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

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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RE: [Ifeffit] Errors from Webatoms?
by Barton, David (DG) 18 Feb '06

18 Feb '06

Feng, Attached is a CIF file for alpha-SiO2 with the same space group (P3121) that you are attempting to use. The major difference that I see in this file compared with your input file is the Si location (0.465 0 1/3) vs. (-.465 .465 1/3). I am no crystallographer so I cannot tell you if a shift vector would make these equal, but this CIF file imports directly into Artemis and does give a 4-coordinate Si-O. Dave > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov > [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf > Of Feng Wang > Sent: Saturday, February 18, 2006 2:28 AM > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Errors from Webatoms? > > > 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, > z+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 > ========================================================= > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

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R-space
by Marcos Eleoterio 12 Feb '06

12 Feb '06

Good morning, I have a question about the R-range in Artemis, i want to fit the first shell region only, but what are the criteria to select the R-range? if i select the first peak just a,little bit different to one fit from the other, the fit get very different. reagards Marcos Eleotério

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Athena 0.8.048, Artemis 0.8.005, Hephaestus 0.13
by Bruce Ravel 11 Feb '06

11 Feb '06

Hi, Today I have released version 060 of the source code tarball, which includes Athena 0.8.048, Artemis 0.8.005, Hephaestus 0.13. This is mostly a bug fix release, although both Athena and Hephaestus have minor new features. The problem with displaying documentation should be solved. Please read the release notes at http://cars9.uchicago.edu/iffwiki/HoraeVersion060 New versions of the tarball are at SourceForge and at my website. I built new Windows executables -- a new updater is available and should install the next time you fire up one of the programs. As always, let me know if you run into any problems or have any great new suggestions. 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/exafs/

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sample holders
by Silvio Levy 09 Feb '06

09 Feb '06

I beg the indulgence of the list owner to post a question not directly related to Ifeffit. Where can on purchase sample holders to be used in the SSRL beam (both for liquid samples and solid ones)? I've asked some researchers at SSRL and at UCB but they use ones milled at their respective institutions, and I don't have this option. Silvio Levy Cal State University East Bay Mathematical Sciences Research Institute

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Mac OS X installation
by Bradley Roberts 09 Feb '06

09 Feb '06

Bottom line - I was able to install - hopefully my comments below help someone in the future. > >I'm not sure I understand the full sequence of events, but I'd >definitely recommend re-installing from the binary installer. >Building from source is possible, of course, but once you run into a >problem it's a lot harder to guess what's wrong. I'm trying to avoid building from source, and was trying to re-install from binary. > > I am able to load ifeffit and execute commands, however when I >try to load any of >> the ancillary programs there are failures (see printout below). > >It looks like the core ifeffit is installed fine, but not the perl >libraries needed by athena, artemis, etc. Do you have any ideas why >that might be the case? What, if anything, is in /Library/Perl? /Library/Perl had (and has) a full installation of 5.8.6 although since starting this, there is now a 5.8.1 folder with the dir darwin-thread-multi-2level which I think I'll just leave alone for now. > > As per previous posts, I've installed and updated g77 via fink, >as well as tk and tk::pod via >> cpan. I also had to install LWP via cpan before I could get >>ifeffit to run. > >OK.... but none of this should be needed for athena to run. It did appear that LWP was necessary to get ifeffit to run. It also didn't start to work until g77 was installed, somewhat confirmed with this page: http://cars9.uchicago.edu/cgi-bin/ifeffit/faqwiz?req=show&file=faq02.010.htp tk, tk::pod did not appear to be necessary > > From the install notes I see that ifeffit's intall program >trashes the LWP directory in perl, > >Hmmm, where do you see this? (and I'd hope it doesn't trash >anything!!) The installer does write a bunch of perl modules to >/Library/Perl. "trash" was probably the wrong word. I can't find where I was concerned about LWP specifically, but this note is the closest: If you are using Perl on Mac OS X for other purposes, you may want to consult with Matt and/or Bruce before installing this package. > > so I'm curious if I've caused this problem myself (and if so, how >do I fix it?). Secifically, the >> ifeffit.pm and Tk/Pod.pm files cannot be found anywhere in the >>@INC directories. Also, >>running the locate command I cannot find the files on the drive >>anywhere else. > >They should be in /Library/Perl. still not seen by the locate command, however as I note below, the programs run. > > Additionally, I tried to download and re-install ifeffit from the > > disk image and it cannot install - the error says "you cannot >> continue. there is nothing to install." > >You probably need to delete the "installation receipt" by removing >the /Library/Receipt/Ifeffit-1.2.*****.pkg folder(s). Then you should >be able to do a full re-install. >After that happens, check the contents of /Library/Perl. I re-downloaded the 1.2.8 binary package from sourceforge and removed the previous receipt. Upon re-installation, athena/artemis/etc appear as applications (with icons, etc) and are properly launched either via double click or command line. I can't say what, specifically, caused it to install correctly this time, or what steps I went through that were unnecessary, but hopefully these notes will help someone else next time. Thanks for your help - now I've got to learn how to use the program. >Hope that helps. Let us know how it works out. > >Cheers, > >--Matt > -- 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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Athena
by lkh＠ensm-douai.fr 09 Feb '06

09 Feb '06

Hi, I'm working with Athena (00.8.046 version). I have two questions about xanes treatment : 1- When I open a file as xanes(E) the self absorption correction is not accessible. I must open it as mu(E). Why? 2- About Peak fit, It's possible to introduce new functions? Thank you very much. L. Khouchaf Analyse Physique Centre de Recherche de l'Ecole des Mines de Douai. Douai France. khouchaf(a)ensm-douai.fr

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Re: using FEFF8 to calculate the xanes spectra of solid solutions
by Bruce Ravel 09 Feb '06

09 Feb '06

On Thursday 09 February 2006 09:24, Valmor Mastelaro wrote: > >Hello Bruce, > > could you please help me with the following question: > > I truing to calculate the xanes spectra of Pb1-xLaxTiO3 solid solutions. I > calculated the PbTiO3 xanes spectra and is quite similar to published one. > When I substitute some Pb atoms by La atoms, even for x=15%, I only > observed few changes on the calculated spectra compared with the undoped > one. > > Please, could you verify if I´m using a correct feff imput file (in > attach)... > > thanks for your help > > Regards Hi Valmor, I hope you don't mind that I am CCing my response to the Ifeffit mailing list. Your question is one that I see often, so I think that others would benefit by seeing this discussion. In a solid solution, one expects the dopant to substitute stochastically into the lattice. That is, in the absence of some kind of structural phase transition that leads to a different crystal symmetry, we expect the dopant to enter randomly into the crystal. In your case, each Pb site in the crystal has a 15% chance of being replaced by a La atom. If we ignore La-La correlations, the probability of a Pb site being replaced by La is unaffected by the occupancy of the adjacent Pb sites. Here are the first several lines of the feff.inp file you sent me, with several lines not related to this discussion deleted: TITLE PLT10 Com lantânio,a=3.885,c=4.139 HOLE 1 1.0 POTENTIALS * ipot z label 0 22 Ti 2 3 0.01 1 8 O 2 3 3.00 2 82 Pb 3 3 0.90 3 22 Ti 2 3 0.99 4 57 La 3 3 0.10 ATOMS .00000 .00000 .00000 0 Ti .00000 .00000 .00000 -1.87041 1 axial 1.87041 -1.95921 .00000 .33980 1 Planar 1.98846 .00000 -1.95921 .33980 1 Planar 1.98846 1.95921 .00000 .33980 1 Planar 1.98846 .00000 1.95921 .33980 1 Planar 1.98846 .00000 .00000 2.15145 1 axial 2.15145 1.95921 -1.95921 1.91754 4 La 3.36956 1.95921 1.95921 1.91754 2 Pb 3.36956 -1.95921 -1.95921 1.91754 2 Pb 3.36956 -1.95921 1.95921 1.91754 2 Pb 3.36956 1.95921 -1.95921 -2.10432 2 Pb 3.47925 -1.95921 -1.95921 -2.10432 2 Pb 3.47925 1.95921 1.95921 -2.10432 2 Pb 3.47925 -1.95921 1.95921 -2.10432 2 Pb 3.47925 .00000 -3.91842 .00000 3 Ti 3.91842 .00000 3.91842 .00000 3 Ti 3.91842 3.91842 .00000 .00000 3 Ti 3.91842 -3.91842 .00000 .00000 3 Ti 3.91842 .00000 .00000 4.02186 3 Ti 4.02186 .00000 .00000 -4.02186 3 Ti 4.02186 This feff.inp file does NOT adequately represent a solid solution. The Pb sites here are NOT occupied by La 15% of the time. In this example, there is one Pb site that is occupied by La 100% of the time and all the rest are never occupied by La. That's NOT a solid solution -- that's a different crystal. Thus, this feff.inp file might be some kind of approximation of a solid solution, but probably not a very good one. Unfortunately, Feff does not allow you to put 15% of an atom at a site. Each site is either all or nothing. That doesn't mean that Feff is not helpful in the case of a solid solution -- it just means that you have to do more work. One way of better approximating a solid solution is to use a random number generator and to run Feff many times. Each time you run feff, pre-process the feff.inp file, using a random number generator to decide for *every* lead site whether it should be replaced with a La atom. If you run enough feff calculations with Pb randomly substituted in this way, the ensemble will be a good representation of a solid solution. You can add up the subsequent calculations until the sum of spectra converges. There is at least one person out there in Ifeffit-land who has done some work on approximating solid solutions in this way. He might be inspired to comment further on this topic. There is an additional issue that you are not considering in the feff.inp file that you sent me. It is quite unlikely that the La atoms rests exactly on the Pb site. Much more likely is that the La atom introduces some kind of local disorder, moving off-site, pushing surrounding atoms away or drawing them closer. Those distortions might be large enough to be significantly effect the local environment about the Ti atom. If so, ignoring them in the feff.inp file is obviously incorrect. One last thing: take a look at the PDF file of a talk I have been giving recently on multiple scattering theory: http://cars9.uchicago.edu/~ravel/talks/pimst.pdf. In section 3, I show a simple sequence of calculations on PbTiO3. One rule of thumb that I try to get across in that part of the talk is that light atoms tend to effect the XANES more than heavy atoms. I don't want to overstate this issue, but it is quite possible that the difference between Pb and La in the XANES of an oxide is pretty subtle. That is, the XANES is probably more sensitive to where the oxygen atoms are than to whether a Pb site is occupied by Pb or La. If that is the case, then, of the two issues I discuss above, the more serious is the possibility that La introduces distortions to the oxygen octahedra. Although your feff.inp file certainly does not do a complete job at modelling a solid solution, the more serious issue is probably that it does not introduce new distortions. And that is my best guess for why your feff.inp file does not seem to replicate the changes you see in your Ti-edge spectra. 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/exafs/

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Re: [Feffusers] Fwd: Some question about FMS calculation with FEFF
by Bruce Ravel 09 Feb '06

09 Feb '06

On Thursday 09 February 2006 01:57, Michel Jaouen wrote: > Now a question about Hephaestus: for f' and f" one has rodio buttons > allowing to select among various set (Crmer Liberman, Henke, ..). I > have try to select several and it always return CL! Why and how to > fix this (not sure it is a bug but?). To quote from the Hephaestus document about the f'/f" utility: This utility plots the complex corrections to the scattering factors for the elements. i.e. the energy dependent f'(E) and f"(E) terms. These functions are tabulated from the Cromer-Liberman calculations for the isolated, neutral atom. The selection in the Resource menu is ignored. That's by design. The reason is that I have never been able to figure out how to do the interpolation off of Chantler's ffast tables near the absorption edges such that the f' function is well behaved near the absorption edge. The dteails are at http://physics.nist.gov/PhysRefData/FFast/Text/cover.html. The last time I looked at this in detail, my implementation gave very poor results in the region of f' that was changing quickly. 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/exafs/

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Re: [Ifeffit] Installation troubles on OS X
by Matt Newville 08 Feb '06

08 Feb '06

Hi Brad, I'm not sure I understand the full sequence of events, but I'd definitely recommend re-installing from the binary installer. Building from source is possible, of course, but once you run into a problem it's a lot harder to guess what's wrong. > I am able to load ifeffit and execute commands, however when I try to load any of > the ancillary programs there are failures (see printout below). It looks like the core ifeffit is installed fine, but not the perl libraries needed by athena, artemis, etc. Do you have any ideas why that might be the case? What, if anything, is in /Library/Perl? > As per previous posts, I've installed and updated g77 via fink, as well as tk and tk::pod via > cpan. I also had to install LWP via cpan before I could get ifeffit to run. OK.... but none of this should be needed for athena to run. > From the install notes I see that ifeffit's intall program trashes the LWP directory in perl, Hmmm, where do you see this? (and I'd hope it doesn't trash anything!!) The installer does write a bunch of perl modules to /Library/Perl. > so I'm curious if I've caused this problem myself (and if so, how do I fix it?). Secifically, the > ifeffit.pm and Tk/Pod.pm files cannot be found anywhere in the @INC directories. Also, >running the locate command I cannot find the files on the drive anywhere else. They should be in /Library/Perl. > Additionally, I tried to download and re-install ifeffit from the > disk image and it cannot install - the error says "you cannot > continue. there is nothing to install." You probably need to delete the "installation receipt" by removing the /Library/Receipt/Ifeffit-1.2.*****.pkg folder(s). Then you should be able to do a full re-install. After that happens, check the contents of /Library/Perl. Hope that helps. Let us know how it works out. Cheers, --Matt

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secondary notes
by Bradley Roberts 08 Feb '06

08 Feb '06

My previous post was incomplete, after looking at last night's late late late notes: 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 (I thought they'd be autoinstalled if they're needed?) Other error messages at the beginning indicate that Test::More and Test::Without::Moderate were not installed. Hopefully this additional information will be helpful? -- 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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Installation troubles on OS X
by Bradley Roberts 08 Feb '06

08 Feb '06

I've spent the past few days going through the backlogs of this list and have been able to solve many problems so far. However, I've hit a point where I don't see a record of this problem/solution and am hoping someone can help. I am able to load ifeffit and execute commands, however when I try to load any of the ancillary programs there are failures (see printout below). As per previous posts, I've installed and updated g77 via fink, as well as tk and tk::pod via cpan. I also had to install LWP via cpan before I could get ifeffit to run. From the install notes I see that ifeffit's intall program trashes the LWP directory in perl, so I'm curious if I've caused this problem myself (and if so, how do I fix it?). Secifically, the ifeffit.pm and Tk/Pod.pm files cannot be found anywhere in the @INC directories. Also, running the locate command I cannot find the files on the drive anywhere else. Additionally, I tried to download and re-install ifeffit from the disk image and it cannot install - the error says "you cannot continue. there is nothing to install." My setup is: PB 15" G4 OS X 10.4.4 ifeffit 1.2.8 perl 5.8.6 fink and cpan selfupdated to the latest via cvs epic-glory:~ apple$ athena Can't locate Ifeffit.pm in @INC (@INC contains: /sw/lib/perl5 /sw/lib/perl5/darwin /System/Library/Perl/5.8.6/darwin-thread-multi-2level /System/Library/Perl/5.8.6 /Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 /Library/Perl /Network/Library/Perl/5.8.6/darwin-thread-multi-2level /Network/Library/Perl/5.8.6 /Network/Library/Perl /System/Library/Perl/Extras/5.8.6/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at /Applications/Ifeffit/bin/athena line 54. BEGIN failed--compilation aborted at /Applications/Ifeffit/bin/athena line 58. epic-glory:~ apple$ artemis Can't locate Ifeffit.pm in @INC (@INC contains: /sw/lib/perl5 /sw/lib/perl5/darwin /System/Library/Perl/5.8.6/darwin-thread-multi-2level /System/Library/Perl/5.8.6 /Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 /Library/Perl /Network/Library/Perl/5.8.6/darwin-thread-multi-2level /Network/Library/Perl/5.8.6 /Network/Library/Perl /System/Library/Perl/Extras/5.8.6/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at /Applications/Ifeffit/bin/artemis line 49. BEGIN failed--compilation aborted at /Applications/Ifeffit/bin/artemis line 53. epic-glory:~ apple$ hephaestus Can't locate Tk/Pod.pm in @INC (@INC contains: /sw/lib/perl5 /sw/lib/perl5/darwin /System/Library/Perl/5.8.6/darwin-thread-multi-2level /System/Library/Perl/5.8.6 /Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 /Library/Perl /Network/Library/Perl/5.8.6/darwin-thread-multi-2level /Network/Library/Perl/5.8.6 /Network/Library/Perl /System/Library/Perl/Extras/5.8.6/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at /Library/Perl/5.8.6/darwin-thread-multi-2level/Tk/widgets.pm line 14. at /Applications/Ifeffit/bin/hephaestus line 66 BEGIN failed--compilation aborted at /Applications/Ifeffit/bin/hephaestus line 66. -- 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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FEFF8 vrs FEFF6
by Kelly, Shelly D. 06 Feb '06

06 Feb '06

Hello Ifeffit friends, It is my understanding that FEFF6 or equivalently FEFF7 are considered the standard for Extended X-ray Absorption Fine Structure Analysis. In my experience, FEFF8 is a dangerous tool for EXAFS analysis as it has the ability to produce results that differ significantly from FEFF6 or FEFF7. In the review of EXAFS manuscripts where FEFF8 is the tool of choice, what parameters should be reported to give the reader some confidence that the authors have not tweaked the code to cover-up some errors in the model(s). A Big Thanks 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 60439

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Again _ for help with Webatoms input_sorry for incomplete information
by Feng Wang 03 Feb '06

03 Feb '06

Hi Everyone, I had a trouble with the input for webatoms in trying to get feff.inp from it. I got the crystal structure information from papers, as attached below, would you please suggest what should I input for the items listed below: Shift: Alpha= Beta= Gamma= The table of Crystallgraphic sites: Would Dr. Ravel or some of you can help with that? Thank you so much in advance. Best regards, Feng Crystal structure information: Iron trifluorine has a ReO3 type structure (hexagonal), with spac group of R- 3C, with two Fe atoms at (0 0 0) and (0.5 0.5 0.5)and 6 fluorines at (x, 0.5- x, 0.25), -(x, 0.5-x, 0.25), (0.5-x,0.25 x),-(0.5-x,0.25 x), (0.25 x, 0.5- x), -(0.25 x, 0.5-x), and with x=-0.164. ================================== Feng Wang fwang(a)phys.ualberta.ca Electron Microscopy Group Department of Physics University of Alberta =========================================================

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for help with Webatoms input
by Feng Wang 02 Feb '06

02 Feb '06

Hi Everyone, I had a trouble with the input for webatoms in trying to get feff.inp from it. I got the crystal structure information from papers, as attached below, would you please suggest what should I input for the items listed below: Shift: Alpha= Beta= Gamma= The table of Crystallgraphic sites: Thank you so much in advance. Best regards, Feng Crystal structure information: Iron trifluorine has a ReO3 type structure (hexagonal), with spac group of R- 3C, with two Fe atoms at (0 0 0) and (0.5 0.5 0.5)and 6 fluorines at (x, 0.5- x, 0.25), -(x, 0.5-x, 0.25), (0.5-x,0.25 x),-(0.5-x,0.25 x), ( ================================== Feng Wang fwang(a)phys.ualberta.ca Electron Microscopy Group Department of Physics University of Alberta =========================================================

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correlated Einstein model and Debye model
by Renato Canha Ambrosio 01 Feb '06

01 Feb '06

Good afternoon everybody I have questions about the Einstein and Debye correlated models in IFEFFIT. As described in page 80 of the EXAFS ANALYSIS WITH FEFF AND FEFFIT - PART 2: COMMENTARY by Bruce Ravel the eins function is a function evaluated in the context of the current path. So the reduced mass is calculated with the mass of the atoms in the path. Its ok but I have several scans at different temperatures so I would like to refine not only the Theta (Einstein temperature) but also the reduced mass and perhaps the static disorder. Can I do it in the context of the path or I have to perform a non - xafs refinement with the file containing the temperatures and sigma^2. I make the same question for the Debye correlated model. Thank you very much for your kind attention Renato Canha Universidade Federal do Rio Grande do Norte Natal - RN - BRASIL Open WebMail Project (http://openwebmail.org) ---------- Original Message ----------- From: ifeffit-request(a)millenia.cars.aps.anl.gov To: ifeffit(a)millenia.cars.aps.anl.gov Sent: Wed, 1 Feb 2006 12:00:12 -0600 Subject: Ifeffit Digest, Vol 36, Issue 1 > 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: FEFF8 vrs FEFF6 (Matt Newville) > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 1 Feb 2006 08:54:22 -0600 > From: Matt Newville <newville(a)cars.uchicago.edu> > Subject: Re: [Ifeffit] FEFF8 vrs FEFF6 > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: > <b8522e3d0602010654j195cf712hf30b878a67bac08e(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > HI Shelly, > > I wouldn't say it's wrong to use Feff8 for EXAFS analysis, just > rarely necessary. > > Feff8 was definitely designed for XANES, and improvements for EXAFS > were not the main goal. But there are a few cases where Feff8 _is_ > known to be better for EXAFS than Feff6. (I'll leave out Feff7 as it > seems no one is using this much). Clusters with H is one, and > transuranic elements is another. I've heard a few people claim that > Feff8 gives "better E0's", which I think means that E0 refines to a > value closer to 0 (that is, to where the it's arbitrarily assigned in > the data processing). Since E0 has to be refined and has little > physical significance, I don't find this to be a compelling advantage > for Feff8. > > Early versions of Feff8 (pre-release? Including 8.00?? I'm not sure) > were much worse for EXAFS.This did get fixed, but I'm not sure when > (I have a hard time understanding Feff8 version numbers and can never > really tell which get released and widely used: I've given up > complaining and live wih the fact that "Feff8" means one snapshot of > 8 years worth of work.). By Feff8.1 for sure, and maybe eralier, there > were essentially no difference between Feff6, 7, and 8 for EXAFS. > That was based on analysis of data on metal foils (Cu, Ag, Au), and > could hardly be called thorough and possibly not even 'highly > relevent to real-world problems', as it doesn't even test changes in > exchange or overlap of metal-oxygen potentials. Better testing and > comparisons would be very good. > > Anyway, I think it's fine to use Feff6, 7, or 8 for EXAFS. > > I don't think anything should change for these versions in the > reporting of how a Feff calculation was done for EXAFS. Most EXAFS > work using Feff give no details about the calculation, and I think > that's mostly OK, as the Feff/Atoms/Artemis default parameters are > generally quite reasonable. If the work discusses comparing > different Feff calculations, then obviously more detail on what was > changing would be needed. > > That's my opinion, anyway. > > --Matt > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > End of Ifeffit Digest, Vol 36, Issue 1 > ************************************** ------- End of Original Message -------

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RESTRAINTS IN IFEFFIT
by Renato Canha Ambrosio 25 Jan '06

25 Jan '06

Hi Folks, this is my first message on the list. Perhaps someone could help me. The subject is how to include restraints on exafs refinement. There is just scanty information about this on the ifeffit reference manual. I'm trying to refine the exafs data of a rhombohedral perovskite. The main MS contributions to the signal at about 3.5 A (non phase correct) arise from M O M interactions being M the absorber . We have a significant SS path, a two-legged and a three-legged path. The structural parameters of these three terms are correlated since all refers to the same A-B-C triangle and the A-B and B-C distances must be that found for M-O1 nearest-neighbor configurations. For these reasons we constrained the photo electron path length for three-legged to the M-O nearest-neighbor distance:R(three-leg = 2*RM-O). I'm trying to intoroduce the quantity defined as delta = R(three-legged)-R(two-legged) and thus define the SS half path length as a function of delta R(SS) = R (three-legged) - 2*delta. I think it is a restraint not a constraint. So I defined (def) the delta function on the line above the command FEFFIT also delr for the SS path. I introduced the restraint in the line FEFFIT as restraint = delrSS). The fit produce the same results as obtainde without the definition of delta and delrSS (function of delta). So I need to know how to introduce this restraint in the fit in order to calculate de M - O - M bond angle (this angle should be calculated using simple geometric relationships) - perhaps introduce the bond angle as a restraint. Someone can say me where I introduce the definitions of restraint parameters? Thank you very much for your kind attention Renato Canha Universidade Federal do Rio Grande doNorte Departamento de Quimica Natal - RN - BRAZIL Open WebMail Project (http://openwebmail.org) ---------- Original Message ----------- From: ifeffit-request(a)millenia.cars.aps.anl.gov To: ifeffit(a)millenia.cars.aps.anl.gov Sent: Mon, 23 Jan 2006 12:00:13 -0600 Subject: Ifeffit Digest, Vol 35, Issue 14 > 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: Re: I should be able to find this somewhere... (Bruce Ravel) > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 22 Jan 2006 16:58:07 -0600 > From: Bruce Ravel <bravel(a)anl.gov> > Subject: Re: [Ifeffit] Re: I should be able to find this somewhere... > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <200601221658.07513.bravel(a)anl.gov> > Content-Type: text/plain; charset="iso-8859-1" > > Hi, > > In fact, Artemis and Athena both attempt to deal correctly with input > chi(k) data that is not on the expected grid. Both codes perform a > test to see if the data is on the standard grid and, if not, > front-loads the data with zeros and uses Ifeffit's boxcar rebinning > function to put the data on the expected grid. > > Alas, there was a bug in the rebinning macro used by A&A which caused > it to fail in a particular situation met by the data in Matthew's > example. This bug will be fixed in the next release. > > If you import mu(E) data into Athena and then import data from the > Athena project file into Artemis, you will never see the problem that > Matthew reported. > > B > > On Tuesday 17 January 2006 16:09, Matt Newville wrote: > > Hi Matthew, Bruce, > > > > OK, I think it's a bug. Well, maybe it's just a consequence of a > > "known but not well advertised" problem. > > > > The chi(k) data you have doesn't start at k=0. By itself, this should > > be OK, and the fit seems to be mostly fine. There seems to be a bug > > in Ifeffit that the output fit chi(k) has the same number of data > > points as the input chi(k) data. In this case is incorrect -- it > > should go to the last data point in k. From looking at the code, I'm > > pretty sure this has no effect on the fit and is only an error in the > > output array. But the shortened chi_fit(k) will have an impact on the > > way Bruce is calculating the residual. Even if that were fixed, the > > residual would still be wrong, as the residual in Artemis is > > calculated as > > set(data0_res.k = data0.k) > > set(data0_res.chi = data0.chi - data0_fit.chi) > > > > and then Fourier transforming to R-space. Since the data and fit > > aren't aligned in k-space, the residual is incorrect. It should be > > > > set(data0_res.chi = data0.chi - interp(data0_fit.k, data0_fit.chi, > > data0.k)) > > > > or some variation on that. > > > > Sorry for the trouble. It's definitely a result of narrow-mindedly > > expecting that all chi(k) data comes from Ifeffit/Athena and will > > always start at k=0. We should get this fixed (it's mostly there!) so > > that data from other sources can be used. Right now, the easiest > > work-around is to pre-pack the chi(k) data with zeros (starting from > > k=0.00) > > > > --Matt > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > -- > 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/ > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > End of Ifeffit Digest, Vol 35, Issue 14 > *************************************** ------- End of Original Message -------

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RE: [Ifeffit] RESTRAINTS IN IFEFFIT
by Kelly, Shelly D. 25 Jan '06

25 Jan '06

Hi Renato, See below for some comments: > > Hi Folks, this is my first message on the list. Perhaps someone could help > me. The subject is how to include restraints on exafs refinement. There is > just scanty information about this on the ifeffit reference manual. > > I'm trying to refine the exafs data of a rhombohedral perovskite. > > The main MS contributions to the signal at about 3.5 A (non phase correct) > arise from M - O - M interactions being M the absorber . We have a > significant SS path, a two-legged and a three-legged path. The structural > parameters of these three terms are correlated since all refers to the > same > A-B-C triangle and the A-B and B-C distances must be that found for > M-O1 nearest-neighbor configurations. For these reasons > we constrained the photo electron path length for three-legged to the > M-O nearest-neighbor distance:R(three-leg = 2*RM-O). [Kelly, Shelly D.] The three-leg path length is given by half the total path length. Calculated as R = (distance_AB + distance_BC + distance_AC) * 0.5 You know the distance from A-B and the distance from B-C but the distance from A-C is dependent on the angle of the triangle path. You can write an equation to determine the angle A. a^2 = b^2 + c^2 -2bc cos(A) where a=distance_AC, b=distance_AB, c=distance_BC and A is the angle opposite of the AC side of the triangle. Then the four leg path has a path length defined as R = (2*distance_AB + 2*distance_BC)*0.5 The single path from A to B has the distance R = (2*distance_AB)*0.5 The single path from A to C has the distance R = (2*distance_AC)*0.5 Which also depends on the angle A and distance_AB as defined above. So for your case you have one unknown length and one unknown bond angle to describe these path lengths. i.e. distance_AB=distance_BC is unknown and angle A is unknown. HTH Shelly I'm trying to > intoroduce the quantity defined as delta = R(three-legged)-R(two-legged) > and thus define the SS half path length as a function of delta R(SS) = R > (three-legged) - 2*delta. I think it is a restraint not a constraint. > So I defined (def) the delta function on the line above the command FEFFIT > also delr for the SS path. I introduced the restraint in the line FEFFIT > as > restraint = delrSS). The fit produce the same results as obtainde without > the definition of delta and delrSS (function of delta). > So I need to know how to introduce this restraint in the fit in order to > calculate de M - O - M bond angle (this angle should be calculated using > simple geometric relationships) - perhaps introduce the bond angle as a > restraint. > Someone can say me where I introduce the definitions of restraint > parameters? > > Thank you very much for your kind attention > > Renato Canha > > Universidade Federal do Rio Grande doNorte > Departamento de Quimica > Natal - RN - BRAZIL > Open WebMail Project (http://openwebmail.org) > > > ---------- Original Message ----------- > From: ifeffit-request(a)millenia.cars.aps.anl.gov > To: ifeffit(a)millenia.cars.aps.anl.gov > Sent: Mon, 23 Jan 2006 12:00:13 -0600 > Subject: Ifeffit Digest, Vol 35, Issue 14 > > > 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: Re: I should be able to find this somewhere... (Bruce Ravel) > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Sun, 22 Jan 2006 16:58:07 -0600 > > From: Bruce Ravel <bravel(a)anl.gov> > > Subject: Re: [Ifeffit] Re: I should be able to find this somewhere... > > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > > Message-ID: <200601221658.07513.bravel(a)anl.gov> > > Content-Type: text/plain; charset="iso-8859-1" > > > > Hi, > > > > In fact, Artemis and Athena both attempt to deal correctly with input > > chi(k) data that is not on the expected grid. Both codes perform a > > test to see if the data is on the standard grid and, if not, > > front-loads the data with zeros and uses Ifeffit's boxcar rebinning > > function to put the data on the expected grid. > > > > Alas, there was a bug in the rebinning macro used by A&A which caused > > it to fail in a particular situation met by the data in Matthew's > > example. This bug will be fixed in the next release. > > > > If you import mu(E) data into Athena and then import data from the > > Athena project file into Artemis, you will never see the problem that > > Matthew reported. > > > > B > > > > On Tuesday 17 January 2006 16:09, Matt Newville wrote: > > > Hi Matthew, Bruce, > > > > > > OK, I think it's a bug. Well, maybe it's just a consequence of a > > > "known but not well advertised" problem. > > > > > > The chi(k) data you have doesn't start at k=0. By itself, this should > > > be OK, and the fit seems to be mostly fine. There seems to be a bug > > > in Ifeffit that the output fit chi(k) has the same number of data > > > points as the input chi(k) data. In this case is incorrect -- it > > > should go to the last data point in k. From looking at the code, I'm > > > pretty sure this has no effect on the fit and is only an error in the > > > output array. But the shortened chi_fit(k) will have an impact on the > > > way Bruce is calculating the residual. Even if that were fixed, the > > > residual would still be wrong, as the residual in Artemis is > > > calculated as > > > set(data0_res.k = data0.k) > > > set(data0_res.chi = data0.chi - data0_fit.chi) > > > > > > and then Fourier transforming to R-space. Since the data and fit > > > aren't aligned in k-space, the residual is incorrect. It should be > > > > > > set(data0_res.chi = data0.chi - interp(data0_fit.k, data0_fit.chi, > > > data0.k)) > > > > > > or some variation on that. > > > > > > Sorry for the trouble. It's definitely a result of narrow-mindedly > > > expecting that all chi(k) data comes from Ifeffit/Athena and will > > > always start at k=0. We should get this fixed (it's mostly there!) so > > > that data from other sources can be used. Right now, the easiest > > > work-around is to pre-pack the chi(k) data with zeros (starting from > > > k=0.00) > > > > > > --Matt > > > > > > _______________________________________________ > > > Ifeffit mailing list > > > Ifeffit(a)millenia.cars.aps.anl.gov > > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > -- > > 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/ > > > > ------------------------------ > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > End of Ifeffit Digest, Vol 35, Issue 14 > > *************************************** > ------- End of Original Message ------- > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Re: Possible bug in Artemis. (Bruce Ravel)
by joshua jason kas 24 Jan '06

24 Jan '06

Hi Bruce, Thanks for the tips. I fooled around with the feff.inp and found that artemis somehow has a problem when feff is run with the RMULTIPLIER card. This card is purely for convenience, so I took it out and things work fine. This card was used in feff6 although the code runs very slowly with it for some reason. Anyway, here is the feff.inp file that I was using for feff6 or feff8 (they both have the problem). Thanks, Josh TITLE GeCl4 HOLE 1 1.0 CONTROL 1 1 1 1 1 1 (feff8) CONTROL 1 1 1 1 (feff6) PRINT 1 0 0 0 0 3 EXCHANGE 0 1 1 CORRECTIONS 1.2427845974 0.0041969513 RMAX 10.0 RMULTIPLIER 1.01 POTENTIALS 0 32 Ge -1 -1 1 1 17 Cl -1 -1 4 ATOMS 0.0000000000 0.0000000000 0.0000000000 0 1.1568027 1.1568027 1.1568027 1 Cl 1.1568027 -1.1568027 -1.1568027 1 Cl -1.1568027 1.1568027 -1.1568027 1 Cl -1.1568027 -1.1568027 1.1568027 1 Cl END > From: Bruce Ravel <bravel(a)anl.gov> > Subject: Re: [Ifeffit] Possible bug in Artemis. > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <200601231845.59426.bravel(a)anl.gov> > Content-Type: text/plain; charset="iso-8859-1" > > On Monday 23 January 2006 17:47, joshua jason kas wrote: >> Hi, >> When I import a feff calculation, or run feff, the paths show up in >> artemis, but the description is garbled. What I mean is that the path >> description under Scattering Path which normally looks like >> >> [+] Cl [+] O ... >> >> looks like >> >> [+] <?> [+] <?> ... > > This looks like another version of a bug that has cropped up here and there. > The algorithm for generating the interpretation page parses the feff.inp file > and a couple of feff's output files. Every so often, someone throws a > hand-made feff.inp file at Artemis that works in feff but breaks the rather > crufty parser I wrote. > > If you can send me the feff.inp file that would help. The artemis project > file might help also, so send that along. Even if it is one that makes > Artemis do bad things when you try to read, I can still peak on the inside and > figure out what's going on. > > 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/ > > > > ------------------------------ > > Message: 2 > Date: Mon, 23 Jan 2006 20:18:42 -0500 > From: "TAO, Ye" <yetao(a)chem.uga.edu> > Subject: Re: [Ifeffit] Possible bug in Artemis. > To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <00f001c62084$1d8d28c0$3b05c080@RASD800> > Content-Type: text/plain; format=flowed; charset="iso-8859-1"; > reply-type=original > > Josh, > > Have a try to set the absorber coordinate as origin (0 0 0) in feff.inp, > then it should work. > > Ye > ----- Original Message ----- > From: "joshua jason kas" <hebhop(a)u.washington.edu> > To: <ifeffit(a)millenia.cars.aps.anl.gov> > Sent: Monday, January 23, 2006 6:47 PM > Subject: [Ifeffit] Possible bug in Artemis. > > >> Hi, >> When I import a feff calculation, or run feff, the paths show up in >> artemis, but the description is garbled. What I mean is that the path >> description under Scattering Path which normally looks like >> >> [+] Cl [+] O ... >> >> looks like >> >> [+] <?> [+] <?> ... >> >> and if I save the project file and reopen it, it can't >> I have attached a screenshot. >> Here is some info on my software >> 1) artemis 0.8.004 >> 2) ifeffit 1.2.8 >> 3) perl -e 'use Tk; print $Tk::VERSION,$/' gives 804.027 >> 4) perl v5.8.7 >> >> I tried updating Tk, and that works about as well as it always has on my >> system. Most of the tests passed, a few failed. >> This may be a problem with my version of Linux, or my version of perl/Tk. >> Anyway, any help would be much appreciated. >> Thank you very much, >> Josh Kas > > > -------------------------------------------------------------------------------- > > >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> > > > > ------------------------------ > > Message: 3 > Date: Tue, 24 Jan 2006 11:43:30 -0300 > From: "Renato Canha Ambrosio" <rcanha(a)ccet.ufrn.br> > Subject: [Ifeffit] RESTRAINTS IN IFEFFIT > To: ifeffit(a)millenia.cars.aps.anl.gov > Message-ID: <20060124142316.M21887(a)ccet.ufrn.br> > Content-Type: text/plain; charset=iso-8859-1 > > Hi Folks, this is my first message on the list. Perhaps someone could help > me. The subject is how to include restraints on exafs refinement. There is > just scanty information about this on the ifeffit reference manual. > > I'm trying to refine the exafs data of a rhombohedral perovskite. > > The main MS contributions to the signal at about 3.5 A (non phase correct) > arise from M � O � M interactions being M the absorber . We have a > significant SS path, a two-legged and a three-legged path. The structural > parameters of these three terms are correlated since all refers to the same > A-B-C triangle and the A-B and B-C distances must be that found for > M-O1 nearest-neighbor configurations. For these reasons > we constrained the photo electron path length for three-legged to the > M-O nearest-neighbor distance:R(three-leg = 2*RM-O). I'm trying to > intoroduce the quantity defined as delta = R(three-legged)-R(two-legged) > and thus define the SS half path length as a function of delta R(SS) = R > (three-legged) - 2*delta. I think it is a restraint not a constraint. > So I defined (def) the delta function on the line above the command FEFFIT > also delr for the SS path. I introduced the restraint in the line FEFFIT as > restraint = delrSS). The fit produce the same results as obtainde without > the definition of delta and delrSS (function of delta). > So I need to know how to introduce this restraint in the fit in order to > calculate de M - O - M bond angle (this angle should be calculated using > simple geometric relationships) - perhaps introduce the bond angle as a > restraint. > Someone can say me where I introduce the definitions of restraint parameters? > > Thank you very much for your kind attention > > Renato Canha > > Universidade Federal do Rio Grande doNorte > Departamento de Quimica > Natal - RN - BRAZIL > Open WebMail Project (http://openwebmail.org) > > > ---------- Original Message ----------- > From: ifeffit-request(a)millenia.cars.aps.anl.gov > To: ifeffit(a)millenia.cars.aps.anl.gov > Sent: Mon, 23 Jan 2006 12:00:13 -0600 > Subject: Ifeffit Digest, Vol 35, Issue 14 > >> 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: Re: I should be able to find this somewhere... (Bruce Ravel) >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Sun, 22 Jan 2006 16:58:07 -0600 >> From: Bruce Ravel <bravel(a)anl.gov> >> Subject: Re: [Ifeffit] Re: I should be able to find this somewhere... >> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >> Message-ID: <200601221658.07513.bravel(a)anl.gov> >> Content-Type: text/plain; charset="iso-8859-1" >> >> Hi, >> >> In fact, Artemis and Athena both attempt to deal correctly with input >> chi(k) data that is not on the expected grid. Both codes perform a >> test to see if the data is on the standard grid and, if not, >> front-loads the data with zeros and uses Ifeffit's boxcar rebinning >> function to put the data on the expected grid. >> >> Alas, there was a bug in the rebinning macro used by A&A which caused >> it to fail in a particular situation met by the data in Matthew's >> example. This bug will be fixed in the next release. >> >> If you import mu(E) data into Athena and then import data from the >> Athena project file into Artemis, you will never see the problem that >> Matthew reported. >> >> B >> >> On Tuesday 17 January 2006 16:09, Matt Newville wrote: >>> Hi Matthew, Bruce, >>> >>> OK, I think it's a bug. Well, maybe it's just a consequence of a >>> "known but not well advertised" problem. >>> >>> The chi(k) data you have doesn't start at k=0. By itself, this should >>> be OK, and the fit seems to be mostly fine. There seems to be a bug >>> in Ifeffit that the output fit chi(k) has the same number of data >>> points as the input chi(k) data. In this case is incorrect -- it >>> should go to the last data point in k. From looking at the code, I'm >>> pretty sure this has no effect on the fit and is only an error in the >>> output array. But the shortened chi_fit(k) will have an impact on the >>> way Bruce is calculating the residual. Even if that were fixed, the >>> residual would still be wrong, as the residual in Artemis is >>> calculated as >>> set(data0_res.k = data0.k) >>> set(data0_res.chi = data0.chi - data0_fit.chi) >>> >>> and then Fourier transforming to R-space. Since the data and fit >>> aren't aligned in k-space, the residual is incorrect. It should be >>> >>> set(data0_res.chi = data0.chi - interp(data0_fit.k, data0_fit.chi, >>> data0.k)) >>> >>> or some variation on that. >>> >>> Sorry for the trouble. It's definitely a result of narrow-mindedly >>> expecting that all chi(k) data comes from Ifeffit/Athena and will >>> always start at k=0. We should get this fixed (it's mostly there!) so >>> that data from other sources can be used. Right now, the easiest >>> work-around is to pre-pack the chi(k) data with zeros (starting from >>> k=0.00) >>> >>> --Matt >>> >>> _______________________________________________ >>> Ifeffit mailing list >>> Ifeffit(a)millenia.cars.aps.anl.gov >>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> >> -- >> 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/ >> >> ------------------------------ >> >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> >> End of Ifeffit Digest, Vol 35, Issue 14 >> *************************************** > ------- End of Original Message ------- > > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 35, Issue 16 > *************************************** >

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Possible bug in Artemis.
by joshua jason kas 23 Jan '06

23 Jan '06

Hi, When I import a feff calculation, or run feff, the paths show up in artemis, but the description is garbled. What I mean is that the path description under Scattering Path which normally looks like [+] Cl [+] O ... looks like [+] <?> [+] <?> ... and if I save the project file and reopen it, it can't I have attached a screenshot. Here is some info on my software 1) artemis 0.8.004 2) ifeffit 1.2.8 3) perl -e 'use Tk; print $Tk::VERSION,$/' gives 804.027 4) perl v5.8.7 I tried updating Tk, and that works about as well as it always has on my system. Most of the tests passed, a few failed. This may be a problem with my version of Linux, or my version of perl/Tk. Anyway, any help would be much appreciated. Thank you very much, Josh Kas

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Re: I should be able to find this somewhere...
by Bruce Ravel 22 Jan '06

22 Jan '06

On Friday 13 January 2006 20:25, you wrote: > By what factor is the residual multiplied when plotted in Artemis? I can't > find that figure quoted. > mam The residual is saved in k-space and Fourier transformed. 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: moving the legend in Athena
by Bruce Ravel 19 Jan '06

19 Jan '06

On Thursday 19 January 2006 14:05, Carlo Segre wrote: > When I plot data using athena, I would like to move the legend. How can I > do this? Go to the preferences, then to the plot branch. key_x and key_y are the xy coordinates of the upper left corner of the legend box. key_dy is the spacing between lines. The answer is the same for Artemis. 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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Enabling auto-updater for Artemis etc on startup (Windows)
by Simon Granville 19 Jan '06

19 Jan '06

Hello and Happy New Year all, my first of possibly many questions to this list (so please be gentle!) should hopefully be an easy one. When at Matt's iFEFFIT session in Melbourne at the start of December, I changed something in the updater.inifile (in the config directory of ifeffit) so that Artemis and Athena didn't attempt to look for updates when those programs are started. Of course I did this from a hint by Matt - now I'd quite like to reenable that auo-update and I don't know what to change. I know there's a newer version or two out there (my Artemis version is 0.8.002). Here's what my updater.ini file looks like [updater] next_checktime = tomorrow update_site = http://cars9.uchicago.edu/ifeffit/updates/ timestamp = 1137635213.22 http_proxy = timeout_connect = 60.0 timeout_download = 2400.0 Cheers, Simon. Simon Granville PhD student MacDiarmid Institute for Advanced Materials and Nanotechnology Victoria University of Wellington Wellington New Zealand

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