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

Fwd: problems by using Artemis and Demeter
by Bruce Ravel 28 Jul '14

28 Jul '14

Marika, I am responding via the Ifeffit mailing list, which is the appropriate venue for questions about the software. Please use it. It is to your significant benefit to use the mailing list as it exposes you to other people who may be able to answer your questions. This is particularly useful at a time when I am on vacation, as I was for the last several days. You did not identify the version of Artemis that you are using, although your email suggests that you are not using the most current version. I simply do not have the resources to provide support for any but the most recent version of my software. Your postscript comment is similarly ambiguous in that you did not tell me what file you were attempting to import nor what actions you took. See this page of the document: http://bruceravel.github.io/demeter/artug/startup/main.html#thefilemenu and, in particular, note the explanation of the "Import" submenu, which provides a tool for importing project files (.apj) from the very old version of Artemis. As I have discussed many times on the mailing list, .apj file import is spotty, but has imporved over time as people have reported problems in a way that is clear and actionable. Cheers, B -------- Forwarded Message -------- Subject: problems by using Artemis and Demeter Date: Thu, 24 Jul 2014 17:26:57 +0200 From: Vespa, Marika (INE) <marika.vespa(a)kit.edu> To: bravel(a)bnl.gov <bravel(a)bnl.gov> Dear Bruce, I encountered a problem that Artemis is only showing the fit results in the top of the results window: Later where a summary is usually shown it is left blank: R-factor for this data set = 0.46013 pathdegen amp sigma^2 e0 reff delta_R R ------------------------------------------------------------------------ I started a new project sequentially reading the FEFF paths and the problem appear after I have read in the fist C-path (U_oxo_carboante.prj). Would you have any idea? Best regards, Marika P.S. I have tried to use Demeter, but there I was not able to open a saved project -- 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://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

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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 15 Jul '14

15 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 11 Jul '14

11 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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Re: [Ifeffit] trial release #9 for Windows for Demeter 0.9.20 (Bruce Ravel)
by Badari Rao 11 Jul '14

11 Jul '14

Dear Dr. Bruce, I am not able to download the installation file from the link provided by you. It gives some kind of "access denied" error. I don't know if this is caused by some firewall from my institute or is a genuine problem. I have attached a screenshot of the error. Could you perhaps provide another link to download the file? [image: Inline image 2] Thanking You, -- Yours Sincerely, Badari Narayana. A. R. Ph.D Student, Nanoscience and Nanotechnology, c/o Prof Rajeev Ranjan, Electroceramics Lab, Department of Materials Engineering, Indian Institute of Science.

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trial release #9 for Windows for Demeter 0.9.20
by Bruce Ravel 09 Jul '14

09 Jul '14

As I promised Badari yesterday, I have a new trial release for Demeter on Windows: 64 bit: https://s3.amazonaws.com/demeter4xas/Demeter_Installer_for_Windows_0.9.20_(… 32 bit: https://s3.amazonaws.com/demeter4xas/Demeter_Installer_for_Windows_0.9.20_(… This fixes both of the issues Badari reported. It also fixes Margaret Anne's problem with the Spec file with a really long line without needing a plugin. There are also a number of improvements to Atoms even compared to the previous trial release. An update to demeter-devel on MacPorts is not yet available, but will be soon. Those who build Demeter from source can clonw from the head of the github repository. Cheers, 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-devel Athena on OS 10.9.4
by Emmanuelle Montarges-Pelletier 08 Jul '14

08 Jul '14

Dear all I have just installed Demeter-devel on a computer Mac OS X 10.9.4, following the suggestions of Frank Schima and the different steps for installing xcode and command tools, macports, Xquartz. The mailing list was really helpful, thanks! After having written Athena on a terminal window I have apparently the same "freezing" phenomena reported earlier by Margaret Hinkle, July 4th 2014 " With the new demeter-devel Macports download, Athena freezes upon opening. Opening up Athena via Terminal brought up perl5.16 -- I could see the GUI, the Tip of the Day, and the Athena startup box, but the system just froze. I had to force quit every time, getting the following notice in my Terminal: 'Terminated: 15'.". I don't know how to solve this Athena blocking and completely lost when I read the solution provided by Bruce " Look for the '[athena]' section of demeter.ini, which should be in '$HOME/.horae'. Set the "tips" parameter to "false". That will suppress the tips dialog." I really tried to do on my own,...but I have to be honest, I don't know how to change the tips parameter. I would need a specific lesson, something entitled "demeter for dummies". So, could someone help me? Thanks for your answer Best Regards Emmanuelle -- ................................................. Emmanuelle Montarges-pelletier CR CNRS LIEC UMR 7360 CNRS-Université Lorraine 15 avenue du Charmois BP40 54500 Vandoeuvre les Nancy France tel 33 (0)3 83 59 62 52 fax 33 (0)3 83 59 62 55 mob 33 (0)6 31 33 10 30 emmanuelle.montarges(a)univ-lorraine.fr Zone Atelier Moselle http://www.ensic.inpl-nancy.fr/Zam/

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Possibly will join, I am from MPI- Stuttgart. EOM
by Devender 08 Jul '14

08 Jul '14

On Tue, Jul 8, 2014 at 12:54 PM, Edmund Welter <edmund.welter(a)desy.de> wrote: > Dear mail list users, > > > as you probably know the next XAFS conference (XAFS 16) will be held > from August 23rd to 28th 2015 in Karlsruhe, Germany. Around the main > conference a small number of Satellite meetings will be organised. One of > these meetings will be organised at the DESY site in Hamburg, Germany. The > title of this Satellite meetings is: “Data acquisition, treatment, storage > – quality assurance in XAFS spectroscopy“. Almost 5 years after the Q2XAFS > workshop in Tsukuba, Japan the idea behind this meeting is, to recapitulate > the developments during the last 5 years and to discuss strategies for > further improvement of XAFS data taking and XAFS data evaluation and > storage. > > First information about the meeting is summarised in the attached flyer > and on the meeting's webpage (see: > https://indico.desy.de/conferenceDisplay.py?confId=10169) The > information on the webpage will be updated and further information > especially about registration, travel and accommodation added as soon as it > becomes available. > > Please send me a mail if you have any comment, suggestions for further > session topics and/or questions! I am also interested in getting a first > impression about the possible number of participants and would therefore > appreciate if you send me (edmund.welter(a)desy.de) a short notice if you > could imagine to participate in the meeting. > > > Best regards > > Edmund Welter > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > -- Devender Graduate Student, Materials Science and Engineering Rensselaer Polytechnic Institute, Troy, NY Website <https://sites.google.com/site/devendermaun/>

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XAFS 16 Sat. Meeting announcement
by Edmund Welter 08 Jul '14

08 Jul '14

Dear mail list users, as you probably know the next XAFS conference (XAFS 16) will be held from August 23rd to 28th 2015 in Karlsruhe, Germany. Around the main conference a small number of Satellite meetings will be organised. One of these meetings will be organised at the DESY site in Hamburg, Germany. The title of this Satellite meetings is: "Data acquisition, treatment, storage -- quality assurance in XAFS spectroscopy". Almost 5 years after the Q2XAFS workshop in Tsukuba, Japan the idea behind this meeting is, to recapitulate the developments during the last 5 years and to discuss strategies for further improvement of XAFS data taking and XAFS data evaluation and storage. First information about the meeting is summarised in the attached flyer and on the meeting's webpage (see: https://indico.desy.de/conferenceDisplay.py?confId=10169) The information on the webpage will be updated and further information especially about registration, travel and accommodation added as soon as it becomes available. Please send me a mail if you have any comment, suggestions for further session topics and/or questions! I am also interested in getting a first impression about the possible number of participants and would therefore appreciate if you send me (edmund.welter(a)desy.de) a short notice if you could imagine to participate in the meeting. Best regards Edmund Welter

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Re: [Ifeffit] How to distinguish whether the coordination
by Michael Weir 07 Jul '14

07 Jul '14

Hi Matt and Zhan, I think this is the point where adding another approach would be very useful. In my limited experience, XAFS was much more powerful when combined with other techniques to eliminate potential models. We also needed to use our "chemical sense". Is there a reason you would suspect Se, Ge, Ga, or any of the other elements in your material? Could you use your beamline to look for these elements by a quick scan of one of their stronger transitions? If there is a full coordination shell, detecting the other element this way is feasible. However, as someone else mentioned recently, dopants would be much more difficult to detect. Is there another analytical technique you could use to narrow down the possible elements in your system? I hope that answering those questions helps you answer your question about the system. Also, thank you Bruce, Matt, Scott and others for the very useful discussions on this list. Michael Weir Hi Zhan, On Mon, Jul 7, 2014 at 3:40 AM, ZHAN Fei <zhanfei(a)ihep.ac.cn> wrote: > Hi Matti? > Thanks for your attention and patience. > The back fourier transform of the specific peak (use window)of Chi(R) > gives the amplitude,donated by amp_bft?As in previous mails,I ask whether > the compare the amp_bft and the amplitude of specific Z number element can > determine the Z. > Sorry, I'm not sure I understand this. I didn't understand the figure you attached in your earlier mail. Generally speaking, I find back-transformed data to be not very useful -- making any sense of these requires very well isolated shells of atoms. The amplitude of the back-transformed chi(k) (is that what you mean by amp_bft??) has many contributions, and is not simply f(k). It will have Z dependence, but it will have other dependencies too. > And thanks for telling me the useful trick using the total phase shift of > the specific element. > > > The discrepancy between R and Rphcor is below,the Zn and Br is close to > Se(the best fit)'s 0.013, > Yes, Ge actually gives the closest match, and Se the second closest match, and I left Ga out of the test. I would probably say that anything closer that 0.015 Ang (and, really, maybe 0.02 Ang) is pretty darn close. So the phase-correction approach appears to be (in this case) not as sensitive to Z as the reduced chi-square, but does provides a check on self-consistency. The fits with Zn and Rb are noticeably worse than the fit with Se... hence Z +/- 3 or perhaps 5 seems like a reasonable rule of thumb, and sometimes one might be able to do better. > should the enot also be important criterion in this trick?and dose the > plus or minus of enot indicate the lighter or higher element relative to > the specific coordination shell? > Well, an E0 shift > 10 eV probably indicating that something is off .... but that could be just the selection of E0 for the experimental data. I wouldn't put much meaning of the absolute value of E0 though for any single fit. "a bond valence sum can be an independent check on the consistency of N, > R, and valence",can your give the ref. paper of this method? Thanks > > http://en.wikipedia.org/wiki/Bond_valence_method The idea is that N, R, and valence are not independent. --Matt --

2 1

Multiple phases in samples
by Dien.Li＠srs.gov 07 Jul '14

07 Jul '14

Hi, All "Assuming" there are multiple phases in one sample, saying, U on goethite, U on organic matter, and uraninite, how to fit the EXAFS data using Artemis? Thanks. Dien Li, Ph.D. Environmental Sciences and Biotechnology Savannah River National Laboratory Aiken, South Carolina, 29808 Tel: 803-725-7520

2 1

Re: [Ifeffit] Bug Report: Error while handling files in Athena in the latest version, Demeter 0.9.20_pre7
by Badari Rao 07 Jul '14

07 Jul '14

Dear Chris, I am facing the same problem in both windows xp (32 bit) as well as windows 7 (64 bit) operating systems. Dear Matt, These two problems are not file specific since I have confirmed it with many files and also with different systems. (windows xp as well as windows 7). Dear Bruce, Thank you for taking note of the problem. - Badari

1 0

Demeter-devel MacPorts Athena issues & work-around
by Margaret Hinkle 07 Jul '14

07 Jul '14

Dear OS X Users, First let me thank Frank Schima for fixing the issues with Artemis and ATOMS with his new demeter-devel Macports download -- I (and all Mac users) greatly appreciate it! I thought I would bring two issues with Macports Athena to your attention... FYI, I am using Mac OS X Mavericks v. 10.9.4, with an Intel processor. I followed the directions found here today to delete the old version of demeter and download the new one: http://www.mail-archive.com/ifeffit%40millenia.cars.aps.anl.gov/msg04404.ht… Issue 1. With the new demeter-devel Macports download, Athena freezes upon opening. Opening up Athena via Terminal brought up perl5.16 -- I could see the GUI, the Tip of the Day, and the Athena startup box, but the system just froze. I had to force quit every time, getting the following notice in my Terminal: 'Terminated: 15'. I had a feeling it was an issue with the Tip of the Day popping up, so I edited the Athena.pm file (in the UI folder), and edited line 197 from ‘$app->show_tip if Demeter->co->default('athena', 'tips');’ TO ‘$app->show_tip if Demeter->co->default('athena', 'tip');’ (honestly, I don't know enough about this code to be able to give it a real option that would turn off the Tip of the Day as the default, so I just hoped this would make the program give me general error in the GUI but that Athena could still load). Luckily, my not-fix fix worked. I get an error every time I open it, but after clicking 'OK', Athena behaves just like normal. I hope you can use this information to provide a real fix to the problem! Issue 2. I can only load data files into Athena if there are no headers of any sort -- commenting out each header line with a # or % does not work. When I try to load in a .dat file with a commented-out header, I get the following error message in Terminal: 'At line 436 of file iff_show.f Fortran runtime error: End of record' followed by Athena quitting itself. This is an issue with both the regular Macports demeter download and the demeter-devel download. These data files loaded in just fine to the old iXAFS version of Athena, and on a PC. Is there a plugin I should be using in the Demeter versions? If I delete the header, or load it in from a .prj file, everything works just fine. So it is not huge issue, as I do have a work around. Thank you, Frank, for the new version of Demeter, and thank you all for any thoughts you have on Issue 2. Best regards, Margaret Anne ------------------------------------ Margaret Anne G. Hinkle Ph.D. Candidate Earth and Planetary Sciences Washington University in St. Louis Rudolph Hall Campus Box 1169 1 Brookings Drive St. Louis, MO 63130 email: mhinkle(a)eps.wustl.edu website: aqgeochem.wustl.edu

5 11

Bug Report: Error while handling files in Athena in the latest version, Demeter 0.9.20_pre7
by Badari Rao 07 Jul '14

07 Jul '14

Dear Sir, I am facing two problems while handling files in Athena. First of all, when I freshly open Athena and import a file, it gives some kind of warning, which says can't locate Encoding/FixLatin/XS.pm in @NIC.. etc. I have attached a screenshot of the warning message. However, I could continue with my work without any problem, and importing more files did not give this warning. The second problem, which is a major one is that I am not able to use the "align data" option. Whenever I select my data and click on "align data", the software crashes and closes. kindly look into this issue. I would also like to mention that both these bugs were not present in the earlier version: Demeter 0.9.20_pre5. Thanking You, -- Yours Sincerely, Badari Narayana. A. R. Ph.D Student, Nanoscience and Nanotechnology, c/o Prof Rajeev Ranjan, Electroceramics Lab, Department of Materials Engineering, Indian Institute of Science. [image: Inline image 2]

4 3

How to distinguish whether the coordination element is heavy or light
by ZHAN Fei 07 Jul '14

07 Jul '14

Dear all, when I try to solve my question{[Ifeffit] path contribution to fit in low R-space position, but the fit bond length is much longer than that},I find a method from Prof.Calvin to distinguish whether coordination shell is composed by light or heavy element: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2007-December/007983.html A clue can perhaps be obtained by noting the relative height of the peak near 2.3 angstroms compared with the large peak you've fit. As k- weight is raised from 0 to 1 to 2 to 3, the peak at 2.3 angstroms does not grow relative to the first peak. That suggests the scattering may be from another low-Z element like oxygen. But I still don't know ,why it works. Thanks for your patience, Sincerely, zhanfei

4 8

Athena crash report
by George Sterbinsky 04 Jul '14

04 Jul '14

Hello, I am running Athena 0.9.20 on OSX 10.8.5. Selecting the difference spectra tool from the drop-down menu causes Athena to crash and the following message to print to the terminal. Usage: Wx::ComboBox::GetClientData(THIS, n) at /opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level/Demeter/UI/Athena/Difference.pm line 215, <F> line 339. I've tried this with several different projects and it appears to be general behavior. If I can provide any additional information please let me know. Thank you, George

2 1

Re: [Ifeffit] Matthew Marcus Ifeffit Digest, Vol 137, Issue 5
by Teck Kwang Choo 03 Jul '14

03 Jul '14

To: Matthew Marcus Hi Matthew, would you be able to send me the executable file and manual for PCA? My spectra files are in .dat form . Thanks and kind regards. Teck Kwang Choo PhD Candidate Department of Chemical Engineering Room 225, Building 36 Monash University Mobile No.: 04-11489904 On 3 July 2014 16:19, Teck Kwang Choo <teck.kwang.choo(a)monash.edu> wrote: > Thanks everyone for the suggestions! I will give Six pack a go first since > I have that software. If that doesn't work, I'll send another message. > > I wish you all a pleasant day. > > Teck Kwang Choo > PhD Candidate > Department of Chemical Engineering > Room 225, Building 36 > Monash University > Mobile No.: 04-11489904 > > > On 3 July 2014 01:33, <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: Principal Component Analysis (PCA) for XANES >> (fred.mosselmans(a)diamond.ac.uk) >> 2. Re: Principal Component Analysis (PCA) for XANES (Matthew Marcus) >> 3. Re: Ifeffit Digest, Vol 137, Issue 4 (Abhijeet Gaur) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Wed, 2 Jul 2014 07:48:29 +0000 >> From: <fred.mosselmans(a)diamond.ac.uk> >> To: <ifeffit(a)millenia.cars.aps.anl.gov> >> Subject: Re: [Ifeffit] Principal Component Analysis (PCA) for XANES >> Message-ID: >> < >> CF65047C5B0562499EAFF9FBBC542D64757859A1(a)EXCHMBX01.fed.cclrc.ac.uk> >> Content-Type: text/plain; charset="us-ascii" >> >> >> Dear Teck, >> >> ITFA does transformation factor analysis as well, if you just want to do >> PCA, the PCA module in Sam Webb's sixpack is quite intuitive to use. >> https://home.comcast.net/~sam_webb/sixpack.html >> >> cheers >> 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 >> >> >> >> >> >> >> >> ------------------------------ >> >> Message: 2 >> Date: Wed, 02 Jul 2014 08:33:25 -0700 >> From: Matthew Marcus <mamarcus(a)lbl.gov> >> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >> Subject: Re: [Ifeffit] Principal Component Analysis (PCA) for XANES >> Message-ID: <53B42645.5040005(a)lbl.gov> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >> Athena (IFEFFIT package) does it. So does the ALS Beamline 10.3.2 >> software package at >> https://sites.google.com/a/lbl.gov/microxas-lbl-gov/software . >> If you can't get at it there, I can send the executable and manual. >> mam >> >> On 7/1/2014 10:59 PM, Teck Kwang Choo wrote: >> > Hi Everyone, >> > >> > Does anyone know what software I should use to perform a Principal >> Component Analysis (PCA) on my K-edge XANES spectra (for sulfur)? The >> reason I need to use this technique is because I have a couple of reference >> compound spectra but am not sure which of those I should use to fit my >> unknown sample spectrum. >> > >> > Any help is appreciated. >> > >> > Thanks and kind regards. >> > >> > >> > Teck Kwang Choo >> > PhD Candidate >> > Department of Chemical Engineering >> > Room 225, Building 36 >> > Monash University >> > Mobile No.: 04-11489904 >> > >> > >> > _______________________________________________ >> > Ifeffit mailing list >> > Ifeffit(a)millenia.cars.aps.anl.gov >> > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> > >> >> >> ------------------------------ >> >> Message: 3 >> Date: Wed, 2 Jul 2014 21:03:17 +0530 >> From: Abhijeet Gaur <abhijeetgaur9(a)gmail.com> >> To: ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >> Subject: Re: [Ifeffit] Ifeffit Digest, Vol 137, Issue 4 >> Message-ID: >> <CAEq27Q2UkMuFScofU8w20jO= >> 7A34MkyKkimSgy5+h+7B_NCZ-w(a)mail.gmail.com> >> Content-Type: text/plain; charset="utf-8" >> >> Hi Teck Kwang Choo, >> >> For PCA analysis you can use SixPack >> data analysis package by Dr. Sam Webb available at >> https://home.comcast.net/~sam_webb/sixpack.html. >> >> Also you can use Dmeter by Dr Bruce Ravel >> available at http://bruceravel.github.io/demeter/. >> >> With best wishes >> >> Dr Abhijeet Gaur >> >> >> >> >> On Wed, Jul 2, 2014 at 12:52 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. spam on our mailing list (Bruce Ravel) >> > 2. Re: to use scattering path in different model or to construct >> > a new model which is the combination of different simple compound >> > (Bruce Ravel) >> > 3. Principal Component Analysis (PCA) for XANES (Teck Kwang Choo) >> > 4. Re: Principal Component Analysis (PCA) for XANES >> > (Amayri, Dr. Samer) >> > >> > >> > ---------------------------------------------------------------------- >> > >> > Message: 1 >> > Date: Tue, 01 Jul 2014 13:31:59 -0400 >> > From: Bruce Ravel <bravel(a)bnl.gov> >> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >> > Subject: [Ifeffit] spam on our mailing list >> > Message-ID: <53B2F08F.7000401(a)bnl.gov> >> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> > >> > >> > Hi all, >> > >> > Over the years we've done a pretty good job of keeping spam off this >> > mailing list. As you saw, one slipped through this afternoon. Hopefully >> > it was a one-time event and it will not be necessary to change the >> > friendly nature of security on the list. >> > >> > 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: Tue, 01 Jul 2014 15:16:20 -0400 >> > From: Bruce Ravel <bravel(a)bnl.gov> >> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >> > Subject: Re: [Ifeffit] to use scattering path in different model or to >> > construct a new model which is the combination of different >> simple >> > compound >> > Message-ID: <53B30904.5030207(a)bnl.gov> >> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> > >> > On 07/01/2014 10:43 AM, ZHAN Fei wrote: >> > > 1 In the example,multiplet scattering path comes from two model >> > > respectively,if use path from different model in different shell's >> > > fit,there is risk of ignore important multiple path across >> models.Should >> > > construct a cluster ,run feff to ensure? >> > >> > I don't completely understand the question, but I'll give it a try. >> > >> > In the example of Shelly's paper, she had a situation where she >> > *couldn't* write a single feff.inp file. Her local environment was the >> > average of all possible ways that the uranyl ion could bond to biomass. >> > The uranyl binding disproportionated into a pH-dependent mixture of >> > carboxyl, phosphoryl, and hydroxyl sites. There was simply no way to >> > write a feff.inp file for that. So her solution was to run Feff more >> > than once, picking and choosing paths that represented her best guess >> > for modeling the average bonding environment. >> > >> > I think what you are really getting at, though, is whether it was right >> > for Shelly to use parts of Feff calculations on a crystals to model >> > something else. If you were to read up on the theory used in Feff, you >> > would find that the important thing is that the muffin tin radii of the >> > scatterers get calculated reasonably. Unless Shelly had a reason to >> > think that the interatomic distances in her biomass sample were VERY >> > different than in the crystals she used to run Feff, then the scattering >> > amplitudes and phase shifts were almost certainly computed quite well >> > enough. >> > >> > > 2 I have confusion of the relationship pf N between single path and >> > > multiple path,for example I think U-Oe-C U-Oe-Pshould be 1 2 >> > > respectively,instead 2 4 in paper. >> > >> > I think Scott's explanation is correct. In real-space, >> > multiple-scattering theory, both ways around a three-legged path have to >> > be counted. >> > >> > 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: 3 >> > Date: Wed, 2 Jul 2014 15:59:25 +1000 >> > From: Teck Kwang Choo <teck.kwang.choo(a)monash.edu> >> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >> > Subject: [Ifeffit] Principal Component Analysis (PCA) for XANES >> > Message-ID: >> > < >> > CAHXRQWDT2LvAsBVBuu7HmAg0oWCC9u8fKBChzDamyw14-uyJ_Q(a)mail.gmail.com> >> > Content-Type: text/plain; charset="utf-8" >> > >> > Hi Everyone, >> > >> > Does anyone know what software I should use to perform a Principal >> > Component Analysis (PCA) on my K-edge XANES spectra (for sulfur)? The >> > reason I need to use this technique is because I have a couple of >> reference >> > compound spectra but am not sure which of those I should use to fit my >> > unknown sample spectrum. >> > >> > Any help is appreciated. >> > >> > Thanks and kind regards. >> > >> > >> > Teck Kwang Choo >> > PhD Candidate >> > Department of Chemical Engineering >> > Room 225, Building 36 >> > Monash University >> > Mobile No.: 04-11489904 >> >

1 0

Re: [Ifeffit] Ifeffit Digest, Vol 137, Issue 5
by Teck Kwang Choo 03 Jul '14

03 Jul '14

Thanks everyone for the suggestions! I will give Six pack a go first since I have that software. If that doesn't work, I'll send another message. I wish you all a pleasant day. Teck Kwang Choo PhD Candidate Department of Chemical Engineering Room 225, Building 36 Monash University Mobile No.: 04-11489904 On 3 July 2014 01:33, <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: Principal Component Analysis (PCA) for XANES > (fred.mosselmans(a)diamond.ac.uk) > 2. Re: Principal Component Analysis (PCA) for XANES (Matthew Marcus) > 3. Re: Ifeffit Digest, Vol 137, Issue 4 (Abhijeet Gaur) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 2 Jul 2014 07:48:29 +0000 > From: <fred.mosselmans(a)diamond.ac.uk> > To: <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Principal Component Analysis (PCA) for XANES > Message-ID: > < > CF65047C5B0562499EAFF9FBBC542D64757859A1(a)EXCHMBX01.fed.cclrc.ac.uk> > Content-Type: text/plain; charset="us-ascii" > > > Dear Teck, > > ITFA does transformation factor analysis as well, if you just want to do > PCA, the PCA module in Sam Webb's sixpack is quite intuitive to use. > https://home.comcast.net/~sam_webb/sixpack.html > > cheers > 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 > > > > > > > > ------------------------------ > > Message: 2 > Date: Wed, 02 Jul 2014 08:33:25 -0700 > From: Matthew Marcus <mamarcus(a)lbl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Principal Component Analysis (PCA) for XANES > Message-ID: <53B42645.5040005(a)lbl.gov> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Athena (IFEFFIT package) does it. So does the ALS Beamline 10.3.2 > software package at > https://sites.google.com/a/lbl.gov/microxas-lbl-gov/software . > If you can't get at it there, I can send the executable and manual. > mam > > On 7/1/2014 10:59 PM, Teck Kwang Choo wrote: > > Hi Everyone, > > > > Does anyone know what software I should use to perform a Principal > Component Analysis (PCA) on my K-edge XANES spectra (for sulfur)? The > reason I need to use this technique is because I have a couple of reference > compound spectra but am not sure which of those I should use to fit my > unknown sample spectrum. > > > > Any help is appreciated. > > > > Thanks and kind regards. > > > > > > Teck Kwang Choo > > PhD Candidate > > Department of Chemical Engineering > > Room 225, Building 36 > > Monash University > > Mobile No.: 04-11489904 > > > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > ------------------------------ > > Message: 3 > Date: Wed, 2 Jul 2014 21:03:17 +0530 > From: Abhijeet Gaur <abhijeetgaur9(a)gmail.com> > To: ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Ifeffit Digest, Vol 137, Issue 4 > Message-ID: > <CAEq27Q2UkMuFScofU8w20jO= > 7A34MkyKkimSgy5+h+7B_NCZ-w(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Teck Kwang Choo, > > For PCA analysis you can use SixPack > data analysis package by Dr. Sam Webb available at > https://home.comcast.net/~sam_webb/sixpack.html. > > Also you can use Dmeter by Dr Bruce Ravel > available at http://bruceravel.github.io/demeter/. > > With best wishes > > Dr Abhijeet Gaur > > > > > On Wed, Jul 2, 2014 at 12:52 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. spam on our mailing list (Bruce Ravel) > > 2. Re: to use scattering path in different model or to construct > > a new model which is the combination of different simple compound > > (Bruce Ravel) > > 3. Principal Component Analysis (PCA) for XANES (Teck Kwang Choo) > > 4. Re: Principal Component Analysis (PCA) for XANES > > (Amayri, Dr. Samer) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Tue, 01 Jul 2014 13:31:59 -0400 > > From: Bruce Ravel <bravel(a)bnl.gov> > > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > > Subject: [Ifeffit] spam on our mailing list > > Message-ID: <53B2F08F.7000401(a)bnl.gov> > > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > > > Hi all, > > > > Over the years we've done a pretty good job of keeping spam off this > > mailing list. As you saw, one slipped through this afternoon. Hopefully > > it was a one-time event and it will not be necessary to change the > > friendly nature of security on the list. > > > > 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: Tue, 01 Jul 2014 15:16:20 -0400 > > From: Bruce Ravel <bravel(a)bnl.gov> > > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > > Subject: Re: [Ifeffit] to use scattering path in different model or to > > construct a new model which is the combination of different > simple > > compound > > Message-ID: <53B30904.5030207(a)bnl.gov> > > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > On 07/01/2014 10:43 AM, ZHAN Fei wrote: > > > 1 In the example,multiplet scattering path comes from two model > > > respectively,if use path from different model in different shell's > > > fit,there is risk of ignore important multiple path across > models.Should > > > construct a cluster ,run feff to ensure? > > > > I don't completely understand the question, but I'll give it a try. > > > > In the example of Shelly's paper, she had a situation where she > > *couldn't* write a single feff.inp file. Her local environment was the > > average of all possible ways that the uranyl ion could bond to biomass. > > The uranyl binding disproportionated into a pH-dependent mixture of > > carboxyl, phosphoryl, and hydroxyl sites. There was simply no way to > > write a feff.inp file for that. So her solution was to run Feff more > > than once, picking and choosing paths that represented her best guess > > for modeling the average bonding environment. > > > > I think what you are really getting at, though, is whether it was right > > for Shelly to use parts of Feff calculations on a crystals to model > > something else. If you were to read up on the theory used in Feff, you > > would find that the important thing is that the muffin tin radii of the > > scatterers get calculated reasonably. Unless Shelly had a reason to > > think that the interatomic distances in her biomass sample were VERY > > different than in the crystals she used to run Feff, then the scattering > > amplitudes and phase shifts were almost certainly computed quite well > > enough. > > > > > 2 I have confusion of the relationship pf N between single path and > > > multiple path,for example I think U-Oe-C U-Oe-Pshould be 1 2 > > > respectively,instead 2 4 in paper. > > > > I think Scott's explanation is correct. In real-space, > > multiple-scattering theory, both ways around a three-legged path have to > > be counted. > > > > 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: 3 > > Date: Wed, 2 Jul 2014 15:59:25 +1000 > > From: Teck Kwang Choo <teck.kwang.choo(a)monash.edu> > > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > > Subject: [Ifeffit] Principal Component Analysis (PCA) for XANES > > Message-ID: > > < > > CAHXRQWDT2LvAsBVBuu7HmAg0oWCC9u8fKBChzDamyw14-uyJ_Q(a)mail.gmail.com> > > Content-Type: text/plain; charset="utf-8" > > > > Hi Everyone, > > > > Does anyone know what software I should use to perform a Principal > > Component Analysis (PCA) on my K-edge XANES spectra (for sulfur)? The > > reason I need to use this technique is because I have a couple of > reference > > compound spectra but am not sure which of those I should use to fit my > > unknown sample spectrum. > > > > Any help is appreciated. > > > > Thanks and kind regards. > > > > > > Teck Kwang Choo > > PhD Candidate > > Department of Chemical Engineering > > Room 225, Building 36 > > Monash University > > Mobile No.: 04-11489904 > >

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