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

Fwd: from Rui Si at SSRF: help needed
by Bruce Ravel 18 Jul '14

18 Jul '14

Hi Rui, I am CCing my answer to you and to the Ifeffit Mailing List. It's always a good idea to use the mailing list as it greatly increases the number of eyes that get to look at your question. If you reply to this, please do so via the mailing list. In the PDF file you attached, you asked these two questions: (1) Why the second peak (ca. 3 Å) in experimental data is missing in the Co3O4 model? I do not know anything about your sample, so this is a tough question. Are you certain of its phase purity? Could there be another form of cobalt oxide present in the sample? (2) Why need to add the “shift vector” suggested by Artemis? Actually, no action is required and the software change the Co core from 0.125, 0.125, 0.125 to 0.5 0.5 0.5, and keep the shift vector as 0 0 0. The purpose of the shift vector is explained here: http://bruceravel.github.io/demeter/artug/atoms/space.html#multipleoriginsa… In the case of the CIF file you attached, the shift vecotr does not seem required. The list of atomic coordinates without the shift vecotr looks right to me. B -------- Original Message -------- Subject: from Rui Si at SSRF: help needed Date: Tue, 15 Jul 2014 07:33:31 +0000 From: 司锐 <sirui(a)sinap.ac.cn> To: bravel(a)bnl.gov <bravel(a)bnl.gov> Hi Bruce, Here, I have a question needs your help on the EXAFS fittings. When I tried to fit the Co3O4 standard (cif and apj file attached), there was a "shift vector" problem, which has been resulted in the mismatch between experimental data and theoretic model. Please see the details in the attachment. I am not familiar with crystal models, and thus I cannot find the key. Could you please help me? Many thanks! Best, Rui ---------------------------------------------------------- Dr. Rui Si Shanghai Institute of Applied Physics, Chinese Academy Sciences Shanghai Synchrotron Radiation Facility Address: 239 Zhangheng Rd, Pudong District Shanghai 201204, China E-mail: sirui(a)sinap.ac.cn Tel: (86)21-33932079 Cell:(86)13301753969

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demeter-devel: Athena autosave hang issue
by Jennifer Carter 16 Jul '14

16 Jul '14

Installed the newest version of the software for the Mac OS X earlier this week. v129-22-124-229:~ jwc137$ port installed ifeffit p5.16-ifeffit demeter-devel The following ports are currently installed: demeter-devel @0.9.20pre10_0 (active) ifeffit @1.2.11c_0+gcc48 ifeffit @1.2.13_0+gcc48 (active) p5.16-ifeffit @1.0.0_0 p5.16-ifeffit @2_0 (active) Now when I try to run athena the software hangs on an autosave file. I am unable to click either button the the pop-up menu to advance the software and I get the "application not responding" error. I searched for an athena.autosave file, as discussed in a previous thread about this issue, but don't find one. v129-22-124-229:~ jwc137$ find athena.autosave find: athena.autosave: No such file or directory Cheers Jennifer ᐧ

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Re: [Ifeffit] crystallite size determination by EXAFS
by Rana, Jatinkumar Kantilal 16 Jul '14

16 Jul '14

Dear Prof. Frenkel, Many thanks for your detailed explanation about my queries. I would appreciate if you could send me the electronic copy of your article (at Jatinkumar.rana(a)helmholtz-berlin.de ): D. Glasner and A. I. Frenkel Geometrical characteristics of regular polyhedra: Application to EXAFS studies of nanoclusters AIP Conf. Proc. 882, 746-748 (2007). We may have further discussion on this topic, once I go through the suggested literature. With best regards, Jatin -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: 16 July, 2014 03:19 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 137, Issue 42 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: ATOM and GDS (Sin Yuen Chang) 2. Re: ATOM and GDS (Bruce Ravel) 3. Re: crystallite size determination by EXAFS (Anatoly I Frenkel) ---------------------------------------------------------------------- Message: 1 Date: Tue, 15 Jul 2014 17:27:50 +0000 From: Sin Yuen Chang <sinyuen.chang(a)postgrad.manchester.ac.uk> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] ATOM and GDS Message-ID: <62C8FAC78934514E930100B52B3D4A17010AC2C612(a)MBXP05.ds.man.ac.uk> Content-Type: text/plain; charset="us-ascii" Hi Dien Li, I had the same problem with ATOM in Demeter version 0.9.18 used in Windows 7, the "Add a site" icon doesn't work for me for some reasons. To add another row of atomic coordinate, what works for me is: 1. right click on any space on the table of atomic coordinate. 2. choose "Copy site" 3. right click again 4. choose "Paste site" [cid:image001.png@01CFA05A.7CE0C5C0] Hope this helps, Sin Yuen -- Sin Yuen, Chang PhD Student, School of Chemical Engineering and Analytical Science, The University of Manchester, M13 9PL Manchester. From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Dien.Li(a)srs.gov Sent: 14 July 2014 21:26 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] ATOM and GDS HI, Bruce and Matt For the Demeter version I am using, I found that I could just enter 8 atoms in ATOM, and define 12 variables in GDS. Could I enter more atoms in ATOMS, and define more variables in GDS? and How? Thanks. Dien Li, Ph.D. Environmental Sciences and Biotechnology Savannah River National Laboratory Aiken, South Carolina, 29808 Tel: 803-725-7520

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crystallite size determination by EXAFS
by Rana, Jatinkumar Kantilal 16 Jul '14

16 Jul '14

Dear all, I have some questions regarding crystallite size determination by EXAFS. I am investigating a system where there is a formation of metallic Cu in the system. I could see the presence of metallic Cu in the sample by XRD and EXAFS. However, high resolution TEM does not show any evidence of metallic Cu, perhaps the crystallite size is much smaller than the resolving power of the microscope and/or these crystallites are highly disordered. Nevertheless, I thought of estimating the size of Cu crystallites by EXAFS. I know at least two approaches described by two prominent members of the mailing list, Scott Calvin and Anatoly Frenkel. The approach by Scott Calvin (http://link.aip.org/link/JAPIAU/v94/i1/p778/s1&Agg=doi) estimates crystallite size based on an assumption that they are spherical in shape. On the other hand, Anatoly Frenkel’s approach estimates both size and shape of crystallites based on the number of neighbors in each coordination shell obtained from EXAFS fit http://pubs.acs.org/doi/abs/10.1021/jp012769j I have questions about the second approach. I would like to know how to calculate the number of neighbors in various coordination shells as a function of cluster size for different shapes ? Conversely, if one knows the number of neighbors in various shells from EXAFS fits, then how to correlate those numbers to clusters of different sizes and shapes as discussed by Anatoly Frenkel. I know my questions are very specific, but I am sure many in the list would have already tried both these approaches and may provide some valuable insights. Many thanks in advance ! With best regards, Jatin ________________________________ Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph Geschäftsführung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de

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ATOM and GDS
by Dien.Li＠srs.gov 15 Jul '14

15 Jul '14

HI, Bruce and Matt For the Demeter version I am using, I found that I could just enter 8 atoms in ATOM, and define 12 variables in GDS. Could I enter more atoms in ATOMS, and define more variables in GDS? and How? Thanks. Dien Li, Ph.D. Environmental Sciences and Biotechnology Savannah River National Laboratory Aiken, South Carolina, 29808 Tel: 803-725-7520

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Re: [Ifeffit] Ifeffit Digest, Vol 137, Issue 36
by Dien.Li＠srs.gov 15 Jul '14

15 Jul '14

Hi, Bruce With your instruction, we solved the GDS issue. However, for ATOM, I was screened out to the link you posted. Is there any way to just send me an ATOM file that has many more atom entry lines, I can use it as a template. Thanks you so much. Dien Li, Ph.D. Environmental Sciences and Biotechnology Savannah River National Laboratory Aiken, South Carolina, 29808 Tel: 803-725-7520 From: ifeffit-request(a)millenia.cars.aps.anl.gov To: ifeffit(a)millenia.cars.aps.anl.gov, Date: 07/14/2014 07:10 PM Subject: Ifeffit Digest, Vol 137, Issue 36 Sent by: ifeffit-bounces(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. Re: ATOM and GDS (Bruce Ravel) 2. Re: ATOM and GDS (Carter Abney) 3. Re: Macports ifeffit and Demeter Update (Jennifer Carter) ---------------------------------------------------------------------- Message: 1 Date: Mon, 14 Jul 2014 18:28:43 -0400 From: Bruce Ravel <bravel(a)bnl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] ATOM and GDS Message-ID: <53C4599B.4090601(a)bnl.gov> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 07/14/2014 04:25 PM, Dien.Li(a)srs.gov wrote: > For the Demeter version I am using, I found that I could just enter 8 > atoms in ATOM, and define 12 variables in GDS. Could I enter more atoms > in ATOMS, and define more variables in GDS? and How? Thanks. The fact that the "add site" button on the atoms page was broken is among the things on the list of changes for the version I have been working to get tested and released. https://github.com/bruceravel/demeter/blob/master/Changes.org As for the GDS page, there are several ways of adding a new GDS entry, described here http://bruceravel.github.io/demeter/artug/gds.html On the path page, in the box which contains the math expression for a path parameter, try right clicking on GDS parameter. It'll pop up a menu that allows you to define a new parameter. It seems I neglected to put that last thing in the document -- that needs to be fixed. 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 ------------------------------ Message: 2 Date: Mon, 14 Jul 2014 22:40:12 +0000 From: Carter Abney <abneycw(a)uchicago.edu> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] ATOM and GDS Message-ID: <B4E36C4B6D5E674FB469E2B23AC64D723729B06C(a)xm-mbx-04-prod.ad.uchicago.edu> Content-Type: text/plain; charset="us-ascii" Dr Li, If I'm understanding the questions properly, there should be some fairly straightforward fixes. Simplest first: in GDS, there should be a button on the right side that says "Add GDS." Clicking on it will give you additional variables (or definitions, restraints, etc.) in GDS. Otherwise, you could right-click on the numbers to the left of the "type" column. You'll get options like "insert blank line above (or below) current row." This is convenient for keeping your variables grouped intelligently while fitting. To the best of my knowledge, there is no maximum number of lines in GDS, though your number of variables should be limited by 2/3 the number of independent points available from your data. Additionally, you're only allowed a maximum of 10 restraints at any time in a fit. Regarding Atoms, it sounds like you're trying to manually add elements to the coordination sphere of your absorbing element. There should be a button, "add a site" which will allow you to add more than 8 elements. That said, I've never prepared my scattering pathways in this fashion (this probably says more about my inexperience than anything else). Most of the time, I call Atoms from Artemis, input a cif file, run atoms, run feff, and have a list of scattering pathways afterwards. If your system isn't crystalline, you can run several Feff calculations with different cif files which have the correct absorbing atom and an appropriate scattering atom. (You have to add each of these Feff calculations in Artemis individually.) Then, use the generated scattering paths to model your data. Also, Atoms allows a person to modify the input file (I believe they're referred to as "cards") as a text document from within the Atoms program. So, if I have a model with no cif file, I can run atoms with any other cif file to generate some sort of card for feff, then I can edit the card appropriately by copy/pasting the Cartesian coordinates and defining the appropriate ipot value for each element. If you have the card already generated from another cif file, it's fairly straightforward to edit it to represent your model. - Carter Message: 2 Date: Mon, 14 Jul 2014 16:25:40 -0400 From: Dien.Li(a)srs.gov To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] ATOM and GDS Message-ID: <OF5F2EDED2.B07C6B62-ON85257D15.006FF11D-85257D15.007036E1(a)srs.gov> Content-Type: text/plain; charset="us-ascii" HI, Bruce and Matt For the Demeter version I am using, I found that I could just enter 8 atoms in ATOM, and define 12 variables in GDS. Could I enter more atoms in ATOMS, and define more variables in GDS? and How? Thanks. Dien Li, Ph.D. Environmental Sciences and Biotechnology Savannah River National Laboratory Aiken, South Carolina, 29808 Tel: 803-725-7520

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Macports ifeffit and Demeter Update
by Schima, Frank 15 Jul '14

15 Jul '14

Mac OS X users, Thanks to help from Bruce Ravel and Matt Newville, I have updated ifeffit and Demeter-devel in Macports to fix a number of problems reported. To update from your current version type the following: sudo port selfupdate sudo port upgrade outdated To install from scratch after installing Macports [1]: sudo port selfupdate sudo port install demeter-devel When done, your should see the following ports installed: $ port installed ifeffit p5.16-ifeffit demeter-devel The following ports are currently installed: demeter-devel @0.9.20pre10_0 (active) ifeffit @1.2.13_0+gcc48 (active) p5.16-ifeffit @2_0 (active) Please reply to the list (NOT to me directly) about how this works for you. Cheers! Frank [1] <https://www.macports.org/install.php>

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Re: [Ifeffit] ATOM and GDS
by Carter Abney 14 Jul '14

14 Jul '14

Dr Li, If I'm understanding the questions properly, there should be some fairly straightforward fixes. Simplest first: in GDS, there should be a button on the right side that says "Add GDS." Clicking on it will give you additional variables (or definitions, restraints, etc.) in GDS. Otherwise, you could right-click on the numbers to the left of the "type" column. You'll get options like "insert blank line above (or below) current row." This is convenient for keeping your variables grouped intelligently while fitting. To the best of my knowledge, there is no maximum number of lines in GDS, though your number of variables should be limited by 2/3 the number of independent points available from your data. Additionally, you're only allowed a maximum of 10 restraints at any time in a fit. Regarding Atoms, it sounds like you're trying to manually add elements to the coordination sphere of your absorbing element. There should be a button, "add a site" which will allow you to add more than 8 elements. That said, I've never prepared my scattering pathways in this fashion (this probably says more about my inexperience than anything else). Most of the time, I call Atoms from Artemis, input a cif file, run atoms, run feff, and have a list of scattering pathways afterwards. If your system isn't crystalline, you can run several Feff calculations with different cif files which have the correct absorbing atom and an appropriate scattering atom. (You have to add each of these Feff calculations in Artemis individually.) Then, use the generated scattering paths to model your data. Also, Atoms allows a person to modify the input file (I believe they're referred to as "cards") as a text document from within the Atoms program. So, if I have a model with no cif file, I can run atoms with any other cif file to generate some sort of card for feff, then I can edit the card appropriately by copy/pasting the Cartesian coordinates and defining the appropriate ipot value for each element. If you have the card already generated from another cif file, it's fairly straightforward to edit it to represent your model. - Carter Message: 2 Date: Mon, 14 Jul 2014 16:25:40 -0400 From: Dien.Li(a)srs.gov To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] ATOM and GDS Message-ID: <OF5F2EDED2.B07C6B62-ON85257D15.006FF11D-85257D15.007036E1(a)srs.gov> Content-Type: text/plain; charset="us-ascii" HI, Bruce and Matt For the Demeter version I am using, I found that I could just enter 8 atoms in ATOM, and define 12 variables in GDS. Could I enter more atoms in ATOMS, and define more variables in GDS? and How? Thanks. Dien Li, Ph.D. Environmental Sciences and Biotechnology Savannah River National Laboratory Aiken, South Carolina, 29808 Tel: 803-725-7520

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Energy shift in exported data
by George Sterbinsky 12 Jul '14

12 Jul '14

Hello, I have noticed the following behavior in Athena 0.9.20 on OSX 10.8.5. If a group with an energy shift applied is exported as norm(E) using the export marked groups option then the energy shift is not preserved in the .nor file. If the export current group option is used then the energy shift is preserved. This seems to be general behavior and should be straightforward to reproduce, but I can provide an example project if needed. Thank you, George

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Athena/Artemis/Atoms OSX (10.9.3) issues
by Jennifer Carter 11 Jul '14

11 Jul '14

I am running into the following issues (screen shots for each are attached) *1st) starting athena from the terminal* I get the following message but the software hangs (rainbow wheel of death) and I am unable to advance to the main page "Athena found and autosave file. Would you like to import" I tried uninstalling in terminal: sudo port uninstall xorg-server demeter and reinstalling in terminal: sudo port install xorg-server demeter but the program still hangs *2nd) The screens for artemis and atoms have black backgrounds so that the text is hidden.* As a new user I am having a hard time using the software in a semi-blind mode. Thanks Jennifer ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Jennifer L.W. Carter Assistant Professor Department of Materials Science and Engineering Case Western Reserve University *500B White Building* *10900 Euclid Ave.Cleveland, OH 44106-4901phone: (216) 368-4214email: jennifer.w.carter(a)case.edu <jennifer.w.carter(a)case.edu>* [image: Inline image 3] [image: Inline image 4] ᐧ

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