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

Bug when adding feff calculations
by Georges Siddiqi 31 Oct '13

31 Oct '13

Hi, I'd like to report 2 bugs that I have when dealing with Feff calculations. One is critical (program crashes), the other is more troublesome, but i've found ways around it. OS: Windows 7, SP1 Demeter version: 0.9.18 *1) Critical - Trying to add single scattering paths of arbitrary lengths. This used to work with an older version of the program, but now, no matter what I do, when I add a single scattering path with any length, the program crashes* I've attached the log file (dartemis.log)* * * * How to replicate: -import any file (i've attached Cu.inp for ease of comparison) -run atoms -run feff -load an athena file (i've attached Cu foil.apj) -go to "Path like" tab -input any bond distance, and drag path over to the path list *-*program should crash This problem occurs both with cif files and inp files (and several of both file types have been tried), and (so far) any type of data set I try to import into athena. I've just chosen the attached files for their simplicity. 2) Not critical - I deal with a lot of organometallic compounds whose cif files correspond of only 1 absorbing atom surrounded by a network of non-absorbing atoms. i.e. not a regular, repeating lattice.* *When I import the cif file for one of these compounds (*see attachment, schrock 1.cif*), the Atoms page is fine, but in the Feff page, the "potentials" lists the absorbing atom as ipot 0 and 1: POTENTIALS * ipot Z tag 0 74 W 1 74 W 2 8 O 3 7 N 4 6 C 5 1 H while in the atoms list, it only appears once as ipot 0. Naturally, if I just click "run Feff", the program returns an error. My workaround to this has been to copy the atoms list into notepad, save, import into excel, subtract 1 from the ipot column (besides ipot 0), and replace the old atoms list with the corrected atoms list. then I manually change the potentials to: POTENTIALS * ipot Z tag 0 74 W 1 8 O 2 7 N 3 6 C 4 1 H after this it works fine. So this isn't a big burden, after a bit of practice I've gotten pretty fast at editing the Feff file, but if there's some easier solution it would be great. This problem occurs with any monomeric compounds. If I run the feff on a dimeric organometallic compound, there's no problems. Please let me know if there's any additional information I can supply that would help with this. thanks, Georges Siddiqi

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Re: [Ifeffit] Ifeffit Digest, Vol 128, Issue 22
by Kyler Carroll 30 Oct '13

30 Oct '13

Hi Stefan, I had help from Tsu-Chein Weng (tsuchien(a)slac.stanford.edu) with this issue and his solution worked for me. Basically I had to unistall both iXAFS and XQuartz and reinstall and do a similar trick in terminal. Hope this helps! 1. Drag /Applications/iXAFS.app into the trash bin 2. Download iXAFS3.0.3.dmg and install the package 3. Drage /Applications/XQuartz.app and /opt/X11 into the trash bin 4. Download XQuartz-2.7.4.dmg and install the package 5. Launch Terminal.app 5.1 cd /Applications/Utilities 5.2 sudo rm -fr X11.app 5.3 sudo mkdir X11.app 5.4 cd X11.app 5.5 sudo ln -s ../XQuartz.app/Contents 5.6 open -a X11 5.7 open -a ixafs Thank you, Kyler J. Carroll, Ph.D. Research Scientist Chemical Engineering Massachusetts Institute of Technology, On Mon, Oct 28, 2013 at 10:47 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. Did anyone upgraded to SeaLion aka Mavericks (MacOS 10.9) > (Mangold, Stefan) > 2. Athena crash report (George Sterbinsky) > 3. Re: Athena crash report (Bruce Ravel) > 4. Re: Athena crash report (George Sterbinsky) > 5. Re: Athena crash report (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 27 Oct 2013 18:00:28 +0100 > From: "Mangold, Stefan" <stefan.mangold(a)kit.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] Did anyone upgraded to SeaLion aka Mavericks (MacOS > 10.9) > Message-ID: <6C20978B-32DC-4C87-A900-2499DFFF4EC9(a)kit.edu> > Content-Type: text/plain; charset="us-ascii" > > Dear all, > > one question to the early adopter. Did anyone tried ifeffit already on > Mavericks? Is there any known issue beside the X11/Quartz issue? I have it > installed ifeffit on MoutainLion with the know trick to "emulate" the old > X11 (was on the mailing list). > > Best regards > > Stefan Mangold > > > Karlsruhe Institute of Technology (KIT) > ANKA Synchrotron Radiation Facility >

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Did anyone upgraded to SeaLion aka Mavericks (MacOS 10.9)
by Mangold, Stefan 27 Oct '13

27 Oct '13

Dear all, one question to the early adopter. Did anyone tried ifeffit already on Mavericks? Is there any known issue beside the X11/Quartz issue? I have it installed ifeffit on MoutainLion with the know trick to "emulate" the old X11 (was on the mailing list). Best regards Stefan Mangold Karlsruhe Institute of Technology (KIT) ANKA Synchrotron Radiation Facility

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Artemis Software Issue
by James Apollo 25 Oct '13

25 Oct '13

Hello, Bruce and co I am a user of extended xray edge EXAFS spectroscopy and I have what I hope is a well formulated question regarding your software that you have developed. I recently downloaded a fresh copy of Iffefit from the CARS website, but the same issue continues to persist. In version 0.8.012 of Atena, I have noticed that if I ever close the "graphics window #1" the program alerts me that "the window was closed" and the software shuts down. Afterwards, I cannot restart the software no matter how hard I try. I have lost a great deal of my extended xray XAFS and XANES work from this aggreviating software issue. Is there some kind of patch I can download? The updates don't seem to work when I startup the software. Is there a newer version of the software I could use? Please let me know how to fix the problem. Thanks!

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Problem with PCA tool in Athena
by Ismael Graff 25 Oct '13

25 Oct '13

Dear fellows, I have an issue with the PCA tool of Athena (using 0.9.18 version of Demeter, windows XP sp2). When I try to target-transform a standard/model compound the program simply ignores my choice of standard. The target transform is applied to the first sample file that I have used to get the different components, even having highlighted the standard compound of my choice. Also, there is no output for the TT coefficients in the text box. Is it a problem of my Demeter installation? Has anyone had the same issue? All the best, Ismael. -- ************************************ * Ismael Graff * * * * Universidade Federal do Paraná * * Departamento de Física, CP 19044 * * 81531-980, Curitiba, Brazil. * * Tel (office): +55 41 3361 3278 * * Tel (Lab): +55 41 3361 3427 * * Fax: +55 41 3361 3418 * * http://fisica.ufpr.br/graff * * * * "DOCENDO DISCIMUS" * ************************************

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Re: [Ifeffit] Report problem in Demeter install
by Bruce Ravel 25 Oct '13

25 Oct '13

Charles, It is a bad use of my time to answer questions about the software other than on the mailing list http://cars9.uchicago.edu/mailman/listinfo/ifeffit/ You'll notice this email is CCed to the mailing list. Any further conversation on this topic must use the mailing list. On 10/25/2013 04:38 PM, Charles Le Losq wrote: > Hello, > > I tried to install the demeter software but when I seach for > dependencies with > > ./Build installdeps > > (as described here: > http://bruceravel.github.io/demeter/pods/installation.pod.html#Installing_f…) Am I to assume that you are trying to build from source? The link is to the part of that page that discusses NOT building from source.... > (step 3b) > > > > this command actually don't work and don't exist... I seach for > other commands with ./Build help but I did not found anything. What > should I do to fix that ? > All the standard questions apply. You really have to give me something to work with.... * Is this linux? * What version of linux? Or whatever operating system you are using. * What version of perl? (perl -v) * What version of gcc? (gcc -v) * Did you successfully install Ifeffit and Pgplot? (Step 1) * What happened when you did "perl Build.PL"? * Is cpan configured reasonably? (Step 3a) * Did you read this: https://gist.github.com/waveform80/3959252 ? It's really helpful -- Dave Hughes did a bang-up job. > In addition, I wanted to use this version in order to get the latest > version of Athena... I have a issue with the one I got, it did not > work when asking for normalization of more than 200 spectra in one > run... On linux and mac... Is it a memory limitation ? How can I > overpass that? I've answered this question over a billion times times on the mailing list. Ifeffit, the backend Athena uses for its XAS functionality, is written in Fortran. Fortran has static memory allocation. As normally delivered Ifeffit can handle about 60 groups, given the way Athena uses memory. You have two options. (1) Compile Ifeffit to use more memory. Instructions can be found by searching the mailing list. (2) Live with the fact that you cannot do 200 spectra at a time. As Matt has pointed out many times, Larch will fix this problem. The day when Athena can use Larch is fast approaching. I'm getting there, but I have a lot of things to do each day. So it takes time. 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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FW: Problem opening Demeter in Windows - doesn't work at all
by Arjen van Veelen 25 Oct '13

25 Oct '13

Dear Bruce, Regarding my earlier mail this week, the log files of my problem. Also, when I go to command window in Windows 7, it says that it can't find the path specified. What should I do? Should I fix the paths and if yes, how do I do that? Arjen From: Arjen van Veelen Sent: 22 October, 2013 5:04 PM To: 'ifeffit(a)millenia.cars.aps.anl.gov' Subject: Problem opening Demeter in Windows - doesn't work at all Dear Bruce, > > I reinstalled Demeter today, since it didn't want to start up (it worked before as far as I know). I > re-installed it and still does not start up. > > I see a window appearing and disappearing, but not Athena or Artemis. > I am running this also at linux, but like to be able to use it in > windows as well, since I write and work mostly in Windows.... > > Is there a way around it, or is there a bug in the software? For the mean-time I am using linux > > Best wishes, > > Arjen ir. A. (Arjen) van Veelen | PhD student | University of Manchester | School of Earth, Atmospheric and Environmental Sciences | Oxford Road | Manchester | M13 9PL | United Kingdom | M +44 77 2037 3237 | arjen.vanveelen(a)postgrad.manchester.ac.uk<mailto:arjen.vanveelen@postgrad.manchester.ac.uk> | www.manchester.ac.uk<http://www.manchester.ac.uk>

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calculating particle size from coordination numbers
by Georges Siddiqi 24 Oct '13

24 Oct '13

Hi All, I'm trying to use EXAFS data I have of Cu nanoparticles dispersed on SiO2 and ZnO to calculate their particle size. Searching the archives, i've come by these topics and papers, which have helped immensely, but I'm still a little bit in the dark about the specifics of the fits: http://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg02994.html http://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg03430.html http://pubs.acs.org/doi/full/10.1021/jp012769j http://pubs.rsc.org/en/Content/ArticleLanding/1999/CP/a904654b#!divAbstract So these discussions and papers make it clear that CNs for the 2nd or 3rd coordination shells will give a more accurate picture of the particle size (and even shape). Also, just comparing SO2s between a foil and the sample isnt the most accurate. My initial thought was to get a good fitting model on Cu foil, obtain coordination numbers which are very close to 1, then apply that same fitting model to the Cu nanoparticles (for the Cu-SiO2 species we have TEM data I can again calibrate myself with) However, my specific problem is getting reasonable coordination numbers for the Cu foil. - I can set the SO2 to 1 and get a very good fit for the data, but this is not useful for the nanoparticles - I can give all paths the same SO2 variable, and get a fitted value close to 1, but this isnt useful for comparing first and second shell CNs, as the ratio will always be the same. - And finally, when I try to give each scattering shell its own independent CN, I again get a good fit, but while the first shell SO2 is close to 1, the 2nd shell value is closer to 1.5 I've been playing with which variables are the same between paths, etc, and I can get more reasonable numbers, but the problem then becomes that I cant easily justify my fitting model. Attached is my Artemis file for Cu foil. Any help or suggestions with how to proceed (specifically with how to group variables) would be much appreciated. I apologize in advance if i'm asking about a topic that's been covered extensively. thanks, Georges Siddiqui

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Problem opening Demeter in Windows - doesn't work at all
by Arjen van Veelen 22 Oct '13

22 Oct '13

Dear Bruce, > > I reinstalled Demeter today, since it didn't want to start up (it worked before as far as I know). I > re-installed it and still does not start up. > > I see a window appearing and disappearing, but not Athena or Artemis. > I am running this also at linux, but like to be able to use it in > windows as well, since I write and work mostly in Windows.... > > Is there a way around it, or is there a bug in the software? For the mean-time I am using linux > > Best wishes, > > Arjen ir. A. (Arjen) van Veelen | PhD student | University of Manchester | School of Earth, Atmospheric and Environmental Sciences | Oxford Road | Manchester | M13 9PL | United Kingdom | M +44 77 2037 3237 | arjen.vanveelen(a)postgrad.manchester.ac.uk<mailto:arjen.vanveelen@postgrad.manchester.ac.uk> | www.manchester.ac.uk<http://www.manchester.ac.uk>

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Problem opening Demeter in Windows - doesn't work at all (Arjen van Veelen)
by fred.mosselmans＠diamond.ac.uk 22 Oct '13

22 Oct '13

Hi Arjen the most common cause of this is the lack of a directory for the log file for either artemis or athena to write to. in windows 7. see the link bruce sent. if that directory doesn't exist ( or for some bizarre reason they cant write to it) ,neither program will create it and when you attempt to start them a "dos" window " opens then closes as it finds it cant create the log file. Obviously there could well be a different reason but the symptoms you describe are associated with this problem. 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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