June 2014 - Ifeffit - millenia.cars.aps.anl.gov

Crystallographic input for a structure having screw axis and co-ordinates shifted by certain amount
by madhusmita sahoo 12 Jun '14

12 Jun '14

Dear Members, I would like to know, *Q1)* If there is a screw axis in the system, like the anatase phase of TiO2, whose space group is I41/amd, how should I enter that in the atoms for feff calculation. Kindly tell me which is the correct way. When I entered 141(the space group number) and I41/amd, both generated separate set of atomic positions. The older version of artemis, now the new one(latest version), both generates different set of atomic position with the same crystallographic input, i.e if I enter 141(or I41/amd) in place of space group and run atoms, it generates two different set of co-ordinates in Artemis 0.8.012 and in Demeter 0.9.18. Ideally this should be same. *Q2)* And when co-ordinates is shifted by certain amount, do we have to enter that in the shift vector as well as while defining the (x y z) of a particular site. Or I should just enter the shift vector and define the co-ordinates at its usual position ( I feel this one is correct). For example in anatase crystal structure the co-ordinates are shifted by (0,0.25,-0.125). So, the inputs can be For shift vector 0,0.25,-0.125 and in place of sites Ti(core) x=0, y=0, z= 0 and O (scatterer) x= 0, y=0, z=0.20806 (Or) shift vector 0,0,0 and in place of sites Ti(core) x=0, y=0.25, z= -0.125 and O (scatterer) x= 0, y=0.25, z=0.08160 Ideally both should give the same result. But it gives different set of atomic positions. Even the same input in different version of artemis is yielding different results(in Artemis 0.8.012 and in Demeter 0.9.18) . I am confused about how atoms work in artemis. I request you to elucidate the correct method. Warm wishes Madhusmita India

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Scattering paths in XANES calculations
by Stefanie Roese 12 Jun '14

12 Jun '14

Dear all, I am performing XANES calculations for silver clusters with FEFF. Aditional to my XANES results, I would like to get information about the participating scattering paths and how they influence my spectra. In detail I want to get the same pictures that Bruce ravel used in his talk "a practical introduction to multiple scattering theory" from page 11. I have performed calculations for XANES using the rpath algorithm to obtain the feffnnnn.dat files. I already checked, that the course of the rpath spectra agrees to the fms calculations in ordner to make sure that the algorithm converged. But now I fail at getting the plots with the Energy at the x-axis and the normailzed mu at the y-axis likle Bruce did it in his talk. Which program was used there? Athena? And how can I get the energy/mu-information out of my feffnnn.dat files to compare to the total spectrum? I think I am quite close to the solution, but it does not work. Thanks in advance for every help! Steffi

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Demeter on Mac OS X
by Juliana Fonseca de Lima 06 Jun '14

06 Jun '14

Hi all, I have used Athena on my Mac since last month, but from last week I have had the below problem to open the software. Could you help me to solve that? perl5.16(423,0x7fff75854310) malloc: *** mach_vm_map(size=18446744071562072064) failed (error code=3) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug Out of memory! PS: I have 8 GB of physical memory. Cheers, Juliana

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Demeter-devel port added in Macports for OS X
by Schima, Frank 06 Jun '14

06 Jun '14

OS X Users, I have created a new port in Macports for demeter-devel based on the 0.9.20 version which is still in development. This has important fixes for the black window problem in Artemis. To install it, simply run the following commands in Terminal: sudo port selfupdate sudo port uninstall demeter sudo port install demeter-devel Feedback appreciated. I have only tested it on OS X 10.9.3 so far. Just keep in mind that the “devel” part means that this is not a release version and problems may exist. Cheers! Frank

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Help
by Dien.Li＠srs.gov 06 Jun '14

06 Jun '14

HI, all I am a beginner user of Athena and Artemis and ATOMS. It is very nice to find Athena and Artemis manuals, they are helpful: 1. Do you have FeS2 and other Fe mineral EXAFS data as described in your manual, and associated data files, so that I can practice following your manual. 2. When I ran ATOMS standing alone, to input the crystal structure data that have more than 7 atom sites. I could not add a site by clicking "Add a Site" button, is there a problem for ATOMS, or it may be related to our SRNL security system. 3. Currently, my project is to study U adsorption to natural organic matter and minerals (e.g., goethite) surfaces, do you have any template files available for calculating FEFF or if you can instruct me where I can start for such systems: for example, uranyl-C or uranyl-goethite surfaces. 4. How to define the fitting models and GDS parameters for such U systems. Thanks you so much for your help. Dien Li, Ph.D. Fellow Scientist Environmental Sciences and Biotechnology Savannah River National Laboratory Aiken, South Carolina, 29808 Tel: 803-725-7520

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Aligning EXAFS E0 to Theory
by Carter Abney 05 Jun '14

05 Jun '14

Hello, Everyone - This is my first time trying to work through EXAFS analysis of experimental data, and I've got what (I think) should be a fairly straightforward question. I'm trying to minimize my delta E0 by aligning the EXAFS data with my best fit (i.e. - align the k-grid of the data with the k-grid of the theory to obtain a small delta E0). However, I have been unsuccessful in "reading the theoretical chi(k) spectrum into Athena<http://www.mail-archive.com/ifeffit%40millenia.cars.aps.anl.gov/msg02494.ht…>" to accomplish this. I assume the crux of the problem is the format in which I am exporting my theoretical chi(k) spectrum from Artemis. The only way I have been able to export the data with Artemis so Athena can import it is to click the "Save next plot to a file" button, which then allows me to save the data as a text file. I know I need chi(k) data that is not k-weighted<http://www.mail-archive.com/ifeffit%40millenia.cars.aps.anl.gov/msg01623.ht…>, so I plot the best fit with k-weight of 0 in k space with deltaE0 equal to 0. Considering the problems I've had, I'm assuming somewhere in this process is where I'm going wrong. When I import this data, I have four columns: k, experimental data, fit, window. Since k is the wavenumber of the photoelectron, I choose that as "Energy." Then I select column 3, the best fit, as "Numerator," and change the data type to chi(k). I then import the data. I've attached two pngs to this e-mail which, assuming they come through, should display the Athena data import window and the corresponding plot of chi(k). When I plot this data in k-space or R-space using Artemis, the resulting plots look appropriate. When I try to align the experimental EXAFS data in Athena, I know it aligns the first derivative of E for the selected data to the first derivative of E for the standard. I want my best fit to be the standard to which the data is aligned. However, I cannot plot chi(k) data in E, which causes me to believe I shouldn't be able to align data to the first derivative of E. True enough, when I try to auto align, I get impossible values for E0 adjustment. Clearly I'm doing something wrong - possibly even several somethings wrong. Any guidance would be greatly appreciated. Thanks, - Carter

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Re: [Ifeffit] Aligning EXAFS E0 to Theory
by Carter Abney 05 Jun '14

05 Jun '14

Edmund & Drew, thanks for your insights on the matter. I think between the combination of your responses, things are making more sense. Edmund, your question "Why?" is valid. The answer is: "I misunderstood what was being done in the tutorials/literature." There is plenty of documentation discussing E0 correction, I'm just new to EXAFS and thought this is what I was trying to do in the alignment menu (and thought this is what they were asking for in the tutorials, etc). Drew, as you pointed out I don't actually want to adjust the whole spectrum in energy, just the position of E0 to better align the experimental data to the theoretical first shell. So, to answer my own question (and make sure I'm actually understanding you): 1.) I imported the data acceptably, but 2.) should adjust the E0 value for the experimental data by changing the pre-edge range, normalization range, and Rbkg. I should be able to see the effects of these changes by plotting in k-space with my imported theoretical first shell. Someone please (re)correct me if I'm still not getting it right. Thanks again for the help. - Carter

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Artemis Feff calculation error
by Schima, Frank 04 Jun '14

04 Jun '14

Hi all, I’m running Demeter 0.9.18.3 from Macports on Mac OS X 10.9.3. We are seeing an error in a Feff calculation that we don’t understand and we are hoping someone can point out what we are doing wrong. STEPS TO REPRODUCE: 1. Launch artemis 2. Open File->Import->Chi(k) data and select the file chi.dat (attached). This file is our data. 3. Notice that a plot window opens that looks good. 4. In the Artemis [Data] chi window, press “Import crystal data or a Feff calculation” 5. Select the feff.inp file for Cu (attached). This file is from the EXAFS Cu example. 6. In the "Artemis [Feff] Atoms and Feff" window that appears, press the “Run Feff” button. Here is the error from the output console: -------------------------------------------------------------------------------------------------------------------------------- ********** Feff calculation beginning at 2014-06-02T15:04:27 Feff 6L.02 Error reading input, bad line follows: HOLE k 1.0 Fatal Error: at RDINP (Feff executable: feff6) ********** Feff calculation finished at 2014-06-02T15:04:27 Your Feff calculation took 0 seconds. -------------------------------------------------------------------------------------------------------------------------------- The line “ HOLE k 1.0” does not appear in either data file. Ideas? Cheers! Frank

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Data for Cr selenide?
by Matthew Marcus 04 Jun '14

04 Jun '14

Does anyone have EXAFS data to at least k=12 for Cr selenide of known phase? I'm working on fitting the EXAFS of Cr doped into Bi2Se3, and using Feff6L, the S02 comes out to 0.65 if I assume a substitutional site, which seems a bit low. mam

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Re: [Ifeffit] Demeter on Ubuntu 14.04
by Denis Testemale 02 Jun '14

02 Jun '14

Bruce, thanks for looking into that. And my apologies for the dodgy and incomplete bug report. Right to the point: - the command env | grep LC returns nothing... - the command: perl -e 'printf("%.3f\n", 5.23456)' returned 5.23456. So you're stumped, right? :-) - but env | grep LANG returns: LANG=fr_FR.UTF-8 GDM_LANG=fr_FR LANGUAGE=fr_FR So your trick to export language variables to en_US did it. And _solved my problem_. So thank you. I'd like to raise a related issue to complete my initial bug report and try to understand better those problems (which could occur again in the future). To install demeter initially (last year I think) I followed this procedure: https://gist.github.com/waveform80/3959252 One thing that I could not understand (and still cannot, it is somehow beyond my limited knowledge of linux) are the subtle differences between installing the code locally or system-wide and in particular this cryptic (to me) command: eval $(perl -I$HOME/perl5/lib/perl5 -Mlocal::lib) Indeed, the procedure I followed created a perl5 folder in my home folder. That is the reason why, when I mentionned that I erased all the folders to reinstall everything, I was referring to the folders demeter and perl5 in my home folder, as suggested in the 'Removing installation' chapter in the same page. And I'm pretty sure that many of my problems are related to that. As always, being a numb, I tried different fixes, in particular a root installation. Everything is probably a mixture of approximate fixes now and makes it hard to source the problems. The thing is I actually don't need this perl5 folder anymore. Everything now runs smoothly (with the en_US LANGUAGE trick), but I sometimes have warning messages (in dathena for example) that it can't locate Encoding/FixLatin/XS.pm in @INC for example. I copied the file from the local perl5 folder to the system wide folder in /usr/local/lib and the warning disappeared. In fact I was wondering if I should reinstall from zero with a system-wide install, or if the local install made sense in some situations. As I understood it at the time, it was to be able to erase the local perl install. Sorry for the long message. The bottom line is that you unlocked my situation. Cheers denis Le 29/05/2014 16:40, ifeffit-request(a)millenia.cars.aps.anl.gov a écrit : > 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: Demeter on Ubuntu 14.04 (Bruce Ravel) > 2. Re: Demeter on Ubuntu 14.04 (Bruce Ravel) > 3. Fitting EXAFS simulation to experimental (Carl Brozek) > 4. Re: Fitting EXAFS simulation to experimental (Bruce Ravel) > 5. Re: Fitting EXAFS simulation to experimental (Scott Calvin) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 28 May 2014 14:24:06 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Demeter on Ubuntu 14.04 > Message-ID: <538629C6.7080907(a)bnl.gov> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > Hi Denis, > > On 05/26/2014 10:11 AM, Denis Testemale wrote: >> Context: I'm running Ubuntu 64 bits 14.04. Demeter version 0.9.20. I >> followed Ubuntu specific instructions found here: >> https://gist.github.com/3959252 >> Demeter once worked but I cannot guarantee that it did just before the >> upgrade to 14.04. After the upgrade, both trying to run dathena or to >> rebuild the package ran into errors such as: > These: > >> denis@huchet4:~/demeter$ ./Build >> Building Demeter >> Perl API version v5.14.0 of DateTime does not match v5.18.0 at >> /usr/share/perl/5.18/XSLoader.pm line 92. >> ... etc... > and >> denis@huchet4:~/demeter$ dathena >> Perl API version v5.14.0 of Wx does not match v5.18.0 at >> /usr/lib/perl/5.18/DynaLoader.pm line 207. >> ... etc... > mean that you had built the DateTime and Wx modules for an older > version of perl. The compiled bits are not, in general, forward > compatible. That is, when a new version of perl is installed, the > various modules must be rebuilt. This is the sort of thing that > package managers (like apt-get) take care of and why it would be > lovely if a package for Demeter existed. > > In your case, I suspect that you ran "./Build installdeps" once upon a > time when you have perl 5.14 on your computer. Normally, running > "./Build installdeps" again would do the right thing because it would > install to a version-specific subdirectory in someplace like > /usr/local/lib/perl/. > > You didn't tell me what "perl -V" had to say, so I can only guess why > that didn't work for you. My best guess is that you instruct the perl > Build script to install to some location in your home directory and > then you have modified perl's include list. > > That is, when you say > >> So I erased the folders and reinstalled everything. > I presume that "the folders", whatever you mean by that, are something > other than the system folder that perl would normally install into. > Of course, it is hard for me to know for sure because you have not > provided enough information to diagnose the problem. > >> The installation ran >> smoothly (except I had to install missing deps several times, but no >> error messages at the end). Now I can start the programs but run into >> problems: >> >> Attribute (bkg_nc0) does not pass the type constraint because: >> Validation failed for 'LaxNum' with value 0,00000000000000 at >> /usr/local/lib/perl/5.18.2/Moose/Exception.pm line 37 > This appears to be a localization problem. In fact, it is true that > "0,000" is not a number when a dot is expected as a decimal point. > > I am guessing that you have LC_ALL or LC_NUMERIC set to something like > "fr_FR" and that is causing some module used by Demeter to use French > localization for formatting a character string intended to represent a > number. The reason I suspect this is because your stack trace points > to a line of code that looks like this: > > $self->bkg_nc0(sprintf("%.14f", $self->fetch_scalar("norm_c0"))); > > The fetch_scalar method is used to grab a value from Ifeffit and > returns a floating point number. I then use sprintf to control the > number of decimal places. 14 digits is a lot, making this line a bit > silly, but I use this idiom extensively throughout the code, usually > with much less precision. With one of the LC_* environment variables > set to fr_FR (or whatever), a comma gets used. > > It would not be hard to make this idiom tolerant of commas-as-decimal- > points. > > I suspect that there is a fairly simple work-around you could try: > > * Open a new terminal window. (You want to try this in its own shell > so it doesn't affect the rest of the programs running on your > computer.) Do "env | grep LC" to see whether and how the LC_* > variables are set. > > * do > perl -e 'printf("%.3f\n", 5.23456)' > What gets printed? "5.235" or "5,235"? > > * If the latter, do the following two commands: > * export LC_ALL="" > * export LC_NUMERIC="" > If the former, then I'm stumped. > > * try running Athena again. > > You should take a look at ~/.horae/demeter.ini. If any of the values > in there use commas as the decimal point, then you will either need to > edit or delete the file. > > Of course, I may be way off base. Let me know if that works. > > B > > >

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