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

Re: [Ifeffit] Yttrium in alumina GBs
by Scott Calvin 20 Dec '06

20 Dec '06

Hi Shan, Nothing at all surprising here. In fact, you're getting pretty good results, in my opinion. Your CN insists on being "about" 4.8. When you push the ss, with which CN is correlated, to the top of its fitted range, the CN increases to about 5.2. To me, that says your CN is 4.8 +/ 0.4. A 10% uncertainty in CN is quite good for EXAFS! Of course, your real uncertainty is greater than that, because there are some possible systematic errors (e.g. normalization, sample effects) that might be present. But still, you're doing about as well as can be expected. Of course, that's assuming that CN's are what you're after. If finding out whether it's Alumina or Yttria is what you're after, the quality of fit and CN are not distinguishing between the two possibilities. That leaves bond distance as the best EXAFS indicator of which phase is present. --Scott Calvin Sarah Lawrence College At 05:49 PM 12/20/2006, you wrote: >Thanks Carlo and Scott for ur response. > >Some numbers from my fits in this regard and some more queries. > >When I make a cluster based on the Alumina structure (replacing the >central Al with Y with relaxed lattice parameters) I get DW 0.0025 +- >0.002, without any restraint. While I restrain the DW to 0.005, my CN >jumps from 4.8 to 5.2. > >When I make a cluster based on Yttria structure, I get DW factor of >0.008 +- 0.002, unrestrained. While I restrain the DW to 0.01, it >again jumps from 4.8 to 5.2. > >First query...if you can pin down on the CN change (Carlo..you wanted >some numbers) >Second...what are ur comments on the above 2 models and the change in >DW factors. > >I might add that ther is no appreciable difference with k=2, 3 or 2&3 >fittings. All the fits produce red-chi-sqr less than 100 (~50-70), all >R-factors are <0.01 and no unphysical reports after the fit. And I >have only 1 peak to worry about, there is no second shell correlation >seen. > >I would appreciate your 2 cents on this.

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RE: [Ifeffit] Athena problem
by Barton, David (DG) 20 Dec '06

20 Dec '06

The oddity that Jeff describes also occurs on the Windows platform (Athena 0.8.050). If you hit the "OK" button in the File-Open window a couple of times while a dataset is being loaded you will multiple instances loaded into the data group list that cannot be selected or deleted. The message trapped by Athena message can be seen in attached image. Dave >-----Original Message----- >From: ifeffit-bounces(a)millenia.cars.aps.anl.gov >[mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf >Of Jeff Terry >Sent: Wednesday, December 20, 2006 12:55 PM >To: XAFS Analysis using Ifeffit >Subject: Re: [Ifeffit] Athena problem > >Since everyone is bringing up oddities in Athena, at least >under Debian, if you click on the load file button a second >time after setting up the input file parameters before it has >completed loading, you get a second group with the identical >name but it is not selectable and cannot be deleted. > >Jeff > > >On Dec 20, 2006, at 11:39 AM, Matt Newville wrote: > >> Hi, >> >> I agree that there have been several unrelated "issues" brought up >> here. Some of them are definitely reproducible, if not necessarily >> easy to capture as an isolated bug report. >> >> The "out of memory" problem that Paul Fons mentioned is >definitely due >> to ifeffit's limited, and fixed memory. This can be changed changed >> at compile time, but is (sadly) unavoidable in the current >> implementation. Someday there will be an Ifeffit 2 that eliminates >> this problem. >> >> The problem with 'clicking on the file/group area' in Athena on >> Windows is a long-standing issue. It's fairly common (for >me, anyway) >> to get an Athena session in this state, in which clicking on an >> existing group does not highlight it or make it current, and moving >> the mouse over it does not change the font. Sometimes a group can >> still be chosen as a member of a set. I don't know of an foolproof >> way to get to this state, but it seems to be more common >when reading >> in several data sets, and after a project has been open and >used for a >> while. This is definitely an irritation and it's been >like this for >> awhile. The rest of athena still runs fine. The easiest and most >> reliable workaround (that I know of) is to click into a real >widget in >> the Main Panel (so that it actually responds) and then go >back to the >> group list and click on another group. >> >> I haven't experienced very many random crashes of Athena. >> >> --Matt >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > >_______________________________________________ >Ifeffit mailing list >Ifeffit(a)millenia.cars.aps.anl.gov >http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

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Athena problem
by Maura H. Jordao 20 Dec '06

20 Dec '06

Dear all, Im having some problems to run Athena (Ifeffit 1.2.9) in my Windows XP (Home Edition, Version 2002), and Im writing to this list to get a help. One of them is if I plot a graph using different options (E or k for example) for many times, the graphics window freeze and I need obligatory to close the program. The other is the Pre and Post-edge lines do not appear when I marked them to plot. If somebody had experienced similar problems and know how to solve, please, write me. Ill be glad to receive some solution. Thanks, Maura ____________________________________________________________________________________ Want to start your own business? Learn how on Yahoo! Small Business. http://smallbusiness.yahoo.com/r-index

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RE: [Ifeffit] Athena problem
by Barton, David (DG) 20 Dec '06

20 Dec '06

Bruce, I believe I have a sequence of events that you can reproduce this problem of the data selection window locking up in Windows (tested in XP-SP2 and Win2000-SP4) using Athena 0.8.050. #1) Open three data sets #2) Right-click on first dataset choose Plot This Curve..In energy (Left click to choose) #3) The other datasets are now locked. Cannot select another dataset. #4) The fix: Right-click on any other dataset. Data selection begins working fine again. It appears that Athena is waiting for another Right-click after something is chosen off the popup context menu. This glitch is reproducible on WinXP and Win2000 platforms. Dave >-----Original Message----- >From: ifeffit-bounces(a)millenia.cars.aps.anl.gov >[mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf >Of Bruce Ravel >Sent: Wednesday, December 20, 2006 9:06 AM >To: XAFS Analysis using Ifeffit >Subject: Re: [Ifeffit] Athena problem > > >Hi folks, > >I have been following the discussion in the last few days >about problems people are having on Windows with Athena and >Artemis. I trust that everyone appreciates that my commitment >to providing useful, usable software is strong and that I work >very hard to meet that commitment. Unfortunately, nothing in >this thread has provided me with actionable information. >While I understand that some of you are having problems, no >one has yet provided enough information for me even to begin >solving the problem (whatever it might be). >The fundamental rule of good bug reporting is that you need to >provide sufficient information that I can reproduce the >problem on my computer. If I cannot reproduce the problem, I >cannot understand it and cannot solve it. > >On my bug reporting page >(http://cars9.uchicago.edu/~ravel/software/bugs.html) >there is a box on the left side of the screen with links to >two excellent articles in how to communicate with software >developers. If you are interested in how to best help me to >understand and solve problems with my software, please read >through those articles and take the authors' suggestions to heart. > >Regards, >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/ > >_______________________________________________ >Ifeffit mailing list >Ifeffit(a)millenia.cars.aps.anl.gov >http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

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Re: [Ifeffit] High Correlation betn SO2 and ss
by Scott Calvin 20 Dec '06

20 Dec '06

Hi Sham, I agree with Carlo. I would also add that you should try different k-weights, including multiple k-weights at once. Since the dependence of S02 and ss on k is quite different, that can often reduce the correlation between the two. --Scott Calvin Sarah Lawrence College At 11:58 PM 12/19/2006, Shantanu Behera wrote: >Hi Folks > >I have a small doubt. I work on the structural features of Y that are >segregated to Alumina grain boundaries (very dilute amounts of Yttrium >in polycrystalline alumina). > >In some of my fits, I find a correlation ~0.85 between SO2 and ss. If >I restrain the ss, from 0.004 to 0.007, the CN changes by ~0.5 (not >considering +/-0.3). I would appreciate if someone can explain me how >to interpret the results from a structural point of view.

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High Correlation betn SO2 and ss
by Shantanu Behera 20 Dec '06

20 Dec '06

Hi Folks I have a small doubt. I work on the structural features of Y that are segregated to Alumina grain boundaries (very dilute amounts of Yttrium in polycrystalline alumina). In some of my fits, I find a correlation ~0.85 between SO2 and ss. If I restrain the ss, from 0.004 to 0.007, the CN changes by ~0.5 (not considering +/-0.3). I would appreciate if someone can explain me how to interpret the results from a structural point of view. Warm regards Shan -- ||||||||||||||||||||||||||||||||| Shantanu Behera Center for Advanced Materials and Nanotechnology Lehigh University 5, East Packer Avenue Bethlehem, PA 18015, USA

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XAFS: Industrial Career Opportunity
by Barton, David (DG) 19 Dec '06

19 Dec '06

The Dow Chemical Company has openings for Ph.D. Chemists, Polymer Scientists and Materials Scientists in our Global Analytical Sciences Laboratory. If you are highly qualified and are interested in this job, please submit your electronic resume directly to tdominowski att dow.com Location of Jobs: Midland, Michigan and Freeport, Texas Job Title: Senior Research Scientist Degree: Ph.D Discipline: Analytical Chemistry, Physical Chemistry, Inorganic Chemistry, Materials Science, Physics, Chemical Physics or Polymer Science Job Description Overview: Candidate will be responsible for providing advanced Materials Characterization by developing new techniques in the area of surface science and/or Synchrotron techniques (XAFS, XRD, tomography). For this position we are seeking candidates who are strong in Materials Science and Materials Characterization. Candidates must be proficient in characterization techniques. Candidates must have significant analytical chemistry and thin film characterization specialization and excellent problem solving skills. Qualifications: Ph.D. in Analytical Chemistry, Physical Chemistry, Inorganic Chemistry, Materials Science. Experience and deep capability in Materials Characterization is preferred. Capability in techniques such as XPS/TEM/EXAFS. Experience and expertise in one or more of the following is highly valued: inorganic chemistry, ceramics, materials science. Candidates must have strong quantitative analysis and analytical problem solving skills. Feel free to email me with any questions (dgbarton att Dow.com) Regards, Dave _________________________________ David Barton The Dow Chemical Company Catalysis R&D 1776 Building Midland, MI 48674 USA Ph: (989) 636-4753 Fax: (989) 638-6225 dgbarton att dow.com

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staff position available for BLADE beamline at Diamond Light Source
by Van Der Laan, G (Gerrit) 16 Dec '06

16 Dec '06

Dear Collegue, We are currently looking for a beamline scientist for BLADE (BeamLine for Advanced Dichroism Experiments) at Diamond, which will be operational in 2010/11 at the Diamond Light Source, near Oxford, United Kingdom. I would be very grateful if you could pass on the following advert (see below for the text of the announcement). http://www.diamond.ac.uk/Jobs/CurrentVacancies/Scientific/DIA0271SB.htm Deadline for applications is 5 January 2007. Informal enquiries can be made to Dr Paul Steadman (Paul.Steadman(a)diamond.ac.uk, Tel: +44 (0)1235 778156), who is the principal beamline scientist of BLADE. Best Regards, Gerrit van der Laan Chair of the BLADE user working group Daresbury Laboratory, UK Tel: +44 (0)1925 603448 email: g.vanderlaan(a)dl.ac.uk -------------------------------- Text of the announcement: DIA0239/LV - Beamline Scientist: Beamline for advanced dichroism experiments (BLADE) A beamline for the study of magnetic dichroism and magnetic structure using soft x-ray resonant scattering (reflection and diffraction) and x-ray absorption, allowing a broad range of novel studies focused on the spectroscopic properties and magnetic ordering of novel nanostructured systems This beamline will provide variable linear and circular polarised x-rays covering the energy range 0.4 to 2 KeV, which includes important absorption edges such as 3d transition metal L2,3 and rare earth M4,5 edges. The highly brilliant source of polarised soft x-rays will allow ultrasensitive studies using magnetic dichroism in x-ray absorption, soft x-ray resonant scattering and (resonant) photoemission. The beamline will comprise two branches for (i) a 9T superconducting magnet with UHV environment, cooling to 1K for x-ray magnetic circular and linear dichroism (XMCD and XMLD) and (ii) a multi-circle UHV diffractometer with liquid helium cooling and sample magnetisation for soft x-ray resonant magnetic scattering (SXRMS). There will also be the possibility of attaching user stations such as for photoemission and resonant Raman scattering. This beamline, which will be world leading in terms of its flux, coherence and design for extreme sample conditions, provides a ke! y resource to scientists in the national and international research communities and will have a very significant impact in some of the most topical subjects of contemporary solid state. The combination of XMCD/ XMLD and SXRMS will enable a broad range of exciting new phenomena in novel nanostructures and correlated materials to be explored using soft x-ray spectroscopy and diffraction. Key Duties Working in support of the Principal Beamline Scientist in the following areas: * To assist in the design, testing, installation and commissioning of the Beamline * Assist in the procurement of the beamline components * Liaise with the suppliers of the beamline components * Assist in the testing, installation and commissioning of the beamline components. * Support the operation of the beamline and interact closely with the users of this facility * Carry out own research in an area relevant to the beamline Skills and experience Essential * Appropriate first degree or equivalent qualification * Relevant synchrotron research experience * Experience or knowledge of synchrotrons * Ability and initiative to get to the heart of the problem and take it effectively through to completion * Good interpersonal, communication and presentational skills * Ability to interact effectively with staff at all levels * Ability to work as part of a multi-disciplinary team * Self motivated * Desirable * Experience of beamline design * Experience of magnetic circular dichroism and magnetic linear dichroism * Experience of soft X-ray scattering * Experience of working with high magnetic fields * Experience of low temperature measurements * Experience of ultra high vacuum * Second degree in appropriate subject * Ability to manage a small team * Project management experience * Further Information * Must be available to travel occasionally within the UK and abroad, including overnight absences Salary c£30,000 If you would like to apply please visit our website at <http://www.diamond.ac.uk/Jobs/How+to+apply/ApplicationForm.htm>

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Re: Ifeffit Digest, Vol 46, Issue 7
by Mehdi Ali 14 Dec '06

14 Dec '06

I have a question what does Rbkg option in athena does. What is its physical significance. I am new to exaf data analysis. Thanks Mehdi Mehdi Ali, PHD Canditate, Department of Physics, Illinois Institute of Technology, Chicago,IL (773)-895-6144 ----- Original Message ----- From: ifeffit-request(a)millenia.cars.aps.anl.gov Date: Thursday, December 7, 2006 12:00 pm Subject: Ifeffit Digest, Vol 46, Issue 7 > 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: Re: question on Athena data import (Gerrit Schmithals) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Thu, 07 Dec 2006 15:15:27 +0100 > From: Gerrit Schmithals <schmithals(a)hmi.de> > Subject: Re: [Ifeffit] Re: question on Athena data import > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <457821FF.30400(a)hmi.de> > Content-Type: text/plain; charset="iso-8859-1" > > Matt Newville schrieb: > >> Very nice! I'd be happy to give you some space on > >> http://cars9.uchicago.edu/~ravel/software/contrib.html, if that > would>> help. > > > > You could use the wiki for this. > Hello Bruce, Hello Matt, > > I appended the script file along with a couple of textfiles for > testing.There is a description at the top of the file that explains > how to use it. > > I think both the wiki and the Athena homepage are good places to offer > it. Can I leave it up to you where you want to have it? > > I only tested it on Windows so maybe you want to give it a try on > Linux/Mac first. > > Cheers, > Gerrit > >

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FEFF and XANES
by Frommer Jakob 11 Dec '06

11 Dec '06

Dear all, I have a FEFF related question (I know that this is an IFEFFIT list, but I guess the subjects are closely related). I try to model some of my Cr XANES data with FEFF (following the procedure outlined in an excellent publication in Chem Phys 300 (2004) 13-22 the authors have shown that it is possible to explain the Cr XANES spectra at least qualitatively by the means of FEFF calculations). I have however still some trouble to understand the difference (or the relation) between the XANES results given in the xmu.dat file and the l-projected density of states results (ldosXX.dat). Due to rho(E)=rho_0(E)[1+chi(E)] I would expect them to conincide (if the rho is calculated for the correct l i.e. if the matrix element is non-zero). However I observed that the ldos and the xmu do not always coincide is this possible? Furthermore at the white line position (from what I know, the white line is commonly interpreted as being due to the transition into unoccupied but bound states) the xmu shows strong intensity whereas the ldos do not (maybe one comment: I assume that the e-scales in the ldos-file and in the xmu-file are the same). I am using FEFF8.2 with the SCF, DOS, XANES and FMS card. I would be obliged for your help. Thanks Jakob P.s.: for hydroxide structures FEFF is always returning bad counts if I include the protons into the FEFF calculation however this might be also due to bad input structures. ___________________________________________________ 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 Email: jakob.frommer(a)env.ethz.ch http://www.ito.ethz.ch/SoilChem/

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