Dear all, I recently performed FEFF calculations to model chi(k) spectra. The generated chi.dat files had chi(k) data starting at 1.4k. When importing the data (chi.dat) in Athena (version 0.8.056) using IFEFFIT 1.2.11 (XP OS), Athena was not able to interpolate the data from 0 to xk (x being the starting k value of the file, in my case 1.4). Thus Athena could only read the data in but no changes were visible in the plot window when changing parameters (e.g. k-weight, looking at the FT). The plot window just froze. Yet the echo and Ifeffit buffer indicated that the changes had been taken into account. I tried to uncheck the buffering and storing options in the plot window without success. In contrast, with the newest version of Artemis (i.e. 0.8.012, or previous versions of Athena, e.g. 0.8.054), I was able to read and play with any chi data. To look at the data in Athena 0.8.056 I simply added a 0-1.4k interval with a 0.05k grid and set chi(k) to 0 in this interval. Do you also experience this tiny Athena 0.8.056 (XP OS) bug? Or is there a workaround? Best regards, Oli ++++++++++++++++++++++++++++++++++++:-) Olivier Jacquat Soil Chemistry group Institut of Biogeochemistry and Pollutant Dynamics ETH Zürich Universitätstrasse 16, CHN F71 8092 Zürich-Switzerland Tel: +41 44 633 60 28 Fax: +41 44 633 11 18 Email: olivier.jacquat@env.ethz.ch
Olivier, This is a bit confusing. I want to be sure I understand the most salient point: 1. You have a file of chi(k) that does not start at 0 2. The current version of Athena fails to read this correctly. 3. The current version of Artemis is able to read this correctly. Is that right? Can I see the data file? (Once again: problems can't be fixed if I cannot reproduce them on my own computer.) B On Wednesday 03 September 2008 19:33:31 Olivier wrote:
Dear all,
I recently performed FEFF calculations to model chi(k) spectra. The generated chi.dat files had chi(k) data starting at 1.4k.
When importing the data (chi.dat) in Athena (version 0.8.056) using IFEFFIT 1.2.11 (XP OS), Athena was not able to interpolate the data from 0 to xk (x being the starting k value of the file, in my case 1.4). Thus Athena could only read the data in but no changes were visible in the plot window when changing parameters (e.g. k-weight, looking at the FT). The plot window just froze. Yet the echo and Ifeffit buffer indicated that the changes had been taken into account. I tried to uncheck the buffering and storing options in the plot window without success.
In contrast, with the newest version of Artemis (i.e. 0.8.012, or previous versions of Athena, e.g. 0.8.054), I was able to read and play with any chi data.
To look at the data in Athena 0.8.056 I simply added a 0-1.4k interval with a 0.05k grid and set chi(k) to 0 in this interval.
Do you also experience this tiny Athena 0.8.056 (XP OS) bug?
Or is there a workaround?
Best regards,
Oli
++++++++++++++++++++++++++++++++++++:-) Olivier Jacquat Soil Chemistry group Institut of Biogeochemistry and Pollutant Dynamics ETH Zürich Universitätstrasse 16, CHN F71 8092 Zürich-Switzerland Tel: +41 44 633 60 28 Fax: +41 44 633 11 18 Email: olivier.jacquat@env.ethz.ch
-- 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 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/
Hi Bruce, Yes, you're right. Here one of the files (sorry for the omission). Note that with other files of chi(k) (either measured or simulated), the same "problem" appears. Best regards, Oli ++++++++++++++++++++++++++++++++++++:-) Olivier Jacquat Soil Chemistry group Institut of Biogeochemistry and Pollutant Dynamics ETH Zürich Universitätstrasse 16, CHN F71 8092 Zürich-Switzerland Tel: +41 44 633 60 28 Fax: +41 44 633 11 18 Email: olivier.jacquat@env.ethz.ch Url:http://www.ibp.ethz.ch/people/ojacquat/index -----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Bruce Ravel Sent: jeudi, 4. septembre 2008 14:50 To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] chi(k) Athena bug? Olivier, This is a bit confusing. I want to be sure I understand the most salient point: 1. You have a file of chi(k) that does not start at 0 2. The current version of Athena fails to read this correctly. 3. The current version of Artemis is able to read this correctly. Is that right? Can I see the data file? (Once again: problems can't be fixed if I cannot reproduce them on my own computer.) B On Wednesday 03 September 2008 19:33:31 Olivier wrote:
Dear all,
I recently performed FEFF calculations to model chi(k) spectra. The generated chi.dat files had chi(k) data starting at 1.4k.
When importing the data (chi.dat) in Athena (version 0.8.056) using IFEFFIT 1.2.11 (XP OS), Athena was not able to interpolate the data from 0 to xk (x being the starting k value of the file, in my case 1.4). Thus Athena could only read the data in but no changes were visible in the plot window when changing parameters (e.g. k-weight, looking at the FT). The plot window just ?froze?. Yet the echo and Ifeffit buffer indicated that the changes had been taken into account. I tried to uncheck the buffering and storing options in the plot window without success.
In contrast, with the newest version of Artemis (i.e. 0.8.012, or previous versions of Athena, e.g. 0.8.054), I was able to read and play with any chi data.
To look at the data in Athena 0.8.056 I simply added a 0-1.4k interval with a 0.05k grid and set chi(k) to 0 in this interval.
Do you also experience this tiny Athena 0.8.056 (XP OS) bug?
Or is there a workaround?
Best regards,
Oli
++++++++++++++++++++++++++++++++++++:-) Olivier Jacquat Soil Chemistry group Institut of Biogeochemistry and Pollutant Dynamics ETH Zürich Universitätstrasse 16, CHN F71 8092 Zürich-Switzerland Tel: +41 44 633 60 28 Fax: +41 44 633 11 18 Email: olivier.jacquat@env.ethz.ch
-- 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 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/ _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Hi Olivier,
This sounds like it might be due to bugs in both Feff and
Ifeffit/Athena. That is,
a) Feff's chi.dat should start at k=0, not at k=1.4Ang^-1. Any ideas
why this might have happened?? If you'd like us to understand this
issue better, post the feff.inp file.
b) Ifeffit/Athena is able to read chi(k) data that starts at k>0, in
general. But I can believe that it might recognize a chi.dat file
from Feff, and read it in expecting it to start at k=0. That could
cause the trouble you're seeing, though I would not expect athena to
freeze because of such a problem.
--Matt
On Wed, Sep 3, 2008 at 6:33 PM, Olivier
Dear all,
I recently performed FEFF calculations to model chi(k) spectra. The generated chi.dat files had chi(k) data starting at 1.4k.
When importing the data (chi.dat) in Athena (version 0.8.056) using IFEFFIT 1.2.11 (XP OS), Athena was not able to interpolate the data from 0 to xk (x being the starting k value of the file, in my case 1.4). Thus Athena could only read the data in but no changes were visible in the plot window when changing parameters (e.g. k-weight, looking at the FT). The plot window just "froze". Yet the echo and Ifeffit buffer indicated that the changes had been taken into account. I tried to uncheck the buffering and storing options in the plot window without success.
In contrast, with the newest version of Artemis (i.e. 0.8.012, or previous versions of Athena, e.g. 0.8.054), I was able to read and play with any chi data.
To look at the data in Athena 0.8.056 I simply added a 0-1.4k interval with a 0.05k grid and set chi(k) to 0 in this interval.
Do you also experience this tiny Athena 0.8.056 (XP OS) bug?
Or is there a workaround?
Best regards,
Oli
++++++++++++++++++++++++++++++++++++:-) Olivier Jacquat Soil Chemistry group Institut of Biogeochemistry and Pollutant Dynamics ETH Zürich Universitätstrasse 16, CHN F71 8092 Zürich-Switzerland Tel: +41 44 633 60 28 Fax: +41 44 633 11 18 Email: olivier.jacquat@env.ethz.ch
_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Hi Matt,
1) This is not a FEFF related bug. I just had the CORRECTION CARD in the
calculation.
2) This tiny "problem" is not related to chi.dat file. If I save a .chi file
(from raw, mue,... data), then remove the first k values and then try to
read it in again in Athena, the same bug is occurring.
For example, I opened one raw spectrum given as example with the package
(e.g. under Ifeffit\examples\Athena\Fe\Fe.060), saved it as chi spectrum
(without doing any changes), removed the first chi(k) data, then opened the
.chi file back in Athena: I did experience the same "problem".
HTH,
Oli
++++++++++++++++++++++++++++++++++++:-)
Olivier Jacquat
Soil Chemistry group
Institut of Biogeochemistry and Pollutant Dynamics
ETH Zürich
Universitätstrasse 16, CHN F71
8092 Zürich-Switzerland
Tel: +41 44 633 60 28
Fax: +41 44 633 11 18
Email: olivier.jacquat@env.ethz.ch
Url:http://www.ibp.ethz.ch/people/ojacquat/index
-----Original Message-----
From: ifeffit-bounces@millenia.cars.aps.anl.gov
[mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Matt
Newville
Sent: jeudi, 4. septembre 2008 16:28
To: XAFS Analysis using Ifeffit
Subject: Re: [Ifeffit] chi(k) Athena bug?
Hi Olivier,
This sounds like it might be due to bugs in both Feff and
Ifeffit/Athena. That is,
a) Feff's chi.dat should start at k=0, not at k=1.4Ang^-1. Any ideas
why this might have happened?? If you'd like us to understand this
issue better, post the feff.inp file.
b) Ifeffit/Athena is able to read chi(k) data that starts at k>0, in
general. But I can believe that it might recognize a chi.dat file
from Feff, and read it in expecting it to start at k=0. That could
cause the trouble you're seeing, though I would not expect athena to
freeze because of such a problem.
--Matt
On Wed, Sep 3, 2008 at 6:33 PM, Olivier
Dear all,
I recently performed FEFF calculations to model chi(k) spectra. The generated chi.dat files had chi(k) data starting at 1.4k.
When importing the data (chi.dat) in Athena (version 0.8.056) using IFEFFIT 1.2.11 (XP OS), Athena was not able to interpolate the data from 0 to xk (x being the starting k value of the file, in my case 1.4). Thus Athena could only read the data in but no changes were visible in the plot window when changing parameters (e.g. k-weight, looking at the FT). The plot window just "froze". Yet the echo and Ifeffit buffer indicated that the changes had been taken into account. I tried to uncheck the buffering and storing options in the plot window without success.
In contrast, with the newest version of Artemis (i.e. 0.8.012, or previous versions of Athena, e.g. 0.8.054), I was able to read and play with any chi data.
To look at the data in Athena 0.8.056 I simply added a 0-1.4k interval with a 0.05k grid and set chi(k) to 0 in this interval.
Do you also experience this tiny Athena 0.8.056 (XP OS) bug?
Or is there a workaround?
Best regards,
Oli
++++++++++++++++++++++++++++++++++++:-) Olivier Jacquat Soil Chemistry group Institut of Biogeochemistry and Pollutant Dynamics ETH Zürich Universitätstrasse 16, CHN F71 8092 Zürich-Switzerland Tel: +41 44 633 60 28 Fax: +41 44 633 11 18 Email: olivier.jacquat@env.ethz.ch
_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Hi Olivier,
1) This is not a FEFF related bug. I just had the CORRECTION CARD in the calculation.
Posting the feff.inp file sure would help here.
2) This tiny "problem" is not related to chi.dat file. If I save a .chi file (from raw, mue,... data), then remove the first k values and then try to read it in again in Athena, the same bug is occurring.
Sending data files that expose the problem would let us help you out here. As Bruce has mentioned several times on this mailing list recently, we really do need to see the input files, data files, or project files to be able to fix any problem such as these. --Matt
Hi Matt, Alright, Here additional files to the one (Athena_chi.dat) I send in a previous email. 1) one feff.inp file and the related chi.dat file. 2) the original and manually cut chi(k) spectrum of Fe.060 (generated from Ifeffit\examples\Athena\Fe\Fe.060). As this tiny bug is occurring for all types of data (measured & simulated), I do not believe that there is any relation to FEFF. It only seems that the newest version of Athena is not able to "interpolate" the "missing" chi(k) data, while Artemis does. Thanks for your help. Oli ++++++++++++++++++++++++++++++++++++:-) Olivier Jacquat Soil Chemistry group Institut of Biogeochemistry and Pollutant Dynamics ETH Zürich Universitätstrasse 16, CHN F71 8092 Zürich-Switzerland Tel: +41 44 633 60 28 Fax: +41 44 633 11 18 Email: olivier.jacquat@env.ethz.ch
On Thursday 04 September 2008 14:21:16 Olivier wrote:
As this tiny bug is occurring for all types of data (measured & simulated), I do not believe that there is any relation to FEFF. It only seems that the newest version of Athena is not able to "interpolate" the "missing" chi(k) data, while Artemis does.
That is certainly possible. Armed with your test files, I can now look into it. I'll let everyone know what I find. Olivier, I want to stress that Matt and I are not being assholes by insisting on good documentation of the problem you are running into. I genuinely want to fix the problems in the code, but it is usually impossible for me to do so only on the basis of a description of the problem. By submitting a good bug report, which includes examples of how to trigger the bug, you are doing a great service to me and to everyone who uses my code. Without good and useful feedback from my many users over the years, my codes would suck a lot more than actually do. So ... thank you for participating constructively in this process. 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 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/
Dear Bruce and Matt, Thanks again for your help. Sorry if my mails seemed impolite. It was not my intention. Iffefit, Athena, Artemis and co are (and will always be :-)) excellent data analysis tools. I know how much effort you put into them (including the mailing list). Thank you again for generating them!!! Many thanks and sorry again. Oli a happy Iffefit/Athena user.
Hi Olivier, Bruce,
I agree that this is a bug in Athena. It is almost certainly Windows
specific. That is, I have no problem reading in the Athena_chi.dat
file or the chi.dat file you sent with Athena 0.8.054 on Linux.
Actually I am pretty sure it is a bug that is shared between Ifeffit
and Athena that is a left-over mistake from testing versions that
Bruce and I made this summer in preparing ifeffit 1.2.11
First, I noticed that there is a problem with the current Ifeffit
windows distribution that, while not the direct cause of the problem,
gives a hint:
- The ifeffit.dll in the distribution is dated 2007, and the
ifeffit shell says 'ifeffit 1.2.10' which is definitely out of date.
These are both my fault, and I'll make an update to fix these
omissions.
- Athena, artemis, etc report 'ifeffit-1.2.11' which means they
are not actually reading the dll. This is a
problem, as changes to the backend require a rebuild of the
horae applications.
For now, I put a zip file with ifeffit.exe, ifeffit_12.dll, and
ifeffit_12.lib at
http://cars9.uchicago.edu/~ifeffit/src/ifeffit_1.2.11a.zip
Again, I could make an update out of these so that everyone gets the
latest versions, though I think we might want to wait for new versions
of Athena and Artemis too...
In Athena, reading in the chi data starting at k=1.4 (Athena_chi.dat,
as Olivier attached) definitely causes problems. In fact, as Olivier
suggested "it totally hoses the session" (I'm paraphrasing). Perhaps
this is what was causing Nirawat's troubles too???
By "totally hoses the session", I mean these symptoms: Reading the
data file Olivier attached, selected [ chi(k) ] for data type, the
plot shows the column plot view, but the data arrays never get set.
In fact, "show @arrays" in the ifeffit buffers shows nothing, as if no
data was read at all. In addition, no data could be read into this
session after that and no plots were performed. The Athena GUI
appeared to be responsive, but typing into the ifeffit gave pretty
much nothing. That is, Ifeffit appeared to be dead.
Copying the ifeffit buffer session into an ifeffit script (attached, I
trimmed out the log-ratio macros but left the others in tact) I can
run this in an ifeffit shell and it works correctly. Hmmmmm.....
Looking at that more closely and knowing that this Athena/Ifeffit
works _sometimes_ (no, really), I figured it might be due to
"fix_chik" and remembered that the July debug sessions were mostly
about playing with dimensions and that macros can be horribly fragile.
Replacing fix_chik with one that had 1 "set" command per line (also attached):
macro fix_chik
"repair chi(k) data group that is not on a uniform k grid"
set(fix___a.k = range(0, ceil($1.k), 0.05) )
set(fix___floor = floor($1.k) - 0.05)
set(fix___a.kk = range(0, fix___floor, 0.05))
set(fix___n = npts(fix___a.kk))
set(fix___a.cc = zeros(fix___n))
set(fix___a.x = join(fix___a.kk, $1.k))
set(fix___a.y = join(fix___a.cc, $1.chi))
set(fix___a.chi = rebin(fix___a.x, fix___a.y, fix___a.k))
set($1.k = fix___a.k)
set($1.chi = fix___a.chi)
erase @group fix___a fix___floor fix___n
end macro
in a fresh Athena session (that is, before reading any chi(k) into
Athena) worked, even for chi(k) data that started at k>0!!
To check this, save the "fix_chik" macro into a file (say,
fix_chik.txt) and on starting Athena, open the Ifeffit buffer and type
load fix_chik.txt
before reading in the chi(k) data. That should work.
My guess is that the Athena, Artemis, Hephaestus executables are built
with a slightly out-of-date ifeffit-1.2.11 dll (ie, that prevented the
longer command lines), and in fact are statically build with that dll.
I would guess that rebuilding Athena, etc and then making an update
from that would be the best option.
--Matt
On Thu, Sep 4, 2008 at 1:21 PM, Olivier
Hi Matt,
Alright,
Here additional files to the one (Athena_chi.dat) I send in a previous email.
1) one feff.inp file and the related chi.dat file.
2) the original and manually cut chi(k) spectrum of Fe.060 (generated from Ifeffit\examples\Athena\Fe\Fe.060).
As this tiny bug is occurring for all types of data (measured & simulated), I do not believe that there is any relation to FEFF. It only seems that the newest version of Athena is not able to "interpolate" the "missing" chi(k) data, while Artemis does.
Thanks for your help. Oli
++++++++++++++++++++++++++++++++++++:-) Olivier Jacquat Soil Chemistry group Institut of Biogeochemistry and Pollutant Dynamics ETH Zürich Universitätstrasse 16, CHN F71 8092 Zürich-Switzerland Tel: +41 44 633 60 28 Fax: +41 44 633 11 18 Email: olivier.jacquat@env.ethz.ch
_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
participants (3)
-
Bruce Ravel -
Matt Newville -
Olivier