October 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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Fwd: problem compiling ifeffit
by Bruce Ravel 10 Nov '13

10 Nov '13

Rene, Support for the software is done via the Ifeffit Mailing List. This and all other questions should be asked in that forum. http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit please note that I am CCing my answer to the mailing list. All follow-up discussion should be on the mailing list rather than by responding to me directly. Regarding the problem with png files and PGPLOT, the solution of installing libpng12-devel is the much better solution. Regarding the problem compiling the file decod.f, I am going to blame Matt for that one. It seems he made a change to that file in August of 2012 (which is more recently than the last time I did a "git pull" on ifeffit!) Pulling and attempting to rebuild, I get the same result. Fixing the problem required editing the file encod.h to define the missing symbol "jtait". I just forked ifeffit, fixed the problem, and sent Matt a pull request. Here it is: https://github.com/newville/ifeffit/pull/4 If you follow the little link that says "97f6458", you'll see the diff. If you make the edit yourself, you should be able to finish compilation. Or wait for Matt to merge the pull request, do a git pull, then finish building. Regards, B -------- Original Message -------- Subject: problem compiling ifeffit Date: Thu, 31 Oct 2013 17:36:24 +0100 From: René Genz <liebundartig(a)freenet.de> To: <bravel(a)bnl.gov> Dear Mr. Ravel, today I tried to install the latest version of Demeter on Fedora 18 x86_64 following the instructions: http://bruceravel.github.io/demeter/pods/installation.pod.html In the past I could install ifeffit on Fedora 16 x86_64. But now I need your help. I encountered a problem in compiling ifeffit. This problem is reproducible on Ubuntu 12.04 i686. Furthermore, there are two minor things that I would like to mention as well: - PGPLOT_install does not set return code, if PGPLOT was not properly installed - ./configure of ifeffit echos the following line and continues without a problem "./configure: line 3355: #include: command not found" Details about the problem follow: I used the default installation selection for Fedora (Gnome Desktop). After installation I executed the following commands $ sudo yum install -y perl gnuplot gcc gcc-gfortran libX11-devel ncurses ncurses-devel libpng libpng-devel giflib wxGTK-devel git $ cd $ git clone https://github.com/newville/ifeffit.git $ cd ifeffit $ sudo ./PGPLOT_install The compilation started by the script fails. The attached file Demeter__F20__x86-64__PGPLOT_install.txt shows the last part of the output. I could work around this problem in two ways. Either a) sudo ./PGPLOT_install --no-png OR b) sudo yum install libpng12-devel ; sudo ./PGPLOT_install I used 'a)' and PGPLOT could be installed by the script. So I continued with the compilation of ifeffit. This is where I encountered a problem that I could not solve. $ ./configure was OK, just one line catched my attention "./configure: line 3355: #include: command not found" $ make The full output is in Demeter__F20_x86-64__ifeffit-configure-make.txt Here is the last part of the output: gfortran -g -O2 -fPIC -c iff_sync.f gfortran -g -O2 -fPIC -c decod.f decod.f:191.26: elseif (ic.eq.jtait) then 1 Error: Symbol 'jtait' at (1) has no IMPLICIT type make[3]: *** [decod.o] Error 1 make[3]: Leaving directory `/home/user/ifeffit/src/lib' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/user/ifeffit/src' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/user/ifeffit' make: *** [all-recursive-am] Error 2 The error message refers to ./src/lib/decod.f I do not know how to solve this problem. Do you have a suggestions how to solve this? -- Kind regards, René

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modeling significant defects and molecules
by Carl Brozek 31 Oct '13

31 Oct '13

dear listhost, I would like to use Artemis/Atoms to simulate EXAFS of a crystalline material with significant defects that include additional atoms to the unit cell. Can I simulate this material without making a new cif file? Ideally, I would be able to input a DFT-optimized model cluster as xyz coordinates only -- no crystallographic information. This problem seems analogous to modeling discrete molecules. Can molecules be simulated by atoms/artemis? I know FEFF is capable of this, but I would like to use atoms for making my input file for feff. Carl -- PhD Candidate | Chemistry | MIT SB | 2010 | University of Chicago

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Athena crash report
by George Sterbinsky 31 Oct '13

31 Oct '13

Hello, I am writing to report a crash of Athena 0.9.18 running on Ubuntu 12.04 as a virtual machine. The terminal output is below. Let me know if I can provide any additional information. Thanks, George parallels@parallels-Parallels-Virtual-Platform:~$ dathena Attribute (bkg_nor1) does not pass the type constraint because: Validation failed for 'Num' with value 15. at accessor Demeter::Data::bkg_nor1 (defined at /home/parallels/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data.pm line 264) line 12, <F> line 1. Demeter::Data::bkg_nor1(Demeter::Data=HASH(0xd26a1b0), 15.) called at /home/parallels/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena/Main.pm line 843 Demeter::UI::Athena::Main::OnParameter(Demeter::UI::Athena::Main=HASH(0xaf7f780), Wx::CommandEvent=SCALAR(0xc130520), Demeter::UI::Athena=HASH(0x186fad0), "bkg_nor1") called at /home/parallels/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena/Main.pm line 341 Demeter::UI::Athena::Main::__ANON__(Demeter::UI::Athena::Main=HASH(0xaf7f780), Wx::CommandEvent=SCALAR(0xc130520)) called at /home/parallels/perl5/bin/dathena line 47 eval {...} called at /home/parallels/perl5/bin/dathena line 47 parallels@parallels-Parallels-Virtual-Platform:~$

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calculating particle size from coordination numbers
by Georges Siddiqi 31 Oct '13

31 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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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 31 Oct '13

31 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 26 Oct '13

26 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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