Re: [Ifeffit] Energy shift after deglitch
Hi Bruce, Thanks for your reply. Are there any plans to update the macports package in the future? Thanks, George On Tue, Aug 11, 2015 at 7:55 AM, Bruce Ravel bra...@bnl.gov wrote: I don't see the behavior you describe when I follow your recipe. Perhaps it got fixed when I fixed this fellow's issue...? http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2015-May/012496.html Of course, the Mac package is a fair bit behind at this point. B On 08/06/2015 06:10 PM, George Sterbinsky wrote: Hello, I am writing to report a bug in Athena running on OSX 10.10.4. Here are the steps to reproduce the problem. I'm not sure that all steps are necessary. 1. Open Athena and import the attached project, which contains two groups that are both marked. 2. Change plot range to plot from -30 to 30 eV. 3. Select the deglitch and truncate window. 4. Select group Ref data.merge. 5. In deglitch many points, set margin to 0.05, Emin to -24, and Emax to -20. 6. Click replot margins. 7. Click remove points. 8. Click return to main window. 9. Click the derivative check box to plot marked groups as normalized derivative. 10. Click mu(E) button to plot marked groups as derivative of mu(E). When the last step is done the groups appear to shift with respect to each other. One can switch between Normalized and mu(E) and see the shift come and go. Thank you, George ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
[Ifeffit] Energy shift after deglitch
Hello, I am writing to report a bug in Athena running on OSX 10.10.4. Here are the steps to reproduce the problem. I'm not sure that all steps are necessary. 1. Open Athena and import the attached project, which contains two groups that are both marked. 2. Change plot range to plot from -30 to 30 eV. 3. Select the deglitch and truncate window. 4. Select group Ref data.merge. 5. In deglitch many points, set margin to 0.05, Emin to -24, and Emax to -20. 6. Click replot margins. 7. Click remove points. 8. Click return to main window. 9. Click the derivative check box to plot marked groups as normalized derivative. 10. Click mu(E) button to plot marked groups as derivative of mu(E). When the last step is done the groups appear to shift with respect to each other. One can switch between Normalized and mu(E) and see the shift come and go. Thank you, George BugDemo.prj Description: Binary data ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Energy shift in exported data
On 07/11/2014 06:56 PM, George Sterbinsky wrote: Hello, I have noticed the following behavior in Athena 0.9.20 on OSX 10.8.5. If a group with an energy shift applied is exported as norm(E) using the export marked groups option then the energy shift is not preserved in the .nor file. If the export current group option is used then the energy shift is preserved. This seems to be general behavior and should be straightforward to reproduce, but I can provide an example project if needed. You are correct. Yikes! I will try to get that fixed soon enough that Frank can get the fix into the next demeter-devel release for Mac. Thanks, B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage:http://xafs.org/BruceRavel Software:https://github.com/bruceravel ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Energy shift
Your attachment do not help in this case...
Do you know something more about sample? I suppose it is a thin layer.
Have you checked if you have no defects, vacancies, etc?
I suppose that you can follow instructions given in this post
http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2009-January/008522.html
but you can be also interested in this topic:
http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2009-June/004293.html
and especially in last posts.
you can also try this suggestion
http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2010-June/009471.html
In general - could you precise, what is k_{min} for your fit, and did
you use self consistent potential in calculations?
W dniu 11-10-06 02:28, JeongEunSuk pisze:
Thank Dariuz and Bruce.
TiO is deposited on Si substrate and PtO is fabricated on TiO2.
I measered EXAFS with Pt L3 edge(11563eV) and The model is decided
from FEFF8.0.
PtO has only fist shell like attached files So I chose the simple
model with octahedral structure (probe atom Pt, others O)
When the EXAFS was fitted by feffit, the variables were three eo(Enot
in Artemis, energy shift), do1(distance factor), sigo1(debye-waller
factor).
the results of fit is as following
variablebest fit valueuncertainty initial guess
eo = 19.2833981.7264260.00
do1= -0.0232270.0095570.096000
sigo1 =0.0037900.0005830.003047
r-factor: 11
reduced-chi square: 95
Energy shift by fit shows an amount of difference from Pt L3 edge. It
is my problem.
To reduce the energy shift, I tried to remove background carefully
again and to change distance Pt-O.
However the result was failed.
Date: Wed, 5 Oct 2011 08:24:16 +0200
From: ki...@ifj.edu.pl
To: ifeffit@millenia.cars.aps.anl.gov
Subject: Re: [Ifeffit] Energy shift
Hi,
could say more precise what kind of energy shift you are talking
about? the position of the white line or the Enot in Artemis. How big
it is? Which version of Feff do you use? What do you mean writing
removing background carefully? Background in the EXAFS fit? Any
pictures to illustrate problem are welcome
W dniu 11-10-05 03:25, JeongEunSuk pisze:
Hell all
I have the study for PtO nanoparticles with EXAFS.
When I fitted the data to model, I had a problem for energy shift.
I thought that the energy shift obtained from fitting must be
below White line. However it was over white line.
Although I removed background carefully and changed bond length in
model, the energy shift was still big.
I want to know other factors which affect energy shift.
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Re: [Ifeffit] Energy shift
Hi, could say more precise what kind of energy shift you are talking about? the position of the white line or the Enot in Artemis. How big it is? Which version of Feff do you use? What do you mean writing removing background carefully? Background in the EXAFS fit? Any pictures to illustrate problem are welcome W dniu 11-10-05 03:25, JeongEunSuk pisze: Hell all I have the study for PtO nanoparticles with EXAFS. When I fitted the data to model, I had a problem for energy shift. I thought that the energy shift obtained from fitting must be below White line. However it was over white line. Although I removed background carefully and changed bond length in model, the energy shift was still big. I want to know other factors which affect energy shift. ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Energy shift
On Tuesday, October 04, 2011 09:25:18 pm JeongEunSuk wrote: Hell all I have the study for PtO nanoparticles with EXAFS. When I fitted the data to model, I had a problem for energy shift. I thought that the energy shift obtained from fitting must be below White line. However it was over white line. Although I removed background carefully and changed bond length in model, the energy shift was still big. I want to know other factors which affect energy shift. As Darek said, it is hard to know what you are talking about without some more information. There are a lot of things that can lead to weird values of E0 in an EXAFS fit, for instance: * You expect an oxide, but your sample has a large metallic component * You expect an oxide, but your sample has a large sulfide component * You run Feff on the Pt K edge rather than the Pt L3 edge, resulting in an incorrect phase shift in the theory * You mistyped a number while inputing crystal data into Atoms, resulting in icorrect distances in the feff.inp file * You took crystal data from an untrustworthy source, resulting in icorrect distances in the feff.inp file * Your material as a nanoparticle is substantially different from the bulk analogue I, of course, have no idea if any of those suggestions apply. The bottom line is that a disturbingly large E0 value is usually a suggestion that you have made an error of procedure or assumption while creating your fitting model. Sometimes it indicates a systematic problem in the data collection -- certain monochromator problems can introduce a periodic but non-EXAFS signal into the data. On occassion it even suggests a bug in the software -- but usually not. Usually there is some problem in the fitting model. I should also point out that going through the excercise of documenting the problem clearly, as Darek suggested, is valuable not only because it provides the information that makes it likely that someone can actually answer your question, but because doing so forces you to carefully examine your work, which may turn expose the problem. B -- Bruce Ravel bra...@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/ifeffit/Demeter ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
[Ifeffit] Energy shift
Hell all I have the study for PtO nanoparticles with EXAFS. When I fitted the data to model, I had a problem for energy shift. I thought that the energy shift obtained from fitting must be below White line. However it was over white line. Although I removed background carefully and changed bond length in model, the energy shift was still big. I want to know other factors which affect energy shift. ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
[Ifeffit] Energy shift
Hi all, I finished simulations of Er(OH)3, ErO(OH) and Er2O3, when I compared the spectras with the samples and I found a shift in energy equal to 5.5 eV.Even between the meassured and calculated spectra of Er2O3, which was previously calibrated with a niquel film standard. Is this shift part of the bussines? Thanks, euG ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Energy shift (???)
Hi eunsuk1986 (unfortunately you did not share your full name with us...) I had some trouble with reading your feff.inp. Nevertheless the problem of the absolute alignment of FEFF xmu and experimental data has been the subject of earlier questions. I' am citing form a list contribution of J. Rehr (Aug 3rd 2003): The FEFF calculation of the absolute energy is not meant to be highly accurate, and errors of several eV for K-shells of large Z atoms are not unusal. Thus you did nothing wrong in the input file. To match FEFF and experiment you *always* have to shift the FEFF absolute threshold to match experiment.. There is no way (I am aware of) to tell FEFF do this absolute shift (you can and you often need to shift the position of the Fermi level though) but you can do this with every plot program. Thus you should not worry too much about the absolute energies in your xmu but a lot about relative energies (i.e. the positions of the single resonances). HTH Jakob ___ Jakob Frommer Soil Chemistry Group Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich Universitätstrasse 16, CHN F19 CH - 8092 Zürich Tel: +41 44 632 87 58 Fax: +41 44 633 11 18 web: http://www.ibp.ethz.ch/research/soilchemistry From: [EMAIL PROTECTED] on behalf of [EMAIL PROTECTED] Sent: Mon 8/18/2008 09:46 To: ifeffit@millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 66, Issue 9 Send Ifeffit mailing list submissions to ifeffit@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 [EMAIL PROTECTED] You can reach the person managing the list at [EMAIL PROTECTED] When replying, please edit your Subject line so it is more specific than Re: Contents of Ifeffit digest... Today's Topics: 1. Energy shift (???) -- Message: 1 Date: Mon, 18 Aug 2008 16:46:26 +0900 From: ??? [EMAIL PROTECTED] Subject: [Ifeffit] Energy shift To: ifeffit@millenia.cars.aps.anl.gov Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ks_c_5601-1987 Hi everyoneI am studying XANES at Zn K-edge in ZnO nanocrystal by using FEFF8. I wrote FEFF8 as following, and got xmu.dat. I found that there was a difference between experimental data and xmu.dat (check file) for the energy. I dont understand why the energy is shifted. I wish to adjust xmu.dat in FEFF8 to my experimental dat. If someone knows how to do, please contact me. * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * TITLE name: zincite ZnO TITLE formula: ZnO TITLE sites:Zn1,O1 TITLE refer1: wyckoff, vol 1, ch III, p 111 TITLE refer2: TITLE schoen: TITLE notes1: EDGE K S02 1.0 * potxsph fms paths genfmt ff2chi CONTROL 1 1 1 1 1 1 PRINT 1 0 0 0 0 0 * r_scf [ l_scf n_scf ca ] SCF 5.03864 0 15 0.1 * ixc [ Vr Vi ] EXCHANGE 2 0 0*EXAFS*RPATH 9.07729 * kmax [ delta_k delta_e ] XANES 4.0 ! 0.07 0.5 * r_fms [ l_fms ] FMS 5.53864 0 * *RPATH 0.1 * emin emax resolution LDOS -2020 0.1 POTENTIALS * ipot z [ label l_scmt l_fms stoichiometry ] 0 30 Zn -1 -1 0 18O -1 -1 1 2 30Zn -1 -1 1 ATOMS 0.0 0.0 0.00 Zn1 0.0 0.0 0.0 2.063021 O1 2.06302 -1.95951 0.0-0.651481 O1 2.06497 0.97978-1.69700-0.651481 O1 2.06500 0.97978 1.69700-0.651481 O1 2.06500 0.97978-1.69700 -2.714502 Zn1 3.34788 0.97978 1.69700 2.714502 Zn1 3.34788 0.97978 1.69700-2.714502 Zn1 3.34788 0.97978-1.69700 2.714502 Zn1 3.34788 _ ???, ?? ??? Windows Live Hotmail! ?? ???! http://www.hotmail.com http://www.hotmail.com/ -- next part -- An HTML attachment was scrubbed... URL: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20080818/aac9c4ad/attachment.html -- next part -- A non-text attachment was scrubbed... Name: data and FEFF_model.jpg Type: image/jpeg Size: 24357 bytes Desc: not available Url : http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20080818/aac9c4ad/attachment.jpg -- ___ Ifeffit mailing list
[Ifeffit] Energy shift
Hi everyoneI am studying XANES at Zn K-edge in ZnO nanocrystal by using FEFF8. I wrote FEFF8 as following, and got xmu.dat. I found that there was a difference between experimental data and xmu.dat (check file) for the energy. I dont understand why the energy is shifted. I wish to adjust xmu.dat in FEFF8 to my experimental dat. If someone knows how to do, please contact me. * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * TITLE name: zincite ZnO TITLE formula: ZnO TITLE sites:Zn1,O1 TITLE refer1: wyckoff, vol 1, ch III, p 111 TITLE refer2: TITLE schoen: TITLE notes1: EDGE K S02 1.0 * potxsph fms paths genfmt ff2chi CONTROL 1 1 1 1 1 1 PRINT 1 0 0 0 0 0 * r_scf [ l_scf n_scf ca ] SCF 5.03864 0 15 0.1 * ixc [ Vr Vi ] EXCHANGE 2 0 0*EXAFS*RPATH 9.07729 * kmax [ delta_k delta_e ] XANES 4.0 ! 0.07 0.5 * r_fms [ l_fms ] FMS 5.53864 0 * *RPATH 0.1 * emin emax resolution LDOS -2020 0.1 POTENTIALS * ipot z [ label l_scmt l_fms stoichiometry ] 0 30 Zn -1 -1 0 18O -1 -1 1 2 30Zn -1 -1 1 ATOMS 0.0 0.0 0.00 Zn1 0.0 0.0 0.0 2.063021 O1 2.06302 -1.95951 0.0-0.651481 O1 2.06497 0.97978-1.69700-0.651481 O1 2.06500 0.97978 1.69700-0.651481 O1 2.06500 0.97978-1.69700 -2.714502 Zn1 3.34788 0.97978 1.69700 2.714502 Zn1 3.34788 0.97978 1.69700-2.714502 Zn1 3.34788 0.97978-1.69700 2.714502 Zn1 3.34788 _ 강력해진 보안성, 아웃룩을 닮아 편리해진 기능들로 무장한 Windows Live Hotmail! 지금 로그인해 보세요! http://www.hotmail.comattachment: data and FEFF_model.jpg___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
