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

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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