June 2013 - Ifeffit - millenia.cars.aps.anl.gov

Re: [Ifeffit] Launching Athena on Mountain Lion (Mac OS 10.8)
by Kyler Carroll 05 Dec '14

05 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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DAthena crashes when reconstructing data from PCA
by Scott Calvin 29 Jul '13

29 Jul '13

Hi Bruce, Athena is crashing every time I try to "Reconstruct Data" in the PCA dialog. It doesn't seem to matter what data I use, or what space I'm working in (mu or chi), or how many components I use in the reconstruction. I'm using Demeter 0.9.17 with Ifeffit 1.2.11d, under Windows 8 running in Parallels 8 running under OS 10.8.4 on a MacBook Pro. The log file for the latest crash is below. If you'd like a project file too, let me know, but it happens, e.g., with the gold cyanobacteria project file, and with every data set I've tried. --Scott Calvin Sarah Lawrence College

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Basic EXAFS question
by Darren Dale 13 Jul '13

13 Jul '13

Hello All, If I have a Ta(1-x)Ge(x)O(y) thin film, with Germanium concentration of a few percent, is it possible in principle to get useable fluorescence-mode EXAFS spectra around the Ge K edge (11.1 keV)? Or is it likely that the spectra would be complicated by additional Ge fluorescence excited by processes triggered by Tantalum L edge absorption (9.88, 11.13, 11.68 keV)? Thanks, Darren

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Unable to import data from HXMA beamline at CLS into Athena
by Anthony Ardizzi 27 Jun '13

27 Jun '13

Hello, I am currently at the HXMA beamline at the CLS facility in Saskatoon, Canada. I have attempted to import some of the data we have taken here into Athena (demeter version 0.9.17), however I continue to receive the following error: "C:\...\xxxxx.dat could not be read as data". I suspect that this might be a problem with the latest demeter release, as an associate of mine seems to have no problem importing these data files into Athena 0.8.056. I have attached a .dat file so that you can verify that the formatting is readable by Athena. Hopefully someone can provide some help. I would prefer not to have to go back to an older version of Athena if possible. Also, I am running Windows 7 64-bit, in case that is relevant Thanks in advance, Anthony

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Disable duplicate data group check
by Jason Gaudet 21 Jun '13

21 Jun '13

Hi all, Not a bug this time, but a feature that occasionally frustrates me. Artemis does a sanity check prior to fitting, and if it detects a project has two instances of the same Athena data group, it will refuse to fit the new data. IME this is not a particularly helpful warning, and a major hassle if I'm trying a couple different treatments of the same data to see how the FEFF fit is affected. (The message is "This data came from the the same source as another data group. You seem to be trying to increase your number of independent points by fitting the same data more than once in a multiple data set fit." But of course I'm not doing this; only one dupe is being fitted at a time.) I don't see any option in the Artemis preferences to disable this warning, which means I have to spend effort deleting and loading data sets, and keeping a "dummy" data set I don't really care about to collect all my paths in. Is the possibility of extremely novice users trying to fit multiple instances of the same data such a serious threat that this function needs to exist? Is there any possibility of disabling this check, or giving an option to disable it in the Preferences? It would save me from the occasional headache ... Thanks, Jason

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bond angle
by washington gomes 21 Jun '13

21 Jun '13

Dear Colleagues, I am structure characterized of La0.8Ba0.2CoO3 by x-ray spectroscopy, used program IFFEFIT 1.2. 10. I wonderif it is possible to determine the bond angle Co-O-CO,used IFFEFIT code in the extended x -ray absorption fine structure EXAFS. If possible, I would like you to indicate the material that shows examples of how to determine the bond angle Co-O-CO. Sincerely yours, Wahington

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Re: [Ifeffit] no so2 term in Artemis
by Bruce Ravel 14 Jun '13

14 Jun '13

On 06/14/2013 02:59 AM, Lei Cheng wrote: > Dear Dr. Bruce Ravel, > > My name is Lei Cheng, I am a graduate student in UC-Berkeley and doing > my research in LBNL. > > I started to learn how to use Demeter for data processing and fitting. I > got this very bizarre problem with Artemis (please see the attached > screen shot). The so2 term is not showing up. (For your information, I > tried with two different computers, Win 7 64-bit, Win 8 64-bit, Demeter > version 0.9.17 and 0.9.13, Demeter is installed in E:\strawberry\ or > C:\strawberry\) > > Thanks for your time and looking forward to your reply > > -Lei Lei, The Ifeffit mailing list exists to handle questions like this one. I am CCing my reply to the mailing list. Please subscribe to and use the mailing list for any follow-up to this issue. Here is information about the list: http://cars9.uchicago.edu/mailman/listinfo/ifeffit/ If I understand your issue, it is a fairly minor one. The label that says "S02" is not being displayed, but otherwise Artemis works as expected. Is that correct? Are you able to perform fits with Artemis? Are you able to access the context menu (normally, one would right click on that label -- see about halfway down this page: http://bruceravel.github.io/demeter/artug/path/mathexp.html)? I have not observed this behavior on any of my windows machines nor on those of any of the folks who visit my beamline. So I am not sure how to proceed. I am suspicious that this is a locale issue, that is, an issue with how fonts and unicode characters are displayed on your machine. Your name suggests that you may be Chinese. Do you have your computers configured to display something other than English? In applications like Word or Explorer, are the menus and buttons labeled in English or some other language? The reason I ask is that it is possible that I have never observed this problem because none of my computers are configured to display an eastern language. B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods 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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Athena Deglitch Problem
by George Sterbinsky 11 Jun '13

11 Jun '13

Hello, I am writing to report what I believe to be two bugs in Athena 0.9.17. In the attached project file, attempting to use the Deglitch feature to remove the point at ~816 eV (the obvious glitch) returns the attached error message and does not remove the point. Also, when selecting "linespoints" for the "datastyle" in the gnuplot preferences, the data continues to be plotted as lines only. Thank you, George

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Re: [Ifeffit] Very large exafs amplitude in collected data - cause unknown (Jason Alvino)
by Jason F. Alvino 11 Jun '13

11 Jun '13

Hi Matt, As I pointed out before, in the attached zipfile, there is a file called "AuNP_anatase_Au.D" which has the data in two columns of energy vs mu, comma separated underneath the "EV RAW" header. It also already has all the bad channels removed from the averaged data. Cheers, Jason Hi Jason, > > On Fri, Jun 7, 2013 at 9:25 AM, Jason F. Alvino > <jason.alvino(a)adelaide.edu.au> wrote: > > Hi all, > > > > There seemed to have been abit of a misunderstanding with the data > format, > > sorry about that. I was not really sure what format was going to be best > to > > share with people, I thought the raw data would have been useful so that > > people were able to see all the channels. > > > > I have attached a data file from average (AuNP_anatase_Au.D) which has > the > > data in columns of energy vs u(E). > > > > The second data format (.ssrl) has data in the following columns; > > > > 1 = real time clock > > 2 = Mono angle (requested) > > 3 = Energy (eV) > > 4 = I0 > > 5 = I1 > > 6 = I2 > > 7-9 = blank > > 10-44 - fluor channels (SCA) > > 45-79 - ICRs for the det element > > > > I have attached these two data sets to this new email. > > I still am completely unwilling to work with that file. Send a file > with no more than 5 columns, and do not expect anyone to add columns > together or know how you would use the different columns in your file. > It's best to send a file with only energy and xmu. > > > Now to try to answer some of the questions that have been asked of the > data. > > > > The samples are chemically synthesised Au8, Au9, Au11 clusters protected > by > > PPh3 ligands. We then support these samples on various oxides, in this > case > > anatase at a % weight loading of 0.17% cluster/anatase. The loading is > > typically quite low as we discovered that higher loadings lead to greater > > levels of Au agglomeration. The samples can then undergo various > treatments, > > in an attempt to remove the protective ligand groups, however harsher > > treatments can also lead to agglomeration of the Au clusters. The > currently > > attached example is of Au9 on anatase at 0.17% loading after being > calcined > > at 200 C under an oxygen atmosphere. There was potentially an issue > > initially about releasing all the info of the samples which has now been > > sorted out. > > > > "Perhaps there is some sort of coupling in the signal chain between the > Ge > > detector and IO" - I wouldn't really know how to start with that one, > > however I could have another chat with the beamline scientists over this > and > > see if they may have some ideas as to the cause. > > > > We were actually analysing some of the data as we went, but unfortunately > > not all of it. However this problem of large k2 or k3 weighted exafs > > amplitude only occurs in samples that we know begin to agglomerate into > > larger particles of gold (this has been determined from a similar study > we > > have done at the SXR). We have multiple samples that display this > behaviour. > > > > The values I get for sigma2 when trying to fit using XFIT are 2 or > greater, > > if I maintain debye waller factors greater than 0.001 and maintain > sensible > > coordination numbers <=12. > > > > The samples were cooled to 12 K using a cryostat, however the Au foil > data > > is not cooled. > > That alone could explain the difference. > > > --Matt > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 124, Issue 8 > *************************************** > -- Jason F. Alvino PhD Candidate (Chemistry) School of Chemistry and Physics University of Adelaide, AUSTRALIA 5005 Ph : +61 8 8313 3707 E-mail: jason.alvino(a)adelaide.edu.au

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Re: [Ifeffit] Very large exafs amplitude in collected data - cause unknown (Jason Alvino)
by Jason F. Alvino 07 Jun '13

07 Jun '13

Hi all, There seemed to have been abit of a misunderstanding with the data format, sorry about that. I was not really sure what format was going to be best to share with people, I thought the raw data would have been useful so that people were able to see all the channels. I have attached a data file from average (AuNP_anatase_Au.D) which has the data in columns of energy vs u(E). The second data format (.ssrl) has data in the following columns; 1 = real time clock 2 = Mono angle (requested) 3 = Energy (eV) 4 = I0 5 = I1 6 = I2 7-9 = blank 10-44 - fluor channels (SCA) 45-79 - ICRs for the det element I have attached these two data sets to this new email. Now to try to answer some of the questions that have been asked of the data. The samples are chemically synthesised Au8, Au9, Au11 clusters protected by PPh3 ligands. We then support these samples on various oxides, in this case anatase at a % weight loading of 0.17% cluster/anatase. The loading is typically quite low as we discovered that higher loadings lead to greater levels of Au agglomeration. The samples can then undergo various treatments, in an attempt to remove the protective ligand groups, however harsher treatments can also lead to agglomeration of the Au clusters. The currently attached example is of Au9 on anatase at 0.17% loading after being calcined at 200 C under an oxygen atmosphere. There was potentially an issue initially about releasing all the info of the samples which has now been sorted out. "Perhaps there is some sort of coupling in the signal chain between the Ge detector and IO" - I wouldn't really know how to start with that one, however I could have another chat with the beamline scientists over this and see if they may have some ideas as to the cause. We were actually analysing some of the data as we went, but unfortunately not all of it. However this problem of large k2 or k3 weighted exafs amplitude only occurs in samples that we know begin to agglomerate into larger particles of gold (this has been determined from a similar study we have done at the SXR). We have multiple samples that display this behaviour. The values I get for sigma2 when trying to fit using XFIT are 2 or greater, if I maintain debye waller factors greater than 0.001 and maintain sensible coordination numbers <=12. The samples were cooled to 12 K using a cryostat, however the Au foil data is not cooled. Also it seems my first response email directly replied to Bruce, sorry about that I simply hit the reply button on the forum page instead of writing a new email to the mailing list. I had attached a data file from average (AuNP_anatase_Au.average) which had the data in columns of energy vs u(E), to Bruce, which may have been overlooked. If anything needs further clarification please let me know. As I'm sure you are already aware this was only our first trip using XAFS so our experience is quite limited. Cheers for all the input so far! Jason

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