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

RE: [Ifeffit] Amplitude in Artemis
by Kelly, Shelly D. 28 Feb '06

28 Feb '06

Hi Paul, How close are the distances for the 6 ligands? It is usually not possible to fit a single peak in the EXAFS spectrum by 6 independent signals. It sound like the distribution of distances for these 6 ligands is incorrect. I suggest that you try to fit just the first peak with one and then with two different shells with unknown coordination numbers and distances. This will give you some more information about what the data indicate the structure is like. If you send me an artemis file, I'll take a peak at it. Shelly skelly(a)anl.gov ________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Paul Sent: Monday, February 27, 2006 6:31 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Amplitude in Artemis Hi Shelly Unfortunately the coordination number is 1 for all atoms present. I have the crystal structure of the complex, so I am currently including 6 ligating atoms all at distances defined by the structure in the input file. It seems to be the first shell that is causing the problems, with a quickfit first shell artemis fit giving nominally 13 ligating species (which is of course absurd). So I believe something else must be the problem. Cheers Paul ----- Original Message ----- From: Kelly, Shelly D. <mailto:SKelly@anl.gov> To: XAFS Analysis using Ifeffit <mailto:ifeffit@millenia.cars.aps.anl.gov> Sent: Tuesday, February 28, 2006 12:55 AM Subject: RE: [Ifeffit] Amplitude in Artemis Hi Paul, It seems possible that one of the other amplitude terms is also incorrect. Scott already mentioned the step height but what about the coordination number? The amplitude of the model is given by coordination number * S02. You mentioned that the S02 value was somewhere between 2 and 4. What is the value for coordination number * S02? If the coordination number is 1, then it is possible that the parameters are switched. Maybe the coordination number should be between 2 and 4 and S02 should be around 1. HTH, Shelly ________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Paul Sent: Sunday, February 26, 2006 6:52 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Amplitude in Artemis I have just started a PhD and have been given alot of EXAFS data to simulate but I don't know much about artemis. I have tried to fit the data for quite some time now, but can't get any kind of good fit unless the amplitude is above 1. Is there any way amp can be above 1 and rationally explained? Cheers, Paul ________________________________ _______________________________________________ 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] Amplitude in Artemis
by Kelly, Shelly D. 28 Feb '06

28 Feb '06

Hi Paul, It seems possible that one of the other amplitude terms is also incorrect. Scott already mentioned the step height but what about the coordination number? The amplitude of the model is given by coordination number * S02. You mentioned that the S02 value was somewhere between 2 and 4. What is the value for coordination number * S02? If the coordination number is 1, then it is possible that the parameters are switched. Maybe the coordination number should be between 2 and 4 and S02 should be around 1. HTH, Shelly ________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Paul Sent: Sunday, February 26, 2006 6:52 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Amplitude in Artemis I have just started a PhD and have been given alot of EXAFS data to simulate but I don't know much about artemis. I have tried to fit the data for quite some time now, but can't get any kind of good fit unless the amplitude is above 1. Is there any way amp can be above 1 and rationally explained? Cheers, Paul

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Amplitude in Artemis
by Paul 27 Feb '06

27 Feb '06

I have just started a PhD and have been given alot of EXAFS data to simulate but I don't know much about artemis. I have tried to fit the data for quite some time now, but can't get any kind of good fit unless the amplitude is above 1. Is there any way amp can be above 1 and rationally explained? Cheers, Paul

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SPAM score=47.4*** Fonts in document pods
by Dave Baker 22 Feb '06

22 Feb '06

-------------------- Start SpamAssassin results ---------------------- Content analysis details: (score=47.4,required=5.3) -2.6 BAYES_00 BODY: Bayesian spam probability is 0 to 1% [score: 0.0000] 50 STOCKS_APS FULL: Hot Stocks Spam -------------------- 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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Re: How to change the spline knots in Athena
by Bruce Ravel 21 Feb '06

21 Feb '06

On Tuesday 21 February 2006 03:08, you wrote: > I am using Athena (0.8.048) software for XAFS analysis. > It is greatly helpful to me for XAFS characterization. > > I have a question on the background estimation. > Spline knots is displayed by "About current group" menu. > Could you tell me how to change the spline knots, if possible. > Changing the knots is useful to suppress the long-range variation. This is the kind of question that is better sent to the mailing list, so I am CCing my answer there. The number of knots is determined by the values of the k-range of the spline fit and by the value of Rbkg. The number of knots is delta_k * Rbkg * 2 / pi and the knots are evenly spaced in k. Ifeffit (and so Athena) does not allow you to move the knots to different locations nor does it allow you add or remove knots. The AUTOBK algorithm works by making a distinction between data and background in terms of Fourier components. Consequently it *cannot* allow you to move the knots or use more knots, since doing so would change the Fourier components included in the background spline. B -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advanced 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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error message in help
by Bradley Roberts 21 Feb '06

21 Feb '06

With Ifeffit 1.2.8, Athena 0.8.047, Artemis 0.8.004 running on OS X and plotting correctly, I'm not able to pull up any of the help windows. In either of the GUI programs, when I click on the Help menu and choose Document (or any of the sub-menu items in Athena) X11 beeps in error, and a window opens with the title "pod" and nothing displayed within the window. I mentioned before that I could not get tk::pod to install correctly via CPAN (the response being) Installing tk::pod FAILED windows would pop up during the make test routine that said: Can't find Pod 'perl' with an OK button and that the Text::English and Tk::HistEntry modules were not installed (though they are installed, says CPAN) I recognize that this is probably more of a Perl/CPAN related question but perhaps someone has seen this problem before. -- Bradley Roberts (br2(a)u.washington.edu) Graduate Student, Department of Materials Science & Engineering Roberts Hall 302 Box 352120 University of Washington Seattle, WA 98195 206-616-7485 lab 206-543-3100 fax

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Re: [Ifeffit] pgplot+Kubuntu+/XWINDOW /XSERVE
by Bruce Ravel 21 Feb '06

21 Feb '06

On Monday 20 February 2006 23:48, Denis Testemale wrote: > I've been using Ifeffit+horae (VERY GOOD) stuff for a while on my > previous Mandrake linux distro. I've changed to Kubuntu now. I have > difficulties to install everything on this new laptop. [Please be > aware that I use Linux for quite some time now but still consider > myself as an "everyday beginner"] > > I'm stuck at the installation of PGPLOT. > I've tried then to install from Mat's PGPLOT_install script but ran > into the same kind of error. Here it is: Kubuntu is debian-based and, I think, can use any debian repository. So I think you should be able to use Carlo's debian repository to install the software. Just point kynoptic at the repositories mentioned here: http://cars9.uchicago.edu/~ravel/software/downloads.html#debian Hope that helps, B -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advanced 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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Re: How to change the spline knots in Athena
by Bruce Ravel 21 Feb '06

21 Feb '06

On Tuesday 21 February 2006 03:08, you wrote: > I am using Athena (0.8.048) software for XAFS analysis. > It is greatly helpful to me for XAFS characterization. > > I have a question on the background estimation. > Spline knots is displayed by "About current group" menu. > Could you tell me how to change the spline knots, if possible. > Changing the knots is useful to suppress the long-range variation. This is the kind of question that is better sent to the mailing list, so I am CCing my answer there. The number of knots is determined by the values of the k-range of the spline fit and by the value of Rbkg. The number of knots is delta_k * Rbkg * 2 / pi and the knots are evenly spaced in k. Ifeffit (and so Athena) does not allow you to move the knots to different locations nor does it allow you add or remove knots. The AUTOBK algorithm works by making a distinction between data and background in terms of Fourier components. Consequently it *cannot* allow you to move the knots or use more knots, since doing so would change the Fourier components included in the background spline. B -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advanced 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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pgplot+Kubuntu+/XWINDOW /XSERVE
by Denis Testemale 21 Feb '06

21 Feb '06

Hello. I've been using Ifeffit+horae (VERY GOOD) stuff for a while on my previous Mandrake linux distro. I've changed to Kubuntu now. I have difficulties to install everything on this new laptop. [Please be aware that I use Linux for quite some time now but still consider myself as an "everyday beginner"] I'm stuck at the installation of PGPLOT. I've tried then to install from Mat's PGPLOT_install script but ran into the same kind of error. Here it is: -if I try to install without any driver but the /NULL one, this what it tells: g77 -fno-backslash -o pgdemo1 /usr/local/src/pgplot/examples/pgdemo1.f -L`pwd` -lpgplot -L/usr/X11R6/lib -lX11 /usr/bin/ld: ne peut trouver -lX11 collect2: ld a retourné 1 code d'état d'exécution - if I try with the /XWINDOW and /XSERVE: gcc -c -Wall -fPIC -DPG_PPU -O -I. -I/usr/X11R6/include /usr/local/src/pgplot/drivers/xwdriv.c /usr/local/src/pgplot/drivers/xwdriv.c:127:21: erreur: X11/Xos.h : Aucun fichier ou répertoire de ce type /usr/local/src/pgplot/drivers/xwdriv.c:128:22: erreur: X11/Xlib.h : Aucun fichier ou répertoire de ce type /usr/local/src/pgplot/drivers/xwdriv.c:129:23: erreur: X11/Xutil.h : Aucun fichier ou répertoire de ce type /usr/local/src/pgplot/drivers/xwdriv.c:130:24: erreur: X11/keysym.h : Aucun fichier ou répertoire de ce type /usr/local/src/pgplot/drivers/xwdriv.c:131:23: erreur: X11/Xatom.h : Aucun fichier ou répertoire de ce type ... make: *** [xwdriv.o] Erreur 1 Let me add that my examples here are taken from an installation from the PGPLOT source, but I would have the same kind of error messages with Mat's script. In my long struggle I remember I had PGPLOT installed and working correctly (i.e. the demo would work) but without /XWINDOW neither /XSERVE. If I remember well, at that time my desperate attempt had been to delete "|X11" from a LIBS line in the make file. But of course, following up to the installation of horae, I could not have the plotting interface in athena/artemis. I read somewhere that Bruce had some Kubuntus running some where. Maybe somebody else? Did you face this kind of difficulties. Thanks for any kind of advice and please feel free to ask any additional information needed. Cheers denis ps: I'm not a 64 bit linux.

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Errors from Webatoms?
by Feng Wang 20 Feb '06

20 Feb '06

Hi everyone: I used WEBATOMS(version 1.8), to calculated the feff.inp for Si-K of alpha-SiO2 (quartz phase), using the crystal structure (as listed below) from Wyckoff's Crsytal Structures(P312-313), however, I could not get correct atomic configuration, such as, I did not get the tetrahedron (of 4 nearest neighboring oxygen atoms), I got two n.n. oxygen atoms only, please refer to the results on the bottom. As suggested by Dr. Ravel, I tried the atoms in Artemis, but still I could not get correct feff.inp.Would you please help me to check and suggest, thank you so much. Best regards, Feng alpha-SiO2 crystal structure (from Wyckoff's book): hexagonal, a=4.91304, c=5.40463, space group: p3121 (#152). Si (3a): (-u,- u,1/3), (u,u,0) (0,u,2/3); O: (6c): (x,y,z), (y-x, -x, z+1/3), (-y, x-y, z+2/3), (x-y, -y,-z), (y,x,2/3-z), (-x,y-x,1/3-z). In which, u(si)=0.465, x=0.415, y=0.272, z=0.120. According to it, I used the input for WEBATOMS: Space group: p3121 OUTPUT type: feff8.inp Edge: K shift: 0 0 0 A=4.91304, c=5.40463 Crystallographic Sites: Si (-0.465 -0.465, 1/3) O (0.415, 0.272, 0.12). And I got the atomic configuration in feff.inp as below: ATOMS * this list contains 449 atoms * x y z ipot tag distance 0.00000 0.00000 0.00000 0 Si 0.00000 0 -0.51058 -0.99735 -1.15297 2 O 1.60771 1 0.21274 1.45917 -0.64854 2 O 1.61091 2 0.00000 0.00000 1.80158 1 Si 1.80158 3 -2.27633 0.97033 0.00004 1 Si 2.47451 4 1.97849 -1.48619 0.00004 1 Si 2.47451 5 0.82118 -2.40002 0.64857 2 O 2.61822 6 -1.11902 0.05650 -2.45008 2 O 2.69412 7 0.82118 2.51302 0.64857 2 O 2.72218 8 -1.66789 1.91117 1.15301 2 O 2.78637 9 1.37005 -0.54535 2.45012 2 O 2.85964 10 2.58693 -0.54535 1.15301 2 O 2.88428 11 -2.27633 0.97033 -1.80153 1 Si 3.06084 12 -0.29784 2.45652 -1.80153 1 Si 3.06083 13 1.97849 -1.48619 -1.80153 1 Si 3.06083 14 -0.29784 -2.45652 -1.80153 1 Si 3.06083 15 -0.29784 2.45652 1.80154 1 Si 3.06084 16 -0.29784 -2.45652 1.80154 1 Si 3.06084 17 -1.11902 0.05650 2.95455 2 O 3.15987 18 1.37005 -0.54535 -2.95451 2 O 3.30206 19 -3.43364 0.05650 0.64857 2 O 3.49481 20 0.21274 -3.45387 -0.64854 2 O 3.52066 21 0.00000 0.00000 -3.60305 1 Si 3.60305 22 -1.66789 -3.00187 1.15301 2 O 3.62250 23 1.97849 3.42685 0.00004 1 Si 3.95698 24 -0.51058 3.91569 -1.15297 2 O 4.11372 25 3.74424 1.45917 -1.15297 2 O 4.18065 26 -4.04208 -0.99735 -0.64854 2 O 4.21352 27 -2.88477 1.91117 2.45012 2 O 4.23999 28 3.95698 0.00000 -1.80153 1 Si 4.34778 29 1.97849 3.42685 -1.80153 1 Si 4.34778 30 3.95698 0.00000 1.80154 1 Si 4.34779 31 -0.29784 2.45652 -3.60309 1 Si 4.37098 32 -0.29784 -2.45652 -3.60309 1 Si 4.37098 33 -2.27633 0.97033 3.60310 1 Si 4.37099 34 -0.29784 2.45652 3.60310 1 Si 4.37099 35 1.97849 -1.48619 3.60310 1 Si 4.37099 36 -0.29784 -2.45652 3.60310 1 Si 4.37099 37 -0.51058 -0.99735 4.25166 2 O 4.39682 38 -2.88477 1.91117 -2.95451 2 O 4.55012 39 -2.27633 -3.94271 0.00004 1 Si 4.55265 40 4.46756 -0.99735 -0.64854 2 O 4.62325 41 ================================== Feng Wang fwang(a)phys.ualberta.ca Electron Microscopy Group Department of Physics University of Alberta =========================================================

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