February 2006 - Ifeffit - millenia.cars.aps.anl.gov

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 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: 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 02 Feb '06

02 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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