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

Looking for reviewers for XAFS textbook chapters
by Scott Calvin 09 Mar '11

09 Mar '11

Hi all, I am looking for people interested in reviewing portions of the XAFS textbook I am working on. I am particularly hoping that some people less experienced in XAFS will volunteer, so that I can get feedback on how well it teaches and how well it covers the topics you'd like to know more about. Experts are also welcome! The first chapter I've got ready is the chapter on sample preparation. If you are interested in reviewing this chapter and can get feedback back to me within two weeks, please email me at SCalvin(a)slc.edu . --Scott Calvin Sarah Lawrence College

4 3

Re: [Ifeffit] Looking for reviewers for XAFS textbook chapters
by Scott Calvin 08 Mar '11

08 Mar '11

Darn it! I did not mean to send the packet to the whole list. If anyone is interested in reviewing, please send a request to SCalvin(a)slc.edu . I apologize for spamming you all with a multi-MB file. --Scott On Mar 8, 2011, at 12:24 PM, Scott Calvin wrote: > Great! > > I'm attaching the review packet. The page numbering is a bit > chaotic, because it's actually several documents stitched together: > > The copyright notice. My publisher is allowing me to distribute > review copies, but only on the condition that reviewers not > redistribute them. > A detailed table of contents. This is more detailed than the final > version will be, but gives context to reviewers as to what will be > covered elsewhere. > An excerpt from the preface explaining the origin of the cartoon > characters. (Yes, there are cartoon characters...) > An introduction to the cartoon characters. > Chapter 3, on sample preparation. > References > > In the chapter, I've placed numbers along the margin to aid in > making comments. For example, you might want to comment on page 18, > lines 6-7. The numbers won't appear in the final version. > > If you have any questions about the context of the chapter, the > intended audience, or whatever, feel free to ask! > > --Scott Calvin > Sarah Lawrence College > <XAFSforEveryone_Chapter3_v2.pdf> > > On Mar 8, 2011, at 11:27 AM, Prof. Dr. Peter Leinweber wrote: > >> hello, i am interested in reviewing this. i am not experienced but i >> want to learn more. >> i look forward to hearing from you, peter leinweber >> >> Am 08.03.2011 04:13, schrieb Scott Calvin: >>> Hi all, >>> >>> I am looking for people interested in reviewing portions of the XAFS >>> textbook I am working on. I am particularly hoping that some people >>> less experienced in XAFS will volunteer, so that I can get >>> feedback on >>> how well it teaches and how well it covers the topics you'd like to >>> know more about. Experts are also welcome! >>> >>> The first chapter I've got ready is the chapter on sample >>> preparation. >>> If you are interested in reviewing this chapter and can get feedback >>> back to me within two weeks, please email me at SCalvin(a)slc.edu . >>> >>> --Scott Calvin >>> Sarah Lawrence College >>> _______________________________________________ >>> Ifeffit mailing list >>> Ifeffit(a)millenia.cars.aps.anl.gov >>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >>> >> >> >> -- >> Prof. Dr. Peter Leinweber >> Soil Science >> Institute for Land Use >> University of Rostock >> D-18051 Rostock/Germany >> Tel.: +49 381 498 3120 >> Fax: +49 381 498 3122 >> >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

1 0

FEFF6L input keyword question
by YOON Zin Seok 03 Mar '11

03 Mar '11

Dear FEFF users, Hi, I am a beginner of FEFF6L. Usually depending on the manual provided by web site, I am managing to calculate spectrum, and there are too many difficulties...I would like to be advised from you, senior members. I have three questions. (1) I would like to control the temperature. In the manual, I see DEBYE 190 315 (Calculate Debye-Waller factors for Cu at 190 K??). Can I change the temperature simply by modifying the number "190"? Can I find a reference paper for this? (2) Where can I find Debye-Waller factors in the output files? (3) How can I change the ionic state? I would like to compare the output file, chi dat., between SF6 and SF6+ molecules. I hope I could have answers for my questions... Best wishes, Zin

3 2

International Workshop on Improving Data Quality and Quantity , for XAFS Experiments (Q2XAFS2011), Tsukuba, Apr. 12-13, 2011
by Yohei Uemura 02 Mar '11

02 Mar '11

Dear ifeffit mailing list users, This is Yohei Uemura at Photon Factory, KEK, Japan. "Q2XAFS" workshop is going to be held on 12-13 April 2011 in Photon Factory, Tsukuba, Japan. This workshop aims to have worldwide discussions about measurements and data collection of XAFS to improve data quality and quantity. There will be also presentations about XAFS experiments on bio-systems and recent beamline developments. Please read the message from the organisers below. **************************************************************** Dear Colleagues It is our pleasure to inform you that "International Workshop on Improving Data Quality and Quantity for XAFS Experiments (Q2XAFS2011)" will be held during April 12-13, 2011 in Tsukuba, Japan. As you have been of great significance in the related topics of XAFS, we would be honored to ask your attendance and participation in our efforts aimed at quality and quantity improvements. We will welcome your early registration (reduced fee) at the Q2XAFS2011 web (http://pfwww.kek.jp/Q2XAFS2011/index.html) by February 28. The workshop is jointly organized by the IUCr XAFS Commission and the IXAS, inviting outstanding researchers representing synchrotron radiation facilities all over the world. Q2XAFS2011 focuses on Q2 (quality and quantity) control of EXAFS data collection, analyzing and exchange. Our goal is to assess the current status, to find fundamental problems and to propose a solution through standards and/or recommendation. The workshop will provide opportunities to fully discuss and exchange opinions on important categories of Q2 control. As the topics of the workshop are strongly dependent on beamlines and experimental stations, participation of experienced scientists based at facilities is essential. In particular, we will have a dedicated session for standard data format that would dramatically improve efficiency and security of data collection and exchange. Your participation in the workshop will be greatly appreciated. We look forward to seeing you in Tsukuba. Sincerely, yours Soich Wakatsuki, Chair of Q2XAFS2011, Director of Photon Factory Isabella Ascone, IUCr XAFS Commission, Chair Hiroyuki Oyanagi, IXAS, Chair **************************************************************** -- =========================================== 上村洋平所属: 高エネルギー加速器研究機構　物質構造科学研究所放射光科学研究施設（Photon Factory) 住所: 茨城県つくば市大穂1-1 Yohe'i Uemura (Ph.D) Affiliation : Photon Factory, Institute of Materials Science, KEK Adress : 1-1 Oho, Tsukuba-Shi, Ibaraki, Japan 305-0801 TEL&FAX: 029-879-6105 PHS: 029-864-5200 + 4956 Email : yuemura(a)post.kek.jp ===========================================

1 0

Purple & Red E Derivatives
by Andrew Korinda 25 Feb '11

25 Feb '11

While working in Athena today I noticed something peculiar while looking at the derivative plots of mu(E) data. When I plot the current group (red button) the plot can be spiky. However, when I plot as marked group (purple button) everything is much smoother and more rounded. Smoothed data will do the same thing. It always happens whether I have mu(E) or norm(E) selected. I have never noticed a difference in how any of the other plots current when switching between marked and active plotting. I didn't see anything in the documentation about how the derivatives are calculated so I'm turning to all of you. Have any of you noticed this? Does anyone know if there is a difference in how the derivatives are calculated in each plotting function? Andy Korinda Notestein Lab Northwestern University

4 6

parseval's theorem and athena
by kirshstein＠googlemail.com 17 Feb '11

17 Feb '11

Hello, I would like to use parseval's theorem (as described in a document called: Error Reporting Recommendations: A Report of the Standards and Criteria Committee, Adopted by the IXS Standards and Criteria Committee July 26, 2000 ) to quantify the statistical noise in my spectra. In section 3 (as shown in the attachment), it says that for the formula to work, the forward FT has to be normalized by sqrt(deltak/Pi). (delta k is the spacing of points in k space) What is the normalization used for FFT in athena? if it is not sqrt(deltak/Pi), what is it? how does the parseval theorem formula need to be modified as a function of FT normalization? Many thanks for answers! Regina

2 3

FEFF question Te K edge
by Andrea L Foster 16 Feb '11

16 Feb '11

Hello All, sorry if this is not the correct venue...I tried to join a feffusers list I saw at http://leonardo.phys.washington.edu/feff/html/mailing_list.html but I got bounces when I subscribed and tried to post. my problem is below, and I'm sure one of the many knowledgeable folks on this group can help: I am starting to run FEFF6L calculations for Tellurium phases. I used published structure report of calaverite (AuTe2) and Na2TeO3_5H2O to generate ATOMS.INP files which I then used to generate FEFF.inp files. These two very different Te minerals gave me the following error when running FEFF6L (following is a copy of a little of the FEFF output): Running "C:\Program Files\Ifeffit\bin\feff6l.exe" feff.inp Feff 6L.02 Disodium Tellurite 5-hydrate Calculating potentials and phases... free atom potential and density for atom type 0 free atom potential and density for atom type 1 free atom potential and density for atom type 2 free atom potential and density for atom type 3 overlapped potential and density for unique potential 0 overlapped potential and density for unique potential 1 overlapped potential and density for unique potential 2 overlapped potential and density for unique potential 3 muffin tin radii and interstitial parameters phase shifts for unique potential 0 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. phase shifts for unique potential 1 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. phase shifts for unique potential 2 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. phase shifts for unique potential 3 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. Preparing plane wave scattering amplitudes... ...I have stopped copying the FEFF output there. I do not think that the problem is with the crystal structures as they are pretty simple (though human error is never to be minimized, especially mine ;). ATOMS returned no errors when it ran. The interatomic distances generated in feff match those reported in the crystal structure report...and the coordination numbers appear to be correct (for example the sodium tellurite structure should have 3 closest oxygen neighbors, and does, at the correct distances)... so I don' t know how to troubleshoot this error when nothing appears wrong geometrically. I have attached the 2 feff.inp files (which list the xtal structure info) in case that helps. They are slightly renamed. thanks for any help, andrea ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Andrea L. Foster, Ph.D. U.S.G.S. WMESC 345 Middlfield Rd., MS 901 Menlo Park, CA 94025 T: 650-329-5437 F: 650-329-5491

1 0

Re: [Ifeffit] Fe in glassy ceramics
by Scott Calvin 16 Feb '11

16 Feb '11

Hi Andrei, It's not unreasonable to model such a thing. Use a highly constrained model for the spinel, not allowing coordination numbers to float and using very few sigma2 parameters. I've published a model like that for fitting spinels here: http://prb.aps.org/abstract/PRB/v66/i22/e224405 My model is more complicated than yours needs to be, because you don't really have site disorder; all the sites are Fe. Then multiply the amplitudes by a guessed parameter representing the fraction of the iron that is in the spinel phase. The remaining amplitude gets used for the glassy phase, which can possibly be fit by a single iron-oxygen path, which can be cloned from one of the spinel near neighbor paths, but now with most parameters floated. You may very well need to fix S02 based on the value from a standard. Fit over a wide range in the Fourier transform, so that you take advantage of high R peaks to pin down the spinel part. Worth a shot, anyway. The key is being aggressive with assumptions and constraints, and then being honest about how that affects your uncertainties in the end. --Scott Calvin Faculty at Sarah Lawrence College Currently on sabbatical at Stanford Synchrotron Radiation Laboratory On Feb 16, 2011, at 4:53 AM, Andrei Shiryaev wrote: > Dear colleagues, > > Probably similar questions were already asked, but nevertheless I > would appreciate some advice how to solve the problem. > > We are looking at Fe environment in complex glasses, which underwent > partial crystallization. A fraction of Fe has precipitated as spinel- > like nanocrystals, another fraction remains in glass. Spinel itself > is already challenging for XAFS, but our task is to understand the > Fe fraction in glass (e.g., Fe-O bond length). > > We do not know the exact composition of the crystalline phases, thus > we can not record a suitable standard. Does anybody have an idea how > could we try to separate the Fe in glass from Fe(cryst) contributions? > > I fully realize that the problem is ill-posed, perhaps, some people > had somehow solved this problem. > > Thanks a lot, > Andrei Shiryaev > > Instituteof Physical Chemistry > Moscow > Russia

1 0

Fe in glassy ceramics
by Andrei Shiryaev 16 Feb '11

16 Feb '11

Dear colleagues, Probably similar questions were already asked, but nevertheless I would appreciate some advice how to solve the problem. We are looking at Fe environment in complex glasses, which underwent partial crystallization. A fraction of Fe has precipitated as spinel-like nanocrystals, another fraction remains in glass. Spinel itself is already challenging for XAFS, but our task is to understand the Fe fraction in glass (e.g., Fe-O bond length). We do not know the exact composition of the crystalline phases, thus we can not record a suitable standard. Does anybody have an idea how could we try to separate the Fe in glass from Fe(cryst) contributions? I fully realize that the problem is ill-posed, perhaps, some people had somehow solved this problem. Thanks a lot, Andrei Shiryaev Instituteof Physical Chemistry Moscow Russia

2 1

compiling feff 9
by Eugenio Otal 11 Feb '11

11 Feb '11

Hello, I am trying to compile the feff9 with ifort linux compiler but I find that the code is split in more than one file unlike feff84 that is only one file, feff84.f. I read the manual and I cannot find any help in feff9 manual, in feff84 manual there are more information but it is also not so useful. Would you help me to know how to compile the code with all this files. Kind Regards, euG 8<- - - - - - 8<- - - - - - 8<- - - - - - 8<- - - - - - Dr. Eugenio H. Otal Solid State Chemistry and Catalysis Laboratory, Empa - Swiss Federal Laboratories for Materials Science and Technology, Ueberlandstrasse 129, CH-8600 Duebendorf, Switzerland, Tel +41 44 823 41 31, Fax +41 44 823 40 19, eugenio.otal(a)empa.ch, www.empa.ch/abt131,

1 0