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

Re: Artemis Fit Questions
by Scott Calvin 17 Aug '04

17 Aug '04

> >Hi Dan, > >At 12:27 PM 8/16/2004 -0700, you wrote: >> Should I add more paths? > >I always feel more paths are better, until the fit stops working. They will >reduce correlations and uncertainties in general, and also reduce the >incidence of false minima. That does mean you'll have to include some >multiple scattering once you get far enough out, but IMHO poorly >constrained multiple scattering is better than none at all. > >>Is there other parameters that I should add? >>Was it Ok to make 2 separate e0's? > >This is an ongoing debate--it cropped up again on the Ifeffit list >recently. I am not enamored of separate E0's without a very good reason, >but others use them more freely. On the other hand, a separate ss for the >nearest-neighbors from paths further out (I can't tell from your >description if there's a significant separation between the three paths) is >often called for. You might also consider fitting a third cumulant; the >effect on a spectrum is not unlike fitting a separate E0. > >>I think this is a pretty good fit, but I >>feel like there has to be something to improve it. >> > >Seems not unreasonable, although it's hard to tell without uncertainties. >That r-factor is a bit high for a three-path, five parameter fit, though. > >--Scott Calvin >Sarah Lawrence College > >

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Artemis Fit Questions
by Scott Calvin 17 Aug '04

17 Aug '04

Hi all, I've been exchanging emails with Dan Carter, a recent newcomer to EXAFS analysis, and I thought some of the other novices out there might find pieces of it useful. Also, it's always interesting to watch the interplay of the advice from the more experienced users on these basic issues! Therefore, I'm forwarding (with Dan's permission) our exchanges so far to this list (don't worry, there's only a handful!). --Scott Calvin Sarah Lawrence College >Hi Scott, > > Here at Hunter we are trying to make some Li -- MoS2 batteries. >Therefore, I'm trying to do EXAFS on MoS2 and running Artemis on the same. >Basically, I'm trying to create the best fit possible and I was hoping that if >I gave you what I know so far you might be able to give me some suggestions to >improve the fit. > > MoS2 is trigonal or hexagonal depending on who you talk to. >I have 3 paths -- All single scattering below reff = 4 Angstroms. >I made two e0's one for the first path and one for the second, it improved the >fit. All parameters are guesses. > > This is the result I got: >Reduced Chi-square = 809.564600728 >R-factor = 0.039774809 > amp = 0.7511730 > e0 = -1.0221910 > delr = 0.0010090 > ss = 0.0031050 > e0_1 = 2.3828120 > > Should I add more paths? Is there other parameters that I should add? >Was it Ok to make 2 separate e0's? I think this is a pretty good fit, but I >feel like there has to be something to improve it. > > Please help, Dan Carter > >

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a message
by Bruce Ravel 16 Aug '04

16 Aug '04

Hi, A couple weeks ago I received an email from a student at one of the Sao Paolo University campuses named Luis Silva. Luis asked me a question about how to obtain the Ifeffit software. I tried a couple of times to respond to his email, the mail keeps bouncing back with an error message of "Host or domain name not found." I feel badly because he probably thinks I am ignoring him! Does anyone (perhaps one of the Brazilians) on the list know Luis Silva? If so, could you contact him and tell him where to download the Ifeffit package. Thanks! B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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Topical issue for XAFS 12
by Scott Calvin 12 Aug '04

12 Aug '04

Hi all, I contacted the Physica Scripta staff about when the XAFS 12 topical issue will be out...thought you might want to know it will be some time next year. --Scott Calvin Sarah Lawrence College > >Dear Dr Calvin, > >The proceedings will be published during the first half of 2005. > >Sincerely, > >Katarina Lundin >Production Editor, Physica Scripta >The Royal Swedish Academy of Sciences >Box 50005 >SE-10405 STOCKHOLM, Sweden >Email: kat(a)physica.kva.se >Voice: +46 8673 9528 >Facsimile: +46 8673 9590 >

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It works great now -- Re: Running Feff
by dmc＠pdx.edu 11 Aug '04

11 Aug '04

Hi, I just clicked on the default value under the "Feff Executable" branch under "Feff" under "Setting." The default is "Feff6I" with an "I" not a "1" and it works great now. Also, next time I forget about the output window, just say so. I was looking in the Artemis Palletes for an output since it pops up and did not see the window behind. Thanks again, Dan

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Running Feff in Artemis -- More info
by dmc＠pdx.edu 11 Aug '04

11 Aug '04

Hi guys, Thanks for the help, I'm sorry I wasnt completely clear. I thought there might be an easy answer and there still may. I will elaborate. I have tried to 'Run Feff' several times. Including several of the Cu database files one your suggestion. Every time, I 'run Atoms' without a hitch and then when I 'run Feff' I get the error message: There are no feffNNNN.dat files...etc. The output window says: 'feff6' is not recognized as an internal or external command, operable program or batch file. I am indeed operating in Windows. I do have the latest updated for Ifeffit. The Feff.INP file does get created in this directory: C:\Ifeffit\horae\stash\artemis.project.3\data0.feff0 It is 6 KB. Maybe this helps some, I will look at some more of your comments to see if I can figure it out. Thanks Again, Dan

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Running Feff -- In Artemis
by dmc＠pdx.edu 10 Aug '04

10 Aug '04

Hi Feff guys, I'm sure you've answered this question before, but I was wondering about the error message "There are no FeffNNNN.dat files! Something has gone wrong with your feff calculation." I entered all the information into Atoms correctly and Atoms ran fine, but when I run Feff I get this message. Is there a directory that I have to place my Feff.INP file in to make this work? I can't figure it out. Thanks, Dan Carter

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Re: Ifeffit Digest, Vol 18, Issue 2
by m.bondin＠pgrad.unimelb.edu.au 03 Aug '04

03 Aug '04

Hi Shelly - thankyou for your detailed response - it helps greatly and is most appreciated. Cheers, Mark -- Mark Bondin PhD student School of Chemistry, University of Melbourne (03) 8344 7015 (Tower lab) 0409 252 983 (mobile)

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info sought regarding file locking
by Bruce Ravel 03 Aug '04

03 Aug '04

Hi! In the recent release of Athena and Artemis, I believe I fixed the problem that Windows users were observing that files would get locked when in use by one of my programs. This would be a problem if, say, you imported a file into Athena and then wanted to rename or move that file using the file manager. I am interested to know if anyone is still experiencing any problems of this sort. If so, please describe to me in as much detail as possible what lead to a file getting locked by my program. I will assume that if I do not hear from anyone regarding this, that means that this is working properly. Thanks, B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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RE: [Ifeffit] Re: EXAFS analysis of homonuclear metal clusters
by Kelly, Shelly D. 02 Aug '04

02 Aug '04

Dear mailing list - This is a general EXAFS question I decided to post in regards to your collective thoughts and/or experience with this EXAFS analysis approach. I am currently attempting to model a number of Fe-S clusters with nuclearities of 2, 3, 4, 5, and 6. In some cases (where all the Fe atoms are chemically equivalent i.e. same oxidation state and coordination geometry) it is easy to approach this by assuming a single Fe absorber model. When the Fe atoms become inequivalent (oxidation states which may be a mixture of I, II or III, and different coordination geometry) I can average the environments (by including all interactions and ajusting coordination numbers for the different iron atoms accordingly) again into a single Fe absorber model. The fits go well, giving realiable bond lengths (when compared to available crystallographic data), DW's, and statistics (I am also keeping in mind the number of refined parameters to ensure a well over-determined fit for each of the models). My only hesitation, and main reason I am posting this question, is that I am not completely sure this is a reasonable assumption as the Fe atoms are in different oxidation states and will have different E0's. What I do know is there is a shift of roughly 2 to 3 eV in E0 to higher energy for every increase, by one, in oxidation state (i.e. Fe(I) to Fe(II)). Is there any way of determining if this small difference in energy, and hence E0, between the Fe atoms in the clusters can or cannot be neglected in modelling the EXAFS? Regards, Mark -- Hi Mark, I liked Bruce's response, but since you asked again. I will go out on a limb. I believe that your assumption is justified. The theoretical models built using Feff7 or less do not have different Ezero values based on the valence state of the absorbing atom. The difference is made by choosing a slightly different Ezero at the edge, rather than a difference in K=0 in the theoretical model. In addition, different Ezero's become important at low k-values. Using a kmin of 3.0 inverse angstrom or greater, I would not expect you to need different Ezero's. If you move kmin from something like 3.0 inverse angstroms to 1.5 inverse angstroms you might find that your model no longer works with one Ezero. Also, Ezero and Delr are correlated. So say you know delr then you might be able to "see" a few eV shift in Ezero, assuming that you are using a lot of low k in the data range. If you want to see the shift. Then I would get my hands on the metal oxides for each valence state. And then simultaneously fit each oxidation state together with the mixture...You might be able to pull the info out this way. -As Bruce suggested. It is unlikely that your data range and fit range will support more than one Ezero. To verify that only one Ezero is needed: Try several models with a each shell having it's own Ezero, or two Ezeros or one Ezero. Compare the reduced chi square values of the different models. If the reduced chi square value decreases by a factor of two or more then your data will supports more than one Ezero. Also check the uncertainty in the values for Ezero. If the values overlap considering the error then these Ezero-values are the same and should be only one variable instead of two. I am sure that you can find EXAFS papers of mixed Fe(II)/Fe(III) oxides such as magnetite, Fe2O3. I would guess that they are modeled with a single Ezero. HTH Shelly

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