April 2007 - Ifeffit - millenia.cars.aps.anl.gov

question concerning Hephaestus
by I.Reitz 17 Apr '07

17 Apr '07

Dear list members, can you please tell me, what the ion chamber utility calculates. I did not understand the perl code. Does it give me first the percentage absorbed via Beers law und then give me the Nbofphotonsabsorbed, that means the flux absorbed in the chamber or is the result that gives the program out the "number of transmitted photons" after the chamber? Thank you Irmi -- ********************************************* I. Reitz German Cancer Research Center DKFZ, E0401 Dept. of Medical Physics in Radiation Therapy Im Neuenheimer Feld 280 D – 69120 Heidelberg Phone: +49 - 6221 42-2455 Fax: +49 - 6221 42-2572 Email: I.Reitz(a)dkfz.de *********************************************

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Doubts
by Shiju N. R. 16 Apr '07

16 Apr '07

Hi, I am Shiju and I work as a research associate at the Chemical Engineering department of University of Cincinnati. We are working on the conversion of light alkanes using mixed oxide catalysts. We are trying to understand the structure of a Mo based mixed oxide catalyst that is highly active for this reaction using XAFS and have some data of this catalyst, collected at NSLS. Since I am new to XAFS, I am trying to learn it myself. I am using Athena and Artemis. I am trying to use MoO3 as a model compound for understanding the Mo local structure in my catalyst. By following Scott Calvin's ZnO example (which is highly helpful for beginners like me), I was able to get a reasonable fit for MoO3 structure. For the next step (fitting my Mo catalyst), I would like to seek help regarding the procedure I should follow. I would like to describe my understanding to approach the fitting of my Mo catalyst and please let me know if I am right or wrong. I am going to take same MoO3 structure to form the theory and import the same paths which were used to fit model MoO3 structure. Then I will set the values of S02 and sigma2 to that obtained for MoO3 and allow E0 and delr to vary during the fitting. Please let me know if this is right approach. I tried once this way, also introducing the concept suggested by Bruce Ravel to find the coordination in one of the earlier posts. I used the expression S02 = ni*amp, where i represents each path, keeping the degeneracy of each path as 1. I was able to get a fit, however, ni are fractions and their sum is much less than 6, while I am expecting an octahedral coordination of Mo in my catalyst. Is it due to any mistake in my approach? what should I do to correct it? Please excuse if these questions seem silly... I am just a beginner in XAFS! Shiju Dr. Shiju. N. R. Research associate Chemical and Material Engineering University of Cincinnati Ohio USA --------------------------------- Yahoo! Mail is the world's favourite email. Don't settle for less, sign up for your freeaccount today.

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Platinum Rhenium EXAFS in Artemis
by Edward L. Kunkes 16 Apr '07

16 Apr '07

Hi everyone, I am new to EXAFS and have been working with Athena to process my data and trying to fit it with Artemis. I have LIII edge EXAFS data from monometallic carbon supported Pt, Re and bi-metallic PtRe nanoparticles (1-3nm). My objective to perform a first coordination shell fit, and i have been successful with the monometallic data and reference samples (Pt and Re foils and salts). Unfortunately success with PtRe bimetallics has been limited so far, and I can not get a good fit with reasonable delEo values. Did anyone work with platinum/rhenium before and can offer some helpful advice? The literature says that even though the backscattering properties of Pt and Re are similar (given their proximity on the periodic table), they should still be distinguishable with k0-weighted fitting. I was also if its possible to use Athena or Artemis to extract the back-scattering properties of Pt and Re from reference samples, and use these properties in fitting a Pt-Re path. Thank you very much for your help -Ed Kunkes Graduate Student University of Wisconsin-Madison Chemical Engineering

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Platinum and Rhenium EXAFS in Artemis
by Edward L. Kunkes 15 Apr '07

15 Apr '07

Hi everyone, Sorry for the formatting error in my last e-mail. I am new to EXAFS and have been working with Athena to process my data and trying to fit it with Artemis. I have LIII edge EXAFS data from monometallic carbon supported Pt, Re and bi-metallic PtRe nanoparticles (1-3nm). My objective to perform a first coordination shell fit, and i have been successful with the monometallic data and reference samples (Pt and Re foils and salts). Unfortunately success with PtRe bimetallics has been limited so far, and I can not get a good fit with reasonable delEo values. Did anyone work with platinum/rhenium before and can offer some helpful advice? The literature says that even though the backscattering properties of Pt and Re are similar (given their proximity on the periodic table), they should still be distinguishable with k0-weighted fitting. I was also if its possible to use Athena or Artemis to extract the back-scattering properties of Pt and Re from reference samples, and use these properties in fitting a Pt-Re path. Thank you very much for your help -Ed Kunkes Graduate Student University of Wisconsin-Madison Chemical Engineering

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max number of restraints
by Victor.Streltsov＠csiro.au 15 Apr '07

15 Apr '07

> Hi Victor, > > It should be > restraint_sum = restraint1 + restraint2 + restraint3 + ... > > That is, a restraint should be a value that you'd like to me made as > small as possible, but can take either sign. The restraints are > simply appended to the "vector to be minimized" in the least squares > sense. > > I'm not sure that will fully solve the issue of having different > results between 10+ individual restraints and fewer summed restraints. > But I'm interested to hear and see more.... >--Matt >Given that individual restraints might be of either sign, you might >consider adding them in quadrature and using the square root of that >as the restraint. As Matt said, the details matter, but I think that >would be a serviceable work around for more than 10 restraints. >B I am confused. I thought I did exactly what Bruce said. I added them in quadrature and used square root of that as the restraint in artemis: After summing in quadrature: restraint_sum = sqrt((restraint1)^2 + (restraint2)^2 + (restraint3)^2...) I asked artemis "to build restraint from "restraint_sum"" and artemis added line: res_restraint_sum=penalty(restraint_sum,n1,n2)*scale This way of summing them seems closer to the way of adding them individually squared to the "vector to be minimized", provided artemis/ifeffit squares them before appending to the "vector" (you don't need to square them before). I guess the questions is what artemis does when asked to "build restraint from ..."? Victor Dr Victor Streltsov CSIRO Molecular & Health Technologies 343 Royal Parade Parkville VIC 3052 Australia Phone: +61 3 96627311 Fax: +61 3 96627101 victor.streltsov(a)csiro.au

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max number of restraints
by Victor.Streltsov＠csiro.au 13 Apr '07

13 Apr '07

Hi Matt, Thanks for your reply. Following Bruce's instructions, I have re-compiled Ifeffit with a larger "max_restraint" number on a Linux Machine. It works fine. Now, I can compare fits obtained with a set of multiple restraints (more elegant) and with a combined (limited to 10) set of restraints. I did combine restraints before in the way almost as you suggested. Assuming that each restraint is squared before adding to chi-square, I used sum as follows restraint_sum = sqrt((restraint1)^2 + (restraint2)^2 + (restraint3)^2...) for group of similar atoms and bond lengths. I guess, the difference in sums should not have a significant effect on fit. However, the difference in fits with multiple and combined restraints is surprisingly noticeable. I expected that the mathematical distinction should be pretty small as you said. But it is not at least in this test. I should explore it a bit more. The restraints combined were for similar sets of both lengths in independent molecular units and should not be strongly anti-correlated. I wonder if when stereochemical restraint relations are used and a large number of independent not equally important (close to zero elements) restraints imposed, convergence and stability of minimization algorithm are affected by such a sparse normal-equations matrix. Regarding the examples with possible more than 10 restraints, I have a data for a solution of Cu(II)complex with two almost geometrically identical organic molecules. The crystal structure and total 28 bond distances with uncertainties are available in the literature. This amount can be reduced to 14 assuming 2-fold symmetry between molecules. I wanted to apply in XAFS fit bit more rigorous independent restraints using available from crystal structure bond distances with uncertainties. In addition, for proper sterochemical restraints (e.g. in "rigid-body" refinement) some bond angles and planar groups restraints may be required, which may be important for multiple scattering paths. I guess, to have a bit more flexibility in the amount of restraints (more than 10) can be useful when fitting data for bio-molecular systems. Victor Dr Victor Streltsov CSIRO Molecular & Health Technologies 343 Royal Parade Parkville VIC 3052 Australia Phone: +61 3 96627311 Fax: +61 3 96627101 victor.streltsov(a)csiro.au >Hi Victor, >As Bruce said, the limit of 10 restraints is compiled-in. It could >certainly be increased. >But I'm impressed that you have more than 10 independent restraints to >impose! Depending on the nature of your restraints, it might be >possible to combine some of them. That is, using one restraint of > restraint_sum = (restraint1) + (restraint2) + (restraint3) >(where each restraint might be an elaborate calculation) is only >different from using three restraints if the three restraints are >strongly anti-correlated, so that they compete against one another. >If you're restraining different bond lengths, some of them probably >can be combined. >It's definitely better, and more elegant, to use multiple restraints, >but I think the mathematical distinction may be pretty small. >--Matt

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multiple k-weights refinments
by marie-helene.tuilier＠uha.fr 13 Apr '07

13 Apr '07

I try multiple k-weights refinments with ARTEMIS of Al K EXAFS of ternary aluminium and titanium nitrides films. This system is rather disordered and textured with large grain boundaries that contribute to EXAFS. Consequently only few parameters can be varied simultaneously. I think that the k**3 weighting plays the major role in the multiple k-weights calculation. There is no great dfference between the results of k**3 weight and multiple k-weights fits. Best regards Marie-Hélène Tuilier Laboratoire MMPF (Mécanique, matériaux et Procédés de Fabrication) Pôle STIC-SPI-Maths, Université de Haute Alsace, IUT de Mulhouse, 61 rue Albert Camus, F-68093 Mulhouse Cedex Tel : 33 (0)3 89 33 75 16 Fax : 33 (0)3 89 33 75 05

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my last message....
by Bruce Ravel 11 Apr '07

11 Apr '07

Sigh.... If any of you had any lingering doubts about what kind of an idiot I am, my last message -- mistakenly sent here rather than to the individual in question -- should clear that right up! Sorry for filling up your mail boxes.... B -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advanced Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/

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Mehmet Alper Sahiner/FAC/SHU is out of the office.
by Mehmet Sahiner 11 Apr '07

11 Apr '07

I will be out of the office starting 04/09/2007 and will not return until 04/15/2007. I will be at the MRS2007 Meeting in San Francisco between 4/9/07-4/15/07 Alper

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max number of restraints
by Victor.Streltsov＠csiro.au 11 Apr '07

11 Apr '07

Hi, I wonder if there is a way to change a max number of restraints in Artemis or Ifeffit. If you have more than 10 restraints in Artemis (which is possible to input in Artemis without a warning), the Ifeffit gives the following message in "ifeffit interaction buffer": *** feffit:: too many restraints restraint will be ignored: and ignores all restraints after the 10th in the Artemis list. Often, you need more than 10 restraints when fitting data for biological samples (e.g. bond length restraints etc.) Thanks Victor

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