August 2013 - Ifeffit - millenia.cars.aps.anl.gov

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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FEFF report: Hard tests failed in fovrg.
by Naumova, Maria 07 Aug '13

07 Aug '13

Dear EXAFS people, I have a question that appeared in FEFF and IFEFFIT several times. Still I didn't get an answer. Here are some links to this question discussed or asked previously: http://cars9.uchicago.edu/feff/feffusers/msg00255.html http://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg02675.html http://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg01532.html http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2005-October/002080.html I have EXAFS of several similar organic complexes - copper which has S, N and Hal (Cl or I), and sometimes copper in its first coordination shell and more C and N in ligands. I have structural data for them which I use as a model for FEFF. When I run FEFF via Artemis I get the following report for all my substances (I have 6 potentials in the list): Calculating potentials and phases... free atom potential and density for atom type 0 free atom potential and density for atom type 1 ...and so on... overlapped potential and density for unique potential 0 overlapped potential and density for unique potential 1 ...and so on... muffin tin radii and interstitial parameters phase shifts for unique potential 0 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. phase shifts for unique potential 1 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. ...and so on... Feff done. Have a nice day. In FEFF documentation I read the following: "To save time the code calculates the overlapped atom potential for each unique potential only once, using as a sample geometry the first atom in the atom list with a given unique potential index. Thus it is essential that the neighborhood of that sample atom be representative. Failure to do so may cause the code to perform poorly. " http://leonardo.phys.washington.edu/feff/Docs/feff6/feff6-4.html#pot I think that at least for copper and halogen or sulfur geometry of every atom in the atom list is representative. "Often we receive reports by users of older versions of FEFF of bugs that are fixed in the latest releases. Other code failures can often be traced to input file errors, sometimes quite subtle. An example would be non-physical widely spaced distributions of atoms. Symptoms of this common problem are very large muffin-tin radii (see the header of any .dat file) and possibly a failure of the phase-shift program to converge." http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2005-October/002080.html Here the reason is explained. Since it's an organic complex local distances between neighrours are small, but distances between parts of molecule can be quite big. Still it's not "non-physical widely spaced distributions of atoms". For example distance from copper to the first shell is 2 - 2.3 A (2.6-2.7 to I and Cu). To the "second shell" (ligand atoms connected to the first shell atoms or not connected but close to central atom) - 2.9 - 3.4 A. Finally what I want to know: May I use this FEFF calculation as a valid base for future fit? Or this error means that FEFF doesn't work correct and I can't rely on its output? If the phase-shift program failed to converge does it mean that it could stop in some completely unrealistic result? I attach several FEFF inp files which have this problem. Thanks for your help, Maria Naumova PhD student in DESY

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linear combination fitting
by Shaofeng Wang 07 Aug '13

07 Aug '13

Dear Bruce, I am using Dathena to do some linear combination fitting. In your program, you give three methods for fitting, nomal, derivate and chi(k). I got three different results using these methods. My question is which one is better to obtain more reasonable result or what the purpose of each method is. Regards, Shaofeng

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Re: [Ifeffit] linear combination fitting (Matt Newville)
by fred.mosselmans＠diamond.ac.uk 07 Aug '13

07 Aug '13

Matt wrote "Please avoid asking "why is the blue curve always lower than the red curve"?" By using a negative offset in Athena you can get the red curve below the blue curve :-) cheers Fred I hope Matt doesn't have the monopoly on jokes. -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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. Re: Split white line in TcO2 spectra and similar Tc(IV)
by fred.mosselmans＠diamond.ac.uk 07 Aug '13

07 Aug '13

Dear Wayne Thanks for your explanation Fred -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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