April 2011 - Ifeffit - millenia.cars.aps.anl.gov

Re: [Ifeffit] Scripting - Python
by Andrew Korinda 21 Jul '11

21 Jul '11

Thanks for the help. Sorry it took so long to report back but I can only do must of my work on this on weekends. The corrected code worked great and I'm moving forward again. No message was given when the code wasn't working. Andy Korinda On Nov 1, 2010 1:55 PM, "Matt Newville" <newville(a)cars.uchicago.edu> wrote: Hi Andrew, On Mon, Nov 1, 2010 at 12:01 PM, Andrew Korinda <a-korinda(a)northwestern.edu> wrote: > I'm looking t... This is almost certainly due to space in the filename, and is really more of a problem with the fortran than python (or perl for that matter). That is, with a space in the file name, you should explicitly use read_data(file=...., group=...) This should work better:: import Ifeffit iff = Ifeffit.Ifeffit() ret = iff.ifeffit("read_data(file=C:\Program Files\Ifeffit\examples\Ifeffit\data\cu.xmu, group=c)") If it doesn't, let use know. > >From this experience I have some questions: > > ~First does anyone have some debugging tips for ... There should have been a printed message that might have altered you that the file hadn't been read in correctly: *** read_data: no file name given! was that message not given? > ~Secondly, Does anyone have any example Python scripts for Ifeffit > that they would like to shar... I sort of deliberately have left the base Ifeffit python module bare-bones. It would certainly be possible to add more functionality to that, or distribute add-on packages. It sort of depends what people would find desirable. I have many example scripts using Ifeffit + Python, mostly scripts, not documented, reliable code. Of course, there is also sixpack. I had some older GUIs as well. Would it be helpful to add some small examples on a wiki page? > ~Finally, would I be better off coding in Perl and using Demeter? That's a difficult question. The relative merits of Perl v Python are sort of a topic all on their own. For what it's worth, I believe (far) more people have used Python than Perl, but several very notable Ifeffit programs are written in Perl ;). --Matt PS: The next version of Ifeffit will be in python. Progress is slow, and when it will start to look like an EXAFS analysis program is a fair question. It probably shouldn't sway your decision much. _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.g...

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Bug in Athena merge preferences?
by Scott Calvin 28 Apr '11

28 Apr '11

Hi Bruce (and Ifeffiteers), I'm not positive this is a bug--maybe I'm just misunderstanding how the features are supposed to work. (It wouldn't be the first time!) In Athena 0.8.061 on a Mac running OS 10.5.8, I tried the following (I tried it in more than one project, to make sure it's not an intermittent bug): --Under Edit Preferences/Merge/Merge_Weight, choose "n" and apply to future sessions --Close Athena and reopen --Open a project --Mark two data sets. --Change the "importance" of one of them. --Under the merge menu, choose "weight by importance." --Under the merge menu, "merge marked data in chi(k)" The result for me is that the merged file ignores the importance I've assigned. I've also tried it in mu(E), with the same result. It seems that perhaps the "n" value in the preferences overrides the "weight by importance" option in the menu? If so, that's not the way I expect preferences and menu options to interact. Trying it with applying the "n" only to the current session also has an interesting behavior, although not necessarily the "wrong" one: it seems to just change the radio button in the menu. Also, if I change the radio button in the menu directly, the option under Preferences changes to match. For the current session, I can understand the argument that this is a reasonable behavior. But it is likely to cause confusion if a user changes it in the menu and then tries to use the preferences to check what the future sessions value is set to--if they haven't previously changed the preferences directly during the session, they might naturally assume that the value there is the value for future sessions, but in reality it just represents the most recent menu choice they made, and could be different in a future session. My suggested fix to both issues: the preferences should control what value the radio button takes on when Athena is first opened, and changes to the preferences should cause an immediate change to the status of the radio button. Subsequent changes to the radio button should not change the value under the preferences. And the behavior of the merge function should always reflect the current value of the radio button. --Scott Calvin Sarah Lawrence College

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GAANN Fellowships
by Carlo Segre 27 Apr '11

27 Apr '11

Dear All: Illinois Institute of Technology still has some GAANN Fellowships available in Physics and specifically for students interested in synchrotron radiation research. More information is available at http://www.iit.edu/research/undergraduate_research/news/gaan_award.shtml Note that the deadlines are not in force at this time, we will still accept applications. Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Graduate Admissions, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre(a)iit.edu http://phys.iit.edu/~segre segre(a)debian.org

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Re. Cofigurationally averaged EXAFS from MD
by Marcus Karolewski 22 Apr '11

22 Apr '11

> From: Francisco Garcia <garcia.ff.000(a)gmail.com> > I want to compute the ?average EXAFS spectra? using 500 snapshots of > atomic coordinates from my MD simulations. Dear Francisco and others, I am still exploring this area myself, but as suggested by Matt Newville, the best approach probably is to search through the MD configuration file for each absorber atom, generate its feff.inp file (based on a neighbour list), then execute FEFF and add the resulting chi(k) to an accumulator. I have a Windows program that will do this for a system with up to 3 atom types (e.g. O, Zn, H only) for both FEFF 7 and 8. It is easy to use, but does not recognize bonds that cross periodic boundaries. It is thus necessary to specify a central region of interest that is representative of the "bulk" of the system. This could be a problem if you have used a small MD simulation cell. Typically 10,000 absorbers require about 1 day of execution time, so doing 500 snapshots should be fairly easy. This is not the end of the fitting problem, unfortunately. Before making a comparison of the "synthetic" XAFS spectrum with experimental data, you need to fit E0 and S02. FEFF cannot necessarily calculate these accurately, but they have no bearing on the accuracy of your MD structural model. I feel that the E0 and S02 fits are best done using experimental standards. Attempting to fit them without knowledge of structure (e.g. by alignment-type operations between experimental and MD data) produces only approximate values - such fits also attempt to compensate, inappropriately, for any MD-related errors. After adjusting the MD-XAFS spectra for E0 and S02, you will likely find that the R-space peaks differ significantly from the experimental values in terms of position, height and width. Assuming your snapshots are representative of the canonical distribution, these remaining differences reflect the limitations of the potential. The structural sensitivity of XAFS is such that even quite small differences between potentials (e.g. cut-off distance) can produce visibly significant results. There are at least 2 ways to compare the experimental and (adjusted) MD XAFS spectra. (a) Visible or least-squares comparison of the spectra (in the R range of interest). (b) Direct extraction of cumulants from the MD data (by statistical analysis of atoms in the same region used to generate the XAFS), which are then used (with the inclusion of global scaling factors for dR and C2) to fit/reconstruct the experimental spectrum in Artemis (good MD data should produce not only good fits, but also scale factors near 1.0). Please contact me directly if you are interested to discuss further, or in using the code. I have glossed over some minor details (e.g. input data format, FEFF versions, chik.dat quirks, how to extract cumulants). Regards, Marcus Karolewski Message: 2 Date: Mon, 11 Apr 2011 13:18:04 -0700 From: Francisco Garcia <garcia.ff.000(a)gmail.com> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Strategy to obtain cofigurationally averaged EXAFS from MD simulations Message-ID: <BANLkTinqbsgn6_JL_iVTcL1dfN39g1_Pig(a)mail.gmail.com> Content-Type: text/plain; charset=windows-1252 Dear users, I want to compute the ?average EXAFS spectra? usin 500 snapshots of atomic coordinates from my MD simulations. The idea is to compute the EXAFS spectra for each snapshot and then average the spectra over all snapshots (the so-called "MD EXAFS" approach). I know how to use Artemis to generate the EXAFS spectrum of a single snapshot. However, generating the EXAFS data for each of the 500 snapshots individually will be too time consuming and messy (this is essentially a book-keeping approach). I was wondering if there is a time-saving strategy/script for computing the average EXAFS instead of the snapshot-by-snapshot approach. For example, is it possible to include the coordinates of all the snapshots in a single feff.inp file and feed it to Artemis? Or if I have the feff.inp file for each snapshot, is it possible to write a script for Artemis that will compute each EXAFS spectra individually and dump them in a specified directory? Thank you very much.

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Re: [Ifeffit] Peak fitting to XANES data
by Bruce Ravel 21 Apr '11

21 Apr '11

Hi Zhixi, I am responding to your question on the Ifeffit mailing list (http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit) which is the appropriate venue for questions about the software. I encourage you to join the mailing list and use it for future questions about XAS or the use of our software. As for your questions, there are at least two options. The button labeled "Write a log file" actually exports a column data file with the results of the fit in the header and columsn of data containing the data, the fit, and each of the lineshapes. This file can be imported easily into Origin or most any other plotting program. The header also provides the parameters and formulas of the lineshapes, so you can easily replicate the fitted functions. The other option is that the tab labeled has the parameter values from the fit, so you can use those to replicate the line shapes. HTH, B On Thursday, April 21, 2011 11:04:10 am you wrote: > Good morning, > > Thank you for your attention. I use the peak fitting to some XANES data > using an arc-tangent and a Lorentzian. I got the fitting results and > analytical line shapes at Graphics Window #1, i.e. fit, step, peak 1. I > want to obtain the data of these lines, but I did not find the method. I > have no idea about this problem because I have to use the data in Origin > soft. > > Thank you for your help. > > Sincerely, > > Zhixi Zhao > Institute of Applied Ecology -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

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Fwd: atoms.inp Mn3O4
by Bruce Ravel 20 Apr '11

20 Apr '11

Angelika, As you can see, I am responding to this email via the Ifeffit mailing list, which is the appropriate venue for questions about the software. It seems as though you took the crystal data from Matt's Atoms.inp database. It was not our intention to vouch for all the data you find there. Caveat lector, and all that. That particular file was something I converted from a public database from American Mineralogist. The citation for those data are included in the atoms.inp file. There are several CIF files for Mn3O4 available from http://www.crystallography.net/. I'm afraid that I am not clear what is wrong with the feff.inp file you attached. It looks like a plausible structure to me, although I am not particularly familiar with what Mn3O4 should look like. Perhaps someone else on the list is familiar with this material and can help Angelika better than I can .... Regards, B ---------- Forwarded Message ---------- Subject: atoms.inp Mn3O4 Date: Wednesday, April 20, 2011, 12:33:37 pm From: "Frau Dr. A. Chasse" <angelika.chasse(a)physik.uni-halle.de> To: bravel(a)bnl.gov Dear prof. Ravel, I have used atoms.f to produce a file for calculations af O K-edge XAS of Mn3O4 with the attached input file. I my opinion the constructed structure is not correct. I have also tried the file with shift, but no improvement. Look for the first two Mn atoms! If you look in feff.inp, you do not see the tetraeder of Mn atoms around O, which we should see in the spinel-like structure. May be you can help me. With best regards, Angelika Chasse -- , PD Dr. Angelika Chasse Martin-Luther-Universität Halle-Wittenberg Naturwissenschaftliche Fakultät II Institut für Physik D-06099 Halle (Saale) Telefon: +49 (0)345 55 25436 Telefax: +49 (0)345 55 25446 Email : angelika.chasse(a)physik.uni-halle.de ----------------------------------------- -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/ title name: Mn3O4 hausmannite title formula: Mn3O4 title sites: Mn1--2,O1 title refer1: Baron V, Gutzmer J, Rundlof H, Tellgren R title refer2: American Mineralogist 83 (1998) 786-793 title schoen: D_4h^19 space I 41/a m d a = 5.7691 b = 5.7691 c = 9.4605 rmax = 6.00 core = O1 atom Mn 0.00000 0.75000 0.12500 Mn1 Mn 0.00000 0.00000 0.50000 Mn2 O 0.00000 0.47230 0.25920 O1 ------ * This feff.inp file generated by ATOMS, version 2.50 * ATOMS written by and copyright (c) Bruce Ravel, 1992-1999 * Space group "I 41/A M D" may be referenced to a different origin. * If the atom list seems incorrect, put this line in your input file * shift 0 0.25 -0.125 * and run atoms again.- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * * total mu = 22991.6 cm^-1, delta mu = 22978.8 cm^-1 * specific gravity = 4.827, cluster contains 77 atoms. * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * * mcmaster corrections: 0.00766 ang^2 and 0.365E-04 ang^4 * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * TITLE name: Mn3O4 hausmannite TITLE formula: Mn3O4 TITLE sites: Mn1--2,O1 TITLE refer1: Baron V, Gutzmer J, Rundlof H, Tellgren R TITLE refer2: American Mineralogist 83 (1998) 786-793 TITLE schoen: D_4h^19 EDGE K S02 1.0 * pot xsph fms paths genfmt ff2chi CONTROL 1 1 1 1 1 1 PRINT 1 0 0 0 0 0 * r_scf [ l_scf n_scf ca ] SCF 4.25031 0 15 0.1 * ixc [ Vr Vi ] EXCHANGE 0 0 0 EXAFS RPATH 8.50062 * kmax [ delta_k delta_e ] *XANES 4.0 0.07 0.5 * r_fms [ l_fms ] *FMS 4.25031 0 * *RPATH 0.10000 * emin emax resolution *LDOS -20 20 0.1 POTENTIALS * ipot z [ label l_scmt l_fms stoichiometry ] 0 8 O -1 -1 0 1 25 Mn -1 -1 3 2 8 O -1 -1 4 ATOMS 0.00000 0.00000 0.00000 0 O1 0.00000 1.44228 -1.28247 -0.08704 1 Mn2 1.93196 -1.44228 -1.28247 -0.08704 1 Mn2 1.93196 0.00000 1.60208 -1.26960 1 Mn1 2.04415 0.00000 0.15980 2.27809 1 Mn2 2.28369 0.00000 -2.56494 0.00000 2 O1 2.56494 -1.28247 -1.28247 2.19105 2 O1 2.84432 1.28247 -1.28247 2.19105 2 O1 2.84432 2.88455 0.00000 -0.17407 2 O1 2.88980 -2.88455 0.00000 -0.17407 2 O1 2.88980 1.28247 1.60208 2.36512 2 O1 3.13133 -1.60208 -1.28247 -2.36513 2 O1 3.13133 1.60208 -1.28247 -2.36513 2 O1 3.13133 -1.28247 1.60208 2.36512 2 O1 3.13133 0.00000 3.20416 0.00000 2 O1 3.20416 1.60208 1.60208 -2.53920 2 O1 3.40306 -1.60208 1.60208 -2.53920 2 O1 3.40306 2.88455 1.60208 1.09553 1 Mn1 3.47670 -2.88455 1.60208 1.09553 1 Mn1 3.47670 0.00000 -2.72475 2.27809 1 Mn2 3.55161 2.88455 0.15980 -2.45216 1 Mn2 3.78936 -2.88455 0.15980 -2.45216 1 Mn2 3.78936 0.00000 3.04435 2.27809 1 Mn2 3.80234 0.00000 -1.28247 -3.63472 1 Mn1 3.85434 2.88455 -2.56494 -0.17407 2 O1 3.86392 -2.88455 -2.56494 -0.17407 2 O1 3.86392 -2.88455 3.20416 -0.17407 2 O1 4.31481 2.88455 3.20416 -0.17407 2 O1 4.31481 0.00000 -4.16702 -1.26960 1 Mn1 4.35614 -4.32683 -1.28247 -0.08704 1 Mn2 4.51373 4.32683 -1.28247 -0.08704 1 Mn2 4.51373 0.00000 0.31961 4.55618 2 O1 4.56737 -2.88455 -2.72475 -2.45216 1 Mn2 4.66454 2.88455 -2.72475 -2.45216 1 Mn2 4.66454 2.88455 -1.28247 3.46065 1 Mn1 4.68417 -2.88455 -1.28247 3.46065 1 Mn1 4.68417 -1.44228 4.48663 -0.08704 1 Mn2 4.71355 1.44228 4.48663 -0.08704 1 Mn2 4.71355 -2.88455 3.04435 -2.45216 1 Mn2 4.85817 2.88455 3.04435 -2.45216 1 Mn2 4.85817 0.00000 0.31961 -4.90432 2 O1 4.91473 -4.16702 -1.28247 -2.36513 2 O1 4.96010 1.28247 -4.16702 2.36512 2 O1 4.96010 4.16702 -1.28247 -2.36513 2 O1 4.96010 -1.28247 -4.16702 2.36512 2 O1 4.96010 -1.44228 1.60208 4.64321 1 Mn2 5.11920 1.44228 1.60208 4.64321 1 Mn2 5.11920 -4.16702 1.60208 -2.53920 2 O1 5.13598 4.16702 1.60208 -2.53920 2 O1 5.13598 -1.60208 -4.16702 -2.53920 2 O1 5.13598 1.60208 -4.16702 -2.53920 2 O1 5.13598 1.28247 4.48663 2.19105 2 O1 5.15512 -4.48663 -1.28247 2.19105 2 O1 5.15512 4.48663 -1.28247 2.19105 2 O1 5.15512 -1.28247 4.48663 2.19105 2 O1 5.15512 -2.88455 -4.16702 1.09553 1 Mn1 5.18506 2.88455 -4.16702 1.09553 1 Mn1 5.18506 1.44228 1.60208 -4.81729 1 Mn2 5.27760 -1.44228 1.60208 -4.81729 1 Mn2 5.27760 4.48663 1.60208 2.36512 2 O1 5.31886 -1.60208 4.48663 -2.36513 2 O1 5.31886 1.60208 4.48663 -2.36513 2 O1 5.31886 -4.48663 1.60208 2.36512 2 O1 5.31886 0.00000 -2.88455 4.55618 2 O1 5.39253 0.00000 2.88455 4.55618 2 O1 5.39253 -2.88455 0.31961 4.73025 2 O1 5.54960 -2.88455 0.31961 -4.73025 2 O1 5.54960 2.88455 0.31961 -4.73025 2 O1 5.54960 2.88455 0.31961 4.73025 2 O1 5.54960 0.00000 -2.88455 -4.90432 2 O1 5.68973 0.00000 2.88455 -4.90432 2 O1 5.68973 5.76910 0.00000 0.00000 2 O1 5.76910 0.00000 -5.76910 0.00000 2 O1 5.76910 0.00000 5.76910 0.00000 2 O1 5.76910 -5.76910 0.00000 0.00000 2 O1 5.76910 0.00000 4.48663 -3.63472 1 Mn1 5.77417 0.00000 -1.28247 5.82578 1 Mn1 5.96527 END

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Looking for reviewers for another chapter
by Scott Calvin 19 Apr '11

19 Apr '11

Hi all, I have completed the draft of another chapter of my textbook, and am again interested in reviewers (repeat reviewers are fine!). The chapter I've currently got ready is about the parameters of the EXAFS equation, covering physical meaning, effect on graphs, a bit on common constraint schemes, etc.. This will be chapter 10 in the book, and so it's not suitable for absolute beginners. I am interested, though, in hearing from people who are still learning to fit, as well as experts. If you are interested in reviewing the chapter and can get feedback back to me by 4 May, please contact me directly at SCalvin(a)slc.edu . --Scott Calvin Sarah Lawrence College

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Re: [Ifeffit] Problem with running FEFF in Artemis
by Jatinkumar Rana 15 Apr '11

15 Apr '11

On 15.04.2011 17:29, ifeffit-request(a)millenia.cars.aps.anl.gov wrote: Dear Bruce, Thank you very much for your reply. The feff.inp file with shift (0,0,0) is quite right. I was just alarmed by that message everytime i ran ATOMS. But it is clear now. :-) Thanks a lot. With best regards, Jatin Rana Berlin -- Jatinkumar Rana Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Institut für angewandte Materialforschung FI-1 Mikrostruktur Hahn-Meitner-Platz 1 D-14109 Berlin Germany Tel: +49 30 8062-43217 Fax: +49 30 8062-43059 eMail: jatinkumar.rana(a)helmholtz-berlin.de **************************************************************************************** Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Vorsitzender des Aufsichtsrats: Prof. Dr. Dr. h.c. mult. Joachim Treusch Stellvertretende Vorsitzende: Dr. Beatrix Vierkorn-Rudolph Geschäftsführer: Prof. Dr. Anke Rita Kaysser-Pyzalla, Prof. Dr. Dr. h.c. Wolfgang Eberhardt, Dr. Ulrich Breuer Sitz der Gesellschaft: Berlin Handelsregister: AG Charlottenburg, 89 HRB 5583

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Soft XAS PhD studentship at the University of Manchester
by Sven Schroeder 15 Apr '11

15 Apr '11

Dear colleagues I would be grateful if you could bring the following PhD opportunity in soft XAS of crystal nucleation from solution to the attention of potential candidates: http://www.jobs.ac.uk/job/ACJ915/4-phd-studentships-available-at-leeds-manc… ================================= Applications close on 16 May 2011 ================================= Background information about the project is available here: http://gow.epsrc.ac.uk/ViewGrant.aspx?GrantRef=EP/I013563/1 and here: http://gow.epsrc.ac.uk/ViewGrant.aspx?GrantRef=EP/I014446/1 Interested candidates can also contact me directly by email. -- Dr Sven L.M. Schroeder (mailto:s.schroeder@manchester.ac.uk) Reader School of Chemical Engineering and Analytical Science (CEAS) The University of Manchester, Manchester M13 9PL, United Kingdom http://www.slmslab.info Also at: School of Chemistry, The University of Manchester, Manchester M13 9PL, United Kingdom Tel +44 (161) 306 4502 Fax +44 (161) 306 8867 Office: Room C57 (Jackson's Mill) DISCLAIMER The views expressed within this message are those of the sender, not those of The University of Manchester or one of its units. While all emails and attachments are scanned for viruses before sending, we cannot accept any responsibility for viruses, so please scan all emails and attachments. This email is intended for the addressee only. If you are not the intended recipient, please notify the sender and delete this email immediately. END OF MESSAGE

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Problem with running FEFF in Artemis
by Jatinkumar Rana 15 Apr '11

15 Apr '11

Dear Ifeffit users, I am facing a strange problem in running ATOMS for the "F d-3 m" space group. It gives me following message : "F d -3 m" appears in the International Tables with multiple choices of origin. If the atoms list seems wrong, you should use a shift vector of: -0.125, -0.125, -0.125 After i add shift vector on ATOMS page and run FEFF in ARTEMIS, it gives me error and shows that many pairs of atoms are close together. The crystallographic data used to run FEFF were obtained using Neutron diffraction experiments. I do not understand the reason for this since i have never come across such a problem. Can anyone help me to comeout of this problem ? I have attached the Artemis project file with this mail for further detail. With best regards, Jatin Rana Berlin -- Jatinkumar Rana Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Institut für angewandte Materialforschung FI-1 Mikrostruktur Hahn-Meitner-Platz 1 D-14109 Berlin Germany Tel: +49 30 8062-43217 Fax: +49 30 8062-43059 eMail: jatinkumar.rana(a)helmholtz-berlin.de **************************************************************************************** Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Vorsitzender des Aufsichtsrats: Prof. Dr. Dr. h.c. mult. Joachim Treusch Stellvertretende Vorsitzende: Dr. Beatrix Vierkorn-Rudolph Geschäftsführer: Prof. Dr. Anke Rita Kaysser-Pyzalla, Prof. Dr. Dr. h.c. Wolfgang Eberhardt, Dr. Ulrich Breuer Sitz der Gesellschaft: Berlin Handelsregister: AG Charlottenburg, 89 HRB 5583

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