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

Manganese oxide EXAFS modelin
by Ebrahim Rezaei 13 Jul '12

13 Jul '12

Hi everyone, I am working with bulk and nano-particles manganese oxides. Basically I have collected EXAFS of Mn K-edge for my reference material (Mn2O3, bixibyite) and also the catalyst (Mn supported on alumina). The catalyst shows formation of nanoparticles of bixibyite on alumina with size around 20 nm. My first question is about modeling the reference material in order to find So which will be used as a fixed parameter to find oxygen and manganese first and second shell CNs for the catalyst. The difficulty with modeling the reference material arises due to the rather complex atomic coordinates of Mn2O3 containing oxygen atoms at different but very close distances. Basically Mn2O3 has two sites (25% and 75% occupancy for site 1 and 2 respectively) with the following coordinates: Site 1 Site 2 Atom R (Å) CN Atom R (Å) CN O 1.993 6 O 1.899 2 Mn 3.104 6 O 1.985 2 Mn 3.565 6 O 2.249 2 Mn 3.115 6 Mn 3.575 6 I am aware that in order to fit the EXAFS equation I should considers paths from both sites and multiply their amplitudes by their site occupancy. But to make the life easier I simplified the atom coordinates of Mn2O3 to be able to extract the CNs from the catalyst. To my understanding one can expect to have 6 oxygen atoms in average at the first shell (0.25*6 + 0.75*6 = 6), 6 Mn atoms at the second shell and 6 Mn atoms at the third shell regardless of the site occupancy. Therefore I ignored the site occupancy and considered the following atomic coordinates assuming that there is only one site in the in the model developed for the reference material: Atom R (Å) CN O 1.985 4 O 2.249 2 Mn 3.115 6 Mn 3.565 6 The model works fairly acceptable and I am able to get CN from the catalysts as well. But I am not sure if my assumptions could be acceptable or not. I was wondering if I can have idea of the EXAFS community experts on this. My other question is about dealing with σ2 as a fixed parameter. I have noticed that after fitting the catalysts, σ2 of paths in the catalysts are almost close to that of the reference material. Therefore I tried to fix the values of σ2 for the catalyst and use the ones I have obtained from the reference material. This increases the degree of freedom of the fit and results in smaller error bars in CN while χ2 increases by 2.5%. Basically I have always kept number of variables to almost less than half of the number of the independent points either with fixing or relaxing σ2. I was wondering if estimation of σ2 in the catalysts from the reference material might be a good assumption in my case or not. I think it should not be a bad idea since size of Mn2O3 nano-particles on alumina is fairly large (around 20 nm) showing formation of complete crystalline of Mn2O3 on the catalyst. I have my project file in hand and I can send it for further discussion as well. I appreciate your time and help in advance. Best Regards, Ebrahim Rezaei, PhD Student, Chemical Engineering Department, University of Saskatchewan, Saskatoon, SK, Canada

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Athena Request
by BradleyW Miller 11 Jul '12

11 Jul '12

Hi, If my memory is correct there was a period of time you were taking request for improvements on Athena. This may be too late however I would like to see the LCF function of Athena capable of running multiple models (sequential models e.g. Sample A followed by B, C...) using a similar set of standards. For instances, I may have 25-40 spectra (environmental samples), one set of standards which may be plausible, and currently I have to run the model wait for the LCF model for sample A to finish before starting Sample B. If there was a way to write a script or add the functionality of multiple scans from the same set of standards, I (and maybe others) could set up a computer and leave for several hours instead of returning every 5-30 mins to execute a new LCF model. A conversation was posted about running models with a large number of standards (and whether it was appropriate), similarly running multiple samples is cumbersome. In a related comment I have tried to take advantage of access to high speed computing, but Athena's code does not appear to be capable of taking advantage of increased resources (either RAM and CPU) in order to decrease computational time. All the same thanks (to the many of you working on Ifeffit) for the shareware and all your support. Thanks for your time. Respectfully, Bradley W. Miller, Ph.D. Post Doctoral Fellow Oak Ridge Institute for Science and Education U. S. Environmental Protection Agency National Risk Management Research Laboratory Land Remediation and Pollution Control Division 5995 Center Hill Avenue, Cincinnati, OH 45224-1702 Office: (513) 487-2889 Miller.BradleyW(a)epa.gov Fax: (513) 569-7879 www.epa.gov www.tinyurl.com/bwmiller The great tragedy of Science—the slaying of beautiful hypothesis by an ugly fact.— Thomas H. Huxley Views or Opinions expressed in this email is solely representative of the sender and does not represents those of the EPA or any other agency.

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Crash when Discarding Feff Calculation
by Andrew Korinda 08 Jul '12

08 Jul '12

I have an Arthemis project (started in Demeter) with several feff calculations with the input written by me into a feff.inp boiler plate. The calculations themselves were fine but now when I show a calculation and click discard, I get the pop-up asking me if I want to discard this calculation, I click yes, then everything closes. Attached is the log file, project file, and demeter.mru. Let me know if there's anything I can do to help debug this. Andy Korinda

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FEFF83 question
by Pal, Rhitankar 05 Jul '12

05 Jul '12

Dear Professor Ravel, I am using FEFF83 and IFEFFIT recently to calculate the EXAFS spectra of Mn-cluster in PhotosystemII. I would like to know what is the E0 value FEFF83 uses for a Mn atom. Does it use the same E0 for all the absorbing atoms if there are multiple Mn atoms in a cluster. Please let me know if you or any of your group member can help me with this. Thanks and best regards Rhitankar Pal Postdoc, Batista Group Yale University

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Re: [Ifeffit] Fitting XANES spectrun with standards (Adrien Couet)
by adrien couet 03 Jul '12

03 Jul '12

Thanks for the answer Bruce! I think one thing I did not understand about the single fit is that it tries to use all standards (although some of the standard's weights can be equal to 0 in the results), which can be detrimental to the fitting. Thanks a lot for the precisions, things are clearer now! -- Adrien Couet Graduate Student Dept of Nuclear Engineering, Penn State University +1 814 865 9709 axc1019(a)psu.edu

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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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