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

A feff question
by Scott Calvin 08 Jul '06

08 Jul '06

Hi all, I know how to handle doping in feff/ifeffit/artemis, but I'm not so confident with crystal structures that have a large fraction of vacancies. Suppose a site has a SOF of 0.50...and no other atom that substitutes. I could run atoms with the site filled, and then run feff, and then use Artemis to cut the amplitude of paths involving that scatterer in half...but will the feff calculation be anywhere near correct? It seems to me like this is a little like running a 6 angstrom cluster and then taking paths out to 6 angstroms--in that case, those last paths aren't very accurate because feff treats those atoms as if they are missing some neighbors. In this case, we have the opposite problem, with feff treating atoms as having more neighbors than they do. I guess one solution would be to go into the feff.inp file and remove roughly the right fraction of the atoms in question. Is that the standard way on handling this? --Scott Calvin Sarah Lawrence College P.S. I'll look forward to seeing many of you in a couple of days!

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Fwd: Re: FW: [Ifeffit] Undergraduates and EXAFS
by Scott Calvin 03 Jul '06

03 Jul '06

Thanks for the references, Anatoly! And, what the heck, I might as well give my opinion on the general topic. While the referee's argument is understandable, I think there are few "physics" fields in which undergrads can make greater contributions than in the characterization of materials using EXAFS. I think that to be good at using EXAFS, a researcher must have very strong general research skills. For example, they have to be able to read the literature, communicate in both directions with those in other fields (e.g., chemists), visualize, be able to distinguish real effects from noise, be able to devise tests to establish the cause of observed effects, etc.. The technique itself requires a substantial learning curve; 80 hours seems about right to be able to =begin= to use it productively. But not a lot of specific Ph.D., or even advanced undergraduate, material is required. How could it be? Although a lot of EXAFS experts were trained in physics, we're seeing more who come out of a variety of disparate fields. And you, Bruce, and others have offered EXAFS short courses for years. So this makes it perfect for a talented undergraduate. Undergraduate interns have the time to spare for that 80-hour learning curve; that only takes the first two weeks of a summer internship. And there's no reason that the best of them shouldn't have better general research skills than a mediocre graduate student. And that's what I've found. The average quality of work does depend on the level of the student in the expected way: high school < undergrad < masters < Ph.D.. But the variation within groups is considerably greater than the variation between groups. In fact, the best member of my research group I ever had, the one who did the most sophisticated work, was a high school student! That's my two cents, anyway. :) --Scott Calvin Sarah Lawrence College > >In short, the referee's argument is of course strong one, but a good >planning of undergraduate research can help make use of undergrads. >Since these are EXAFS papers, you can definitely use them to support >your claim that EXAFS research can be done with undergrads. We have >several professors at YU who publish their research, not EXAFS >related, with undergraduates in top journals. > >Anatoly

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Right way of choosing E0 in Athena
by Vadim G Palshin 03 Jul '06

03 Jul '06

>Since you know the spectra are well calibrated relative >to one another, I would use a single E0 for all >background subtractions. In such a situation, I tend to >play with the background parameters for one of the >spectra and then apply these background >parameters to all other spectra. Thanks, Matt! Yes, that’s pretty much what I have been doing, just had some trouble getting reasonable fit values for E0’s in my last set of samples. Aligning chi(k) of the standard to theory – great guide, Shelly! – and then applying the same parameters to the other spectra helped solve this. Now, more questions: 1. Many experts advise to do multiple k-weight fitting to deal with correlated variables. Should one always use multiple k-weights, or is it better to switch to one kw value once the correlations are taken care of – to refine the remaining variables? Does it make any difference? 2. When modeling the Debye-Waller factors for multiple-scattering paths, is it possible to express them in terms of the sigma^2’s of single-scattering paths that correspond to the atoms involved in the multiple scattering events; i.e. for a core—atomA—atomB—core path, can sigma^2 be obtained by some combination of core—atomA and core—atomB sigmas? It seems intuitively that they should be related, and also that the amplitudes of multiple scattering paths should be more sensitive to disorder. Does this make any sense? Thanks again for your replies! Vadim.

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E0 and background subtraction
by Vadim G Palshin 29 Jun '06

29 Jun '06

Hi everyone, I have the following question: I have a set of spectra collected in transmission with 3 ionization chambers and a standard between 2nd and 3rd ion chambers for calibration, so I know my spectra are nicely calibrated relative to each other. Should I then force Athena(/autobk) to use the same E0 for all of them (e.g. use the atomic value) or let it find E0 independently for each sample? Thanks! Vadim.

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Fwd: Re: r-factor
by Bruce Ravel 23 Jun '06

23 Jun '06

On Friday 23 June 2006 05:01, you wrote: > I have a question about Artemis log file. I noticed that two r-factors are > reported in the log file. One is in the fifth line and it is called > 'R-factor' and the other one is under the data set fitting conditions and > it is called 'r-factor for this data set'. They have in general different > values. What does it mean? Which is the difference between the two? It probably means that I am calculating something wrongly. Here's the concept. If you do a multiple data set fit and you have some value of R-factor, you would like to know how that misfit is partitioned among the data sets. That is, you'd like to know if one set is contributing to the misfit for significantly than the others. When Ifeffit computes the R-factor, it is for the entire fit. My idea in Artemis was to use the formula for R factor from page 18 of http://cars9.uchicago.edu/~newville/feffit/feffit.ps on each data set in a multiple data set fit and report that in the log file. At some point, I must have convinced myself that I was doing the calulcation in Artemis identically to how it is done in Ifeffit. If you are seeing different values, it would seem I was mistaken. I'll make an entry in my to do list to look into that. 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/exafs/

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data file format
by emmanuelle montarges-pelletier 22 Jun '06

22 Jun '06

Hello I have some problems with data file format as I try to import exafs files in Artemis or in Athena. I am working on a powerbook G4, with OSX 10.4.6. I installed the ifeffit package, including Athena and Artemis. Athena could open any XAS "raw" file from fluorescence or transmission measurements. However, if I perform any modifications on these raw files with exterior programs (Michalowicz programs, Kaleidagraph) and try to import the new files , saved as text files, Athena or Arthemis can not open them. I guess it may come from the encoding of the text file. Do you have any clue on this encoding issue? Do you know any program which would allow me to transform these text files in readable files for Artemis? Thank you for your answer sincerely Emmanuelle ********************************************* Emmanuelle Montargés-Pelletier CR CNRS LEM UMR7569 CNRS-INPL-ENSG 15 avenue du charmois BP40 54501 Vandoeuvre les Nancy cedex France Tel 33 (0)3 83 59 62 52 fax 33 (0)3 83 59 62 55 emmanuelle.montarges(a)ensg.inpl-nancy.fr http://www.ensg.inpl-nancy.fr/lem/ **************************************************

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The most important fitting parameters
by Bridget Ingham 21 Jun '06

21 Jun '06

Hi Bruce and Shelly, thanks for your replies. The problem I am encountering is that we know virtually nothing about the crystallography, only the elements that are present. We expect the structure to be quite different to CuWO4, even though this is the stoichiometry obtained. Addressing some of your questions/comments: Shelly: 1) I will try this. In other systems I've tried the second oxygen shells don't contribute significantly, so maybe they are unnecessary and only adding to the uncertainty in the other shells. 2) & 3) As mentioned above, we don't even know this about the structure. But it is worth me having a go at restricting the delr's to relate to CuWO4. I am loathe to do the same with the amplitudes however, as I expect the co-ordination numbers to be completely different. 4) Yes, I ran a CuWO4 standard at the same time. It looks completely different ;) 5) & 6) Thanks for these tips! Bruce: I have kept E0 the same for all shells, hence 13 parameters (4 shells x amp, delr, ss; plus E0). Sorry for not making that clear enough. The data stops at 9 Ang-1 because there seems to be some Zn edge impurity :( I will play around with the constraints a bit more (starting with the CuWO4 standard) and let you know how I get on. Thanks again for your help! Bridget This electronic transmission and any documents accompanying this electronic transmission contain confidential information belonging to the sender. This information may be legally privileged. The information is intended only for the use of the individual or entity named above. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution or the taking of any action in reliance on or regarding the contents of this electronically transmitted information is strictly prohibited. This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

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Debian packages of ifeffit and horae
by Carlo Segre 20 Jun '06

20 Jun '06

It has taken a bit of time but the Debian packages of ifeffit and horae are now uploaded to my apt repository. Note that horae requires a new Perl module to be installed (libtext-glob-per) and so will have to be upgraded expplicitly. Also note that if you are using the "etch" or "sid" versions of the packages, that a new version of pgplot5 will be also installed. This is to correct a serious bug that exists in the Debian version at this time. Thanks to Ken McIvor for fixing this. hopefully a new official Debian version will be coming out soon to fix this officially. The repositories for the various distributions are, as always: # For the stable (sarge) distribution deb http://fermi.phys.iit.edu/debian/sarge binary/ deb-src http://fermi.phys.iit.edu/debian/sarge source/ # For the testing (etch) distribution deb http://fermi.phys.iit.edu/debian/etch binary/ deb-src http://fermi.phys.iit.edu/debian/etch source/ # For the unstable (sid) distribution deb http://fermi.phys.iit.edu/debian/sid binary/ deb-src http://fermi.phys.iit.edu/debian/sid source/ Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 Carlo.Segre(a)iit.edu http://www.iit.edu/~segre

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how to creat a chi.dat
by tony vitova 19 Jun '06

19 Jun '06

Hi, I will be very thankful, if you tell me how to create a chi.dat file with Artemis. My PRINT and CONTROL cards in feff.inp are: CONTROL 1 1 1 1 PRINT 5 1 1 1 I am expecting it to be in D:\Program Files\Ifeffit\horae\stash\artemis.project.3\data0.feff1 but it is not there? Is there another way ...? Thank you very much for the help! Tonya Vitova --------------------------------- Yahoo! Messenger with Voice. PC-to-Phone calls for ridiculously low rates.

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The most important fitting parameters
by Bridget Ingham 16 Jun '06

16 Jun '06

Dear all, I am trying to use EXAFS, along with other techniques, to attempt to find information about an unknown structure. It is an organic-inorganic hybrid material, EDX reveals Cu1-W1-O4 as the stoichiometry of the inorganic component, which we are most interested in structurally. We have not been able to solve the structure from XRD, although not for want of trying. I started off with CuWO4 as the model compound and constrained the fitting parameters: - take all 1st oxygen shells (x6 at slightly different distances) and give them all amp1, dr1*reff, enot and ss1 - take all 1st copper shells (x2) and give them both amp2, dr2*reff, enot and ss2 - take all 2nd oxygen shells (x6), amp3, dr3*reff, enot, ss3 - take all 1st tungsten shells (x6), amp4, dr4*reff, enot, ss4 This gave me 13 parameters with 14.8 independent points. (Other factors: fitted in kw=2&3, k-range 2-9, used Athena with default background subtraction parameters as the chi(k) from that seemed sensible. The data were collected at SSRL, beamline 11-2, in transmission.) I was happy with the final result (R-factor 0.014), but am just wondering if this is a sensible way to go about doing things - bearing in mind I am not sure of the structure in the first place. Any hints or advice would be much appreciated. I should have collected data at the tungsten edge as well, as it is not that much higher in energy from Cu, but this didn't occur to me until later. Regards, Bridget This electronic transmission and any documents accompanying this electronic transmission contain confidential information belonging to the sender. This information may be legally privileged. The information is intended only for the use of the individual or entity named above. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution or the taking of any action in reliance on or regarding the contents of this electronically transmitted information is strictly prohibited. This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

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