January 2014 - 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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Re: [Ifeffit] MacPorts install of Demeter
by Martha W Schaefer 29 Jan '14

29 Jan '14

Hi Bruce, After fetching the new Demeter from MacPorts this morning, Atoms is now opening normally. I will be trying it out later today. I have been using Athena, just to plot and merge EXAFS data, and it is working well. The labels and spacing all look just like the Windows version, except that the buttons for plotting individual or sets of E, k, R, q, and kq have no color to them. The colors do show below that in the backgrounds of the mu(E), Background, pre-edge line, etc checkboxes. Thanks for all your hard work! Martha W. Schaefer Louisiana State University On Jan 28, 2014, at 12:00 PM, ifeffit-request(a)millenia.cars.aps.anl.gov wrote: > > Yay, indeed! Hopefully you and others will put Athena through her > paces (some LCF, some PCA, some aligning, some merging, ...) and let > me know if things look right. > > Also, if you see any places where labels don't seem to be written > properly or the spacing between controls seems weird, I'd like to see > a screenshot. >

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Demeter 0.9.18.3 on Mac OS X
by Schima, Frank 28 Jan '14

28 Jan '14

Hello Mac OS X users, I have updated the Demeter port in Macports on OS X to version 0.9.18.3 so that artemis and hephaestus now work! I also added symlinks to atoms and datoms. Thanks to Bruce Ravel for providing some quick fixes! If you already have the demeter port installed, this is how to update to the latest version. 1. Launch Terminal 2. Type: sudo port selfupdate 3. Type: sudo port upgrade outdated If you are installing for the first time, please see Bruce’s instructions on the wiki [1]. Cheers! Frank [1] <http://bruceravel.github.io/demeter/#mac>

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MacPorts install of Demeter
by Martha W Schaefer 27 Jan '14

27 Jan '14

First of all, thank you Frank so much for making the MacPorts install possible for Demeter! I have installed it on my MacBook Pro running MacOS 10.8.5, and here is a short report in how well it is running. Hope this is of use. Athena opens and looks normal so far. I have no trouble loading data and plotting. Yay! I think feff and feffit also work, but I don't know how to use the command line version so I haven't been able to test them yet. Artemis fails (as we were warned) with segmentation fault that crashed Perl. Hephaestus also fails (as warned), in the same way. Atoms does not open, and the following errors are produced: Attribute (txx) does not pass the type constraint because: Validation failed fo 'Num' with value 1.0000000 at /opt/local/lib/perl5/vendor_perl/5.16.1/darwinthread-multi-2level/Moose/Exception.pm line 37 Moose::Exception::_build_trace('Moose::Exception::ValidationFailedForInineTypeConstraint=HASH(0x7fcb4fe83b40)') called at reader Moose::Exception::trae (defined at /opt/local/lib/perl5/vendor_perl/5.16.1/darwin-thread-multi-2leve/Moose/Exception.pm line 9) line 7 Moose::Exception::trace('Moose::Exception::ValidationFailedForInlineTypConstraint=HASH(0x7fcb4fe83b40)') called at /opt/local/lib/perl5/vendor_perl/5.6.1/darwin-thread-multi-2level/Moose/Exception.pm line 49 Moose::Exception::BUILD('Moose::Exception::ValidationFailedForInlineTypConstraint=HASH(0x7fcb4fe83b40)', 'HASH(0x7fcb4fe839f0)') called at /opt/local/ib/perl5/vendor_perl/5.16.1/darwin-thread-multi-2level/Class/MOP/Method.pm line128 Class::MOP::Method::execute('Moose::Meta::Method=HASH(0x7fcb4ff6fac8)','Moose::Exception::ValidationFailedForInlineTypeConstraint=HASH(0x7fcb4fe83b40), 'HASH(0x7fcb4fe839f0)') called at /opt/local/lib/perl5/vendor_perl/5.16.1/darin-thread-multi-2level/Moose/Object.pm line 56 Moose::Object::BUILDALL('Moose::Exception::ValidationFailedForInlineTypConstraint=HASH(0x7fcb4fe83b40)', 'HASH(0x7fcb4fe839f0)') called at /opt/local/ib/perl5/vendor_perl/5.16.1/darwin-thread-multi-2level/Moose/Meta/Class.pm line282 Moose::Meta::Class::new_object('Moose::Meta::Class=HASH(0x7fcb4fe873b0), 'HASH(0x7fcb4fe839f0)') called at /opt/local/lib/perl5/vendor_perl/5.16.1/darin-thread-multi-2level/Moose/Object.pm line 27 Moose::Object::new('Moose::Exception::ValidationFailedForInlineTypeConsraint', 'type_constraint_message', 'Validation failed for \'Num\' with value .0000000', 'class_name', 'Xray::Crystal::Cell', 'attribute_name', 'txx', 'value, ' 1.0000000') called at /opt/local/lib/perl5/vendor_perl/5.16.1/darwin-threa-multi-2level/Moose/Util.pm line 51 Moose::Util::throw_exception('ValidationFailedForInlineTypeConstraint','type_constraint_message', 'Validation failed for \'Num\' with value 1.000000', 'class_name', 'Xray::Crystal::Cell', 'attribute_name', 'txx', 'value', ' 1.000000') called at accessor Xray::Crystal::Cell::txx (defined at /opt/local/libperl5/site_perl/5.16.1/darwin-thread-multi-2level/Xray/Crystal/Cell.pm line 133 line 9 Xray::Crystal::Cell::txx('Xray::Crystal::Cell=HASH(0x7fcb4b01e998)', ' 1.0000000') called at /opt/local/lib/perl5/site_perl/5.16.1/darwin-thread-multi2level/Xray/Crystal/Cell.pm line 170 Xray::Crystal::Cell::geometry('Xray::Crystal::Cell=HASH(0x7fcb4b01e998)) called at /opt/local/lib/perl5/site_perl/5.16.1/darwin-thread-multi-2level/Xry/Crystal/Cell.pm line 73 Xray::Crystal::Cell::__ANON__('Xray::Crystal::Cell=HASH(0x7fcb4b01e998), 0, 0) called at accessor Xray::Crystal::Cell::b (defined at /opt/local/lib/pel5/site_perl/5.16.1/darwin-thread-multi-2level/Xray/Crystal/Cell.pm line 75) lie 15 Xray::Crystal::Cell::b('Xray::Crystal::Cell=HASH(0x7fcb4b01e998)', 0) clled at /opt/local/lib/perl5/site_perl/5.16.1/darwin-thread-multi-2level/Xray/Cystal/Cell.pm line 64 Xray::Crystal::Cell::__ANON__('Xray::Crystal::Cell=HASH(0x7fcb4b01e998), 0, 0) called at accessor Xray::Crystal::Cell::a (defined at /opt/local/lib/pel5/site_perl/5.16.1/darwin-thread-multi-2level/Xray/Crystal/Cell.pm line 69) lie 15 Xray::Crystal::Cell::a('Xray::Crystal::Cell=HASH(0x7fcb4b01e998)', 0) clled at /opt/local/lib/perl5/site_perl/5.16.1/darwin-thread-multi-2level/Xray/Cystal/Cell.pm line 144 Xray::Crystal::Cell::clear('Xray::Crystal::Cell=HASH(0x7fcb4b01e998)') alled at /opt/local/lib/perl5/site_perl/5.16.1/darwin-thread-multi-2level/Demetr/Atoms.pm line 302 Demeter::Atoms::clear('Demeter::Atoms=HASH(0x7fcb4b016358)') called at opt/local/lib/perl5/site_perl/5.16.1/darwin-thread-multi-2level/Demeter/Atoms.p line 316 Demeter::Atoms::read_inp('Demeter::Atoms=HASH(0x7fcb4b016358)') called t /opt/local/lib/perl5/site_perl/5.16.1/darwin-thread-multi-2level/Demeter/Atom.pm line 169 Demeter::Atoms::__ANON__('Demeter::Atoms=HASH(0x7fcb4b016358)', 'atoms.np') called at constructor Demeter::Atoms::new (defined at /opt/local/lib/perl5site_perl/5.16.1/darwin-thread-multi-2level/Demeter/Atoms.pm line 926) line 103 Demeter::Atoms::new('Demeter::Atoms', 'file', 'atoms.inp') called at /ot/local/bin/atoms line 72 Martha W. Schaefer Louisiana State University

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Absorption-coefficient data repository?
by Damon Turney 27 Jan '14

27 Jan '14

Dear XAFS Community, I'm looking for values of absorption coefficient (or mass absorption coefficient) of ZnO in the XANES region of the Zn edge, but all the publications give XANES plots in "arbitrary units", so I have no way of knowing the absorption coefficient for ZnO. Does anybody know a data repository where absorption coefficients are collected? Thanks, Damon -- Damon Turney PhD Energy Institute, Department of Chemical Engineering City University of New York New York, NY 10031 dturney(a)che.ccny.cuny.edu office: (212) 650-5470 cell: (805) 571-3764 fax: (805) 823-4593

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Demeter on Mac OS X via Macports
by Schima, Frank 27 Jan '14

27 Jan '14

Hello Mac users, I finally have launched a Mac OS X version of Demeter 0.9.18.2 on Macports. I have not tested it very much because I’m not actually a Demeter user. It builds, launches and opens some example data but beyond that, it is untested. If the Mac version interests you, fire up your Terminal and follow these instructions: 1. *Carefully* follow the steps to install Macports. <http://www.macports.org/install.php> 2. Open a new Terminal window and type the following. It will take a while depending on your computer and network speed. sudo port install demeter 3. When it is done, launch Athena by typing the following in Terminal. Note: Make sure you are in a directory you have write permission to (like your home directory) because it creates hidden log files at launch time. athena It is a known issue that artemis and hephaestus do not launch right now, but Bruce is working on a fix that will be added soon. I'm not going to have time to debug people's Macports issues when installing Demeter with Macports, but tech support is available on the Macports Users mailing list [1]. You should not need any help installing if you correctly follow the intructions. Please let Bruce and I know if it works for you or not after you have it installed. I have only tested on OS X Mavericks and Mountain Lion so far. Keep in mind that this is the first working release candidate of Demeter on Mac OS X, so problems are going to be expected. Cheers! Frank [1] <https://lists.macosforge.org/mailman/listinfo/macports-users>

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Re: [Ifeffit] Ifeffit Digest, Vol 131, Issue 30
by Noffke, Louisa 27 Jan '14

27 Jan '14

Thanks Bruce, I had tried what Jeff had suggested and I got a response for 'echo $DISPLAY’ , but I’ve installed xquartz 2.7.5 now and am getting the plot window. Cheers, Louisa > > As for the missing plot window, have you tried following Jeff's advice > to George from over the weekend? > > B > >

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no plot window in athena Re: Demeter on Mac OS X via Macports
by Noffke, Louisa 27 Jan '14

27 Jan '14

Hi Frank, I’ve successfully completed the install of Demeter using Macports under Mavericks following your very clear instructions. Athena starts and imports data, but , similar to George’s experience, does not generate a plot. However, the plot buffer shows that plotting actions seem to be carried out, such as ## plot formatting set style line 20 linecolor rgb "#cccccc" set grid ls 20 set key top right width 1 height 1 box set label 99 '{/*0.6 Demeter 0.9.18 {\251} Bruce Ravel 2006-2013}' at screen 0.7, screen 0.02 font 'Arial' ## gnuplot script set title "{/*1.5 merge in k space}" set xlabel "{/*1.2 Wavenumber&{aa}({\305}^{-1})}" set ylabel "{/*1.2 k^{2} {\267} {/Symbol c}(k)&{aa}({\305}^{-2})}" set xrange [ 0 : 15 ] # merge: ifeffit group = zccvv plot '/Users/LouNo/.horae/stash/gp_igzcvjge' using 1:2 with lines ls 1 title "merge" … but there is no plot window. Also, the following error is printed to the bash terminal when a plot is requested: <2014-01-25 20:09:36.898 perl5.16[28306:507] CoreText performance note: Client called CTFontCreateWithName() using name "Lucida Grande" and got font with PostScript name "LucidaGrande". For best performance, only use PostScript names when calling this API.> Hope this info is helpful. Louisa Message: 1 Date: Fri, 24 Jan 2014 20:22:09 +0000 From: "Schima, Frank" <frank.schima(a)nist.gov<mailto:frank.schima@nist.gov>> To: "ifeffit(a)millenia.cars.aps.anl.gov<mailto:ifeffit@millenia.cars.aps.anl.gov>" <ifeffit(a)millenia.cars.aps.anl.gov<mailto:ifeffit@millenia.cars.aps.anl.gov>> Subject: [Ifeffit] Demeter on Mac OS X via Macports Message-ID: <FCAA45CB-E764-43F3-BF8D-6BD8BD605A36(a)nist.gov<mailto:FCAA45CB-E764-43F3-BF8D-6BD8BD605A36@nist.gov>> Content-Type: text/plain; charset="windows-1252" Hello Mac users, I finally have launched a Mac OS X version of Demeter 0.9.18.2 on Macports. I have not tested it very much because I?m not actually a Demeter user. It builds, launches and opens some example data but beyond that, it is untested. If the Mac version interests you, fire up your Terminal and follow these instructions: 1. *Carefully* follow the steps to install Macports. <http://www.macports.org/install.php> 2. Open a new Terminal window and type the following. It will take a while depending on your computer and network speed. sudo port install demeter 3. When it is done, launch Athena by typing the following in Terminal. Note: Make sure you are in a directory you have write permission to (like your home directory) because it creates hidden log files at launch time. athena It is a known issue that artemis and hephaestus do not launch right now, but Bruce is working on a fix that will be added soon. I'm not going to have time to debug people's Macports issues when installing Demeter with Macports, but tech support is available on the Macports Users mailing list [1]. You should not need any help installing if you correctly follow the intructions. Please let Bruce and I know if it works for you or not after you have it installed. I have only tested on OS X Mavericks and Mountain Lion so far. Keep in mind that this is the first working release candidate of Demeter on Mac OS X, so problems are going to be expected. Cheers! Frank [1] <https://lists.macosforge.org/mailman/listinfo/macports-users>

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Re: [Ifeffit] Ifeffit Digest, Vol 131, Issue 26
by Danilo Oliveira de Souza 23 Jan '14

23 Jan '14

Dear Bruce and Matt, I really appreciate for your patience and answers. I always knew that all messages on the mailing list have been archived and I've tried to check in the archives for an answer, but I can't proceed with it because it seems that the link to the old discussions was broken on IFEFFIT site at that time! Anyway, I thank you guys again! *Danilo OLIVEIRA DE SOUZA* (PhD student) Université de Sciences et Technologies de Lille (Université Lille 1) UCCS - Unité de Catalise et Chimie du Solid, Bat. C3, Bureau 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 2014/1/22 <ifeffit-request(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. "Save marked groups as..." command (Danilo Oliveira de Souza) > 2. Re: "Save marked groups as..." command (Bruce Ravel) > 3. Re: "Save marked groups as..." command (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 22 Jan 2014 16:40:56 +0100 > From: Danilo Oliveira de Souza <danilo.olsouza(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] "Save marked groups as..." command > Message-ID: > < > CANbKcaVUm4ZQVq+zWeiOfMhU3APEcFCn0t+Uz6SeHiQyM05xTw(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear list, > > I have a big collection of data from a catalytic reaction. > I tried to export all the spectra (about 200) to a unique file containing > the normalized ones. I used the "File>Save marked groups as>norm(E)" > option. > Unfortunately, Athena (Demeter 0.9.18) is not able to make one unique file > (it crashes and I have to initialize it again), instead I had to creat 4 > different files of 45 spectra each (the maximum group I could gather on a > file). Is there any bug on it or some kind of limitation to creat these > kind of files? > > Best regards, > > > *Danilo OLIVEIRA DE SOUZA* (PhD) > Universit? de Sciences et Technologies de Lille (Universit? Lille 1) > UCCS - Unit? de Catalise et Chimie du Solid, Bat. C3, 110. > Cit? Scientifique, 59655, VIlleneuve d'Ascq CEDEX, France. > > danilo.olsouza(a)gmail.com > d.oliveira-de-souza(a)ed.univ-lille1.fr > tel: +33 06.63.55.86.12 >

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"Save marked groups as..." command
by Danilo Oliveira de Souza 22 Jan '14

22 Jan '14

Dear list, I have a big collection of data from a catalytic reaction. I tried to export all the spectra (about 200) to a unique file containing the normalized ones. I used the "File>Save marked groups as>norm(E)" option. Unfortunately, Athena (Demeter 0.9.18) is not able to make one unique file (it crashes and I have to initialize it again), instead I had to creat 4 different files of 45 spectra each (the maximum group I could gather on a file). Is there any bug on it or some kind of limitation to creat these kind of files? Best regards, *Danilo OLIVEIRA DE SOUZA* (PhD) 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, France. danilo.olsouza(a)gmail.com d.oliveira-de-souza(a)ed.univ-lille1.fr tel: +33 06.63.55.86.12

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