HOON Kim | 18 Sep 13:06 2014
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Inconsistency of the amplitude reduction factor

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Hello, 

I am a bit confused about the amplitude reduction factor (S0^2), in a sense that whether this factor must be determined by fitting or constrained by a reference value for a specific element. I'm dealing with a cathode composite (for lithium-ion battery) comprised of two crystal phases. During charge-discharge, the amplitude reduction factor changes and at a certain state of charge (SOC) it changes a lot  such as from 0.77 to 0.67. My understanding is that it may reflect the phase transition of the material into the amplitude reduction factor. But, I'm not sure ... I need advice on this. 

Thank you !

Kind Regards,
HOON
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Bruce Ravel | 15 Sep 21:12 2014

Re: problems re-opening Athena project

Could I have a data file or two?  That way so I could try to walk 
through what you did.  I need to be able to reproduce the problem here 
in front of myself in order to have a hope of fixing it.

It is certainly true that Athena is not completely reliable noticing 
that chi(k) data is chi(k) data.  You certainly should make sure the 
data type is set correctly.

Thanks for taking the time to report the problem.
B

On 09/15/2014 03:02 PM, Foster, Andrea wrote:
> Hi Bruce,
>
> thanks for your response..I think that my problem is in the
> specification of energy unit and/or the numerator/denominator.  In the
> project I sent, I imported the files specifying energy as "k" and
> nothing for numerator/denominator.  The plotter would then display the
> EXAFS as k2 weighted and I found that I couldn't change the plot display.
>
> in a later attempt at importing data, I still specified energy as "k"
> but then checked "chi" for the numerator. The result is still
> strange...the data will be imported, but when I try to change
> k-weighting and replot, I can't re-plot. I can plot the data in "R" or
> "q" space, but can't ever go back to k...
>
> anyway, here is the screen shot you requested.  The data are sixpack
> generated, I would think totally compatible.
>
> thanks for the help, andrea
>
> Inline image 1
>
> ________________________________________
> Andrea L. Foster, PhD
> U.S. Geological Survey, GMEG Science Center
> 345 Middlefield Rd., MS 901
> Menlo Park, CA 94025
> 650-329-5437 (t)
> 650-329-5491 (f)
>
> On Sat, Sep 13, 2014 at 12:20 PM, Bruce Ravel <bravel@...
> <mailto:bravel@...>> wrote:
>
>
>     Andrea,
>
>     Your project file is horribly, unrecoverably broken.  A project file
>     in that state is unusual in the sense that I do not know how you got
>     there and I do not know how to replicate it.
>
>     To understand what went awry, I would have to know more about how
>     you got to that point.  For starters, it would help to see the data
>     that you imported into Athena to begin with.  A screenshot of the
>     state of the column selection dialog right before clicking the OK
>     button would probably help also.  I'll probably have more questions
>     after that.
>
>     Bottom line, you found a neat, new (to me) way of breaking my
>     program. Clearly the work of an experienced EXAFS person!! :P
>
>     On 09/12/2014 08:51 PM, Foster, Andrea wrote:
>
>         Hello all,
>
>         I am an experienced EXAFS person, but not having a lot of luck
>         using Athena.
>
>         I am trying to set up an Athena project for linear combo fitting.
>
>         I can get the data + model compounds imported, and I can save a
>         project
>         file.  However, after saving and closing the file, the next time
>         I try
>         to open, I am asked to re-import the data from the project file
>         (I think
>         this is a normal part of Athena)...
>         Inline image 4
>
>         ...but when I try to select importing as chi(k) instead of u(E),
>         I get
>         the following message
>
>
>     This is certainly not related to the problem with the project file,
>     but I want to point out that the box in the project selection dialog
>     is labelled "Plot as", not "Import as".  Its purpose is to display
>     the data in different ways to help you decide what data you might
>     want to import.  Data is always imported from a project file in the
>     same manner as it was imported from the raw data file regardless of
>     how you choose to plot it before clicking the import selection button.
>
>     B
>
>         Inline image 2>
>         after "ok-ing" this message away, I can't get any farther.
>         Importing
>         the data as u(E) doesn't give the appropriate results.
>
>         I am also attaching the aforementioned project file.
>
>         thanks for any help with this, andrea
>
>         __________________________________________
>         Andrea L. Foster, PhD
>         U.S. Geological Survey, GMEG Science Center
>         345 Middlefield Rd., MS 901
>         Menlo Park, CA 94025
>         650-329-5437 (t)
>         650-329-5491 (f)
>
>
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>         http://millenia.cars.aps.anl.__gov/mailman/listinfo/ifeffit
>         <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit>
>
>
>
>     --
>       Bruce Ravel  ------------------------------__------ bravel@...
>     <mailto:bravel@...>
>
>       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/
>     <http://bruceravel.github.io/home/>
>       Software: https://github.com/bruceravel
>       Demeter: http://bruceravel.github.io/__demeter/
>     <http://bruceravel.github.io/demeter/>
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>
>
>
>
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--

-- 
  Bruce Ravel  ------------------------------------ bravel@...

  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/
Foster, Andrea | 13 Sep 02:51 2014
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problems re-opening Athena project

Hello all, 

I am an experienced EXAFS person, but not having a lot of luck using Athena.

I am trying to set up an Athena project for linear combo fitting.

I can get the data + model compounds imported, and I can save a project file.  However, after saving and closing the file, the next time I try to open, I am asked to re-import the data from the project file (I think this is a normal part of Athena)...


...but when I try to select importing as chi(k) instead of u(E), I get the following message


after "ok-ing" this message away, I can't get any farther.  Importing the data as u(E) doesn't give the appropriate results.

I am also attaching the aforementioned project file.  

thanks for any help with this, andrea

________________________________________
Andrea L. Foster, PhD
U.S. Geological Survey, GMEG Science Center
345 Middlefield Rd., MS 901
Menlo Park, CA 94025
650-329-5437 (t)
650-329-5491 (f)
Attachment (recon2_OSU.prj): application/octet-stream, 4194 bytes
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Katarina Norén | 9 Sep 08:10 2014
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Open position in XAFS spectroscopy at MAX IV

Hi,

At the MAX IV Laboratory we are looking for a beamline scientist in XAFS
spectroscopy with profile in Environmental science for the BALDER
beamline at the new 3 GeV ring that will be taken in operation in 2016.


Best regards,
Katarina Norén
__________________________________________________

Katarina Norén, PhD
Manager Hard X-ray Group

MAX IV Laboratory
Lund University
P.O. Box 118, SE-221 00 Lund, Sweden
Visiting address: Ole Römers väg 1, 223 63 Lund
Telephone +46 46 222 68 09
Mobile: +46 709 32 34 23
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Godfrey, Ian | 5 Sep 17:58 2014
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Cursor Issue in Athena Data Import Window

Dear All,

 

This bug report is for a very minor cosmetic issue, but I’m reporting it as it fooled me into thinking Athena had hung and doing a lot of unnecessary troubleshooting – hopefully I can save someone else from the same fate!

 

I experienced this issue with Demeter 0.9.20 on Windows 8 x64 and Windows 7 x64. I don’t recall this issue on previous versions of Demeter, but I could be wrong. The bug is as follows. When you open the Athena “Import” window (file > import data) the cursor over the data import window changes to the Windows’ busy cursor indefinitely (see screenshot) when it should be the normal cursor (it doesn’t impair functionality in anyway – you’re still fully able to interact with the window, create plots etc.).

 

Like I said, not a big bug but it led to me wasting a bit of time so I thought I’d report it.

 

Regards,

 

Ian Godfrey (UCL)

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Matthias Filez | 5 Sep 16:18 2014
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extract backscattering amplitude and phase shift files after feff calculation

Dear mailing list user,
 
I would like to obtain the backscattering amplitude and phase shift files, generated during feff calculations, for photo-electron paths used during modelling. These files (containing F(k), j(k)) should be located in some directory but I really cannot find them back.
 
I know this question has been asked before, but no conclusive answer was provided. I use Windows 7, Intel(R) Core(TM) i5-2520M CPU <at> 2.5 GHz, 64-bit OS, 4 GB RAM. Currently I employ Demeter 0.9.13.
 
Please provide me your suggestions/solutions,
Many thanks in advance,
 
Matthias Filez
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Badari Rao | 5 Sep 15:03 2014
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Implementing constraints in EXAFS analysis

Dear Dr. Bruce,
I have collected EXAFS data on a ferroelectric perovskite Sodium Bismuth Titanate which has an average rhombohedral R3c structure and am trying to fit the data with R3c as the starting model. But I am having trouble in implementing constraints for the fit.
I found a paper authored by you, titled "Local structrue and phase transitions of BaTiO3, Ferroelectrics, 1998, 206-207, pp 407-430". I want to do similar kind of analysis using Artemis on my data. However, I am finding difficulty in understanding how the constraints have been implemented for the refinement of the barium K edge EXAFS, especially those for the bond lengths (Page 416 in the above mentioned article in particular is unclear). Could you please explain how the GDS window and the variables for different paths in this case would look like. Also how do you decide what parameters to refine and what to keep fixed (table IV in the article)?

Also can you please suggest some literature for beginners which can guide me in implementing such constraints?

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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Bruce Ravel | 3 Sep 21:38 2014

Re: Athena data exporting

On 09/03/2014 03:21 PM, Dissanayake, Amila C wrote:
> Dear Bruce,
>
> I am Amila Dissanayake, a Ph.D intern at Pacific Northwest National Lab.
> I am analyzing XAS data using Athena. But when I am trying to save a
> list of data group (about 6 data group) using “  Save marked group
> as..”  command, all the data groups are not saving into different
> columns. When I try to load this file into Origin I could find only just
> two columns of data. Could you help me to sort out this problem.

I am CCing my answer to the Ifeffit Mailing List, which is the 
appropriate place to ask questions about the software.

    http://cars9.uchicago.edu/mailman/listinfo/ifeffit/

You should address any follow up questions to the list.

You've not offered enough information that I can even venture a guess as 
to what is happening.  You have not told me what version of the software 
you are using.  You've not provided an example of a project file that 
triggers the problem.  You have not provided a recipe that would allow 
me to reproduce the problem on my computer.  Alas, there's nothing for 
me to comment on.

The "Save marked groups" feature works for me -- I just tried it on both 
the linux and Windows machines here in my office.  Works fine.  No one 
else has ever raised this problem.

The one thing that occurs to me is that you may not understand what is 
meant by the phrase "marked groups".  Have you read this page from the 
document?

    http://bruceravel.github.io/demeter/aug/ui/mark.html

B

--

-- 
  Bruce Ravel  ------------------------------------ bravel@...

  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/
Javier Alonso | 3 Sep 17:34 2014
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Maghemite, hematite and magnetite XANES standards

Dear all,

Is there a place where I can download some good XANES standards for these samples? I know that this has been a problem for some time and I have found in the literature recent articles which show different XANES spectra for the "same" iron oxide, so I was wondering about this.

The only one I have managed to find is hematite: 
http://cars9.uchicago.edu/~ravel/software/doc/Standards/fe.html 

Thanks in advance,

Javier



--
Javier Alonso Masa
Research Associate
Basque center for materials, applications & nanostructures



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pushkar shejwalkar | 31 Aug 07:50 2014
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Regarding installation of demeter on Mac Mavericks system

Dear All,
            I am new to the mac and mac apps as well as not a techie either. I am trying to install the latest version of demeter (artemis, athena and heph) on my macbook using Mavericks OS. For this I followed the steps given on the site with Macports installation, then its activation step. and then I used terminal to connect and download the athena. However there was error which I thought might because of not having the windowing environment ( I am using all the words from site and dont know anything what it means). So I clicked to download X11 from XQuartz site. After that I logged out from terminal and logged in again. to check if anything changes but the following message was observed (the complete message is attached as word document but some part essentially the last portion talking about the error is pasted below.

--->  Activating xorg-libXau <at> 1.0.8_0

Error: org.macports.activate for port xorg-libXau returned: Image error: /opt/local/lib/libXau.6.dylib already exists and does not belong to a registered port.  Unable to activate port xorg-libXau. Use 'port -f activate xorg-libXau' to force the activation.

Error: Failed to install xorg-libXau

Please see the log file for port xorg-libXau for details:

    /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_x11_xorg-libXau/xorg-libXau/main.log

Error: The following dependencies were not installed: quartz-wm xorg-libAppleWM xorg-libXext xorg-libX11 xorg-libXau xorg-libXdmcp xorg-libxcb python27 bzip2 db46 db_select gettext expat libiconv ncurses libedit openssl zlib python_select sqlite3 xorg-libpthread-stubs xorg-xcb-proto libxml2 xz xorg-xextproto xorg-libXinerama xorg-xineramaproto xorg-libXrandr xorg-randrproto xrender xorg-renderproto xinit mkfontdir mkfontscale freetype libpng xorg-libfontenc xauth xorg-libXmu xorg-libXt xorg-libsm xorg-libice xrdb xset xorg-libXfontcache xorg-fontcacheproto xorg-libXp xorg-printproto xorg-libXxf86misc xorg-xf86miscproto xkeyboard-config xkbcomp xorg-libxkbfile xorg-fonts font-adobe-100dpi fontconfig font-adobe-75dpi font-adobe-utopia-100dpi font-adobe-utopia-75dpi font-adobe-utopia-type1 font-alias font-arabic-misc font-bh-100dpi font-bh-75dpi font-bh-lucidatypewriter-100dpi font-bh-lucidatypewriter-75dpi font-bh-ttf font-bh-type1 font-bitstream-100dpi font-bitstream-75dpi font-bitstream-speedo font-bitstream-type1 font-cronyx-cyrillic font-cursor-misc font-daewoo-misc font-dec-misc font-ibm-type1 font-isas-misc font-jis-misc font-micro-misc font-misc-cyrillic font-misc-ethiopic font-misc-meltho font-misc-misc font-mutt-misc font-schumacher-misc font-screen-cyrillic font-sony-misc font-sun-misc font-winitzki-cyrillic font-xfree86-type1 xorg-encodings xorg-libXfixes xorg-fixesproto xorg-libXfont xorg-fontsproto

To report a bug, follow the instructions in the guide:

    http://guide.macports.org/#project.tickets

Error: Processing of port xorg-server failed

Pushkar-Shejwalkars-MacBook:~ Pushkar$

 

Please help me installing it properly. Really very sorry for the long email but I thought it will be more helpful this way.
Waiting for the replies.
Thank you very much

--
Best Regards,
Pushkar Shejwalkar.
Post-doctoral -Researcher,JSPS Fellow
Hokkaido University,
Sapporo,
Japan

Attachment (Computing dependencies for xorg.docx): application/vnd.openxmlformats-officedocument.wordprocessingml.document, 221 KiB
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Bruce Ravel | 29 Aug 16:50 2014

Re: save Artemis project and cannot find Path List information when reopen

On 08/29/2014 10:40 AM, huyanyun@... wrote:
>
> Now I understand why it happens --I re-run the feff calculation after
> running a fit.

Why do you do that?

I am not criticizing, I am trying to understand what you are trying to 
accomplish.  As you can tell from my earlier comments, re-running the 
feff calculation is an action that surprises both me and Artemis, so I'd 
like to understand what you are aiming to do.

B

--

-- 
  Bruce Ravel  ------------------------------------ bravel@...

  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/

Gmane