December 2015 - Ifeffit - millenia.cars.aps.anl.gov

Solution to running Demeter on an ORNL computer
by Mullins, David R. 17 Dec '15

17 Dec '15

After having run Athena and Artemis for years on my office computer in Oak Ridge they suddenly stopped working. The command prompt window and "credits window" appeared briefly and then shut down. I tried upgrading from v 9.21 to v 9.24. This didn't help. The problem appears to be similar to what was reported in October 2015 by Matt Noerpel on EPA computers. The problem is related to the restricted Administrator privileges imposed by ORNL IT. To install new software we temporarily obtain Administrator privileges. When we do this it changes our User Directory from our standard User Directory to Admin. Demeter's default is to install in the current User Directory which is now the Admin directory and apparently programs installed there won't run when Administrator privileges are gone. To solve the problem I changed the installation directory from Admin to my User Directory name in the long line "Install Demeter in ...". Note that I just substituted my User Directory name for Admin and didn't change any of the other directory specifications. Hope this helps. I suspect that as time goes by many other national labs and companies will institute similarly restrictive Admin privileges. Dave ********************** David R. Mullins Oak Ridge National Laboratory PO Box 2008, MS 6201 Oak Ridge, TN 37831-6201 PH: 865-574-2796 FAX: 865-241-5152 E-MAIL: mullinsdr(a)ornl.gov<mailto:mullinsdr@ornl.gov> WWW:http://www.ornl.gov/sci/csd/Research_areas/SCC_group.html

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Measurment of size of nanoparticles using one measurement of sample
by pushkar shejwalkar 17 Dec '15

17 Dec '15

Dear All, I am currently trying to find out the size of my Pd nanoparticles using EXAFS analysis. But I am totally new to this field and I have no physics background as well. With this I started digging into the email archives as to if it is possible to speculate the size of the nanoparticles that I have. My preliminary information from SEM lets me start from the point where the nanoparticles are around 2-3 nm in size and about spherical in nature. I started with the following thread from archive http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2013-October/011474.html and it was pretty useful as well. I read the documents and other threads involved in it. and then I realized that with the knowledge of amplitude of known (lets say in this case Pd foil) and my sample I can find out the extent to which the Pd atoms are present at the farthest distance. by doing so I can find out what the nanoparticles size. To be specific I am talking about this particular paper. http://scitation.aip.org/docserver/fulltext/aip/journal/jap/94/1/1.1581344.… (http://dx.doi.org/10.1063/1.1581344) I am using this paper since it works with spherical nanoparticles and hence my assumptions can best be supported by this model. I am open to other references as well and I would cite them all if they are useful. Now my question is, in order to make up to the reduced amplitude, it is recommended that for spherical nanoparticles only two variables in fitting parameteres are needed 1) Radius 2) amplitude reduction factor (SO2) I think I have understood the basic concept as to why the amplitude is reduced and somehow we need to increase the number N of number of paths/number of atoms in the cluster so that the amplittude will now increase so much so that it would match the theory. BUT what I have not understood is how to do so? e,g do we do that during fitting? in artemis? in which case the amplitude is by default adjusted to get the fit and now there is no difference in the absolute value of x(R) (A-3Ao) Y-axis. OR have I misunderstood something? Could someone shine a light on this please. Best Pushkar -- Best Regards, Pushkar Shejwalkar. Post-doctoral -Researcher, Tokyo Engineering University, Tokyo-to Japan

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Mac woes
by Bruce Ravel 15 Dec '15

15 Dec '15

If someone would like to contribute a write-up on how to install the Mac package and how to troubleshoot the most common problems, that would be helpful. I could then replace the text that exists on the Demeter homepage, which does not appear to be sufficient for many Mac users. 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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No Plot window (Mac El Capitan)
by Laila Al-Madhagi [fy11lham] 15 Dec '15

15 Dec '15

Hello there, I have installed Demeter with Macports on my Mac recently. My operating system is El Capitan. My issue is that I cannot see the plot area. I have followed two threads discussing this issue. The first one is ''No plot window in Athena/ Demeter on Mac OS X Yosemite'' (http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2015-September/012739.ht… where George suggested to change the gnuplot to x11 on the Athena preferences menu. I could not find Athena preference menu and I was wondering if anyone could help with that. The second thread is ''No plot window on Mac El Capitan'' (http://www.mail-archive.com/ifeffit%40millenia.cars.aps.anl.gov/msg05261.ht… where Chloe could not find Athena Preferences menu as well. Best regards, Laila

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[ANN] Larch 0.9.27
by Matt Newville 13 Dec '15

13 Dec '15

Hi Folks, Though I've resisted making an announcement about each minor release of Larch, I wanted to let everyone know about an important change starting with the latest release. As both Bruce and I (and Sam, and probably anyone who has tried) have experienced, and many of you have witnessed from discussions on this list, building and maintaining binary installers for various Windows and Macintosh generations is a painful and time-/resource-consuming. For Larch, as with Demeter, Windows installers have been possible but real work, and Macintosh installers have been much more difficult. Starting with Larch 0.9.27, I'm recommending that folks using Mac OSX and Windows use the free version of Anaconda Python 2.7 from ContinuumIO ( https://www.continuum.io/) Anaconda Python comes with a very large set of the standard scientific Python libraries as well as visualization and development tools. I highly recommend this package for anyone interested in learning scientific programming. For Larch, the main benefits of this approach are 1) very easy installation and upgrades to packages, and 2) that the default installation goes into the users home directory, and so can easily be modified (or deleted) by the user without administrative privileges. To install Larch with Anaconda Python, the instructions (see http://xraypy.github.io/xraylarch/installation/index.html) are: 1. Download and Install Anaconda Python from https://www.continuum.io/downloads 2. Open a Command Line Terminal Windows: From the Start Menu, open an Anaconda Shell Mac OSX: Applications->Utilities->Terminal and type: conda install -c newville xraylarch This will install all the basic software for Larch, and all the installed programs can be run from this terminal. 3. To create "clickable icons" (Windows shortcuts or Mac Applications) type: larch_makeicons in the same Terminal window. This will create a Folder named Larch on your desktop with several Larch applications in it. Because these are on your desktop, you can move, rename, or delete these without affecting any other software. 4. To update Larch at any time, you will be able to open a Terminal and type: conda update -c newville xraylarch For Linux, Anaconda is a fine choice, but seems slightly less important as the standard package managers have most of the required packages available, and a source installation of Larch is very easy. Installing with Anaconda includes all the source code for the Larch plugins in "share/larch/plugins" under the anaconda folder in your home directory (or under AppData on Windows). These are dynamically loaded by Larch, so you can still explore and modify the analysis procedures. However, installing with Anaconda does not include local copies of the documentation or examples. This may change in future release, but for now these will be made available for each release at http://cars.uchicago.edu/xraylarch/downloads/docs/ Let me know if you have any questions or trouble with any of this. --Matt

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Athena 0.9.24 (64-bit) on Windows: Problems with Alignment and with plotting window
by Voegelin, Andreas 11 Dec '15

11 Dec '15

Dear Bruce After upgrading from Demeter 0.9.22 to Demeter 0.9.24 (64-bit) on two PCs with Windows 7 Enterprise, I now encounter two problems that I did not observe before: 1) In Athena, auto-align does not seem to work properly: In the attached project file, the first spectrum is a reference Fe foil spectrum. Trying to align the reference spectra linked with the sample spectra to this reference foil, the "auto-align" function results in an obviously wrong alignment (see jpg file). Even if I first manually correctly align the reference spectra, "auto align" again shifts the spectrum to a wrong place. 2) Plotting window is always set to small size when plotting a graph and zooming does not work: Working with Athena, I normally used the left half of the screen to display the GUI and the right half to display the plotting window. After I installed Demeter 0.9.24, the plotting window is always reduced in size and moved to the left part of the screen when I try to plot a graph from Athena. Furthermore, within the plotting window, the zoom function does not seem to work anymore. Best regards, Andreas °°° °°° °°° °°° °°° °°° °°° °°° °°° °°° Andreas Voegelin, PhD Eawag - Swiss Federal Institute of Aquatic Science and Technology Ueberlandstrasse 133, CH-8600 Duebendorf, Switzerland Tel: +41 58 765 54 70 mailto:andreas.voegelin@eawag.ch http://www.eawag.ch/~voegelan

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Athena 0.9.24 (64-bit) on Windows: Problems with Alignment and with plotting window
by Voegelin, Andreas 11 Dec '15

11 Dec '15

Dear Bruce In the project file I sent with my previous email, the E0 of the standard Fe foil spectrum was set to 7128.5 eV, and the E0 of the foil spectra associated with the sample spectra were set to 7112 eV. If I set the E0 value of the standard Fe foil spectrum to 7112 eV as well, the "auto-align" function works properly again. Playing around a little bit further, it appears that the auto align function finds the correct solution as long as the difference between the E0 values assigned to the standard foil and the foil spectrum to be aligned is less than or equal to 5 eV. However, I wonder why the choice of E0 should affect the alignment function? Best regards, Andreas °°° °°° °°° °°° °°° °°° °°° °°° °°° °°° Andreas Voegelin, PhD Eawag - Swiss Federal Institute of Aquatic Science and Technology Ueberlandstrasse 133, CH-8600 Duebendorf, Switzerland Tel: +41 58 765 54 70 mailto:andreas.voegelin@eawag.ch http://www.eawag.ch/~voegelan

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Unable to export flattened normalized XANES spectra from Athena 0.9.24
by Jeff Catalano 09 Dec '15

09 Dec '15

I am looking for some help with a possible error on my part or bug associated with exporting normalized mu(E) spectra from Athena 0.9.24 64-bit on Windows 10 Pro 64-bit. I have some Si XANES data with a challenging background shape that is well removed through careful normalization in Athena, as long as the "Flatten normalized data" option is checked. When I save the current group as norm(E), what is saved is the non-flattened normalized data. The checkbox for flattening the data has no effect on what is exported despite changing what is plotted. I have verified this by comparing the files exported the the flatten box checked or unchecked. I have tried this with multiple data files loaded in multiple formats (raw beamline data, simple two-column E and mu data, PRJ files) and the effect is always the same. It is also unaffected by the normalization ranges I select. No matter what options I select Athena 0.9.24 will only save non-flattened norm(E) data. This behavior is different from what I remember, and I have verified that in version 0.8 of Athena the exported norm(E) was the flattened data, provided that the flatten box was checked (of course). I have been unable to determine if I have any errors in the settings in version 0.9.24 but all parameters that I can find are identical in both 0.9.24 and 0.8. I have also uninstalled and reinstalled Athena 0.9.24 and the effect is still the same. Has anyone else noticed this problem? Is this a bug? Thank you, Jeff -- Jeffrey G. Catalano, Associate Professor Department of Earth and Planetary Sciences Washington University 1 Brookings Drive, Campus Box 1169 Saint Louis, MO 63130 USA http://aqgeochem.wustl.edu/

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Most probably a bug or something.
by pushkar shejwalkar 02 Dec '15

02 Dec '15

Dear All, I have recently found this particular problem with plotting my graphs in k fitting. This is a problem with athena as well as artemis. When I plot the graphs in R or E or q there is no problem, but when I do so in k suddenly these four black circles show up on the left side of the graph. Interestingly this has appeared suddenly just now and after this (probably i can recollect exactly) I could not maximize my plotting window at all. although if I drag the corners it can be resized and these four circles then appears relatively smaller (basically it does not exapnds with the window. Anybody else have this problem? is there a quick fix? I am not sure if this is a bug or not so I am sending this here. my operating system is Windows 10, Athena and artemis 0.9.22 8GB RAM. (Please let me konw if anything else is needed) Pictures of these problem is attached below. I am attaching R-space just to show that it doesnt happen for the R-space. First picture is Athena, second is from Artemis fitting. [image: Inline image 4] [image: Inline image 2][image: Inline image 3] -- Best Regards, Pushkar Shejwalkar. Post-doctoral -Researcher, Tokyo Engineering University, Tokyo-to Japan

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Re: [Ifeffit] Ifeffit Digest, Vol 154, Issue 5
by Enyuan Hu 02 Dec '15

02 Dec '15

Dear all, Thank you all for the kind help. I didn't know CuO is so useful in the sense that asking for its spectrum would reveal the abundant kindness in this community :) Enyuan On Wed, Dec 2, 2015 at 10:26 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: Ifeffit Digest, Vol 154, Issue 1 (Soma Chattopadhyay) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 2 Dec 2015 20:14:04 -0600 > From: Soma Chattopadhyay <soma.tifr(a)gmail.com> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Ifeffit Digest, Vol 154, Issue 1 > Message-ID: > <CAMYsB8ucwLRpSNGFK1aA8LbuWb03t5fOajSjdPU= > SGerD30jQQ(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Enyuan > Attached is my athena project file with Cu foil, CuO and Cu2O data in > athena. > They have references foils with them. > best > Soma > > On Wed, Dec 2, 2015 at 7:38 PM, Enyuan Hu <enhu(a)bnl.gov> wrote: > > > Dear Matt, > > > > I'm sorry to be persistent but I noticed that the reference spectrum (Cu > > foil I assume) for these two CuO data doesn't seem to correct. I conclude > > this after I made comparison using the Cu foil data from the database and > > my own previous measurement. If it's not bothering you, can you help me > > look into that? Thanks. > > > > Enyuan > > > > On Wed, Dec 2, 2015 at 8:08 PM, Enyuan Hu <enhu(a)bnl.gov> wrote: > > > >> Dear Riti and Matt, > >> > >> Thank you two very much for the timely help. I didn't even know the > >> existence of these two libraries. Thanks again for letting me know such > a > >> valuable resource. > >> > >> regards, > >> Enyuan > >> > >> On Wed, Dec 2, 2015 at 7:40 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. CuO XAS spectrum (Enyuan Hu) > >>> 2. Re: CuO XAS spectrum (Ritimukta Sarangi) > >>> 3. Re: CuO XAS spectrum (Matthew Marcus) > >>> 4. Fwd: Most probably a bug or something. (pushkar shejwalkar) > >>> > >>> > >>> ---------------------------------------------------------------------- > >>> > >>> Message: 1 > >>> Date: Wed, 2 Dec 2015 18:32:11 -0500 > >>> From: Enyuan Hu <enhu(a)bnl.gov> > >>> To: ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > >>> Subject: [Ifeffit] CuO XAS spectrum > >>> Message-ID: > >>> < > >>> CAJud35MbtedoHtgoN3yFJgJ3squ+L5LCVpp1uNm0Tf4vwpWENA(a)mail.gmail.com> > >>> Content-Type: text/plain; charset="utf-8" > >>> > >>> Dear all, > >>> > >>> I'm analyzing some Cu compounds spectra and was wondering if anyone has > >>> the > >>> CuO XAS spectrum and is willing to share. Thanks. > >>> > >>> best regards, > >>> Enyuan > >>>

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