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

Re: [Ifeffit] _Mn3O4 EXAFS fitting
by 이국승 01 Jun '15

01 Jun '15

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Mn3O4 EXAFS fitting
by 이국승 01 Jun '15

01 Jun '15

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Re: [Ifeffit] Ifeffit Digest, Vol 147, Issue 20
by Raj kumar 29 May '15

29 May '15

Hi Bruce, The comments are very helpful to assure my data processing and for future experiments. Yes, all measurements were obtained in Dispersive EXAFS mode. As for i know (at least until my preparation time) the bulk sample (first one) doesn't contain the Hf impurities. However, i will double check that point. Regards, Raj On Fri, May 29, 2015 at 7:00 PM, <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: Peak at short distance in FT - YbVO4 nanoparticles > (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 29 May 2015 12:52:38 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Peak at short distance in FT - YbVO4 > nanoparticles > Message-ID: <55689956.8040302(a)bnl.gov> > Content-Type: text/plain; charset=windows-1252; format=flowed > > On 05/29/2015 11:54 AM, Raj kumar wrote: > > Recently, i have performed EXAFS for YbVO4 bulk (prepared through > > sintering process) and nanoparticles (at room temperature). > > Nanoparticles were synthesized by co-precipitation technique and their > > EXAFS was measured by passing the prepared solution using peristaltic > > pump. After all subtraction (background and solvent), nanoparticles XAS > > data were recovered and processed for the fitting. After Fourier > > transform, it was observed that both nanoparticles posses an additional > > short peak (or shoulder) at about 1.2 A from bulk. Since the peak > > appears much closer to 1 A, i suspect this may due to artifact or bad > > background subtraction. Hence, i would like to know the way to eliminate > > this peak at short distance. > > Hi Raj, > > A few comments: > > 1. Your bulk sample (the first one in the list) may have a bit of Hf > in it it. It's hard to tell, but the mu(E) seems to be trending > upward right at the end of the data, which is the approximate edge > energy of Hf L3. I got a slightly better background removal by > changing the end of the spline range to 600. But this a minor > detail. The real story seems to be that .... > > 2. You data are pretty noisy. If you plot chi(R) out to 10 Angstroms > (which is, presumably, well beyond where you should expect to see > good signal in your data), you get a sense of how the level of > noise manifests itself in chi(R). To my eye, the peak/shoulder at > about 1.2 that you are asking about is of about the same size as > the level of noise in your data. > > You are asking how to get rid of a feature in the data that is > aesthetically unpleasing. I don't think that's the right question. > > Your data are what they are. Your data are noisy and measured over a > rather short energy range. That doesn't give you a lot of choices > about how aesthetically appealing you can make the Fourier transform > be. > > You seem to be operating Athena correctly and there aren't any magic > buttons that will make your short, noisy data longer or less noisy. I > don't see anything obviously wrong in how you are processing your data > and -- short of using PhotoShop ;) -- I don't see any defensible way of > making the feature at 1.2 go away. > > > > Am I correct in thinking that these data are measured in the > dispersive geometry? If so, my suggestion is to reconsider how you > make your samples. This kind of experiment is VERY sensitive to the > homogeneity of the sample. You have to take extraordinary care to make > your samples as homogeneous as possible. I suspect most of the > glitchy little points in your data are indicative of sample > inhomogeneity. > > You also should worry about purity of your source material. Granted, > it canbe very difficult to obtain rare earth metal samples that are > elementally pure. But if your data range is short because of other > edges, then you need samples that are more pure. > > HTH, > B > > > -- > Bruce Ravel ------------------------------------ bravel(a)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(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 147, Issue 20 > **************************************** >

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Peak at short distance in FT - YbVO4 nanoparticles
by Raj kumar 29 May '15

29 May '15

Dear All, Recently, i have performed EXAFS for YbVO4 bulk (prepared through sintering process) and nanoparticles (at room temperature). Nanoparticles were synthesized by co-precipitation technique and their EXAFS was measured by passing the prepared solution using peristaltic pump. After all subtraction (background and solvent), nanoparticles XAS data were recovered and processed for the fitting. After Fourier transform, it was observed that both nanoparticles posses an additional short peak (or shoulder) at about 1.2 A from bulk. Since the peak appears much closer to 1 A, i suspect this may due to artifact or bad background subtraction. Hence, i would like to know the way to eliminate this peak at short distance. Regards, Raj

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Output of data fit in k-space from current version of Artemis
by Rosalie Hocking 27 May '15

27 May '15

Hi Guys, I am embarrassed to ask this question, but I am fairly new to Artemis (moving over from the dark side of EXAFSPak) Could anyone advise me how to export a fit in k-space? If I go to the Artemis data window and go Data “save data and fit as” it doesn’t seem to match up with the simulations on the window. Exports in R-space seem sensible, but no amount of repetition and changes alternation, of fits etc seems to result in similarly sensible output in k-space. If anyone could help I would appreciate it- I can email you my fit file if it would help. kind regards, Rosalie

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polarization in Artemis
by Bruce Ravel 25 May '15

25 May '15

Hi, Everything in the discussion between Eugenio and Matt is stuff I agree with, except ... When I rewrote Artemis, one of the motivations was that I wanted to write my own pathfinder rather than to continue using the one in Feff. My main motivation was fuzzy degeneracy (http://bruceravel.github.io/demeter/artug/extended/fuzzy.html) plus I wanted to correct a few other things I saw as shortcomings. When I was writing it years ago, I didn't immediately see an easy way to consider polarization correctly while also doing fuzzy degeneracy correctly. I have since figured that out, but years went by and only one person ever asked me about polarized feff calculations in Artemis. So I never implemented it. It's a funny thing, when you wait for a bus, none comes, then two show up at once. A month ago, I was asked about polarization in Artemis, and now Eugenio brings it up! Polarization works (although it needs testing) in the very latest code in github. But I did that work since the last time I built a Windows installer. Ellipticity does not yet work (in Artemis -- it works just fine in Feff, but Artemis does not deliver the ellipticity-dependent calculation to the user). Anyway, I will try to find a few hours this week to build a new Windows installer, which will included the ability to consider linear polarization. > Artemis used to make this very easy (sum paths without fitting), but > I don't recall how to do this in the latest version. Still is easy. Well, I think it is. YMMV :) http://bruceravel.github.io/demeter/artug/plot/vpaths.html B -- Bruce Ravel ------------------------------------ bravel(a)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/

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polarization on FEFF calculation
by Eugenio Paris 24 May '15

24 May '15

Dear all, i have a question about polarization vector in performing the FEFF calculation in Artemis. I am studying the system CeOBiS2 using Bi L3-edge EXAFS. Starting from *.cif file i'm creating the *.inp file which atoms list come out as follows: ATOMS * this list contains 35 atoms * x y z ipot tag distance 0.00000 0.00000 0.00000 0 bi 0.00000 0.00000 0.00000 2.50509 4 s2.1 2.50509 2.81711 0.00000 -0.12006 4 s1.1 2.81967 -2.81711 0.00000 -0.12006 4 s1.1 2.81967 0.00000 2.81711 -0.12006 4 s1.1 2.81967 0.00000 -2.81711 -0.12006 4 s1.1 2.81967 0.00000 0.00000 -3.31180 4 s1.2 3.31180 ... Bismuth has a S atom sitting on top of him (s2) and it is square coordinated with other four S atoms (s1). I made measurements on single crystals using fluorescence yield. The experimental geometry consist of the x-ray beam coming at (almost) normal incidence which corresponds to electric field vector lying on the crystal's ab plane. If I perform the FEFF calculation without taking account of polarization I obtain the first scattering paths which are 1) @S2.1@, Degen = 1, Reff = 2.5051, Rank = 100 2) @S1.1@, Degen = 4, Reff = 2.8197, Rank = 100 3) @S1.2@, Degen = 1, Reff = 3.3118, Rank = 14.78 4) ...... When I insert the line "POLARIZATION 1 0 0" in the imput file i get 1) @S2.1@, Degen = 1, Reff = 2.5051, Rank = 100 2) @S1.1@, Degen = 4, Reff = 2.8197, Rank = 100 3) @S1.2@, Degen = 1, Reff = 3.3118, Rank = 3.67 4) ...... which is exactly the same result for the first 2 scatterings, even if the rank of higher shells is changed... Now, my question is: If the components of the polarization vector has to be written in the same reference frame of the atom list i'm expecting to see a strong suppression of the rank factor for the @S2.1@ scattering whose bond is along the z-direction, is it correct? the .cif file is attached Thank you in advance, Eugenio

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Plucking issue in the deglitching
by Shoaib Muhammad 23 May '15

23 May '15

Dear all, I am using Demeter Athena 0.9.21 on Windows 8.1 x64. Recently I measured some XAS data in which there are some glitches. Somehow pluck tool is working very inaccurate for me during deglitching. I can't select the point where I click, so I have to remove several points in order to get rid of one point. I have attached a short screen cast video along with sample XAS dataset in which I am trying to remove a point from pre-edge for demo purpose. I would be thankful if you could look into it. Regards, /Shoaib

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Re: [Ifeffit] Ifeffit Digest, Vol 147, Issue 10
by kakarla chandu 21 May '15

21 May '15

Dear all I am Dr. Chandrasekhar working on experimental condensed matter physics in NSYSU-Taiwan. As a part of my research, I am carrying XAS experiments for some multiferoic and strongly correlated systems. This is very new topic for me. As a part of my research I am studying one system. In that particular system, I face a situation where Cu2+ ions surrounded by five oxygen ligand atoms in different ligand geometries. That is CuIO5 is in square pyramid and CuIIO5 in trigonal bipyramid. So I did the EXAFS spectrum now how can I analyze the data, since XAS is element specific the Cu element scan I got one spectrum but I don’t know whether it is coming from CuIO5 or CuIIO5. So if you have any suggestion please help me Waiting for your reply. With Regards Dr. Chandu On Thu, May 21, 2015 at 6:31 PM, <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. Plucking issue in the deglitching (Shoaib Muhammad) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 22 May 2015 10:31:23 +0900 > From: "Shoaib Muhammad" <mshoaibce(a)gmail.com> > To: "'XAFS Analysis using Ifeffit'" > <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] Plucking issue in the deglitching > Message-ID: <002b01d0942f$05b44b60$111ce220$(a)gmail.com> > Content-Type: text/plain; charset="us-ascii" > > > > Dear all, > > > > I am using Demeter Athena 0.9.21 on Windows 8.1 x64. Recently I measured > some XAS data in which there are some glitches. Somehow pluck tool is > working very inaccurate for me during deglitching. I can't select the point > where I click, so I have to remove several points in order to get rid of > one > point. I have attached a short screen cast video along with sample XAS > dataset in which I am trying to remove a point from pre-edge for demo > purpose. > > > > I would be thankful if you could look into it. > > > > Regards, > > /Shoaib > >

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help
by Jagadesh K Kesavan 12 May '15

12 May '15

Hi I have windows 8 (32 bit) operating system in my laptop. I am not able to istall the six pack software, It is not working in my pc. What is the problem? how could i resolve this problem? Do i get the proper six pack software for windows 8 (32 bit)? Kindly suggest me. Looking for your reply. Thank you. With Best Regards, ----------------------------- *JAGADESH KOPULA KESAVAN* PhD Research Scholar Material Science and Nanotechnology Department of Science University of Rome 3 Via della Vasca Navale 84, 00146, Rome, Italy. E-mail: jagadesh.kopulakesvan(a)uniroma3.it Tel: 06/57337054 Mob: +39 3207769588 -----------------------------

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Re: [Ifeffit] Ca EXAFS with Ge220 or InSb111 (Lisa Bovenkamp)
by Lisa Bovenkamp 11 May '15

11 May '15

Hello. No, the resolution is fine. I can do XANES fine with InSb111. We use those for years. Just had problems with EXAFS because for this long range the flux has to be more stable from the crystals. Lisa

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Ca EXAFS with Ge220 or InSb111
by Lisa Bovenkamp 11 May '15

11 May '15

Hello. After having some troubles recording a good EXAFS spectrum with some old InSb111 crystals I started wondering if it might be better to use Ge220 instead. Anybody have some experience with that? Lisa

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Scatter Plot in Athena
by Shoaib Muhammad 05 May '15

05 May '15

Dear All, In Athena documentation section I can see data plotted as scatter instead of line type plot (for example the plot shown in the attached file). This feature seems to be helpful in deglitching the bad data points but I could not figure out how to do it! Can anybody guide me how to plot data as scatter in Athena? My platform is Windows8 x64. Thanks, /Shoaib

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Re: [Ifeffit] Self absorption Correction
by Richard Mayes 04 May '15

04 May '15

Farzana, I'm copying the IFEFFIT mail list, they may have the information buried in the archives somewhere. That link points to Grant Bunker's webpage containing his XAFS tutorials and it will not open for me at the moment either. However, there are several very good books that have come out lately on XAFS that explain self absorption quite well. If you're not interested in getting a copy of the books, there is a discussion thread from when I was a newbie to overabsorption that is found on the XAFS.org tutorials page. I suggest going through it as several contributed substantial knowledge in that thread (http://www.xafs.org/Experiment/OverAbsorption) Cheers, -Rich On Mon, May 4, 2015 at 7:47 PM, Farzana Nasreen <farzana6109(a)gmail.com> wrote: > Dear Rich, > > http://cars9.uchicago.edu/pipermail/ifeffit/2009-February/008631.html > > I was looking at this above link to find out similar information that Jen > had. Unfortunately, I couldn't open the link in the reply that you gave to > her. > Do you know where I can download this paper by > > *http://gbxafs.iit.edu/training/Self_Absorption_effects.pdf <http://gbxafs.iit.edu/training/Self_Absorption_effects.pdf>* > > I am working on some PFY-XAS data on some uranium compounds. > > Thanks > > Farzana > > > > >

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Demeter Package for mac
by ebonturim＠usp.br 29 Apr '15

29 Apr '15

Hi everyone! I would like to know if the Demeter Package is already working into the mac (2015). Someone could use it? How do install the right way files? Thank you. Everton Bonturim

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Re: [Ifeffit] energy resolution
by Lisa Bovenkamp 20 Apr '15

20 Apr '15

Hello all. I am getting confused with different comments how to determine the energy resolution of an XAS beamline. I think using peak fitting to determine the line width is a reasonable method. The basis of a XAS peak is the Voigt profile (a combination of a Lorenzian and Gaussian) The width of the Lorenzian equals the natural line width while the width of the Gaussian represents the experimental line width and some features Now here is question 1: What is the combination of the two profiles in the Athena peak fitting routine for the Pseudo-Voigt? Question 2: Is the sigma (Gaussian width) that delta E that represents the resolution - (E /delta E) ? Using a different program (Igor Pro) to determine the width gives different results because can only use a simple combination of Lorentz and Gauss (1:1). Thanks. Lisa

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Athena reporting incorrect element on import
by Kenneth Latham 20 Apr '15

20 Apr '15

Hi, I am having a number of issues with importing my data into Athema, the data that I collected was on the carbon K edge. As there is an issue with recording carbon (as it builds up on the mirrors), the synchrotron that I performed my measurments at (Australian Synchrotron) has developed software to perform a double normalization to remove these effects. The problem comes when importing the now normalized data into Athena. As it doesn't require normalization again, I select the norm(E) data type and the correct column for energy and response which produces the correct plot of the data. When I click OK it attempts to produce the other plots, sometimes it manages to make a k-space and R-space but q-space is never displayed and other times it only manages the energy plot. Additionally, the word element is lit up red and it has selected beryllium as the element on the L2 edge. Changing this to carbon does not seem to fix the problem as it reverts back to beryllium as soon as I leave the main page. Finally, when I go to peak fitting, any value added for peaks informs me that it is out of range. I have attached some normalized data. Any help with this would be greatly appreciated. Regards, Ken Latham

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Re: [Ifeffit] Problems installing demeter in Manjaro Linux
by Ramiro Moreira Toja 16 Apr '15

16 Apr '15

Bruce, force-installing with cpan did the trick, thanks! I still wonder if the apache/src thing may give me trouble some day. When installing the XMLRPC::Lite module, I hit on that again, but everything worked in the end. Thanks for your help (and for this great software, too!) Ramiro I'm not familiar with Manjaro. Are there package in its packaging system for those two perl modules? If so, just install them that way. If not, you could try running the cpan program and doing: force install Regexp::Assemble and force install XMLRPC::Lite Another option is to download those two packages from metacpan.org and install them by hand. As for the pgplot installation -- I believe I had to do the same thing the last time I built Ifeffit. Glad you figured it out! Good luck! Let us know if you run into other problems. B On 04/15/2015 09:40 PM, Ramiro Moreira Toja wrote: Hi, I'm using Manjaro 0.8.12 x64. I tried to install the demeter collection (following these instructions <https://bruceravel.github.io/demeter/pods/installation.pod.html>), but keep failing to do so. Also, I've checked to have installed all the reccomended packages, including apache and gnuplot. When installing PGPLOT, I've had to edit the configuration to use gif instead of png, because it kept failing to install. Once I did this, it went smoothly. I add this piece of information here hoping this helps to solve later problems. I'm having a little trouble installing dependencies. At the "sudo ./Build installdeps", it kept having trouble to find the apache/src. After a little Web search, it seems like I need to manually download the httpd sources, so I got them from here <http://apache.xfree.com.ar//httpd/httpd-2.4.12.tar.bz2>, but now it indicates I need Apache 1.3.0 version! If I do "perl Build.PL", I get: perl Build.PL Checking prerequisites... requires: ! Regexp::Assemble is not installed ! XMLRPC::Lite is not installed ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the versions of the modules indicated above before proceeding with this installation So, I guess I'm having some more problems with the dependencies, apart from the Apache ones. What should be my next move to fix this? I've been even considering using a Ubuntu LiveUSB with persistence, just to get this working in a proven system, but really would like to get it working on my OS of choice. Thanks in advance Ramiro _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- Bruce Ravel ------------------------------------ bra...(a)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(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Problems installing demeter in Manjaro Linux
by Ramiro Moreira Toja 16 Apr '15

16 Apr '15

Hi, I'm using Manjaro 0.8.12 x64. I tried to install the demeter collection (following these instructions <https://bruceravel.github.io/demeter/pods/installation.pod.html>), but keep failing to do so. Also, I've checked to have installed all the reccomended packages, including apache and gnuplot. When installing PGPLOT, I've had to edit the configuration to use gif instead of png, because it kept failing to install. Once I did this, it went smoothly. I add this piece of information here hoping this helps to solve later problems. I'm having a little trouble installing dependencies. At the "sudo ./Build installdeps", it kept having trouble to find the apache/src. After a little Web search, it seems like I need to manually download the httpd sources, so I got them from here <http://apache.xfree.com.ar//httpd/httpd-2.4.12.tar.bz2>, but now it indicates I need Apache 1.3.0 version! If I do "perl Build.PL", I get: perl Build.PL Checking prerequisites... requires: ! Regexp::Assemble is not installed ! XMLRPC::Lite is not installed ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the versions of the modules indicated above before proceeding with this installation So, I guess I'm having some more problems with the dependencies, apart from the Apache ones. What should be my next move to fix this? I've been even considering using a Ubuntu LiveUSB with persistence, just to get this working in a proven system, but really would like to get it working on my OS of choice. Thanks in advance Ramiro

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FEFF calculation for two inequivalent absorbing sites
by Eugenio Paris 10 Apr '15

10 Apr '15

Hello everybody, I'm trying to make Co K-edge EXAFS fitting for the Co3O4 compound (*.cif file is attached). The nearest neighbour of Co is oxigen at about 1.93 Angstrom distance. Cobalt sits in two inequivalent sites in the unit cell. When I perform the FEFF calculation in Artemis for either one or the other site i get the same path with Reff = 1.93 and degeneracy = 4. So i wonder what is the correct way to take account of the presence of both sites. At the beginning i was thinking to put 2*amp as S0^2 parameter to take account for twice the coordination number. Then i tried to use the "Aggregate" option in Artemis. When I use this option i get exactly the same result, i.e. a SS path with Reff = 1.92 and degeneracy = 4... I was expecting to get twice the degeneracy.. (the margin and beta parameters are set to default) My question is: Why do i get the same path list when I do use the "Aggregate" pathfinder and when I don't? What is wrong in my interpretation? Thank you in advance! Sincerely, Eugenio

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error message by import
by Zimina, Anna (IKFT) 09 Apr '15

09 Apr '15

I get the following error message when I read the txt file with two columns of data (energy and intensity): "11:42:20: Use of uninitialized value $line in pattern match (m//) at C:/strawberry/perl/site/lib/Demeter/Files.pm line 188." Still the data can be read. What is the problem? Thanks in advance, Anna Zimina. ______________________________________________________________________________________ Karlsruhe Institute of Technology (KIT) Institute of Catalysis Research and Technology (IKFT) Dr. Anna Zimina Beamline scientist Hermann-von-Helmholtz-Platz 1 Building 345, Office 108 76344 Eggenstein-Leopoldshafen Phone: +49 721 608 28673 Fax: +49 721 608 26789 E-Mail anna.zimina(a)kit.edu<mailto:anna.zimina@kit.edu> [cid:image001.jpg@01D071F1.C77B7BC0]

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Atoms
by Zimina, Anna (IKFT) 08 Apr '15

08 Apr '15

In the last version Atoms is not present as a separate program. Is it correct? Mit freundlichen Grüßen, Anna Zimina ______________________________________________________________________________________ Karlsruhe Institute of Technology (KIT) Institut für Katalyseforschung und -technologie (IKFT) Dr. Anna Zimina Wissenschaftlerin Hermann-von-Helmholtz-Platz 1 Geb. 345 Zi. 108 76344 Eggenstein-Leopoldshafen Fon: +49 721 608 28673 Fax: +49 721 608 26789 E-Mail anna.zimina(a)kit.edu<mailto:anna.zimina@kit.edu> [cid:image001.jpg@01D071F0.3A2FB840]

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Evaluation of uncertainty using correlated Debye model + advices for the fitting of an hexagonal Co-foil
by Samy OuldChikh 07 Apr '15

07 Apr '15

Dear all, I would like to go beyond the fitting of the first shell for a cobalt metallic foil acquired at FAME beamlime (ESRF). It's not mandatory for the determination of So in this case, but I just would like to improve myself in EXAFS fitting. The cobalt foil has an hexagonal structure (P 63/mmc, a =b=2.507 A, c= 4.068 A) according to the supplier. The first 49 scattering paths calculated with FEFF were selected to cover the R range up to 5.1 A. This include multiple scattering paths. The parametrization of those scattering paths is as follow (.apj enclosed) : - Distances : 1) a spherical expansion term was used to describe distance variation in [hkl] direction (reff*alpha1) with l considered as "large" when compared to h,k (reff*alpha1) 2) another spherical expansion term was used to describe distance variation in pure [hk0] direction (reff*alpha2) 3) a rough average of two previous expansion terms for [hkl] direction when h,k are comparable to l (reff*(alpha2+alpha1)/2). - For modeling disorder, the correlated Debye model was used with 3 parameters dt, dt2, dt3 (t =293K): 1) [hkl] direction with l considered as "large" : debye(t,dt) 2) pure [hk0] direction: debye(t,dt2) 3) for [hkl] direction with h,k comparable to l : debye(t,(dt+dt2)/2) But does this choice of parametrization is really reasonable? It seems very rough to me but when I look at the fit results it looks ok. - Uncertainty on : 1) Distances : is it simply delta(r) = reff*delta(alpha) ? 2) Debye-Waller : I can't figure out how to relate the uncertainty computed for the Debye temperatures (dt, dt2) to the uncertainties of the debye-waller terms for each scattering paths. Although I spent some times trying to understand this paper, http://journals.aps.org/prb/pdf/10.1103/PhysRevB.20.4908, I can't write a simple relation at the end. Many thanks for your kind help, Best Regards, Samy Ould-Chikh KAUST Catalysis Center Bldg.3,Level 4, #4231 4700 King Abdullah University of Science & Technology Thuwal 23955-6900 Kingdom of Saudi Arabia Tel: +966 12 8084486 E-mail: samy.ouldchikh(a)kaust.edu.sa Website: http://kcc.kaust.edu.sa/Pages/Home.aspx ________________________________ This message and its contents including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

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Re: [Ifeffit] Importing data with the new version of Athena [SEC=UNCLASSIFIED]
by Ravel, Bruce 06 Apr '15

06 Apr '15

Zhaoming, This conversation should be happening on the Ifeffit Mailing List. I did not notice that last night when I replied to your first email. Yet another reason not to answer email late at night! I continue to be sceptical of your claims. I have no problems with the data file you sent on either Windows or Linux once I correctly select the columns in the column selection dialog. Once imported, the default values for normalization are set as I expect and the data is interactive in the normal manner. Here are some hints about how to provide a useful bug report: http://bruceravel.github.io/demeter/pods/bugs.pod.html Please read it carefully. If there is more to this conversation, please use the mailing list. B -- Bruce Ravel ------------------------------------ bravel(a)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 ________________________________ From: ZHANG, Zhaoming [zzx(a)ansto.gov.au] Sent: Thursday, April 02, 2015 1:00 AM To: Ravel, Bruce Subject: RE: [Ifeffit] Importing data with the new version of Athena [SEC=UNCLASSIFIED] Hi Bruce, Sorry, I did have to specify column 4 as energy, 7 as Io and 8 as It. The new version of Athena does read the .dat file in, but the default values for normalization are way wrong, and it doesn’t work by manually change them either. I’m happy to send you screen shots if necessary. Thanks again for your help. Zhaoming From: Ravel, Bruce [mailto:bravel@bnl.gov] Sent: Thursday, 2 April 2015 12:43 PM To: ZHANG, Zhaoming Subject: RE: [Ifeffit] Importing data with the new version of Athena [SEC=UNCLASSIFIED] Zhaoming, I'm afraid I am sceptical of your story. I have no trouble reading this file and I don't believe that any change I've made since 0.9.20 would have affected this. Who knows, though. I'll take a lok on a windows machine when I get into work tomorrow morning. It's a rather awkward file. The first column is an index, not energy. That's one of my pet peeves -- just a ridiculous way to present the data and kind of mean-spirited to the user. When something is measured in energy, the first column should be energy. That means you have to explicitly select column 2 as the energy. Column 2 appears to be in keV, so you need to explicitly set that in the column selection dialog. Because column 1 was not the energy, Athena had no way of figuring that out. I have no idea which columns have data in them. 7 and 8 look rather like I0 and It. So you need to explicitly set your data columns, as well. I've attached a screenshot of the column selection dialog with all those settings. When data are presented as obfuscated as they are in this data file, it is not reasonable to expect that Athena will magically know how to disentangle everything without your help. You have to be responsible for knowing which columns to combine to turn your raw data into mu(E). B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov<mailto:bravel@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 ________________________________ From: ZHANG, Zhaoming [zzx(a)ansto.gov.au] Sent: Wednesday, April 01, 2015 7:34 PM To: Ravel, Bruce Subject: [Ifeffit] Importing data with the new version of Athena [SEC=UNCLASSIFIED] Dear Bruce, I’ve encountered the same problem as Sander Bruun. My data were obtained from the Australian Synchrotron. In the past, I could read the .dat file (see attached example) directly into Athena. But it doesn’t work with the new version (0.9.20), and the beamline scientist doesn’t know why either. I would really appreciate if you could let me know what ‘fix’ we need! Thanks so much. Warm regards, Zhaoming

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Possible Error on 0.9.21
by Clark, Adam 01 Apr '15

01 Apr '15

Hi I have recently encountered an error in displaying the path geometry in the latest version of artemis, 0.9.21. When running feff and then selecting a path and viewing the geometry of this path an incorrect path is shown. This does not occur when using the same feff.inp file on the older 0.9.20 version. The problem is limited to the numbering and showing of the path geometry in the feff calculation window. Attached is the feff.inp, feff.txt files and a screenshot showing the produced feff.txt ‘show geometry for this path window’ for a selected @ O.1 @ path (instead showing the @ Zn.1 @ path) and ‘atoms and feff’ window showing the discrepancy in path numbering between the feff.txt file and feff window. Thanks Adam

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