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

ODP: EXAFS with multiple absorbers
by Kicaj 22 Feb '14

22 Feb '14

You compute the EXAFS signal for each absorber, also for different sublattices. As result you get the superimpose of all signals. Sent from mobile -------- Oryginalna wiadomość -------- Temat:[Ifeffit] EXAFS with multiple absorbers Od:Francisco Garcia <garcia.ff.000(a)gmail.com> Do:ifeffit@millenia.cars.aps.anl.gov DW: Dear users, I would like to know if FEFF8 or FEFF9 can compute the EXAFS when multiple absorbers are present in the sample. Thank you.

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Re: [Ifeffit] [ifeffit] XAS lectures
by fred.mosselmans＠diamond.ac.uk 21 Feb '14

21 Feb '14

Hi Velea I am pleased to say that the videos of the esteemed Dr Ravel giving his lectures at Diamond in November 2011 are now available again on our new Diamond website but at a new page http://www.diamond.ac.uk/Beamlines/Spectroscopy/Techniques/XAS.html Please Bruce and anyone else who links to these videos update those links. We find the vlc media player is good for viewing these. Regards Fred Prof. J F W Mosselmans Principal Beamline Scientist I18 Diamond Light Source Diamond House Harwell Campus Didcot Oxon OX11 ODE UK T 00 44 1235 778568 M 00 44 7785510211 E fred.mosselmans(a)diamond.ac.uk F 00 44 1235 778448 Never mind the W it's the tax that counts -- 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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XAS lectures
by Velea Alin 20 Feb '14

20 Feb '14

Hi Bruce, I was watching yesterday your lectures from XAS workshop (http://www.diamond.ac.uk/Home/Events/Past_events/XAS-workshop-2011.html?mgn…) hosted by Diamond. I was just finishing your tutorials on Athena and today I was planning to start on Artemis. The surprise was that the link is not working anymore ("The page may have been moved or deleted permanently"). Do you know anything about this? They've decided to take them down? Can I get somewhere else a copy of the videos? Thanks, Alin

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job opening at PETRA III / University Paderborn: XES
by Matthias Bauer 13 Feb '14

13 Feb '14

Dear mailing list users, please find attached a job offer for a postdoc at PETRA III, funded by the university of Paderborn. Main task will be the set-up of a dispersive spectrometer for X-ray emission an application of the technique to study chemical reactions in the wide field of sustainable processes and energy conversion. Please do not hesitate to contact me in case of questions, best regards, Matthias -- Prof. Dr. Matthias Bauer Universität Paderborn Naturwissenschaftliche Fakultät Department Chemie Warburger Straße 100 33098 Paderborn Tel.: 05251-605614 matthias.bauer(a)upb.de

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Demeter not open in Windows and can't import raw data in Mac
by Mengling Stuckman 12 Feb '14

12 Feb '14

Hi, all, I'm a new user of Demeter and unfortunately I have problems with installing and using Demeter for both operating systems. In Windows 7 enterprise, all of my Demeter programs (updated to version 0.9.18.2) can't open. In the %APPDATA%\Roaming\demeter\dathena.log, the following message showed up if I tried to open Athena: "Can't load 'C:/strawberry/perl/site/lib/auto/Wx/Wx.dll' for module Wx: load_file:The network path was not found at C:/strawberry/perl/lib/DynaLoader.pm line 200. at C:/strawberry/perl/site/lib/Wx/Perl/SplashFast.pm line 60 Compilation failed in require at C:\strawberry\perl\site\bin\dathena.bat line 23. BEGIN failed--compilation aborted at C:\strawberry\perl\site\bin\dathena.bat line 23." If I tried to open Artemis, the same error message showed up. I did go through the mailing list to search for similar topics, but I can't find any .mru file or .cwd file in folder %APPDATA%\Roaming\demeter\ to delete. Is there anything else I can do to solve this problem? In my mac OS X 10.7.5, I did successfully install Demeter onto my system and was able to open any files in the .prj file in Athena. However, when I tried to import the raw XANES data files, like sample.0001 or sample.0002, Athena would close. At the same time on Terminal, the follow message showed up: "At line 436 of file iff_show.f Fortran runtime error: End of record" The mac version is very new, I don't know if any user has similar issue to not? Thank you very much! Any reply would be highly appreciated! Mengling -- Mengling Stuckman ORISE Research Fellow National Energy Technology Laboratory U.S. Department of Energy Pittsburgh, PA STUCKMAN.MENGLING(a)CONTR.NETL.DOE.GOV Office: 412-386-7387

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Problem opening demeter in Windows 7
by Arjen van Veelen 12 Feb '14

12 Feb '14

Dear Bruce, In October last year (October 22) I reported a problem in Demeter. I couldn't open Artemis or Athena. The only thing happening was two screens popping up quickly before disappearing. You replied that you had never seen this problem before. Since then I have used Demeter in Ubuntu. Now, first I have to be honest. I haven't read all the threads posted about windows problems with Demeter lately, so I do apologize if you have this solution already posted somewhere. I have been looking into this problem today on my computer again as I found it very frustrating switching between two OS. So, I checked my local environment settings and for some reason there was a whole list of crappy paths accumulated under PATHS. Don't ask me why, I have no idea how this happened. I deleted, after uninstalling Demeter first, everything related to strawberry in PATHS. I also deleted strawberry in C:\strawberry. Then I reinstalled Demeter and everything seems to work fine. Maybe this will be helpful for some people experiencing a similar problem. 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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Re: [Ifeffit] Correct Crystallographic parameters for Todorokite EXAFS fit
by Sathish Mayanna 09 Feb '14

09 Feb '14

Dear Dr. Robert Thanks a lot for your information that's very helpful. I checked the ICSD, but unfortunately we don't have access to the crystal data. It would be great, if you or someone has the access to the crystal data to provide me the coordinates, the *collection code: 202727, Author: Post, Year: 1988. * *Please let me know, if someone has the access to the data.* Regards Sathish On Thu, Feb 6, 2014 at 11:05 PM, <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. Re: Correct Crystallographic parameters for Todorokite EXAFS > fitting in Artemis (Robert Gordon) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 06 Feb 2014 16:05:30 -0600 > From: Robert Gordon <ragordon(a)alumni.sfu.ca> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Correct Crystallographic parameters for > Todorokite EXAFS fitting in Artemis > Message-ID: <52F4072A.1070008(a)alumni.sfu.ca> > Content-Type: text/plain; charset="iso-8859-1"; Format="flowed" > > Hi Satty, > > The crystal data in your inp file came from the paper. I checked the > International > Crystal Structure Database (ICSD) - printout attached. The structure > data in the paper > are not in standard form - atoms might not give the correct results if > the input is bad- and there > are typos for two of the O5 coordinates according to the ICSD warning. > Does your institution have access to the ICSD - Online or on disc? If you > are not familiar with it, try talking to one of your institution's > reference librarians. > > I'm not certain what you mean by the corner-corner Mn. You were choosing > Mn1 > as the core in your inp. When I look at the structure, Mn1 sits in the > middle of > the set of 3 octahedra that make up a side of the tunnel. Where would > the corner-corner > distance be relative to the middle of the chain? You have 4 different Mn > sites. > > Fitting in R-space is common. > > As for learning about crystal structures, try sitting in on a > coordination chemistry > or solid state chemistry course. For a basic learning book, I like > West's "Basic Solid > State Chemistry" or Muller's "Inorganic Structural Chemistry" (again, > try the library > if you don't want to buy a copy). More recent books may be available. > A bit of > googling may reveal some online lessons, like: > http://www.seas.upenn.edu/~chem101/sschem/solidstatechem.html > > > regards, > Robert > > > On 2/6/2014 3:16 AM, Sathish Mayanna wrote: > > Hi > > > > I am having some problem to get the real crystallographic parameters > > for Todorokite (I know there are many literature available) I used the > > parameters from Post et al 1988 (/Rietveld refinement of the > > Todorokite structure/) and others as well (*attached Todorokite.inp > > file*). > > > > I except the corner corner Mn in Todorokite, since its a tunnel > > structure, but the Feff calculations do not provide any corner corner > > Mn, in addition I cannot fit exactly even Mn-O or Mn-Mn. > > > > But If I use Ramsdellite (*attached Ramsdellite.inp file*), which is > > also a tunnel structure, I could get the Corner-Corner Mn and can fit > > perfectly the Mn-O, Mn-Mn, but cannot fit in K space. > > > > It would be really great, if anyone could provide me the model Tunnel > > type-Mn oxide crystallographic parameters to fit the data *(attached > > Mn Spectra.prj)* > > > > p.s: I tried my best to learn and understand the crystallographic > > parameters and miller indices, but still I feel that I am very poor, > > it would be nice, if someone suggest some good and basic source to > > learn more about pure mineralogy (which is crucial to know the basic > > parameters for fitting in Artemis). > > -- > > Satty > > > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > -- > Dr. Robert Gordon > Staff Scientist, PNCSRF > APS Sector 20 (PNC/XSD) > 9700 S Cass Ave. 435E > Argonne, IL, USA 60439 > > 630-252-0581 > 630-252-0580 fax > >

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Athena doesn't open anymore
by Kuri, Ulises 07 Feb '14

07 Feb '14

I am having problems opening Athena. Reading the iffefit mailing list I found a similar problem posted by Roberto Rodriguez on 29 May 2013. I tried to delete the .mru file. but still I have same problem dathena.log says: Failed to load YAML document from 'C:\Users\Sof\AppData\Roaming\demeter\athena.cwd' at C:/strawberry/perl/vendor/lib/YAML/Tiny.pm line 593 YAML::Tiny::LoadFile('C:\Users\Sof\AppData\Roaming\demeter\athena.cwd') called at C:/strawberry/perl/site/lib/Demeter/UI/Athena.pm line 81 Demeter::UI::Athena::OnInit('Demeter::UI::Athena=HASH(0x270eb0c)') called at C:/strawberry/perl/site/lib/Wx/App.pm line 36 eval {...} called at C:/strawberry/perl/site/lib/Wx/App.pm line 36 Wx::App::new('Demeter::UI::Athena') called at C:\strawberry\perl\site\bin\dathena.bat line 57 I will appreciate any help. Sorry if the issue is already solved in the mailing list, but I did not find it Ulises

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Correct Crystallographic parameters for Todorokite EXAFS fitting in Artemis
by Sathish Mayanna 06 Feb '14

06 Feb '14

Hi I am having some problem to get the real crystallographic parameters for Todorokite (I know there are many literature available) I used the parameters from Post et al 1988 (*Rietveld refinement of the Todorokite structure*) and others as well (*attached Todorokite.inp file*). I except the corner corner Mn in Todorokite, since its a tunnel structure, but the Feff calculations do not provide any corner corner Mn, in addition I cannot fit exactly even Mn-O or Mn-Mn. But If I use Ramsdellite (*attached Ramsdellite.inp file*), which is also a tunnel structure, I could get the Corner-Corner Mn and can fit perfectly the Mn-O, Mn-Mn, but cannot fit in K space. It would be really great, if anyone could provide me the model Tunnel type-Mn oxide crystallographic parameters to fit the data *(attached Mn Spectra.prj)* p.s: I tried my best to learn and understand the crystallographic parameters and miller indices, but still I feel that I am very poor, it would be nice, if someone suggest some good and basic source to learn more about pure mineralogy (which is crucial to know the basic parameters for fitting in Artemis). -- Satty

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EXAFS simulations - peak too high
by Lisa Bovenkamp 03 Feb '14

03 Feb '14

Hello. I am running some EXAFS simulations Au L3 on Au clusters with SR coating. In the outer shell Au sits between 2 S atoms. 4 Au atoms are in the neighborhood up to 3.5 Angström. Expecting two peaks in the chi(R) - one for Au-S and one for Au-Au (here it can be several little ones) I find that for 1 out of 5 sites the Au-Au peak is way too high. Is something in the FEFF code weighing an Au-Au path for this site too much? Does anyone have some ideas on that? Thanks, Lisa

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Re: [Ifeffit] EXAFS simulations - peak too high
by Lisa Bovenkamp 03 Feb '14

03 Feb '14

Dear Anatoly. Yes, I know that paper. In order to expand that study from pure gold to bimetallic clusters I want to be sure and repeat the results that this group found. Thanks for mentioning it. Dear Scott, That was the answer I was looking for. I believe the paths are reinforcing each other. This is now obvious from the Im chi(R). Thanks for the presentation of yours. Now one question remains: Do I discard/disregard this site from my calculations (in the averaging process) or not? Thanks. Lisa

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How can I fit the results obtained from FEFF9 to the experimental data using the ARTEMIS.
by Abhijeet Gaur 03 Feb '14

03 Feb '14

Hi, I have started using FEFF9 recently. I am using it to generate theoretical model for some copper compounds and complexes. As you have mentioned in one of research article' Nuclear Instruments and Methods in Physics Research A 619(2010)28-32' How can I fit the results obtained from FEFF9 to the experimental data using the ARTEMIS. I have tried to search the answer on the ifeffit mailing list but unable to find a satisfactory one. With thanks in advance -- Dr. Abhijeet Gaur

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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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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 15 Jan '14

15 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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Connecting Artemis to FEFF9.6.4
by Bao Nguyen 12 Jan '14

12 Jan '14

Dear all, I'm new and have a daff question which must have been asked before: Can I refer Artemis to FEFF9.6.4, which I have, rather than the standard-issued FEFF6 for more streamlined structural refinement? Many thanks! Bao Nguyen Tenure-track Research Fellow School of Chemistry University of Leeds Woodhouse Lane Leeds, UK Tel: +44 (0)1133430109

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