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

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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about 0.9.19
by Bruce Ravel 21 Jan '14

21 Jan '14

I want to thank Shoaib, Georges, Robert, and Kevin for their helpful feedback on the various problems with the 0.9.19 installer package. In light of these issues, I have rolled back the Demeter home page at http://bruceravel.github.io/demeter/. It again lists and links to 0.9.18 as the current version. There is a link to the problematic 0.9.19 package at the bottom of the page. I will keep working on these problems and hope to have a new and well-functioning installer package soon. 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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Demeter not working on Windows 8.1 64bit
by Shoaib Muhammad 14 Jan '14

14 Jan '14

Hi, I have recently upgraded my computer to Windows 8.1 Pro x64 and after this upgrade I can't run Athena and Artemis. The problem symptoms are: 1- If I use Demeter version 0.9.13, Athena opens but when I try to open previously saved file, Athena simply crashes without showing any error. Artemis also shows similar behavior. 2- By using latest build Demeter 0.9.19, Athena behavior is slightly different it opens the files and show the plot. But pressing the E,k,R buttons does not change the plot. Artemis still crashes by opening any project file without any error. I have tried following things, installed in compatibility mode of Windows7. Athena worked fine only once after installing in compatibility mode. Installed in different drives but situations remains the same. Tried to "run as Admin" but no improvement. Installed Demeter on three different computers running Windows 8.1 x64 but similar behavior is received. Kindly suggest me some work around because I have to use Demeter on almost daily basis. I have attached log file obtained from Demeter 0.9.13 running under Window 8.1 x64. Thanks, Shoaib Muhammad Department of Energy Science Sungkyunkwan University South Korea

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Re: [Ifeffit] Demeter 0.9.19
by Bruce Ravel 14 Jan '14

14 Jan '14

On 01/09/2014 08:24 AM, Stefano Luciano Ciurli wrote: > Hello Bruce and thank you for your hard work! > instructions to install on OS X 10.6.8? There is not a Mac package. I do not own a Mac and and so do not have the ability to develop a Mac package on my own. Over the years, no one has ever stepped up to help me develop a Mac package for Demeter. (Or Debian packages, or RedHat packages, for that matter.) Frankly, the work I do on the Windows package takes a lot of time. The only way I can claim that time fits in my job description is because my group uses Windows machines at our beamlines. Help would be welcome to develop packages for Mac and other platforms, but despite repeated requests over many years, no one has ever volunteered and actually seen it through to completion. So, you have four choices here: 1. Find other software 2. Use a virtual machine and run the Windows package 3. Install Demeter from source, including all the dependencies 4. If you do #3, then you might as well step up and help make a package happen on the platform of your choice 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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