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

Re: [Ifeffit] LCF
by Jason Gaudet 07 Nov '13

07 Nov '13

It depends how you want to set up your guess-def-set parameters. For argument I'll describe a system of BCC Mo metal and MoO3, where you want to determine what fraction of Mo is in each. My usual method is just to set each path as N=1, SO2=amp_O for Mo-O, and N=1, SO2=amp_Mo for Mo-Mo. Then, in guess-def-set, I'd GUESS N_Mo = 8 N_O = 6 SET (SO2 as determined by my standards) so2=0.87 and DEFINE my amplitudes amp_Mo = N_Mo*so2 amp_O = N_O*so2 (And of course you want all the other parameters as well, I'm just showing the amplitude ones.) Then, once I get my N_Mo and N_O I can scale these to my expected coordination numbers and see if I get reasonable contributions for each. (Is N_Mo/8 + N_O/6 = 1?) If I had a really good reason to believe all Mo metal in my sample had an average Mo-Mo coordination of exactly 8 and all Mo oxide had an average Mo-O coordination of exactly 6, I could define things another way. SET N_Mo = 8 N_O = 6 so2=0.87 DEFINE amp_Mo = N_Mo*so2*Frac_metal amp_O = N_O*so2*(1-Frac_metal) GUESS Frac_metal=0.5 And that constrains all the amplitude parameters so the only result is what atomic fraction of Mo is present in the metal phase. Makes sense? -Jason On Thu, Nov 7, 2013 at 2:05 PM, KONG Qingyu < qingyu.kong(a)synchrotron-soleil.fr> wrote: > Hello Jason, > > Thanks a lot for your reply. > > What I can get from Artemis is the fitted parameters (amp, enot, ss^2, > delr) of each path, Mo-O, Mo-Mo, how can one get the percentage of Mo, x > from Li2MoO3 and 100-x from MoO3, from the fitted information. > > Best regards, > > > Qingyu > > Beamline ODE > Société civile Synchrotron SOLEIL > L'Orme des Merisiers > Saint-Aubin - BP 48 > 91192 GIF-sur-YVETTE CEDEX > Tel: +33 (0)1 69 35 97 84 (office) > +33 (0)1 69 35 97 16 (beamline) > email: kong(a)synchrotron-soleil.fr >

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linear combination fitting
by KONG Qingyu 06 Nov '13

06 Nov '13

Hello, We measured EXAFS of a mixed sample of Li2MoO3 and MO3, with Artemis we fitted the data with two FEFF calculations using the crystal structures of Li2MoO3 and MO3, the fitting results are quite good. We would like to know the weight of Li2MoO3 and MO3 in the sample, how can we get this value from Artemis? Thanks a lot in advance. Qingyu Kong Beamline ODE Société civile Synchrotron SOLEIL L'Orme des Merisiers Saint-Aubin - BP 48 91192 GIF-sur-YVETTE CEDEX Tel: +33 (0)1 69 35 97 84 (office) +33 (0)1 69 35 97 16 (beamline) email: kong(a)synchrotron-soleil.fr

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Re: [Ifeffit] Is it possible to use ATOMS to solve this problem?
by Matt Newville 05 Nov '13

05 Nov '13

Hi Aderson, On Tue, Nov 5, 2013 at 8:16 AM, Áderson Miranda <aderson.mir(a)gmail.com>wrote: > Dear Prof. Newville, > I am a PhD. student from Brazil and I am trying to use ATOMS to a solve a > particular problem in my thesis. I would like to generate a big cubic > unitary cell with a S2O3 molecule surrounded by six water molecules in the > center of cell and to put heliums atoms in their six vertices. > > I have all the atoms positions optimized to my problem, except by the > helium atoms, that I want to place in a enough distance to have only one > molecule of S2O3 surrounded by water in the simulation of EXAFS. I tried to > insert the data in atoms and generate an input for the simulation of > EXAFS. I was not successful in my try, so is it possible to construct this > kind of cell and simulating the "EXAFS" for this specific problem? > > Sincerely, > > Áderson Miranda > > Yes, it should be possible to do this. It would be most helpful to see what you've tried and what worked and what did not. It's not obvious to me that helium will give a noticeable contribution to the EXAFS, but it's worth being able to calculate. I am using the Ifeffit mailing list to respond to this mail, as many people reading this have extensive experience constructing such molecular coordinates. --Matt

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Header information data Lepidocrocite
by Florian Werner 05 Nov '13

05 Nov '13

Hi All, I'm trying to find my way into XAFS data processing with Athena, but I'm new to the topic. I hope someone can help me out with my questions. As background information: Currently I'm planning my beamtime experiment for XANES spectra about phosphorus speciation at SLRI in Thailand. I have made a tutorial with data from Bruce Ravel from scans of Lepidocrocite. I have a question regarding this data. For example in the header information of file Fe_lepidocrocite.000 (from Bruce Ravel's github site) there can be found the abbreviations SRB, SRSS and SPP. So my first question is: What do this abbreviations stand for? SRB is the sampling range (SR..?!), i guess, so what does 15k stand for (data ends at 7971.35723 keV, but how is this connected to "15k"?)? SRSS manages the step size (..SS?), but how does "0.05k" result in the given steps? I assume that this kind of "k"-settings may be limited to X-23A2 beamline (or BNL), but still I'm anxious to know how the data has been collected. Best regards, Florian

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Lead reference compounds
by Luxton, Todd 01 Nov '13

01 Nov '13

Hi All, I am looking for spectra of three lead compounds, and I am hoping someone has one or all of the spectra. I am looking for Coronadite (lead manganese oxide), Plumboferrite, (lead iron oxide), and Magnetoplumbite (Iead iron oxide). Any help would be greatly appreciated. Best Regards Todd Luxton "A nation that destroys its soils, destroys itself" Franklin D. Roosevelt

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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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