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

"FEFF+IFEFFIT" and "cumulant expansion+ratio method" approaches
by Leandro Araujo 20 Jul '06

20 Jul '06

Dear all, I'm stuck on a peculiar situation and would appreciate any kind of help available. I need to "translate" EXAFS analysis results obtained with IFEFFIT/FEFF into the "language" of the cumulant expansion/ratio method approach. More specifically, I have to relate my mean interatomic distance R obtained with IFEFFIT to the first cumulants (mean interatomic distances) that show up in the ratio method formalism. I'm saying the cumulantS because the ratio method makes a distinction between the so called "effective P(r,lambda)" and "real rho(r)" distributions of interatomic distances, which are related by: P(r,lambda)=rho(r)*[[exp(-2r/lambda)]/r^2] . For the second cumulant (Debye-Waller factor or sigma^2) and higher terms, the difference between "effective" and "real" values is not significant unless the disorder in the sample is really big. But for the first cumulant it is significant (at least at not very low temperatures), being the "real" first cumulant bigger than the "effective" one by a term like [(2*sigma^2)/r]*[1+(r/lambda)]. My dilemma is: how my mean interatomic distance R from IFEFFIT relates to the "effective" and "real" first cumulants? Should it be the same as one of them? Which one? Or it doesn't correspond exactly to any of them? Any comments will be welcome... Regards, Leandro

3 2

Job Opening
by Amitava Roy 19 Jul '06

19 Jul '06

Hi Ifeffit users, We have a job opening related to X-ray absorption spectroscopy, described below. Information about the Center for Advanced Microstructures and Devices (CAMD) can be found at the following website: http://www.camd.lsu.edu/ Thanks, Amitava Roy CAMD/LSU _____ Application Deadline: July 31, 2006, or Until candidate is selected Assistant Professor-Research/Associate Professor-Research Ref: Log #0647 The Center for Advanced Microstructures and Devices (CAMD) at Louisiana State University (LSU) in Baton Rouge, Louisiana, invites applications for the position of Assistant Professor-Research/Associate Professor-Research as a beamline scientist in the X-ray spectroscopy group. Responsibilities: Responsible for maintenance and daily operation of X-ray beamlines at the CAMD storage ring; optimization of the beamlines, the experimental stations and the data reduction software for continued routine operation; support of the users; participates in ongoing research projects and develop his/her own "in house" research program according to the candidate's scientific interests; prepares and writes grant proposals for other staff, and especially users. Special Requirements: Willingness and ability to work flexible hours which may occasionally require evening and weekend shifts for completion of experiments. Required qualifications: Ph.D. in Physics Chemistry, Biological Sciences or a related field; experience in the field of X-ray absorption spectroscopy using synchrotron radiation demonstrated by refereed publications etc; familiarity with the theoretical background and the state-of-the-art computer codes (e.g. FEFF and SPRKKR) that are commonly used for data evaluation and interpretation; experience with the operation of synchrotron radiation beamlines and monochromators, including knowledge of vacuum technology, electronics, and computing. Additional qualifications desired: Experience with the techniques of X-ray fluorescence and/or X-ray diffraction and/or small angle scattering (SAXS). Salary and level will be commensurate with qualifications and experience. An offer of employment is contingent on a satisfactory pre-employment background check. Level will be determined based on qualifications and experience. Review of applications will begin immediately. For full consideration, applications must be submitted by July 31, 2006. Applications will be accepted until candidate is selected. Please submit letter of application, C. V. (including e-mail address and publication list), and three references with telephone numbers to: CAMD/LSU Attn.: Craig Stevens 6980 Jefferson Hwy. Baton Rouge, LA 70806 Ref: Log #0647 Louisiana State University Contact info: E-mail: evstev(a)lsu.edu 225-578-4603 Tel. 225-578-6954 Fax For further technical information, you may contact Amitava Roy <mailto:reroy@lsu.edu> via e-mail. LSU IS AN EQUAL OPPORTUNITY/EQUAL ACCESS EMPLOYER

1 0

status of ifeffit on Intel-based Mac's
by aslowey＠pangea.Stanford.EDU 18 Jul '06

18 Jul '06

Hi there, I just sifted through the email archives, but it's not clear whether there's an ifeffit installer that will install useable versions of Athena, etc. As a recent PC-to-Mac convert, thanks to all who are working on this issue. with patience, Aaron Slowey

2 1

Re: phase shift
by Bruce Ravel 17 Jul '06

17 Jul '06

On Friday 14 July 2006 03:03, you wrote: > I'm using Athena for fitting my EXAFS data. I have a problem: I need the > phase shift corrections for Ni as a function of the photon energy in the > range (38-44) keV. In fact, I'm studying the La K edge in LaNi_5 and so I > have to put the phase correction relative to the Ni-La scattering. May you > help me, please? Thank you and excuse me. Antonio, This is the sort of question that you should consider asking on the ifeffit mailing list. That way, when I'm out of town, as I was last week, someone else might be able to answer your question. http://cars9.uchicago.edu/mailman/listinfo/ifeffit/ I believe that the thing you are looking for is answered in the documentation for both Ifeffit and Feff. Here is a link from the Feff6 document that explains what the columns are in a feffNNNN.dat file: http://feff.phys.washington.edu/feff/Docs/feff/feff6-6.html#ss6.7 The language in that document is a bit cryptic, but you can see that the third and fourth columns of that file are the magnitude and phase of the effective scattering function for the path. Here is a link where Ifeffit explains what happens you you directly read a feffNNNN.dat file: http://cars9.uchicago.edu/~ifeffit/refman/node24.html Again, we see that the third and fourth columns of the file contain the magnitude and phase of the effective scattering function. So it would seem, by my understanding of your question, that you need to find the feffNNNN.dat file for the scatterer you are interested in and use the fourth column of that file. HTH, 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/

1 0

ifeffit & horae now officially in Debian distribution
by Carlo Segre 08 Jul '06

08 Jul '06

Hello All: As of today, the ifeffit and horae programs are in the Debian archives. because of their dependence on pgplot which is non-free, they are in the contrib section of the unstable distribution. Please make sure that you have "main contrib non-free" in your apt sources line. If all goes smoothly, they will be available for all the Debian-supported architectures and in 10 days or so will migrate to the testing distribution. I expect that they will also be available under Ubuntu soon. Because of this, I will stop providing ifeffit and horae on my private repository. New versions installable on the stable distribution will continue to be built. If you have any questions or problems installing, please contact me. Cheers, 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

1 0

A feff question
by Scott Calvin 07 Jul '06

07 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!

1 0

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

2 1

Right way of choosing E0 in Athena
by Vadim G Palshin 02 Jul '06

02 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.

4 3

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.

4 3

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/

1 0