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

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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