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

amorphous metal alloys EXAFS spectra to be fitted with Artemis
by "Piotr J. Bardziński" 25 Aug '13

25 Aug '13

Dear Sir or Madam, I got a normalized Fe K-edge EXAFS spectrum for my amorphous 7-component alloy sample, for which I know its atomic percent composition. I need to find out the interatomic distances between the Fe and the other atoms present in the alloy (identify the peaks in R-space) as well as how many atoms of each element is surrounding the absorbing iron atom (coordination number). To meet my goal, I think I need to fit the R-space Fourier transform of my EXAFS spectrum in a program like Artemis. Unfortunately, I haven`t found any tutorial discussing how to deal with amorphous sample with unknown organization of the atoms. When you are about to prepare an atomic model in Artemis for fitting, you need to build a model with an initial interatomic distances, atomic coordination number, etc, but all that is obviously unknown to me. I know nothing about the short range order in my material and I want to learn it from the experiment itself (note that itcan be and most probably is different from the one present in crystalline structures). So, my question is, could somebody tell me how to deal with such system using the Artemis, what type of initial models for fitting should be prepared? All of your help will be greatly appreciated. Best regards, Piotr Bardziński,

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Recommendations for DFT/computational chemistry software?
by Scott Calvin 22 Aug '13

22 Aug '13

Hi all, I know many of you use DFT calculations to help model EXAFS data for molecular compounds. Do you have recommendations for good computational chemistry packages, commercial or otherwise, to use for that purpose? --Scott Calvin Sarah Lawrence College

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Lecture/tutorials required on FeFF 9.x
by S. Gautam 22 Aug '13

22 Aug '13

Dear All, I have been trying to find out some lectures/tutorials on FeFF 9.x (J.J. Rehr) to deliver my XAFS users, other than it's UserGuide as available on the website. If someone has made for their users, it would help me to deliver with acknowledging you. thanks in advance sincerely Sanjeev ----- Dr. Sanjeev Gautam KIST -PAL , South Korea -------------- http://orcid.org/0000-0003-3123-9906 -----

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(D) Atoms crashing while running feff
by Matt Frith 18 Aug '13

18 Aug '13

Dear All, I have been trying to run a feff calculation on FeAl2O4 with Fe as the absorbing atom. Every time I attempt the calculation in Artemis crashes. Atoms also crashes if it is run independently. The dartemis and datoms log files both read: "At line 90 of file istprm.f Fortran runtime error: End of file Can't close(GLOB(0x931c6cc)) filehandle: '' at C:/strawberry/perl/site/lib/Demeter/Feff.pm line 1015" Can someone please tell me what I need to edit to solve this problem? Can editing something on the input file fix this problem? The cif file and datoms log file for the problem are attached. Problem occurred on Win 7 32bit computer. Thank you for your time. Sincerely, Matt Frith Graduate Student Princeton University

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Linear Combination Fitting using ATHENA
by Teck Kwang Choo 15 Aug '13

15 Aug '13

Hello, I have been using ATHENA to perform Linear Combination Fitting (LCF) on my XANES spectrum to quantify the amounts of Fe (II) and Fe (III) in my samples using only FeO and Fe2O3 as standards. The results showed a majority of Fe (II), which is contrary to what was expected. This made me wonder if the LCF results from XANES is a molar percentage (mol %) or weight percentage (wt%). Could anyone enlighten me on this matter? Thanks! -- Teck Kwang Choo PhD Student Department of Chemical Engineering Room 225, Building 36 Monash University Mobile No.: 04-11489904

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Re: [Ifeffit] Recommendations for DFT/computational chemistry software?
by Ryan Nelson 12 Aug '13

12 Aug '13

Hi Scott, Gaussian is a pretty solid program. The input files are easy to write, and it's popularity make it easy to find support. It is a commercial product, though, which can be a problem if your on a tight budget. Several years back, I tried Gamess, which worked fine. Its biggest drawback for me was writing input files. It was cumbersome to use mixed/custom basis sets, which is probably key for anything you'll be doing for EXAFS. I haven't tried Gamess recently, so the situation may have changed. I hear good things about Orca as well. I think this package does a lot of interesting stuff related to XAS, but I haven't spent much time with it. A couple years back, Orca couldn't do analytical frequency calculations, which, in my experience, led to very slow frequency calculations. However, according to the website, it seems like that feature will be coming soon, so I would like to find some time to really play around with this program again. My colleague uses WebMO, which is a web-based frontend to many electronic structure packages. I haven't used it myself, but it may make for a more unified experience for many of these packages. Just my two cents... Good luck. Ryan > Hi all, > > I know many of you use DFT calculations to help model EXAFS data for > molecular compounds. Do you have recommendations for good computational > chemistry packages, commercial or otherwise, to use for that purpose? > > --Scott Calvin > Sarah Lawrence College > > >

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Re: [Ifeffit] Recommendations for DFT/computational chemistry software?
by Eric Breynaert 12 Aug '13

12 Aug '13

Dear Scott, The answer to this question depends on the compounds you're interested with and probably also on the software you have access to. In principle all computational chemistry software can export a molfile of the optimised structure. Using xyz coordinates in the molfile you can easily rig a feff input file. Best advice is probably to get in touch with a molecular modelling group and ask them to do the structure optimisations. If that's not an option, you could try Gaussian. Fairly expensive, but in combination with Gaussview it's reasonably easy to get the structure optimisation going. Gamess should do the trick for free. ADF is also an option and VASP can even handle periodic systems decently. But as i said initially, the best advice is to collaborate with a good molecular modelling group. Regards, Eric -- Eric Breynaert Centrum voor Oppervlaktechemie en Katalyse Departement Microbiële en moleculaire systemen (M²S) - KU Leuven Kasteelpark Arenberg 23 - bus 2461 B-3001 Leuven Tel: +3216321598 Fax: +3216321998

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issues with Athena (new Demeter package)
by Adrian Gainar 12 Aug '13

12 Aug '13

Hi All, I experience two issues with Athena of the updated new Demeter package, which it would be easier to describe: 1) when I open successively two .prj files that contain each a fitted spectrum, Athena seems to remember only the positions, widths and amplitudes of arctan and gaussian curves of the spectrum I open first; this translates to the fact that for the other fitted spectra that I open afterwards, it remembers the peak positions, widths and amplitudes of the curves belonging to the initially opened spectrum. The result of this issue is that I need to enter manually each time these values in order to get the fits back again - do you have any suggestions how this can be fixed?; 2) another issue is that after spectra calibrations, the spectrum does not appear to be calibrated. More specifically, when one checks the centroid positions of arctan or gaussian curves directly on the spectrum, the values don't correspond with the ones in the boxes, which I believe that means the calibration did not happen after all. Thank you very much in advance for any suggestions or ideas! Best wishes, Adrian ******************* Adrian Gainar PhD student Office: D37 School of Chemical Engineering and Analytical Science Jackson's Mill University of Manchester Manchester M13 9PL UK e-mail address contact: adrian.gainar(a)postgrad.manchester.ac.uk<mailto:adrian.gainar@postgrad.manchester.ac.uk> office telephone no.: +44(0)161 306 4362

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Fwd: Linear Combination Fitting using ATHENA
by Scott Calvin 09 Aug '13

09 Aug '13

I just noticed part of this thread went off-list. That's easy to do by mistake sometimes. I'm forwarding this part of the exchange to the list so that we don't start talking too much in circles. --Scott Calvin Sarah Lawrence College Begin forwarded message: From: Scott Calvin <scalvin(a)sarahlawrence.edu<mailto:scalvin@sarahlawrence.edu>> Subject: Re: [Ifeffit] Linear Combination Fitting using ATHENA Date: August 9, 2013 8:54:59 AM EDT To: Teck Kwang Choo <teck.kwang.choo(a)monash.edu<mailto:teck.kwang.choo@monash.edu>> Hi Teck Kwang, An Fe3O4 spectrum is available at the CARS XAFS database: http://cars.uchicago.edu/~newville/ModelLib/search.html --Scott Calvin Sarah Lawrence College On Aug 9, 2013, at 8:35 AM, Teck Kwang Choo <teck.kwang.choo(a)monash.edu<mailto:teck.kwang.choo@monash.edu>> wrote: Hi Scott, My spectrum standard fits extremely well with FeO: the sample spectrum's conformation to FeO's can be seen even by just superimposing both spectra together. Through XRD, it was confirmed that Ferrite (-Fe2O4) is the primary form of Fe but unfortunately I did not have any Ferrite standard compound with me during the actual XANES analysis. I am now suspecting that both FeO and -Fe2O4's spectra might be similar to each other. Do you have the spectrum for ferrite (Mg-ferrite if possible) by any chance? Thanks and kind regards. Teck Kwang On 9 August 2013 21:00, Scott Calvin <scalvin(a)sarahlawrence.edu<mailto:scalvin@sarahlawrence.edu>> wrote: Hi Teck Kwang, Molar percent by absorbing atom. In other words, if the best fit is 60% Fe(II), that corresponds to 60% of the iron atoms being Fe(II). But note that XANES depends on more than just valence state. Does the FeO and Fe2O3 combination fit the XANES well? Do those compounds correspond well to the actual compounds expected in the material? Did you try other iron standards? --Scott Calvin Sarah Lawrence College On Aug 8, 2013, at 11:37 PM, Teck Kwang Choo <teck.kwang.choo(a)monash.edu<mailto:teck.kwang.choo@monash.edu><mailto:teck.kwang.choo@monash.edu<mailto:teck.kwang.choo@monash.edu>>> wrote: Hello, I have been using ATHENA to perform Linear Combination Fitting (LCF) on my XANES spectrum to quantify the amounts of Fe (II) and Fe (III) in my samples using only FeO and Fe2O3 as standards. The results showed a majority of Fe (II), which is contrary to what was expected. This made me wonder if the LCF results from XANES is a molar percentage (mol %) or weight percentage (wt%). Could anyone enlighten me on this matter? Thanks! --

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tracking atom positions
by Bruce Ravel 08 Aug '13

08 Aug '13

Matthew said: > As it is now, if you want to describe your unknown structure as a > distorted version of the one for which FEFF was run, you have to > enter formulas for distances by hand. For instance, suppose you're > doing a substitutional dopant and you want to use Artemis to fit the > displacement of the impurity off-site and the dilation/contraction > of the first-neighbor shell. As it is now, you have to do the > algebra yourself to compute all the distances in terms of the > distortion parameters. It would be really nice if there were some > syntax for describing the alteration of atom positions, from which > Artemis would automatically compute the displacements. This might > have to be a new class of parameters. Such a computation would > cover the MS paths as well. What it would still NOT do is account > for the effect of leg-to-leg angles on MS paths (deviation from > focusing/backscatter), but it would be a step. I realize that this > would be a big job to implement in a nice way that wouldn't break > everything that came before, but it would be super useful and make > the IFEFFIT team (yet again) heros to the community It's nice to start a new thread when you start a new thread, so I'm starting a new thread. :) I understand exactly what you are asking for. In short, you would like to be able to parameterize atom positions, possibly even crystallographic parameters, and have those propagated through to the math expressions for delta_R for the paths. In fact, Demeter has some of what's needed already built in. There are two things needed to implement that with the way things currently work. 1. The pathfinder needs to remember the all the scattering geometries that contribute to a degenerate set of paths so that a parameterization has the possibility of breaking degeneracies. 2. In the case of using crystal data, Atoms needs to remember the symmetry operations that were done to place each atom in the cluster. This would allow Demeter to propagate a change in a crystal parameter through to delta_R. #1 already exists in Demeter. #2 is something I worked on in the past, but never got working to my satisfaction. The point is that most of #2 is in there, but commented out. That is, it's reasonably close. As you suggest, the hard part is presenting this to the user. I have actually been thinking about this problem lately and am interested in getting back to it. I have another big feff-interface improvement to work on first (an idea for dealing with Feff calculations over multiple, inequivalent sites in a user-friendly and user-efficient way), but I'll think about it. I should mention that Shelly has implemented something like this before for use with Matt's ancient feffit program. You might be able to get her to chime in.... B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science 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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