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

Re: [Ifeffit] IFEFFIT update (windows7)
by hemantha aranwela 19 Aug '10

19 Aug '10

Hi Todd, Thanks for the information. But I have already tried that. Doesn't work for me. But since it has worked for you I guess the problem is still in my computer. Unfortunately I do not know what it is. So, I am going to download and install updates directly as Matt has suggested. Thanks. Aranwela Date: Tue, 17 Aug 2010 08:52:28 -0600 From: "Monson, Todd" <tmonson(a)sandia.gov> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] updating Athena in Win 7 Message-ID: <AC050BA7EAC9A34E9A05BC31C3AA2E8B186774E38A(a)ES02SNLNT.srn.sandia.gov> Content-Type: text/plain; charset="us-ascii" Aranwela, It sounds like you're having the same problem that I was having. You need to change the permissions in the Ifeffit folder under program files. There is a good discussion of this that worked for me under Vol. 90, Issue 5 of the Ifeffit digest. This is a copy of the portion of that conversion that you need: "Right click on the IFEFFIT folder in Program Files and select Properties. Select the Security tab and then click the Edit button. For all of the group or user names listed make sure Allow is marked for all permissions (Checking Full Control should select all of the permissions in the list below it). Hit the Apply button and then the OK button. Then try opening Athena again and see if it successfully runs through the update process. " Todd Monson Sandia National Labs Nanomaterials Sciences P.O. Box 5800, MS 1415 Albuquerque, NM 87185-1415 (505) 845-2129 Fax: (505) 844-5470

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Help with cif file
by Kleper Rocha 18 Aug '10

18 Aug '10

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updating Athena in Win 7
by Monson, Todd 17 Aug '10

17 Aug '10

Aranwela, It sounds like you're having the same problem that I was having. You need to change the permissions in the Ifeffit folder under program files. There is a good discussion of this that worked for me under Vol. 90, Issue 5 of the Ifeffit digest. This is a copy of the portion of that conversion that you need: "Right click on the IFEFFIT folder in Program Files and select Properties. Select the Security tab and then click the Edit button. For all of the group or user names listed make sure Allow is marked for all permissions (Checking Full Control should select all of the permissions in the list below it). Hit the Apply button and then the OK button. Then try opening Athena again and see if it successfully runs through the update process. " Todd Monson Sandia National Labs Nanomaterials Sciences P.O. Box 5800, MS 1415 Albuquerque, NM 87185-1415 (505) 845-2129 Fax: (505) 844-5470

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Help with cif file
by Kleper Rocha 17 Aug '10

17 Aug '10

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Re: [Ifeffit] PYTHON scripting on MacOS & XP (Joel Brugger)
by Brugger, Joel (SAM) 17 Aug '10

17 Aug '10

Hi Matt, Thanks for the update. We had trouble getting the XP version to work. We're running Win XP under parallels on the Mac. Ifeffit (1.2.11), python (2.5) and the wrapper installed successfully. The ifeffit.py shell (in the python/scripts directory) does not recognise any python commands. And opening python in the ifeffit directory - it does not recognise ifeffit in the "import ifeffit" command. What are we doing wrong? Thanks, Joel & Barbara

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incorporating feff 8 into Artemis
by Jatinkumar Rana 17 Aug '10

17 Aug '10

Dear All, Recently, I have decided to upgrade to Feff8.20. We have got Feff820a.exe file. I would like to know if there is any specific procedure to replace older Feff6 with this Feff820a.exe in artemis ? Thank you very much in advance !!! Best regards, Rana

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problem with the current Ifeffit installer for windows
by Bruce Ravel 16 Aug '10

16 Aug '10

Hi all, Last week, I discovered a problem that might affect some of you. The current Windows installer package, ifeffit-1.2.11.exe, has a problem to do with how the ifeffit library was compiled. Fortunately, this problem was subsequently fixed. If you have installed the updates that have come out since ifeffit-1.2.11.exe was released, then you are fine. If, however, you have installed the installer *without* installing the updates, then your version of Artemis will be performing its fits slightly incorrectly. To find out if your installation is affected, start Artemis and select "About Ifeffit" from the Help menu. * If the version number for Ifeffit displayed in the echo area at the bottom of the Artemis window says "1.2.11" then you need to update. * If the version number says "1.2.11c" then you are fully updated and will not suffer from this problem. If you need to update but are, for some reason, unable to do so by the normal channel, there are instructions for updating by hand at this wiki page: http://cars9.uchicago.edu/ifeffit/IfeffitOnWindows/WinUpdater If you are using the incorrect version of the Ifeffit library, your fits will still be reasonable, but the best fit values of your parameters and all statistical parameters will be calculated differently from the normal version of Ifeffit. In my limited experience, best fit values tend not to different outside of their error bars, but they are different. The reason I noticed this problem is because here at Brookhaven, our internet access goes through a proxy server. If you are not configured to have the runner go through the proxy server, then it will be unable to find and download the updates. The solution I found for my colleague's computer was to set the http_proxy variable in C:\Program Files\Ifeffit\config\updater.ini to the address and port of the local proxy. I will work on making a new installer next week when I return from an experiment at the APS. For those affected by this long-standing but recently-discovered problem, I apologize. B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

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Re: [Ifeffit] Ifeffit Digest, Vol 90, Issue 7
by hemantha aranwela 16 Aug '10

16 Aug '10

Message: 4 Date: Thu, 12 Aug 2010 12:47:50 -0400 From: Bruce Ravel <bravel(a)bnl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Cc: "Beauchemin, Suzanne" <Suzanne.Beauchemin(a)nrcan-rncan.gc.ca> Subject: [Ifeffit] Fwd: Windows 7? Message-ID: <201008121247.50747.bravel(a)bnl.gov> Content-Type: Text/Plain; charset="iso-8859-1" Hi all, This afternoon I was asked the following: > They are talking here to move us all from XP to Window 7... I checked on > your website and Athena is compatible with XP, Windows 2000, Windows > 95/98/ME but there is no mention of Window 7. Is it also adapted for > Window 7? Not having used Windows 7 myself, I don't have a lot to say. I know that everything worked OK with Vista, so I presume that the same is true of 7. Would anyone else like to comment to Suzanne on this issue? Thanks, B Hi Suzanne and Bruce, It works fine with Windows 7. But the updating is the problem. Runner.exe doesn't work properly. The window (runner) opens and download the files but does not install. Initially I thought it is due to the security settings and changed those. Still, no improvement. Thanks. Aranwela

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Haha
by Scott Calvin 15 Aug '10

15 Aug '10

Hi all, For a little comic relief, I just came across this graph: http://www.usablemarkets.com/wp-content/uploads/2010/06/fed-rate-3.jpg I have never seen a graph unrelated to XAFS looks more like (noisy) XAFS data... --Scott Calvin Sarah Lawrence College

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Re: [Ifeffit] updating Athena in Windows 7
by Monson, Todd 13 Aug '10

13 Aug '10

My difficulty in updating Athena was indeed a permissions problem. After following Laurent's suggestions, I was able to edit and save the updater.ini file as well as successfully download and install the updates to Athena while starting up the program. Thanks for all the help! Todd ---------------------------------------------------------------------- Message: 1 Date: Wed, 11 Aug 2010 07:13:23 -0500 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] updating Athena in Windows 7 (Matt Newville) Message-ID: <AANLkTin3bADHAyZX8g2jRZ5WvcJvKOhPF1mGS0qFMwCF(a)mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Hi Todd, That sounds like a permissions problem to me. Some account needs to be able to write to that file.... If updating the updater.ini file is not working, and Laurent's suggestions don't let you edit that file, you could also try downloading and installing the update zip files by hand. This is a bit more work (compared to editing updater.ini!), but the description at http://cars9.uchicago.edu/ifeffit/IfeffitOnWindows/WinUpdater guides you through it. Hope that helps, --Matt ------------------------------ _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit End of Ifeffit Digest, Vol 90, Issue 6 **************************************

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PYTHON scripting on MacOS & XP
by Brugger, Joel (SAM) 13 Aug '10

13 Aug '10

We used python scripting in 2005 (Win XP). However trying to get back into it we ran into trouble: - We're now using MacOS X, but could not find a python wrapper in the current iXAFS or IFEFFIT installs; is python scripting supported on the mac at all? - We then tried to get back to the PC version, only to discover that the wrapper also seems to be absent from the latest install. Can you please help us to get going again with python scripting? If this option is not supported anymore, can you recommend an alternative? Thanks, Joel & Barbara

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two measurements of the same compound in different beam-lines
by María Elena Montero Cabrera 13 Aug '10

13 Aug '10

Hi all! I have performed two independent XAFS measurements of Cr K-edge of the same Fe-Cr sample at two different beam-lines at SSRL. I have obtained the Fe-K edge data only once. The quality of data are different in each measurement. However, I cannot average spectra from different Cr-K measurements, and I don't know if I could take somehow advantage from having almost twice the information for the Cr- K adge, or I have to use only the better quality data and discard the other. What do you advice? If I can use both measurements, how can I do the fitting in Artemis? Thank you very much and all take care -- María Elena Dra. María Elena Montero Cabrera Departamento de Medio Ambiente y Energía Centro de Investigación en Materiales Avanzados (CIMAV) Miguel de Cervantes 120, Compl. Ind. Chihuahua Chihuahua CP 31109, Chih. México Tel (614) 4391123

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S K-edge of CdS(ZnOOH) Thin Films
by Kevin McPeak 12 Aug '10

12 Aug '10

Hi all, On Aug 22nd I will acquiring S K-edge XANES spectra (at APS 9-BM) of CdS(ZnOOH) thin films that I have grown in my lab. The films are grown in such a way that their composition and thickness vary as a function of position. View the following pdfs for details on thickness and composition: http://dunx1.irt.drexel.edu/~kmm333/cdzns/figure1.pdf http://dunx1.irt.drexel.edu/~kmm333/cdzns/figure3.pdf The idea is to take scans at various position along the middle of the substrate and observe how the different amounts of oxygen affect the Sulfur species present. Foreseeable issues are: 1). The CdS(ZnOOH) films are deposited on FTO (250 nm F:SnO2 film deposited on 2 mm of soda lime glass). There is 0.2 wt% SO3 (0.05 at% S) in the glass according to the manufacturer. We will run a scan on the bare FTO before starting work on CdS(ZnOOH), hopefully the SO3 in the glass is below the detection level. 2). If the SO3 in the glass is an issue I also have a sample where the CdS(ZnOOH) film is deposited on <100> Silicon. In earlier work I tried using this sample at the Cd and Zn K-edge at the APS 10-BM (to reduce scatter from the glass) but I ended up getting Bragg peaks in the spectra. Outside of spinning the substrate (not really an option here) do you have any suggestions for avoiding the Si Bragg peaks? I read one paper where they discussed deglitching but I am not sure how well that would go over with reviewers. Furthermore, grazing-incidence is not an option at 9-BM. All of the measurements above either have been (Cd and Zn) or will be (S) acquired in fluorescence. I am meeting with the beamline scientist to discuss this next Thursday but I figured it was a good idea to get input from the list as well. Any advice is most appreciated. Regards, Kevin McPeak kmm333(a)drexel.edu 312.371.5477 -- PhD Candidate Chemical Engineering Drexel University

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Fwd: Windows 7?
by Bruce Ravel 12 Aug '10

12 Aug '10

Hi all, This afternoon I was asked the following: > They are talking here to move us all from XP to Window 7... I checked on > your website and Athena is compatible with XP, Windows 2000, Windows > 95/98/ME but there is no mention of Window 7. Is it also adapted for > Window 7? Not having used Windows 7 myself, I don't have a lot to say. I know that everything worked OK with Vista, so I presume that the same is true of 7. Would anyone else like to comment to Suzanne on this issue? Thanks, B ------------------------------------------------------- -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

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amplitude values too high (>>100%)
by Edgar Macias 11 Aug '10

11 Aug '10

Hello, I am looking for some help on trying to understand what is wrong with our data. We are very impressed with the high values of amplitude (up to 390.24) that we got working with Artemis and we know are wrong. Hope somebody could help us and take a look into these files, we will appreciate it. Thank you in advance!

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Re: [Ifeffit] updating Athena in Windows 7 (Matt Newville)
by Monson, Todd 11 Aug '10

11 Aug '10

Matt, I tried resetting the timestamp to 0 under: Ifeffit\config\updater.ini. However, I could not save the changed updater.ini file. I verified that I have administrator privileges on my computer. Could something else be preventing me from updating the updater.ini file and in turn updating Athena? Todd Date: Wed, 28 Jul 2010 07:37:52 -0500 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] updating Athena in Windows 7 Message-ID: <AANLkTinxBX3aCXUGdN5XZCajMuK5gWCyftb9N-6YvpVz(a)mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Hi Todd, On Mon, Jul 26, 2010 at 3:39 PM, Monson, Todd <tmonson(a)sandia.gov> wrote: > On Saturday, while starting up Athena, I was informed that there was > an update to Athena available.? I tried installing the update but > failed.? I am afraid this is due to some user permission issue in > windows 7.? How can I try to reinstall the update and ensure that it works? You can change the file current.dat in C:\Program Files\Ifeffit\config. It probably reads 013 right now, and you could change that to 012 or even lower. That will cause an update the next time ifeffit looks for updates, which only happens when one of the programs starts and if the time in Ifeffit\config\updater.ini is past. To force a check for updates the next time ifeffit runs, change updater.ini to read timestamp = 0 In general, I believe this should work for Windows 7 (I have access to two Windows 7 64-bit machines, and all seems to be working on them, though I admit to not stressing them too much). So, as you say, I would also guess that the trouble you had was "only" permission issues. But, please let us know how it goes, Sorry for the trouble, --Matt ------------------------------ _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit End of Ifeffit Digest, Vol 89, Issue 19 ***************************************

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How to analyze this data
by Elsa E. Sileo 10 Aug '10

10 Aug '10

I have some measurements at the As edge of As(V) adsorbed onto pure goethite (alfa-FeOOH), Mn partially substituted Goethite (alfa-Mn,Fe.OOH), Al substituted goethite (alfa-Al,FeOOH) and Mn and Al goethite (alfa-Al,Mn,FeOOH) The EXAFS signals change from one spectrum to another. I have refined the distances As-Fe on pure goethite, but when I try to refine Mn-FeOOH or Al,FeOOH, the analysis gets more difficult because As forms different complexes with Al and Fe. Unfortunately for me is almost impossible to have the pure phases alfa-MnOOH or alfa-AlOOH, and measured the As adsorbed. How can I analyze the spectra and have some knowledge about the As-surface complexes formed? Thanks, Elsa Dra. Elsa E. Sileo Solidos Inorganicos INQUIMAE - Dto. Qca. Inorganica, Analitica y Qca. Fisica; FCEN, UBA Int. Güiraldes 2160, Pabellón 2, Piso 3, Ciudad Universitaria - C1428EHA CABA - Argentina Tel: (54 11) 4576 3380 ext. 113 Fax: (54 11) 4576 3341 e-mail: sileo(a)qi.fcen.uba.ar

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Re: [Ifeffit] Physical meaning of POLARIZATION card 0 0 1
by Joshua Kas 06 Aug '10

06 Aug '10

Does this POL card > setting mean that the electric vector is along the z/c axis of the > crystal axis? Not quite. FEFF doesn't really know about crystal symmetry. The coordinates in the POLARIZATION card are the same as those in the feff.inp file under the ATOMS card. If the c axis of the crystal happens to be along the z direction, then POLARIZATION 0 0 1 sets the electric field vector along the c axis. You will have to look at the coordinates in the feff.inp to figure out which direction the c axis is. I may be wrong, but I think atoms/webatoms puts the c-axis in the z direction by default. Cheers, Josh Kas > I did read the Feff manual and the POL card but I am > still confused how to relate these to the crystal structure and > orientation. > > Thank you all in advance, > > -- > Chris Patridge > PhD. Candidate > Dept. of Chemistry > SUNY University at Buffalo > Buffalo, NY 14260 > Contact: 315-529-0501 > >

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Physical meaning of POLARIZATION card 0 0 1
by Chris Patridge 06 Aug '10

06 Aug '10

Hello everyone, I am working on modeling HfO2 using L3 Hf edge data. Using the default Feff input generated in Artemis, there is some significant mismatch between the data and theory so I augmented the Feff file by adding the POLARIZATION card setting the values of x y z to (0 0 1). Summing the theoretical paths in this calculation looked much closer and fitting the theory gives the results pasted in the text file. Does this POL card setting mean that the electric vector is along the z/c axis of the crystal axis? I did read the Feff manual and the POL card but I am still confused how to relate these to the crystal structure and orientation. Thank you all in advance, -- Chris Patridge PhD. Candidate Dept. of Chemistry SUNY University at Buffalo Buffalo, NY 14260 Contact: 315-529-0501

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Stoichiometry from EXAFS data
by Peter Zalden 02 Aug '10

02 Aug '10

Dear Feff users, lately, we measured a sample containing Sb and Te at EXAFS beamline CEMO, Hasylab and are wondering whether one can determine the stoichiometry from the height of the different K edges´ steps, if one normalizes the values on the edge steps of the elements (cf. http://physics.nist.gov/PhysRefData/XrayMassCoef/tab3.html) The absorption gases and the specimen were not changed for the different K edges. Of course, I have already tried doing so and from statistical reproducibility and from the resulting values compared to the expected ones I would estimate an error of this method of about 1%. A source of error that I could imagine originates from the different beam position at different energies combined with a slight inhomogenity in the pressed sample powder. Now my question is: Are there any other sources of error that I should take into accout? Is there any reference on this method from a more experienced user that I could cite? Kind regards, Peter --- Dipl.-Phys. Peter Zalden I. Physikalisches Institut IA, RWTH Aachen, 52056 Aachen EMAIL: zalden(a)physik.rwth-aachen.de

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Large Amplitude Values
by Gavin Garside 31 Jul '10

31 Jul '10

Fellow X-Ray Absorption Enthusiasts, I have recently compiled a model that gives excellent visual fits in R, q, and k space for bond spacing in a BCC structure. This model gives bond spacings that make sense, and are very close to what would be expected from this set. The R factors are very low, and the enot values correspond quite well to the edge. However, our amplitude values are much larger than typically expected. They come in at the range of 1.8 up to 5.0, but only on a few data sets. On all the rest the amplitude values are 0.4 to 1.0. Could this increase in amplitude be attributed to the fact that we ran florescence measurements instead of transmission, and have a weaker signal coming to the detector? What else could be causing this in only one data set? All samples used in this model have the same structure. Thanks in advance to any replies, your help and time is appreciated. Gavin gavin_garside(a)yahoo.com

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Large Amplitude Values
by Gavin Garside 30 Jul '10

30 Jul '10

Group, I have recently compiled a model that gives excellent visual fits in R, q, and k space. This model also bond spacings that make sense, and are very close to what would be expected from this set. The R factors are very low, and the enot values correspond quite well to the edge. However, our amplitude values are much larger than typically expected. They come in at the range of 1.8 up to 5.0, but only on a few data sets. On all the rest the amplitude values are 0.4 to 1.0. Could this increase in amplitude be attributed to the fact that we ran florescence measurements instead of transmission? What else could be causing this in only one data set, where they all have the same structure. Thanks in advance to any replies, your help and time is appreciated. Gavin gavin_garside(a)yahoo.com

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Re: [Ifeffit] Case of "nonequivalent multiple atomic sites of absorbing atoms"
by Jatinkumar Rana 29 Jul '10

29 Jul '10

Dear Matt, Dear Scott, Thank you very much for the detailed explanation on Delta E0 and S02. Now, things are becoming more clear to me. Best regards, Rana On 28.07.2010 19:00, ifeffit-request(a)millenia.cars.aps.anl.gov wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. Re: Case of "nonequivalent multiple atomic sites of absorbing > atoms" (Matt Newville) > 2. Re: Case of "nonequivalent multiple atomic sites of absorbing > atoms" (Scott Calvin) > 3. Re: updating Athena in Windows 7 (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 28 Jul 2010 06:46:24 -0500 > From: Matt Newville<newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Case of "nonequivalent multiple atomic sites of > absorbing atoms" > Message-ID: > <AANLkTikm-ufMHua8Tpoq3ja7Xr0Bc+XxFPWfSh75RZgO(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Dear Rana, > > Delta E0 is a shift in the Energy origin of k, that is where k=0. For > the experimental data, this was chosen empirically (and so somewhat > arbitrarily) from the measured data. For the FEFF calculation, it was > chosen at the calculated absorption threshold (lowest available > electronic level), but is known to not be perfect at this, especially > in Feff6. > > Though E0 is meant to be the absorption threshold, it is more > important that the FEFF calculation and measured data agree. Because > of this, Delta E0 is best left as an adjustable parameter in the > analysis. > > It is generally found that a single Delta E0 parameter is needed *per > measured data set and per FEFF calculation*, because measured data can > be shifted in energy and because each calculation can have a different > definition of E0. It is possible to read the FEFF outputs and try to > figure out how different these energies are and so set (not allow to > float) the different E0 values. I believe this can work well, but it > is not automated, and so not often used. In addition, usually one > uses a different Delta E0 for each data set, but well-aligned data > that re-use a FEFF calculation (say, data taken on the same system at > different external conditions) can often get by with sharing a single > Delta E0 parameter. > > S02 is meant to express the incomplete overlap of the "passive > electrons" in the absorbing atom. Removing the deep core electron can > allow the other (L, M, N, O) electrons to relax slightly from their > ground state. That relaxation reduces the overlap of the "initial" > and "final" states of the transition that gives rise to XAFS, and so > reduces the full effect. FEFF6 does not do a very good job of > estimating this effect. > > In practice, S02 can also mask other "amplitude issues", some > theoretical (the inelastic losses that fold into the mean-free-path > are not perfect) and some experimental (it is easier to mis-measure > the amplitude than the phase of an oscillation). For XAFS, these > experimental problems all tend to spoil the amplitude of the > meaurement more than the phase: pin-holes in the sample, slight > misalignment of the sample, over-absorption for fluorescence > measurements, energy bandwidth of the incident beam and harmonic > content of the incident beam. > > The rule of thumb is that it is OK to use the same S02 for all samples > of a particular absorbing atom. Many would add "measured at the same > beamline" to that rule, so that effects of energy bandwidth and > harmonic content are compensated. > > Cheers, > > --Matt > > > ------------------------------ > > Message: 2 > Date: Wed, 28 Jul 2010 08:05:23 -0400 > From: Scott Calvin<SCalvin(a)slc.edu> > To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Case of "nonequivalent multiple atomic sites of > absorbing atoms" > Message-ID:<8295E519-0FC0-4D2C-8C33-944E9BF0F53D(a)slc.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > Hi Rana, > > Currently, S02 is usually described as being due to the relaxation of > the other electrons in an atom when a core electron is removed, > resulting in incomplete overlap of initial and final states. This > appears to be a fairly good description, as careful experiments show > good agreement with theoretical calculations based on this idea. > > Note, however, that there could be some other contributors to S02. A > photon could, in addition to exciting the core electron at the edge, > also excite a valence electron. > > There's a small thread on the transferability of S02 here: > > http://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg01626.html > > E0 is a tricky concept, in my opinion: it is the energy origin in the > EXAFS equation. Perhaps a theorist can give me a pithy physical > interpretation of what happens at that energy, but I don't know there > needs to be anything; at k near 0, the path expansion is not > convergent, so I'm not sure we should expect anything special to > happen exactly at 0. In other words, it's not exactly the Fermi level > or any other special energy. > > E0 is dependent on oxidation state; it can shift by an electron volt > or two when oxidation states vary. > > Note that oxidation state is a simplistic measure of what's happening > with the electron distribution in a material. Suppose fluorine is > substituted for iodine in some material. Formally, the oxidation state > of the atom they are bonded to is not changed by the substitution. But > in reality, the electron distribution is different, and a small E0 > shift would not be surprising. > > I think the bottom line, then, is this: > > S02 is completely transferable for the same element at multiple > absorbing sites. > > Delta E0 is transferable with some caution for the same element at > multiple absorbing sites if the oxidation state is the same. > > One other note: there's no rule that when trying constraints, you have > to start unconstrained and add constraints to see the effect on the > fit. With complicated systems like yours, it often pays to start with > unrealistically simple constrains (not only E0's and S02's the same, > but also sigma2's), and see if you're on the right track. Then look at > the effect of relaxing constraints. > > --Scott Calvin > Sarah Lawrence College > > > > On Jul 28, 2010, at 4:00 AM, Jatinkumar Rana wrote: > > >> Dear Users, >> >> Since long, i was trying to understand the physical meaning of term >> "Delta E0" and "S02" in EXAFS equation. I have little bit of idea >> about both of them. for example, S02 is element specific and it is >> transferable between samples (if we consider same absorbing atom). >> >> However, I am not able to realize their importance in terms of their >> "physical meaning" as far as interaction of photoelectron is >> concerned. Therefore, it is difficult for me to understand their >> influence on EXAFS. >> >> I am dealing with a case of "nonequivalent multiple atomic sites of >> absorbing atoms". It is quite obvious that in such kind of case no. >> of variables are more than no. of independent points and there is a >> need to constrain the parameters to solve such problems. >> >> I have following questions : >> >> How do i understand "Delta E0" and "S02" theoretically (in terms of >> photoelectron interaction) ? >> >> Can i constrain "Delta E0" for all absorbing atomic site as same ? >> (my assumption : all absorbing atoms are at same oxidation level) >> >> your comments and suggestions would be highly appreciated... >> >> Best regards, >> Rana >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> >> > > > ------------------------------ > > Message: 3 > Date: Wed, 28 Jul 2010 07:37:52 -0500 > From: Matt Newville<newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] updating Athena in Windows 7 > Message-ID: > <AANLkTinxBX3aCXUGdN5XZCajMuK5gWCyftb9N-6YvpVz(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi Todd, > > On Mon, Jul 26, 2010 at 3:39 PM, Monson, Todd<tmonson(a)sandia.gov> wrote: > >> On Saturday, while starting up Athena, I was informed that there was an >> update to Athena available.? I tried installing the update but failed.? I am >> afraid this is due to some user permission issue in windows 7.? How can I >> try to reinstall the update and ensure that it works? >> > You can change the file current.dat in C:\Program > Files\Ifeffit\config. It probably reads > > 013 > > right now, and you could change that to 012 or even lower. That will > cause an update the next time ifeffit looks for updates, which only > happens when one of the programs starts and if the time in > Ifeffit\config\updater.ini is past. To force a check for updates the > next time ifeffit runs, change updater.ini to read > > timestamp = 0 > > In general, I believe this should work for Windows 7 (I have access to > two Windows 7 64-bit machines, and all seems to be working on them, > though I admit to not stressing them too much). So, as you say, I > would also guess that the trouble you had was "only" permission > issues. But, please let us know how it goes, > > Sorry for the trouble, > > --Matt > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 89, Issue 19 > *************************************** > > >

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updating Athena in Windows 7
by Monson, Todd 28 Jul '10

28 Jul '10

On Saturday, while starting up Athena, I was informed that there was an update to Athena available. I tried installing the update but failed. I am afraid this is due to some user permission issue in windows 7. How can I try to reinstall the update and ensure that it works? Thanks, Todd Todd Monson Sandia National Labs Nanomaterials Sciences P.O. Box 5800, MS 1415 Albuquerque, NM 87185-1415 (505) 845-2129 Fax: (505) 844-5470

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Case of "nonequivalent multiple atomic sites of absorbing atoms"
by Jatinkumar Rana 28 Jul '10

28 Jul '10

Dear Users, Since long, i was trying to understand the physical meaning of term "Delta E0" and "S02" in EXAFS equation. I have little bit of idea about both of them. for example, S02 is element specific and it is transferable between samples (if we consider same absorbing atom). However, I am not able to realize their importance in terms of their "physical meaning" as far as interaction of photoelectron is concerned. Therefore, it is difficult for me to understand their influence on EXAFS. I am dealing with a case of "nonequivalent multiple atomic sites of absorbing atoms". It is quite obvious that in such kind of case no. of variables are more than no. of independent points and there is a need to constrain the parameters to solve such problems. I have following questions : How do i understand "Delta E0" and "S02" theoretically (in terms of photoelectron interaction) ? Can i constrain "Delta E0" for all absorbing atomic site as same ? (my assumption : all absorbing atoms are at same oxidation level) your comments and suggestions would be highly appreciated... Best regards, Rana

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