Re: [Ifeffit] Ifeffit Digest, Vol 116, Issue 13

24 Oct 2012


      Thanks a lot, Bruce. I checked your new version 0.9.13.1 on my computers
and both yield good fits. Now I can move on to work on real data. Ku-Ding


On 2012/10/23 下午 06:24, ifeffit-request@millenia.cars.aps.anl.gov wrote:
...
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When replying, please edit your Subject line so it is more specific
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Today's Topics:
1. Re: Running (D)Artemis yields different result from that
       shown in (D)Artemis instruction videos (Bruce Ravel)
    2. release 0.9.13.1 (Bruce Ravel)
    3. DORIS III operation ended (Edmund Welter)
    4. Re: DORIS III operation ended (Voegelin, Andreas)
----------------------------------------------------------------------
Message: 1
Date: Mon, 22 Oct 2012 16:12:43 -0400
From: Bruce Ravel 
To: XAFS Analysis using Ifeffit 
Subject: Re: [Ifeffit] Running (D)Artemis yields different result from
         that    shown in (D)Artemis instruction videos
Message-ID: <3508041.vaaWmxvES8@lachesis.bnl.gov>
Content-Type: text/plain; charset="utf-8"
OK, you've convinced me.
When I got into the lab this afternoon, I tried the same fit on a
Windows computer.  Much to my surprise, the result on Windows was
quite different from the result on my linux computers at home.
After a few hours of investigation, I found a problem in how Ifeffit
had been compiled on the Windows machine that I use to build the
Windows installer.
I was able to come up with a short-term solution and then built a new
installer package for 0.9.13 which i think works correctly.
I will be announcing a new release shortly.
B
On Monday, October 22, 2012 06:41:26 AM Tsuei, Ku-Ding wrote:
...
Bruce,
Perhaps you noticed the "Fit color" was red (large R-factor 0.074496,
poor fit, also seen in the attached figure in the last email) when you
loaded in the project file I sent you. When you hit Fit button again the
"Fit color" might turn to green indicating good fit as shown in your
result of a much smaller R-factor (0.004265).
I did the following test on various versions of Demeter on my desktop
and notebook computers both installed with Windows 7 SP1. Of course I
uninstalled one version first before installing another. I tried to use
Uninstall within the Program menu or use the Program manager. I tried to
reboot or not to reboot after uninstallation or installation. Neither
shows any difference.
Fit color
0.9.10 green
0.9.11 red
0.9.12 red
0.9.13 red
Only version 0.9.10 yields good fit. The latter versions would not give
good fits even with repeated hitting the "Fit" button. I have no idea
what causes these results but perhaps this observation provides a clue.
Ku-Ding
On 2012/10/22 ?? 01:00, ifeffit-request@millenia.cars.aps.anl.gov wrote:
...
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ifeffit@millenia.cars.aps.anl.gov
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or, via email, send a message with subject or body 'help' to
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You can reach the person managing the list at
ifeffit-owner@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: Running (D)Artemis yields different result from that
shown in (D)Artemis instruction videos (Ravel, Bruce)
----------------------------------------------------------------------
Message: 1
Date: Sun, 21 Oct 2012 12:36:10 +0000
From: "Ravel, Bruce"
To: XAFS Analysis using Ifeffit
Subject: Re: [Ifeffit] Running (D)Artemis yields different result from
that shown in (D)Artemis instruction videos
Message-ID:
     <47CED3CD722C2A439C0D1D1056B2132517C3B082@EX10-MB1.BNL.GOV>
Content-Type: text/plain; charset="us-ascii"
Ku-Ding,
I don't know what to tell you.  On the computer I am sitting in front of
right now, I opened your two project files and hit the fit buttons, I get
the same fit with only numerical differences.  Here I am cutting and
pasting from the two log files:>
old artemis:
    Chi-square                  =    4334.684537717
    Reduced Chi-square          =     691.819976095
    R-factor                    =       0.004250325
amp             =     0.8649100   +/-      0.0412220    (1.0000)
    enot            =     5.6049380   +/-      0.2950270    (0.0000)
    delr            =    -0.0226780   +/-      0.0023790    (0.0000)
    ss              =     0.0082230   +/-      0.0003250    (0.0030)
new artemis:
    Chi-square                  : 4348.7359268
    Reduced chi-square          : 694.0625918
    R-factor                    : 0.0042652
amp                =   0.86526150    # +/-   0.04129645     [1.00000]
    enot               =   5.61081742    # +/-   0.29527844     [0]
    delr               =  -0.02266589    # +/-   0.00238341     [0]
    ss                 =   0.00822546    # +/-   0.00032571     [0.00300]
I don't acknowledge that there is a problem.
B
________________________________________
From:ifeffit-bounces@millenia.cars.aps.anl.gov
[ifeffit-bounces@millenia.cars.aps.anl.gov] on behalf of Tsuei, Ku-Ding
[tsuei@nsrrc.org.tw] Sent: Thursday, October 18, 2012 1:15 PM
To:ifeffit@millenia.cars.aps.anl.gov
Subject: [Ifeffit] Running (D)Artemis yields different result from that
shown in (D)Artemis instruction videos
Hi Bruce,
I went through your (D)Artemis instruction videos and ran the latest
Demetris 0.9.12 with 0.9.13 update side by side to reproduce the
results. However, my running yields much poorer fitting results on Au
foil EXAFS, even the first shell (video 03). Actually it happened using
the older 0.9.11 too. I also went through your Lecture videos shot at
Diamond and ran (D)Artemis but could reproduce your results closely. I
have felt puzzled for quite a while why the simplest case Au foil does
work well. Today I tried to run the same Au data and fitting by the old,
last version of Artemis 0.8.014. I could produce very good fitting on
the first shell with the R-factor very near that shown in the video. I
made sure the math expressions for the fitting parameters amp, enot,
delr and ss are set exactly the same, with fitting range exactly the
same, in both programs. Their screen outputs file is attached. The saved
respective project files are also attached. I copied the fit outputs
into their journals. I would appreciate if you may review these results
and help clear my puzzle.
Best regards,
Ku-Ding
------------------------------
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End of Ifeffit Digest, Vol 116, Issue 11
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--
Bruce Ravel  ------------------------------------ bravel@bnl.gov
National Institute of Standards and Technology
  Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2
  Building 535A
  Upton NY, 11973
Homepage:    http://xafs.org/BruceRavel
  Software:    https://github.com/bruceravel
------------------------------
Message: 2
Date: Mon, 22 Oct 2012 16:20:16 -0400
From: Bruce Ravel 
To: XAFS Analysis using Ifeffit 
Subject: [Ifeffit] release 0.9.13.1
Message-ID: <2108483.PEeEN70mtK@lachesis.bnl.gov>
Content-Type: text/plain; charset="us-ascii"
Hi,
As a result of a problem brought to my attention by Ku-Ding Tsuei, I
built a new installer of my software for Windows.  The new installer,
release 0.9.13.1 can now be downloaded from
http://bruceravel.github.com/demeter/
This is an installer package.  There is not a package for updating
from 0.9.12.  You must download and install the new installer package.
This new installer is essential for anyone using Artemis.  As Ku-Ding
discovered, versions 0.9.11 through 0.9.13 all suffer from the same
problem.  If you are using Artemis from any of the affected versions,
you *must* upgrade.
I apologize for making three flawed releases of my software and I hope
that no one has been too inconvenienced by my mistake.  Once again,
this mailing list and its most excellent community proves to be the
best feature of our software!
As a bit of consolation, I want to direct your attention to the
Artemis Users' Guide.  I have put a lot of effort into it in recent
weeks.  It is still not complete, but it is much enhanced.
http://bruceravel.github.com/demeter/artug/index.html
Regards,
B
--
Bruce Ravel  ------------------------------------ bravel@bnl.gov
National Institute of Standards and Technology
  Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2
  Building 535A
  Upton NY, 11973
Homepage:    http://xafs.org/BruceRavel
  Software:    https://github.com/bruceravel
------------------------------
Message: 3
Date: Tue, 23 Oct 2012 09:35:25 +0200
From: Edmund Welter 
To: XAFS Analysis using Ifeffit 
Subject: [Ifeffit] DORIS III operation ended
Message-ID: <508648BD.3020804@desy.de>
Content-Type: text/plain; charset="iso-8859-1"
Dear fellow XAFS user,
yesterday (October 22^nd 2012, 8 am) the DORIS III storage ring in
Hamburg was switched of for good. That means our 3 EXAFS beamlines are
left without photons and user operation at these beamlines had to end.
In the next 2 years we will build 2 new EXAFS beamlines at the PETRA III
storage ring that will hopefully equally well serve the demands of our
large user community as the 3 closed beamlines did during the last 20+
years.
I know this mailing list is mainly about software and number crunching,
but I thought the end of operation of a machine that produced so many
beautiful numbers to be crunched with IFEFFIT/Athena/Artemis etc. might
justify a short notice on this list.
Anyway, to close the circle to the software, the end of user operation
of HASYLAB's DORIS beamlines finally gives our users the chance to use
this software and produce many nice papers during the coming months
(Ah,wait, that was something different, New York, July 1977 :-).
I am looking forward to see you all back at our PETRA extension
beamlines in autumn 2014! Let me close this mail with the last line of
data ever measured at the A1 EXAFS beamline:
7893.277    0   0    0   0   0   0    0   0   0   0   0   0   0
5.489   13.22
Best regards,
Edmund Welter
--
--------------------------------------------------------
Dr. Edmund Welter      Deutsches Elektronen-Synchrotron
DESY FS-Do
Notkestr. 85            Email: edmund.welter@desy.de
D-22607 Hamburg         Phone: +49 40 8998 4510
Germany                 Fax  : +49 40 8998 2787
--------------------------------------------------------