chi square do not really care. Technically, if two models give similar r-factors and chi-square, the one that has better fit in the peak region, the other - in the interstitial, one will examine the r-space fit and choose the one that fits peaks better over the one that fits interstititial region better. However, this information, localized in r-space, is distributed in k-space. Thus, if you look at the graph where data and fit are shown together, either in raw unfiltered k-space or in q-space, the misfit is difficult to interpret. It is, however, possible to interpret the misfit in r-space, and that what often helps to refine the model or choose the better one. Anatoly Anatoly Frenkel Department of Physics Yeshiva University -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov]On Behalf Of Michel Schlegel Sent: Tuesday, September 20, 2005 9:07 AM To: Ravel, Bruce; XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Fit in R and k space Hello Bruce, >Although I prefer to think about the EXAFS problem in R space, I don't think >this is the reason to do the fit in R space. Regardless of which fitting >space you use, you are relying on Feff to supply some fraction of all the >Fourier components in the data. We could also used reference-derived phase and amplitude function, as in the good ol'time ;) > The first-shell feff path only has Fourier >components (or frequencies, if you prefer) corresponding to the first-shell >portion of chi(R). Thus that feff path can only fit those frequencies. >That's true in k-space as well as in R-space True in R-space, and that's why Athena-Ifeffit are doing such a wonderful job at providing windows to fit only selected area of the fourier transform. Almost true also in q-space. In k-space... hmmm, well, I would love to see the mathematical demonstration of it for a limited k-range and a Feff(k) (eventhoug I agree that many people have performed tha fit in k- and R-spaces, and found about the same paramters, so it must be verified somehow). >What's more, I think the problem of non-modelled shells affecting the >modelled >portion of the data exists in R-space just as much as in k-space. Because of >sigma^2 and the finite data range, peaks have width. In R-space, a given >path is centered at a particular R-value (or, in other words, its >contribution to the spectrum is dominated by a particular frequency). >However, the peak has width (it contains frequencies below and above the >dominant frequency). Thus longer paths always interfere with shorter paths >to some extent. I think the effect of interfering contributions in the Konigsberger and Prins. What I noticed, though, is that the fit of closer shells can affect that of the furthest shell because of the "spillof" from the first peak. The recciprocal I was not aware of. But I do agree with you on the whole. However, I think that in the FT case, these interences are limited to the nearest shells, whereas in k-space, nothing protects you from shells at, say, 2R and 3R (so to speak. Best regards, Michel -- Michel Schlegel Commissariat à l'énergie atomique CEN de Saclay, DEN/DANS/DPC/SCP/LRSI Bat 391 - Piece 205B F91 191 Gif-sur-Yvette Cedex, France Ph: +33 (0)1 69 08 93 84 Fax: +33 (0)1 69 08 54 11 _______________________________________________ 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] Ifeffit installer for Mac 10.4 (Tiger)
by Matt Newville 20 Sep '05

20 Sep '05

Hi Stefano, If you've already done 'sudo horae_update' (and thanks for the correction!!) and have the latest versions of Athena and Artemis installed, I would say that you don't need to use the binary installer. The changes in the binary installer are tiny. --Matt

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