reads the copy. The original data is untouched, the copy is
deleted once Athena reads it in. Athena is happy and so, I hope, are you!
Let me know if you have any problems with the plugin. It worked for me
on my linux computer. I suspect it'll work for you as well, but one
never
messg is defined just above that as character*256. I interpreted this
as attempting to put a 330 character string in a character*256 variable.
But, in truth, I did not examine the code all that closely.
I suppose I could have worked on fixing Ifeffit, but the plugin took way
less time. An
that both these bugs were not
> present in the earlier version: Demeter 0.9.20_pre5.
This is actually the same problem that George reported on the Mac late
last week. I believe that I fixed it last week. I will build a new
trial release later today and let you know when it is availabl
;
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
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t 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 bra...@bnl.gov
National Institute of Standards and Technology
Synchrotron Science Group at NSLS --- Beamline
On 07/08/2014 03:37 PM, Bruce Ravel wrote:
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_(64)_pre9.exe
32 bit:
https://s3.amazonaws.com/demeter4xas
platforms. It has a command line switch, "-8",
which does what you want.
http://bruceravel.github.io/demeter/pods/datoms.pl.html
B
--
Bruce Ravel bra...@bnl.gov
National Institute of Standards and Technology
Synchrotron Science Group at NS
cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
--
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National Institute of Standards and Technology
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Building 535A
Upton NY, 11973
Homepag
ry if this is frustrating for you. I am working on it just as
fast as I can.
B
--
Bruce Ravel bra...@bnl.gov
National Institute of Standards and Technology
Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2
Building 535A
Upton NY, 11973
Hom
next demeter-devel release for Mac.
Thanks,
B
--
Bruce Ravel bra...@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
ocument -- that
needs to be fixed.
B
--
Bruce Ravel bra...@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/Bruce
http://cars9.uchicago.edu/atomsdb/Bamfordite.inp
B
--
Bruce Ravel bra...@bnl.gov
National Institute of Standards and Technology
Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2
Building 535A
Upton NY, 11973
Homepage:http://bruce
any of the trial versions that
have been discussed on the list in the recent weeks, you will find that
has been fixed.
B
--
Bruce Ravel bra...@bnl.gov
National Institute of Standards and Technology
Synchrotron Science Group at NSLS --- Beamlines U7A
es/no question. There's a lot
of those.
It's tough for me to figure out Mac-specific problems without
help. I'd need a patient volunteer to help track this down.
B
--
Bruce Ravel bra...@bnl.gov
National Institute of Standard
re
works on the Mac without my ever having tried it myself. Wx really has
solved the cross-platform problem quite well.
B
--
Bruce Ravel bra...@bnl.gov
National Institute of Standards and Technology
Synchrotron Science Group at NSLS --- Beamlines U7A, X
ew 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
--
B
of Athena is "dathena". (When spoken out loud, the "d" is silent!)
During the years I was developing Demeter, the silent "d" allowed one
to have both the old and new versions of my software on the same
computer. Clearly, you have a copy of the very old version still
terial, I would like to set degeneracy as a
variable like the amplitude, deltE0, e.g.. However, I can assign a
letter to N and define it. Do you have any idea how I should do it?
Thanks for your reply,
Peng
--
Bruce Ravel bra...@bnl.gov
National Institu
s/bugs.pod.html#Capturing_error_messages_from_Demete
Is anything written to the screen if you try to launch Athena
from a command window?
B
--
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National Institute of Standards and Technology
Synchrotron Science Group at NSLS --- Beamlines U
ve an undo function.
This:
http://bruceravel.github.io/demeter/aug/ui/frozen.html
helps in certain situations where an undo would be used, but it wouldn't
have helped in your case.
B
--
Bruce Ravel bra...@bnl.gov
National Institute of Standards and
.html
although perhaps not in the most useful manner. The wikipedia page is
also useful for resolving a Schoenflies symbol to the corresponding
Hermann-Maguin symbol.
You can also simply use the Schoenflies symbol in Artemis. The string
"D^9_4h" should be recognized by A
om/ifeffit%40millenia.cars.aps.anl.gov/msg03717.html
Searching for "normalization" on the mailing list archive turns up a lot
more information:
http://www.mail-archive.com/search?q=normalization&l=ifeffit%40millenia.cars.aps.anl.gov
B
--
Bruce Ravel bra...@bnl.gov
the systematic effect of inconsistent normalization -- the purely
statistical uncertainties represented by the reported error bars
are much smaller, thus your error budget is dominated by
systematics
HTH,
B
--
Bruce Ravel bra...@bnl.gov
plugin_path('wx')
from plotter import newplot, plot
with this error message:
file , line 0
ImportError: cannot import name newplot
add_plugin('f85ut')
What am I not understanding? newplot (and plot) seem to be exported
by wx/plotter.py the same way that feffpath i
owards answering the
questions you both are asking. Granted, you have to look at my ugly
face for a long time, which is pretty horrifying. But I think you
might find them helpful.
B
--
Bruce Ravel bra...@bnl.gov
National Institute of Standards and Tec
it?
If it does use FEFF in the fitting, how do you/is it possible to have
Artemis call to FEFF9 instead of FEFF6L?
Thanks all for your time,
Nate Turner
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http://mi
ile->import menu for importing an external Feff calculation. There
is a reason that comes with a lengthy warning message before allowing
you to do so. It's not a robust, well-tested part of Demeter.
B
--
Bruce Ravel bra...@bnl.gov
National I
:
suggest a missing library that is being referenced but which cannot be
linked to. Perhaps you are missing some package associated with
gfortran...?
I'd likely know how to solve this problem on Ubuntu, but on macports.
B
--
Bruce Ravel
know as I
don't yet understand the problem) is to occassionally select "Save
current fit" from the File menu. This writes a project file with only
the current fitting model and none of the history.
B
--
Bruce Ravel bra...@bnl.gov
National
-- I'll take a look
and let you know.
B
--
Bruce Ravel bra...@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.git
-run
feff after running a fit. In fact, you should /never/ re-run feff
after you have started dragging and dropping paths onto the data page.
B
Best,
Yanyun
Quoting Bruce Ravel :
On 08/28/2014 07:51 PM, huyan...@physics.utoronto.ca wrote:
I encountered a serious problem with saving an Arte
, 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 bra...@bnl.gov
National Institute of Standards and Technology
Synchrotron Science Group at
nly
involves a lot more code than what I did this afternoon!
Cheers,
B
--
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National Institute of Standards and Technology
Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2
Building 535A
Upton NY, 11973
RPATH 8 and NLEG 8, but the same problem occurs and the agreement
with experiment in the low-k region 3-6 A-1 does not become better using
FMS (compared to the path expansion).
Thanks in advance,
Best wishes,
Renske
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Building 535A
Upton NY, 11973
Homepage:http://bruceravel.
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exafs
ifeffit: https://github.com/newville/ifeffit
larch: https://github.com/xraypy/xraylarch
B
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National Institute of Standards and Technology
Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2
Building 535A
0.1103/PhysRevB.66.224405
http://dx.doi.org/10.1016/S0016-7037(02)00947-X
While neither of those papers are on the topic of titanate
perovskites, you would do well to read them carefully and understand
the analysis strategies that Scott or Shelly describe.
HTH,
B
his was happening. Another one of those odd and tiny
differences between linux and Windows.
The cursor will work correctly in the column selection dialog in the
next release. Thanks!
B
--
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National Institute of Standards
vey, GMEG Science Center
345 Middlefield Rd., MS 901
Menlo Park, CA 94025
650-329-5437 (t)
650-329-5491 (f)
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650-329-5437 (t)
650-329-5491 (f)
On Sat, Sep 13, 2014 at 12:20 PM, Bruce Ravel mailto:bra...@bnl.gov>> 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
th
ction dialog. Importing multiple raw data or mu(E)
files certainly works fine.
The work-around is slightly annoying. If you open the chi(k) data files
one at a time, that works fine.
I want to do a bit more investigating, but that'll have to wait until
tomorrow.
B
--
B
ks for your patience and thanks for reporting the problem in the
first place. Demeter would be much much worse were it not for patient
people reporting their problems using the codes.
Cheers,
B
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National Institute of Stan
Ifeffit mailing list
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Building
would not be properly captured in the statistical
error bars -- as I mentioned in my last post.
Remember: ALWAYS cite error bars with numbers from a fit!
B
--
Bruce Ravel bra...@bnl.gov
National Institute of Standards and Technology
Synchrotron Sc
orber. As Matt
said, take care not to overwrite your results.
Were this my problem, I would prefer to organize and perform N
calculation, then add them up myself. That said, Feff does provide a
simple sort of configuration average. Look up "CFAVERAGE" in the Feff
document.
B
without an actionable recipe for
replicating the problem, there is simply nothing that I can do to help.
B
--
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National Institute of Standards and Technology
Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2
Building 5
re "helped" you by reformatting the file.
If you have copies of the data exactly as written at the
beamline, start over from scratch and don't do whatever broke up
that line.
B
--
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National Institute of
each path has 1 coordination number (deg)
I don't know what to do, I need some help.
Thank.
Jhonny Huertas Flores
Rio de Janeiro-Brasil
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u can get to the root of the problem with this.
Regards,
Badari
On Tue, Sep 30, 2014 at 10:30 PM,
mailto:ifeffit-requ...@millenia.cars.aps.anl.gov>> wrote:
Date: Tue, 30 Sep 2014 08:21:18 -0400
From: Bruce Ravel mailto:bra...@bnl.gov>>
To: XAFS Analysis using Ifeffit mailt
ion would help in solving this
problem.
Thank you!
Ellen
--
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Research Assistant
Department of Chemistry
Colorado State University
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ster, 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 Tue, Sep 16, 2014 at 1:36 PM, Bruce Ravel mailto:bra...@bnl.gov>> wrote:
On 09/15/2014 03:39 PM, Foster, Andrea wrote:
Bruce, attached are
://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg04636.html
EXAFS analysis isn't simply a matter of learning which buttons to push.
You need to develop some understanding of the physics and the methods
of the technique before diving into challenging analysis problems.
B
--
file that Feff writes out.
That even made it into the document!
http://bruceravel.github.io/demeter/aug/import/columns.html#datatypesandenergyunits
B
--
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National Institute of Standards and Technology
Synchrotron Science Group at NSLS
really appreciate help on this.
I'll add this to my list of things to look into, but I may not get to it
this week.
B
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National Institute of Standards and Technology
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ov/mailman/listinfo/ifeffit
--
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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/
That is,
make sure you ran Feff for the L3 edge rather than the K edge!
B
--
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National Institute of Standards and Technology
Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2
Building 535A
Upton NY,
g list for
some hints on how to address your problem. Not being a Mac owner
myself, I surely don't know how to solve it.
Another option is to use a recent, supported version of the software:
http://bruceravel.github.io/demeter/#mac
B
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National Institute of Standards and Technology
Synchrotron Science Group at NSLS-II
Building 535A
Upton NY, 11973
Homepage:http://bruceravel.github.io/home/
Software:
decent tool
for a lot of XAS jobs, it's not the right tool for every job. If your
stacks are only 12 images deep, Athena may not be the right tool for
you.
B
--
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National Institute of Standards and Technology
Synchrotron S
ia.cars.aps.anl.gov
<mailto:Ifeffit@millenia.cars.aps.anl.gov>
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
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og
file in %APPDATA%\demeter complains about a problem in
"C:/strawberry/perl/site/lib/Config/INI/Reader.pm", then the work-around
is what I suggested to Kurinji.
Kurinji, thanks again for reporting this bug.
Cheers,
B
--
Bruce Ravel bra...@bnl.gov
t closed. And then, after several attempts, started
working again, as if by magic, before I'd saved a log file If I
can figure out how to reproduce this I'll send more info...
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links that say "<< 64 bit installer >>" or
"<< 32 bit installer >>". The link buttons in the side bar point at
the 0.9.20 installer.
On 10/27/2014 10:10 AM, Bruce Ravel wrote:
Ian,
I am starting a new thread for your email. It is only peripherall
hings that Athena /could/ do in this
area, I have found that being adept at the features described on those
manual pages takes most of the tedium out of the sort of chore you are
asking about.
HTH,
B
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National Institute of Sta
I can't reopen - artemis testing.fpj
Log file from trying to open it (0.9.21) - dartemis.log
Project file saved in 0.9.20 that I can't reopen - dualedgefitting.fpj
Log file from trying to open it (0.9.20) - dartemis_current.log
I will look into this, but not today. I was in a meeting si
bruceravel.github.io/demeter/ or follow
along at github: https://github.com/bruceravel/demeter
If you just can't wait, the formula is pretty simple:
energy = E0 + k^2 / 0.2624682917
where the 0.26 number is the right combination of hbar and c to
convert between eV and inverse Angstrom. k i
Mac package. It seems that Frank has done the
bulk of the work. The MacPort ecosystem seems to be well supported
and well documented, so I would think that someone else could readily
step into that role.
B
--
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National Institute o
open it (0.9.20) - dartemis_current.log
Couldn't reproduce your problem, so this will take more attention.
That's a job for tomorrow.
B
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National Institute of Standards and Technology
Synchrotron Science Group at NSLS-II
novation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
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in
England and Wales with its registered office at Diamond House, Harwell
Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
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On 11/03/2014 01:51 PM, Bruce Ravel wrote:
Simply shortening the distance, even by 1% via "RMULTIPLIER 0.99"
allows Feff to run to completion.
Except that Artemis does not seem to process the RMULTIPLIER parameter
correctly. Drat!
Using the RMULTIPLIER works when running Feff6
l the platforms. Still, a more graceful
failure and a useful message to the Feff console should go a long way
towards making the original problem more understandable.
Stephen: thanks for the bug report.
B
On 11/03/2014 01:55 PM, Bruce Ravel wrote:
On 11/03/2014 01:51 PM, Bruce Ravel
for me on my Ubuntu machine.
Are you sure that you have pulled the very latest from Matt's github
site? My suspicion is that you have not done so recently enough....
B
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National Institute of Standards and Technology
Sincerely,
zhanfei
ihep of China
R space of spectrum
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r your time.
Best,
Kate Davis
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On 11/11/2014 10:19 AM, Bruce Ravel wrote:
Rbkg>1.1 can avoid the first peak,but the remaining curve is somewhat
not smooth.How to distinguish whether a long wavelength oscillation
appear as a real peak or false one?I am confused about it.
I find when I avoid the first scattering p
0.00707 -2.326 0.00911 2.09150 2.10061
--
Best Regards,
Pushkar Shejwalkar.
Post-doctoral -Researcher,JSPS Fellow
Hokkaido University,
Sapporo,
Japan
Inline image 3
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age you to, as Matt suggested, figure out how to ask a more
targeted question. Broad, open-ended questions are hard for the rest
of us to answer. Well-focused questions tend to get better answers.
HTH,
B
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National Institute of Stan
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Nation
On 12/09/2014 04:46 AM, Jean-Baptiste ABBE wrote:
Athena once crashed, (in the terminal, it was sait « Terminated 15 »)
Is that the only thing it said? Were there no further error messages?
B
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y issues.
Thank you
ABBE J-Baptiste
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mailto:i.godf...@jaist.ac.jp>
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Synch
lder with a space and see what happens for myself.
B
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Synchrotron Science Group at NSLS-II
Building 535A
Upton NY, 11973
Homepage:http://bruceravel.github.io/home/
Softwa
you can actually plot it with your own data.
On Windows it can be found in
C:\strawberry\perl\site\lib\Demeter\share\standards\data
On linux, from the command line, you can find the data by doing
ls `perl -e 'use Demeter::Here; print Demeter::Here::here,
$/'`/sh
d the local perl directory, and tried installing
demeter again, this time with root privileges following Bruce Ravel's guide.
Any help would be appreciated, thank you in advance!
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National Institute of Standards and Techn
Doing ./Build touch_wrapper does not change anything - all tests pass,
demeter installs, but athena crashes again...
Looking forward to your reply and suggestions on how to solve this problem.
Kind regards,
Stevan
--
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Nanoparticle Process Technology
Department of Engineering Sc
master branch unless you do a "git pull". If you follow one
of the download links, those just point to the most recently tagged
release, which only gets updated when I tag a new release.
If you clone or pull from the head of the master branch, you will find
that the mistakes in the te
another shell):
alias athena='(export LANG=en_US/UTF-8 && /usr/local/bin/athena)'
That will leave LANG untouched in the shell, but run Athena in a way
that will not trigger the issue that started this conversation. That's
bash syntax, it may be a bit
that
would be a welcome contribution. This file can be found on your machine
at C:\strawberry\site\perl\lib\Demeter\share\standards\standards.ini.
The location and people are the same for all the Ag data in that project
file.
B
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imits your usable data range, which
severely limits the information content of the data.
Other than a few technical issues (mostly choice of FT range) you seem
to be thinking about the problem correctly. Your best bet is to
figure out how to make a better measurement at you next visit to the
.uk> i.godf...@jaist.ac.jp
<mailto:i.godf...@jaist.ac.jp>
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.
Thanks!
Yael Kirsch
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Bruce Ravel bra...@bnl.gov
National Institute of Standards and Techno
tached a log file and a problematic project file.
Ian,
Thanks for the bug report. Shouldn't be a tough one.
B
--
Bruce Ravel bra...@bnl.gov
National Institute of Standards and Technology
Synchrotron Science Group at NSLS-II
Building 5
B
PS: No progress yet on the plotting problem reported the other day that
I thought was a gnuplot bug.
--
Bruce Ravel bra...@bnl.gov
National Institute of Standards and Technology
Synchrotron Science Group at NSLS-II
Building 5
aller.
B
--
Bruce Ravel bra...@bnl.gov
National Institute of Standards and Technology
Synchrotron Science Group at NSLS-II
Building 535A
Upton NY, 11973
Homepage:http://bruceravel.github.io/home/
Software:https://github.com/bruceravel
De
PS: If you subscribe to the mailing list (see
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mail will be posted to the list without my intervention.
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Bruce Ravel bra...@bnl.gov
National Institute of Standards and Technology
Synchrotron Scienc
that
starts "Sorry ... another bug report!", an unambiguous explanation
makes me very happy.
As for the problem you are reporting -- yikes! That's really
troubling. I'll look into it.
Cheers,
B
--
Bruce Ravel bra...@bnl.gov
Nationa
my change logs that I ever actually addressed that complaint.
Apparently patience is a virtue. :)
B
--
Bruce Ravel bra...@bnl.gov
National Institute of Standards and Technology
Synchrotron Science Group at NSLS-II
Building 535A
Upton NY, 11973
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