June 2012 - Ifeffit - millenia.cars.aps.anl.gov

lecture videos at the Diamond Light Source
by Bruce Ravel 13 Aug '12

13 Aug '12

Hi, Last fall, the excellent folks at the Diamond Light Source invited me to present a three day XAS training course. All of my lectures and software demonstrations were recorded on camera, as were the desktop sessions on the presentation computer. The Diamond technical staff did a great job assembling all of this information into streaming videos, which they are now hosting on their web site. Here is the URL: http://www.diamond.ac.uk/Home/Events/Past_events/XAS-workshop-2011.html In total, there are several hours of videos of me presenting lectures and teaching the audience how to use the most recent versions of Athena and Artemis. The editing is great -- it transitions very nicely between the camera and the desktop. Really the only problem with the videos is that you will have to watch many hours of my ugly mug :) I'd like to thank Paul Quinn, Fred Mosselmans, and Shu Hayama for inviting me, organizing the event, and making the videos happen. If you find the videos helpful, be sure to let them know. For folks just learning XAS and for those wanting to learn how to use the newest versions of Athena and Artemis, the Diamond folk have done a very kind thing. Regards, B PS: As a Linux user, it was not immediately obvious to me how to use the Microsoft Media Server (mms:) links on the Diamond web page. Here is a hint that worked for me for viewing them from Firefox: http://support.mozilla.org/en-US/questions/747274 I configured Firefox to send the video to VLC, although any video player should work. Presumably, something similar can be done in other browsers. -- 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 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel

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Problems with fit in pyrite structure with Se substitution
by Adriana Matamoros Veloza 03 Jul '12

03 Jul '12

Dear all, I am fitting a crystal pyrite structure with Se substitution in one of the sulphur atoms. I am sharing my projects in artemis. In the AMV1 project, all the parameters are sensible except for the large amplitude. I would like to know if that could be the effect of the substitution. In the second project AMV-2, I am finding large E0, which I tried to overcome by aligning the spectra with the theory in Athena. However, the fitting afterwards is worse than without such correction. https://docs.google.com/open?id=0B6dBCadbyZwFS0tDTmdDSXlWVVU (AMV-1) https://docs.google.com/open?id=0B6dBCadbyZwFYlc2c3FKT0YtbXc (AMV-2) Any ideas to help to solve these problems will be very much appreciated. Kind regards, Adriana Dr Adriana Matamoros-Veloza School of Earth and Environment University of Leeds Leeds, LS2 9JT

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Re: [Ifeffit] Fitting XANES spectrun with standards (Adrien Couet)
by adrien couet 29 Jun '12

29 Jun '12

Thanks for the quick answer Bruce. I'll definetely take into account your point on the pre and post edge ranges and I will check if it makes any changes in the normalization next time I go to APS (in a few days actually). Going back to the original question, I did select 8 standards for both cases (single fit with "fit this group" and combination of fits with "fit all combinations"), which gives me 247 combinations (see Excel file attached). In the case of the single fit I get a R-factor of 2.0x10-3 whereas for the best fit from the combinations I got 1.8x10-3 (the weights of each standards are also different in both cases). I selected the whole range of the spectrum for the fit and forced the weights to be equal to 1. The 8 standards are put in the following order in the library: Fe3O4(4), Pure Fe2O3, SM Fe in pure Zr metal, SM Fe in Zr-4 SPP, SM SA Fe in Zr-4 matrix, Fe3O4(2), Fe2O3(4), Pure Fe (4). I hope this is enough information for you to reproduce what I am doing. Thanks again, -- Adrien Couet Graduate Student Dept of Nuclear Engineering, Penn State University +1 814 865 9709 axc1019(a)psu.edu

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Fitting XANES spectrun with standards
by adrien couet 29 Jun '12

29 Jun '12

Hi all, I am having some troubles when I fit XANES spectra with a library of standards. The unknown spectrum has been processed (background removal, normalization,...). If I understand correctly the documentation, I have two ways to fit the unknown spectra: - using "fit this group" and I will get the best fit using my standards library - using "fit all combinations" and I will get all the different fit results from the best to the worst. However, it appears that the result given by "fit this group" does not correspond to the best fit given by "fit all combinations" (it often corresponds to a higher R factor fit), and thus "fit this group" does not give me the best fit possible. Are these two fitting processes using a different fitting algorithm? I attached one example to this email. I am using a library of 8 different Fe standards to fit the unknown spectra. Thanks for your attention -- Adrien Couet Graduate Student Dept of Nuclear Engineering, Penn State University +1 814 865 9709 axc1019(a)psu.edu

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Larch / Ifeffit2 development status
by Matt Newville 28 Jun '12

28 Jun '12

Hi Folks, I wanted to give an update on progress of my Ifeffit 2 project, which I've been developing under the code name Larch, a name which I think might stick. This has been a long, slow (and sometimes nearly stopped) process over several years, but a few events have conspired so that I've focused enough attention on it over the past month or so that enough progress has actually been made to report on it. One of the conspiring events is the upcoming XAFS conference, where I will present several features of Larch. First, a summary: Larch is a complete rewrite of the functionality of Ifeffit. It has a much richer and flexible syntax, and much better data processing functionality. Though currently focused on XAFS analysis, the intention is to add functionality for related techniques such as XRF. Like Ifeffit, Larch works either as a command-line with a scriptable interface, or as a library, allowing GUIs to be built upon this foundation. Larch is written entirely in Python, using a large set of existing and supported scientific computing libraries. By throwing out all of Ifeffit1 and Fortran and re-implementing in Python, a number of recurring problems we've add with Ifeffit 1 go away. The most import of these is that there is no built-in limits on memory usage. A secondary issue is that the macro language exposed to the user is much, much better -- you can write real programs in Larch (it is a dialect of Python itself) and have much richer data structures. A third part of the enhancement is that development and extending functionality is simpler, and the code is much more modular. This not only means that maintenance is easier for me, but that many existing libraries can be immediately used. It also means that others should have a much easier time playing with the code, which I encourage. Though it may be easy to see that replacing Fortran for Python would give code that is more flexible, easier to read and maintain, it might be counter-intuitive to expect it to be more efficient. But it turns out that for basic data processing (not including graphics), Larch is often considerably faster than Ifeffit 1. A typical "read data, do background subtractions, and FFTs" is about 2.5x faster in my tests. That should make processing large amounts of QEXAFS and hyper-spectral data noticeably faster. As an aside, the graphics are slower, but are of much better quality. Larch is still in active development, but here's a short list of what is currently working: Basic functionality: 1. basic mathematical, array manipulation. 2. reading / writing data from ASCII files. 3. reading data from HDF5. 4. line plotting of x, y data, with much better graphics than Ifeffit, with interactive zooming, plot configuration, etc. 5. simple 2d image display of 2d array data, I(x,y). 6. a complete python-like language for writing complex scripts. 7. an easy-to-use interface to general-purpose fitting of data, for example to Gaussian lineshapes. 8. running either as a command-line program or as a Python library, or in 'server mode', so that another process may interact with a background server process. 9. There is a start of a proof-of-principle general purpose GUI, but it's not very far along. XAFS Functionality: 1. Pre-edge subtraction, normalization. Currently done as in Ifeffit, and ready to be expanded. 2. Autobk background subtraction. A few missing features here. 3. XAFS Fourier transforms (forward and reverse) with a variety of window types. 4. Feffit fits to sums of Feff Paths from feff.dat files. Support for multiple-k-weight fits and multiple-data-set fits are included. 5. Uncertainties calculations are automatically included and match very closely to those from Feffit/Ifeffit despite being a new implementation. 6. Standard reference data for several x-ray values can be retrieved from tables of Elam etal (absorption coefficients, x-ray edges and lines), Chantler etal (f', f''), Waasmaier and Kirfel (f0), and Keski-Rahkonen and Krause (core-hole widths). Where possible, the syntax of the XAFS functionality is largely unchanged. Some of the functionality listed above is an incomplete port of Ifeffit's functionality. For example, the autobk() function does not yet support spline clamps, and may have an error when and there is not yet an equivalent of the Cromer-Libermann Background, ala MBACK. Some functionality is much better, of course. In essence, all of Ifeffit has been ported and is approximately ready for testing for the brave. The build and installation process is not highly streamlined yet -- a windows executable does not yet exist. But code has been actively developed on Windows, Mac OS X, and Linux, and installs and runs without modification (there are some built in Windows-specific code but the user never needs to think about this). The documentation is fairly scant, especially for the EXAFS functions. This will improve over the next months. Much of the current status is expected to be the starting point for further expansion, so this is the right time to think about and propose real enhancements. For example, including better linear algebra / PCA methods would be near the top of list of things to add. My own needs include XRF Analysis, data collection, and I fully expect Larch to be able to all of these things. Since most people here are mostly using the Athena/Artemis/Dathena/Dartemis GUIs I'll point out that the 'server mode' mentioned above will allow Demeter to communicate with Larch, and even allow Demeter to use 2 or more instances of background Larch processes running at the same time (say, one per core of your machine). That is not yet all worked out, but we know how to do it. Code and Documentation so far are at http://github.com/xraypy/xraylarch and http://xraypy.github.com/xraylarch At this point, I'm looking for a couple types of feedback: 1. comments and suggestions on the process and design so far. 2. suggestions for enhancements or features. This is the time to send your wish list! 3. collaborators on implementing these features or adding new functionality. --Matt

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Unsuccessful launching of (D)Athena, (D)Artmis and (D)Hephaestus
by Huaming Guo 28 Jun '12

28 Jun '12

> Hello Bravel, > > Attached please find the log reports. These may be the issues leading to the > unsuccessful launching of (D)Athena, (D)Artmis and (D)Hephaestus. It would > be great if you can give me hands. Thanks. > > Regards > > Huaming > > > ------------------------------------------- > Prof.Dr. Huaming Guo > School of Water Resources & Environment > China University of Geosciences > Beijing 100083 > P.R.China > Tel: 0086-10-82321366 > Fax: 0086-10-82321081 > Email: hmguo(a)cugb.edu.cn > ------------------------------------------- ------------------------------------------- Prof.Dr. Huaming Guo School of Water Resources & Environment China University of Geosciences Beijing 100083 P.R.China Tel: 0086-10-82321366 Fax: 0086-10-82321081 Email: hmguo(a)cugb.edu.cn -------------------------------------------

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HELP
by Diego Fernando 27 Jun '12

27 Jun '12

For some time I'm using FEFF8.4 for calculations of absorption-XANES and DOS in some superconducting materials for which it has been successful, now I have the need to include in the'' input "of some impurity atoms in interstitial positions by Example: *A* *1.16* *B* where *A* and *B* are two different species of atoms, I made several attempts in trying to implement this using ATOMS3.0 on the web: http://millenia.cars.aps.anl.gov/cgi-bin/atoms/atoms.cgi but I have not had consistent results, in ATOMS3.0 manual explains that the program has been designed for this, but suggests that it may be possible. I appeal to you to see if I can help solve this problem. Thanks for your attention. Diego Fernando Mulato Gómez. Estudiante de doctorado en Física Teórica, CINVESTAV, Unidad Mérida, México.

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Problem occurs in ARTEMIS
by Ashok Yadav 27 Jun '12

27 Jun '12

Dear All, I am using windows 7 professional in my desktop. My ARTEMIS (0.8.014 free available) is not working properly even Athena is working very well. When I am opening my project files which is fitted and saved day before, artemis is not opening it and showing an error massage "Artemis trapped one or more errors! Error message dumped to the screen" , but I couldn't see such error message on the screen. This same massage is also occurring when I try to quit from Artemis window and it isn't quitting. When I opened this project files using artemis installed in another PC and my laptop these project files are working very well (even I can refine fitting in another PC using same artemis version). I have re installed the software but the same problem occurs again and again. If anyone encountered problem like this please help me to resolve it. Thank you Ashok

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Histograms with Demeter -- meaning of fit values
by Walter Fu 25 Jun '12

25 Jun '12

Hi all, I'm trying to do a preliminary fit to the first shell of an amorphous material, using a histogram generated from diffraction data. I've been using a script similar to the one given here: http://bruceravel.github.com/demeter/dpg/examples/histo.html When I run my script, it creates an SS path for each histogram bin and then performs the fit, as expected. However, if I then query the fit object for a summary, I get a list of fitted values back. My question is, what is the meaning of these values? Do they refer to the fit as a whole, or individual paths within the fit? For instance, is the "delR" value the one which, when applied uniformly to all of the paths generated, produces the best fit? Or is it merely the value calculated for the last-used path (presumably the one corresponding to last bin in the histogram), which may be different for the second-to-last path or for the first path? I'm also a bit confused as to how the "amp" variable (line 30 in the script from the link given above) comes into play. Is the reported value a single multiplicative factor which is applied to the histogram-generated amplitudes of all the paths, or is there a separate "amp" for each path, with only the one corresponding to the last-accessed path being reported? I've tried looking through the Demeter source to get the answers, but given my limited knowledge of Perl, my search is proving less than conclusive. Any explanations you could give would be greatly appreciated. -Walter

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PCA component determination
by Santiago José Alejandro Figueroa 23 Jun '12

23 Jun '12

Dear all, Determine the number of components in Principal Component Analysis decomposition is usually a hard work, close to an art. Recently Malinowski discuss some methods in a paper that is proposed a new method (DRMAD): DOI: 10.1002/cem.1182 This last method has in the program developed by Carmelo Prestipino PCA_GUI.py (http://code.google.com/p/prestopronto/) developed with some advices of Marcos Fernandez-Garcia. There are many methods better than use the empirical IND funtion. The better is have a good knowledge of your system by other techniques or by the behavior, this additional information can be of the extreme importance if you have more than 2 components. Best regards, Santiago -------------------------------------------- Dr. Santiago J. A. Figueroa Pesquisador - Laboratório Nacional de Luz Síncrotron (LNLS) Centro Nacional de Pesquisa em Energia e Materiais (CNPEM) Rua Giuseppe Máximo Scolfaro, 10000 Caixa Postal 6192 - CEP 13083-970, Campinas(SP), BRASIL Tels.: (sala)19 3517-5063 / (xafs2)19 3512-1246 / (xafs1)1139 / (dxas)1141 Fax: 19 3512-1006 WEB: http://www.lnls.br BLOG: http://www.marevero.blogspot.com/

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