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

Re: [Ifeffit] error in ATOMS
by Ravel, Bruce 10 Nov '13

10 Nov '13

Julius, I am CCing my response to the Ifeffit mailing list (http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit) which is the appropriate venue for questions about the software. The problem you report is surprising to me and certainly not something I see normally. I will need to see an example on my own computer. If you could post an example of crystal data that triggers this, that would help. When you send this to the mailing list, also let us know what version of the software you are using. B Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel ________________________________ From: Julius Campecino [jcampecino(a)gmail.com] Sent: Saturday, November 09, 2013 11:58 AM To: Ravel, Bruce Subject: error in ATOMS Hi Bruce, I am a new user of ATOMS (as well as Athena and Artemis). Whenever I try to run atoms it gives me this error "Can't call method "tag" on an undefined value at C:/strawberry/perl/site/lib/Demeter/Atoms.pm line 662." I do not know how to fix that or go around it. Hopefully you can help. Thank you, Bruce. Julius

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re Athena: Target transform function not working
by fred.mosselmans＠diamond.ac.uk 10 Nov '13

10 Nov '13

Dear Bruce, Following the instructions you gave John Hayes, I tried installing this fix on both a windows XP and Windows 7 machine today. Installing the PCA.pm file in the strawberry\perl\site\lib\Demeter folder seems to result in the crashing Athena when the pca tab is selected. I initially replaced both PCA.pm files and crashed the program then replaced one at a time and it is this file which causes the crash. Looking at github I see it was last changed yesterday I think, so suspect you may have altered it recently in a less than perfect manner. Log file attached. Thanks Fred -- 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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Re: [Ifeffit] Ifeffit Digest, Vol 129, Issue 9
by KONG Qingyu 08 Nov '13

08 Nov '13

Hello Jason, Thank you. Could one obtain x% directly from Artemis? We have tried to use a separate program to do linear combination fitting using feff calculated paths, but not the same quality of fitting from Artemis. Best regards, Qingyu Kong -----Message d'origine----- De : ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] De la part de ifeffit-request(a)millenia.cars.aps.anl.gov Envoyé : jeudi 7 novembre 2013 19:00 À : ifeffit(a)millenia.cars.aps.anl.gov Objet : Ifeffit Digest, Vol 129, Issue 9 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. linear combination fitting (KONG Qingyu) 2. Re: linear combination fitting (Jason Gaudet) ---------------------------------------------------------------------- Message: 1 Date: Wed, 6 Nov 2013 19:57:07 +0000 From: KONG Qingyu <qingyu.kong(a)synchrotron-soleil.fr> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] linear combination fitting Message-ID: <30F62EE734A9EA45A3F211513CB62003B134D787(a)SUN-DAG1.synchrotron-soleil.fr> Content-Type: text/plain; charset="iso-8859-1" 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 Soci?t? 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 ------------------------------ Message: 2 Date: Wed, 6 Nov 2013 18:03:53 -0500 From: Jason Gaudet <jason.r.gaudet(a)gmail.com> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] linear combination fitting Message-ID: <CANMcWtP0z6vALK5XMWtXp1TawruMo3NeMxNeZNoA1kvZpjT3wA(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Hi Qingyu, Each Mo absorber contributes to the spectrum equally, so if you think you have a good analysis that indicates x% of Mo scatterers are most similar to Li2MoO3 and 100-x% are most similar to MoO3, those are simply atomic percentages. All you have to do is convert the atomic% to mass% using the formula weight of your components. -Jason On Wed, Nov 6, 2013 at 2:57 PM, KONG Qingyu < qingyu.kong(a)synchrotron-soleil.fr> wrote: > 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 >

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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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