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

update for Windows, fixing problems with Athena/Artemis
by Matt Newville 01 Oct '08

01 Oct '08

Hi Folks, I just put up a Windows updater with new versions of Athena and Artemis which (should / seems to) fix the "Athena is stuck" problems seen be various people. Details on what else changed are below. All windows users with Ifeffit 1.2.10 and 1.2.11 should install this update. If you're still using an older version, beware that this update will be binary incompatible with that version, and you should upgrade to 1.2.11 before installing this update. If you've been having troubles with Athena/Artemis "getting stuck" and these persist after installing this update, please let us know!! --Matt =========== This update to Ifeffit 1.2.11 for Windows corrects several problems with the prior release related to building the Athena et al executables against the wrong version of the Ifeffit library. This update includes newly rebuilt executables for Athena, Artemis, Hephaestus, and Atoms. Additionally, the following features have been added to Athena: 1. Filename are sorted when importing multiple files. 2. Corrected a problem related to importing chi(k) data that do not start at 0. 3. Filetype plugins have been added for: - SSRL binary files - SSRL ASCII files - SSRL MicroEXAFS files - files from the CLS HXMA beamline - files from Photon Factory beamline 12C Enjoy! Bruce Ravel 25 Sep. 2008 ===========

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Broadening
by Eugenio Otal 01 Oct '08

01 Oct '08

Hello everybody, I have a doubt about the LDOS broadening, in xmu.dat I found that core-hole broadening is 4.163, which value should I use in LDOS broadening to reproduce the experimental spectra. Thanks, euG

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Independence of scattering paths?
by van der Veen Renske 01 Oct '08

01 Oct '08

Hello! I have a question concerning the independence of scattering pathways. I fitted the EXAFS signal of a molecule consisting of 30 atoms (the related FEFF calculation is called calc 1). To see the effect of the surrounding solvent molecules in the chi(k) data, I added an O-atom in the coordinate list of the FEFF input file at an arbitrary distance from the absorbing atom (in this case Pt) and I re-ran FEFF (calc 2). As a check within calc 2, I generated the sum of the same scattering paths that were used in the fitting model of calc 1 using the therein obtained structural fit parameters. The new O-atom was not included in this sum. I expected the sum within calc 2 to be identical to the fit of calc 1 based on the fact that the original atoms can not sense the presence of the new O-atom (independence of scattering paths). BUT: the resulting sum was significantly different from the fit! Am I overlooking something here? Aren't the calculated backscatter amplitudes and phases independent from each other? I am using Artemis version 0.8.007, Windows XP, Ifeffit 1.2.9. Thank you! Best regards, Renske Renske M. van der Veen PhD student EPFL / PSI Paul Scherrer Institut Swiss Light Source WSLA/210 5232 Villigen PSI Switzerland Phone: +41 56 310 5362 Fax: +41 56 310 3151 E-mail: renske.vanderveen(a)psi.ch Web: http://lsu.epfl.ch http://femto.web.psi.ch

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Re: [Ifeffit] Independence of scattering paths? (van der Veen Renske)
by Frommer Jakob 30 Sep '08

30 Sep '08

Hi Renske, I am not sure whether I fully understand your question but here is my *two-cent-explanation*: FEFF's first step is to calculate the potentials - since it is a real space code based on the muffin-tin approximation the surrounding of an atom determines the actual scattering potential (even if you are not doing a self-consistent calculation). Since the potentials in turn determine the backscattering amplitudes and phase shifts, placing an additional atom randomly in a structure is certainly not a good idea. A possible work-around may be to find a *similar* (but known) structure with oxygen ligands and combine these two calculations in artemis (for multiple scattering however the geometry can matter a lot). If your solvent contains oxygen already you may (at least as a first approximation and for single scattering) just duplicate that path in artemis. Regards Jakob ___________________________________________________ Jakob Frommer Soil Chemistry Group Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich Universitätstrasse 16, CHN F19 CH - 8092 Zürich Tel: +41 44 632 87 58 Fax: +41 44 633 11 18 web: http://www.ibp.ethz.ch/research/soilchemistry

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plot linetypes option in athena windows version
by Malte Schulz 22 Sep '08

22 Sep '08

Hi there, I would like to export graphics from Athena to use them in my b&w printed thesis. Therefore it would be really useful to have Athena cycle through linetypes instead of colors. I found the "linetypes" option in the "plot" section of the preferences menu. However it doesn't seem to have any effect. I am using Athena v. 0.8.056 for windows. Malte

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export from large Athena projects
by shiryaev＠crys.ras.ru 19 Sep '08

19 Sep '08

Hi, It seems that there is a problem in exporting normalised data files from large (i.e. >10 curves) Athena projects: Exported data are cut in energy. When one exports the files one by one, this problem does not occurs. All the best, Andrei

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[ATOMS] supercell input file
by Mauro Rovezzi 19 Sep '08

19 Sep '08

Dear all, I would like to submit to your attention a problem with Atoms that I still do not understand. What I would like to do is to generate a FEFF input file starting from a supercell, that is repeating the unit cell NXxNYxNZ times and create the crystal with the resulting box. An example is given in the attached _test-atoms.inp_ created following this procedure: from wurtzite GaN (a,c cell parameters) that we describe with 2 atoms I reduce the symmetry and I use 4 atoms, then I create a 72 atoms supercell - 4*(3x3x2) - that has 3ax3ax2c dimensions and finally I tell atoms to use "P1" space group in order to replicate the supercell in x,y,z space and shift at the center the absorbing atom. Here the *problem*: the resulting _test-feff8.inp_ present good values of distances but strangely it has generated an additional Fe potential (there is just 1 Fe absorbing atom in the box/list). This is annoying because I have to remove manually the wrong "ipot" to run FEFF. Is it a stupid mistake generating the Atoms input file or is it an odd behaviour? Cheers, Mauro PS: Atoms 3.0.1 (linux) 05/08/15 PPS: Do not pay attention to coordinates and distances, these are just test-files! -- Mauro Rovezzi <rovezzi(a)esrf.fr> PhD student - GILDA BM08 c/o ESRF (Grenoble, FR)

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XANES peak fitting
by Dominik Samuelis 18 Sep '08

18 Sep '08

Dear Jenny, although it doesn't exactly look like the software in your attached word file (this probably is some special XPS instrument software), peak fitting can very nicely be done with the Athena program (Analysis -> Peak fit). It's got all the features that you'd expect from a peak fitting software (difference plot, component plot, the possibility to fix certain values, and an almost arbitrary number of gaussians :-) ). If you are not restricted to the ifeffit package, the Peak Fitting Module in OriginLab's Origin Pro also produces nice results. It's not free software, though. Cheers, dominik Am 18.09.2008 um 21:45 schrieb ifeffit- request(a)millenia.cars.aps.anl.gov: > From: Jenny Cai <jennyh_cai(a)yahoo.ca> > Subject: [Ifeffit] XANES peak fitting > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <407251.2113.qm(a)web88208.mail.re2.yahoo.com> > Content-Type: text/plain; charset="us-ascii" > > Hi guys, > > Could anyone tell me which software in Ifeffit package can do peak > fitting like the one shown in the attached file? > > Thank you in advance! > > Jenny Cai > -- Dr. Dominik Samuelis d.samuelis(a)fkf.mpg.de Max-Planck-Institut für Festkörperforschung Heisenbergstr. 1 70569 Stuttgart Germany Phone +49-711-689-1769 Fax +49-711-689-1722 Web http://www.fkf.mpg.de/maier/

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Re: [Ifeffit] CFAVERAGE CARD
by joshua jason kas 18 Sep '08

18 Sep '08

Hi Cammelli, feff8 is hard coded to accept only 1000 atoms or less. The error message is not very informative and I don't think it applies to your case. What you want to do is recompile change the parameter natx in the source code to something larger, maybe 3000, and recompile. If you do not have the source code, you can find it at the feff webpage with the same username and password that was used to obtain your executable. Cheers, Josh Kas On Thu, 18 Sep 2008, ifeffit-request(a)millenia.cars.aps.anl.gov wrote: > 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. CFAVERAGE CARD (Cammelli Sebastiano) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 18 Sep 2008 15:59:43 +0200 > From: "Cammelli Sebastiano" <Sebastiano.Cammelli(a)psi.ch> > Subject: [Ifeffit] CFAVERAGE CARD > To: <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: > <AD99CE4B84C4D3468F69B0E4FB345D58048FE174(a)MAILBOX0A.psi.ch> > Content-Type: text/plain; charset="us-ascii" > > Dear Iffefit user > > I have a question about CFAVERAGE card used in FEFF8.4 for EXAFS > simulations. > > I need to simulate a cluster with 1481 atoms, let's say in a first > moment, composed of only Cu atoms. > > Without this card the simulations crashed and it was suggested to "Use > or reduce rclabs in CFAVERAGE card Or increase parameter natx and > recompile". > > I tried with different indexes: > > CFAVERAGE 1 -1 7 > > CFAVERAGE 0 -1 6... > > I could run EXAFS simulations but I could not get xmu.dat. > > FEFF8.4 works perfectly when <1000 atoms are involved (and CFAVERAGE is > NOT used). But how could I simulate larger clusters (with more then > 1000atoms)? > > Here I send you a copy of the feff.inp, I do not write here below all > the atoms between the 1st and the 37th shell because I do not want to > make this mail too large, but I attach the original file. > > > > TITLE A > > *cluster 1481 atoms > > CONTROL 1 1 1 1 1 1 > > PRINT 0 0 0 0 0 0 > > RMULTIPLIER 1 > > LDOS -30 20 0.2 > > EDGE K > > S02 1.0 > > SCF 4 0 30 0.2 1 > > NLEG 5 > > DEBYE 15 343 0 > > EXAFS > > RPATH 10.0 > > POTENTIALS > > 0 29 Cu 3 3 0.0010 > > 1 29 Cu 3 3 1.0 > > > > ATOMS * this list contains 1481 atoms > > * x y z ipot tag distance > > 0.00000 0.00000 0.00000 0 Cu_1 0.00000 > > 1.80753 1.80753 0.00000 1 Cu_1 2.55623 > > -1.80753 1.80753 0.00000 1 Cu_1 2.55623 > > 1.80753 -1.80753 0.00000 1 Cu_1 2.55623 > > -1.80753 -1.80753 0.00000 1 Cu_1 2.55623 > > 1.80753 0.00000 1.80753 1 Cu_1 2.55623 > > -1.80753 0.00000 1.80753 1 Cu_1 2.55623 > > 0.00000 1.80753 1.80753 1 Cu_1 2.55623 > > 0.00000 -1.80753 1.80753 1 Cu_1 2.55623 > > 1.80753 0.00000 -1.80753 1 Cu_1 2.55623 > > -1.80753 0.00000 -1.80753 1 Cu_1 2.55623 > > 0.00000 1.80753 -1.80753 1 Cu_1 2.55623 > > 0.00000 -1.80753 -1.80753 1 Cu_1 2.55623 > > .... > > 3.61505 9.03763 -12.65268 1 Cu_37 15.96364 > > -3.61505 9.03763 -12.65268 1 Cu_37 15.96364 > > 9.03763 -3.61505 -12.65268 1 Cu_37 15.96364 > > -9.03763 -3.61505 -12.65268 1 Cu_37 15.96364 > > 3.61505 -9.03763 -12.65268 1 Cu_37 15.96364 > > -3.61505 -9.03763 -12.65268 1 Cu_37 15.96364 > > END > > > > > > Best > > Sebastiano Cammelli > > > >

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CFAVERAGE CARD
by Cammelli Sebastiano 18 Sep '08

18 Sep '08

Dear Iffefit user I have a question about CFAVERAGE card used in FEFF8.4 for EXAFS simulations. I need to simulate a cluster with 1481 atoms, let's say in a first moment, composed of only Cu atoms. Without this card the simulations crashed and it was suggested to "Use or reduce rclabs in CFAVERAGE card Or increase parameter natx and recompile". I tried with different indexes: CFAVERAGE 1 -1 7 CFAVERAGE 0 -1 6... I could run EXAFS simulations but I could not get xmu.dat. FEFF8.4 works perfectly when <1000 atoms are involved (and CFAVERAGE is NOT used). But how could I simulate larger clusters (with more then 1000atoms)? Here I send you a copy of the feff.inp, I do not write here below all the atoms between the 1st and the 37th shell because I do not want to make this mail too large, but I attach the original file. TITLE A *cluster 1481 atoms CONTROL 1 1 1 1 1 1 PRINT 0 0 0 0 0 0 RMULTIPLIER 1 LDOS -30 20 0.2 EDGE K S02 1.0 SCF 4 0 30 0.2 1 NLEG 5 DEBYE 15 343 0 EXAFS RPATH 10.0 POTENTIALS 0 29 Cu 3 3 0.0010 1 29 Cu 3 3 1.0 ATOMS * this list contains 1481 atoms * x y z ipot tag distance 0.00000 0.00000 0.00000 0 Cu_1 0.00000 1.80753 1.80753 0.00000 1 Cu_1 2.55623 -1.80753 1.80753 0.00000 1 Cu_1 2.55623 1.80753 -1.80753 0.00000 1 Cu_1 2.55623 -1.80753 -1.80753 0.00000 1 Cu_1 2.55623 1.80753 0.00000 1.80753 1 Cu_1 2.55623 -1.80753 0.00000 1.80753 1 Cu_1 2.55623 0.00000 1.80753 1.80753 1 Cu_1 2.55623 0.00000 -1.80753 1.80753 1 Cu_1 2.55623 1.80753 0.00000 -1.80753 1 Cu_1 2.55623 -1.80753 0.00000 -1.80753 1 Cu_1 2.55623 0.00000 1.80753 -1.80753 1 Cu_1 2.55623 0.00000 -1.80753 -1.80753 1 Cu_1 2.55623 .... 3.61505 9.03763 -12.65268 1 Cu_37 15.96364 -3.61505 9.03763 -12.65268 1 Cu_37 15.96364 9.03763 -3.61505 -12.65268 1 Cu_37 15.96364 -9.03763 -3.61505 -12.65268 1 Cu_37 15.96364 3.61505 -9.03763 -12.65268 1 Cu_37 15.96364 -3.61505 -9.03763 -12.65268 1 Cu_37 15.96364 END Best Sebastiano Cammelli

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