- 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

2 2

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

2 1

Artemis on Yosemite
by George Sterbinsky 26 Mar '15

26 Mar '15

Hello, When I attempt to open Artemis on OSX Yosemite (10.10.2) the error message copied below prints to the terminal. The initial image that indicates Artemis is opening does appear, although Artemis fails to open. Athena and Hephaestus open without error. Any suggestions as to how this could be resolved would be appreciated. Thanks, George $ artemis Can't locate Math/Round.pm in @INC (@INC contains: /opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/site_perl/5.16.3 /opt/local/lib/perl5/vendor_perl/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/vendor_perl/5.16.3 /opt/local/lib/perl5/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/5.16.3 /opt/local/lib/perl5/site_perl /opt/local/lib/perl5/vendor_perl .) at /opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level/Demeter/ScatteringPath.pm line 44. BEGIN failed--compilation aborted at /opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level/Demeter/ScatteringPath.pm line 44. Compilation failed in require at /opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level/Demeter.pm line 306. BEGIN failed--compilation aborted at /opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level/Demeter/UI/Artemis.pm line 26. Compilation failed in require at /opt/local/bin/artemis line 34. BEGIN failed--compilation aborted at /opt/local/bin/artemis line 34.

2 2

Incomplete source tarballs for larch?
by Johan Nilsson 24 Mar '15

24 Mar '15

Dear all, Today I helped a colleague install larch on OSX Yosemite but we ran into some problems using the source tarball from CARS (larch-0.9.24.tar.gz). It was a bit of a learning curve for me as a linux user but we managed to install the prerequisites (exept for epics) using macports and then ran the larch installer without noticing any warnings or errors. The problem after that was that we could not locate the larch binary. The source tarball does not include a 'bin' directory and some other things that are found in the github source so we went ahead and installed larch from the github source instead. After that we could locate the binery and start the interpreter. Did we make some mistake here or are there things missing in the source tarballs? Best regards, Johan Nilsson

2 2

amplitude parameter S02 larger than 1
by huyanyun＠physics.utoronto.ca 23 Mar '15

23 Mar '15

Hi all, I know this question has been asked for many times. S02 is expected to be around, but smaller than 1, a fact that has been explained, such as in the following previous emails, in our mailing list. http://www.mail-archive.com/ifeffit%40millenia.cars.aps.anl.gov/msg02237.ht… http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2003-February/000230.html However, I am continually get S02 value larger than 1 for a series of similar samples when I fit data in Artemis. I think my fit is very good, because my suspected model(based on other technique) could be verified in XAFS analysis (i.e., defensible in physics), the statistics is good ( R=0.01, reduced chi-square=31.4, fit-range:1.5~6 Angstrom, k-range: 3~14 angstrom-1) and all the parameters such as the bond length, sigma2 are physically reasonable. The only thing makes me uncomfortable is that parameter S02 keeps between 1.45 to 1.55 during the fitting. In my system, the absorber atom occupies two crystallographic sites. So I built a model with paths generated from two FEFF calculations. For paths generated from the 1st and 2nd FEFF calculation, the amplitude parameters are set to be S02*P% and S02*(1-P%) respectively, where P% is the first site occupancy percentage. Both S02 and P are free parameters during the fit, and P is an important conclusion I want to extract from XAFS fitting. However, the fit result gives me S02=1.45 ~ 1.55 and P=0.51 ~ 0.56 all the time (i.e., for each path the 'total amplitude' S02*P% or S02*(1-P%) are about 0.7~0.8, smaller than 1). It looks to me that I got a 'perfect' fit but I am not sure if S02 larger than one is defensible. So I have to ask: 1) Is my current fit with S02 larger than one reasonable? If not, what could be suggested to get around it? 2) What's the meaning of S02? It is interpreted in physics that it is a reduced electron excitation parameter, but is it possible that S02 will be affected by any experimental condition? 3) Can anyone share whether you had the multiple site system that gets S02 larger than one? Looking forward to your help. Best, Yanyun

6 23

Installing demeter from source on Yosemite?
by Anders Glans 23 Mar '15

23 Mar '15

Dear all, Has anybody succeeded with installing demeter from source on a Mac? I have attempted to install demeter from source on OS X 10.10.2, but so far without success. I have followed the installation procedure for Installing source code at http://bruceravel.github.io/demeter/pods/installation.pod.html <http://bruceravel.github.io/demeter/pods/installation.pod.html>, except I installed pgplot from source instead of using the install script provided through ifeffit. I don’t get any errors installing either pgplot or ifeffit. All dependencies for demeter should be met: $ sudo perl ./Build.PL Password: Created MYMETA.yml and MYMETA.json Creating new 'Build' script for 'Demeter' version '0.9.21' If all dependencies are met, build and install Demeter by doing: <snip> The build seems to go fine: $ sudo ./Build Simple test for presence of gnuplot ---> found it! Using gnuplot with the x11 terminal. Building Demeter Building Artemis User's Guide Building Athena User's Guide But the tests fail miserably. Already before the actual testing starts, there is a message that loading of Ifeffit.bundle fails: $ sudo ./Build test t/000_ifeffit.t ......... Can't load '/Library/Perl/5.18/darwin-thread-multi-2level/auto/Ifeffit/Ifeffit.bundle' for module Ifeffit: dlopen(/Library/Perl/5.18/darwin-thread-multi-2level/auto/Ifeffit/Ifeffit.bundle, 2): Symbol not found: _ifeffit Referenced from: /Library/Perl/5.18/darwin-thread-multi-2level/auto/Ifeffit/Ifeffit.bundle Expected in: flat namespace in /Library/Perl/5.18/darwin-thread-multi-2level/auto/Ifeffit/Ifeffit.bundle at /System/Library/Perl/5.18/darwin-thread-multi-2level/DynaLoader.pm line 194. at t/000_ifeffit.t line 9. Compilation failed in require at t/000_ifeffit.t line 9. BEGIN failed--compilation aborted at t/000_ifeffit.t line 12. # Looks like your test exited with 255 before it could output anything. t/000_ifeffit.t ......... Dubious, test returned 255 (wstat 65280, 0xff00) Failed 6/6 subtests <snip> However, the bundle exists: $ ls -l /Library/Perl/5.18/darwin-thread-multi-2level/auto/Ifeffit/ total 152 -r-xr-xr-x 1 root wheel 76208 Mar 18 13:09 Ifeffit.bundle and the symbol in question is part of the bundle (well, at least the string exists): $ grep _ifeffit /Library/Perl/5.18/darwin-thread-multi-2level/auto/Ifeffit/* Binary file /Library/Perl/5.18/darwin-thread-multi-2level/auto/Ifeffit/Ifeffit.bundle matches Does anybody know what is going on? Am I missing something? A couple of more bits of information: $ which ifeffit /usr/local/bin/ifeffit $ ifeffit Ifeffit 1.2.12 Copyright (c) 2005 Matt Newville, Univ of Chicago command-line shell version 1.1 with GNU Readline Ifeffit> testplot %PGPLOT, Unrecognized device type %PGPLOT, Invalid device specification: /AQT %PGPLOT, PGBBUF: selected graphics device is not open %PGPLOT, PGQCI: selected graphics device is not open %PGPLOT, PGQFS: selected graphics device is not open %PGPLOT, PGSCI: selected graphics device is not open %PGPLOT, PGSFS: selected graphics device is not open %PGPLOT, PGSVP: selected graphics device is not open %PGPLOT, PGBBUF: selected graphics device is not open %PGPLOT, PGEBUF: selected graphics device is not open %PGPLOT, PGSVP: selected graphics device is not open %PGPLOT, PGSCI: selected graphics device is not open %PGPLOT, PGSFS: selected graphics device is not open %PGPLOT, PGEBUF: selected graphics device is not open ** plot error: cannot open device: %PGPLOT, Unrecognized device type %PGPLOT, Invalid device specification: /AQT ** plot error: cannot open device: Ifeffit> exit $ which athena /usr/local/bin/athena $ athena dyld: lazy symbol binding failed: Symbol not found: _iff_exec Referenced from: /Library/Perl/5.18/darwin-thread-multi-2level/auto/Ifeffit/Ifeffit.bundle Expected in: flat namespace dyld: Symbol not found: _iff_exec Referenced from: /Library/Perl/5.18/darwin-thread-multi-2level/auto/Ifeffit/Ifeffit.bundle Expected in: flat namespace Trace/BPT trap: 5 Regards, Anders

3 7

Re: [Ifeffit] Breaking down correlationships between parameters
by Rana, Jatinkumar Kantilal 23 Mar '15

23 Mar '15

Hi Bruce, Thanks for your comments and links of your lectures. I forgot to mention that I use Artemis for fitting my data. Best regards, Jatin -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: 23 March, 2015 15:37 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 145, Issue 45 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: Breaking down correlationships between parameters (Bruce Ravel) 2. Re: Breaking down correlationships between parameters (Rana, Jatinkumar Kantilal) ---------------------------------------------------------------------- Message: 1 Date: Mon, 23 Mar 2015 09:27:05 -0400 From: Bruce Ravel <bravel(a)bnl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Breaking down correlationships between parameters Message-ID: <551014A9.4090604(a)bnl.gov> Content-Type: text/plain; charset=utf-8; format=flowed On 03/23/2015 08:54 AM, Rana, Jatinkumar Kantilal wrote: > The term N*S02 is fitted for each path of the FEFF calculation. So my > question is, even if we know N with a great certainty for some path, > how can we vary both N and S02 for other paths ? or Did I understand > it wrong ? At no point in your emails did you say that you are using Artemis to do your fitting. The comment I am about to make may not, therefore, be relevant to you. In Ifeffit and Larch -- and therefore in Artemis -- we DO NOT fit N*SO2. Fits in Ifeffit, Larch, and Artemis use a set of user-defined parameters as the variables of the fit. As part of the fitting model, the user relates the variables of the fit to the parameters of the EXAFS equation using math expression. This benefit of the generality of the fitting model allows the user to easily encode prior knowledge into a fit. The cost is that the parameters have to be interpreted in some kind of physical context. To answer you question specifically, Artemis allows you to set or float parameters for N and S02 and to define the amplitude term of the EXAFS equation for each path in any way that you see fit. In that way, you can implement all the suggestions that Matt, Scott, and Chris have made. I discuss this in some detail starting at page 35 of this presentation. https://speakerdeck.com/bruceravel/advanced-topics-in-exafs-analysis Among the lectures at http://www.diamond.ac.uk/Beamlines/Spectroscopy/Techniques/XAS.html, this is the one called "Fit Evaluation and Fitting multiple structures". 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/ ------------------------------ Message: 2 Date: Mon, 23 Mar 2015 14:36:31 +0000 From: "Rana, Jatinkumar Kantilal" <jatinkumar.rana(a)helmholtz-berlin.de> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Breaking down correlationships between parameters Message-ID: <DA4C7D90F90BC249A03505C87F2EB8AB230EE7F0@didag1> Content-Type: text/plain; charset="utf-8" Hi Scott, Thanks for your explanation. It means the reverse can also be true, i.e., I can guess N1 (nearest-neighbors in the first shell) and S02 by setting N2, N3 and N4 to values known from other analysis. I did a quick check by fitting the data. I conducted two fits: 1) setting S02 and guessing only N1 2) guessing both N1 and S02. To my surprise, both the fits gave very similar results, except that the fit#1 refined value of N1 to a higher side, while fit#2 estimated N1 closer to a physically reasonable value (as expected). I always constrained S02 when refining N for any path, due to 100% correlation between them. However, I am surprised to know that they can be refined independently. Best regards, Jatin -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: 23 March, 2015 14:19 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 145, Issue 44 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: Breaking down correlationships between parameters (Scott Calvin) ---------------------------------------------------------------------- Message: 1 Date: Mon, 23 Mar 2015 09:18:21 -0400 From: Scott Calvin <scalvin(a)sarahlawrence.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Breaking down correlationships between parameters Message-ID: <78C1636C-91CF-4C8C-9D48-3EC361BB7237(a)slc.edu> Content-Type: text/plain; charset="utf-8" Hi Jatin, The key is that S02 should be the same for all paths. For example: Suppose you are very confident path 1 has a coordination number of 6, because of prior knowledge you have about the system. Paths 2, 3, and 4 have unknown coordination numbers, however. N1 (i.e. the degeneracy of path 1) you set to 6. You guess S02, N2, N3, and N4. Of course, the way Artemis and Ifeffit implement that, you're writing N1*S02 for the S02 field of Path 1, N2*S02 for the S02 field of Path 2, etc., and then setting N1 = 6 and guessing S02, N2, N3, and N4. There is now enough information for S02, N2, N3, and N4 to each be fitted without 100% correlation. ?Scott Calvin Sarah Lawrence College > On Mar 23, 2015, at 8:54 AM, Rana, Jatinkumar Kantilal <jatinkumar.rana(a)helmholtz-berlin.de> wrote: > > Hi Chris, > > The term N*S02 is fitted for each path of the FEFF calculation. So my question is, even if we know N with a great certainty for some path, how can we vary both N and S02 for other paths ? or Did I understand it wrong ? > > Best regards, > Jatin > > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov > [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of > ifeffit-request(a)millenia.cars.aps.anl.gov > Sent: 23 March, 2015 12:16 > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Ifeffit Digest, Vol 145, Issue 42 > > 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: Breaking down correlationships between parameters > (Rana, Jatinkumar Kantilal) > 2. Re: Breaking down correlationships between parameters > (Chris Patridge) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 23 Mar 2015 11:00:19 +0000 > From: "Rana, Jatinkumar Kantilal" > <jatinkumar.rana(a)helmholtz-berlin.de> > To: "ifeffit(a)millenia.cars.aps.anl.gov" > <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Breaking down correlationships between > parameters > Message-ID: <DA4C7D90F90BC249A03505C87F2EB8AB230EE777@didag1> > Content-Type: text/plain; charset="utf-8" > > Hi Scott, > > Thank you for your comments. Can you please elaborate a little bit more on this "In cases like that, both N for all paths but one and S02 can be fit without 100% correlation." > > Best regards, > Jatin > > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov > [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of > ifeffit-request(a)millenia.cars.aps.anl.gov > Sent: 23 March, 2015 10:16 > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Ifeffit Digest, Vol 145, Issue 41 > > 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: Breaking down correlationships between parameters > (Scott Calvin) > 2. Re: Breaking down correlationships between parameters > (Matt Newville) > 3. Re: Breaking down correlationships between parameters > (Rana, Jatinkumar Kantilal) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 22 Mar 2015 13:44:28 -0400 > From: Scott Calvin <scalvin(a)sarahlawrence.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Breaking down correlationships between > parameters > Message-ID: <E0C66911-7AD2-448C-9F64-F03E262D04D7(a)slc.edu> > Content-Type: text/plain; charset="utf-8" > > One side-comment from me: > > On Mar 22, 2015, at 12:52 PM, Matt Newville <newville(a)cars.uchicago.edu<mailto:newville@cars.uchicago.edu>> wrote: > > N and S02 are always 100% correlated (mathematically, not merely by the finite k range). > > Matt is saying that N and S02 are always 100% correlated for a single path. But in some situations you might know N for one path but not others. For example, you might know that the absorbing atom is octahedrally coordinated to oxygen but not be as certain as to next-nearest neighbors, or that there are copper atoms on the corners of a simple cubic lattice with a mixture of atoms at other positions. In cases like that, both N for all paths but one and S02 can be fit without 100% correlation. > > The degeneracy of multiple-scattering paths can often be constrained in terms of the coordination numbers for direct-scattering paths, which can further reduce (not ?break?) the correlation. > > In terms of the main question, I agree with Matt: I don?t think there?s much point in using the line-crossing technique nowadays; fitting using multiple k-weights simultaneously accomplishes the same thing but is a bit easier to interpret statistically. > > ?Scott Calvin > Sarah Lawrence College > -------------- next part -------------- An HTML attachment was > scrubbed... > URL: > <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/201503 > 22/f4e7b7e4/attachment-0001.htm> > > ------------------------------ > > Message: 2 > Date: Sun, 22 Mar 2015 15:56:20 -0500 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Breaking down correlationships between > parameters > Message-ID: > > <CA+7ESbq_s0X3L9rPDDnwAdhx7h6Ptx5-8guCUFTM2OjwkYEerA(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > On Sun, Mar 22, 2015 at 12:44 PM, Scott Calvin > <scalvin(a)sarahlawrence.edu> > wrote: > >> One side-comment from me: >> >> On Mar 22, 2015, at 12:52 PM, Matt Newville >> <newville(a)cars.uchicago.edu> >> wrote: >> >> N and S02 are always 100% correlated (mathematically, not merely by >> the finite k range). >> >> >> Matt is saying that N and S02 are always 100% correlated *for a >> single path*. But in some situations you might know N for one path >> but not others. For example, you might know that the absorbing atom >> is octahedrally coordinated to oxygen but not be as certain as to >> next-nearest neighbors, or that there are copper atoms on the corners >> of a simple cubic lattice with a mixture of atoms at other positions. >> In cases like that, both N for all paths but one and S02 can be fit without 100% correlation. >> >> > Yes, I completely agree with Scott -- this is a good point that I > neglected. In addition to looking at multiple shells, one might also > consider using temperature or pressure dependence to separate N*S02 and > sigma2. Those aren't without assumptions, and still don't remove the > inherent correlation, but are useful approaches. > > The degeneracy of multiple-scattering paths can often be constrained > in >> terms of the coordination numbers for direct-scattering paths, which >> can further reduce (not ?break?) the correlation. >> >> In terms of the main question, I agree with Matt: I don?t think >> there?s much point in using the line-crossing technique nowadays; >> fitting using multiple k-weights simultaneously accomplishes the same >> thing but is a bit easier to interpret statistically. >> >> ?Scott Calvin >> Sarah Lawrence College >> >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> >> > --Matt > -------------- next part -------------- An HTML attachment was > scrubbed... > URL: > <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/201503 > 22/3dd3f763/attachment-0001.htm> > > ------------------------------ > > Message: 3 > Date: Mon, 23 Mar 2015 09:16:02 +0000 > From: "Rana, Jatinkumar Kantilal" > <jatinkumar.rana(a)helmholtz-berlin.de> > To: "ifeffit(a)millenia.cars.aps.anl.gov" > <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Breaking down correlationships between > parameters > Message-ID: <DA4C7D90F90BC249A03505C87F2EB8AB230EE755@didag1> > Content-Type: text/plain; charset="utf-8" > > Hi Matt, > > Thank you very much for your detailed explanation. As you pointed out that this approach ignores the statistical significance of fits and assumes that all fits are "good" fits. Also, the point that this approach yields a value of the parameter which is only slightly less correlated with the other one, but not completely removes the correlation. It makes it really clear to me that how this approach works and what are the pros and cons. > > Well, I myself has never tried this approach of minimizing the correlation between N*S02 and sigma2, but I read a lot about it in the literature. With my limited knowledge about the method, I could not judge this approach, although I had my own doubts. > > I truly appreciate your efforts in providing me a deeper insight into this approach. > > Best regards, > Jatin > > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov > [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of > ifeffit-request(a)millenia.cars.aps.anl.gov > Sent: 22 March, 2015 18:00 > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Ifeffit Digest, Vol 145, Issue 40 > > 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: Breaking down correlationships between parameters > (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 22 Mar 2015 11:52:30 -0500 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Breaking down correlationships between > parameters > Message-ID: > > <CA+7ESbqcyQHf9XUh2uhk=Lv09An7E9LXxqDTX-X6kRJHy9PFzw(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Jatin, > > > On Sat, Mar 21, 2015 at 10:41 AM, Rana, Jatinkumar Kantilal < jatinkumar.rana(a)helmholtz-berlin.de> wrote: > >> Hi Matt, >> >> Thanks a lot for your prompt reply. The method I am referring to is >> not the multiple k-weight fits by constraining N*S02. My apologies >> for not being clear enough. Let's do it again. I am actually >> referring to an approach where we take an advantage of a different >> k-dependence of various parameters to breakdown correlations between >> them. For example, S02 and sigma2. S02 is k-independent and Sigma2 has k^2 dependence. >> >> > Yes, I am familiar with this approach, and I understand that this is what you are using. What I am saying is that this does not work nearly as well as (sometimes) claimed, and is sort of cheating. It ignores the measures of statistical significance. > > In this case, to breakdown correlation between S02 and sigma2, > > > The correlation between N*S02 and sigma2 is inherent to the finite k-range of the EXAFS signal. It cannot be "broken", though it might be reduced. > > >> one can assume a series of S02 values and perform fits using a single >> k-weight each time (say k-weight 1,2 and 3) and record corresponding >> sigma2 values. > > Let us say for k-weight =1, a series of preset S02 values will result > in a >> series of corresponding sigma2 values refined in fits, which can be >> plotted as a straight line in sigma2 vs. S02 plot. > > > OK, one can fit sigma2 with a series of preset values on N*S02. That's fine. But it does NOT lead to an infinitely thin line of sigma2 vs. > N*S02. Each sigma2 value on that line has a width, corresponding to its > uncertainty. In fact, the line you produce nicely demonstrates and > measures the correlation of N*S02 and sigma2 as the slope of this line. > > >> Similar straight lines can be obtained for fits using k-weight = 2 >> and then 3. > > Now, these three lines may intersect at or near some point, which will >> determine the "true" value of parameters independent of k-weight. > > > The different lines (each with finite thickness) will give a *range of > values* for N*S02 and sigma2, not a single value. > > The biggest problem with this approach is that it ignores the relative goodness-of-fits (let's just assume that is 'chi-square' for the purpose of > this discussion) for the fits along these lines. Some fits are better > than others, and this approach completely ignores that fact, and equally importantly ignores the fact that there is a range of values for chi-square > that are consistent with "good". If you include these values, your > linear plot will become contours of chi-square as a function of N*S02 and > sigma2. And, yes, by using different k-weights and k-ranges and so on you > can get overlapping contour plots which may reduce the correlation a small amount when looked at as an ensemble. And you can find a best set of values for N*S02 and sigma2, but *each* of these will have an uncertainty. > > So, you can use this approach to find a good value for N*S02, but it is not breaking the correlation. You can do this by hand. Or you can just do a > fit with datasets with different k-weights and k-ranges. When you do this > as a fit, you will see that the correlation is still fairly large. > > Also, just to be clear, this is absolutely not a "true" value. It is a measured value. Not at all the same thing. > > One can then constrain S02 to a value obtained from the point of >> intersection of three lines and vary sigma2 in a fit. > > > Well, one can certainly set N*S02 to some value and fit sigma2. As I said earlier, this ignores the correlation of N*S02 and sigma2, but does not remove that correlation. > > >> In this particular case, however, the advantage is, S02 does not >> depend on changes inside sample and we have very good estimate of its >> range (say 0.7 >> - 1.0). >> >> Now suppose instead of S02 (which i now set to a reasonable value), I >> am interested in determining N, but it is highly correlated with >> sigma2. Each time when disorder in the sample increases, the sigma2 >> increases and due to its high correlation, N is also overestimated. >> On the other hand, when the disorder in the sample decreases, the >> sigma2 decreases and I can have a "true" estimation of N in the >> sample. Can I still apply the above mentioned approach to break the correlationship between N and sigma2 and get a "true" >> estimation of N, even if disorder is high in my samples ? or it is >> simply not possible due to the fact that both N and sigma2 varies >> with changes inside the sample. >> >> > N and S02 are always 100% correlated (mathematically, not merely by the finite k range). So, to the extent that the approach works at all, you can use it for "N" or "S02". Really, the approach is comparing N*S02 and sigma2, in one case you asserted a value of "N" and projected all changes to "S02" -- you can equally assert "S02" and project all changes to "N". > > To be clear, this is not going to find the "true" value of anything, because no analysis is ever going to find the "true" value -- it's going to find a measured value. > > Finally, the correlation of N*S02 and sigma2 does not imply a bias in the values for N*S02. N*S02 is NOT overestimated because it is highly correlated with sigma2. > > Hope that helps, > > --Matt > -------------- next part -------------- An HTML attachment was > scrubbed... > URL: > <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/201503 > 22/86f5b809/attachment.html> > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 145, Issue 40 > **************************************** > > ________________________________ > > Helmholtz-Zentrum Berlin f?r Materialien und Energie GmbH > > Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. > > Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, > stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph > Gesch?ftsf?hrung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas > Frederking > > Sitz Berlin, AG Charlottenburg, 89 HRB 5583 > > Postadresse: > Hahn-Meitner-Platz 1 > D-14109 Berlin > > http://www.helmholtz-berlin.de > > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 145, Issue 41 > **************************************** > > ________________________________ > > Helmholtz-Zentrum Berlin f?r Materialien und Energie GmbH > > Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. > > Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, > stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph > Gesch?ftsf?hrung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas > Frederking > > Sitz Berlin, AG Charlottenburg, 89 HRB 5583 > > Postadresse: > Hahn-Meitner-Platz 1 > D-14109 Berlin > > http://www.helmholtz-berlin.de > > > > ------------------------------ > > Message: 2 > Date: Mon, 23 Mar 2015 07:15:05 -0400 > From: Chris Patridge <patridge(a)buffalo.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Breaking down correlationships between > parameters > Message-ID: <29942DF9-8043-424E-BDCC-9CA19EB4AC9B(a)buffalo.edu> > Content-Type: text/plain; charset=utf-8 > > I think Scott was pointing out that first neighbors may be known with high certainty and therefore you can set this value thereby removing it and slightly reducing the correlations. > > Chris > > Sent from my iPhone > >> On Mar 23, 2015, at 7:00 AM, Rana, Jatinkumar Kantilal <jatinkumar.rana(a)helmholtz-berlin.de> wrote: >> >> Hi Scott, >> >> Thank you for your comments. Can you please elaborate a little bit more on this "In cases like that, both N for all paths but one and S02 can be fit without 100% correlation." >> >> Best regards, >> Jatin >> >> -----Original Message----- >> From: ifeffit-bounces(a)millenia.cars.aps.anl.gov >> [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of >> ifeffit-request(a)millenia.cars.aps.anl.gov >> Sent: 23 March, 2015 10:16 >> To: ifeffit(a)millenia.cars.aps.anl.gov >> Subject: Ifeffit Digest, Vol 145, Issue 41 >> >> 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: Breaking down correlationships between parameters >> (Scott Calvin) >> 2. Re: Breaking down correlationships between parameters >> (Matt Newville) >> 3. Re: Breaking down correlationships between parameters >> (Rana, Jatinkumar Kantilal) >> >> >> --------------------------------------------------------------------- >> - >> >> Message: 1 >> Date: Sun, 22 Mar 2015 13:44:28 -0400 >> From: Scott Calvin <scalvin(a)sarahlawrence.edu> >> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >> Subject: Re: [Ifeffit] Breaking down correlationships between >> parameters >> Message-ID: <E0C66911-7AD2-448C-9F64-F03E262D04D7(a)slc.edu> >> Content-Type: text/plain; charset="utf-8" >> >> One side-comment from me: >> >> On Mar 22, 2015, at 12:52 PM, Matt Newville <newville(a)cars.uchicago.edu<mailto:newville@cars.uchicago.edu>> wrote: >> >> N and S02 are always 100% correlated (mathematically, not merely by the finite k range). >> >> Matt is saying that N and S02 are always 100% correlated for a single path. But in some situations you might know N for one path but not others. For example, you might know that the absorbing atom is octahedrally coordinated to oxygen but not be as certain as to next-nearest neighbors, or that there are copper atoms on the corners of a simple cubic lattice with a mixture of atoms at other positions. In cases like that, both N for all paths but one and S02 can be fit without 100% correlation. >> >> The degeneracy of multiple-scattering paths can often be constrained in terms of the coordination numbers for direct-scattering paths, which can further reduce (not ?break?) the correlation. >> >> In terms of the main question, I agree with Matt: I don?t think there?s much point in using the line-crossing technique nowadays; fitting using multiple k-weights simultaneously accomplishes the same thing but is a bit easier to interpret statistically. >> >> ?Scott Calvin >> Sarah Lawrence College >> -------------- next part -------------- An HTML attachment was >> scrubbed... >> URL: >> <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20150 >> 3 >> 22/f4e7b7e4/attachment-0001.htm> >> >> ------------------------------ >> >> Message: 2 >> Date: Sun, 22 Mar 2015 15:56:20 -0500 >> From: Matt Newville <newville(a)cars.uchicago.edu> >> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >> Subject: Re: [Ifeffit] Breaking down correlationships between >> parameters >> Message-ID: >> >> <CA+7ESbq_s0X3L9rPDDnwAdhx7h6Ptx5-8guCUFTM2OjwkYEerA(a)mail.gmail.com> >> Content-Type: text/plain; charset="utf-8" >> >> On Sun, Mar 22, 2015 at 12:44 PM, Scott Calvin >> <scalvin(a)sarahlawrence.edu> >> wrote: >> >>> One side-comment from me: >>> >>> On Mar 22, 2015, at 12:52 PM, Matt Newville >>> <newville(a)cars.uchicago.edu> >>> wrote: >>> >>> N and S02 are always 100% correlated (mathematically, not merely by >>> the finite k range). >>> >>> >>> Matt is saying that N and S02 are always 100% correlated *for a >>> single path*. But in some situations you might know N for one path >>> but not others. For example, you might know that the absorbing atom >>> is octahedrally coordinated to oxygen but not be as certain as to >>> next-nearest neighbors, or that there are copper atoms on the >>> corners of a simple cubic lattice with a mixture of atoms at other positions. >>> In cases like that, both N for all paths but one and S02 can be fit without 100% correlation. >> Yes, I completely agree with Scott -- this is a good point that I >> neglected. In addition to looking at multiple shells, one might also >> consider using temperature or pressure dependence to separate N*S02 and >> sigma2. Those aren't without assumptions, and still don't remove the >> inherent correlation, but are useful approaches. >> >> The degeneracy of multiple-scattering paths can often be constrained >> in >>> terms of the coordination numbers for direct-scattering paths, which >>> can further reduce (not ?break?) the correlation. >>> >>> In terms of the main question, I agree with Matt: I don?t think >>> there?s much point in using the line-crossing technique nowadays; >>> fitting using multiple k-weights simultaneously accomplishes the >>> same thing but is a bit easier to interpret statistically. >>> >>> ?Scott Calvin >>> Sarah Lawrence College >>> >>> _______________________________________________ >>> Ifeffit mailing list >>> Ifeffit(a)millenia.cars.aps.anl.gov >>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> --Matt >> -------------- next part -------------- An HTML attachment was >> scrubbed... >> URL: >> <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20150 >> 3 >> 22/3dd3f763/attachment-0001.htm> >> >> ------------------------------ >> >> Message: 3 >> Date: Mon, 23 Mar 2015 09:16:02 +0000 >> From: "Rana, Jatinkumar Kantilal" >> <jatinkumar.rana(a)helmholtz-berlin.de> >> To: "ifeffit(a)millenia.cars.aps.anl.gov" >> <ifeffit(a)millenia.cars.aps.anl.gov> >> Subject: Re: [Ifeffit] Breaking down correlationships between >> parameters >> Message-ID: <DA4C7D90F90BC249A03505C87F2EB8AB230EE755@didag1> >> Content-Type: text/plain; charset="utf-8" >> >> Hi Matt, >> >> Thank you very much for your detailed explanation. As you pointed out that this approach ignores the statistical significance of fits and assumes that all fits are "good" fits. Also, the point that this approach yields a value of the parameter which is only slightly less correlated with the other one, but not completely removes the correlation. It makes it really clear to me that how this approach works and what are the pros and cons. >> >> Well, I myself has never tried this approach of minimizing the correlation between N*S02 and sigma2, but I read a lot about it in the literature. With my limited knowledge about the method, I could not judge this approach, although I had my own doubts. >> >> I truly appreciate your efforts in providing me a deeper insight into this approach. >> >> Best regards, >> Jatin >> >> -----Original Message----- >> From: ifeffit-bounces(a)millenia.cars.aps.anl.gov >> [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of >> ifeffit-request(a)millenia.cars.aps.anl.gov >> Sent: 22 March, 2015 18:00 >> To: ifeffit(a)millenia.cars.aps.anl.gov >> Subject: Ifeffit Digest, Vol 145, Issue 40 >> >> 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: Breaking down correlationships between parameters >> (Matt Newville) >> >> >> --------------------------------------------------------------------- >> - >> >> Message: 1 >> Date: Sun, 22 Mar 2015 11:52:30 -0500 >> From: Matt Newville <newville(a)cars.uchicago.edu> >> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >> Subject: Re: [Ifeffit] Breaking down correlationships between >> parameters >> Message-ID: >> >> <CA+7ESbqcyQHf9XUh2uhk=Lv09An7E9LXxqDTX-X6kRJHy9PFzw(a)mail.gmail.com> >> Content-Type: text/plain; charset="utf-8" >> >> Hi Jatin, >> >> >>> On Sat, Mar 21, 2015 at 10:41 AM, Rana, Jatinkumar Kantilal < jatinkumar.rana(a)helmholtz-berlin.de> wrote: >>> >>> Hi Matt, >>> >>> Thanks a lot for your prompt reply. The method I am referring to is >>> not the multiple k-weight fits by constraining N*S02. My apologies >>> for not being clear enough. Let's do it again. I am actually >>> referring to an approach where we take an advantage of a different >>> k-dependence of various parameters to breakdown correlations between >>> them. For example, S02 and sigma2. S02 is k-independent and Sigma2 has k^2 dependence. >> Yes, I am familiar with this approach, and I understand that this is what you are using. What I am saying is that this does not work nearly as well as (sometimes) claimed, and is sort of cheating. It ignores the measures of statistical significance. >> >> In this case, to breakdown correlation between S02 and sigma2, >> >> >> The correlation between N*S02 and sigma2 is inherent to the finite k-range of the EXAFS signal. It cannot be "broken", though it might be reduced. >> >> >>> one can assume a series of S02 values and perform fits using a >>> single k-weight each time (say k-weight 1,2 and 3) and record >>> corresponding >>> sigma2 values. >> >> Let us say for k-weight =1, a series of preset S02 values will result >> in a >>> series of corresponding sigma2 values refined in fits, which can be >>> plotted as a straight line in sigma2 vs. S02 plot. >> >> >> OK, one can fit sigma2 with a series of preset values on N*S02. That's fine. But it does NOT lead to an infinitely thin line of sigma2 vs. >> N*S02. Each sigma2 value on that line has a width, corresponding to its >> uncertainty. In fact, the line you produce nicely demonstrates and >> measures the correlation of N*S02 and sigma2 as the slope of this line. >> >> >>> Similar straight lines can be obtained for fits using k-weight = 2 >>> and then 3. >> >> Now, these three lines may intersect at or near some point, which >> will >>> determine the "true" value of parameters independent of k-weight. >> >> >> The different lines (each with finite thickness) will give a *range >> of >> values* for N*S02 and sigma2, not a single value. >> >> The biggest problem with this approach is that it ignores the relative goodness-of-fits (let's just assume that is 'chi-square' for the purpose of >> this discussion) for the fits along these lines. Some fits are better >> than others, and this approach completely ignores that fact, and equally importantly ignores the fact that there is a range of values for chi-square >> that are consistent with "good". If you include these values, your >> linear plot will become contours of chi-square as a function of N*S02 and >> sigma2. And, yes, by using different k-weights and k-ranges and so on you >> can get overlapping contour plots which may reduce the correlation a small amount when looked at as an ensemble. And you can find a best set of values for N*S02 and sigma2, but *each* of these will have an uncertainty. >> >> So, you can use this approach to find a good value for N*S02, but it is not breaking the correlation. You can do this by hand. Or you can just do a >> fit with datasets with different k-weights and k-ranges. When you do this >> as a fit, you will see that the correlation is still fairly large. >> >> Also, just to be clear, this is absolutely not a "true" value. It is a measured value. Not at all the same thing. >> >> One can then constrain S02 to a value obtained from the point of >>> intersection of three lines and vary sigma2 in a fit. >> >> >> Well, one can certainly set N*S02 to some value and fit sigma2. As I said earlier, this ignores the correlation of N*S02 and sigma2, but does not remove that correlation. >> >> >>> In this particular case, however, the advantage is, S02 does not >>> depend on changes inside sample and we have very good estimate of >>> its range (say 0.7 >>> - 1.0). >>> >>> Now suppose instead of S02 (which i now set to a reasonable value), >>> I am interested in determining N, but it is highly correlated with >>> sigma2. Each time when disorder in the sample increases, the sigma2 >>> increases and due to its high correlation, N is also overestimated. >>> On the other hand, when the disorder in the sample decreases, the >>> sigma2 decreases and I can have a "true" estimation of N in the >>> sample. Can I still apply the above mentioned approach to break the correlationship between N and sigma2 and get a "true" >>> estimation of N, even if disorder is high in my samples ? or it is >>> simply not possible due to the fact that both N and sigma2 varies >>> with changes inside the sample. >> N and S02 are always 100% correlated (mathematically, not merely by the finite k range). So, to the extent that the approach works at all, you can use it for "N" or "S02". Really, the approach is comparing N*S02 and sigma2, in one case you asserted a value of "N" and projected all changes to "S02" -- you can equally assert "S02" and project all changes to "N". >> >> To be clear, this is not going to find the "true" value of anything, because no analysis is ever going to find the "true" value -- it's going to find a measured value. >> >> Finally, the correlation of N*S02 and sigma2 does not imply a bias in the values for N*S02. N*S02 is NOT overestimated because it is highly correlated with sigma2. >> >> Hope that helps, >> >> --Matt >> -------------- next part -------------- An HTML attachment was >> scrubbed... >> URL: >> <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20150 >> 3 >> 22/86f5b809/attachment.html> >> >> ------------------------------ >> >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> >> >> End of Ifeffit Digest, Vol 145, Issue 40 >> **************************************** >> >> ________________________________ >> >> Helmholtz-Zentrum Berlin f?r Materialien und Energie GmbH >> >> Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. >> >> Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, >> stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph >> Gesch?ftsf?hrung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas >> Frederking >> >> Sitz Berlin, AG Charlottenburg, 89 HRB 5583 >> >> Postadresse: >> Hahn-Meitner-Platz 1 >> D-14109 Berlin >> >> http://www.helmholtz-berlin.de >> >> >> >> ------------------------------ >> >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> >> >> End of Ifeffit Digest, Vol 145, Issue 41 >> **************************************** >> >> ________________________________ >> >> Helmholtz-Zentrum Berlin f?r Materialien und Energie GmbH >> >> Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. >> >> Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, >> stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph >> Gesch?ftsf?hrung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas >> Frederking >> >> Sitz Berlin, AG Charlottenburg, 89 HRB 5583 >> >> Postadresse: >> Hahn-Meitner-Platz 1 >> D-14109 Berlin >> >> http://www.helmholtz-berlin.de >> >> _______________________________________________ >> 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 > > > End of Ifeffit Digest, Vol 145, Issue 42 > **************************************** > > ________________________________ > > Helmholtz-Zentrum Berlin f?r Materialien und Energie GmbH > > Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. > > Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, > stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph > Gesch?ftsf?hrung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas > Frederking > > Sitz Berlin, AG Charlottenburg, 89 HRB 5583 > > Postadresse: > Hahn-Meitner-Platz 1 > D-14109 Berlin > > http://www.helmholtz-berlin.de > > _______________________________________________ > 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 End of Ifeffit Digest, Vol 145, Issue 44 **************************************** ________________________________ Helmholtz-Zentrum Berlin f?r Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph Gesch?ftsf?hrung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de ------------------------------ _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit End of Ifeffit Digest, Vol 145, Issue 45 **************************************** ________________________________ Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph Geschäftsführung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de

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Re: [Ifeffit] Breaking down correlationships between parameters
by Rana, Jatinkumar Kantilal 23 Mar '15

23 Mar '15

Hi Scott, Thanks for your explanation. It means the reverse can also be true, i.e., I can guess N1 (nearest-neighbors in the first shell) and S02 by setting N2, N3 and N4 to values known from other analysis. I did a quick check by fitting the data. I conducted two fits: 1) setting S02 and guessing only N1 2) guessing both N1 and S02. To my surprise, both the fits gave very similar results, except that the fit#1 refined value of N1 to a higher side, while fit#2 estimated N1 closer to a physically reasonable value (as expected). I always constrained S02 when refining N for any path, due to 100% correlation between them. However, I am surprised to know that they can be refined independently. Best regards, Jatin -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: 23 March, 2015 14:19 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 145, Issue 44 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: Breaking down correlationships between parameters (Scott Calvin) ---------------------------------------------------------------------- Message: 1 Date: Mon, 23 Mar 2015 09:18:21 -0400 From: Scott Calvin <scalvin(a)sarahlawrence.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Breaking down correlationships between parameters Message-ID: <78C1636C-91CF-4C8C-9D48-3EC361BB7237(a)slc.edu> Content-Type: text/plain; charset="utf-8" Hi Jatin, The key is that S02 should be the same for all paths. For example: Suppose you are very confident path 1 has a coordination number of 6, because of prior knowledge you have about the system. Paths 2, 3, and 4 have unknown coordination numbers, however. N1 (i.e. the degeneracy of path 1) you set to 6. You guess S02, N2, N3, and N4. Of course, the way Artemis and Ifeffit implement that, you're writing N1*S02 for the S02 field of Path 1, N2*S02 for the S02 field of Path 2, etc., and then setting N1 = 6 and guessing S02, N2, N3, and N4. There is now enough information for S02, N2, N3, and N4 to each be fitted without 100% correlation. ?Scott Calvin Sarah Lawrence College > On Mar 23, 2015, at 8:54 AM, Rana, Jatinkumar Kantilal <jatinkumar.rana(a)helmholtz-berlin.de> wrote: > > Hi Chris, > > The term N*S02 is fitted for each path of the FEFF calculation. So my question is, even if we know N with a great certainty for some path, how can we vary both N and S02 for other paths ? or Did I understand it wrong ? > > Best regards, > Jatin > > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov > [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of > ifeffit-request(a)millenia.cars.aps.anl.gov > Sent: 23 March, 2015 12:16 > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Ifeffit Digest, Vol 145, Issue 42 > > 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: Breaking down correlationships between parameters > (Rana, Jatinkumar Kantilal) > 2. Re: Breaking down correlationships between parameters > (Chris Patridge) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 23 Mar 2015 11:00:19 +0000 > From: "Rana, Jatinkumar Kantilal" > <jatinkumar.rana(a)helmholtz-berlin.de> > To: "ifeffit(a)millenia.cars.aps.anl.gov" > <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Breaking down correlationships between > parameters > Message-ID: <DA4C7D90F90BC249A03505C87F2EB8AB230EE777@didag1> > Content-Type: text/plain; charset="utf-8" > > Hi Scott, > > Thank you for your comments. Can you please elaborate a little bit more on this "In cases like that, both N for all paths but one and S02 can be fit without 100% correlation." > > Best regards, > Jatin > > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov > [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of > ifeffit-request(a)millenia.cars.aps.anl.gov > Sent: 23 March, 2015 10:16 > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Ifeffit Digest, Vol 145, Issue 41 > > 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: Breaking down correlationships between parameters > (Scott Calvin) > 2. Re: Breaking down correlationships between parameters > (Matt Newville) > 3. Re: Breaking down correlationships between parameters > (Rana, Jatinkumar Kantilal) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 22 Mar 2015 13:44:28 -0400 > From: Scott Calvin <scalvin(a)sarahlawrence.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Breaking down correlationships between > parameters > Message-ID: <E0C66911-7AD2-448C-9F64-F03E262D04D7(a)slc.edu> > Content-Type: text/plain; charset="utf-8" > > One side-comment from me: > > On Mar 22, 2015, at 12:52 PM, Matt Newville <newville(a)cars.uchicago.edu<mailto:newville@cars.uchicago.edu>> wrote: > > N and S02 are always 100% correlated (mathematically, not merely by the finite k range). > > Matt is saying that N and S02 are always 100% correlated for a single path. But in some situations you might know N for one path but not others. For example, you might know that the absorbing atom is octahedrally coordinated to oxygen but not be as certain as to next-nearest neighbors, or that there are copper atoms on the corners of a simple cubic lattice with a mixture of atoms at other positions. In cases like that, both N for all paths but one and S02 can be fit without 100% correlation. > > The degeneracy of multiple-scattering paths can often be constrained in terms of the coordination numbers for direct-scattering paths, which can further reduce (not ?break?) the correlation. > > In terms of the main question, I agree with Matt: I don?t think there?s much point in using the line-crossing technique nowadays; fitting using multiple k-weights simultaneously accomplishes the same thing but is a bit easier to interpret statistically. > > ?Scott Calvin > Sarah Lawrence College > -------------- next part -------------- An HTML attachment was > scrubbed... > URL: > <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/201503 > 22/f4e7b7e4/attachment-0001.htm> > > ------------------------------ > > Message: 2 > Date: Sun, 22 Mar 2015 15:56:20 -0500 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Breaking down correlationships between > parameters > Message-ID: > > <CA+7ESbq_s0X3L9rPDDnwAdhx7h6Ptx5-8guCUFTM2OjwkYEerA(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > On Sun, Mar 22, 2015 at 12:44 PM, Scott Calvin > <scalvin(a)sarahlawrence.edu> > wrote: > >> One side-comment from me: >> >> On Mar 22, 2015, at 12:52 PM, Matt Newville >> <newville(a)cars.uchicago.edu> >> wrote: >> >> N and S02 are always 100% correlated (mathematically, not merely by >> the finite k range). >> >> >> Matt is saying that N and S02 are always 100% correlated *for a >> single path*. But in some situations you might know N for one path >> but not others. For example, you might know that the absorbing atom >> is octahedrally coordinated to oxygen but not be as certain as to >> next-nearest neighbors, or that there are copper atoms on the corners >> of a simple cubic lattice with a mixture of atoms at other positions. >> In cases like that, both N for all paths but one and S02 can be fit without 100% correlation. >> >> > Yes, I completely agree with Scott -- this is a good point that I > neglected. In addition to looking at multiple shells, one might also > consider using temperature or pressure dependence to separate N*S02 and > sigma2. Those aren't without assumptions, and still don't remove the > inherent correlation, but are useful approaches. > > The degeneracy of multiple-scattering paths can often be constrained > in >> terms of the coordination numbers for direct-scattering paths, which >> can further reduce (not ?break?) the correlation. >> >> In terms of the main question, I agree with Matt: I don?t think >> there?s much point in using the line-crossing technique nowadays; >> fitting using multiple k-weights simultaneously accomplishes the same >> thing but is a bit easier to interpret statistically. >> >> ?Scott Calvin >> Sarah Lawrence College >> >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> >> > --Matt > -------------- next part -------------- An HTML attachment was > scrubbed... > URL: > <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/201503 > 22/3dd3f763/attachment-0001.htm> > > ------------------------------ > > Message: 3 > Date: Mon, 23 Mar 2015 09:16:02 +0000 > From: "Rana, Jatinkumar Kantilal" > <jatinkumar.rana(a)helmholtz-berlin.de> > To: "ifeffit(a)millenia.cars.aps.anl.gov" > <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Breaking down correlationships between > parameters > Message-ID: <DA4C7D90F90BC249A03505C87F2EB8AB230EE755@didag1> > Content-Type: text/plain; charset="utf-8" > > Hi Matt, > > Thank you very much for your detailed explanation. As you pointed out that this approach ignores the statistical significance of fits and assumes that all fits are "good" fits. Also, the point that this approach yields a value of the parameter which is only slightly less correlated with the other one, but not completely removes the correlation. It makes it really clear to me that how this approach works and what are the pros and cons. > > Well, I myself has never tried this approach of minimizing the correlation between N*S02 and sigma2, but I read a lot about it in the literature. With my limited knowledge about the method, I could not judge this approach, although I had my own doubts. > > I truly appreciate your efforts in providing me a deeper insight into this approach. > > Best regards, > Jatin > > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov > [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of > ifeffit-request(a)millenia.cars.aps.anl.gov > Sent: 22 March, 2015 18:00 > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Ifeffit Digest, Vol 145, Issue 40 > > 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: Breaking down correlationships between parameters > (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 22 Mar 2015 11:52:30 -0500 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Breaking down correlationships between > parameters > Message-ID: > > <CA+7ESbqcyQHf9XUh2uhk=Lv09An7E9LXxqDTX-X6kRJHy9PFzw(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Jatin, > > > On Sat, Mar 21, 2015 at 10:41 AM, Rana, Jatinkumar Kantilal < jatinkumar.rana(a)helmholtz-berlin.de> wrote: > >> Hi Matt, >> >> Thanks a lot for your prompt reply. The method I am referring to is >> not the multiple k-weight fits by constraining N*S02. My apologies >> for not being clear enough. Let's do it again. I am actually >> referring to an approach where we take an advantage of a different >> k-dependence of various parameters to breakdown correlations between >> them. For example, S02 and sigma2. S02 is k-independent and Sigma2 has k^2 dependence. >> >> > Yes, I am familiar with this approach, and I understand that this is what you are using. What I am saying is that this does not work nearly as well as (sometimes) claimed, and is sort of cheating. It ignores the measures of statistical significance. > > In this case, to breakdown correlation between S02 and sigma2, > > > The correlation between N*S02 and sigma2 is inherent to the finite k-range of the EXAFS signal. It cannot be "broken", though it might be reduced. > > >> one can assume a series of S02 values and perform fits using a single >> k-weight each time (say k-weight 1,2 and 3) and record corresponding >> sigma2 values. > > Let us say for k-weight =1, a series of preset S02 values will result > in a >> series of corresponding sigma2 values refined in fits, which can be >> plotted as a straight line in sigma2 vs. S02 plot. > > > OK, one can fit sigma2 with a series of preset values on N*S02. That's fine. But it does NOT lead to an infinitely thin line of sigma2 vs. > N*S02. Each sigma2 value on that line has a width, corresponding to its > uncertainty. In fact, the line you produce nicely demonstrates and > measures the correlation of N*S02 and sigma2 as the slope of this line. > > >> Similar straight lines can be obtained for fits using k-weight = 2 >> and then 3. > > Now, these three lines may intersect at or near some point, which will >> determine the "true" value of parameters independent of k-weight. > > > The different lines (each with finite thickness) will give a *range of > values* for N*S02 and sigma2, not a single value. > > The biggest problem with this approach is that it ignores the relative goodness-of-fits (let's just assume that is 'chi-square' for the purpose of > this discussion) for the fits along these lines. Some fits are better > than others, and this approach completely ignores that fact, and equally importantly ignores the fact that there is a range of values for chi-square > that are consistent with "good". If you include these values, your > linear plot will become contours of chi-square as a function of N*S02 and > sigma2. And, yes, by using different k-weights and k-ranges and so on you > can get overlapping contour plots which may reduce the correlation a small amount when looked at as an ensemble. And you can find a best set of values for N*S02 and sigma2, but *each* of these will have an uncertainty. > > So, you can use this approach to find a good value for N*S02, but it is not breaking the correlation. You can do this by hand. Or you can just do a > fit with datasets with different k-weights and k-ranges. When you do this > as a fit, you will see that the correlation is still fairly large. > > Also, just to be clear, this is absolutely not a "true" value. It is a measured value. Not at all the same thing. > > One can then constrain S02 to a value obtained from the point of >> intersection of three lines and vary sigma2 in a fit. > > > Well, one can certainly set N*S02 to some value and fit sigma2. As I said earlier, this ignores the correlation of N*S02 and sigma2, but does not remove that correlation. > > >> In this particular case, however, the advantage is, S02 does not >> depend on changes inside sample and we have very good estimate of its >> range (say 0.7 >> - 1.0). >> >> Now suppose instead of S02 (which i now set to a reasonable value), I >> am interested in determining N, but it is highly correlated with >> sigma2. Each time when disorder in the sample increases, the sigma2 >> increases and due to its high correlation, N is also overestimated. >> On the other hand, when the disorder in the sample decreases, the >> sigma2 decreases and I can have a "true" estimation of N in the >> sample. Can I still apply the above mentioned approach to break the correlationship between N and sigma2 and get a "true" >> estimation of N, even if disorder is high in my samples ? or it is >> simply not possible due to the fact that both N and sigma2 varies >> with changes inside the sample. >> >> > N and S02 are always 100% correlated (mathematically, not merely by the finite k range). So, to the extent that the approach works at all, you can use it for "N" or "S02". Really, the approach is comparing N*S02 and sigma2, in one case you asserted a value of "N" and projected all changes to "S02" -- you can equally assert "S02" and project all changes to "N". > > To be clear, this is not going to find the "true" value of anything, because no analysis is ever going to find the "true" value -- it's going to find a measured value. > > Finally, the correlation of N*S02 and sigma2 does not imply a bias in the values for N*S02. N*S02 is NOT overestimated because it is highly correlated with sigma2. > > Hope that helps, > > --Matt > -------------- next part -------------- An HTML attachment was > scrubbed... > URL: > <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/201503 > 22/86f5b809/attachment.html> > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 145, Issue 40 > **************************************** > > ________________________________ > > Helmholtz-Zentrum Berlin f?r Materialien und Energie GmbH > > Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. > > Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, > stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph > Gesch?ftsf?hrung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas > Frederking > > Sitz Berlin, AG Charlottenburg, 89 HRB 5583 > > Postadresse: > Hahn-Meitner-Platz 1 > D-14109 Berlin > > http://www.helmholtz-berlin.de > > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 145, Issue 41 > **************************************** > > ________________________________ > > Helmholtz-Zentrum Berlin f?r Materialien und Energie GmbH > > Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. > > Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, > stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph > Gesch?ftsf?hrung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas > Frederking > > Sitz Berlin, AG Charlottenburg, 89 HRB 5583 > > Postadresse: > Hahn-Meitner-Platz 1 > D-14109 Berlin > > http://www.helmholtz-berlin.de > > > > ------------------------------ > > Message: 2 > Date: Mon, 23 Mar 2015 07:15:05 -0400 > From: Chris Patridge <patridge(a)buffalo.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Breaking down correlationships between > parameters > Message-ID: <29942DF9-8043-424E-BDCC-9CA19EB4AC9B(a)buffalo.edu> > Content-Type: text/plain; charset=utf-8 > > I think Scott was pointing out that first neighbors may be known with high certainty and therefore you can set this value thereby removing it and slightly reducing the correlations. > > Chris > > Sent from my iPhone > >> On Mar 23, 2015, at 7:00 AM, Rana, Jatinkumar Kantilal <jatinkumar.rana(a)helmholtz-berlin.de> wrote: >> >> Hi Scott, >> >> Thank you for your comments. Can you please elaborate a little bit more on this "In cases like that, both N for all paths but one and S02 can be fit without 100% correlation." >> >> Best regards, >> Jatin >> >> -----Original Message----- >> From: ifeffit-bounces(a)millenia.cars.aps.anl.gov >> [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of >> ifeffit-request(a)millenia.cars.aps.anl.gov >> Sent: 23 March, 2015 10:16 >> To: ifeffit(a)millenia.cars.aps.anl.gov >> Subject: Ifeffit Digest, Vol 145, Issue 41 >> >> 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: Breaking down correlationships between parameters >> (Scott Calvin) >> 2. Re: Breaking down correlationships between parameters >> (Matt Newville) >> 3. Re: Breaking down correlationships between parameters >> (Rana, Jatinkumar Kantilal) >> >> >> --------------------------------------------------------------------- >> - >> >> Message: 1 >> Date: Sun, 22 Mar 2015 13:44:28 -0400 >> From: Scott Calvin <scalvin(a)sarahlawrence.edu> >> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >> Subject: Re: [Ifeffit] Breaking down correlationships between >> parameters >> Message-ID: <E0C66911-7AD2-448C-9F64-F03E262D04D7(a)slc.edu> >> Content-Type: text/plain; charset="utf-8" >> >> One side-comment from me: >> >> On Mar 22, 2015, at 12:52 PM, Matt Newville <newville(a)cars.uchicago.edu<mailto:newville@cars.uchicago.edu>> wrote: >> >> N and S02 are always 100% correlated (mathematically, not merely by the finite k range). >> >> Matt is saying that N and S02 are always 100% correlated for a single path. But in some situations you might know N for one path but not others. For example, you might know that the absorbing atom is octahedrally coordinated to oxygen but not be as certain as to next-nearest neighbors, or that there are copper atoms on the corners of a simple cubic lattice with a mixture of atoms at other positions. In cases like that, both N for all paths but one and S02 can be fit without 100% correlation. >> >> The degeneracy of multiple-scattering paths can often be constrained in terms of the coordination numbers for direct-scattering paths, which can further reduce (not ?break?) the correlation. >> >> In terms of the main question, I agree with Matt: I don?t think there?s much point in using the line-crossing technique nowadays; fitting using multiple k-weights simultaneously accomplishes the same thing but is a bit easier to interpret statistically. >> >> ?Scott Calvin >> Sarah Lawrence College >> -------------- next part -------------- An HTML attachment was >> scrubbed... >> URL: >> <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20150 >> 3 >> 22/f4e7b7e4/attachment-0001.htm> >> >> ------------------------------ >> >> Message: 2 >> Date: Sun, 22 Mar 2015 15:56:20 -0500 >> From: Matt Newville <newville(a)cars.uchicago.edu> >> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >> Subject: Re: [Ifeffit] Breaking down correlationships between >> parameters >> Message-ID: >> >> <CA+7ESbq_s0X3L9rPDDnwAdhx7h6Ptx5-8guCUFTM2OjwkYEerA(a)mail.gmail.com> >> Content-Type: text/plain; charset="utf-8" >> >> On Sun, Mar 22, 2015 at 12:44 PM, Scott Calvin >> <scalvin(a)sarahlawrence.edu> >> wrote: >> >>> One side-comment from me: >>> >>> On Mar 22, 2015, at 12:52 PM, Matt Newville >>> <newville(a)cars.uchicago.edu> >>> wrote: >>> >>> N and S02 are always 100% correlated (mathematically, not merely by >>> the finite k range). >>> >>> >>> Matt is saying that N and S02 are always 100% correlated *for a >>> single path*. But in some situations you might know N for one path >>> but not others. For example, you might know that the absorbing atom >>> is octahedrally coordinated to oxygen but not be as certain as to >>> next-nearest neighbors, or that there are copper atoms on the >>> corners of a simple cubic lattice with a mixture of atoms at other positions. >>> In cases like that, both N for all paths but one and S02 can be fit without 100% correlation. >> Yes, I completely agree with Scott -- this is a good point that I >> neglected. In addition to looking at multiple shells, one might also >> consider using temperature or pressure dependence to separate N*S02 and >> sigma2. Those aren't without assumptions, and still don't remove the >> inherent correlation, but are useful approaches. >> >> The degeneracy of multiple-scattering paths can often be constrained >> in >>> terms of the coordination numbers for direct-scattering paths, which >>> can further reduce (not ?break?) the correlation. >>> >>> In terms of the main question, I agree with Matt: I don?t think >>> there?s much point in using the line-crossing technique nowadays; >>> fitting using multiple k-weights simultaneously accomplishes the >>> same thing but is a bit easier to interpret statistically. >>> >>> ?Scott Calvin >>> Sarah Lawrence College >>> >>> _______________________________________________ >>> Ifeffit mailing list >>> Ifeffit(a)millenia.cars.aps.anl.gov >>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> --Matt >> -------------- next part -------------- An HTML attachment was >> scrubbed... >> URL: >> <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20150 >> 3 >> 22/3dd3f763/attachment-0001.htm> >> >> ------------------------------ >> >> Message: 3 >> Date: Mon, 23 Mar 2015 09:16:02 +0000 >> From: "Rana, Jatinkumar Kantilal" >> <jatinkumar.rana(a)helmholtz-berlin.de> >> To: "ifeffit(a)millenia.cars.aps.anl.gov" >> <ifeffit(a)millenia.cars.aps.anl.gov> >> Subject: Re: [Ifeffit] Breaking down correlationships between >> parameters >> Message-ID: <DA4C7D90F90BC249A03505C87F2EB8AB230EE755@didag1> >> Content-Type: text/plain; charset="utf-8" >> >> Hi Matt, >> >> Thank you very much for your detailed explanation. As you pointed out that this approach ignores the statistical significance of fits and assumes that all fits are "good" fits. Also, the point that this approach yields a value of the parameter which is only slightly less correlated with the other one, but not completely removes the correlation. It makes it really clear to me that how this approach works and what are the pros and cons. >> >> Well, I myself has never tried this approach of minimizing the correlation between N*S02 and sigma2, but I read a lot about it in the literature. With my limited knowledge about the method, I could not judge this approach, although I had my own doubts. >> >> I truly appreciate your efforts in providing me a deeper insight into this approach. >> >> Best regards, >> Jatin >> >> -----Original Message----- >> From: ifeffit-bounces(a)millenia.cars.aps.anl.gov >> [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of >> ifeffit-request(a)millenia.cars.aps.anl.gov >> Sent: 22 March, 2015 18:00 >> To: ifeffit(a)millenia.cars.aps.anl.gov >> Subject: Ifeffit Digest, Vol 145, Issue 40 >> >> 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: Breaking down correlationships between parameters >> (Matt Newville) >> >> >> --------------------------------------------------------------------- >> - >> >> Message: 1 >> Date: Sun, 22 Mar 2015 11:52:30 -0500 >> From: Matt Newville <newville(a)cars.uchicago.edu> >> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >> Subject: Re: [Ifeffit] Breaking down correlationships between >> parameters >> Message-ID: >> >> <CA+7ESbqcyQHf9XUh2uhk=Lv09An7E9LXxqDTX-X6kRJHy9PFzw(a)mail.gmail.com> >> Content-Type: text/plain; charset="utf-8" >> >> Hi Jatin, >> >> >>> On Sat, Mar 21, 2015 at 10:41 AM, Rana, Jatinkumar Kantilal < jatinkumar.rana(a)helmholtz-berlin.de> wrote: >>> >>> Hi Matt, >>> >>> Thanks a lot for your prompt reply. The method I am referring to is >>> not the multiple k-weight fits by constraining N*S02. My apologies >>> for not being clear enough. Let's do it again. I am actually >>> referring to an approach where we take an advantage of a different >>> k-dependence of various parameters to breakdown correlations between >>> them. For example, S02 and sigma2. S02 is k-independent and Sigma2 has k^2 dependence. >> Yes, I am familiar with this approach, and I understand that this is what you are using. What I am saying is that this does not work nearly as well as (sometimes) claimed, and is sort of cheating. It ignores the measures of statistical significance. >> >> In this case, to breakdown correlation between S02 and sigma2, >> >> >> The correlation between N*S02 and sigma2 is inherent to the finite k-range of the EXAFS signal. It cannot be "broken", though it might be reduced. >> >> >>> one can assume a series of S02 values and perform fits using a >>> single k-weight each time (say k-weight 1,2 and 3) and record >>> corresponding >>> sigma2 values. >> >> Let us say for k-weight =1, a series of preset S02 values will result >> in a >>> series of corresponding sigma2 values refined in fits, which can be >>> plotted as a straight line in sigma2 vs. S02 plot. >> >> >> OK, one can fit sigma2 with a series of preset values on N*S02. That's fine. But it does NOT lead to an infinitely thin line of sigma2 vs. >> N*S02. Each sigma2 value on that line has a width, corresponding to its >> uncertainty. In fact, the line you produce nicely demonstrates and >> measures the correlation of N*S02 and sigma2 as the slope of this line. >> >> >>> Similar straight lines can be obtained for fits using k-weight = 2 >>> and then 3. >> >> Now, these three lines may intersect at or near some point, which >> will >>> determine the "true" value of parameters independent of k-weight. >> >> >> The different lines (each with finite thickness) will give a *range >> of >> values* for N*S02 and sigma2, not a single value. >> >> The biggest problem with this approach is that it ignores the relative goodness-of-fits (let's just assume that is 'chi-square' for the purpose of >> this discussion) for the fits along these lines. Some fits are better >> than others, and this approach completely ignores that fact, and equally importantly ignores the fact that there is a range of values for chi-square >> that are consistent with "good". If you include these values, your >> linear plot will become contours of chi-square as a function of N*S02 and >> sigma2. And, yes, by using different k-weights and k-ranges and so on you >> can get overlapping contour plots which may reduce the correlation a small amount when looked at as an ensemble. And you can find a best set of values for N*S02 and sigma2, but *each* of these will have an uncertainty. >> >> So, you can use this approach to find a good value for N*S02, but it is not breaking the correlation. You can do this by hand. Or you can just do a >> fit with datasets with different k-weights and k-ranges. When you do this >> as a fit, you will see that the correlation is still fairly large. >> >> Also, just to be clear, this is absolutely not a "true" value. It is a measured value. Not at all the same thing. >> >> One can then constrain S02 to a value obtained from the point of >>> intersection of three lines and vary sigma2 in a fit. >> >> >> Well, one can certainly set N*S02 to some value and fit sigma2. As I said earlier, this ignores the correlation of N*S02 and sigma2, but does not remove that correlation. >> >> >>> In this particular case, however, the advantage is, S02 does not >>> depend on changes inside sample and we have very good estimate of >>> its range (say 0.7 >>> - 1.0). >>> >>> Now suppose instead of S02 (which i now set to a reasonable value), >>> I am interested in determining N, but it is highly correlated with >>> sigma2. Each time when disorder in the sample increases, the sigma2 >>> increases and due to its high correlation, N is also overestimated. >>> On the other hand, when the disorder in the sample decreases, the >>> sigma2 decreases and I can have a "true" estimation of N in the >>> sample. Can I still apply the above mentioned approach to break the correlationship between N and sigma2 and get a "true" >>> estimation of N, even if disorder is high in my samples ? or it is >>> simply not possible due to the fact that both N and sigma2 varies >>> with changes inside the sample. >> N and S02 are always 100% correlated (mathematically, not merely by the finite k range). So, to the extent that the approach works at all, you can use it for "N" or "S02". Really, the approach is comparing N*S02 and sigma2, in one case you asserted a value of "N" and projected all changes to "S02" -- you can equally assert "S02" and project all changes to "N". >> >> To be clear, this is not going to find the "true" value of anything, because no analysis is ever going to find the "true" value -- it's going to find a measured value. >> >> Finally, the correlation of N*S02 and sigma2 does not imply a bias in the values for N*S02. N*S02 is NOT overestimated because it is highly correlated with sigma2. >> >> Hope that helps, >> >> --Matt >> -------------- next part -------------- An HTML attachment was >> scrubbed... >> URL: >> <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20150 >> 3 >> 22/86f5b809/attachment.html> >> >> ------------------------------ >> >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> >> >> End of Ifeffit Digest, Vol 145, Issue 40 >> **************************************** >> >> ________________________________ >> >> Helmholtz-Zentrum Berlin f?r Materialien und Energie GmbH >> >> Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. >> >> Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, >> stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph >> Gesch?ftsf?hrung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas >> Frederking >> >> Sitz Berlin, AG Charlottenburg, 89 HRB 5583 >> >> Postadresse: >> Hahn-Meitner-Platz 1 >> D-14109 Berlin >> >> http://www.helmholtz-berlin.de >> >> >> >> ------------------------------ >> >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> >> >> End of Ifeffit Digest, Vol 145, Issue 41 >> **************************************** >> >> ________________________________ >> >> Helmholtz-Zentrum Berlin f?r Materialien und Energie GmbH >> >> Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. >> >> Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, >> stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph >> Gesch?ftsf?hrung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas >> Frederking >> >> Sitz Berlin, AG Charlottenburg, 89 HRB 5583 >> >> Postadresse: >> Hahn-Meitner-Platz 1 >> D-14109 Berlin >> >> http://www.helmholtz-berlin.de >> >> _______________________________________________ >> 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 > > > End of Ifeffit Digest, Vol 145, Issue 42 > **************************************** > > ________________________________ > > Helmholtz-Zentrum Berlin f?r Materialien und Energie GmbH > > Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. > > Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, > stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph > Gesch?ftsf?hrung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas > Frederking > > Sitz Berlin, AG Charlottenburg, 89 HRB 5583 > > Postadresse: > Hahn-Meitner-Platz 1 > D-14109 Berlin > > http://www.helmholtz-berlin.de > > _______________________________________________ > 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 End of Ifeffit Digest, Vol 145, Issue 44 **************************************** ________________________________ Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph Geschäftsführung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de

1 0

Re: [Ifeffit] Breaking down correlationships between parameters
by Rana, Jatinkumar Kantilal 23 Mar '15

23 Mar '15

Hi Chris, The term N*S02 is fitted for each path of the FEFF calculation. So my question is, even if we know N with a great certainty for some path, how can we vary both N and S02 for other paths ? or Did I understand it wrong ? Best regards, Jatin -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: 23 March, 2015 12:16 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 145, Issue 42 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: Breaking down correlationships between parameters (Rana, Jatinkumar Kantilal) 2. Re: Breaking down correlationships between parameters (Chris Patridge) ---------------------------------------------------------------------- Message: 1 Date: Mon, 23 Mar 2015 11:00:19 +0000 From: "Rana, Jatinkumar Kantilal" <jatinkumar.rana(a)helmholtz-berlin.de> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Breaking down correlationships between parameters Message-ID: <DA4C7D90F90BC249A03505C87F2EB8AB230EE777@didag1> Content-Type: text/plain; charset="utf-8" Hi Scott, Thank you for your comments. Can you please elaborate a little bit more on this "In cases like that, both N for all paths but one and S02 can be fit without 100% correlation." Best regards, Jatin -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: 23 March, 2015 10:16 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 145, Issue 41 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: Breaking down correlationships between parameters (Scott Calvin) 2. Re: Breaking down correlationships between parameters (Matt Newville) 3. Re: Breaking down correlationships between parameters (Rana, Jatinkumar Kantilal) ---------------------------------------------------------------------- Message: 1 Date: Sun, 22 Mar 2015 13:44:28 -0400 From: Scott Calvin <scalvin(a)sarahlawrence.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Breaking down correlationships between parameters Message-ID: <E0C66911-7AD2-448C-9F64-F03E262D04D7(a)slc.edu> Content-Type: text/plain; charset="utf-8" One side-comment from me: On Mar 22, 2015, at 12:52 PM, Matt Newville <newville(a)cars.uchicago.edu<mailto:newville@cars.uchicago.edu>> wrote: N and S02 are always 100% correlated (mathematically, not merely by the finite k range). Matt is saying that N and S02 are always 100% correlated for a single path. But in some situations you might know N for one path but not others. For example, you might know that the absorbing atom is octahedrally coordinated to oxygen but not be as certain as to next-nearest neighbors, or that there are copper atoms on the corners of a simple cubic lattice with a mixture of atoms at other positions. In cases like that, both N for all paths but one and S02 can be fit without 100% correlation. The degeneracy of multiple-scattering paths can often be constrained in terms of the coordination numbers for direct-scattering paths, which can further reduce (not ?break?) the correlation. In terms of the main question, I agree with Matt: I don?t think there?s much point in using the line-crossing technique nowadays; fitting using multiple k-weights simultaneously accomplishes the same thing but is a bit easier to interpret statistically. ?Scott Calvin Sarah Lawrence College

3 2

Re: [Ifeffit] Breaking down correlationships between parameters
by Rana, Jatinkumar Kantilal 23 Mar '15

23 Mar '15

Hi Scott, Thank you for your comments. Can you please elaborate a little bit more on this "In cases like that, both N for all paths but one and S02 can be fit without 100% correlation." Best regards, Jatin -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: 23 March, 2015 10:16 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 145, Issue 41 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: Breaking down correlationships between parameters (Scott Calvin) 2. Re: Breaking down correlationships between parameters (Matt Newville) 3. Re: Breaking down correlationships between parameters (Rana, Jatinkumar Kantilal) ---------------------------------------------------------------------- Message: 1 Date: Sun, 22 Mar 2015 13:44:28 -0400 From: Scott Calvin <scalvin(a)sarahlawrence.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Breaking down correlationships between parameters Message-ID: <E0C66911-7AD2-448C-9F64-F03E262D04D7(a)slc.edu> Content-Type: text/plain; charset="utf-8" One side-comment from me: On Mar 22, 2015, at 12:52 PM, Matt Newville <newville(a)cars.uchicago.edu<mailto:newville@cars.uchicago.edu>> wrote: N and S02 are always 100% correlated (mathematically, not merely by the finite k range). Matt is saying that N and S02 are always 100% correlated for a single path. But in some situations you might know N for one path but not others. For example, you might know that the absorbing atom is octahedrally coordinated to oxygen but not be as certain as to next-nearest neighbors, or that there are copper atoms on the corners of a simple cubic lattice with a mixture of atoms at other positions. In cases like that, both N for all paths but one and S02 can be fit without 100% correlation. The degeneracy of multiple-scattering paths can often be constrained in terms of the coordination numbers for direct-scattering paths, which can further reduce (not ?break?) the correlation. In terms of the main question, I agree with Matt: I don?t think there?s much point in using the line-crossing technique nowadays; fitting using multiple k-weights simultaneously accomplishes the same thing but is a bit easier to interpret statistically. ?Scott Calvin Sarah Lawrence College

2 1

Re: [Ifeffit] Breaking down correlationships between parameters
by Rana, Jatinkumar Kantilal 23 Mar '15

23 Mar '15

Hi Matt, Thank you very much for your detailed explanation. As you pointed out that this approach ignores the statistical significance of fits and assumes that all fits are "good" fits. Also, the point that this approach yields a value of the parameter which is only slightly less correlated with the other one, but not completely removes the correlation. It makes it really clear to me that how this approach works and what are the pros and cons. Well, I myself has never tried this approach of minimizing the correlation between N*S02 and sigma2, but I read a lot about it in the literature. With my limited knowledge about the method, I could not judge this approach, although I had my own doubts. I truly appreciate your efforts in providing me a deeper insight into this approach. Best regards, Jatin -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: 22 March, 2015 18:00 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 145, Issue 40 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: Breaking down correlationships between parameters (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Sun, 22 Mar 2015 11:52:30 -0500 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Breaking down correlationships between parameters Message-ID: <CA+7ESbqcyQHf9XUh2uhk=Lv09An7E9LXxqDTX-X6kRJHy9PFzw(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Jatin, On Sat, Mar 21, 2015 at 10:41 AM, Rana, Jatinkumar Kantilal < jatinkumar.rana(a)helmholtz-berlin.de> wrote: > Hi Matt, > > Thanks a lot for your prompt reply. The method I am referring to is > not the multiple k-weight fits by constraining N*S02. My apologies for > not being clear enough. Let's do it again. I am actually referring to > an approach where we take an advantage of a different k-dependence of > various parameters to breakdown correlations between them. For > example, S02 and sigma2. S02 is k-independent and Sigma2 has k^2 dependence. > > Yes, I am familiar with this approach, and I understand that this is what you are using. What I am saying is that this does not work nearly as well as (sometimes) claimed, and is sort of cheating. It ignores the measures of statistical significance. In this case, to breakdown correlation between S02 and sigma2, The correlation between N*S02 and sigma2 is inherent to the finite k-range of the EXAFS signal. It cannot be "broken", though it might be reduced. > one can assume a series of S02 values and perform fits using a single > k-weight each time (say k-weight 1,2 and 3) and record corresponding > sigma2 values. Let us say for k-weight =1, a series of preset S02 values will result in a > series of corresponding sigma2 values refined in fits, which can be > plotted as a straight line in sigma2 vs. S02 plot. OK, one can fit sigma2 with a series of preset values on N*S02. That's fine. But it does NOT lead to an infinitely thin line of sigma2 vs. N*S02. Each sigma2 value on that line has a width, corresponding to its uncertainty. In fact, the line you produce nicely demonstrates and measures the correlation of N*S02 and sigma2 as the slope of this line. > Similar straight lines can be obtained for fits using k-weight = 2 and > then 3. Now, these three lines may intersect at or near some point, which will > determine the "true" value of parameters independent of k-weight. The different lines (each with finite thickness) will give a *range of values* for N*S02 and sigma2, not a single value. The biggest problem with this approach is that it ignores the relative goodness-of-fits (let's just assume that is 'chi-square' for the purpose of this discussion) for the fits along these lines. Some fits are better than others, and this approach completely ignores that fact, and equally importantly ignores the fact that there is a range of values for chi-square that are consistent with "good". If you include these values, your linear plot will become contours of chi-square as a function of N*S02 and sigma2. And, yes, by using different k-weights and k-ranges and so on you can get overlapping contour plots which may reduce the correlation a small amount when looked at as an ensemble. And you can find a best set of values for N*S02 and sigma2, but *each* of these will have an uncertainty. So, you can use this approach to find a good value for N*S02, but it is not breaking the correlation. You can do this by hand. Or you can just do a fit with datasets with different k-weights and k-ranges. When you do this as a fit, you will see that the correlation is still fairly large. Also, just to be clear, this is absolutely not a "true" value. It is a measured value. Not at all the same thing. One can then constrain S02 to a value obtained from the point of > intersection of three lines and vary sigma2 in a fit. Well, one can certainly set N*S02 to some value and fit sigma2. As I said earlier, this ignores the correlation of N*S02 and sigma2, but does not remove that correlation. > In this particular case, however, the advantage is, S02 does not > depend on changes inside sample and we have very good estimate of its > range (say 0.7 > - 1.0). > > Now suppose instead of S02 (which i now set to a reasonable value), I > am interested in determining N, but it is highly correlated with > sigma2. Each time when disorder in the sample increases, the sigma2 > increases and due to its high correlation, N is also overestimated. On > the other hand, when the disorder in the sample decreases, the sigma2 > decreases and I can have a "true" estimation of N in the sample. Can I > still apply the above mentioned approach to break the correlationship between N and sigma2 and get a "true" > estimation of N, even if disorder is high in my samples ? or it is > simply not possible due to the fact that both N and sigma2 varies with > changes inside the sample. > > N and S02 are always 100% correlated (mathematically, not merely by the finite k range). So, to the extent that the approach works at all, you can use it for "N" or "S02". Really, the approach is comparing N*S02 and sigma2, in one case you asserted a value of "N" and projected all changes to "S02" -- you can equally assert "S02" and project all changes to "N". To be clear, this is not going to find the "true" value of anything, because no analysis is ever going to find the "true" value -- it's going to find a measured value. Finally, the correlation of N*S02 and sigma2 does not imply a bias in the values for N*S02. N*S02 is NOT overestimated because it is highly correlated with sigma2. Hope that helps, --Matt

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Re: [Ifeffit] Breaking down correlationships between parameters
by Rana, Jatinkumar Kantilal 22 Mar '15

22 Mar '15

Hi Matt, Thanks a lot for your prompt reply. The method I am referring to is not the multiple k-weight fits by constraining N*S02. My apologies for not being clear enough. Let's do it again. I am actually referring to an approach where we take an advantage of a different k-dependence of various parameters to breakdown correlations between them. For example, S02 and sigma2. S02 is k-independent and Sigma2 has k^2 dependence. In this case, to breakdown correlation between S02 and sigma2, one can assume a series of S02 values and perform fits using a single k-weight each time (say k-weight 1,2 and 3) and record corresponding sigma2 values. Let us say for k-weight =1, a series of preset S02 values will result in a series of corresponding sigma2 values refined in fits, which can be plotted as a straight line in sigma2 vs. S02 plot. Similar straight lines can be obtained for fits using k-weight = 2 and then 3. Now, these three lines may intersect at or near some point, which will determine the "true" value of parameters independent of k-weight. One can then constrain S02 to a value obtained from the point of intersection of three lines and vary sigma2 in a fit. In this particular case, however, the advantage is, S02 does not depend on changes inside sample and we have very good estimate of its range (say 0.7 - 1.0). Now suppose instead of S02 (which i now set to a reasonable value), I am interested in determining N, but it is highly correlated with sigma2. Each time when disorder in the sample increases, the sigma2 increases and due to its high correlation, N is also overestimated. On the other hand, when the disorder in the sample decreases, the sigma2 decreases and I can have a "true" estimation of N in the sample. Can I still apply the above mentioned approach to break the correlationship between N and sigma2 and get a "true" estimation of N, even if disorder is high in my samples ? or it is simply not possible due to the fact that both N and sigma2 varies with changes inside the sample. Best regards, Jatin ________________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [ifeffit-bounces(a)millenia.cars.aps.anl.gov] on behalf of ifeffit-request(a)millenia.cars.aps.anl.gov [ifeffit-request(a)millenia.cars.aps.anl.gov] Sent: Saturday, March 21, 2015 3:14 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 145, Issue 38 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: amplitude parameter S02 larger than 1 (Scott Calvin) 2. Breaking down correlationships between parameters (Rana, Jatinkumar Kantilal) 3. Re: Breaking down correlationships between parameters (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Fri, 20 Mar 2015 18:53:06 -0400 From: Scott Calvin <scalvin(a)sarahlawrence.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] amplitude parameter S02 larger than 1 Message-ID: <D2ADF788-9BC6-41E2-BD6B-794BD2E59DBC(a)slc.edu> Content-Type: text/plain; charset="utf-8" Hi Yanyun, Good. So here's the procedure for a Hamilton test. We're comparing the fit with S02 guessed to the one with S02 set to 0.90, because that was your a priori best guess at S02. I take the ratio of the first R-factor to the second. You didn't actually say the R-factor for the fit with S02 guessed, but it's clearly around 0.0055 based on the other information you gave. The R-factor for the 0.90 fit is 0.021. So the ratio is 0.0055/0.021 = 0.26, which we'll call x. For the first fit the degrees of freedom is 31.2 - 24 = 8.2. Take half of that and call that a. So a is 4.1. The first fit guesses 1 parameter that the second one doesn't. Take half of 1 and call that b. So b is 0.5. Find a regularized lower incomplete beta function calculator, like this one: http://www.danielsoper.com/statcalc3/calc.aspx?id=37 Enter x, a, and b. The result is 0.001. This means that there is a 0.1% chance that the fits are actually consistent, and that the difference is just due to noise in the data. So in this case, we can't just explain away the high S02 as insignificant. Of course, you could pretty much eyeball that once you gave me the uncertainties; since your fit said 1.45 +/- 0.14, that's likely to be quite incompatible with S02 = 0.9. Still, it's nice to put that on a firmer statistical basis, and I've personally found the Hamilton test quite helpful for answering "do I need to worry about [X]?" type questions. But in your case, you do need to worry about it. This discussion has generated several suggestions; hopefully one of them is a good lead! --Scott Calvin Sarah Lawrence College > On Mar 20, 2015, at 4:30 PM, huyanyun(a)physics.utoronto.ca wrote: > > Hi Scott, > > In all situations, 31.2 independent data points and 24 variables were > used. In the case of setting S02 to a value, 23 variables were used. > > Let me know if there is any other info needed. > > Best, > Yanyun > > > Quoting Scott Calvin <scalvin(a)sarahlawrence.edu>: > >> Hi Yanyun, >> >> To actually do a Hamilton test, the one other thing I need to know >> the number of degrees of freedom in the fit...if you provide that, >> I'll walk you through how to actually do a Hamilton test--it's not >> that bad, with the aid of an online calculator, and I think it might >> be instructive for some of the other people reading this list who >> are trying to learn EXAFS. >> >> --Scott Calvin >> Sarah Lawrence College >> >> >>> On Mar 20, 2015, at 3:46 PM, huyanyun(a)physics.utoronto.ca wrote: >>> >>> Hi Scott, >>> >>> Thank you so much for giving me your thought again. It is very helpful >>> to know how you and other XAFS experts deal with unusual situations. >>> >>> The floating S02 is fitted to be 1.45+/-0.14, this just means the fit >>> doesn't like the idea of an S02 in a typical range. Instead of setting >>> S02 to 0.9, I have to figure out why it happens and what it might >>> indicate. >>> >>> I guess a Hamilton test is done by adjusting one parameter (i.e., S02) >>> while keeping other conditions and model the same. Is that right? So >>> I record this test as following: >>> >>> 1) Floating S02: S02 fits to 1.45+/-0.14, R=0.0055, reduced >>> chi^2=17.86, Percentage=0.53+/-0.04 >>> 2) Set S02=0.7, R=0.044, reduced chi^2=120.6, percentage=0.81+/-0.2 >>> 3) set S02=0.8, R=0.030, reduced chi^2=86.10, percentage=0.77+/-0.07 >>> 3) set S02=0.9, R=0.021, reduced chi^2=60.16, percentage=0.72+/-0.06 >>> 4) set S02=1.0, R=0.017, reduced chi^2=49.5, percentage=0.67+/-0.05 >>> 5) set S02=1.1, R=0.012, reduced chi^2=35.1, percentage=0.62+/-0.03 >>> 6) set S02=1.2, R=0.009, reduced chi^2=24.9, percentage=0.59+/-0.02 >>> 7) set S02=1.3, R=0.007, reduced chi^2=18.9, percentage=0.57+/-0.02 >>> 8) set S02=1.4, R=0.0057, reduced chi^2=16.1, percentage=0.55+/-0.02 >>> 9) Floating S02 to be 1.45+/-0.14 >>> 10) set S02=1.6, R=0.006, reduced chi^2=17.8, percentage=0.53+/- 0.02 >>> 11) set S02=2.0, R=0.044, reduced chi^2=120.7, percentage=0.37+/-0.06. >>> >>> Therefore, I will say S02 falling in the range 1.2~1.6 gives >>> statistically improved fit, but S02=0.9 is not terrible as well. I >>> agree with you that I could always be confident to say the percentage >>> is 0.64+/-0.15, but I do want to shrink down the uncertainty and think >>> about other possibilities that could cause a large S02. >>> >>> I did double-check the data-reduction and normalization process. I >>> don't think I can improve anything in this step. By the way, I have a >>> series of similar samples and their fittings all shows floating S02 >>> larger than one based on the same two-sites model. >>> >>> Best, >>> Yanyun >>> >>> >>> >>> >>> Quoting Scott Calvin <scalvin(a)sarahlawrence.edu>: >>> >>>> Hi Yanyun, >>>> >>>> Lots of comments coming in now, so I?m editing this as I write it! >>>> >>>> One possibility for why you're getting a high best-fit S02 is that >>>> the fit doesn't care all that much about what the value of S02; i.e. >>>> there is broad range of S02's compatible with describing the fit as >>>> "good." That should be reflected in the uncertainty that Artemis >>>> reports. If S02 is 1.50 +/- 0.48, for example, that means the fit >>>> isn't all that "sure" what S02 should be. That would mean we could >>>> just shrug our shoulders and move on, except that it correlates with >>>> a parameter you are interested in (in this case, site occupancy). So >>>> in such a case, I think you can cautiously fall back on what might >>>> be called a "Bayesian prior"; i.e., the belief that the S02 should >>>> be "around" 0.9, and set the S02 to 0.9. (Or perhaps restrain S02 to >>>> 0.9; then you're really doing something a bit more like the notion >>>> of a Bayesian prior.) >>>> >>>> On the other hand, if the S02 is, say, 1.50 +/- 0.07, then the fit >>>> really doesn?t like the idea of an S02 in the typical range. An S02 >>>> that high, with that small an uncertainty, suggests to me that >>>> something is wrong?although it could be as simple as a normalization >>>> issue during data reduction. In that case, I?d be more skeptical of >>>> just setting S02 to 0.90 and going with that result; the fit is >>>> trying to tell you something, and it?s important to track down what >>>> that something is. >>>> >>>> Of course, once in a while, a fit will find a local minimum, while >>>> there?s another good local minimum around a more realistic value. >>>> That would be reflected by a fit that gave similarly good >>>> quantitative measures of fit quality (e.g. R-factors) when S02 is >>>> fit (and yields 1.50 +/- 0.07) as when its forced to 0.90. That?s >>>> somewhat unusual, however, particularly with a global parameter like >>>> S02. >>>> >>>> A good way to defend setting S02 to 0.90 is to use the Hamilton test >>>> to see if floating S02 yields a statistically significant >>>> improvement over forcing it to 0.90. If not, using your prior best >>>> estimate for S02 is reasonable. >>>> >>>> If you did that, though, I?d think that it would be good to mention >>>> what happened in any eventual publication of presentation; it might >>>> provide an important clue to someone who follows up with this or a >>>> similar system. It would also be good to increase your reported >>>> uncertainty for site occupancy (and indicate in the text what you?ve >>>> done). I now see that your site occupancies are 0.53 +/- 0.04 for >>>> the floated S02, and 0.72 +/-0.06 for the S02 = 0.90. That?s not so >>>> bad, really. It means that you?re pretty confident that the site >>>> occupancy is 0.64 +/- 0.15, which isn?t an absurdly large >>>> uncertainty as these things go. >>>> >>>> To be concrete, if all the Hamilton test does not show statistically >>>> significant improvement by floating S02, then I might write >>>> something like this in any eventual paper: ?The site occupancy was >>>> highly correlated with S02 in our fits, making it difficult to >>>> determine the site occupancy with high precision. If S02 is >>>> constrained to 0.90, a plausible value for element [X] [ref], then >>>> the site occupancy is 0.53 +/- 0.04. If constrained to 1.0, the site >>>> occupancy is [whatever it comes out to be] To reflect the increased >>>> uncertainty associated with the unknown value for S02, we are >>>> adopting a value of 0.53 +/- [enough uncertainty to cover the >>>> results found for S02 = 1.0]. >>>> >>>> Of course, if you do that, I?d also suggest tracking down as many >>>> other possibilities for why your fit is showing high values of S02 >>>> as you can; e.g., double-check your normalization during data >>>> reduction. >>>> >>>> If, on the other hand, the Hamilton test does show the floated S02 >>>> is yielding a statistically significant improvement, I think you >>>> have a bigger issue. Looking at, e.g., whether you may have >>>> constrained coordination numbers incorrectly becomes more critical. >>>> >>>> ?Scott Calvin >>>> Sarah Lawrence College >>>> >>>> >> >> >> _______________________________________________ >> 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 ------------------------------ Message: 2 Date: Sat, 21 Mar 2015 13:06:39 +0000 From: "Rana, Jatinkumar Kantilal" <jatinkumar.rana(a)helmholtz-berlin.de> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] Breaking down correlationships between parameters Message-ID: <DA4C7D90F90BC249A03505C87F2EB8AB230EE6D1@didag1> Content-Type: text/plain; charset="iso-8859-1" Dear All, I have stumbled upon a question regarding correlationships between various parameters in EXAFS fitting. As we know, the parameters S02*N and sigma2 are highly correlated (where N is the number of nearest neighbors). I would like to determine the number of nearest neighbors for a series of sample subjected to some treatment. I can do this by simply setting S02 to a value for a given absorber (based on the literature or my own measurements of some reference compounds) and letting N and sigma2 vary in a fit. However, the problem is the physical process which changes the number of nearest neighbors, also introduces structural disorder in samples. Thus, I always get the values of N overestimated due to its correlationship with sigma2. I know of a method which can be used to breakdown the correlationship between S02 and sigma2 by setting a series of S02 values at different k-weights and refining the corresponding sigma2 as discussed in several literature. However, in this approach the explicit assumption is, S02 is the property of absorbing atoms and thus is independent of changes occurring inside the sample. In my case, however, both sigma2 and N vary with changes inside samples. Is there any way to break this correlationship ? I look forward to your valuable suggestions and comments. Best regards, Jatin ________________________________ Helmholtz-Zentrum Berlin f?r Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph Gesch?ftsf?hrung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de

3 3

Breaking down correlationships between parameters
by Rana, Jatinkumar Kantilal 21 Mar '15

21 Mar '15

Dear All, I have stumbled upon a question regarding correlationships between various parameters in EXAFS fitting. As we know, the parameters S02*N and sigma2 are highly correlated (where N is the number of nearest neighbors). I would like to determine the number of nearest neighbors for a series of sample subjected to some treatment. I can do this by simply setting S02 to a value for a given absorber (based on the literature or my own measurements of some reference compounds) and letting N and sigma2 vary in a fit. However, the problem is the physical process which changes the number of nearest neighbors, also introduces structural disorder in samples. Thus, I always get the values of N overestimated due to its correlationship with sigma2. I know of a method which can be used to breakdown the correlationship between S02 and sigma2 by setting a series of S02 values at different k-weights and refining the corresponding sigma2 as discussed in several literature. However, in this approach the explicit assumption is, S02 is the property of absorbing atoms and thus is independent of changes occurring inside the sample. In my case, however, both sigma2 and N vary with changes inside samples. Is there any way to break this correlationship ? I look forward to your valuable suggestions and comments. Best regards, Jatin ________________________________ Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph Geschäftsführung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de

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Re: [Ifeffit] amplitude parameter S02 larger than 1
by Joshua Kas 20 Mar '15

20 Mar '15

Anatoly makes a very good point, and his example can also be used to show that there could be very large correlation between s02 and your percentage parameter. For example, if you assume that the first shell distances are the same for the two sites, and take Anatoly's example of 4 and 6 nearest neighbors, then your parameter P is 100 percent correlated with s02, i.e., all it does is change the coordination smoothly from 4 to 6. In a real system this probably won't happen, but the correlation could still be large. Have you looked at it? Josh On Fri, Mar 20, 2015 at 10:00 AM, <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: amplitude parameter S02 larger than 1 (Anatoly I Frenkel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 20 Mar 2015 16:57:02 +0000 > From: Anatoly I Frenkel <afrenke2(a)yu.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] amplitude parameter S02 larger than 1 > Message-ID: > < > 545F89325F51764C902D37B42C9F4D530148FDA88C(a)YUWEXCPM11.yuad.uds.yu.edu> > > Content-Type: text/plain; charset="us-ascii" > > One possible scenario: If one site has 6 nearest neighbors and the other - > 4, and if you choose the site with 4 neighbors to construct FEFF to model > your EXAFS data; and if you set your degeneracy equal to 4 and make your > amplitude factor as S02*x of one site + S02*(1-x) of another site, then > your S02 will come out larger than it should be because it will compensate > for the fact that you underestimate the degeneracy of the 6-coordinated > site. > > Anatoly > > ________________________________________ > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [ > ifeffit-bounces(a)millenia.cars.aps.anl.gov] on behalf of > huyanyun(a)physics.utoronto.ca [huyanyun(a)physics.utoronto.ca] > Sent: Friday, March 20, 2015 12:04 PM > To: XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] amplitude parameter S02 larger than 1 > > Hi Chris, > > Thank you for your suggestion. But I don't have a standard. Also, I > wonder whether a multiple-site situation could be different from the > normal one-site case with respect to S02. > > Best, > Yanyun > Quoting Chris Patridge <patridge(a)buffalo.edu>: > > > Hi, > > > > One thing that could be considered is transferring the SO2 factor > > from a reliable source such as a standard and then use that value in > > the fit. Chemical transferability of SO2 to similar systems is often > > acceptable. You could also try constraining the value in the fit as > > well. SO2 and Debye are also correlated so this may also affect the > > value. > > > > Hope that helps, > > > > Chris > > > > > > > > Sent from my iPhone > > > >> On Mar 19, 2015, at 6:32 PM, huyanyun(a)physics.utoronto.ca wrote: > >> > >> Hi all, > >> > >> I know this question has been asked for many times. S02 is expected > >> to be around, but smaller than 1, a fact that has been explained, > >> such as in the following previous emails, in our mailing list. > >> > >> > http://www.mail-archive.com/ifeffit%40millenia.cars.aps.anl.gov/msg02237.ht… > >> > http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2003-February/000230.html > >> > >> However, I am continually get S02 value larger than 1 for a series > >> of similar samples when I fit data in Artemis. I think my fit is > >> very good, because my suspected model(based on other technique) > >> could be verified in XAFS analysis (i.e., defensible in physics), > >> the statistics is good ( R=0.01, reduced chi-square=31.4, > >> fit-range:1.5~6 Angstrom, k-range: 3~14 angstrom-1) and all the > >> parameters such as the bond length, sigma2 are physically > >> reasonable. The only thing makes me uncomfortable is that parameter > >> S02 keeps between 1.45 to 1.55 during the fitting. > >> > >> In my system, the absorber atom occupies two crystallographic > >> sites. So I built a model with paths generated from two FEFF > >> calculations. For paths generated from the 1st and 2nd FEFF > >> calculation, the amplitude parameters are set to be S02*P% and > >> S02*(1-P%) respectively, where P% is the first site occupancy > >> percentage. Both S02 and P are free parameters during the fit, and > >> P is an important conclusion I want to extract from XAFS fitting. > >> > >> However, the fit result gives me S02=1.45 ~ 1.55 and P=0.51 ~ 0.56 > >> all the time (i.e., for each path the 'total amplitude' S02*P% or > >> S02*(1-P%) are about 0.7~0.8, smaller than 1). It looks to me that > >> I got a 'perfect' fit but I am not sure if S02 larger than one is > >> defensible. So I have to ask: > >> > >> 1) Is my current fit with S02 larger than one reasonable? If not, > >> what could be suggested to get around it? > >> > >> 2) What's the meaning of S02? It is interpreted in physics that it > >> is a reduced electron excitation parameter, but is it possible that > >> S02 will be affected by any experimental condition? > >> > >> 3) Can anyone share whether you had the multiple site system that > >> gets S02 larger than one? > >> > >> Looking forward to your help. > >> > >> Best, > >> Yanyun > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> _______________________________________________ > >> 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 > > > > _______________________________________________ > 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 > > > End of Ifeffit Digest, Vol 145, Issue 31 > **************************************** >

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Re: [Ifeffit] amplitude parameter S02 larger than 1
by Joshua Kas 20 Mar '15

20 Mar '15

On Fri, Mar 20, 2015 at 10:00 AM, <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: amplitude parameter S02 larger than 1 (Anatoly I Frenkel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 20 Mar 2015 16:57:02 +0000 > From: Anatoly I Frenkel <afrenke2(a)yu.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] amplitude parameter S02 larger than 1 > Message-ID: > < > 545F89325F51764C902D37B42C9F4D530148FDA88C(a)YUWEXCPM11.yuad.uds.yu.edu> > > Content-Type: text/plain; charset="us-ascii" > > One possible scenario: If one site has 6 nearest neighbors and the other - > 4, and if you choose the site with 4 neighbors to construct FEFF to model > your EXAFS data; and if you set your degeneracy equal to 4 and make your > amplitude factor as S02*x of one site + S02*(1-x) of another site, then > your S02 will come out larger than it should be because it will compensate > for the fact that you underestimate the degeneracy of the 6-coordinated > site. > > Anatoly > > ________________________________________ > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [ > ifeffit-bounces(a)millenia.cars.aps.anl.gov] on behalf of > huyanyun(a)physics.utoronto.ca [huyanyun(a)physics.utoronto.ca] > Sent: Friday, March 20, 2015 12:04 PM > To: XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] amplitude parameter S02 larger than 1 > > Hi Chris, > > Thank you for your suggestion. But I don't have a standard. Also, I > wonder whether a multiple-site situation could be different from the > normal one-site case with respect to S02. > > Best, > Yanyun > Quoting Chris Patridge <patridge(a)buffalo.edu>: > > > Hi, > > > > One thing that could be considered is transferring the SO2 factor > > from a reliable source such as a standard and then use that value in > > the fit. Chemical transferability of SO2 to similar systems is often > > acceptable. You could also try constraining the value in the fit as > > well. SO2 and Debye are also correlated so this may also affect the > > value. > > > > Hope that helps, > > > > Chris > > > > > > > > Sent from my iPhone > > > >> On Mar 19, 2015, at 6:32 PM, huyanyun(a)physics.utoronto.ca wrote: > >> > >> Hi all, > >> > >> I know this question has been asked for many times. S02 is expected > >> to be around, but smaller than 1, a fact that has been explained, > >> such as in the following previous emails, in our mailing list. > >> > >> > http://www.mail-archive.com/ifeffit%40millenia.cars.aps.anl.gov/msg02237.ht… > >> > http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2003-February/000230.html > >> > >> However, I am continually get S02 value larger than 1 for a series > >> of similar samples when I fit data in Artemis. I think my fit is > >> very good, because my suspected model(based on other technique) > >> could be verified in XAFS analysis (i.e., defensible in physics), > >> the statistics is good ( R=0.01, reduced chi-square=31.4, > >> fit-range:1.5~6 Angstrom, k-range: 3~14 angstrom-1) and all the > >> parameters such as the bond length, sigma2 are physically > >> reasonable. The only thing makes me uncomfortable is that parameter > >> S02 keeps between 1.45 to 1.55 during the fitting. > >> > >> In my system, the absorber atom occupies two crystallographic > >> sites. So I built a model with paths generated from two FEFF > >> calculations. For paths generated from the 1st and 2nd FEFF > >> calculation, the amplitude parameters are set to be S02*P% and > >> S02*(1-P%) respectively, where P% is the first site occupancy > >> percentage. Both S02 and P are free parameters during the fit, and > >> P is an important conclusion I want to extract from XAFS fitting. > >> > >> However, the fit result gives me S02=1.45 ~ 1.55 and P=0.51 ~ 0.56 > >> all the time (i.e., for each path the 'total amplitude' S02*P% or > >> S02*(1-P%) are about 0.7~0.8, smaller than 1). It looks to me that > >> I got a 'perfect' fit but I am not sure if S02 larger than one is > >> defensible. So I have to ask: > >> > >> 1) Is my current fit with S02 larger than one reasonable? If not, > >> what could be suggested to get around it? > >> > >> 2) What's the meaning of S02? It is interpreted in physics that it > >> is a reduced electron excitation parameter, but is it possible that > >> S02 will be affected by any experimental condition? > >> > >> 3) Can anyone share whether you had the multiple site system that > >> gets S02 larger than one? > >> > >> Looking forward to your help. > >> > >> Best, > >> Yanyun > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> _______________________________________________ > >> 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 > > > > _______________________________________________ > 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 > > > End of Ifeffit Digest, Vol 145, Issue 31 > **************************************** >

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Data being overwritten in Artemis history window
by Godfrey, Ian 18 Mar '15

18 Mar '15

?Dear All, Sorry... another bug report! Hopefully the last one for a while! In the history window some, but not all, data from previous fits seems to get overwritten when running a new fit. Specifically I've noticed this happening with the information in the "Data set" section. To reproduce run a QFS fit with some R-space fitting windows (say 2-4); at this point the log will be displayed correctly in the history window. Now change the R window (say 1.5-3.5) and run the fit again. When you go to the history window the R window information will be displayed correctly for the most recent fit but, for the previous fit it will have been overwritten by the newer fit. Some of the other info, such as R-factor by k-weight seems to get overwritten too. A video of this behaviour can be found here: https://wwwa-e.ucl.ac.uk/cgi-bin/dropbox/dropbox.cgi?state=pickup_info&id=2… password: 54c8545f System info: Win 8.1 Enterprise x64 running Demeter 0.9.22 pre release x64; log attached. All the best, Ian ---- Ian Godfrey PhD Student, UCL/JAIST Programme Industrial Doctorate Centre in Molecular Modelling and Materials Science, Department of Chemistry, University College London and School of Materials Science, Japan Advanced Institute of Science and Technology i.godfrey(a)ucl.ac.uk<mailto:i.godfrey@ucl.ac.uk> i.godfrey(a)jaist.ac.jp<mailto:i.godfrey@jaist.ac.jp>

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Re: [Ifeffit] (D)Artemis shutting down automatically
by Raj kumar 11 Mar '15

11 Mar '15

Dear Bruce, Thanks for the reply. Please see the attachment for the files which i have used. Regards, Raj On Wed, Mar 11, 2015 at 6:00 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: Increase in uncertainty of Eo and fitting mismatch > (Matt Newville) > 2. Re: Data being overwritten in Artemis history window (Bruce Ravel) > 3. (D)Artemis shutting down automatically (Raj kumar) > 4. Re: (D)Artemis shutting down automatically (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 10 Mar 2015 12:08:24 -0500 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Increase in uncertainty of Eo and fitting > mismatch > Message-ID: > < > CA+7ESbot-UZAgz3WM9EqaNROc7io+KnBE5NbEoMvxVoixPWGcw(a)mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Raj, > > Some comments and suggestions. > > On Tue, Mar 10, 2015 at 11:11 AM, Raj kumar <rajrk37(a)gmail.com> wrote: > > Dear All, > > > > Recently, I recorded Copper foil EXAFS as a reference in (Dispersive > EXAFS) > > transmission mode at Soleil, Paris. For understanding the data quality > (of > > my sample), i started fitting copper EXAFS through Artemis. After the > DATA > > extraction, i fitted copper in Artemis and found a shift in energy. For > this > > reason, i have modeled with and without corrected Copper EXAFS in > Artemis. > > What does "with and without corrected Copper EXAFS" mean? > > > Initially, i started with first shell and progressed to three shell fit > > through step by step. During the course of fitting, some of the following > > troubles have been faced. Please help me to rectify it. > > > > For first shell fit: Everything goes well and converged to reasonable > > physical values of copper foil. Whereas for further increment in copper > > shells leads to increase in Debye-waller factor for all three shells and > > By itself would not worry me too mcuh. > > > increase in uncertainty value of E0 than the actual value. > > What actual value? You mean the uncertainty in E0 increases when you > go from 1 to 3 shells? That increase in uncertainty could easily be > due to a worse overall fit. > > > Moreover, i have noticed that the (increase of shells in the fit) not > only > > changes the physical parameters and also modifies the Fourier transform. > > The Fourier transform of the data depends only on the k-space data, > and the weighting and windowing applied. It doesn't depend on the > values of the fitting parameters -- those affect only the Fourier > transform of the model. > > > The inference are the following: A shift in first and third shell of > Cu-Cu > > are observed, respectively, to larger and shorter distance than the > > experimental spectrum with diminished second shell amplitude. > > Not sure what you mean.... larger and shorter than what? > > I would recommend fitting one spectrum first -- I don't quite > understand why you have 2 spectra with an obvious E0 shift between > them, and no (unless I missed something) shared parameters. > > > --Matt > > > ------------------------------ > > Message: 2 > Date: Tue, 10 Mar 2015 13:50:59 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Data being overwritten in Artemis history > window > Message-ID: <54FF2F03.8060708(a)bnl.gov> > Content-Type: text/plain; charset=windows-1252; format=flowed > > On 03/09/2015 04:17 AM, Godfrey, Ian wrote: > > In the history window some, but not all, data from previous fits seems > > to get overwritten when running a new fit. Specifically I've noticed > > this happening with the information in the "Data set" section. To > > reproduce run a QFS fit with some R-space fitting windows (say 2-4); at > > this point the log will be displayed correctly in the history window. > > Now change the R window (say 1.5-3.5) and run the fit again. When you go > > to the history window the R window information will be displayed > > correctly for the most recent fit but, for the previous fit it will have > > been overwritten by the newer fit. Some of the other info, such as > > R-factor by k-weight seems to get overwritten too. > > I just pushed a fix for this to github and posted new windows installer > candidates at > > http://bruceravel.github.io/demeter/#windows > > If you see any other questionable behavior in the history window let me > know. I think I understood the ramifications of the fix I made, but I am > not 100% certain. > > The windows installers also include the most recent version of gnuplot. > Hopefully that will address your problem regarding zooming and > scrolling. > > If it does not, try changing the gnuplot->terminal configuration > parameter to "qt". qt is one of the other terminal options in the new > version of gnuplot. It makes a pretty plot, but I like the controls on > the wxt terminal more. If you are unsatisfied with that, try setting it > to "windows", which is the third (and to my eye, the worst) of the three > plot terminal options. Hopefully one of them will work for you. > > Cheers, > 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/ > > > ------------------------------ > > Message: 3 > Date: Wed, 11 Mar 2015 09:59:54 +0100 > From: Raj kumar <rajrk37(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] (D)Artemis shutting down automatically > Message-ID: > < > CAAW7+QMAn0kbe0udnpMzyPpqsb0X_t632Qwk7bWuMhtbzY96WQ(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear All, > > Recently, i have faced automatic shutting down of artemis during the import > of chi file. For more clarification, please see the first log file. > > Also, i observed emptying of .fpj files. This happens during the saving of > old .apj to .fpj or/and during the frequent saving of .fpj files after .apj > conversion. Please see the second log file for this problem. > > > Regards, > Raj >

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Re: [Ifeffit] Increase in uncertainty of Eo and fitting mismatch
by Raj kumar 11 Mar '15

11 Mar '15

Dear matt and Bruce, Thanks for the reply. Bruce i am working in new version (facing some problem) and will write to you soon >>"What does "with and without corrected Copper EXAFS" mean? For more clarity, in the new file, i have presented single copper EXAFS fit and showed the result. Please see the attachment for that. >>What actual value? You mean the uncertainty in E0 increases when you go from 1 to 3 shells? That increase in uncertainty could easily be due to a worse overall fit. Here i am mentioning *final fit* value as *actual value* and their *error bar *is uncertainty. If you look at the Eo value from 1 shell (fit 1) to 3 shell (fit 3), it decreases and close to zero whereas the corresponding uncertainty tending to reach more than or equal to 1. This is what i am mentioning here by saying Eo uncertainty increases for the inclusion of shells. >>>The Fourier transform of the data depends only on the k-space data, and the weighting and windowing applied. It doesn't depend on the values of the fitting parameters -- those affect only the Fourier transform of the model. I am really sorry, aforementioned sentence has been written in wrong and misleading way. The point i would like to make here is about the fit in R-space. The trouble i am facing is the following: I*f you look at the fit in R-space, similarly, * from 1 shell (fit1) to 3 shell (fit3) fit, the first shell theoretical shape shifts to larger distance (*for three shell fit (fit 3) in R-space*) compared to the only first shell fit (*fit 1*). If you look the third shell theoretical shape, it is shifted towards the shorter distance than the experimental spectrum (in *fit 3*), while the amplitude of second shell fit is always less than the experimental observation. Why it is occurring so? and what i am missing here? I hope i have conveyed the problem in right way. With regards, Raj On Wed, Mar 11, 2015 at 6:00 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: Increase in uncertainty of Eo and fitting mismatch > (Matt Newville) > 2. Re: Data being overwritten in Artemis history window (Bruce Ravel) > 3. (D)Artemis shutting down automatically (Raj kumar) > 4. Re: (D)Artemis shutting down automatically (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 10 Mar 2015 12:08:24 -0500 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Increase in uncertainty of Eo and fitting > mismatch > Message-ID: > < > CA+7ESbot-UZAgz3WM9EqaNROc7io+KnBE5NbEoMvxVoixPWGcw(a)mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Raj, > > Some comments and suggestions. > > On Tue, Mar 10, 2015 at 11:11 AM, Raj kumar <rajrk37(a)gmail.com> wrote: > > Dear All, > > > > Recently, I recorded Copper foil EXAFS as a reference in (Dispersive > EXAFS) > > transmission mode at Soleil, Paris. For understanding the data quality > (of > > my sample), i started fitting copper EXAFS through Artemis. After the > DATA > > extraction, i fitted copper in Artemis and found a shift in energy. For > this > > reason, i have modeled with and without corrected Copper EXAFS in > Artemis. > > What does "with and without corrected Copper EXAFS" mean? > > > Initially, i started with first shell and progressed to three shell fit > > through step by step. During the course of fitting, some of the following > > troubles have been faced. Please help me to rectify it. > > > > For first shell fit: Everything goes well and converged to reasonable > > physical values of copper foil. Whereas for further increment in copper > > shells leads to increase in Debye-waller factor for all three shells and > > By itself would not worry me too mcuh. > > > increase in uncertainty value of E0 than the actual value. > > What actual value? You mean the uncertainty in E0 increases when you > go from 1 to 3 shells? That increase in uncertainty could easily be > due to a worse overall fit. > > > Moreover, i have noticed that the (increase of shells in the fit) not > only > > changes the physical parameters and also modifies the Fourier transform. > > The Fourier transform of the data depends only on the k-space data, > and the weighting and windowing applied. It doesn't depend on the > values of the fitting parameters -- those affect only the Fourier > transform of the model. > > > The inference are the following: A shift in first and third shell of > Cu-Cu > > are observed, respectively, to larger and shorter distance than the > > experimental spectrum with diminished second shell amplitude. > > Not sure what you mean.... larger and shorter than what? > > I would recommend fitting one spectrum first -- I don't quite > understand why you have 2 spectra with an obvious E0 shift between > them, and no (unless I missed something) shared parameters. > > > --Matt > > > ------------------------------ > > Message: 2 > Date: Tue, 10 Mar 2015 13:50:59 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Data being overwritten in Artemis history > window > Message-ID: <54FF2F03.8060708(a)bnl.gov> > Content-Type: text/plain; charset=windows-1252; format=flowed > > On 03/09/2015 04:17 AM, Godfrey, Ian wrote: > > In the history window some, but not all, data from previous fits seems > > to get overwritten when running a new fit. Specifically I've noticed > > this happening with the information in the "Data set" section. To > > reproduce run a QFS fit with some R-space fitting windows (say 2-4); at > > this point the log will be displayed correctly in the history window. > > Now change the R window (say 1.5-3.5) and run the fit again. When you go > > to the history window the R window information will be displayed > > correctly for the most recent fit but, for the previous fit it will have > > been overwritten by the newer fit. Some of the other info, such as > > R-factor by k-weight seems to get overwritten too. > > I just pushed a fix for this to github and posted new windows installer > candidates at > > http://bruceravel.github.io/demeter/#windows > > If you see any other questionable behavior in the history window let me > know. I think I understood the ramifications of the fix I made, but I am > not 100% certain. > > The windows installers also include the most recent version of gnuplot. > Hopefully that will address your problem regarding zooming and > scrolling. > > If it does not, try changing the gnuplot->terminal configuration > parameter to "qt". qt is one of the other terminal options in the new > version of gnuplot. It makes a pretty plot, but I like the controls on > the wxt terminal more. If you are unsatisfied with that, try setting it > to "windows", which is the third (and to my eye, the worst) of the three > plot terminal options. Hopefully one of them will work for you. > > Cheers, > 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/ > > > ------------------------------ > > Message: 3 > Date: Wed, 11 Mar 2015 09:59:54 +0100 > From: Raj kumar <rajrk37(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] (D)Artemis shutting down automatically > Message-ID: > < > CAAW7+QMAn0kbe0udnpMzyPpqsb0X_t632Qwk7bWuMhtbzY96WQ(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear All, > > Recently, i have faced automatic shutting down of artemis during the import > of chi file. For more clarification, please see the first log file. > > Also, i observed emptying of .fpj files. This happens during the saving of > old .apj to .fpj or/and during the frequent saving of .fpj files after .apj > conversion. Please see the second log file for this problem. > > > Regards, > Raj >

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Re: [Ifeffit] wavelet transformed XAS in Larch-0.9.24
by Danilo Oliveira de Souza 11 Mar '15

11 Mar '15

On Tue, Mar 10, 2015 at 10:43 AM, Matthias Filez <Matthias.Filez(a)ugent.be> wrote: > Dear mailing list user, > > I am currently trying to use the cauchy_wavelet.py plugin of Larch-0.9.24 to > wavelet transform some k-space EXAFS data. In principle, everything works > properly, but I would like to adjust the order of the Cauchy wavelet to 50. > However, a view inside the script does not make clear what changes are > necessary. How can this be done? > > Please provide me your suggestions, > Many thanks, > > Matthias Filez Hi, Matthias You should check the MATLAB script made by Manuel MUÑOZ, François FARGES and Pierre ARGOUL. I think you have such freedom of choice you looking for. It works pretty well! Try this link http://perso.univ-mlv.fr/farges/wav/ Regards, -- *Danilo OLIVEIRA DE SOUZA* (PhD fellow) Université de Sciences et Technologies de Lille (Université Lille 1) UCCS - Unité de Catalise et Chimie du Solid, Bat. C3, 110. Cité Scientifique, 59655, VIlleneuve d'Ascq CEDEX. danilo.olsouza(a)gmail.com d.oliveira-de-souza(a)ed.univ-lille1.fr tel: +33 06.63.55.86.12

3 3

(D)Artemis shutting down automatically
by Raj kumar 11 Mar '15

11 Mar '15

Dear All, Recently, i have faced automatic shutting down of artemis during the import of chi file. For more clarification, please see the first log file. Also, i observed emptying of .fpj files. This happens during the saving of old .apj to .fpj or/and during the frequent saving of .fpj files after .apj conversion. Please see the second log file for this problem. Regards, Raj

2 1

Increase in uncertainty of Eo and fitting mismatch
by Raj kumar 10 Mar '15

10 Mar '15

Dear All, Recently, I recorded Copper foil EXAFS as a reference in (Dispersive EXAFS) transmission mode at Soleil, Paris. For understanding the data quality (of my sample), i started fitting copper EXAFS through Artemis. After the DATA extraction, i fitted copper in Artemis and found a shift in energy. For this reason, i have modeled with and without corrected Copper EXAFS in Artemis. Initially, i started with first shell and progressed to three shell fit through step by step. During the course of fitting, some of the following troubles have been faced. Please help me to rectify it. For first shell fit: Everything goes well and converged to reasonable physical values of copper foil. Whereas for* further increment in copper shells* leads to *increase in Debye-waller factor for all three shells* and *increase in uncertainty value of E0 than the actual value*. Moreover, i have noticed that the (increase of shells in the fit) *not only changes the physical parameters and also modifies the Fourier transform*. The inference are the following: A shift in first and third shell of Cu-Cu are observed, respectively, *to larger and shorter distance than the experimental spectrum* with diminished second shell amplitude. Although Copper foil EXAFS is standard and well known sample, i am stuck with fitting. Please help me to overcome these problems. For your reference, project file of Copper file is attached with this email. Regards. Raj

3 2

wavelet transformed XAS in Larch-0.9.24
by Matthias Filez 10 Mar '15

10 Mar '15

Dear mailing list user, I am currently trying to use the cauchy_wavelet.py plugin of Larch-0.9.24 to wavelet transform some k-space EXAFS data. In principle, everything works properly, but I would like to adjust the order of the Cauchy wavelet to 50. However, a view inside the script does not make clear what changes are necessary. How can this be done? Please provide me your suggestions, Many thanks, Matthias Filez PhD student Ghent University / Laboratory for Chemical Technology Technologiepark 914, B-9052 Ghent - Belgium http://www.lct.UGent.be<http://www.lct.ugent.be/> Disclaimer: http://helpdesk.UGent.be/email/disclaimer.php<http://helpdesk.ugent.be/email/disclaimer.php>

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Importing data with the new version of Athena
by Bruce Ravel 09 Mar '15

09 Mar '15

Hi, This question was sent to our mailing list by someone who is not subscribed. For some reason, it was not in the administration queue on the list server, so I couldn't forward it along in the normal fashion. Here is Sander Bruun's question: > For some reason I am unable to import data directly from *.dat files > in the new version of Athena. It says I may be needing a plugin, but > I do not know how to install it. Can anybody help. It worked fine in > some of the older versions of Athena, but I cannot find and install > them now. Sander, That's not enough information for me to answer the question. "*.dat" is not a file format. A file called "*.dat" can (and usually does!) contain almost anything. Without an example of the sort of file that is giving you trouble, I cannot possibly know what's going on. If your data comes from a particular beamline, it's possible that you simply need to enable that beamline's plugin. There are a couple plugins that come with the software related to specific beamlines at ESRF.... http://bruceravel.github.io/demeter/aug/other/plugin.html#athena%27spluginr… Cheers, B PS: If you subscribe to the mailing list (see http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit) then you mail will be posted to the list without my intervention. -- 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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Re: [Ifeffit] Question about statistics
by Olga Kashurnikova 08 Mar '15

08 Mar '15

Hello, Dr Matt Newville, Thank you very much for the answer. There is a message with some corrections in the next thread - the numbers of my hand try to check am I right about chi_square and error calculation in IFEFFIT, were not right in the first time. I will try to attach the calculation files later, it is not clear for me how they will be shown here. I will write the main question and then about Bayesian analysis for thread splitting if you don't mind. These things are interconnected that's why I didn't split them. The main question was about how IFEFFIT calculates chi_square and to what minimization function it adds restraints, in case of k_space. What is the normalization? I thought it should be (N_idp/N_data)sum[(dat-model)^2/eps^2], and in k space only the real part of data compared with imaginary part of model, but my hand calculation for check this gave the different result. It is necessary for the choice of optimal restraint (it is chi^2 without normalization that I need to compare) and for normalization of errors for them to be covariance matrix of this chi^2, as of Krappe and Rossner. Restraint will change errors, of course, because covariance matrix is (Q+A)^(-1) where A is regularizer in restraint and Q is what should be without restraint. If Q is not invertible (in case of some parametra don't influence spectrum) it is critical, and optimal A can be found to strictly divide the 'parametra space' and verify models. That's why I need to rescale them well, because for bayes it should be chi^2=sum[(dat-model)^2/eps^2]+A*sum(x-x0)**2 (A is connected with a priori ranges of parametra, it should be not one number, but algorithm of finding optimal diagonal A matrix is harder and I think not with IFEFFIT/Larch help). It is the same as your (paramA-A_0)/eps_A restraint, I understood what formula should be for a restraint, but don't understand how to weight data and restraint part. It were Krappe and Rossner who mentioned Tikhonov regularization if I remember right, and it is very close, if I understood the paper about this regularization. That's what I mean in 'doesn't fit': 4 coordination spheres (Gd-O, Gd-Gd,Gd-Hf, next Gd-O for instance, and only first is in separate peak) may be in the N_idp range, but are so correlated that without constraints or other structure model the fit give bad results - some parametra will leave the acceptable range etc, and I'm not sure that without a Bayesian analysis I can define the better model of constraints, and the sphere splitting is even more difficult to define. So, the main question is 'how IFEFFIT calculates this, what is the formula', because FEFFIT manual doesn't give the k-space case, and the check was wrong. I can append calculation files in a while if needed (I need to convert from a program to iff file), though I wrote formulae and they may be can be verified without numerical values. Chi_square in your method is close to what should be minimized and for what the covariance matrix should be found in Bayesian analysis, with the right normalization, that's why I ask if I could use IFEFFIT to calculate this with renormalization of the results. If I put the right normalization to restraint, I need only rescale chi_square and errors and then calculate what I need. It is not that I think IFEFFIT use Bayesian statistics, I understand there are different approaches. Thankful for your assistance, Olga Kashurnikova, MEPhI, Moscow

3 7

Question about statistics
by Ольга Кашурникова 06 Mar '15

06 Mar '15

Good day to developers and users of Ifeffit, I'd like to get help with my question of statistical calculations in Ifeffit (I use the version embedded in Demeter, but in console mode or from my Fortran little program: think of Larch using but there are no some features and I'm not sure). The task is to try making Bayes statistics, in the sense that was published in Krappe et al. papers from 1999,2002,2004 years and the book of Bretthorst. I haven't found the software for it and my own tries to write it are not completed because of no experience. I saw something in papers about BFEFFIT, an extension for such statistics, but haven't found it in the web or any other information. May be somebody knows what stage is it on. I need it because of complicate model (4 spheres, may be splitting of spheres because it is many-phase system with dopant phase) and need of regularization in Tikhonov sense (parametra are correlated and I can not determine which constraint or model is better without statistics, and with nonconstrained parametra it simply will not fit) I understood that it can be emulated in Ifeffit with help of restraints. All thing is to: -minimize chi**2=(dat-model)**2/epsilon_k**2+A*sum(xi-x0i)**2, where A is regularizer, xi - parametra in fit end, x0i - a priori values of parametra. -calculate pair correlations and errors so that we can calculate the second derivatives and variance matrix of chi**2 determines in this sence. But I can not understand about how restraint goes in fit and how IFEFFIT calculates chi_square (not reduced) and errors. From manuals of FEFFIT and IFEFFIT I supposed that there goes: -LS minimisation of (dat-model)**2+restraint**2, may be normed, but it doesn't matter -chi_square is this value divided by eps_k**2, may be divided by points num -for errors found variance of chi_square defined above, but then error bars are scaled to chi_reduced to eliminate noise dependence -pair correlations are corr(i,j)/sqrt(corr(i,i)*corr(j,j) and doesn't depend of normalisations What is right? I need the above defined chi**2=(dat-model)**2/epsilon_k**2+A*sum(xi-x0i)**2 and its variance matrix, because it defines my statistics, optimal A,errors and 'projections' of parametra that I need to verify model. I use the fit in k space (not q) without Fourier transforms or k weight, because it is hard to do for this statistics. (Filtration of high fr3equency components I can do with rectangle windows if needed, I think, but it is not much bigger than noise) I thought (dat-model)**2 in k space is in real part for points from kmax to kmin for defined dat array(my_spectrum.chi for instance) and fit.chi array. But I calculated chi_square in hand from these arrays and there was no right number. for test of 1 sphere chi_square=8e-3, (dat-model)**2=3e-4, (dat-model)**2/noise**2=2,37e1, (dat-model)**2/noise**2=9.5e-2 and so on (regularizer part A(x-x0)**2=0.91). For instance. But if it calculates in real and imaginary part of Fourier transform no meaning what space I use - and this function is used to find variance - then I'm not sure how to find error bars and variance matrix I need. There are many other questions and limitations, I want to make this calculation approximately with what I can (constaint noise, may be +bkg part as Ifeffit gives, two or more spectra - and the other things later), but I hope someone could help the beginner to solve this problem or find the simplest way in existing software... I need to know what is the stage of this topic and need I end my program for it or not. There in mind are such things as mu0 polynome fit, many-spectra fit with PDF and diffraction spectra for model and so on, but may be there is the best program in one step from completeness and I need not to do it. Thanks sincerely, Olga Kashurnikova (from MePHI XAFS group in Moscow)

3 3

calculation of statistics-2
by Ольга Кашурникова 06 Mar '15

06 Mar '15

Good afternoon or other time of day again, I don't know how to add message to the thread (I use online mail service), so will write additions here, sorry, may be somebody will correct me. The chi_square definition in FEFFIT manual is chi_square=N_idp/N_data*sum((dat-model)^2/epsilon_k^2), and to this sum IFEFFIT adds restraint^2 (as of source code). But with 0 restraint I didn't get the right value. If there is 2*N_data, I get the right order, but not exactly the same value (0.6 and 0.8 for instance). chi_reduced=chi_square/(N_idp-N_param) by definition, and it is exact. (N_idp=18, N_param=4 in my case, eps_k=3.6e-3 from FT high-frequency compared with mu0 calculation in real spectrum. I'm not sure about small values, but the test is generated oxygen sphere without noise, so only systematic errors. I will correct it anyhow, but can it be a problem I'm not sure) I found that I need to set Rmin and Rmax for N_idp calculus even if I fit in k space, but it doesn't help. The adding of real part of fit chi (that exists, I don't know why) with 0 data made things only worse. I try to find maths in source code, but it is big, and I can not find all definitions and understand quickly what is the beginning and what is the chain of calls I need. Are files in feffit and lib directories used together? That seems that the fit vector that is LS-fitted is (dat-model)/weight and restraint components, but what of weight. In fitnls.f file there are weight(id) = sigdtk(id) * sigdtk(id) / sigwgt(id) !in k space case. Is it epsilon_k**2 if user-defined epsilon_k? what is this normalization? weight(id) = sqrt ( nptfit(id) * weight(id) / xinfo(id)) !nptfit=N_data without 2 from kmin to kmax? xinfo=N_idp ifeffit variable? !We sum chi_square in m_fit points, is it the same? in fft file there was 2*N_data even in k space? So can I think that weight=sqrt(N_data/N_idp)*epsilon_k, or not? I didn't get the chi_square right with this formula. Also, dat-model is multiplied by window, but I make Hanning window with dk=0 and it doesn't help. It is the main question I wish to find the answer now, because need to make this calculus to publish, for results in my compounds to be confident. I thought of suggesting that chi_square is different only by norm and restraint is added to chi_square and to calculate and renormalize errors and A parameter in restraint for calculation. But it can be a problem if is not proportional, and I'm not sure if A renormalization can help... The question of extending the method can wait a while. I will be very thankful if somebody could help... Thanks sincerely, O.V. Kashurnikova, XAFS group of the MEPhI, Moscow (Moscow Engeneering-Physics Institute)

1 0

Artemis error - xdi is not writable (0.9.21, Windows 8)
by Godfrey, Ian 05 Mar '15

05 Mar '15

Dear All, I've encountered a problem in Artemis 0.9.21 (x64 running under Win 8.1 Pro x64) when I try and load a project file to which I've previously saved changes using this version of Artemis. When double clicking the file to open it the programme begins to open as normal, until it reaches "importing paths" - at which point it simply closes. The log file (attached) shows an error that "xdifile is not writable, no setter defined at...". Opening files saved in older versions of Artemis seems fine though. I've attached a log file and a problematic project file. Regards, Ian

2 3

Two plotting related glitches in Athena
by Godfrey, Ian 04 Mar '15

04 Mar '15

?Dear All, I encountered two (apparent) bugs related to plotting data in Athena. In both cases I think they're best expressed via video screencaps so please see the links with each bug report (both of these links are valid for 10 days only). Both of these are occurring in Athena 0.9.21 x64 on Windows 8.1 Enterprise x64. An Athena log file is attached. 1) Sometimes lines on a plot disappear when zooming/scrolling. This typically happens with steeper lines. In the video you can see it occurring when I scroll up and down - sometimes it also occurs immediately when I try and zoom in. (I guess this could be an issue with GNUPlot, rather than Athena?) Video: https://wwwa-e.ucl.ac.uk/cgi-bin/dropbox/dropbox.cgi?state=pickup_info&id=1… Password: 2725d459 2) When using the pluck function to set indicators (possibly in other situations too, although I haven't noticed it there) if you don't double click to pluck the point fast enough after clicking the pluck button the software plucks a nonsense value instead. (The halo around the cursor is supposed to show when I click, but it seems to show up when I leave the cursor stationary and at some other times too, so don't rely too much on that... when I don't double click the point I've left the cursor entirely off the Athena windows). (Sometimes when this happens it seems that you need to replot the graph to be able to pluck again, but I can't reliably reproduce that behaviour.) Video: https://wwwa-e.ucl.ac.uk/cgi-bin/dropbox/dropbox.cgi?state=pickup_info&id=3… Password: 2725d459 Regards, Ian ---- Ian Godfrey PhD Student, UCL/JAIST Programme Industrial Doctorate Centre in Molecular Modelling and Materials Science, Department of Chemistry, University College London and School of Materials Science, Japan Advanced Institute of Science and Technology i.godfrey(a)ucl.ac.uk<mailto:i.godfrey@ucl.ac.uk> i.godfrey(a)jaist.ac.jp<mailto:i.godfrey@jaist.ac.jp>

2 2

International EXAFS Conference XAFS16
by Lichtenberg, Henning (IKFT) 04 Mar '15

04 Mar '15

Abstract Deadline for the International XAFS Conference in Karlsruhe (www.xafs16.org<http://www.xafs16.org>) extended until March 15,2015 Dear colleagues of earlier XAFS conferences Good news about the XAFS16 conference, which will take place in Karlsruhe/Germany 23 – 28 August 2015: More than 300 abstracts have arrived in our system during the last 3 days just before the deadline. Most popular at the moment are topics like EXAFS in materials science, instrumentation, new spectroscopic methods, energy-related materials and catalysis (please refer to the site: http://www.xafs16.org) The strength of the conference is that theory and instrumentation on the one hand and applications on the other hand talk to each other! Many have asked us about the extension of the deadline so that we have prolonged the abstract submission deadline until March 15, 2015. Please submit your abstract in time! The reviewing process will start immediately afterwards. Later abstracts may be considered as poster but this also depends on whether we still have enough space. During the next days we will also update the plenary and keynote speaker list. So please have a glance on the homepage www.xafs16.org<http://www.xafs16.org> from time to time. Special sessions like an industrial session as well as 3 satellite meetings are planned. We already now look forward to a successful conference and look forward to contributions in all 16 topics. Best regards, in the name of the IXAS society and the local organizing committee. Jan-Dierk Grunwaldt Chairman XAFS16 [cid:image001.jpg@01D0553A.FD9D8F50]<http://www.xafs16.org/> --------------------------------------------------------------------- Prof. Dr. Jan-Dierk Grunwaldt Chair in Chemical Technology and Catalysis grunwaldt(a)kit.edu<mailto:grunwaldt@kit.edu>; www.itcp.kit.edu/grunwaldt/<http://www.itcp.kit.edu/grunwaldt/> Tel.: +49 721 608-42120, Fax: -44805, Sekr. Tel.: -42121, -43064 Karlsruhe Institute of Technology (KIT) Director at the Institute for Chemical Technology and Polymer Chemistry (ITCP) Engesserstr. 20, 76131 Karlsruhe, Germany Director at the Institute for Catalysis Research and Technology (IKFT) Herman-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany KIT - Universität des Landes Baden-Württemberg und nationales Großforschungszentrum in der Helmholtz-Gemeinschaft

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problem plotting in Athena after installation of Demeter 0.9.21 on Windows 64bit
by kirshstein＠gmail.com 03 Mar '15

03 Mar '15

Hello, I have just installed Demeter and the first thing Athena does, when asked to plot (mu(E)) of an averaged standard spectrum (S-K-edge of CaSO4, averaged in sixpack), is to give the following error message: "Use of uninitialized value in multiplication(*) at C:/strawberry/perl/site/lib/Math/Spline.pm line 36." Also E0 is 0 and in front of a red background. So it seems to have trouble finding E0. But why? What does this mean? What do I have to do to get athena to work? attached is the CaSO4 spectrum in question. Thanks! Yael Kirsch

2 2

Feature request - Hephaestus: Plot multiple standards at once
by Godfrey, Ian 02 Mar '15

02 Mar '15

Dear All, I'm using Hephaestus' standards library to help with some XANES fingerprinting and it's very useful. I would find it quite helpful to be able to select two (or more) standards from the list and plot them on the same graph for comparison. Regards, Ian ---- Ian Godfrey PhD Student, UCL/JAIST Programme Industrial Doctorate Centre in Molecular Modelling and Materials Science, Department of Chemistry, University College London and School of Materials Science, Japan Advanced Institute of Science and Technology i.godfrey(a)ucl.ac.uk<mailto:i.godfrey@ucl.ac.uk> i.godfrey(a)jaist.ac.jp<mailto:i.godfrey@jaist.ac.jp>

2 5

Pb compound determination fitting issue
by Pieter Tack 25 Feb '15

25 Feb '15

Hi everyone, I recently acquired an EXAFS data set (albeit somewhat noisy) on the Pb-L3 edge. I have normalized it using Athena, and tried to fit the first shell using Artemis. I attached the Athena project file as well as the Artemis project file of what I obtained thus far. We have reason to believe the unknown compound is PbO or PbS (or a mixture). However, when I look at the R space curve, the first coordination shell is at rather low path distance (1.7 A), whereas one would expect larger bond distances for PbO and PbS. I found that a similar bond distance as to what the experimental spectrum shows can be found in PbCO3, but a fit using the mineral data of PbCO3 also doesn't do the trick. In any case, no matter what I try to fit in Artemis, nothing seems decent. Is the EXAFS fitting simply impossible due to the noisy data, did I extract my Chi(k) wrong or am I encountering some other issue? I realize it's probably not much to go on, but I'm rather new to EXAFS analysis so any help/advice is appreciated. Thanks a lot in advance! Best regards, Pieter Tack -- X-Ray Micro-Spectroscopy and Imaging Group Department of Analytical Chemistry Ghent University Krijgslaan 281 S12 B-9000 Ghent Belgium Phone: +32 (0)9 264 4723 Fax: +32 (0)9 264 49 60

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Re: [Ifeffit] Pb compound determination fitting issue
by fred.mosselmans＠diamond.ac.uk 25 Feb '15

25 Feb '15

-----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: 25 February 2015 10:48 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 144, Issue 11 Hi Pieter Apologies for confusing you, By 1 and 3 I meant fit 3 O, fit 5 S in the history. I had to fix S02 as the data range gives only 3 -4 paras and it flew off initially. Sorry Fred ---------------------------------------------------------------------- Message: 1 Date: Wed, 25 Feb 2015 10:45:15 +0000 From: <fred.mosselmans(a)diamond.ac.uk> To: <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Pb compound determination fitting issue Message-ID: <CF65047C5B0562499EAFF9FBBC542D6485DF0819(a)EXCHMBX01.fed.cclrc.ac.uk> Content-Type: text/plain; charset="us-ascii" Dear Pieter, You wouldn't start with Pb exafs if you had the choice. Pb has a lot of structural disorder in its compounds and is very thermally wobbly leading to poor signal to noise data. I think your dataset is only good to 7 -8 inverse A. That said I think you can learn something about the sample. Was the sample cold? eg in a cryostat when measured this is about the only way to get OK Pb data from anything but a solid state system with ordered atoms. In fit 1 (see the history) in the attached project file I use the first shell of massicot and this doesn't give a good fit but nothing ridiculous , in fit 3 I sued the cerrusite 1st shell and e0 goes along way and the first shell distance contracts a lot. This suggests you are likely have O in the first shell and by playing around more, e.g. Shortening the data range in Athena to improve the data reduction you should be able to get a better fit than with just one button press, however the useable data range is small so it will be not great In accuracy terms. Also you might try comparing the XANES to literature data though the core hole size in Pb L3 washes out xanes a bit so its not the best. Regards Fred ---------------------------------------------------------------------- Message: 1 Date: Wed, 25 Feb 2015 11:20:17 +0100 From: Pieter Tack <Pieter.Tack(a)ugent.be> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Pb compound determination fitting issue Message-ID: <20150225112017.Horde.GS9lWdD6UQ5U7aHhPZgmRhA(a)webmail.ugent.be> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"; DelSp="Yes" Hi everyone, I recently acquired an EXAFS data set (albeit somewhat noisy) on the Pb-L3 edge. I have normalized it using Athena, and tried to fit the first shell using Artemis. I attached the Athena project file as well as the Artemis project file of what I obtained thus far. We have reason to believe the unknown compound is PbO or PbS (or a mixture). However, when I look at the R space curve, the first coordination shell is at rather low path distance (1.7 A), whereas one would expect larger bond distances for PbO and PbS. I found that a similar bond distance as to what the experimental spectrum shows can be found in PbCO3, but a fit using the mineral data of PbCO3 also doesn't do the trick. In any case, no matter what I try to fit in Artemis, nothing seems decent. Is the EXAFS fitting simply impossible due to the noisy data, did I extract my Chi(k) wrong or am I encountering some other issue? I realize it's probably not much to go on, but I'm rather new to EXAFS analysis so any help/advice is appreciated. Thanks a lot in advance! Best regards, Pieter Tack -- X-Ray Micro-Spectroscopy and Imaging Group Department of Analytical Chemistry Ghent University Krijgslaan 281 S12 B-9000 Ghent Belgium Phone: +32 (0)9 264 4723 Fax: +32 (0)9 264 49 60

1 0

Re: [Ifeffit] Pb compound determination fitting issue
by fred.mosselmans＠diamond.ac.uk 25 Feb '15

25 Feb '15

Dear Pieter, You wouldn't start with Pb exafs if you had the choice. Pb has a lot of structural disorder in its compounds and is very thermally wobbly leading to poor signal to noise data. I think your dataset is only good to 7 -8 inverse A. That said I think you can learn something about the sample. Was the sample cold? eg in a cryostat when measured this is about the only way to get OK Pb data from anything but a solid state system with ordered atoms. In fit 1 (see the history) in the attached project file I use the first shell of massicot and this doesn't give a good fit but nothing ridiculous , in fit 3 I sued the cerrusite 1st shell and e0 goes along way and the first shell distance contracts a lot. This suggests you are likely have O in the first shell and by playing around more, e.g. Shortening the data range in Athena to improve the data reduction you should be able to get a better fit than with just one button press, however the useable data range is small so it will be not great In accuracy terms. Also you might try comparing the XANES to literature data though the core hole size in Pb L3 washes out xanes a bit so its not the best. Regards Fred ---------------------------------------------------------------------- Message: 1 Date: Wed, 25 Feb 2015 11:20:17 +0100 From: Pieter Tack <Pieter.Tack(a)ugent.be> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Pb compound determination fitting issue Message-ID: <20150225112017.Horde.GS9lWdD6UQ5U7aHhPZgmRhA(a)webmail.ugent.be> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"; DelSp="Yes" Hi everyone, I recently acquired an EXAFS data set (albeit somewhat noisy) on the Pb-L3 edge. I have normalized it using Athena, and tried to fit the first shell using Artemis. I attached the Athena project file as well as the Artemis project file of what I obtained thus far. We have reason to believe the unknown compound is PbO or PbS (or a mixture). However, when I look at the R space curve, the first coordination shell is at rather low path distance (1.7 A), whereas one would expect larger bond distances for PbO and PbS. I found that a similar bond distance as to what the experimental spectrum shows can be found in PbCO3, but a fit using the mineral data of PbCO3 also doesn't do the trick. In any case, no matter what I try to fit in Artemis, nothing seems decent. Is the EXAFS fitting simply impossible due to the noisy data, did I extract my Chi(k) wrong or am I encountering some other issue? I realize it's probably not much to go on, but I'm rather new to EXAFS analysis so any help/advice is appreciated. Thanks a lot in advance! Best regards, Pieter Tack -- X-Ray Micro-Spectroscopy and Imaging Group Department of Analytical Chemistry Ghent University Krijgslaan 281 S12 B-9000 Ghent Belgium Phone: +32 (0)9 264 4723 Fax: +32 (0)9 264 49 60

1 0

Trouble installing demeter on Mint 17.1
by Stevan Ognjanovic 19 Feb '15

19 Feb '15

Dear list, After upgrading my Linux OS to Mint 17.1, I have trouble installing demeter again (on Mint 14 it used to install and run without problems). sudo ./Build installdeps failed to install a few dependencies even after issuing the command several times (Wx and Regexp:Assemble), so I installed them manually from the Mint repositories. After that, perl ./Build.PL said that all dependencies were satisfied. I then ran ./Build which finished, I think, normally. The only lines that look remotely suspicious are: Chantler data conversion tool 1.2 for Absorption 0.10 Parsing lines ... Parsing element 5Argument "8.20144-01" isn't numeric in numeric le (<=) at lib/Xray/data/chantler2st.PL line 120, <CHANTLER> line 81. 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 Getting energy list keys ... sorting energy list ... and making energy hash Saving new database, lib/Xray/data/../Absorption/chantler.db. However, when I run ./Build test it shows that 2/44 tests fail (5/2681 subtests). Please find the terminal output below. It might be usefull to mention that at first I tried to install demeter without root privileges (following the Dave Hughes' guide), with same tests failing. I went on to ./Build install anyway, and it succeded, but when trying to open previously saved projects, dathena would crash. I then removed demeter and the local perl directory, and tried installing demeter again, this time with root privileges following Bruce Ravel's guide. Any help would be appreciated, thank you in advance! ./Build test terminal output: t/000_ifeffit.t ......... ok t/001_base.t ............ ok t/002_types.t ........... ok # Failed test 'configuration system introspection works: groups 37 artemis' # at t/003_config.t line 61. # Failed test 'configuration system introspection works: main_groups 37' # at t/003_config.t line 63. # Failed test 'introspection after reading new group: groups' # at t/003_config.t line 74. # Failed test 'introspection after reading new group: main_groups' # at t/003_config.t line 76. # Looks like you failed 4 tests of 24. t/003_config.t .......... Failed 4/24 subtests t/004_data.t ............ ok t/005_plot.t ............ ok t/006_gds.t ............. ok t/007_prj.t ............. ok t/008_path.t ............ ok # Failed test 'statistics reporting seems ok' # at t/009_fit.t line 97. # Looks like you failed 1 test of 25. t/009_fit.t ............. Dubious, test returned 1 (wstat 256, 0x100) Failed 1/25 subtests t/010_feff.t ............ ok t/011_sp.t .............. ok t/012_atoms.t ........... ok t/013_spacegroups.t ..... ok t/014_vpath.t ........... ok t/015_sspath.t .......... ok t/016_fspath.t .......... ok t/017_structuralunit.t .. ok t/018_multichannel.t .... ok t/019_provenance.t ...... ok t/020_indicator.t ....... ok t/021_externalfeff.t .... ok t/022_filetypes.t ....... ok t/023_files.t ........... ok t/024_graph.t ........... ok t/025_lcf.t ............. ok t/026_xes.t ............. ok t/028_fpath.t ........... ok t/029_threebody.t ....... ok t/030_xdi.t ............. ok t/031_quench.t .......... ok t/032_miscellany.t ...... ok t/100_elam.t ............ ok t/101_mcmaster.t ........ ok t/102_chantler.t ........ ok t/103_henke.t ........... ok t/104_shaltout.t ........ ok t/105_fluo.t ............ ok t/500_checker.t ......... ok t/501_dataBlock.t ....... ok t/502_dictionary.t ...... ok t/503_filter.t .......... ok t/504_parser.t .......... ok t/505_writer.t .......... ok Test Summary Report ------------------- t/003_config.t (Wstat: 0 Tests: 24 Failed: 4) Failed tests: 17-18, 23-24 t/009_fit.t (Wstat: 256 Tests: 25 Failed: 1) Failed test: 17 Non-zero exit status: 1 Files=44, Tests=2681, 69 wallclock secs ( 0.29 usr 0.06 sys + 67.36 cusr 2.64 csys = 70.35 CPU) Result: FAIL Failed 2/44 test programs. 5/2681 subtests failed. Kind regards, Stevan Ognjanovic -- Stevan Ognjanovic, Dipl.-Ing. Nanoparticle Process Technology Department of Engineering Sciences University Duisburg-Essen Lotharstraße 1, MA 349 D-47057 Duisburg Phone: +49 (0)203 379 1783 Mobile phone: +49 (0)157 3820 6890 Fax: +49 (0)203 379 4453 web: www.nppt.de e-mail: stevan.ognjanovic(a)uni-due.de

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Re: [Ifeffit] Trouble installing demeter on Mint 17.1
by Denis Testemale 19 Feb '15

19 Feb '15

Stevan, Bruce, this Athena crashing (when opening a file or importing data) sounds similar to some trouble I had some months ago. Bruce solved my problem (as usual...) with a solution that I still need to apply and that still works perfectly. Iin the terminal, I type: export LANG=en_US.UTF-8 before launching athena or artemis (from the same terminal). I cannot guarantee that it will sove your problem, and I didn't inspect your error messages carefully, so I might be miles away from the truth, but since like me you're from a non-US country with probably non-US langage environments, I thought it would be worth trying. Cheers denis -- Institut Néel - CNRS http://neel.cnrs.fr/spip.php?rubrique264 +33 476 881 045

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Re: [Ifeffit] Ifeffit Digest, Vol 144, Issue 2
by Khalid, Syed 04 Feb '15

04 Feb '15

Thank you all, many nice suggestions and I will try them all. For the first time the beamline 2-2 at SSRL is being used for XAS. The control software is in LINUX and the output files automatically move to a Windows computer, in binary and ASCII form, sitting next to it. We were also able to see the ASCII file in wordpad and then saved it as text file after deleting all the text and only keeping the data columns. Athena was able to read it then. I will have to write a program to add "#" before text lines. We will need that dealing with lot of data. I will certainly check with the beamline scientist, why things are the way they are. About the offsets, I did notice it was slightly negative, but we had other major problems to deal with, so did not bother. Syed Khalid -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Wednesday, February 04, 2015 1:00 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 144, Issue 2 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: SSRL-data (Shoaib Muhammad) 2. Re: SSRL-data (Matt Newville) 3. Re: SSRL-data (Matthew Marcus) ---------------------------------------------------------------------- Message: 1 Date: Wed, 4 Feb 2015 10:31:56 +0900 From: "Shoaib Muhammad" <mshoaibce(a)gmail.com> To: "'XAFS Analysis using Ifeffit'" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] SSRL-data Message-ID: <002401d0401a$5e97d300$1bc77900$(a)gmail.com> Content-Type: text/plain; charset="us-ascii" Dear Syed Khalid, One simple work around can be to select "Plugin Registry" and enable SSRL related plugins. By doing this I was able to successfully read both the attached files in Demeter Athena. Further details to enable plugins can be found here: http://bruceravel.github.io/demeter/aug/other/plugin.html /Shoaib SKKU (South Korea) From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Khalid, Syed Sent: Monday, February 2, 2015 5:11 AM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] SSRL-data How to handle SSRL, beamline 2-2 data. Attached is a binary and an ASCII file(with under score A). Wordpad reads it, first column is time (data point duration), second energy it must go to, third real energy where mono went, fourth I0 and fifth It. It is gold foil transmission data. Syed Khalid

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SSRL-data
by Khalid, Syed 04 Feb '15

04 Feb '15

How to handle SSRL, beamline 2-2 data. Attached is a binary and an ASCII file(with under score A). Wordpad reads it, first column is time (data point duration), second energy it must go to, third real energy where mono went, fourth I0 and fifth It. It is gold foil transmission data. Syed Khalid

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Exploring XANES data for getting EXAFS results
by Marcelo Alves 16 Jan '15

16 Jan '15

Hi all, I wonder if it is possible from XANES unusual data treatment to get information such as number and distances of neigbhors in the first and second shells. I think that could be very interesting for low Z elements such as P, S, Ca, K, Al, etc in diluted samples. Thanks in advance. Marcelo.

5 4

Demeter installation
by Miller, BradleyW 14 Jan '15

14 Jan '15

Hi, I'm trying to install Demeter software package on my govt. computer which is under a degree of lock down. I have full admin rights but its still not running. Here is the explanation from IT support. "it wants to install on C:\strawberry<file:///C:\strawberry> and the C: drive is locked down here and all our programs need to be installed to C:\program<file:///C:\program> files (x86) and when I tried to install there it told me that it didn't like spaces in the directory and I went ahead and install where it wanted and now program will not run due to security " Any suggestions? Thanks for your time. Respectfully, Bradley W Miller, PhD Environmental Scientist US Environmental Protection Agency National Enforcement Investigations Center Denver Federal Center, Bldg 25 Door E3 PO Box 25227 Denver, CO 80225 Office: 303-462-9150 Mobile: 863-258-7989 Fax: 303-462-9028 The great tragedy of Science-the slaying of beautiful hypothesis by an ugly fact.- Thomas H. Huxley Views or Opinions expressed in this email is solely representative of the sender and does not represents those of the EPA or any other agency.

3 2

is there any ongoing effort to integrate feff and larch?
by Angel Yanguas-Gil 03 Jan '15

03 Jan '15

So far it seems from the sphinx doc that feff cannot be called from larch. Is there any ongoing effort to implement that? The simplest way would be to create a python module to generate the corresponding feff.inp file, but I'd hate to duplicate someone else's work. Thanks! Angel

2 2

Job offer at DESY
by Edmund Welter 22 Dec '14

22 Dec '14

Dear colleagues, DESY offers a postdoc position at the new PETRA III extension EXAFS beamline P64. If you are interested in details please visit: http://www.desy.de/v2/docs/1418221001-e.pdf If you should know of a colleague who might be interested in the advertised position please feel free to forward this mail. In case you have any question please do not hesitate to contact me (preferentially not via this mail list...) Best regards, Edmund Welter

1 0

Handling large data sets in Athena (and energy dispersive calibration)
by Godfrey, Ian 19 Dec '14

19 Dec '14

Dear All, Here's an issue I recently encountered while trying to handle some very large in situ datasets in Athena; it may be by design/an inherent limitation, rather than a bug, though: (I am running Demeter 0.9.21 pre and Demeter 0.9.20 , both x64 on Windows 8.1 x64 on separate machines). Each of my datafiles contains over 300 columns of u(E) data as space delimited plain text, however when I try and import them to Athena the import window will only display checkboxes up to column 87. I've attached an example datafile and a logfile to this email. (The data is very poor, but that shouldn't be an issue for debugging...) I've also attached a copy of the datafile as it came from the beamline - this also displays the issue, so it's nothing I've done to the file. On a related note, is it possible for the energy dispersive data calibration to be added back to Athena? To get the calibration parameters for this data I had to use the (very) old version! Thanks, Ian ---- Ian Godfrey PhD Student, UCL/JAIST Programme Industrial Doctorate Centre in Molecular Modelling and Materials Science, Department of Chemistry, University College London and School of Materials Science, Japan Advanced Institute of Science and Technology i.godfrey(a)ucl.ac.uk<mailto:i.godfrey@ucl.ac.uk> i.godfrey(a)jaist.ac.jp<mailto:i.godfrey@jaist.ac.jp>

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Re: [Ifeffit] non-standard space group P 21/n
by andrea.sanson＠unipd.it 09 Dec '14

09 Dec '14

Dear Wayne, thank you very much for your enlightening answer! Best regards, Andrea Dear Andrea, To convert the atomic positions, use the following equations (starred positions are in the P21/c setting) a* = c b* = b c* = a+b To convert the unit cell,Â A* = C B* = B C* = sqrt{[Ccos(90-beta)]^2+[A-Csin(90-beta)]^2} beta* = 90 - cos-1[Ccos(90-beta)/C*] where cos-1 is the inverse cosine function If you have problems, please double check my geometry for converting the unit cell parameters. Sincerely, Wayne On Fri, Dec 5, 2014 at 9:04 AM, <andrea.sanson(a)unipd.it> wrote: Dear Gordon, thank you for your reply. I tried to use the space group P1, but the resulting local structure around the absorber atoms is completely different from that expected. Andrea HI Andrea, My suggestion, if you know where all the atoms are in the unit cell, is to use space group P1. It may be tedious and brute force in nature, but you won't have to worry about origin choices or non-standard space groups. You will still know which atoms are equivalent and can pick an appropriate one as your target atom. regards, Robert On Fri, Dec 5, 2014 at 8:07 AM, Sanson Andrea <andrea.sanson(a)unipd.it> wrote: Dear all does anyone know if is it possible to create with ATOMS the non-standard space group P 21/n ? Space group keywords are listed at the atoms website http://iffwww.iff.kfa-juelich.de/icp/atoms/atoms.sgml-7.html#ss7.4 but no keyword for P 21/n group is available. Thanks for any suggestion. Best regards, AS _______________________________________________ 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 _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- Wayne Lukens Staff Scientist Lawrence Berkeley National Lab _______________________________________________ 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] non-standard space group P 21/n
by andrea.sanson＠unipd.it 05 Dec '14

05 Dec '14

Dear Gordon, thank you for your reply. I tried to use the space group P1, but the resulting local structure around the absorber atoms is completely different from that expected. Andrea HI Andrea, My suggestion, if you know where all the atoms are in the unit cell, is to use space group P1. It may be tedious and brute force in nature, but you won't have to worry about origin choices or non-standard space groups. You will still know which atoms are equivalent and can pick an appropriate one as your target atom. regards, Robert On Fri, Dec 5, 2014 at 8:07 AM, Sanson Andrea <andrea.sanson(a)unipd.it> wrote: Dear all does anyone know if is it possible to create with ATOMS the non-standard space group P 21/n ? Space group keywords are listed at the atoms website http://iffwww.iff.kfa-juelich.de/icp/atoms/atoms.sgml-7.html#ss7.4 but no keyword for P 21/n group is available. Thanks for any suggestion. Best regards, AS _______________________________________________ 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

2 1

non-standard space group P 21/n
by Sanson Andrea 05 Dec '14

05 Dec '14

Dear all does anyone know if is it possible to create with ATOMS the non-standard space group P 21/n ? Space group keywords are listed at the atoms website http://iffwww.iff.kfa-juelich.de/icp/atoms/atoms.sgml-7.html#ss7.4 but no keyword for P 21/n group is available. Thanks for any suggestion. Best regards, AS

2 1

Re: [Ifeffit] Launching Athena on Mountain Lion (Mac OS 10.8)
by Kyler Carroll 04 Dec '14

04 Dec '14

Hello, I had posted a comment/question a few months back when I had initially installed Mountain Lion on my mac regarding iXAFS compatibility with XQuartz and the new OS not supporting X11 anymore. Since then I have received a few comments back and I found one solution to be the best. This was originally sent by Tsu-Chien Weng from SSRL (tsuchien(a)slac.stanford.edu) Please find the following solution below. Once you install XQuartz the rest will be done in the Terminal.app. This is a one time solution and I havent had any trouble thus far with the program. Hope this works as well for everyone else as it did for me. 1. Install XQuartz from <http://xquartz.macosforge.org/landing/> 2. open Terminal.app 3. cd /Applications/Utilities 4. sudo mkdir X11.app 5. cd X11.app 6. sudo ln -s ../XQuartz.app/Contents Thank you, Kyler J. Carroll, Ph.D. Assistant Project Scientist Department of NanoEngineering University of California, San Diego

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Regarding a fit for Fe(OTf)2
by pushkar shejwalkar 03 Dec '14

03 Dec '14

Dear All, I am experiencing problem during my fit for Fe(OTf)2 anhydrous. The problem is as follows. I collected the data and used a model to fit. The fitting values and other technical information is as below. The basic problem is Fe(OTf)2 in anhydrous condition is probably not cyrstalline because of which there are no crystal data available. Although .cif file is available for hexahydrate and tetra acetonitrile. But obviously it is not directly useful as I am looking for Fe(OTf)2 only. I used hexahydrate for fitting, and the fit information is given. Is this fit acceptable? *Now two questions* 1) Why do I not see any scattering or peak for Fe-S. I expected S to be a strong scatterer and would show a peak. Under given circumstances it looks like Fe is all surrounded by water and no triflate is present near Fe at all. Is this assumption even make sense (when the bottle said anhydrous) The bottle was not kept under inert condition (and its my fault), but does it mean Fe(OTf)2 is so hygroscopic and that it can actually form such hexahydrate to the full extent? OR there is some inherent problem with my fitting and collection itself. I used RBKG=1.0 2) Is anybody working on Fe(OTf)2 and had such or any other problem indicating that Fe(OTf)2 by itself is a bad choice of precursor because of its reactivity. Also any comments on purification method etc. does anybody know if crystal structure is available for Fe(OTf)2 anhydrous? I could not find it on the quick search or on CCDC. Any other site where I can get crystal data and .cif information? Thank you very much for all the help, I hope the question is asked appropriately and all the other information is provided, however, if anybody needs any other information please let me know. Thank you in an anticipation Best Pushkar Independent points : 16.1250000 Number of variables : 4 Chi-square : 7324.9401796 Reduced chi-square : 604.1187777 R-factor : 0.0195782 Measurement uncertainty (k) : 0.0001264 Measurement uncertainty (R) : 0.0004142 Number of data sets : 1 guess parameters: SO = 1.06525455 # +/- 0.05504541 [1.00000] delE = -2.32587026 # +/- 0.59606221 [-2.77870] delR = 0.00911122 # +/- 0.00503027 [-0.02322] ss = 0.00706809 # +/- 0.00071967 [0.00300] Correlations between variables: delr & dele --> 0.9154 ss & so --> 0.9023 All other correlations below 0.4 name N S02 sigma^2 e0 delr Reff R ========================================================================= O1.1 6.000 1.065 0.00707 -2.326 0.00911 2.09150 2.10061 -- Best Regards, Pushkar Shejwalkar. Post-doctoral -Researcher,JSPS Fellow Hokkaido University, Sapporo, Japan [image: Inline image 3]

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Re: [Ifeffit] A small query on constricting mean square displacement in multi-edge EXAFS refinement
by Badari Rao 03 Dec '14

03 Dec '14

Dear Scott, Thank you for the answer. Date: Wed, 3 Dec 2014 08:03:56 -0500 > From: Scott Calvin <scalvin(a)sarahlawrence.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] A small query on constricting mean square > displacement in multi-edge EXAFS refinement > Message-ID: <A7199A7A-EA1B-4396-960B-301A94F68648(a)slc.edu> > Content-Type: text/plain; charset="utf-8" > > Yes. > > The only minor adjustment I can think of to that is something called the > ?McMaster correction,? which adjusts for an oversimplification in the usual > EXAFS method of normalization, and thus can be different for the two edges. > But that correction is generally quite small, and the difference in it > between two edges is even smaller. > > ?Scott Calvin > Sarah Lawrence College > > > On Dec 3, 2014, at 7:54 AM, Badari Rao <badari.rao(a)gmail.com> wrote: > > > > Dear All, > > > > Suppose I have a compound, say AB. I have the EXAFS data from both > A-edge as well as B-edge and I am simultaneously refining these data. > > Would it be correct to force the mean square displacement of the A-B > path in both the edges to be the same? > > > > -- Regards, > > Badari Narayana. A. R. > > Ph.D Student, Nanoscience and Nanotechnology, > > c/o Prof Rajeev Ranjan, > > Electroceramics Lab, > > Department of Materials Engineering, > > Indian Institute of Science. > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

1 0

Fit a mixture
by kaziz sameh 03 Dec '14

03 Dec '14

Dear All,I look for advice or document that can help me to fit the FT EXAFS data of Pd2Au36(SR)24.The situation is as follows:In the sample there is 3 sites of the Pd ( in staples, in surface or in the core). the spectrum that I have presents a first bond of Pd_S and second bond of Pd_Au, so the palladium should be in the staples or in the surface because in core we cannot see Pd-S, but other results of the same sample confirm that the palladium is in core.I concluded that there is a mixture of some nano (x ) with Pd in staple and another nano(y) with Pd in core such y>x.Note that I fit the data with Pd2Au36(SR)24 structure in which I put the 2 palladium in the staple and I have got a good fit (attached) but I think that is not logical.If you can help me with an idea how to fit this mixture, I would be very grateful.Kaziz.

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A small query on constricting mean square displacement in multi-edge EXAFS refinement
by Badari Rao 03 Dec '14

03 Dec '14

Dear All, Suppose I have a compound, say AB. I have the EXAFS data from both A-edge as well as B-edge and I am simultaneously refining these data. Would it be correct to force the mean square displacement of the A-B path in both the edges to be the same? -- Regards, Badari Narayana. A. R. Ph.D Student, Nanoscience and Nanotechnology, c/o Prof Rajeev Ranjan, Electroceramics Lab, Department of Materials Engineering, Indian Institute of Science.

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open position at KIT
by Lichtenberg, Henning (IKFT) 02 Dec '14

02 Dec '14

Dear XAS community, we have an open position in the field of EXAFS and operando spectroscopy in our group. For further information see the attached job description. Please feel to contact us also if you are interested in a beamline scientist position or x-ray microscopy. with best regards, Henning Lichtenberg

1 0

S XANES question
by Matthew Marcus 26 Nov '14

26 Nov '14

A user on ALS 10.3.2 is taking S K-edge XANES and consistently finding a strong peak at 2484eV (calibration: gypsum white line = 2482.75eV). There's a shoulder at the nominal position of the sulfate peak. Now, peaks below sulfate I can understand, but since there's no such thing as heptavalent sulfur, what could give a peak *above* the sulfate white line? Anybody ever seen that? Yes, we checked calibration. mam

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experimental standard
by Yun Xu 18 Nov '14

18 Nov '14

Hi all I have a complex oxide BaTi8-xGaxO16. What standards I should run? Ga is the dopant. I guess I should run the sample without dopant BaTi8O16 as standard, or the simple oxide as BaO, TiO2 Ga2O3? or is the standard necessary? Also, I have colleage working on DFT, I assume the theoretical standard is the result from the DFT calculation, and by using the coordinates of the atoms, I can run FEFF and fit the data. Thanks Yun

3 3

installing Demeter on Yosemite
by Katherine M. Davis 12 Nov '14

12 Nov '14

Dear all, I was wondering whether anyone had tried installing the software on the new Mac OS (10.10 Yosemite)? Everything seems to work fine initially. I installed Macports and checked it installed correctly. At least when I test various commands, it seems to work. The sudo port install xorg-server demeter-devel command ran for about 3 hours until it quit. I tried restarting, but whenever I run the command, the following error message appears: ---> Computing dependencies for xorg-server ---> Cleaning xorg-server ---> Computing dependencies for demeter-devel ---> Configuring demeter-devel Error: org.macports.configure for port demeter-devel returned: configure failure: command execution failed Please see the log file for port demeter-devel for details: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_demeter/demeter-devel/main.log To report a bug, follow the instructions in the guide: http://guide.macports.org/#project.tickets Error: Processing of port demeter-devel failed I will post the log file at the bottom of the email. The last 8 lines are as follows: portbuild::add_automatic_buildsystem_dependencies :debug:clean No need to upgrade! p5.16-term-twiddle 2.730.0_1 >= p5.16-term-twiddle 2.730.0_1 :debug:clean epoch: in tree: 0 installed: 0 :debug:clean p5.16-text-template 1.460.0_1 exists in the ports tree :debug:clean p5.16-text-template 1.460.0_1 is the latest installed :debug:clean p5.16-text-template 1.460.0_1 is active :debug:clean Merging existing variants '' int Would anyone be able to help me with this? Any advice would be useful. Thanks for your time. Best, Kate Davis

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Re: [Ifeffit] Fwd: Re: Re: problem about negative
by Bruce Ravel 12 Nov '14

12 Nov '14

On 11/11/2014 10:19 AM, Bruce Ravel wrote: > Rbkg>1.1 can avoid the first peak,but the remaining curve is somewhat > not smooth.How to distinguish whether a long wavelength oscillation > appear as a real peak or false one?I am confused about it. > I find when I avoid the first scattering peak after white > line(kmin=4.8 maybe too large),the first peak of R space > disappeared.Because usually the first scatering peak is related to the > first coordiantion shell,can I think the first peak in R space less 1A > is a real peak instead of noiseï¼ Zhanfei, As I said yesterday, I don't know anything about your sample, so it is hard for me to know what the "right" answer is to your problem. But I can make some observations and some suggestions. * Your data range is really short. As you seem to have noticed (judging from the very short k-range in your project file), your data has serious systematic problems starting at 9 or 10 inverse Angstroms. I cannot quite tell, but your data appear to be transmission data. Well it is possible that you have some instability or nonlinearity at the beamline, I would guess that your sample is not very homogeneous. It is possible that more disciplined sample preparation might help extend that range of the interpretable data. * You are right that slightly increasing the Rbkg value seems to make a positive difference in the extracted chi(k) data. Your data seem to be an example of the sort of data I was alluding to yesterday. The background subtraction is difficult because it is difficult to distinguish the Fourier components of the background function from the Fourier components of the data. I think that the background subtraction with Rbkg=1.1 looks much better than with Rbkg=1.0, but given how different they are, you have to be concerned about the correlations between the background and the parameters of the data. It is clear that your data are of the sort for which background subtraction is difficult. So how do you know what is an acceptable background subtraction? Well, using only Fourier methods, I think we have demonstrated that you cannot know the right answer without some kind of prior knowledge. So, how do you get that prior knowledge? Well, my advice is to first solve some simpler problems. Measure your standards. Measure the common forms of moly oxide and moly sulfide. Measure moly metal. Analyze all of them. The advantage of the standards is that you know what the answer should be. Do the data processing and data analysis. Make sure that, when you do the analysis, you get the right answers. Having done that exercise, you will then have a lot more knowledge about what the various forms of moly oxide look like and what the challenges are when doing the data processing and data analysis. Some questions: - Are there any forms of moly oxide for which the bond length is as short as 1.6? If so, do the conditions of formation exist in your system? Is your sample of a valence consistent with the valence of the Mo when it has such a short bond? - If you convince yourself that it is possible for moly to have an oxygen atom at 1.6 or 1.7, what did you have to do with your standard to get a sensible analysis of the EXAFS data? Hopefully, that will guide you to doing a sensible analysis of your unknown sample. - If none of your moly oxide standards have an O atom at 1.6 or 1.7, why do you think it is chemically reasonable for your unknown sample to have such a short bond? If, in fact, that short bond doesn't exist elsewhere in nature, why would your sample magically have such a short bond? - If you do not believe in such a short bond, then does your experience with the standards give you the confidence to increase Rbkg such that the low-R signal is removed by the background function? I completely understand that you have a compelling reason to understand your unknown sample and that I am suggesting that you spend a good chunk of time measuring and analyzing a bunch of standards that are not your actual research project. That might seem like time that takes you away from your real goal, but you have already demonstrated that you are stumped by your real goal. I am saying the only way to get over your current hurdle is to take a step back and gain a deeper understanding of the data, the physics of EXAFS, the methods of EXAFS analysis, and the intricacies of your current problem. B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2 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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too small bond length in R space
by ZHAN Fei 11 Nov '14

11 Nov '14

Dear all： I encounter a problem of exafs fit in an example of Mo which have Mo-O Mo-S Mo-Mo bond.The problem is that the Mo-O peak in R space has too small bond length (less than 1.4A(+0.5A for phase correction) ).Because when 1.2>rbkg>0.68 there is little change in spectrum of R and k space,and when I increase the value of rmin of forward Fourier transform the peak changes little,so I think it's not a noise.But when I try to fit it use the 1.35A path of Mo-O,I can't fit it well. Could you give me some advise about fit too small bond length,or recommend papers of similar situation? picture of R space is attached. Thanks Sincerely, zhanfei ihep of China

3 5

Larch-0.9.24 with Python2
by Matthias Filez 05 Nov '14

05 Nov '14

Dear mailing list user, When running an example file of Larch-0.9.24 with Python2 on Ubuntu x86_64, the following error was reported. File "Py_usinglarch.py", line 32, in <module> autobk(xafsdat.energy, xafsdat.mu, rbkg=1.0, _larch=my_larch) File "/usr/local/lib/python2.7/dist-packages/larch/__init__.py", line 37, in wrapper return fcn(*args, **keywords) File "/usr/share/larch/plugins/xafs/autobk.py", line 187, in autobk fit.leastsq() File "/usr/local/lib/python2.7/dist-packages/larch/fitting/minimizer.py", line 395, in leastsq lsout = leastsq(self.__residual, self.vars, **lskws) File "/usr/local/lib/python2.7/dist-packages/larch/fitting/minimizer.py", line 222, in leastsq shape, dtype = _check_func('leastsq', 'func', func, x0, args, n) ValueError: need more than 1 value to unpack Is Larch-0.9.24 compatible with Python2 on Ubuntu x86_64? If not, what packages and dependencies could we install to make it work on Python2? Or is Larch-0.9.24 only compatible with Python3? Many thanks in advance, Matthias

3 8

Reporting the fitting data (uncertainty associated with N)
by pushkar shejwalkar 05 Nov '14

05 Nov '14

Dear All, I have seen and also been told by few professors that when you report the fitting you must report the uncertainty associated with the measurement as evaluated by the program used for the fitting. Now, When I do the fitting I typically get the +/- values for E0, delR, ss and SO2. However, the N value we always put either 1,2 or such whole integers. Is there any way to find out the uncertainty associated with the coordination number (N used in XAFS equation)? If so how to find such uncertainty? can we see this in the log file generated after the fitting is over? Thank you very much for the help Best Regards, Pushkar Shejwalkar. Post-doctoral -Researcher,JSPS Fellow Hokkaido University, Sapporo, Japan

2 2

Structure of Au2O3
by kaziz sameh 04 Nov '14

04 Nov '14

Hi all, I need the structure of Au2O3. if you can help me I would be very grateful. Kaziz

2 1

Re: [Ifeffit] inp file - artemis crashing when running feff calc on manually generated inp file
by stephen.parry＠diamond.ac.uk 03 Nov '14

03 Nov '14

The dartemis output log file -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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inp file - artemis crashing when running feff calc on manually generated inp file
by stephen.parry＠diamond.ac.uk 03 Nov '14

03 Nov '14

Can someone spot the problem with the attached inp file? I have manually reduced a cif file to remove multiple occupancy sites and cut down the unit cell from a large structure. I should be left with the first shell as Cartesian co-ords. I have then overwritten the co-ords and ipots into an old atoms generated inp file. I can't spot any formatting problems but when I run the feff calculation in artemis the program crashes. The feff.run error log file contains nothing obvious. "Feff 6L.02 TITLE Ga_c6h5f TITLE Ga TITLE S TITLE Gallium TITLE Note: mixed occ removed manually SP 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 overlapped potential and density for unique potential 0 overlapped potential and density for unique potential 1 overlapped potential and density for unique potential 2 muffin tin radii and interstitial parameters " Any help appreciated. Regards, Steve ================= Dr Stephen Parry Support Scientist, B18 Diamond Light Source Ltd. -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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Mac support for Demeter
by Bruce Ravel 28 Oct '14

28 Oct '14

Hi gang, I just heard from Frank Schima, the fellow who kindly provided packaging of Demeter via MacPorts. Frank is moving to a new position at NIST Boulder and will no longer be providing IT support for the group out there that does some XAS. That means his availability to maintain and update the MacPorts package will be somewhere between slim and non-existent. Here is what he said: I am no longer working for Quantum Devices as of Friday, 10/31/2014. So I will no longer be involved in updating Demeter and will be unsubscribing from the Ifeffit mailing list. For updates please follow the Macports procedures to request an update in Macports by opening a Trac ticket [1]. I may actually be able to perform the update but I cannot guarantee anything. [1] <https://trac.macports.org/newticket> I know that this support for the Mac was valued by many people in our community, so Frank will be missed. I am not able to provide packaging support for Mac users. Even if I had the time or energy to take on a new packaging responsibility, I simply don't own a Mac. This would be a good time for someone to step up and take over responsibility for the Mac package. It seems that Frank has done the bulk of the work. The MacPort ecosystem seems to be well supported and well documented, so I would think that someone else could readily step into that role. 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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errors importing Artemis project with quick first shell paths
by Bruce Ravel 28 Oct '14

28 Oct '14

Ian, I am starting a new thread for your email. It is only peripherally related to the problem discussed in the other thread. The main problem was two mistakes in how a quick first shell path was brought back to life when importing the project file. I'll explain, although one of the problems is rather technical. Mistake #1 is related to the option for auto-generating variables. That flag was not turned off, so the auto-generated parameters got regenerated, over writing the ones you chose. Yikes! Mistake #2 involved an assumption about the order of entries in a hash data structure while bringing the QFS path back to life. That is extremely sloppy on my part because the order of hash entries is not predictable. This was leading to the intermittent aspects of the behavior. > Dear All, > Sorry for resurrecting this old thread but I've been experiencing a > bug that produces very similar symptoms and that I guess may be > related; but that won't be solved by Bruce's fix. Details are as > follows: > Software: Demeter 0.9.18.2 and 0.9.20 x64 (possibly earlier releases > too) on Windows 8.1 x64 (I've never observed this bug on Windows > versions before 8, but I've been using Windows 8 as my main OS for a > while now so that may be coincidental) > Steps to reproduce: I run a fitting project using quick first shell > fits and save it. When I re-open the project around 80% of the time > the problem occurs. > Symptoms: When I re-open the project around 80-90% of the time one or > more of the following occurs: > - One of the quick shell paths completely loses all its information > (including path information which isn't editable by the user, > parameter info etc; see attached screenshot) I believe that I have fixed this. > - Parameter info for one or more paths is reset to the default > (i.e. if I've named a path delrauau it's renamed dr_ag_au_1) Again, I believe that I have fixed this. > - In the GDS window starting values for parameters that have a > non-zero starting value are set to their previously guessed value, > rather than the starting value I set (ie. If I set ss as 0.003 and > during the fit it is guessed to be 0.001 when I reopen the project > the starting value will be set to 0.001) and "restrain" parameters > are changed to "guess". I have examined the history of your project. At no point is a fit saved with a restraint. The GDS windows is filled correctly according to the contents of your project file. Also, the initial guesses are all entered into the GDS window with the values I see in the history. Are you saying that you have made a restraint, saved the project, then had Artemis fail to remember that you had made a restraint? > - Phase correct fitting boxes are unticked (sometimes in an > "impossible fashion" where the "plot with phase correction" option > is set but no paths have the "use path for phase corrected plotting" > option set) I don't understand how that can be a problem. The default is not to plot with phase correction. I don't save the state of that button in the project file in any case. I need to do a bit more testing, hopefully I'll make a new trial release package for your to test before the end of the day. B > Attachments: > Noinfo.png - screenshot of Artemis when path info is lost > Reset.png - screenshot of Artemis when parameter names are reset > Dartemis.log - Artemis log file when opening a project that has this problem > Artemis.fpj - Artemis project file that displays these symptoms. > Please let me know if you need further info/files. > Thanks, > Ian > Ps: > OK, things got weird while preparing this bug report: The file in > question stopped opening at all - Artemis loaded and went through > loading fit x, x+1 etc., once it finished (not exactly sure what > stage) it just closed. And then, after several attempts, started > working again, as if by magic, before I'd saved a log file.... If I > can figure out how to reproduce this I'll send more info... -- 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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Saving data as chi(E) from Athena?
by Karina Mathisen 28 Oct '14

28 Oct '14

To whom it might concern The older version of Athena had the possibility to save the data as chi(E), which is sorely missed in the newer version. Is there an easy fix for this? Best regards Karina Mathisen ------------------------------------------------------------------------------- Karina Mathisen, PhD Deputy Head for teaching, Department of Chemistry NTNU - Norwegian University of Science and Technology Associate professor Karina.Mathisen(a)ntnu.no<mailto:Karina.Mathisen@ntnu.no> +47 735 96218 Realfagbygget E2-106, Høgskoleringen 5, Trondheim, Norway --------------------------------------------------------------------------------

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Question about using a proper model
by pushkar shejwalkar 28 Oct '14

28 Oct '14

Dear All, I am new to XAFS data analysis and have very limited knowledge about using modelling structures for XAS analysis. I am not sure as to if this question is directly related to Demter or XAFS analysis as such but its a part of it for sure. * Question number one* I am trying to analyze the sample I recently collected at SPring-8 facility. The structure I am hoping to be formed during the reaction is more of a organometallic complex at silica interface. In order to establish the structure I was told that there are two methods I could use. 1) Use a counter part compound which is exact/looks like the structure I am hoping (so basically known compound) and then do traditional comparison method to establish the structure. UNFORTUNATELY I cannot synthesize such compound in lab nor such material is available in literature ( including crystal structure). 2) is to use the model. right now for modelling such structure I am using Spartan program (again I have not used it earlier in my graduate work) So I want to know as to how to generate the models in order to get the correct crystal parameters? (atoms positions?) Is spartan good enough to do job? is there any other method for doing such fitting? * Question number two* In order to get lower E0 values after the fitting, I read that there is a method to use in which delE value can be set to 0 intentionally and then recalibrating the spectra in athena again in order to accurately calibrate the E0. I read paper by Shelly kelly and Bruce Ravel. Also I have seen the steps in one of shelly kellys PDF formatted lecture, although I am still not sure about the exacts steps to take in order to do such calibration. Could someone explain me the steps in details (especially taking artemis files to athena and then using it as STD spectra for calibration purposes, I am confused about that) Thank you very much everyone in advance for your patience to go through such a long email and helping to solve my silly doubts. Your New Bee in this fantastic group Pushkar

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Setting E0 for imported data
by Scott Bechler 27 Oct '14

27 Oct '14

Hello, I am trying to compare a sample with unknown lead bonding with some lead standards. After entering in all of the data and standard scans with reference channels, I aligned the reference channels, which shifted the data scans as well. My question regards the E0 of the data and standard scans. Even though the scan itself shifted, the E0 still remains where it was when I imported it, prior to aligning the reference channels. The peak itself shifted, but the program still marks the E0 at the previous peak position. Is this an issue? If so, how do I adjust the E0 of the scans the same amount that the reference channels shifted? It does say how much the scan shifted, so I went in and manually changed the E0 of each scan so that it correlated with this shift. Would this be an effective solution? If this does solve my problem, is there a less labor-intensive way to solve it in the program? Thanks so much for your help! -Scott

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save Artemis project and cannot find Path List information when reopen
by huyanyun＠physics.utoronto.ca 26 Oct '14

26 Oct '14

Hi all, I encountered a serious problem with saving an Artermis project on my windows 8 64bit desktop. When I am ready to finish my fitting work, I click to save the log file, and go to main window to choose -File-'save project as...', and then close Artemis. But when I reopen this saved project, the Path Page lost all information for each path, and the 'Include path' button has been surprisingly unchecked for all path. The GDS page have all information there. This happened to me several times, but it seems sometime the PathPage data is saved and sometime is not, although I think I was doing the exact something. I attached one of my artemis project file and the most recent log file I saved before I close the program. Can anyone have a look and tell me what I did wrong? As my work is proceeding, this would be a very serious problem if I cannot save my 'hardwork'. Best, Yanyun ----- Attachments (links will expire on 28/02/15): 1. CoedgeforGa0.15 fitting.fpj (7.7 MB) [application/zip] Download link: https://webmail.physics.utoronto.ca/imp/attachment.php?id=53ffbffa-2424-413…

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simulating As K edge XANES using full multi scatering method
by Shaofeng Wang 24 Oct '14

24 Oct '14

Dear all, Does anyone have experience for simulating As K edge XANES using multi-scatering method or some other methods. Please introduce some papers or articles to me. Any help is appreciated. Regards, Shaofeng

2 3

Artemis closes when I try to open a project file or import data
by Kurinji Krishnamoorthy 22 Oct '14

22 Oct '14

Hi, Artemis had been working well on my laptop for a while. But today when I attempted to open a saved project file ( with a *.fpj extension), the program tried to open it for a while but then ultimately closed without any error messages. A similar thing occurred when I tried to import an Athena data file into Artemis. I was wondering if anybody had any idea how to fix this problem? Thanks, Kurinji

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Athena does not React after 2-4 steps
by Michael Kömm 22 Oct '14

22 Oct '14

Dear Bruce and dear mailing list, Athena stops working after doing a maximum of four steps (f.e. removing points, import data,...) when running on my PC with Windows 8. It either says "not responding" or just shuts down. Whenever Athena shuts down the errors in the .txt in the directory of the project differs. But it always looks like this: line 0: warning: Skipping unreadable file "C:\Users\Michael\AppData\Roaming\demeter\stash\gp_leqfnhqh" line 0: No data in plot only the file name changes. But there's never a file with that name in that directory. Sometimes there is as well a window opened that says: gnuplot.exe is not working anymore. I've deleted the Roaming\demeter folder but it didn't end the troubles. Hope there is a way to end this problem. Sincerely yours Michael Koemm PS: There is also one of my projects in the attachment.

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multiple absorber atoms
by Jesús Eduardo Vega Castillo 21 Oct '14

21 Oct '14

Hello, This is my first message to the list so I expect to do it right. I need to generate a path list for EXAFS fitting within ifeffit, based on a crystalline structure that has two different crystallographic positions for the absorber atom (edge K of Mo). Is there any way to do this? I would appreciate any information you could give me. Thanks in advance Jesus

3 3

Importing data to Athena
by Samson Vallerie Ann 20 Oct '14

20 Oct '14

Hi Bruce, I have some trouble importing data to Athena even if it's just ordinary column text file. I have attached two sample data. These are processed data from full-field XANES images. Basically I select a region in the image then write/output the total intensity of that region in a text file and I just iterate over several images. I have tried deleting out the headers, putting back the headers, padding some 0's in the energy column, checking some plugins, but to no avail. Your tips, advice is badly needed. Many thanks, Vallerie

2 1

"PCA not enabled" on Mac version of Demeter: Athena
by Ellen Daugherty 16 Oct '14

16 Oct '14

Hello XAFS community, I recently upgraded to the new version of Demeter (0.9.20) for Mac and am trying to run principal components analysis on my spectra. When I click on "Principle components analysis" from the main menu, the window shows the following message: "PCA is not enabled on this computer. The most likely reason is that the perl modules PDL and/or PDL::Stats are not available." Perhaps the solution here is simple, but I am not familiar with perl modules and do not understand the source of the issue. I could not find information about this problem in the Mail Archive, though I may have missed something. Do I need to download the PDL perl modules separately from the Demeter installation? Could there be files that are not located in the proper directory? Or perhaps PCA is simply not available for Macs? Please let me know if further information would help in solving this problem. Thank you! Ellen -- Graduate Student Research Assistant Department of Chemistry Colorado State University

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XAFS Analysis using Ifeffit
by Ke Yuan 16 Oct '14

16 Oct '14

Hello Drew, Thanks for your suggestions. I just checked my original data without normalization. The edge step is about 0.7 (see pic attached). I did the measurement in fluorescence mode at APS, beamline 12-BMB. What do you think about this pic? For the sample preparation, I think I need to mix UO2 with some other materials to dilute it. Do you have any suggestions on the matrix materials? Best, Ke

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(no subject)
by Ke Yuan 16 Oct '14

16 Oct '14

Hello Pushkar, I think the peak value of the first derivative and the zero value of the second derivative does the same thing. My sec deriv is very noisy so it's easy for my to pick the peak value of the 1st deriv instead. I would suggest you to watch the video from Bruce which explained HOW TO PICK Rbkg at: http://www.diamond.ac.uk/Beamlines/Spectroscopy/Techniques/XAS.html Click the Athena: Data processing II Actually all the other video lectures are very helpful, too! Best, Ke

1 0

iXAFS & xQuartz
by Gaspard Jean-Pierre 16 Oct '14

16 Oct '14

Hi all, On a MacBook under OS X.8.5, I downloaded iXAFS and xQuartz. I start xQuartz. When I try to start iXAFS, it requests X11 that is obviously active, I see it. However iXAFS says : "X11 is not installed". I am missing something but I do not know what. Regards JP

2 1

Ke
by Ke Yuan 16 Oct '14

16 Oct '14

Hello Sin Yuen, Thanks for forwarding me that study materials on E0. I use Athena to find the highest peak on the fist derivative of the spectra and pick that value as E0. I think I did not put E0 above this value. I will try to put it on the high energy side to see what will happen. Tks! Ke

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Ke
by Ke Yuan 15 Oct '14

15 Oct '14

Hi Bruce, Thanks for your comments! I studied Shelly's paper and found my data does looks different, especially the first peak at 1.9 A, seems it splits into two in my case. I prepared this sample by pressing UO2 powder into a hole (2mm deep), which might have significant self-absorption effect, because it's not dilute and thin. Do you think this will change the peak amplitude? Best, Ke

2 1

Possible bug in Athena during alignment
by Leon Clarke 15 Oct '14

15 Oct '14

I'd like to report a possible bug within Athena. Last week I collected Br K-edge data at the APS and have experienced an issue with Athena during data alignment. The beamline energy required calibration and so I did the following data processing steps, in this order: 1. Completed pre- and post-edge corrections, using windows relative to the actual Br K-edge energy, on the raw data exported from the beamline. (In other words these windows were not energy offsets relative to the actual measured edge position). 2. Used the flatten post-edge feature within Athena. 3. 'Calibrated' (Normalised is a better term really) the first derivative of a NaBr measurement to the Br K-edge energy using the calibrate drop-down option. This resulted in the requirement for a -17.39 eV energy offset. 4. Tried to align all of the sample data to the NaBr 'standard' using the align drop-down option. The issue I have had is with step #4. When I aligned, for several samples the XAFS (XANES) plots went wrong. It seems that Athena was not transforming the pre- and post-edge windows correctly for such a large energy shift, i.e. didn't shift these to lower energies by 17.39 eV, and I think this is a bug within Athena. I hope the above makes sense; I can provide an Athena project file, if required. Many thanks, Leon ----- Dr Leon J. Clarke Senior Lecturer in Environmental Analytical Chemistry Division of Chemistry and Environmental Sciences School of Science and the Environment Faculty of Science and Engineering Manchester Metropolitan University John Dalton East Oxford Road Manchester M1 5GD E-mail: l.clarke(a)mmu.ac.uk<mailto:l.clarke@mmu.ac.uk> WWW: http://www.sste.mmu.ac.uk/ Tel: +44 (0)161 247 1412 "Before acting on this email or opening any attachments you should read the Manchester Metropolitan University email disclaimer available on its website http://www.mmu.ac.uk/emaildisclaimer "

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Warning "e0 is greater than 10"
by Ke Yuan 15 Oct '14

15 Oct '14

Hello Feff community, I am practicing on using Artemis to fit a UO2 XAFS data I measured. The parameters I used can be found from the pic attached. The Artemis project file is also attached. I have been getting this "e0 greater than 10" warning on many of my fittings. Will picking a slightly different E0 change the result much? Any suggestions on how to improve this fitting? Thanks! Ke -- Ke Yuan PhD Candidate Department of Earth and Environmental Sciences 1100 North University Ave 3021 C.C Little University of Michigan, Ann Arbor MI 48109-1005

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Using artemis to fit EXAFS data with MD- screen message says perl interpreter has stopped working
by Gill, Simerjeet 14 Oct '14

14 Oct '14

I am trying to fit EXAFS data using MD files. I am able to load my MD file and build the histogram but when I try to transfer my ss path for MD, Artemis fails at last step. I see a message on the screen saying Perl interpreter has stopped working (attached). My artemis log file accessed using C:\Users\<username>\AppData\Roaming\Demeter\artemis.log is empty. I am using the latest version of artemis which is 0.9.20. My system is windows 7 with 32-bit operating system. To repeat what I am doing: I load my project file, then Cu.inp file, run atoms and feff, then I load my MD file, build histogram, when I drag the ss path to the path window, the program fails at last binning stage and I see error message-Perl stopped working. I tried looking into iffefit archive using key words "perl interpreter is not working" but could not find it. I will really appreciate help on this. Thanks, Simer

2 2

error message for Athena lauching on mac os 10.9.5
by emmanuelle Montarges-Pelletier 09 Oct '14

09 Oct '14

dear all Until this morning ATHENA installed through mac ports on my computer (OS 10.9.5) was working rather good. However, I have tried to open a .prj file (too large apparently) and the ATHENA-PERL software froze. I quit and tried to relaunch ATHENA, but I had the following message this morning on the terminal window: perl5.16(1177,0x7fff76dad310) malloc: *** mach_vm_map(size=18446744071562072064) failed (error code=3) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug Out of memory! Could someone tell me what I am supposed to do? Thanks a lot for your answer Best regards Emmanuelle MONTARGES-PELLETIER Chargée de Recherche CNRS LIEC Laboratoire Interdisciplinaire des Environnements Continentaux UMR 7360 CNRS Université de Lorraine 15 avenue du Charmois F-54500 Vandœuvre-lés-Nancy - France tel 33 (0)3 83 59 62 52 mob 33(0)6 31 33 10 30 Directrice de la Zone Atelier du bassin de la Moselle http://apps.ensic.inpl-nancy.fr/Zam/index_fr.html

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Possible problems with athena
by Paul Fons 08 Oct '14

08 Oct '14

Hello all, I am using the latest version of Demeter (@0.9.20pre10)on the Mac put together by Frank Schima (thank you Frank) and I noticed a problem that I thought I would pass along. This is under OS 10.9 Mavericks with the latest Xquartz (X11) installed. If one outputs a standard (in this case for Fe) file from Hephaestus and attempts to read it in as an "xmu" file in athena, the following happens. The element field is identified as Beryllium and E0 is set to 0. The data while looking fine during the input dialog looks fine. Changing the Element to Fe and specifying the K edge results and selecting a change in E0 (to tabulated value for example) results in the tabulated value popping up in the E0 box, however, plotting results in the same screen values returning Be L2 edge and a value of 0 for E0. Note the strange values for the Pre-edge range as well (12106 to 6053 eV). Fixing this is of no use either as soon as one plots, the strange values return. I have tried reading the data in as both norm(E) and xmu (it is an xmu file) to no avail. Any suggestions as to what I might try next? Cheers, Paul p.s. there are attachments demonstrating the values, but if they get dropped the text description should suffice. Dr. Paul Fons Senior Research Scientist Functional Nano-phase-change Research Team Nanoelectronics Research Institute National Institute for Advanced Industrial Science & Technology METI AIST Central 4, Higashi 1-1-1 Tsukuba, Ibaraki JAPAN 305-8568 tel. +81-298-61-5636 fax. +81-298-61-2939 email: paul-fons(a)aist.go.jp The following lines are in a Japanese font 〒305-8562 茨城県つくば市つくば中央東 1-1-1 産業技術総合研究所ナノエレクトロニクス研究部門相変化新規機能デバイス研究チーム上級主究員ポール・フォンス

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Re: [Ifeffit] Trouble creating feff input file for NaTiO3 cubic perovskite structure
by Badari Rao 08 Oct '14

08 Oct '14

Dear Dr. Bruce, I have attached the datoms.log file and the .inp file used. I am using windows platform. I hope you can get to the root of the problem with this. Regards, Badari On Tue, Sep 30, 2014 at 10:30 PM, <ifeffit-request(a)millenia.cars.aps.anl.gov > wrote: > Date: Tue, 30 Sep 2014 08:21:18 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Trouble creating feff input file for NaTiO3 > cubic perovskite structure > Message-ID: <542AA03E.8070701(a)bnl.gov> > Content-Type: text/plain; charset=windows-1252; format=flowed > > On 09/30/2014 05:45 AM, Badari Rao wrote: > > Dear All, > > When I try to feed the following data into the atoms input and run the > > feff calculations, the software just automatically closes. > > space group no: 221 > > a = b = c = 3.88; alpha = beta = gamma = 90; > > atomic coordinates: > > Na: 0.5, 0.5 , 0.5 > > Ti: 0, 0, 0 > > O: 0, 0, 0.5 > > > > Core: Ti > > > > I don't think it is a bug because the calculation works perfectly when I > > replace Na with heavier atoms like K, Mg etc. I would like to know why I > > am not able to create the feff input file using Na. > > I cannot reproduce your problem using the information you've given. > That structural data runs just fine and gives sensible output on both > Windows and linux. > > When making a bug report, you should include the information discussed > in http://bruceravel.github.io/demeter/pods/bugs.pod.html. Without the > information in the error log and without an actionable recipe for > replicating the problem, there is simply nothing that I can do to help. > > B > > > -- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2 > Building 535A > Upton NY, 11973 > > Homepage: http://bruceravel.github.io/home/ > Software: https://github.com/bruceravel > Demeter: http://bruceravel.github.io/demeter/ > -- Badari Narayana. A. R. Ph.D Student, Nanoscience and Nanotechnology, c/o Prof Rajeev Ranjan, Electroceramics Lab, Department of Materials Engineering, Indian Institute of Science.

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Update on importing Hephaestus Fe standard
by Paul Fons 07 Oct '14

07 Oct '14

Hi All, I wanted to add a quick update in that the Fe standard from Hephaestus can be imported as a mu(E) file in athena. Perhaps the file type assigned by Hephaestus is the only problem here. Cheers, Paul

1 0

fitting mixture
by kaziz sameh 06 Oct '14

06 Oct '14

hi, i want to fit Pd2Au36 in KPd edge with artemis. from the data spectrum and think there is a mixture of Pd in staple and in centre. could you help me how to do the fitting mixture.

2 1

ifeffit on Mac 10.8.5
by Gaspard Jean-Pierre 05 Oct '14

05 Oct '14

Hello, I am working on a MacBook under OS X.8.5 I downloaded iXAFS. When I try to start iXAFS, the system answers (in French): "Impossible to open because it comes from an unidentified developer." In the new OS, it is difficult to start an application that is not validated by Apple. Is there a way to start iXAFS ? Thank you for your help. Regards JP Gasaprd

3 2

problems re-opening Athena project
by Foster, Andrea 03 Oct '14

03 Oct '14

Hello all, I am an experienced EXAFS person, but not having a lot of luck using Athena. I am trying to set up an Athena project for linear combo fitting. I can get the data + model compounds imported, and I can save a project file. However, after saving and closing the file, the next time I try to open, I am asked to re-import the data from the project file (I think this is a normal part of Athena)... [image: Inline image 4] ...but when I try to select importing as chi(k) instead of u(E), I get the following message [image: Inline image 2] after "ok-ing" this message away, I can't get any farther. Importing the data as u(E) doesn't give the appropriate results. I am also attaching the aforementioned project file. thanks for any help with this, andrea ________________________________________ Andrea L. Foster, PhD U.S. Geological Survey, GMEG Science Center 345 Middlefield Rd., MS 901 Menlo Park, CA 94025 650-329-5437 (t) 650-329-5491 (f)

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Help
by johnny huertas 03 Oct '14

03 Oct '14

Good afternoon:My name is Jhonny, I work at PUC-Rio in Brazil and I'm having hard difficult to fit the ZrO2 tetragonal. I create the INP file using the follow structural data Space group: p21/ca=5.1490b=5.2070c=5.3160alpha=90beta=99.2250gamma=90Zr (0.2750; 0.03900; 0.2090)O (0.0650; 0.3260; 0.3100)O (0.4610; 0.7570; 0.4790) Several paths were created, but when I start to fit each path a message of ABORT appear saying "you have 3 variables but only 2 independent measurements in 1 data set"One more thing, each path has 1 coordination number (deg)I don't know what to do, I need some help.Thank. Jhonny Huertas Flores Rio de Janeiro-Brasil

2 1

Problems with Athena
by Austin Krehel 02 Oct '14

02 Oct '14

Dear IFEFFIT Representative, I am a graduate student and am just now learning about EXAFS data plotting. I am having a problem with opening the data that I collected last month at Bulk-XANES line X11A (NSLS). I have tried the new and old versions of Athena, and they are both not reading the .001 files, which according to my professor, should be read since this has worked for him in the past on the old version. When I try opening the files, it says they "could not be read by ifeffit as a data file". I have attached one of the .001 files, in case that may help. And help or suggestions will be greatly appreciated. Thanks. -- Austin W. Krehel Kansas State University M.Sc. Geology, Class of 2016 Ph: (810)-358-3505

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Re: [Ifeffit] Problems with Athena
by fred.mosselmans＠diamond.ac.uk 02 Oct '14

02 Oct '14

Hi Austin, Bruce Ravel could surely point out what it is , but there is probably something Athena doesn't like in your header (blank lines??) removing it and then reading the file in works fine (obviously you may want to note of the column headings ) Thanks Fred Mosselmans -----Original Message----- From: ifeffit-request(a)millenia.cars.aps.anl.gov [mailto:ifeffit-request@millenia.cars.aps.anl.gov] Sent: 02 October 2014 13:21 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 140, Issue 2 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. Problems with Athena (Austin Krehel) ---------------------------------------------------------------------- Message: 1 Date: Wed, 1 Oct 2014 21:58:34 -0500 From: Austin Krehel <awkrehel(a)gmail.com> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Problems with Athena Message-ID: <CAOgu4qpAAuzH_hTUn1n_E-MErnhYv96DqjxnzFf1jaHBLSxB2g(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Dear IFEFFIT Representative, I am a graduate student and am just now learning about EXAFS data plotting. I am having a problem with opening the data that I collected last month at Bulk-XANES line X11A (NSLS). I have tried the new and old versions of Athena, and they are both not reading the .001 files, which according to my professor, should be read since this has worked for him in the past on the old version. When I try opening the files, it says they "could not be read by ifeffit as a data file". I have attached one of the .001 files, in case that may help. And help or suggestions will be greatly appreciated. Thanks. -- Austin W. Krehel Kansas State University M.Sc. Geology, Class of 2016 Ph: (810)-358-3505

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Re: [Ifeffit] FEff (Joshua Kas)
by Joshua Kas 30 Sep '14

30 Sep '14

Hi Carlos and Matt, Matt is correct that the CFAVERAGE card averages over a variety of absorbing atoms specified within the input file, with amplitude fixed to 1. In addition, CFAVERAGE only works in FEFF8.4 and earlier, and only if you have the monolithic version (i.e., feff is a single executable, not a script that runs several executables). We intend to improve the capabilities of feff9/jfeff to include more possibilities in terms of averaging over the absorption of different sites within a feff.inp file, or averaging over multiple input files, but for now, you will have to perform the averaging yourself. Cheers, Josh Kas On Tue, Sep 30, 2014 at 10:00 AM, <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: FEff (Matt Newville) > 2. Trouble creating feff input file for NaTiO3 cubic perovskite > structure (Badari Rao) > 3. Re: Trouble creating feff input file for NaTiO3 cubic > perovskite structure (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 29 Sep 2014 12:47:57 -0500 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] FEff > Message-ID: > < > CA+7ESbqpUvDtwnjXumeqWo2DMwvw15nyUOfjPq5jnV8t5EJviw(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > On Mon, Sep 29, 2014 at 11:48 AM, Bruce Ravel <bravel(a)bnl.gov> wrote: > > > On 09/29/2014 11:44 AM, Carlos Triana Estupinan wrote: > > > >> Dear > >> Feff group > >> > >> I am Carlos Triana, and I want ask you the following. > >> I am trying to calculate the feff.inp file for a theoretical amorphous > >> structure composed by a supercell with 24 Ti atoms surrounding by 48 > >> oxygen atoms with different coordination. In amorphous materials or > >> materials with distortions from regular crystals, the absorbing atoms > >> may have different surroundings. > >> My question is how can I build the feff.inp file in this case, shall I > >> define the 24 Ti atoms like absorbing atoms, because in this case the > >> feff does not works. > >> What can I do in this case, how can I build the feff.inp file with > >> different environments > >> > >> I will be very grateful for your help > >> > > > > I'd like to follow up on Matt's comment. > > > > I presume you have some way of knowing a list of Cartesian coordinates > for > > the atoms in your cluster. If so, the discussion on pages 7-10 of this > > talk should be helpful, with the caveat that your input file needs to be > > appropriate to the version of Feff you intend to use. > > > > https://speakerdeck.com/bruceravel/modeling-non- > > crystalline-samples?slide=9 > > > > Make one input file for each Ti atom serving as the absorber. As Matt > > said, take care not to overwrite your results. > > > > Were this my problem, I would prefer to organize and perform N > > calculation, then add them up myself. That said, Feff does provide a > > simple sort of configuration average. Look up "CFAVERAGE" in the Feff > > document. > > > > B > > > > > I believe CFAVERAGE does not work as advertised. I haven't checked this > recently, but my recollection is that using CFAVERAGE always ends up giving > a coordination number that is a whole number, which cannot always be the > case. That might depend on versions of Feff, and I'd be happy to shown to > be wrong about this. > > Can anyone else verify or shed light on this? > > --Matt >

1 0

Trouble creating feff input file for NaTiO3 cubic perovskite structure
by Badari Rao 30 Sep '14

30 Sep '14

Dear All, When I try to feed the following data into the atoms input and run the feff calculations, the software just automatically closes. space group no: 221 a = b = c = 3.88; alpha = beta = gamma = 90; atomic coordinates: Na: 0.5, 0.5 , 0.5 Ti: 0, 0, 0 O: 0, 0, 0.5 Core: Ti I don't think it is a bug because the calculation works perfectly when I replace Na with heavier atoms like K, Mg etc. I would like to know why I am not able to create the feff input file using Na. -- Yours Sincerely Badari Narayana. A. R. Ph.D Student, Nanoscience and Nanotechnology, c/o Prof Rajeev Ranjan, Electroceramics Lab, Department of Materials Engineering, Indian Institute of Science.

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FEff
by Carlos Triana Estupinan 29 Sep '14

29 Sep '14

Dear Feff group I am Carlos Triana, and I want ask you the following. I am trying to calculate the feff.inp file for a theoretical amorphous structure composed by a supercell with 24 Ti atoms surrounding by 48 oxygen atoms with different coordination. In amorphous materials or materials with distortions from regular crystals, the absorbing atoms may have different surroundings. My question is how can I build the feff.inp file in this case, shall I define the 24 Ti atoms like absorbing atoms, because in this case the feff does not works. What can I do in this case, how can I build the feff.inp file with different environments I will be very grateful for your help -- *Carlos Augusto Triana Estupiñan (C.A. Triana-E) Physicist M.Sc. In Physical Sciences-Research PhD Student-Research Ångströmlaboratoriet, Lägerhyddsv. 1 Solid State physics Uppsala University, Box 534 751 21 Uppsala, Sweden Tel: +46 018 471 3144 e-mail:carlos.triana@angstrom.uu.se <e-mail%3Acarlos.triana(a)angstrom.uu.se> web:http://www.uu.se/ <http://www.uu.se/>*

4 4

Inconsistency of the amplitude reduction factor
by HOON Kim 18 Sep '14

18 Sep '14

Hello, I am a bit confused about the amplitude reduction factor (S0^2), in a sense that whether this factor must be determined by fitting or constrained by a reference value for a specific element. I'm dealing with a cathode composite (for lithium-ion battery) comprised of two crystal phases. During charge-discharge, the amplitude reduction factor changes and at a certain state of charge (SOC) it changes a lot such as from 0.77 to 0.67. My understanding is that it may reflect the phase transition of the material into the amplitude reduction factor. But, I'm not sure ... I need advice on this. Thank you ! Kind Regards,HOON

4 11

Open position in XAFS spectroscopy at MAX IV
by Katarina Norén 09 Sep '14

09 Sep '14

Hi, At the MAX IV Laboratory we are looking for a beamline scientist in XAFS spectroscopy with profile in Environmental science for the BALDER beamline at the new 3 GeV ring that will be taken in operation in 2016. Link to the position announcement: http://www.lu.se/lediga-anstallningar-available-jobs?x=0&Dnr=625478&Type=E Best regards, Katarina Norén __________________________________________________ [https://webmail.lu.se/owa/attachment.ashx?id=RgAAAABSBK%2b9jD%2fNQZCL0w%2bj…] Katarina Norén, PhD Manager Hard X-ray Group MAX IV Laboratory Lund University P.O. Box 118, SE-221 00 Lund, Sweden Visiting address: Ole Römers väg 1, 223 63 Lund Telephone +46 46 222 68 09 Mobile: +46 709 32 34 23 www.maxlab.lu.se<http://www.maxlab.lu.se/>

1 0

Cursor Issue in Athena Data Import Window
by Godfrey, Ian 05 Sep '14

05 Sep '14

Dear All, This bug report is for a very minor cosmetic issue, but I'm reporting it as it fooled me into thinking Athena had hung and doing a lot of unnecessary troubleshooting - hopefully I can save someone else from the same fate! I experienced this issue with Demeter 0.9.20 on Windows 8 x64 and Windows 7 x64. I don't recall this issue on previous versions of Demeter, but I could be wrong. The bug is as follows. When you open the Athena "Import" window (file > import data) the cursor over the data import window changes to the Windows' busy cursor indefinitely (see screenshot) when it should be the normal cursor (it doesn't impair functionality in anyway - you're still fully able to interact with the window, create plots etc.). Like I said, not a big bug but it led to me wasting a bit of time so I thought I'd report it. Regards, Ian Godfrey (UCL)

2 2

Implementing constraints in EXAFS analysis
by Badari Rao 05 Sep '14

05 Sep '14

Dear Dr. Bruce, I have collected EXAFS data on a ferroelectric perovskite Sodium Bismuth Titanate which has an average rhombohedral R3c structure and am trying to fit the data with R3c as the starting model. But I am having trouble in implementing constraints for the fit. I found a paper authored by you, titled "Local structrue and phase transitions of BaTiO3, Ferroelectrics, 1998, 206-207, pp 407-430". I want to do similar kind of analysis using Artemis on my data. However, I am finding difficulty in understanding how the constraints have been implemented for the refinement of the barium K edge EXAFS, especially those for the bond lengths (Page 416 in the above mentioned article in particular is unclear). Could you please explain how the GDS window and the variables for different paths in this case would look like. Also how do you decide what parameters to refine and what to keep fixed (table IV in the article)? Also can you please suggest some literature for beginners which can guide me in implementing such constraints? Thanking you, -- Yours Sincerely, Badari Narayana. A. R. Ph.D Student, Nanoscience and Nanotechnology, c/o Prof Rajeev Ranjan, Electroceramics Lab, Department of Materials Engineering, Indian Institute of Science.

2 1

extract backscattering amplitude and phase shift files after feff calculation
by Matthias Filez 05 Sep '14

05 Sep '14

Dear mailing list user, I would like to obtain the backscattering amplitude and phase shift files, generated during feff calculations, for photo-electron paths used during modelling. These files (containing F(k), *(k)) should be located in some directory but I really cannot find them back. I know this question has been asked before, but no conclusive answer was provided. I use Windows 7, Intel(R) Core(TM) i5-2520M CPU @ 2.5 GHz, 64-bit OS, 4 GB RAM. Currently I employ Demeter 0.9.13. Please provide me your suggestions/solutions, Many thanks in advance, Matthias Filez

2 1

Re: [Ifeffit] EXAFS calculation with large RMAX and NLEG - exceeding path finder limit
by van der Veen, Renske 04 Sep '14

04 Sep '14

Dear Bruce and Josh, Many thanks for your help! I have followed Josh's suggestion and increased the limits of the nx and npx parameters to very large values (nx=10^6, npx = 800.000 in path_tot.f90, npx = 100.000 in ff2x_tot.f90), and recompiled. The npatx parameter was set to 8 already, so I didn't change it. In addition, in order to get enough paths included in the fine structure, I had to increase the np1x parameter from 60.000 to 200.000. I am not quite sure what kind of parameter this is, but by checking the path listing in the xmu.dat file, I find that all important paths up to 8 A are included now. The fine structure looks much more like the experiment now – yay! Unfortunately there are so many paths, that a real EXAFS fitting analysis is impossible. Thanks again & best wishes, Renske -- Dr. Renske M. van der Veen Deutsches Elektronen Synchrotron (DESY) Notkestraße 85, 22607 Hamburg and Max Planck Institute for Biophysical Chemistry Am Faßberg 11, 37077 Göttingen Germany Tel (work): 0551 201 1265 Tel (mobile): 0176 315 05894 http://www.mpibpc.mpg.de/11851537/vanderveen

1 0

Re: [Ifeffit] Athena data exporting
by Bruce Ravel 03 Sep '14

03 Sep '14

On 09/03/2014 03:21 PM, Dissanayake, Amila C wrote: > Dear Bruce, > > I am Amila Dissanayake, a Ph.D intern at Pacific Northwest National Lab. > I am analyzing XAS data using Athena. But when I am trying to save a > list of data group (about 6 data group) using “ Save marked group > as..” command, all the data groups are not saving into different > columns. When I try to load this file into Origin I could find only just > two columns of data. Could you help me to sort out this problem. I am CCing my answer to the Ifeffit Mailing List, which is the appropriate place to ask questions about the software. http://cars9.uchicago.edu/mailman/listinfo/ifeffit/ You should address any follow up questions to the list. You've not offered enough information that I can even venture a guess as to what is happening. You have not told me what version of the software you are using. You've not provided an example of a project file that triggers the problem. You have not provided a recipe that would allow me to reproduce the problem on my computer. Alas, there's nothing for me to comment on. The "Save marked groups" feature works for me -- I just tried it on both the linux and Windows machines here in my office. Works fine. No one else has ever raised this problem. The one thing that occurs to me is that you may not understand what is meant by the phrase "marked groups". Have you read this page from the document? http://bruceravel.github.io/demeter/aug/ui/mark.html B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

1 0

Maghemite, hematite and magnetite XANES standards
by Javier Alonso 03 Sep '14

03 Sep '14

Dear all, Is there a place where I can download some good XANES standards for these samples? I know that this has been a problem for some time and I have found in the literature recent articles which show different XANES spectra for the "same" iron oxide, so I was wondering about this. The only one I have managed to find is hematite: http://cars9.uchicago.edu/~ravel/software/doc/Standards/fe.html Thanks in advance, Javier -- *Javier Alonso Masa* Research Associate *Basque center for materials, applications & nanostructures*

1 0

Regarding installation of demeter on Mac Mavericks system
by pushkar shejwalkar 03 Sep '14

03 Sep '14

Dear All, I am new to the mac and mac apps as well as not a techie either. I am trying to install the latest version of demeter (artemis, athena and heph) on my macbook using Mavericks OS. For this I followed the steps given on the site with Macports installation, then its activation step. and then I used terminal to connect and download the athena. However there was error which I thought might because of not having the windowing environment ( I am using all the words from site and dont know anything what it means). So I clicked to download X11 from XQuartz site. After that I logged out from terminal and logged in again. to check if anything changes but the following message was observed (the complete message is attached as word document but some part essentially the last portion talking about the error is pasted below. ---> Activating xorg-libXau @1.0.8_0 Error: org.macports.activate for port xorg-libXau returned: Image error: /opt/local/lib/libXau.6.dylib already exists and does not belong to a registered port. Unable to activate port xorg-libXau. Use 'port -f activate xorg-libXau' to force the activation. Error: Failed to install xorg-libXau Please see the log file for port xorg-libXau for details: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_x11_xorg-libXau/xorg-libXau/main.log Error: The following dependencies were not installed: quartz-wm xorg-libAppleWM xorg-libXext xorg-libX11 xorg-libXau xorg-libXdmcp xorg-libxcb python27 bzip2 db46 db_select gettext expat libiconv ncurses libedit openssl zlib python_select sqlite3 xorg-libpthread-stubs xorg-xcb-proto libxml2 xz xorg-xextproto xorg-libXinerama xorg-xineramaproto xorg-libXrandr xorg-randrproto xrender xorg-renderproto xinit mkfontdir mkfontscale freetype libpng xorg-libfontenc xauth xorg-libXmu xorg-libXt xorg-libsm xorg-libice xrdb xset xorg-libXfontcache xorg-fontcacheproto xorg-libXp xorg-printproto xorg-libXxf86misc xorg-xf86miscproto xkeyboard-config xkbcomp xorg-libxkbfile xorg-fonts font-adobe-100dpi fontconfig font-adobe-75dpi font-adobe-utopia-100dpi font-adobe-utopia-75dpi font-adobe-utopia-type1 font-alias font-arabic-misc font-bh-100dpi font-bh-75dpi font-bh-lucidatypewriter-100dpi font-bh-lucidatypewriter-75dpi font-bh-ttf font-bh-type1 font-bitstream-100dpi font-bitstream-75dpi font-bitstream-speedo font-bitstream-type1 font-cronyx-cyrillic font-cursor-misc font-daewoo-misc font-dec-misc font-ibm-type1 font-isas-misc font-jis-misc font-micro-misc font-misc-cyrillic font-misc-ethiopic font-misc-meltho font-misc-misc font-mutt-misc font-schumacher-misc font-screen-cyrillic font-sony-misc font-sun-misc font-winitzki-cyrillic font-xfree86-type1 xorg-encodings xorg-libXfixes xorg-fixesproto xorg-libXfont xorg-fontsproto To report a bug, follow the instructions in the guide: http://guide.macports.org/#project.tickets Error: Processing of port xorg-server failed Pushkar-Shejwalkars-MacBook:~ Pushkar$ Please help me installing it properly. Really very sorry for the long email but I thought it will be more helpful this way. Waiting for the replies. Thank you very much -- Best Regards, Pushkar Shejwalkar. Post-doctoral -Researcher,JSPS Fellow Hokkaido University, Sapporo, Japan

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Re: [Ifeffit] EXAFS calculation with large RMAX and NLEG - exceeding path finder limit
by Joshua Kas 02 Sep '14

02 Sep '14

Hi Renske, Unfortunately, Bruce's idea will not work for exactly the reason he guessed, i.e., that both path and genfmt have hard coded limits. Luckily, it is not so hard to recompile the code with larger dimensions. If you have access to a fortran compiler, you can just use your favorite find and replace to change the variables in question, or we can do it for you if you send us the details of your operating system. What you will want to search for is parameter (npatx = parameter (nx = parameter (npx = The first parameter (npatx) is the maximum number of atoms in a path, not including the absorbing atom at the beginning and the end, so that the maximum number of legs is npatx + 1. For 8 legs, you will need npatx=7. The second parameter (nx) is the dimension for the heap sort of the paths (maximum number of paths kept). I don't know how large this will need to be for graphite, but I have it set to 60000 in my personal version. I think by default it is set to 10000. The third parameter is the internal path finder limit and can be set quite large. I have it set to 4000000 in my personal version. You will probably want to play with the values so that you can get all the paths you want. If you find at some point that the code fails to run altogether (doesn't even start) you may have exceeded the stack limit. In linux you can set the stack limit to unlimited by running ulimit -s unlimited. Cheers, Josh On Tue, Sep 2, 2014 at 10:00 AM, <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: EXAFS calculation with large RMAX and NLEG - exceeding > path finder limit (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 02 Sep 2014 11:36:53 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] EXAFS calculation with large RMAX and NLEG - > exceeding path finder limit > Message-ID: <5405E415.4010301(a)bnl.gov> > Content-Type: text/plain; charset=windows-1252; format=flowed > > > Hi Renske, > > As you can tell from the lack of response, there is not a lot of depth > of understanding of the fine details of Feff's pathfinder out there. > My vague memory is that there is a hardwired limit of 7-legged paths > in the pathfinder and that increasing that number is tricky due to > some optimizations that were written in to the code to make it fast on > computers in the early 1990s. But that's a vague memory and could be > wrong. > > Matt and I are in the early stages of working on a version of feff 8.5 > which the folks at the Feff Project contributed under redistributable > licensing. https://github.com/xraypy/feff85exafs > > We have a lot of things we want to do, but the most important thing is > to turn genfmt from a free-standing program into a library that can be > wrapped and called from other software, thus allowing recalculation of > scattering paths as part of the fitting loop. That's cool, but not > really to the point of your question. > > I don't know how much effort you want to put into your problem, but if > you do put in the effort to change the pathfinder in Feff's source, I > hope that you'll contribute your effort to feff85exafs. > > In Artemis, I don't actually use Feff's path finder -- I wrote my own to > overcome some other limitations of the original. Unfortunately, my > implementation stops at 4-legged paths. That's not a technical limit -- > I simply stopped writing code once I got 4-legged paths working. As you > probably know, your sort of problem is something of an outlier. Not a > lot of folk work on problems that need more than 4 legs. > > It would be very nice to have a path finder written for Matt's Larch > project. In fact, it's something I am thinking of doing myself (but I > certainly don't need to!). It would be lovely to have a path finder > in Larch with the advantageous features of Artemis' implementation and > no limit of order of scattering. > > I know that wasn't exactly helpful -- just my musings on the scope of > the problem. > > To make a comment that actually is helpful, I can offer a somewhat > tedious solution that may just work. This is entirely untested -- > there could be some reason I don't know about for why it won't work. > > 1. Run the part of Feff that computes the potentials and write the > phase.bin > > 2. Using a paths.dat from a feff calculation you've already made as a > model, keep the header (everything up to and including the line of > dashes), take a "paragraph" like this: > > 11 4 12.000 index, nleg, degeneracy, r= 5.1053 > x y z ipot label rleg beta > eta > 0.000000 -1.805000 -1.805000 1 'Cu ' 2.5527 > 180.0000 0.0000 > 0.000000 0.000000 0.000000 0 'Cu ' 2.5527 > 0.0000 0.0000 > 0.000000 1.805000 1.805000 1 'Cu ' 2.5527 > 180.0000 0.0000 > 0.000000 0.000000 0.000000 0 'Cu ' 2.5527 > 0.0000 0.0000 > > and edit it to look like this: > > 9999 8 12.000 index, nleg, degeneracy, r= 10.2106 > x y z ipot label > 0.000000 -1.805000 -1.805000 1 'Cu ' > 0.000000 0.000000 0.000000 0 'Cu ' > 0.000000 1.805000 1.805000 1 'Cu ' > 0.000000 0.000000 0.000000 0 'Cu ' > 0.000000 1.805000 1.805000 1 'Cu ' > 0.000000 0.000000 0.000000 0 'Cu ' > 0.000000 1.805000 1.805000 1 'Cu ' > 0.000000 0.000000 0.000000 0 'Cu ' > > That's an 8-legged path. The lreg, beta, and eta columns are not > needed -- those were only written for the human reader, anyway. > > 3. Rename your new file with the header and this one path to > "paths.dat" (preserving the old "paths.dat", of course). > > 4. Run the last part of Feff, the part that reads phase.bin and > paths.dat and writes out the feffNNNN.dat. Doing so will make a > file called "feff9999.dat" (the first integer on the first line > of the paragraph is the NNNN number -- it can be anything from 1 > to 9999). > > I am assuming that you have a sense of which paths you want to > consider and can make these paragarphs by hand without too much > difficulty and that you can figure out what the degeneracy is supposed > to be. (in this example, I think 12 is still correct.) > > Obviously, this a lot of work. And it may be that the nleg limit is > hardwired into genfmt as well. But it's something to try. > > B > > > On 08/22/2014 09:32 AM, van der Veen, Renske wrote: > > Dear FEFF users, > > > > Using FEFF8.4, I am trying to perform EXAFS calculations with rather > > large RMAX and NLEG values. The system of interest is graphite. It has > > been shown by Castrucci et al (J. Phys. Chem. C 2009, 113, 4848?4855), > > that convergence of the EXAFS modulations in the region 4-6 A-1 is only > > achieved for a cluster size of RMAX = 8 and including up to 8-body MS > > paths (NLEG = 8). I have tried to reproduce these calculations and > > noticed that the path finder runs into a limit when I use these > > parameters. I can maximally use RMAX = 7.5 and NLEG = 5. With larger > > RMAX or NLEG values I get the message: > > > > "Internal path finder limit exceeded -- path list may be incomplete.", > > > > and the cluster size subsequently truncated at 6-6.5 A (depending on > > NLEG), instead of the desired 8 A. > > > > My path filter criteria are 3% (plane-wave) and 4% (curved-wave). > > However, these values do not affect the appearance of the above message, > > which occurs before the path filter is applied. Consequently, altering > > the 'npx' parameter, as suggested here > > > http://leonardo.phys.washington.edu/feff/wiki/static/c/o/d/Code_Variables_a… > , > > does not help. > > > > Is there a way to increase this internal path limit so I can work with > > RMAX = 8 and NLEG = 8? > > > > P.S.1 I guess graphite is a special case for which MS can be very > > efficient within the graphite planes. In addition, the C-C bond length > > is quite short, which makes higher n-body paths more important. > > P.S.2 I have tried merging XANES and EXAFS using the cards: XANES, FMS > > 6, RPATH 8 and NLEG 8, but the same problem occurs and the agreement > > with experiment in the low-k region 3-6 A-1 does not become better using > > FMS (compared to the path expansion). > > > > Thanks in advance, > > Best wishes, > > Renske > > > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > -- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2 > 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 139, Issue 5 > *************************************** >

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EXAFS calculation with large RMAX and NLEG - exceeding path finder limit
by van der Veen, Renske 02 Sep '14

02 Sep '14

Dear FEFF users, Using FEFF8.4, I am trying to perform EXAFS calculations with rather large RMAX and NLEG values. The system of interest is graphite. It has been shown by Castrucci et al (J. Phys. Chem. C 2009, 113, 4848–4855), that convergence of the EXAFS modulations in the region 4-6 A-1 is only achieved for a cluster size of RMAX = 8 and including up to 8-body MS paths (NLEG = 8). I have tried to reproduce these calculations and noticed that the path finder runs into a limit when I use these parameters. I can maximally use RMAX = 7.5 and NLEG = 5. With larger RMAX or NLEG values I get the message: "Internal path finder limit exceeded -- path list may be incomplete.", and the cluster size subsequently truncated at 6-6.5 A (depending on NLEG), instead of the desired 8 A. My path filter criteria are 3% (plane-wave) and 4% (curved-wave). However, these values do not affect the appearance of the above message, which occurs before the path filter is applied. Consequently, altering the 'npx' parameter, as suggested here http://leonardo.phys.washington.edu/feff/wiki/static/c/o/d/Code_Variables_a…, does not help. Is there a way to increase this internal path limit so I can work with RMAX = 8 and NLEG = 8? P.S.1 I guess graphite is a special case for which MS can be very efficient within the graphite planes. In addition, the C-C bond length is quite short, which makes higher n-body paths more important. P.S.2 I have tried merging XANES and EXAFS using the cards: XANES, FMS 6, RPATH 8 and NLEG 8, but the same problem occurs and the agreement with experiment in the low-k region 3-6 A-1 does not become better using FMS (compared to the path expansion). Thanks in advance, Best wishes, Renske

2 1

spline fitting
by Matthias Filez 29 Aug '14

29 Aug '14

Dear mailing list users, I am trying to fit the spline background function in a proper way to a spectrum (Ga K edge, see attached). However, it doesn't seem to work out, but I don't see why. I already tried the following: * Vary the Rbkg value * Change spline k-weight * Change k-range of spline fitting * Alter the strength of spline clamps ... and the combination of these effects. Since there is a strong white line, I suspect this causes the spline misfit. The data quality is OK. If you have any idea, please post it. Thanks in advance, Matthias _____________________ Matthias Filez Laboratory for Chemical Technology Department of Chemical Engineering Ghent University Technologiepark 914, B-9052 Zwijnaarde, Belgium +32 (0)9 33 11721 www.lct.ugent.be<http://www.lct.ugent.be/> Disclaimer: http://helpdesk.UGent.be/e-maildisclaimer.php<http://helpdesk.ugent.be/e-maildisclaimer.php>

3 2

Demeter OS X plot button colors in Athena
by Schima, Frank 27 Aug '14

27 Aug '14

Hi Bruce, We are seeing an issue in Athena where the plot buttons are not colored correctly. According to section 2.1 of the Athena Users’s Guide, the top row of plot buttons highlighted in the image should be the same color (purple) as the plotting option widgets below them. The 2nd row of plot buttons should be yellowish. However on OS X, all plot buttons appear uncolored. By far the best way to illustrate this is with a screenshot of the Athena UI. I hope the attached image is clear enough to show the issue. I am running Demeter version 0.9.20pre10 via Macports demeter-devel on OS X 10.9.4. BTW, I am happy to work with you on other OS X issues but I am not actually a demeter user and I don’t have much data myself. But if you send me some data, I can follow steps to try to reproduce issues. [cid:F140B9BC-1ABC-4ACE-B222-A833F804F78B] Cheers! Frank

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XAFS short course at Brookhaven
by Anatoly I Frenkel 26 Aug '14

26 Aug '14

Dear subscribers: An annual short course on Methods and Applications of XAFS Spectroscopy will be run at Brookhaven National Laboratory in Nov. 13-15, 2014. The application deadline is Sep. 1. The application form is available at the course web site: http://workshops.ps.bnl.gov/?w=XAFS2014 The application form should filled out first; the 45 participants accepted to the course will be later contacted with registration information. Best regards, Anatoly Anatoly Frenkel, Professor Department of Physics, Yeshiva University 245 Lexington Avenue, New York, NY 10016 https://yu.edu/faculty-bios/frenkel/ Spokesperson, Synchrotron Catalysis Consortium http://yu.edu/scc Office: (212) 340-7827, Lab: (631) 344-3013, Email: anatoly.frenkel(a)yu.edu<mailto:anatoly.frenkel@yu.edu>

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math functions on GDS page
by huyanyun＠physics.utoronto.ca 21 Aug '14

21 Aug '14

Hi there, When I input math expression in the GDS page, I wonder if Artemis recognizes some general math functions, such as 'sqrt', 'cos', 'sin'. Could anyone help me find a list of all math functions covered in Artemis? Best, Yanyun

2 1

Re: [Ifeffit] Questions for Artemis fit
by 이국승 20 Aug '14

20 Aug '14

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Re: [Ifeffit] Artemis and FEFF interaction in fit process
by Nate Turner 19 Aug '14

19 Aug '14

In an instance of Artemis, the Feff executable is run as needed to make the feffNNNN.dat files. That is, the first time you make a plot or a fit (there are a few other actions that will also trigger this), Artemis will run the Feff executable to make the path that is needed. Thus each path plotted or used in a fit requires a system call. I see, so to be clear if I run FEFF9 and make the feffNNNN.dat paths through it, outside of Artemis, then import the feffNNNN.dat files into Artemis, FEFF6L is still called to when I want to plot or use a path in a fit? Thanks for the quick response. Nate Turner

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Artemis and FEFF interaction in fit process
by Nate Turner 19 Aug '14

19 Aug '14

Hello All, I have a question about Artemis' interaction with FEFF. I know you can either run FEFF6L in Artemis to populate a paths list or externally create the FEFFnnnn.dat files in FEFF and import them into Artemis. We currently do the later using FEFF9, the use of the SCF card gives a better Eo initial guess and our compound has fractional occupancy/disorder that requires us to do some altering of the atoms list after its populated in ATOMS, which we find best to do outside of Artemis. My question is once these external FEFF9 paths are brought in does Artemis use FEFF6L in the fit process or is FEFF in Artemis only to populate the paths list? If Artemis doesn't use FEFF in the fit process then there's no issue but while I've read the mailing list and seen that many do not believe there is any improvement in the EXAFS results from FEFF6L to FEFF9, I'd rather be consistent in which version of FEFF we use throughout the analysis. I would have Artemis calling to FEFF9 instead of FEFF6L if in fact Artemis does use FEFF in the fit. The reason I haven't gone ahead with having Artemis call to FEFF9 making this a non issue is I'm not sure how. I know you can direct Artemis to whatever version of FEFF you want under preferences, but then I'm not sure what file I need to direct to specifically for FEFF9. So to summarize, Does Artemis use FEFF in the fitting process or is its only function in Artemis to create the paths for the fit? If it does use FEFF in the fitting, how do you/is it possible to have Artemis call to FEFF9 instead of FEFF6L? Thanks all for your time, Nate Turner

2 1

importing larch functionality
by Bruce Ravel 18 Aug '14

18 Aug '14

This: use_plugin_path('xafs') from feffdat import feffpath works as expected. It adds the path to larch's xafs plugins into the search path and imports "feffdat" such that it can be used in the namespace of the plugin I am working on. This fails use_plugin_path('wx') from plotter import newplot, plot with this error message: file <stdin>, line 0 ImportError: cannot import name newplot add_plugin('f85ut') What am I not understanding? newplot (and plot) seem to be exported by wx/plotter.py the same way that feffpath is exported by xafs/feffdat.py. B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

2 1

Meaning of linear combination fit reports
by Jens Kruse 18 Aug '14

18 Aug '14

Hi everyone, I doing LCF on my XANES data. I wonder if someone can tell me the meaning of the values in parentheses following the weight value in the Fit results window?. I looked into the respective document section of the Manuel but could not find the answer, yet. I am asking because I did a Fitting with over 20 standards (STD) to find all combination of max 4 standards which describe my unknown sample spectra. This results in a lot of combination with similar chi-square(reduced) and R-values. I know a relative changes between these values are more probably meaningful than absolute values. A lot of the possible combinations provided by after the fit yieled combinations with at lest on STD having a weight of 0.000. (Fit 1). I thought that this would mean, that 3 standards are sufficient to describe the system. However, repeating the fit with only the three standards with weight > 0.0 yielded a complete different proportions (Fit 2). How can this be explain and how should I deal with combinations or standards having a weight of 0.000? Thanks a lot for your thoughts and suggesting, Cheers Paul *Results **Fit 1:* 3: STD3 0.324(0.025) 7: STD7 0.686(0.021) 20: STD2O 0.127(0.016) 27: STD27 0.000(0.036) vs. *Results Fit 2:* 3: STD3 0.473(0.019) 7: STD7 0.620(0.023) 20: STD20 0.000(0.030)

3 2

Questions for Artemis fit
by 이국승 18 Aug '14

18 Aug '14

2 1

Questions for Artemis fit
by 이국승 18 Aug '14

18 Aug '14

1 0

problem of normalization of feff calculation and experimental spectrum
by ZHAN Fei 14 Aug '14

14 Aug '14

Hellow,everyone: When the energy range is too short (for instance 60 70 eV,this moment normal normalization in Athena may not be perfect),how to do the normalization of both the feff calculation and experimental spectrum?I want to let feff calculation fit the experiment , so spectrum normalization had better can be express a parameter to be fited,I'm not sure normal edge jump works,anyone have good idea about it ? Thanks, Sincerely, zhanfei

2 1

The missing feff paths
by 史乾涛 14 Aug '14

14 Aug '14

Hi, I have a problem when I used Demeter 9.18 or 9.20. The Artemis window only show parts of the calculated feff paths such as the followed figure (only 0, 4, 5, 6, 7, 10 paths of the first 10 paths were shown, and where is the other paths?). Did anyone meet this problem and how did you treat it? Many thanks! best regards, Qiantao Shi Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences

2 3

help with XAFS spectrum of NbS2
by Yuanyuan Li 09 Aug '14

09 Aug '14

Hi, We have measured some Nb doped MoS2 samples and want to compare Nb edges of these samples with standard NbS2. If someone has it and would like to share it, it would be great help to us. Thank you very much! Best, Yuanyuan Li Physics Department Yeshiva University

1 0

Re: [Ifeffit] space group P 4/mmc ?
by Bruce Ravel 08 Aug '14

08 Aug '14

On 08/08/2014 03:33 PM, Marinkovic, Nebojsa wrote: > Bruce, > I found the PtO strucutre (WJ Moore, JACS 63 (1941) 1392) reported as P > 4/m m c , but Atoms says "invalid space group". Any clues? > Thanks, > Ned > Hi Ned, I am CCing my answer to the Ifeffit Mailing List since I think this question of general interest. The author is using archaic notation, which is a common problem with crystallography references from the early decades of the 20th century. "P 4/m m c" does not exist in the modern International Tables of Crystallography. See http://en.wikipedia.org/wiki/List_of_space_groups Happily the author also gives the Schoenflies notation. "D^9_4h" is "P 42/m m c" in modern notation. The majority of the symbols Artemis recognizes are given in the Artemis Users' Guide: http://bruceravel.github.io/demeter/artug/atoms/space.html although perhaps not in the most useful manner. The wikipedia page is also useful for resolving a Schoenflies symbol to the corresponding Hermann-Maguin symbol. You can also simply use the Schoenflies symbol in Artemis. The string "D^9_4h" should be recognized by Atoms as the same as "P 42/m m c". B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2 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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Undo in Athena
by Peng Liu 01 Aug '14

01 Aug '14

Hello everyone, I have one more question about undo in Athena, e.g. I accidentally deleted one of the good spectra, how I can get it back. In word, I can go to Edit and click undo, but I haven't found it in Athena. Thanks for your time, Peng -- Ph.D. Candidate Earth and Environmental Sciences, CEIT Bldg. Rm. 2026 University of Waterloo Ph: 519-888-4567 ext. 37232 200 University Avenue West Waterloo, Ontario N2L 3G1 Fax:519-746-3882 p26liu(a)uwaterloo.ca

2 1

larch warning about epics plugin
by Johan Nilsson 01 Aug '14

01 Aug '14

Hello, Today I reinstalled larch after upgrading my computer to Ubuntu 14.04. I downloaded the latest source and installed all the recommended dependencies except PyEpics and then continued with the install. Everything went smoothly and larch appears to be working as it should. However when I start the program I get warning messages about the epics plugin $ larch Larch 0.9.23 (8-Apr-2014) M. Newville, T. Trainor using python 2.7.6, numpy 1.8.1, wx-enabled, wx version 2.8.12.1 Warning: /usr/share/larch/plugins/epics/xrfcontrol.py is not a valid plugin error: ImportError('cannot import name ROI',) Warning: /usr/share/larch/plugins/epics/xrf_detectors.py is not a valid plugin error: ImportError('cannot import name ROI',) Warning: /usr/share/larch/plugins/epics/xspress3.py is not a valid plugin error: ImportError('cannot import name ROI',) I have no plans to use this plugin but I tried to install PyEpics to see if anything would change but it did not. Is this a bug or is there some configuration I can change to get rid of the warnings? --Johan

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athena working issues on windows 8 and Ubuntu 14.04
by huyanyun＠physics.utoronto.ca 31 Jul '14

31 Jul '14

Hi All, I am writing to inquire if Demeter(athena, artemis) works on a 64-bit windows 8 system. I was trying to install Demeter 0.9.20 (downloaded from http://bruceravel.github.io/demeter/)on my 64-bit windows 8 laptop. It seems install well, at least there were no problems coming out during the installation. However, when I opened Athena, and imported data (an EXAFS data file end with .dat), there was no graphic window and no data was imported into Arthena, which stopped me proceeding. I had similar problems when I tried to install the Updater package (version 0.9.18.2) after the 0.9.13 Installer package was installed. Has anyone known if this problem was caused by the incompatibility between Demeter and Windows 8, or because I didn't install any supported package? Or how can I resolve this issue? I also tried to install the source code of demeter (version 0.9.20) following the instructions on http://bruceravel.github.io/demeter/pods/installation.pod.html. All procedures (step 1 to 4 in the section 'BUILD DEMETER AND ITS DEPENDENCIES') went smoothly on my Ubuntu 14.04. When it was done, I typed 'athena' or 'artemis' in the terminal under the demeter directory and athena or artemis were launched. But the graphic interface is still PGPLOT, rather than GNUPLOT, although I have installed GNUPLOT before I built demeter. Besides that, the data column window opened through 'open files' cannot be imported, as there is no 'OK' button in the bottom left. Also, the athena version shown is 0.8.061, rather than 0.9.20 which is the version number of demeter I built. I was really confused about these working issues, stopping me at the very beginning of data processing. I'd appreciate a lot if anyone could let me know how to solve the above problems. Does anyone else have similar issues? I look forward to hearing from you soon. All the best, Yanyun Hu PhD student in Physics, University of Toronto

3 3

Import XAFS Data from Farrel Lytle Database (http://ixs.iit.edu/database/)
by Peng Liu 30 Jul '14

30 Jul '14

Hi all, I searched the Farel Lytle Database and looked like I found chalcopyrite spectra for Cu from http://ixs.iit.edu/database/data/Farrel_Lytle_data/RAW/Cu/index.html. I downloaded the data, but I can not import into Athena. I looked into the data, it looked wired for me. The first column doesn't look like energy for Cu. I am wondering if anyone have any idea how to import or transfer the data. I attached the data file. Regards, Peng -- Ph.D. Candidate Earth and Environmental Sciences, CEIT Bldg. Rm. 2026 University of Waterloo Ph: 519-888-4567 ext. 37232 200 University Avenue West Waterloo, Ontario N2L 3G1 Fax:519-746-3882 p26liu(a)uwaterloo.ca

3 2

Quick first shell fit - Artemis
by Karin Julius 30 Jul '14

30 Jul '14

Hello, I'm trying to do a quick first shell fit with Artemis for my EXAFS measurement of 0.1 M auqeous solution of RbCl. I'm especially interested in the first hydration shell of the Rb ion. So I made an atoms input file with Rb and O in Rock salt structure. But how do I consider the Cl ion in the quick first shell fit? I don't think I can overlook the scattering on the Cl ions. Best regards, Karin

3 2

Can the degeneracy (N) in Artemis be a variable?
by Peng Liu 28 Jul '14

28 Jul '14

Hi all, When I model a standard, I know the degeneracy through the other data. But for spectra of unknown material, I would like to set degeneracy as a variable like the amplitude, deltE0, e.g.. However, I can assign a letter to N and define it. Do you have any idea how I should do it? Thanks for your reply, Peng -- Ph.D. Candidate Earth and Environmental Sciences, CEIT Bldg. Rm. 2026 University of Waterloo Ph: 519-888-4567 ext. 37232 200 University Avenue West Waterloo, Ontario N2L 3G1 Fax:519-746-3882 p26liu(a)uwaterloo.ca

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Fwd: problems by using Artemis and Demeter
by Bruce Ravel 28 Jul '14

28 Jul '14

Marika, I am responding via the Ifeffit mailing list, which is the appropriate venue for questions about the software. Please use it. It is to your significant benefit to use the mailing list as it exposes you to other people who may be able to answer your questions. This is particularly useful at a time when I am on vacation, as I was for the last several days. You did not identify the version of Artemis that you are using, although your email suggests that you are not using the most current version. I simply do not have the resources to provide support for any but the most recent version of my software. Your postscript comment is similarly ambiguous in that you did not tell me what file you were attempting to import nor what actions you took. See this page of the document: http://bruceravel.github.io/demeter/artug/startup/main.html#thefilemenu and, in particular, note the explanation of the "Import" submenu, which provides a tool for importing project files (.apj) from the very old version of Artemis. As I have discussed many times on the mailing list, .apj file import is spotty, but has imporved over time as people have reported problems in a way that is clear and actionable. Cheers, B -------- Forwarded Message -------- Subject: problems by using Artemis and Demeter Date: Thu, 24 Jul 2014 17:26:57 +0200 From: Vespa, Marika (INE) <marika.vespa(a)kit.edu> To: bravel(a)bnl.gov <bravel(a)bnl.gov> Dear Bruce, I encountered a problem that Artemis is only showing the fit results in the top of the results window: Later where a summary is usually shown it is left blank: R-factor for this data set = 0.46013 pathdegen amp sigma^2 e0 reff delta_R R ------------------------------------------------------------------------ I started a new project sequentially reading the FEFF paths and the problem appear after I have read in the fist C-path (U_oxo_carboante.prj). Would you have any idea? Best regards, Marika P.S. I have tried to use Demeter, but there I was not able to open a saved project -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

1 0

Fwd: from Rui Si at SSRF: help needed
by Bruce Ravel 18 Jul '14

18 Jul '14

Hi Rui, I am CCing my answer to you and to the Ifeffit Mailing List. It's always a good idea to use the mailing list as it greatly increases the number of eyes that get to look at your question. If you reply to this, please do so via the mailing list. In the PDF file you attached, you asked these two questions: (1) Why the second peak (ca. 3 Å) in experimental data is missing in the Co3O4 model? I do not know anything about your sample, so this is a tough question. Are you certain of its phase purity? Could there be another form of cobalt oxide present in the sample? (2) Why need to add the “shift vector” suggested by Artemis? Actually, no action is required and the software change the Co core from 0.125, 0.125, 0.125 to 0.5 0.5 0.5, and keep the shift vector as 0 0 0. The purpose of the shift vector is explained here: http://bruceravel.github.io/demeter/artug/atoms/space.html#multipleoriginsa… In the case of the CIF file you attached, the shift vecotr does not seem required. The list of atomic coordinates without the shift vecotr looks right to me. B -------- Original Message -------- Subject: from Rui Si at SSRF: help needed Date: Tue, 15 Jul 2014 07:33:31 +0000 From: 司锐 <sirui(a)sinap.ac.cn> To: bravel(a)bnl.gov <bravel(a)bnl.gov> Hi Bruce, Here, I have a question needs your help on the EXAFS fittings. When I tried to fit the Co3O4 standard (cif and apj file attached), there was a "shift vector" problem, which has been resulted in the mismatch between experimental data and theoretic model. Please see the details in the attachment. I am not familiar with crystal models, and thus I cannot find the key. Could you please help me? Many thanks! Best, Rui ---------------------------------------------------------- Dr. Rui Si Shanghai Institute of Applied Physics, Chinese Academy Sciences Shanghai Synchrotron Radiation Facility Address: 239 Zhangheng Rd, Pudong District Shanghai 201204, China E-mail: sirui(a)sinap.ac.cn Tel: (86)21-33932079 Cell:(86)13301753969

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demeter-devel: Athena autosave hang issue
by Jennifer Carter 16 Jul '14

16 Jul '14

Installed the newest version of the software for the Mac OS X earlier this week. v129-22-124-229:~ jwc137$ port installed ifeffit p5.16-ifeffit demeter-devel The following ports are currently installed: demeter-devel @0.9.20pre10_0 (active) ifeffit @1.2.11c_0+gcc48 ifeffit @1.2.13_0+gcc48 (active) p5.16-ifeffit @1.0.0_0 p5.16-ifeffit @2_0 (active) Now when I try to run athena the software hangs on an autosave file. I am unable to click either button the the pop-up menu to advance the software and I get the "application not responding" error. I searched for an athena.autosave file, as discussed in a previous thread about this issue, but don't find one. v129-22-124-229:~ jwc137$ find athena.autosave find: athena.autosave: No such file or directory Cheers Jennifer ᐧ

2 2

Re: [Ifeffit] crystallite size determination by EXAFS
by Rana, Jatinkumar Kantilal 16 Jul '14

16 Jul '14

Dear Prof. Frenkel, Many thanks for your detailed explanation about my queries. I would appreciate if you could send me the electronic copy of your article (at Jatinkumar.rana(a)helmholtz-berlin.de ): D. Glasner and A. I. Frenkel Geometrical characteristics of regular polyhedra: Application to EXAFS studies of nanoclusters AIP Conf. Proc. 882, 746-748 (2007). We may have further discussion on this topic, once I go through the suggested literature. With best regards, Jatin -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: 16 July, 2014 03:19 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 137, Issue 42 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: ATOM and GDS (Sin Yuen Chang) 2. Re: ATOM and GDS (Bruce Ravel) 3. Re: crystallite size determination by EXAFS (Anatoly I Frenkel) ---------------------------------------------------------------------- Message: 1 Date: Tue, 15 Jul 2014 17:27:50 +0000 From: Sin Yuen Chang <sinyuen.chang(a)postgrad.manchester.ac.uk> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] ATOM and GDS Message-ID: <62C8FAC78934514E930100B52B3D4A17010AC2C612(a)MBXP05.ds.man.ac.uk> Content-Type: text/plain; charset="us-ascii" Hi Dien Li, I had the same problem with ATOM in Demeter version 0.9.18 used in Windows 7, the "Add a site" icon doesn't work for me for some reasons. To add another row of atomic coordinate, what works for me is: 1. right click on any space on the table of atomic coordinate. 2. choose "Copy site" 3. right click again 4. choose "Paste site" [cid:image001.png@01CFA05A.7CE0C5C0] Hope this helps, Sin Yuen -- Sin Yuen, Chang PhD Student, School of Chemical Engineering and Analytical Science, The University of Manchester, M13 9PL Manchester. From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Dien.Li(a)srs.gov Sent: 14 July 2014 21:26 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] ATOM and GDS HI, Bruce and Matt For the Demeter version I am using, I found that I could just enter 8 atoms in ATOM, and define 12 variables in GDS. Could I enter more atoms in ATOMS, and define more variables in GDS? and How? Thanks. Dien Li, Ph.D. Environmental Sciences and Biotechnology Savannah River National Laboratory Aiken, South Carolina, 29808 Tel: 803-725-7520

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crystallite size determination by EXAFS
by Rana, Jatinkumar Kantilal 15 Jul '14

15 Jul '14

Dear all, I have some questions regarding crystallite size determination by EXAFS. I am investigating a system where there is a formation of metallic Cu in the system. I could see the presence of metallic Cu in the sample by XRD and EXAFS. However, high resolution TEM does not show any evidence of metallic Cu, perhaps the crystallite size is much smaller than the resolving power of the microscope and/or these crystallites are highly disordered. Nevertheless, I thought of estimating the size of Cu crystallites by EXAFS. I know at least two approaches described by two prominent members of the mailing list, Scott Calvin and Anatoly Frenkel. The approach by Scott Calvin (http://link.aip.org/link/JAPIAU/v94/i1/p778/s1&Agg=doi) estimates crystallite size based on an assumption that they are spherical in shape. On the other hand, Anatoly Frenkel’s approach estimates both size and shape of crystallites based on the number of neighbors in each coordination shell obtained from EXAFS fit http://pubs.acs.org/doi/abs/10.1021/jp012769j I have questions about the second approach. I would like to know how to calculate the number of neighbors in various coordination shells as a function of cluster size for different shapes ? Conversely, if one knows the number of neighbors in various shells from EXAFS fits, then how to correlate those numbers to clusters of different sizes and shapes as discussed by Anatoly Frenkel. I know my questions are very specific, but I am sure many in the list would have already tried both these approaches and may provide some valuable insights. Many thanks in advance ! With best regards, Jatin ________________________________ Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph Geschäftsführung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de

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ATOM and GDS
by Dien.Li＠srs.gov 15 Jul '14

15 Jul '14

HI, Bruce and Matt For the Demeter version I am using, I found that I could just enter 8 atoms in ATOM, and define 12 variables in GDS. Could I enter more atoms in ATOMS, and define more variables in GDS? and How? Thanks. Dien Li, Ph.D. Environmental Sciences and Biotechnology Savannah River National Laboratory Aiken, South Carolina, 29808 Tel: 803-725-7520

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Re: [Ifeffit] Ifeffit Digest, Vol 137, Issue 36
by Dien.Li＠srs.gov 15 Jul '14

15 Jul '14

Hi, Bruce With your instruction, we solved the GDS issue. However, for ATOM, I was screened out to the link you posted. Is there any way to just send me an ATOM file that has many more atom entry lines, I can use it as a template. Thanks you so much. Dien Li, Ph.D. Environmental Sciences and Biotechnology Savannah River National Laboratory Aiken, South Carolina, 29808 Tel: 803-725-7520 From: ifeffit-request(a)millenia.cars.aps.anl.gov To: ifeffit(a)millenia.cars.aps.anl.gov, Date: 07/14/2014 07:10 PM Subject: Ifeffit Digest, Vol 137, Issue 36 Sent by: ifeffit-bounces(a)millenia.cars.aps.anl.gov 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: ATOM and GDS (Bruce Ravel) 2. Re: ATOM and GDS (Carter Abney) 3. Re: Macports ifeffit and Demeter Update (Jennifer Carter) ---------------------------------------------------------------------- Message: 1 Date: Mon, 14 Jul 2014 18:28:43 -0400 From: Bruce Ravel <bravel(a)bnl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] ATOM and GDS Message-ID: <53C4599B.4090601(a)bnl.gov> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 07/14/2014 04:25 PM, Dien.Li(a)srs.gov wrote: > For the Demeter version I am using, I found that I could just enter 8 > atoms in ATOM, and define 12 variables in GDS. Could I enter more atoms > in ATOMS, and define more variables in GDS? and How? Thanks. The fact that the "add site" button on the atoms page was broken is among the things on the list of changes for the version I have been working to get tested and released. https://github.com/bruceravel/demeter/blob/master/Changes.org As for the GDS page, there are several ways of adding a new GDS entry, described here http://bruceravel.github.io/demeter/artug/gds.html On the path page, in the box which contains the math expression for a path parameter, try right clicking on GDS parameter. It'll pop up a menu that allows you to define a new parameter. It seems I neglected to put that last thing in the document -- that needs to be fixed. B -- Bruce Ravel ------------------------------------ bravel(a)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 ------------------------------ Message: 2 Date: Mon, 14 Jul 2014 22:40:12 +0000 From: Carter Abney <abneycw(a)uchicago.edu> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] ATOM and GDS Message-ID: <B4E36C4B6D5E674FB469E2B23AC64D723729B06C(a)xm-mbx-04-prod.ad.uchicago.edu> Content-Type: text/plain; charset="us-ascii" Dr Li, If I'm understanding the questions properly, there should be some fairly straightforward fixes. Simplest first: in GDS, there should be a button on the right side that says "Add GDS." Clicking on it will give you additional variables (or definitions, restraints, etc.) in GDS. Otherwise, you could right-click on the numbers to the left of the "type" column. You'll get options like "insert blank line above (or below) current row." This is convenient for keeping your variables grouped intelligently while fitting. To the best of my knowledge, there is no maximum number of lines in GDS, though your number of variables should be limited by 2/3 the number of independent points available from your data. Additionally, you're only allowed a maximum of 10 restraints at any time in a fit. Regarding Atoms, it sounds like you're trying to manually add elements to the coordination sphere of your absorbing element. There should be a button, "add a site" which will allow you to add more than 8 elements. That said, I've never prepared my scattering pathways in this fashion (this probably says more about my inexperience than anything else). Most of the time, I call Atoms from Artemis, input a cif file, run atoms, run feff, and have a list of scattering pathways afterwards. If your system isn't crystalline, you can run several Feff calculations with different cif files which have the correct absorbing atom and an appropriate scattering atom. (You have to add each of these Feff calculations in Artemis individually.) Then, use the generated scattering paths to model your data. Also, Atoms allows a person to modify the input file (I believe they're referred to as "cards") as a text document from within the Atoms program. So, if I have a model with no cif file, I can run atoms with any other cif file to generate some sort of card for feff, then I can edit the card appropriately by copy/pasting the Cartesian coordinates and defining the appropriate ipot value for each element. If you have the card already generated from another cif file, it's fairly straightforward to edit it to represent your model. - Carter Message: 2 Date: Mon, 14 Jul 2014 16:25:40 -0400 From: Dien.Li(a)srs.gov To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] ATOM and GDS Message-ID: <OF5F2EDED2.B07C6B62-ON85257D15.006FF11D-85257D15.007036E1(a)srs.gov> Content-Type: text/plain; charset="us-ascii" HI, Bruce and Matt For the Demeter version I am using, I found that I could just enter 8 atoms in ATOM, and define 12 variables in GDS. Could I enter more atoms in ATOMS, and define more variables in GDS? and How? Thanks. Dien Li, Ph.D. Environmental Sciences and Biotechnology Savannah River National Laboratory Aiken, South Carolina, 29808 Tel: 803-725-7520

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Macports ifeffit and Demeter Update
by Schima, Frank 15 Jul '14

15 Jul '14

Mac OS X users, Thanks to help from Bruce Ravel and Matt Newville, I have updated ifeffit and Demeter-devel in Macports to fix a number of problems reported. To update from your current version type the following: sudo port selfupdate sudo port upgrade outdated To install from scratch after installing Macports [1]: sudo port selfupdate sudo port install demeter-devel When done, your should see the following ports installed: $ port installed ifeffit p5.16-ifeffit demeter-devel The following ports are currently installed: demeter-devel @0.9.20pre10_0 (active) ifeffit @1.2.13_0+gcc48 (active) p5.16-ifeffit @2_0 (active) Please reply to the list (NOT to me directly) about how this works for you. Cheers! Frank [1] <https://www.macports.org/install.php>

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Re: [Ifeffit] ATOM and GDS
by Carter Abney 14 Jul '14

14 Jul '14

Dr Li, If I'm understanding the questions properly, there should be some fairly straightforward fixes. Simplest first: in GDS, there should be a button on the right side that says "Add GDS." Clicking on it will give you additional variables (or definitions, restraints, etc.) in GDS. Otherwise, you could right-click on the numbers to the left of the "type" column. You'll get options like "insert blank line above (or below) current row." This is convenient for keeping your variables grouped intelligently while fitting. To the best of my knowledge, there is no maximum number of lines in GDS, though your number of variables should be limited by 2/3 the number of independent points available from your data. Additionally, you're only allowed a maximum of 10 restraints at any time in a fit. Regarding Atoms, it sounds like you're trying to manually add elements to the coordination sphere of your absorbing element. There should be a button, "add a site" which will allow you to add more than 8 elements. That said, I've never prepared my scattering pathways in this fashion (this probably says more about my inexperience than anything else). Most of the time, I call Atoms from Artemis, input a cif file, run atoms, run feff, and have a list of scattering pathways afterwards. If your system isn't crystalline, you can run several Feff calculations with different cif files which have the correct absorbing atom and an appropriate scattering atom. (You have to add each of these Feff calculations in Artemis individually.) Then, use the generated scattering paths to model your data. Also, Atoms allows a person to modify the input file (I believe they're referred to as "cards") as a text document from within the Atoms program. So, if I have a model with no cif file, I can run atoms with any other cif file to generate some sort of card for feff, then I can edit the card appropriately by copy/pasting the Cartesian coordinates and defining the appropriate ipot value for each element. If you have the card already generated from another cif file, it's fairly straightforward to edit it to represent your model. - Carter Message: 2 Date: Mon, 14 Jul 2014 16:25:40 -0400 From: Dien.Li(a)srs.gov To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] ATOM and GDS Message-ID: <OF5F2EDED2.B07C6B62-ON85257D15.006FF11D-85257D15.007036E1(a)srs.gov> Content-Type: text/plain; charset="us-ascii" HI, Bruce and Matt For the Demeter version I am using, I found that I could just enter 8 atoms in ATOM, and define 12 variables in GDS. Could I enter more atoms in ATOMS, and define more variables in GDS? and How? Thanks. Dien Li, Ph.D. Environmental Sciences and Biotechnology Savannah River National Laboratory Aiken, South Carolina, 29808 Tel: 803-725-7520

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Energy shift in exported data
by George Sterbinsky 11 Jul '14

11 Jul '14

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. Thank you, George

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Athena/Artemis/Atoms OSX (10.9.3) issues
by Jennifer Carter 11 Jul '14

11 Jul '14

I am running into the following issues (screen shots for each are attached) *1st) starting athena from the terminal* I get the following message but the software hangs (rainbow wheel of death) and I am unable to advance to the main page "Athena found and autosave file. Would you like to import" I tried uninstalling in terminal: sudo port uninstall xorg-server demeter and reinstalling in terminal: sudo port install xorg-server demeter but the program still hangs *2nd) The screens for artemis and atoms have black backgrounds so that the text is hidden.* As a new user I am having a hard time using the software in a semi-blind mode. Thanks Jennifer ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Jennifer L.W. Carter Assistant Professor Department of Materials Science and Engineering Case Western Reserve University *500B White Building* *10900 Euclid Ave.Cleveland, OH 44106-4901phone: (216) 368-4214email: jennifer.w.carter(a)case.edu <jennifer.w.carter(a)case.edu>* [image: Inline image 3] [image: Inline image 4] ᐧ

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Re: [Ifeffit] trial release #9 for Windows for Demeter 0.9.20 (Bruce Ravel)
by Badari Rao 11 Jul '14

11 Jul '14

Dear Dr. Bruce, I am not able to download the installation file from the link provided by you. It gives some kind of "access denied" error. I don't know if this is caused by some firewall from my institute or is a genuine problem. I have attached a screenshot of the error. Could you perhaps provide another link to download the file? [image: Inline image 2] Thanking You, -- Yours Sincerely, Badari Narayana. A. R. Ph.D Student, Nanoscience and Nanotechnology, c/o Prof Rajeev Ranjan, Electroceramics Lab, Department of Materials Engineering, Indian Institute of Science.

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trial release #9 for Windows for Demeter 0.9.20
by Bruce Ravel 09 Jul '14

09 Jul '14

As I promised Badari yesterday, I have a new trial release for Demeter on Windows: 64 bit: https://s3.amazonaws.com/demeter4xas/Demeter_Installer_for_Windows_0.9.20_(… 32 bit: https://s3.amazonaws.com/demeter4xas/Demeter_Installer_for_Windows_0.9.20_(… This fixes both of the issues Badari reported. It also fixes Margaret Anne's problem with the Spec file with a really long line without needing a plugin. There are also a number of improvements to Atoms even compared to the previous trial release. An update to demeter-devel on MacPorts is not yet available, but will be soon. Those who build Demeter from source can clonw from the head of the github repository. Cheers, B -- Bruce Ravel ------------------------------------ bravel(a)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

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Demeter-devel Athena on OS 10.9.4
by Emmanuelle Montarges-Pelletier 08 Jul '14

08 Jul '14

Dear all I have just installed Demeter-devel on a computer Mac OS X 10.9.4, following the suggestions of Frank Schima and the different steps for installing xcode and command tools, macports, Xquartz. The mailing list was really helpful, thanks! After having written Athena on a terminal window I have apparently the same "freezing" phenomena reported earlier by Margaret Hinkle, July 4th 2014 " With the new demeter-devel Macports download, Athena freezes upon opening. Opening up Athena via Terminal brought up perl5.16 -- I could see the GUI, the Tip of the Day, and the Athena startup box, but the system just froze. I had to force quit every time, getting the following notice in my Terminal: 'Terminated: 15'.". I don't know how to solve this Athena blocking and completely lost when I read the solution provided by Bruce " Look for the '[athena]' section of demeter.ini, which should be in '$HOME/.horae'. Set the "tips" parameter to "false". That will suppress the tips dialog." I really tried to do on my own,...but I have to be honest, I don't know how to change the tips parameter. I would need a specific lesson, something entitled "demeter for dummies". So, could someone help me? Thanks for your answer Best Regards Emmanuelle -- ................................................. Emmanuelle Montarges-pelletier CR CNRS LIEC UMR 7360 CNRS-Université Lorraine 15 avenue du Charmois BP40 54500 Vandoeuvre les Nancy France tel 33 (0)3 83 59 62 52 fax 33 (0)3 83 59 62 55 mob 33 (0)6 31 33 10 30 emmanuelle.montarges(a)univ-lorraine.fr Zone Atelier Moselle http://www.ensic.inpl-nancy.fr/Zam/

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Possibly will join, I am from MPI- Stuttgart. EOM
by Devender 08 Jul '14

08 Jul '14

On Tue, Jul 8, 2014 at 12:54 PM, Edmund Welter <edmund.welter(a)desy.de> wrote: > Dear mail list users, > > > as you probably know the next XAFS conference (XAFS 16) will be held > from August 23rd to 28th 2015 in Karlsruhe, Germany. Around the main > conference a small number of Satellite meetings will be organised. One of > these meetings will be organised at the DESY site in Hamburg, Germany. The > title of this Satellite meetings is: “Data acquisition, treatment, storage > – quality assurance in XAFS spectroscopy“. Almost 5 years after the Q2XAFS > workshop in Tsukuba, Japan the idea behind this meeting is, to recapitulate > the developments during the last 5 years and to discuss strategies for > further improvement of XAFS data taking and XAFS data evaluation and > storage. > > First information about the meeting is summarised in the attached flyer > and on the meeting's webpage (see: > https://indico.desy.de/conferenceDisplay.py?confId=10169) The > information on the webpage will be updated and further information > especially about registration, travel and accommodation added as soon as it > becomes available. > > Please send me a mail if you have any comment, suggestions for further > session topics and/or questions! I am also interested in getting a first > impression about the possible number of participants and would therefore > appreciate if you send me (edmund.welter(a)desy.de) a short notice if you > could imagine to participate in the meeting. > > > Best regards > > Edmund Welter > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > -- Devender Graduate Student, Materials Science and Engineering Rensselaer Polytechnic Institute, Troy, NY Website <https://sites.google.com/site/devendermaun/>

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XAFS 16 Sat. Meeting announcement
by Edmund Welter 08 Jul '14

08 Jul '14

Dear mail list users, as you probably know the next XAFS conference (XAFS 16) will be held from August 23rd to 28th 2015 in Karlsruhe, Germany. Around the main conference a small number of Satellite meetings will be organised. One of these meetings will be organised at the DESY site in Hamburg, Germany. The title of this Satellite meetings is: "Data acquisition, treatment, storage -- quality assurance in XAFS spectroscopy". Almost 5 years after the Q2XAFS workshop in Tsukuba, Japan the idea behind this meeting is, to recapitulate the developments during the last 5 years and to discuss strategies for further improvement of XAFS data taking and XAFS data evaluation and storage. First information about the meeting is summarised in the attached flyer and on the meeting's webpage (see: https://indico.desy.de/conferenceDisplay.py?confId=10169) The information on the webpage will be updated and further information especially about registration, travel and accommodation added as soon as it becomes available. Please send me a mail if you have any comment, suggestions for further session topics and/or questions! I am also interested in getting a first impression about the possible number of participants and would therefore appreciate if you send me (edmund.welter(a)desy.de) a short notice if you could imagine to participate in the meeting. Best regards Edmund Welter

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Re: [Ifeffit] How to distinguish whether the coordination
by Michael Weir 07 Jul '14

07 Jul '14

Hi Matt and Zhan, I think this is the point where adding another approach would be very useful. In my limited experience, XAFS was much more powerful when combined with other techniques to eliminate potential models. We also needed to use our "chemical sense". Is there a reason you would suspect Se, Ge, Ga, or any of the other elements in your material? Could you use your beamline to look for these elements by a quick scan of one of their stronger transitions? If there is a full coordination shell, detecting the other element this way is feasible. However, as someone else mentioned recently, dopants would be much more difficult to detect. Is there another analytical technique you could use to narrow down the possible elements in your system? I hope that answering those questions helps you answer your question about the system. Also, thank you Bruce, Matt, Scott and others for the very useful discussions on this list. Michael Weir Hi Zhan, On Mon, Jul 7, 2014 at 3:40 AM, ZHAN Fei <zhanfei(a)ihep.ac.cn> wrote: > Hi Matti? > Thanks for your attention and patience. > The back fourier transform of the specific peak (use window)of Chi(R) > gives the amplitude,donated by amp_bft?As in previous mails,I ask whether > the compare the amp_bft and the amplitude of specific Z number element can > determine the Z. > Sorry, I'm not sure I understand this. I didn't understand the figure you attached in your earlier mail. Generally speaking, I find back-transformed data to be not very useful -- making any sense of these requires very well isolated shells of atoms. The amplitude of the back-transformed chi(k) (is that what you mean by amp_bft??) has many contributions, and is not simply f(k). It will have Z dependence, but it will have other dependencies too. > And thanks for telling me the useful trick using the total phase shift of > the specific element. > > > The discrepancy between R and Rphcor is below,the Zn and Br is close to > Se(the best fit)'s 0.013, > Yes, Ge actually gives the closest match, and Se the second closest match, and I left Ga out of the test. I would probably say that anything closer that 0.015 Ang (and, really, maybe 0.02 Ang) is pretty darn close. So the phase-correction approach appears to be (in this case) not as sensitive to Z as the reduced chi-square, but does provides a check on self-consistency. The fits with Zn and Rb are noticeably worse than the fit with Se... hence Z +/- 3 or perhaps 5 seems like a reasonable rule of thumb, and sometimes one might be able to do better. > should the enot also be important criterion in this trick?and dose the > plus or minus of enot indicate the lighter or higher element relative to > the specific coordination shell? > Well, an E0 shift > 10 eV probably indicating that something is off .... but that could be just the selection of E0 for the experimental data. I wouldn't put much meaning of the absolute value of E0 though for any single fit. "a bond valence sum can be an independent check on the consistency of N, > R, and valence",can your give the ref. paper of this method? Thanks > > http://en.wikipedia.org/wiki/Bond_valence_method The idea is that N, R, and valence are not independent. --Matt --

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Multiple phases in samples
by Dien.Li＠srs.gov 07 Jul '14

07 Jul '14

Hi, All "Assuming" there are multiple phases in one sample, saying, U on goethite, U on organic matter, and uraninite, how to fit the EXAFS data using Artemis? Thanks. Dien Li, Ph.D. Environmental Sciences and Biotechnology Savannah River National Laboratory Aiken, South Carolina, 29808 Tel: 803-725-7520

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Re: [Ifeffit] Bug Report: Error while handling files in Athena in the latest version, Demeter 0.9.20_pre7
by Badari Rao 07 Jul '14

07 Jul '14

Dear Chris, I am facing the same problem in both windows xp (32 bit) as well as windows 7 (64 bit) operating systems. Dear Matt, These two problems are not file specific since I have confirmed it with many files and also with different systems. (windows xp as well as windows 7). Dear Bruce, Thank you for taking note of the problem. - Badari

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Demeter-devel MacPorts Athena issues & work-around
by Margaret Hinkle 07 Jul '14

07 Jul '14

Dear OS X Users, First let me thank Frank Schima for fixing the issues with Artemis and ATOMS with his new demeter-devel Macports download -- I (and all Mac users) greatly appreciate it! I thought I would bring two issues with Macports Athena to your attention... FYI, I am using Mac OS X Mavericks v. 10.9.4, with an Intel processor. I followed the directions found here today to delete the old version of demeter and download the new one: http://www.mail-archive.com/ifeffit%40millenia.cars.aps.anl.gov/msg04404.ht… Issue 1. With the new demeter-devel Macports download, Athena freezes upon opening. Opening up Athena via Terminal brought up perl5.16 -- I could see the GUI, the Tip of the Day, and the Athena startup box, but the system just froze. I had to force quit every time, getting the following notice in my Terminal: 'Terminated: 15'. I had a feeling it was an issue with the Tip of the Day popping up, so I edited the Athena.pm file (in the UI folder), and edited line 197 from ‘$app->show_tip if Demeter->co->default('athena', 'tips');’ TO ‘$app->show_tip if Demeter->co->default('athena', 'tip');’ (honestly, I don't know enough about this code to be able to give it a real option that would turn off the Tip of the Day as the default, so I just hoped this would make the program give me general error in the GUI but that Athena could still load). Luckily, my not-fix fix worked. I get an error every time I open it, but after clicking 'OK', Athena behaves just like normal. I hope you can use this information to provide a real fix to the problem! Issue 2. I can only load data files into Athena if there are no headers of any sort -- commenting out each header line with a # or % does not work. When I try to load in a .dat file with a commented-out header, I get the following error message in Terminal: 'At line 436 of file iff_show.f Fortran runtime error: End of record' followed by Athena quitting itself. This is an issue with both the regular Macports demeter download and the demeter-devel download. These data files loaded in just fine to the old iXAFS version of Athena, and on a PC. Is there a plugin I should be using in the Demeter versions? If I delete the header, or load it in from a .prj file, everything works just fine. So it is not huge issue, as I do have a work around. Thank you, Frank, for the new version of Demeter, and thank you all for any thoughts you have on Issue 2. Best regards, Margaret Anne ------------------------------------ Margaret Anne G. Hinkle Ph.D. Candidate Earth and Planetary Sciences Washington University in St. Louis Rudolph Hall Campus Box 1169 1 Brookings Drive St. Louis, MO 63130 email: mhinkle(a)eps.wustl.edu website: aqgeochem.wustl.edu

5 11

Bug Report: Error while handling files in Athena in the latest version, Demeter 0.9.20_pre7
by Badari Rao 07 Jul '14

07 Jul '14

Dear Sir, I am facing two problems while handling files in Athena. First of all, when I freshly open Athena and import a file, it gives some kind of warning, which says can't locate Encoding/FixLatin/XS.pm in @NIC.. etc. I have attached a screenshot of the warning message. However, I could continue with my work without any problem, and importing more files did not give this warning. The second problem, which is a major one is that I am not able to use the "align data" option. Whenever I select my data and click on "align data", the software crashes and closes. kindly look into this issue. I would also like to mention that both these bugs were not present in the earlier version: Demeter 0.9.20_pre5. Thanking You, -- Yours Sincerely, Badari Narayana. A. R. Ph.D Student, Nanoscience and Nanotechnology, c/o Prof Rajeev Ranjan, Electroceramics Lab, Department of Materials Engineering, Indian Institute of Science. [image: Inline image 2]

4 3

How to distinguish whether the coordination element is heavy or light
by ZHAN Fei 07 Jul '14

07 Jul '14

Dear all, when I try to solve my question{[Ifeffit] path contribution to fit in low R-space position, but the fit bond length is much longer than that},I find a method from Prof.Calvin to distinguish whether coordination shell is composed by light or heavy element: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2007-December/007983.html A clue can perhaps be obtained by noting the relative height of the peak near 2.3 angstroms compared with the large peak you've fit. As k- weight is raised from 0 to 1 to 2 to 3, the peak at 2.3 angstroms does not grow relative to the first peak. That suggests the scattering may be from another low-Z element like oxygen. But I still don't know ,why it works. Thanks for your patience, Sincerely, zhanfei

4 8

Athena crash report
by George Sterbinsky 04 Jul '14

04 Jul '14

Hello, I am running Athena 0.9.20 on OSX 10.8.5. Selecting the difference spectra tool from the drop-down menu causes Athena to crash and the following message to print to the terminal. Usage: Wx::ComboBox::GetClientData(THIS, n) at /opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level/Demeter/UI/Athena/Difference.pm line 215, <F> line 339. I've tried this with several different projects and it appears to be general behavior. If I can provide any additional information please let me know. Thank you, George

2 1

Re: [Ifeffit] Matthew Marcus Ifeffit Digest, Vol 137, Issue 5
by Teck Kwang Choo 03 Jul '14

03 Jul '14

To: Matthew Marcus Hi Matthew, would you be able to send me the executable file and manual for PCA? My spectra files are in .dat form . Thanks and kind regards. Teck Kwang Choo PhD Candidate Department of Chemical Engineering Room 225, Building 36 Monash University Mobile No.: 04-11489904 On 3 July 2014 16:19, Teck Kwang Choo <teck.kwang.choo(a)monash.edu> wrote: > Thanks everyone for the suggestions! I will give Six pack a go first since > I have that software. If that doesn't work, I'll send another message. > > I wish you all a pleasant day. > > Teck Kwang Choo > PhD Candidate > Department of Chemical Engineering > Room 225, Building 36 > Monash University > Mobile No.: 04-11489904 > > > On 3 July 2014 01:33, <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: Principal Component Analysis (PCA) for XANES >> (fred.mosselmans(a)diamond.ac.uk) >> 2. Re: Principal Component Analysis (PCA) for XANES (Matthew Marcus) >> 3. Re: Ifeffit Digest, Vol 137, Issue 4 (Abhijeet Gaur) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Wed, 2 Jul 2014 07:48:29 +0000 >> From: <fred.mosselmans(a)diamond.ac.uk> >> To: <ifeffit(a)millenia.cars.aps.anl.gov> >> Subject: Re: [Ifeffit] Principal Component Analysis (PCA) for XANES >> Message-ID: >> < >> CF65047C5B0562499EAFF9FBBC542D64757859A1(a)EXCHMBX01.fed.cclrc.ac.uk> >> Content-Type: text/plain; charset="us-ascii" >> >> >> Dear Teck, >> >> ITFA does transformation factor analysis as well, if you just want to do >> PCA, the PCA module in Sam Webb's sixpack is quite intuitive to use. >> https://home.comcast.net/~sam_webb/sixpack.html >> >> cheers >> Fred >> >> -- >> This e-mail and any attachments may contain confidential, copyright and >> or privileged material, and are for the use of the intended addressee only. >> If you are not the intended addressee or an authorised recipient of the >> addressee please notify us of receipt by returning the e-mail and do not >> use, copy, retain, distribute or disclose the information in or attached to >> the e-mail. >> Any opinions expressed within this e-mail are those of the individual and >> not necessarily of Diamond Light Source Ltd. >> Diamond Light Source Ltd. cannot guarantee that this e-mail or any >> attachments are free from viruses and we cannot accept liability for any >> damage which you may sustain as a result of software viruses which may be >> transmitted in or with the message. >> Diamond Light Source Limited (company no. 4375679). Registered in England >> and Wales with its registered office at Diamond House, Harwell Science and >> Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom >> >> >> >> >> >> >> >> ------------------------------ >> >> Message: 2 >> Date: Wed, 02 Jul 2014 08:33:25 -0700 >> From: Matthew Marcus <mamarcus(a)lbl.gov> >> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >> Subject: Re: [Ifeffit] Principal Component Analysis (PCA) for XANES >> Message-ID: <53B42645.5040005(a)lbl.gov> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >> Athena (IFEFFIT package) does it. So does the ALS Beamline 10.3.2 >> software package at >> https://sites.google.com/a/lbl.gov/microxas-lbl-gov/software . >> If you can't get at it there, I can send the executable and manual. >> mam >> >> On 7/1/2014 10:59 PM, Teck Kwang Choo wrote: >> > Hi Everyone, >> > >> > Does anyone know what software I should use to perform a Principal >> Component Analysis (PCA) on my K-edge XANES spectra (for sulfur)? The >> reason I need to use this technique is because I have a couple of reference >> compound spectra but am not sure which of those I should use to fit my >> unknown sample spectrum. >> > >> > Any help is appreciated. >> > >> > Thanks and kind regards. >> > >> > >> > Teck Kwang Choo >> > PhD Candidate >> > Department of Chemical Engineering >> > Room 225, Building 36 >> > Monash University >> > Mobile No.: 04-11489904 >> > >> > >> > _______________________________________________ >> > Ifeffit mailing list >> > Ifeffit(a)millenia.cars.aps.anl.gov >> > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> > >> >> >> ------------------------------ >> >> Message: 3 >> Date: Wed, 2 Jul 2014 21:03:17 +0530 >> From: Abhijeet Gaur <abhijeetgaur9(a)gmail.com> >> To: ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >> Subject: Re: [Ifeffit] Ifeffit Digest, Vol 137, Issue 4 >> Message-ID: >> <CAEq27Q2UkMuFScofU8w20jO= >> 7A34MkyKkimSgy5+h+7B_NCZ-w(a)mail.gmail.com> >> Content-Type: text/plain; charset="utf-8" >> >> Hi Teck Kwang Choo, >> >> For PCA analysis you can use SixPack >> data analysis package by Dr. Sam Webb available at >> https://home.comcast.net/~sam_webb/sixpack.html. >> >> Also you can use Dmeter by Dr Bruce Ravel >> available at http://bruceravel.github.io/demeter/. >> >> With best wishes >> >> Dr Abhijeet Gaur >> >> >> >> >> On Wed, Jul 2, 2014 at 12:52 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. spam on our mailing list (Bruce Ravel) >> > 2. Re: to use scattering path in different model or to construct >> > a new model which is the combination of different simple compound >> > (Bruce Ravel) >> > 3. Principal Component Analysis (PCA) for XANES (Teck Kwang Choo) >> > 4. Re: Principal Component Analysis (PCA) for XANES >> > (Amayri, Dr. Samer) >> > >> > >> > ---------------------------------------------------------------------- >> > >> > Message: 1 >> > Date: Tue, 01 Jul 2014 13:31:59 -0400 >> > From: Bruce Ravel <bravel(a)bnl.gov> >> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >> > Subject: [Ifeffit] spam on our mailing list >> > Message-ID: <53B2F08F.7000401(a)bnl.gov> >> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> > >> > >> > Hi all, >> > >> > Over the years we've done a pretty good job of keeping spam off this >> > mailing list. As you saw, one slipped through this afternoon. Hopefully >> > it was a one-time event and it will not be necessary to change the >> > friendly nature of security on the list. >> > >> > B >> > >> > -- >> > Bruce Ravel ------------------------------------ bravel(a)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 >> > >> > >> > ------------------------------ >> > >> > Message: 2 >> > Date: Tue, 01 Jul 2014 15:16:20 -0400 >> > From: Bruce Ravel <bravel(a)bnl.gov> >> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >> > Subject: Re: [Ifeffit] to use scattering path in different model or to >> > construct a new model which is the combination of different >> simple >> > compound >> > Message-ID: <53B30904.5030207(a)bnl.gov> >> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> > >> > On 07/01/2014 10:43 AM, ZHAN Fei wrote: >> > > 1 In the example,multiplet scattering path comes from two model >> > > respectively,if use path from different model in different shell's >> > > fit,there is risk of ignore important multiple path across >> models.Should >> > > construct a cluster ,run feff to ensure? >> > >> > I don't completely understand the question, but I'll give it a try. >> > >> > In the example of Shelly's paper, she had a situation where she >> > *couldn't* write a single feff.inp file. Her local environment was the >> > average of all possible ways that the uranyl ion could bond to biomass. >> > The uranyl binding disproportionated into a pH-dependent mixture of >> > carboxyl, phosphoryl, and hydroxyl sites. There was simply no way to >> > write a feff.inp file for that. So her solution was to run Feff more >> > than once, picking and choosing paths that represented her best guess >> > for modeling the average bonding environment. >> > >> > I think what you are really getting at, though, is whether it was right >> > for Shelly to use parts of Feff calculations on a crystals to model >> > something else. If you were to read up on the theory used in Feff, you >> > would find that the important thing is that the muffin tin radii of the >> > scatterers get calculated reasonably. Unless Shelly had a reason to >> > think that the interatomic distances in her biomass sample were VERY >> > different than in the crystals she used to run Feff, then the scattering >> > amplitudes and phase shifts were almost certainly computed quite well >> > enough. >> > >> > > 2 I have confusion of the relationship pf N between single path and >> > > multiple path,for example I think U-Oe-C U-Oe-Pshould be 1 2 >> > > respectively,instead 2 4 in paper. >> > >> > I think Scott's explanation is correct. In real-space, >> > multiple-scattering theory, both ways around a three-legged path have to >> > be counted. >> > >> > B >> > >> > >> > -- >> > Bruce Ravel ------------------------------------ bravel(a)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 >> > >> > >> > ------------------------------ >> > >> > Message: 3 >> > Date: Wed, 2 Jul 2014 15:59:25 +1000 >> > From: Teck Kwang Choo <teck.kwang.choo(a)monash.edu> >> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >> > Subject: [Ifeffit] Principal Component Analysis (PCA) for XANES >> > Message-ID: >> > < >> > CAHXRQWDT2LvAsBVBuu7HmAg0oWCC9u8fKBChzDamyw14-uyJ_Q(a)mail.gmail.com> >> > Content-Type: text/plain; charset="utf-8" >> > >> > Hi Everyone, >> > >> > Does anyone know what software I should use to perform a Principal >> > Component Analysis (PCA) on my K-edge XANES spectra (for sulfur)? The >> > reason I need to use this technique is because I have a couple of >> reference >> > compound spectra but am not sure which of those I should use to fit my >> > unknown sample spectrum. >> > >> > Any help is appreciated. >> > >> > Thanks and kind regards. >> > >> > >> > Teck Kwang Choo >> > PhD Candidate >> > Department of Chemical Engineering >> > Room 225, Building 36 >> > Monash University >> > Mobile No.: 04-11489904 >> >

1 0

Re: [Ifeffit] Ifeffit Digest, Vol 137, Issue 5
by Teck Kwang Choo 03 Jul '14

03 Jul '14

Thanks everyone for the suggestions! I will give Six pack a go first since I have that software. If that doesn't work, I'll send another message. I wish you all a pleasant day. Teck Kwang Choo PhD Candidate Department of Chemical Engineering Room 225, Building 36 Monash University Mobile No.: 04-11489904 On 3 July 2014 01:33, <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: Principal Component Analysis (PCA) for XANES > (fred.mosselmans(a)diamond.ac.uk) > 2. Re: Principal Component Analysis (PCA) for XANES (Matthew Marcus) > 3. Re: Ifeffit Digest, Vol 137, Issue 4 (Abhijeet Gaur) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 2 Jul 2014 07:48:29 +0000 > From: <fred.mosselmans(a)diamond.ac.uk> > To: <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Principal Component Analysis (PCA) for XANES > Message-ID: > < > CF65047C5B0562499EAFF9FBBC542D64757859A1(a)EXCHMBX01.fed.cclrc.ac.uk> > Content-Type: text/plain; charset="us-ascii" > > > Dear Teck, > > ITFA does transformation factor analysis as well, if you just want to do > PCA, the PCA module in Sam Webb's sixpack is quite intuitive to use. > https://home.comcast.net/~sam_webb/sixpack.html > > cheers > Fred > > -- > This e-mail and any attachments may contain confidential, copyright and or > privileged material, and are for the use of the intended addressee only. If > you are not the intended addressee or an authorised recipient of the > addressee please notify us of receipt by returning the e-mail and do not > use, copy, retain, distribute or disclose the information in or attached to > the e-mail. > Any opinions expressed within this e-mail are those of the individual and > not necessarily of Diamond Light Source Ltd. > Diamond Light Source Ltd. cannot guarantee that this e-mail or any > attachments are free from viruses and we cannot accept liability for any > damage which you may sustain as a result of software viruses which may be > transmitted in or with the message. > Diamond Light Source Limited (company no. 4375679). Registered in England > and Wales with its registered office at Diamond House, Harwell Science and > Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom > > > > > > > > ------------------------------ > > Message: 2 > Date: Wed, 02 Jul 2014 08:33:25 -0700 > From: Matthew Marcus <mamarcus(a)lbl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Principal Component Analysis (PCA) for XANES > Message-ID: <53B42645.5040005(a)lbl.gov> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Athena (IFEFFIT package) does it. So does the ALS Beamline 10.3.2 > software package at > https://sites.google.com/a/lbl.gov/microxas-lbl-gov/software . > If you can't get at it there, I can send the executable and manual. > mam > > On 7/1/2014 10:59 PM, Teck Kwang Choo wrote: > > Hi Everyone, > > > > Does anyone know what software I should use to perform a Principal > Component Analysis (PCA) on my K-edge XANES spectra (for sulfur)? The > reason I need to use this technique is because I have a couple of reference > compound spectra but am not sure which of those I should use to fit my > unknown sample spectrum. > > > > Any help is appreciated. > > > > Thanks and kind regards. > > > > > > Teck Kwang Choo > > PhD Candidate > > Department of Chemical Engineering > > Room 225, Building 36 > > Monash University > > Mobile No.: 04-11489904 > > > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > ------------------------------ > > Message: 3 > Date: Wed, 2 Jul 2014 21:03:17 +0530 > From: Abhijeet Gaur <abhijeetgaur9(a)gmail.com> > To: ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Ifeffit Digest, Vol 137, Issue 4 > Message-ID: > <CAEq27Q2UkMuFScofU8w20jO= > 7A34MkyKkimSgy5+h+7B_NCZ-w(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Teck Kwang Choo, > > For PCA analysis you can use SixPack > data analysis package by Dr. Sam Webb available at > https://home.comcast.net/~sam_webb/sixpack.html. > > Also you can use Dmeter by Dr Bruce Ravel > available at http://bruceravel.github.io/demeter/. > > With best wishes > > Dr Abhijeet Gaur > > > > > On Wed, Jul 2, 2014 at 12:52 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. spam on our mailing list (Bruce Ravel) > > 2. Re: to use scattering path in different model or to construct > > a new model which is the combination of different simple compound > > (Bruce Ravel) > > 3. Principal Component Analysis (PCA) for XANES (Teck Kwang Choo) > > 4. Re: Principal Component Analysis (PCA) for XANES > > (Amayri, Dr. Samer) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Tue, 01 Jul 2014 13:31:59 -0400 > > From: Bruce Ravel <bravel(a)bnl.gov> > > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > > Subject: [Ifeffit] spam on our mailing list > > Message-ID: <53B2F08F.7000401(a)bnl.gov> > > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > > > Hi all, > > > > Over the years we've done a pretty good job of keeping spam off this > > mailing list. As you saw, one slipped through this afternoon. Hopefully > > it was a one-time event and it will not be necessary to change the > > friendly nature of security on the list. > > > > B > > > > -- > > Bruce Ravel ------------------------------------ bravel(a)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 > > > > > > ------------------------------ > > > > Message: 2 > > Date: Tue, 01 Jul 2014 15:16:20 -0400 > > From: Bruce Ravel <bravel(a)bnl.gov> > > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > > Subject: Re: [Ifeffit] to use scattering path in different model or to > > construct a new model which is the combination of different > simple > > compound > > Message-ID: <53B30904.5030207(a)bnl.gov> > > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > On 07/01/2014 10:43 AM, ZHAN Fei wrote: > > > 1 In the example,multiplet scattering path comes from two model > > > respectively,if use path from different model in different shell's > > > fit,there is risk of ignore important multiple path across > models.Should > > > construct a cluster ,run feff to ensure? > > > > I don't completely understand the question, but I'll give it a try. > > > > In the example of Shelly's paper, she had a situation where she > > *couldn't* write a single feff.inp file. Her local environment was the > > average of all possible ways that the uranyl ion could bond to biomass. > > The uranyl binding disproportionated into a pH-dependent mixture of > > carboxyl, phosphoryl, and hydroxyl sites. There was simply no way to > > write a feff.inp file for that. So her solution was to run Feff more > > than once, picking and choosing paths that represented her best guess > > for modeling the average bonding environment. > > > > I think what you are really getting at, though, is whether it was right > > for Shelly to use parts of Feff calculations on a crystals to model > > something else. If you were to read up on the theory used in Feff, you > > would find that the important thing is that the muffin tin radii of the > > scatterers get calculated reasonably. Unless Shelly had a reason to > > think that the interatomic distances in her biomass sample were VERY > > different than in the crystals she used to run Feff, then the scattering > > amplitudes and phase shifts were almost certainly computed quite well > > enough. > > > > > 2 I have confusion of the relationship pf N between single path and > > > multiple path,for example I think U-Oe-C U-Oe-Pshould be 1 2 > > > respectively,instead 2 4 in paper. > > > > I think Scott's explanation is correct. In real-space, > > multiple-scattering theory, both ways around a three-legged path have to > > be counted. > > > > B > > > > > > -- > > Bruce Ravel ------------------------------------ bravel(a)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 > > > > > > ------------------------------ > > > > Message: 3 > > Date: Wed, 2 Jul 2014 15:59:25 +1000 > > From: Teck Kwang Choo <teck.kwang.choo(a)monash.edu> > > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > > Subject: [Ifeffit] Principal Component Analysis (PCA) for XANES > > Message-ID: > > < > > CAHXRQWDT2LvAsBVBuu7HmAg0oWCC9u8fKBChzDamyw14-uyJ_Q(a)mail.gmail.com> > > Content-Type: text/plain; charset="utf-8" > > > > Hi Everyone, > > > > Does anyone know what software I should use to perform a Principal > > Component Analysis (PCA) on my K-edge XANES spectra (for sulfur)? The > > reason I need to use this technique is because I have a couple of > reference > > compound spectra but am not sure which of those I should use to fit my > > unknown sample spectrum. > > > > Any help is appreciated. > > > > Thanks and kind regards. > > > > > > Teck Kwang Choo > > PhD Candidate > > Department of Chemical Engineering > > Room 225, Building 36 > > Monash University > > Mobile No.: 04-11489904 > >

1 0

Principal Component Analysis (PCA) for XANES
by Teck Kwang Choo 02 Jul '14

02 Jul '14

Hi Everyone, Does anyone know what software I should use to perform a Principal Component Analysis (PCA) on my K-edge XANES spectra (for sulfur)? The reason I need to use this technique is because I have a couple of reference compound spectra but am not sure which of those I should use to fit my unknown sample spectrum. Any help is appreciated. Thanks and kind regards. Teck Kwang Choo PhD Candidate Department of Chemical Engineering Room 225, Building 36 Monash University Mobile No.: 04-11489904

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Re: [Ifeffit] Ifeffit Digest, Vol 137, Issue 4
by Abhijeet Gaur 02 Jul '14

02 Jul '14

Hi Teck Kwang Choo, For PCA analysis you can use SixPack data analysis package by Dr. Sam Webb available at https://home.comcast.net/~sam_webb/sixpack.html. Also you can use Dmeter by Dr Bruce Ravel available at http://bruceravel.github.io/demeter/. With best wishes Dr Abhijeet Gaur On Wed, Jul 2, 2014 at 12:52 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. spam on our mailing list (Bruce Ravel) > 2. Re: to use scattering path in different model or to construct > a new model which is the combination of different simple compound > (Bruce Ravel) > 3. Principal Component Analysis (PCA) for XANES (Teck Kwang Choo) > 4. Re: Principal Component Analysis (PCA) for XANES > (Amayri, Dr. Samer) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 01 Jul 2014 13:31:59 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] spam on our mailing list > Message-ID: <53B2F08F.7000401(a)bnl.gov> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > Hi all, > > Over the years we've done a pretty good job of keeping spam off this > mailing list. As you saw, one slipped through this afternoon. Hopefully > it was a one-time event and it will not be necessary to change the > friendly nature of security on the list. > > B > > -- > Bruce Ravel ------------------------------------ bravel(a)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 > > > ------------------------------ > > Message: 2 > Date: Tue, 01 Jul 2014 15:16:20 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] to use scattering path in different model or to > construct a new model which is the combination of different simple > compound > Message-ID: <53B30904.5030207(a)bnl.gov> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > On 07/01/2014 10:43 AM, ZHAN Fei wrote: > > 1 In the example,multiplet scattering path comes from two model > > respectively,if use path from different model in different shell's > > fit,there is risk of ignore important multiple path across models.Should > > construct a cluster ,run feff to ensure? > > I don't completely understand the question, but I'll give it a try. > > In the example of Shelly's paper, she had a situation where she > *couldn't* write a single feff.inp file. Her local environment was the > average of all possible ways that the uranyl ion could bond to biomass. > The uranyl binding disproportionated into a pH-dependent mixture of > carboxyl, phosphoryl, and hydroxyl sites. There was simply no way to > write a feff.inp file for that. So her solution was to run Feff more > than once, picking and choosing paths that represented her best guess > for modeling the average bonding environment. > > I think what you are really getting at, though, is whether it was right > for Shelly to use parts of Feff calculations on a crystals to model > something else. If you were to read up on the theory used in Feff, you > would find that the important thing is that the muffin tin radii of the > scatterers get calculated reasonably. Unless Shelly had a reason to > think that the interatomic distances in her biomass sample were VERY > different than in the crystals she used to run Feff, then the scattering > amplitudes and phase shifts were almost certainly computed quite well > enough. > > > 2 I have confusion of the relationship pf N between single path and > > multiple path,for example I think U-Oe-C U-Oe-Pshould be 1 2 > > respectively,instead 2 4 in paper. > > I think Scott's explanation is correct. In real-space, > multiple-scattering theory, both ways around a three-legged path have to > be counted. > > B > > > -- > Bruce Ravel ------------------------------------ bravel(a)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 > > > ------------------------------ > > Message: 3 > Date: Wed, 2 Jul 2014 15:59:25 +1000 > From: Teck Kwang Choo <teck.kwang.choo(a)monash.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] Principal Component Analysis (PCA) for XANES > Message-ID: > < > CAHXRQWDT2LvAsBVBuu7HmAg0oWCC9u8fKBChzDamyw14-uyJ_Q(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Everyone, > > Does anyone know what software I should use to perform a Principal > Component Analysis (PCA) on my K-edge XANES spectra (for sulfur)? The > reason I need to use this technique is because I have a couple of reference > compound spectra but am not sure which of those I should use to fit my > unknown sample spectrum. > > Any help is appreciated. > > Thanks and kind regards. > > > Teck Kwang Choo > PhD Candidate > Department of Chemical Engineering > Room 225, Building 36 > Monash University > Mobile No.: 04-11489904 >

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Re: [Ifeffit] Principal Component Analysis (PCA) for XANES
by fred.mosselmans＠diamond.ac.uk 02 Jul '14

02 Jul '14

Dear Teck, ITFA does transformation factor analysis as well, if you just want to do PCA, the PCA module in Sam Webb's sixpack is quite intuitive to use. https://home.comcast.net/~sam_webb/sixpack.html cheers Fred -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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to use scattering path in different model or to construct a new model which is the combination of different simple compound
by ZHAN Fei 01 Jul '14

01 Jul '14

Dear all, I have a confusion.For instance,when I want to fit a simple which has Pt-O,Pt-S,Pt-N,Pt-Pt cordination shell;when can not find a compound with all same shell or can not find one with all suitable bond length,can I use different scattering path from different model to fit diffferent shell? and if do so atom may in different pot in feff ,are the phase and amplitude still transformable? Other choice is to use path-like object in demeter to construcr a more suitable distance scattering path,or construct a new cluster model according to several cif files, myself,which proticol is feasible or better ? sincerely zhanfei

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spam on our mailing list
by Bruce Ravel 01 Jul '14

01 Jul '14

Hi all, Over the years we've done a pretty good job of keeping spam off this mailing list. As you saw, one slipped through this afternoon. Hopefully it was a one-time event and it will not be necessary to change the friendly nature of security on the list. B -- Bruce Ravel ------------------------------------ bravel(a)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

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Alexandre dos Santos Anastacio invites you to eM Client
by Alexandre dos Santos Anastacio 01 Jul '14

01 Jul '14

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path contribution to fit in low R-space position, but the fit bond length is much longer than that
by ZHAN Fei 01 Jul '14

01 Jul '14

Dear all, I fit a Zn cluster which RDF has a peak little lower than Zn-S peak,and has a shoulder near Zn-O.This accords with my expection the cluster may have both Zn-S Zn-O bond.But after fit the Zn-O bond length is much larger than reff while it path contribution after fit did in low R.What's wrong with my fit?is it the big delro & delrs =0.7882? sincerely, zhanfei this is the fit log,and puc of fit and path contribution is attached Independent points : 8.0087891 Number of variables : 5 Chi-square : 2276.2312227 Reduced chi-square : 756.5273522 R-factor : 0.0023036 Measurement uncertainty (k) : 0.0002947 Measurement uncertainty (R) : 0.0004735 Number of data sets : 1 Happiness = 100.00/100 color = #D8E796 ***** Note: happiness is a semantic parameter and should ***** ***** NEVER be reported in a publication -- NEVER! ***** guess parameters: enot = 8.99859575 # +/- 1.30831421 [0] ssS = 0.01038392 # +/- 0.00062570 [0.00300] delrS = 0.01271583 # +/- 0.00971686 [0] ssO = 0.02806760 # +/- 0.00277795 [0.00300] delrO = 0.33252269 # +/- 0.01446304 [0] set parameters: amp = 0.85000000 OC = 0.01068708 Correlations between variables: delrs & enot --> 0.9345 delro & enot --> 0.8636 delro & delrs --> 0.7882 sso & enot --> -0.7422 delro & sso --> -0.6014 sso & delrs --> -0.5887 sss & enot --> 0.4980 delrs & sss --> 0.4803 sso & sss --> -0.4737 All other correlations below 0.4 ===== Data set >> CdSe-ZnS(Fe)-Zn << ==================================== : Athena project = C:\04-6-29wulizhu\Zn\athena.prj, 3 : name = CdSe-ZnS(Fe)-Zn : k-range = 3.000 - 10 : dk = 1 : k-window = hanning : k-weight = 1,2,3 : R-range = 1.15 - 3 : dR = 0.0 : R-window = hanning : fitting space = r : background function = no : phase correction = : R-factor by k-weight = 1 -> 0.01310, 2 -> 0.01474, 3 -> 0.02004 name N S02 sigma^2 e0 delr Reff R ========================================================================= O1.1 6.360 0.850 0.02807 8.999 0.33252 1.97800 2.31052 S7.1 3.600 0.850 0.01038 8.999 0.01272 2.34200 2.35472 name ei third fourth ========================================= O1.1 0.00000 0.01069 0.00000 S7.1 0.00000 0.00000 0.00000

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Solid AuCl EXAFS fitting – big N
by Sin Yuen Chang 30 Jun '14

30 Jun '14

Dear all, I have questions on the EXAFS fitting of a spectrum of solid AuCl. I find this quite important to resolve because AuCl is so widely used in the literature as a standard reference compound. I obtained the spectrum from the 2013 XAS workshop in Diamond Light Source. It is one of the reference spectrum in the cyanobacteria tutorial. The XANES in the spectrum looks similar to previously published XANES of AuCl. Lengke, M. F. et al., Can. J. Chem. 85: 651-659 (2007) Each Au in the compound has two Cl atoms attached to it, as seen in the crystal structure below. So I fitted the spectrum using two scattering paths: (i) the Au-Cl single scattering, and (ii) the forward through absorber (Au-Cl- -Cl-Au) multiple scattering path. In the fitting model, I fixed So2 (or amp) at 1. The variables that I used for the paths are: (i) N, drcl, sscl, dele; (ii) N = 2, drcl*2, sscl*2, dele. One would expect N to be 2, or perhaps even a little lower because amp = 1 is quite high, but instead, I get N = 2.35, significantly higher than expected. Reduced chi-square : 1706.6480592 R-factor : 0.0222459 guess parameters: N = 2.34968550 # +/- 0.18385678 [1.00000] dele = 0.82469594 # +/- 0.86953191 [0] drcl = -0.02909926 # +/- 0.00608062 [0] sscl = 0.00349927 # +/- 0.00072012 [0.00300] set parameters: amp = 1.00000000 Fixing the coordination number N at the expected value of 2 leads to unrealistically high amp values, as one would expect because of the strong correlation between the two parameters. Next, I tried adding the third and fourth cumulant terms to perhaps account for anharmonic vibrations. The variables for the two paths are now: (i) N, drcl, sscl, dele, third, fourth; (ii) N = 2, drcl*2, sscl*2, dele, third*2, fourth*2. amp was still fixed at 1. But that doesn’t seem to improve matters much, N is similar to the value found without cumulants. Reduced chi-square : 1114.1247832 R-factor : 0.0106796 guess parameters: N = 2.32392798 # +/- 0.21444748 [1.00000] dele = -2.54795042 # +/- 1.27479319 [0.82470] drcl = -0.07137580 # +/- 0.01429137 [-0.02910] sscl = 0.00338118 # +/- 0.00154424 [0.00300] third = -0.00056160 # +/- 0.00017873 [0] fourth = -0.00000155 # +/- 0.00003392 [0] set parameters: amp = 1.00000000 So I have two questions here: 1. Why is the EXAFS amplitude overall so high? The only possibility I can come up with is that the material is actually a mixture of AuCl3 and AuCl. The bond lengths are very similar and it is well known that AuCl is quite unstable in aqueous solution. I have seen the conversion of [AuCl2]- in solution to Au(III) in my own XAFS experiments. 2. I have tried to include a Au-Au first shell scattering path. But there doesn’t seem to be evidence for Au-Au scattering in the data. If the sample was pure crystalline AuCl, the first Au shell would be at 3.2 Å from the absorber, but I cannot fit such a path to the data. So I am wondering whether the AuCl spectrum is unreliable... Given how many times AuCl XANES has been published before, has anyone else perhaps run into this problem? Has anyone perhaps measured solid AuCl under exclusion of moisture and air, or several times as a function of time to assess beam damage? Does anyone perhaps have suggestions what else may explain the high EXAFS amplitudes and the absence of Au-Au scattering…? Attached are the Athena, Artemis and .cif files. I used Demeter 0.9.18 with perl 5.012003 and using Ifeffit 1.2.11d on Windows 7. Thank you for your attention. Best wishes, Sin-Yuen, Chang PhD Student School of Chemical Engineering and Analytical Science The University of Manchester

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pre-release for Demeter 0.9.20 (Bruce Ravel)
by madhusmita sahoo 28 Jun '14

28 Jun '14

One more problem is there, when i am saving the data in atoms and reopening it, the Z co-ordinate of Ti site is getting changed from -0.125 to 0.875 automatically. Regards Madhusmita Sahoo, SO/C,TFCS/SND/MSG(22171) Indira Gandhi Centre for Atomic Research, Kalpakkam, Tamilnadu On 28 June 2014 17:23, madhusmita sahoo <krushna.chem(a)gmail.com> wrote: > > On 27 June 2014 22:30, <ifeffit-request(a)millenia.cars.aps.anl.gov> wrote: > >> pre-release for Demeter 0.9.20 (Bruce Ravel) > > > I have tried the 64 bit version of Demeter 0.9.20. Initially when i > entered all the details for anatase, it gave the required paths. But when i > pressed first hit button it showed perl has stopped working. so i cancelled > and it got closed. after that when i am trying to run atoms I am not > getting the required paths. rather I am facing the same old problem of > having 6 oxygen atoms in the first co-ordination instead of 4 and 2 oxygen > atoms at different R( i.e 1.9339 and 1.9796). Attaching the input file and > the generated paths. > > Regards > Madhusmita Sahoo, > SO/C,TFCS/SND/MSG(22171) > Indira Gandhi Centre for Atomic Research, > Kalpakkam, Tamilnadu >

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Re: [Ifeffit] Ifeffit Digest, Vol 136, Issue 27
by madhusmita sahoo 28 Jun '14

28 Jun '14

On 27 June 2014 22:30, <ifeffit-request(a)millenia.cars.aps.anl.gov> wrote: > pre-release for Demeter 0.9.20 (Bruce Ravel) I have tried the 64 bit version of Demeter 0.9.20. Initially when i entered all the details for anatase, it gave the required paths. But when i pressed first hit button it showed perl has stopped working. so i cancelled and it got closed. after that when i am trying to run atoms I am not getting the required paths. rather I am facing the same old problem of having 6 oxygen atoms in the first co-ordination instead of 4 and 2 oxygen atoms at different R( i.e 1.9339 and 1.9796). Attaching the input file and the generated paths. Regards Madhusmita Sahoo, SO/C,TFCS/SND/MSG(22171) Indira Gandhi Centre for Atomic Research, Kalpakkam, Tamilnadu

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pre-release for Demeter 0.9.20
by Bruce Ravel 27 Jun '14

27 Jun '14

Hi All, As I said yesterday, I now have trial versions of Demeter 0.9.20 available for both 64 and 32 bit Windows machines. I am happy with how both are working and I think they address all the issues that have come up in recent days. 64 bit: https://s3.amazonaws.com/demeter4xas/Demeter_Installer_for_Windows_0.9.20_(… 32 bit: https://s3.amazonaws.com/demeter4xas/Demeter_Installer_for_Windows_0.9.20_(… List of changes for this version: https://github.com/bruceravel/demeter/blob/master/Changes.org Assuming I don't hear of any problems, I will make a formal release sometime next week and update the website. Cheers, B -- Bruce Ravel ------------------------------------ bravel(a)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

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32 Windows installer for testing
by Bruce Ravel 26 Jun '14

26 Jun '14

Hi all, I just built a 32 bit version of the Demeter installer: https://s3.amazonaws.com/demeter4xas/Demeter_Installer_for_Windows_0.9.20_(… If you have a 32 bit Windows machine, could you give this a try and report back to the list? If you could do a bit more than just fire up the programs, that would be helpful. I think it works, but it would be reassuring to know that it works for someone else besides me. Thanks in advance, B -- Bruce Ravel ------------------------------------ bravel(a)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

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Exchange Dirac Hara on Artemis
by Siri V 25 Jun '14

25 Jun '14

Dear Dr. Bruce Ravel, Thank you for your quick reply. If my problem is using Artemis, do you mean I should not use Run Feff under Artemis [Feff] Atoms and Feff, if I want to incorporate Exchange 1 0 0? My other approach was running the feff.inp on feff6 and have it calculate all the paths with Exchange 1 0 0. Is this the solution you have in mind? However, when I am in Artemis 0.9.13, I cannot find the option for Artemis to pull those pre-calculated paths into the project file. Kind regards, Siri --------------------------------------------------------- Message: 3 Date: Wed, 25 Jun 2014 15:53:39 -0400 From: Bruce Ravel <bravel(a)bnl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Exchange Dirac Hara on Artemis Message-ID: <53AB28C3.6090208(a)bnl.gov> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 06/25/2014 03:45 PM, Siri V wrote: > > - open this data file in Artemis 0.9.13 and ^^^^^^ There's your first problem. B --------------------------------------------------------- Message: 2 Date: Wed, 25 Jun 2014 12:45:00 -0700 From: Siri V <siripunt(a)uw.edu> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Exchange Dirac Hara on Artemis Message-ID: <CAGMtT44vT0pSEJdzcD33W5a37JT-72QCUZktkX2t7fvCLSE=UQ(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Dear Dr. Matt Newville, Thank you for your quick reply and attention to my inquiry. I have change the exchange card so that it has only 3 numbers: EXCHANGE 1 0 0. Please find attached the input file, feff.inp. To replicate my error, please: - open this data file in Artemis 0.9.13 and - refer to Artemis [Feff] Atoms and Feff - click Run Feff You should see the following error report: Feff executable: C:\strawberry\c\bin\feff6.exe) Feff 6.01l exchange exchange Token 0 Keyword unrecognized. See FEFF document -- some old features are no longer available. RDINP-2 ********** Feff calculation finished at 2014-06-25T12:40:41 Kind regards, Siri ---------------------------------------------------- Message: 2 Date: Wed, 25 Jun 2014 07:18:42 -0500 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Exchange Dirac Hara on Artemis Message-ID: <CA+7ESbrgvWpVATmbMCCW+R3iAzO0gRcsD2zLj4YKbzU8TZwy_Q(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Siri, Hmm, not sure -- running feff6L with exchange 1 works for me. The exchange card only takes 3 numbers (index v_real v_imag). If you're still having troubles, please send a complete input file, plain text format, or the complete project file. Sending the full plain text of the output you get would be helpful too. In general: Please don't send screenshots -- they're too hard to read and don't tell the whole story. We're willing to help, but it's very hard for us to guess what might be going on with a partial story. --Matt

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Re: [Ifeffit] Bug report: Artemis cannot re-open saved projects
by Badari Rao 25 Jun '14

25 Jun '14

Dear Sir, The new release is working fine in windows 7 64 bit. I was able to re-open a saved file. Thank you very much. However, there is one more problem happening. When I re-open a previous file and simply press on save and then close it (I did not do anything else at all), all the data is lost. My file size which was 179KB, reduced to 1KB and when I re-opened it, there was nothing stored in it. There is no problem if I do more fitting and then save the data. This is a minor problem but a dangerous as one might lose all his hard-work done in fitting the data. @Matt Newville: I had included a dataset while creating the sample file, but strangely only the Feff input file was stored. I guess the dataset is not saved until we actually run a fit. Also, the problem of not being able to re-open saved project was not only with an empty fits, but also with files with actual fits in them. However, this has been resolved with the new release https://s3.amazonaws.com/demeter4xas/Demeter_Installer_for_Windows_0.9.20_p…. <https://s3.amazonaws.com/demeter4xas/Demeter_Installer_for_Windows_0.9.20_p…> -- Thanks & Regards, Badari Narayana. A. R. Ph.D Student, Nanoscience and Nanotechnology, c/o Prof Rajeev Ranjan, Electroceramics Lab, Department of Materials Engineering, Indian Institute of Science.

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Exchange Dirac Hara on Artemis
by Siri V 25 Jun '14

25 Jun '14

Dear Dr. Matt Newville, Thank you for your quick reply and attention to my inquiry. I have change the exchange card so that it has only 3 numbers: EXCHANGE 1 0 0. Please find attached the input file, feff.inp. To replicate my error, please: - open this data file in Artemis 0.9.13 and - refer to Artemis [Feff] Atoms and Feff - click Run Feff You should see the following error report: Feff executable: C:\strawberry\c\bin\feff6.exe) Feff 6.01l exchange exchange Token 0 Keyword unrecognized. See FEFF document -- some old features are no longer available. RDINP-2 ********** Feff calculation finished at 2014-06-25T12:40:41 Kind regards, Siri Message: 2 Date: Wed, 25 Jun 2014 07:18:42 -0500 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Exchange Dirac Hara on Artemis Message-ID: <CA+7ESbrgvWpVATmbMCCW+R3iAzO0gRcsD2zLj4YKbzU8TZwy_Q(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Siri, Hmm, not sure -- running feff6L with exchange 1 works for me. The exchange card only takes 3 numbers (index v_real v_imag). If you're still having troubles, please send a complete input file, plain text format, or the complete project file. Sending the full plain text of the output you get would be helpful too. In general: Please don't send screenshots -- they're too hard to read and don't tell the whole story. We're willing to help, but it's very hard for us to guess what might be going on with a partial story. --Matt

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Re: [Ifeffit] Question about XAFS resolution
by Matt Newville 25 Jun '14

25 Jun '14

Hi Shoaib, On Wed, Jun 25, 2014 at 7:34 AM, Shoaib Muhammad <mshoaibce(a)gmail.com> wrote: > > Dear Matt Newville, > > Sorry to disturb you by asking one question, hopefully you will mind it. Asking on the ifeffit mailing list is generally better. I am CCing this reply to that list. > I often see that resolution XAFS spectrum of K-edge and especially pre-edge is good for > 3d transition metal but comparatively 4d transition metal XAFS spectra and its pre-edge > spectrum is poor. Is it due to low energy resolution at higher energy level at synchrotron > source or something related with electronic transitions? because as far I understand > pre-edge in 3d transition metal is due to 1s-3d and 4d metals is 1s-4d. > The energy resolution is a convolution of monochromator energy resolution and natural line-width of the core electronic level. Generally speaking, for K edges below 10 keV or so, Si(111) and the core-level widths are comparable, ranging from ~0.5eV to 2 eV. Both the mono resolution and core-width increase with energy, but the core-width increases quadratically and so tends to dominate at higher energies (say, above 20 keV). Core level widths for L3 edges are about 2x that of K edges, so that this term almost always dominates for L3 edges. > I am student in Sungkyunkwan University (Korea) and a beginner of XAFS. Cheers, --Matt

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Exchange Dirac Hara on Artemis
by Siri V 25 Jun '14

25 Jun '14

Dear Dr. Matt Newville, Thank you for your reply. I was able to run the FEFF calculation on Artemis (Demeter 0.9.13), before I included the card below: EXCHANGE 1 0.0 0.0 -1 [image: Inline image 2] I received an error as follow: [image: Inline image 3] I am not sure what I did wrong, should I refer to the EXCHANGE card differently? Please kindly advise, Best regards Siri ---------- Forwarded message ---------- From: Matt Newville <newville(a)cars.uchicago.edu> Date: Mon, Jun 23, 2014 at 12:44 PM Subject: Re: [Ifeffit] Exchange Dirac Hara on Artemis To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Hi Siri, On Mon, Jun 23, 2014 at 2:21 PM, Siri V <siripunt(a)uw.edu> wrote: > Dear ifeffit members, > > I would like to inquire whether the Feff's Exchange card (Dirac Hara) is > supported on Artemis fitting program. > Yes. You can edit the feff input file and change the exchange card (or other cards) before running the calculation. --Matt

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Re: [Ifeffit] Bug report: Artemis cannot re-open saved projects
by Badari Rao 24 Jun '14

24 Jun '14

Hello Sir, I wanted to report that I am facing the same problem as the one faced by Mengling Stuckman (dated: Wed, 19 Mar 2014 11:53:10 -0700.) It does not appear to be problem with the operating system because I am facing the same problem in systems with windows 7 as well as windows xp. I have tried a fresh install on a new system with windows 7 os, and the same problem occurred. Even a simple artemis file in which I have just imported and saved the processed file from athena cannot be re-opened in artemis. Kindly sort out the problem. I have attached one sample artemis file which is giving the problem and also the demeter log file from %APPDATA%\demeter. <https://www.mail-archive.com/search?l=ifeffit%40millenia.cars.aps.anl.gov&q…> Thanking You, -- Yours Sincerely, Badari Narayana. A. R. Ph.D Student, Nanoscience and Nanotechnology, c/o Prof Rajeev Ranjan, Electroceramics Lab, Department of Materials Engineering, Indian Institute of Science.

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Exchange Dirac Hara on Artemis
by Siri V 23 Jun '14

23 Jun '14

Dear ifeffit members, I would like to inquire whether the Feff's Exchange card (Dirac Hara) is supported on Artemis fitting program. Kind regards, Siri University of Washington

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Re: [Ifeffit] Ifeffit Digest, Vol 136, Issue 17
by madhusmita sahoo 22 Jun '14

22 Jun '14

Respected Dr. Bruce, I am looking forward to the updated version with the correction. Regards Madhusmita Regards Madhusmita Sahoo, SO/C,TFCS/SND/MSG(22171) Indira Gandhi Centre for Atomic Research, Kalpakkam, Tamilnadu On 21 June 2014 22:30, <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: Ifeffit Digest, Vol 136, Issue 11 (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 20 Jun 2014 17:47:31 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Ifeffit Digest, Vol 136, Issue 11 > Message-ID: <53A4ABF3.4070901(a)bnl.gov> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > Well, not only was the shift vector not working, it seems I had somehow > neglected to even implement it in Demeter! It's amazing what can go > unnoticed and for how long. > > This will be fixed in the next release. Thank you, Madhusmita, for > bringing this to my attention. > > B > > > On 06/18/2014 09:38 AM, Bruce Ravel wrote: > > On 06/18/2014 07:52 AM, madhusmita sahoo wrote: > >> Contd- Crystallographic input for a structure having screw axis and > >> co-ordinates shifted by certain amount > >> Dear sir, > >> herewith I am attaching two input files. The first one with the name > >> wyckoff .inp generates The first co-ordination sphere at 1.9465 angstrom > >> with degenracy of 6. > >> According to crystal structure data anatase structure should have 4 > >> oxygens at 1.9339 angstrom and 2 oxygens at 1.9796 angstrom. > >> So, I tried with the crystal input from the latest PDF-4+2013 > >> database(attaching the PDF as word file for your ref. > >> That ( inp file - attached)eventually generates the required > >> co-ordination sphere with 4 oxygen at 1.3964( as against the XRD data of > >> 1.9339) and 2 oxygen at 1.8925(aginst the XRD data from PDf-4+2013 of > >> 1.9796 angstrom) > > > > You seem to be asking about Atoms' use of the shift vector. > > Specifically, you seem to be asking whether the shift vector is > > working correctly. > > > > If so, that appears to be a legitimate question and the answer appears > > to be /no/. Sigh.... I will look into it and try to have that fixed > > in time for the next release. > > > > Cheers, > > B > > > > > > > > > -- > Bruce Ravel ------------------------------------ bravel(a)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(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 136, Issue 17 > **************************************** >

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Re: [Ifeffit] Ifeffit Digest, Vol 136, Issue 11
by madhusmita sahoo 20 Jun '14

20 Jun '14

Contd- Crystallographic input for a structure having screw axis and co-ordinates shifted by certain amount Dear sir, herewith I am attaching two input files. The first one with the name wyckoff .inp generates The first co-ordination sphere at 1.9465 angstrom with degenracy of 6. According to crystal structure data anatase structure should have 4 oxygens at 1.9339 angstrom and 2 oxygens at 1.9796 angstrom. So, I tried with the crystal input from the latest PDF-4+2013 database(attaching the PDF as word file for your ref. That ( inp file - attached)eventually generates the required co-ordination sphere with 4 oxygen at 1.3964( as against the XRD data of 1.9339) and 2 oxygen at 1.8925(aginst the XRD data from PDf-4+2013 of 1.9796 angstrom) Regards Madhusmita Sahoo, SO/C,TFCS/SND/MSG(22171) Indira Gandhi Centre for Atomic Research, Kalpakkam, Tamilnadu On 13 June 2014 22:30, <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: Scattering paths in XANES calculations (Bruce Ravel) > 2. Re: Crystallographic input for a structure having screw axis > and co-ordinates shifted by certain amount (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 12 Jun 2014 15:42:22 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Scattering paths in XANES calculations > Message-ID: <539A029E.4050609(a)bnl.gov> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > On 06/12/2014 10:07 AM, Stefanie Roese wrote: > > But now I fail at getting the plots with the Energy at the x-axis and > > the normailzed mu at the y-axis likle Bruce did it in his talk. Which > > program was used there? Athena? And how can I get the > > energy/mu-information out of my feffnnn.dat files to compare to the > > total spectrum? I think I am quite close to the solution, but it does > > not work. > > Stefanie, > > The R-space figures were made using Artemis. I fit the Fe foil data > using the version of Feff6 that comes with Artemis, then plotted the > data and the path relevant to each slide. > > The energy plots were made using Athena back in the early days of Feff8 > (which were also the early days of Athena!). The plots show Fe foil > data and (if I remember correctly) column 4 of the xmu.dat file that was > one of the output files from Feff of that vintage. I imported the data > and the xmu.dat file into Athena to make those plots. The calculation > is offset downwards a bit using the y-axis offset in Athena. > > To answer Matthew's question: interesting? Not sure I'd go that far...! > Here's the link: > > > > https://speakerdeck.com/bruceravel/a-practical-introduction-to-multiple-sca… > > B > > > > -- > Bruce Ravel ------------------------------------ bravel(a)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 > > > ------------------------------ > > Message: 2 > Date: Thu, 12 Jun 2014 15:49:56 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Crystallographic input for a structure having > screw axis and co-ordinates shifted by certain amount > Message-ID: <539A0464.1090102(a)bnl.gov> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > Madhusmita, > > Regarding the first question, I am not clear what the problem is. I > grabbed the crystal data for anatase from Matt's website: > > http://cars9.uchicago.edu/atomsdb/TiO2-ana.inp > > and imported it into Artemis. I certainly don't know what the > interatomic distances for anatase should be off the top of my head, but > what Atoms produced from that input data certainly seems reasonable. If > you think there is a problem, you are going to need to explain it in a > way that I can reproduce easily on my own computer. > > Regarding the second question, the vector specified in the box labeled > "Shift vector" will be added to each site *before* any calculation is made. > > B > > On 06/12/2014 01:45 AM, madhusmita sahoo wrote: > > Dear Members, > > > > I would like to know, > > > > *Q1)* If there is a screw axis in the system, like the anatase phase of > > TiO2, whose space group is I41/amd, how should I enter that in the > > atoms for feff calculation. Kindly tell me which is the correct way. > > > > When I entered 141(the space group number) and I41/amd, both generated > > separate set of atomic positions. > > > > The older version of artemis, now the new one(latest version), both > > generates different set of atomic position with the same > > crystallographic input, i.e if I enter 141(or I41/amd) in place of space > > group and run atoms, it generates two different set of co-ordinates in > > Artemis 0.8.012 and in Demeter 0.9.18. Ideally this should be same. > > > > *Q2)* And when co-ordinates is shifted by certain amount, do we have to > > enter that in the shift vector as well as while defining the (x y z) > > of a particular site. Or I should just enter the shift vector and > > define the co-ordinates at its usual position ( I feel this one is > > correct). > > > > For example in anatase crystal structure the co-ordinates are shifted > > by (0,0.25,-0.125). > > > > So, the inputs can be > > > > For shift vector 0,0.25,-0.125 and in place of sites Ti(core) x=0, y=0, > > z= 0 and O (scatterer) x= 0, y=0, z=0.20806 > > > > (Or) shift vector 0,0,0 and in place of sites Ti(core) x=0, y=0.25, z= > > -0.125 and O (scatterer) x= 0, y=0.25, z=0.08160 Ideally > > > > both should give the same result. But it gives different set of atomic > > positions. > > > > Even the same input in different version of artemis is yielding > > different results(in Artemis 0.8.012 and in Demeter 0.9.18) . > > > > I am confused about how atoms work in artemis. I request you to > > elucidate the correct method. > > > > Warm wishes > > > > Madhusmita > > > > India > > > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > -- > Bruce Ravel ------------------------------------ bravel(a)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(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 136, Issue 11 > **************************************** >

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Postdoctoral position in Yeshiva University and Brookhaven National Laboratory
by Anatoly I Frenkel 20 Jun '14

20 Jun '14

Dear subscribers, Please pass along this information to anyone who may be interested in this opportunity. Physics Department of Yeshiva University in New York City will have an opening for a postdoctoral research associate position, beginning September 2014. The project title is: "Characterization of structure, diffusion mechanism and optoelectronic properties of doped colloidal semiconductor nanocrystals." The postdoc will be stationed at Brookhaven National Laboratory and use advanced facilities of NSLS-II for X-ray spectroscopy and Center for Functional Nanomaterials for electron microscopy measurements. Required qualifications: Ph.D. in physics, chemistry or materials science, expert knowledge of XAS methods and their applications to nanomaterials, and experience with in situ characterization methods. Working knowledge of Raman spectroscopy is a plus. The research will be performed under the direction of Prof. Anatoly Frenkel. Applicants should forward cover letter with contact information of three references and CV to Prof. Frenkel at anatoly.frenkel(a)yu.edu. Yeshiva University is an Equal Opportunity Employer. Anatoly Frenkel, Ph.D., Professor Department of Physics, Yeshiva University 245 Lexington Avenue, New York, NY 10016 http://www.yu.edu/faculty/afrenkel Spokesperson, Synchrotron Catalysis Consortium http://www.yu.edu/scc Office: (212) 340-7827, Lab: (631) 344-3013, Email: anatoly.frenkel(a)yu.edu

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Use of the 3rd and 4th Parameter
by Michael Kömm 16 Jun '14

16 Jun '14

Hello, I'm trying to make an EXAFS analysis on the Structure of Tb in a borogermanate glass System. The reference is an .cif of Terbium-Gallium-Garnet (TGG). I expect some disorder caused to working in glass. Therefore I would like to use the 3rd and/or the 4th parameter. I tried to set a guess parameter to evaluate those parameters. Could you tell me a reasonable value for these parameters? The 3rd only varies a little bit around its guessed value (+- 0.01) and if I try to do the same with the 4th parameter no fit at all takes place. The errors in the GDS-window are exactly 0.00000 with no fit taking place (enot = 0, amp = 0 (guess amp = 1) delr = 0 and ss = 0.003) and the R-factor of the fit is way over the top (>10^20). I've chosen a value of 0.5 for the 3rd and the 4th parameter just to see if they're working and I was only doing a quick first shell fit with the surrounding oxygen-shell. Please can somebody tell me how to deal with this problems. Thanks a lot for your time and efford. Sincerly yours, Michael Kömm

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Re: [Ifeffit] Scattering paths in XANES calculations
by Stefanie Roese 16 Jun '14

16 Jun '14

Ah okay. I think now I get it. Is it correct that in the mu(E) spectrum you plot the total spectrum in blue and in red you chose different fms-radii like 2.5, 3.0, 4.1 to get the XANES spectrum for different shells? Or are the red curves another varied FEFF parameter? Thanks so much for your support! Stefanie

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Re: [Ifeffit] Scattering paths in XANES calculations
by Stefanie Roese 16 Jun '14

16 Jun '14

Dear Bruce, thanks for your answer! My problem is how to get the E/mu information for each single scattering path. If I get it right, the xmu.dat contains the sum of all scattering paths. This is the blue curve in your talk. But there are also the spetra for the first,s econd, third,... path at page 11 in red. I think the information comes from the feff0001.dat. feff0002.dat and so on. But these files do not contain mu! Or do I understand it wrong? I have no data to fit, just the FEFF calculations. Is there any possibility to get the XANES spectrum of all paths and the XANES spectrum of every single path to compare how the single paths influence the complete spectrum? Thanks! Stefanie

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