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

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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