gmane.science.physics.ifeffit

Re: DAthena crashes when reconstructing data from PCA

Bruce Ravel — 2013-06-14T13:18:31





Hi Scott,

I do not see this behavior on any of my computers (which include
native WinXp and Win7 machines and linux) and I am having trouble
guessing from the log file you attached a possible cause of the
problem.

Possibility #1: you are using a configuration that I cannot test.  I
have never used Parallels and none of my computers are running Windows
8.  I'd be surprised if either is the cause of the problem, though.
It seems surprising that Athena would get that deeply into its
operations before running into a platform-related problem.  That said,
I'd be interested to know if you see this on a native Win7 or WinXP
machine.

Possibility #2: you have figured out some combination of mouse clicks
and button presses that I have never tested.  The problem you are
seeing is that the group considered current (i.e. the one that should
be the target of the reconstruction) has become unset.  Typically,
when you click on an item in the group list, Athena will assign that
as the current data set.  It will then r

Re: no so2 term in Artemis

Bruce Ravel — 2013-06-14T12:37:36


Lei,

The Ifeffit mailing list exists to handle questions like this one.  I
am CCing my reply to the mailing list.  Please subscribe to and use
the mailing list for any follow-up to this issue.  Here is information
about the list:

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

If I understand your issue, it is a fairly minor one.  The label that
says "S02" is not being displayed, but otherwise Artemis works as
expected.  Is that correct?  Are you able to perform fits with
Artemis?  Are you able to access the context menu (normally, one would
right click on that label -- see about halfway down this page:
http://bruceravel.github.io/demeter/artug/path/mathexp.html)?

I have not observed this behavior on any of my windows machines nor on
those of any of the folks who visit my beamline.  So I am not sure how
to proceed.

I am suspicious that this is a locale issue, that is, an issue with
how fonts and unicode characters are displayed on your machine.

Your name suggests that you may be Chinese.  Do

DAthena crashes when reconstructing data from PCA

Scott Calvin — 2013-06-12T01:25:46

Hi Bruce,

Athena is crashing every time I try to "Reconstruct Data" in the PCA dialog. It doesn't seem to matter what data I use, or what space I'm working in (mu or chi), or how many components I use in the reconstruction.

I'm using Demeter 0.9.17 with Ifeffit 1.2.11d, under Windows 8 running in Parallels 8 running under OS 10.8.4 on a MacBook Pro.

The log file for the latest crash is below. If you'd like a project file too, let me know, but it happens, e.g., with the gold cyanobacteria project file, and with every data set I've tried.

--Scott Calvin
Sarah Lawrence College

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Re: Athena Deglitch Problem

Bruce Ravel — 2013-06-11T17:02:25

Thanks, George.  Both of these issues will be fixed in the next release.

B

Re: Very large exafs amplitude in collected data - cause unknown (Jason Alvino)

Carlo Segre — 2013-06-11T04:18:23

Hi Jason:

On Tue, 11 Jun 2013, Jason F. Alvino wrote:


Just doing a quick fit of your data with k 2-15 and R 1-6 and a bulk gold 
model (all paths up to 8 A), gives an excellent fit with 5 parameters (R ~ 
2%).  It basically looks like bulk Gold at low temperatures with an 
amplitude reduction factor of 0.77 which is not too small.  You are 
correct that the sigma squared values are samll but that is to be expected 
at 12K.  I used an isotropic expansion/contraction parameter which fits to 
-0.010, again consistent with thermal expansion at low temperatures.

It looks like you indeed have agglomeration because this data does not 
seem to be from nanoparticles of gold.

Cheers,

Carlo

Re: Very large exafs amplitude in collected data - cause unknown (Jason Alvino)

Jason F. Alvino — 2013-06-11T02:00:00

Hi Matt,

As I pointed out before, in the attached zipfile, there is a file called
"AuNP_anatase_Au.D" which has the data in two columns of energy vs mu,
comma separated underneath the "EV RAW" header.

It also already has all the bad channels removed from the averaged data.

Cheers,
Jason

Hi Jason,

Athena Deglitch Problem

George Sterbinsky — 2013-06-10T15:29:52

Hello,

I am writing to report what I believe to be two bugs in Athena 0.9.17. In
the attached project file, attempting to use the Deglitch feature to remove
the point at ~816 eV (the obvious glitch) returns the attached error
message and does not remove the point.

Also, when selecting "linespoints" for the "datastyle" in the gnuplot
preferences, the data continues to be plotted as lines only.

Thank you,
George
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Re: Very large exafs amplitude in collected data - cause unknown (Jason Alvino)

Matt Newville — 2013-06-07T16:25:05

Hi Jason,

On Fri, Jun 7, 2013 at 9:25 AM, Jason F. Alvino
<jason.alvino-sKtvjTG20lXX/JP9YwkgDA< at >public.gmane.org> wrote:

I still am completely unwilling to work with that file.  Send a file
with no more than 5 columns, and do not expect anyone to add columns
together or know how you would use the different columns in your file.
 It's best to send a file with only energy and xmu.


That alone could explain the difference.


--Matt

Re: Very large exafs amplitude in collected data - cause unknown (Jason Alvino)

Jason F. Alvino — 2013-06-07T14:25:23

Hi all,

There seemed to have been abit of a misunderstanding with the data format,
sorry about that. I was not really sure what format was going to be best to
share with people, I thought the raw data would have been useful so that
people were able to see all the channels.

I have attached a data file from average (AuNP_anatase_Au.D) which has the
data in columns of energy vs u(E).

The second data format (.ssrl) has data in the following columns;

1 = real time clock
2 = Mono angle (requested)
3 = Energy (eV)
4 = I0
5 = I1
6 = I2
7-9 = blank
10-44 - fluor channels (SCA)
45-79 - ICRs for the det element

I have attached these two data sets to this new email.

Now to try to answer some of the questions that have been asked of the data.

The samples are chemically synthesised Au8, Au9, Au11 clusters protected by
PPh3 ligands. We then support these samples on various oxides, in this case
anatase at a % weight loading of 0.17% cluster/anatase. The loading is
typically quite low as we discovered that higher load

Re: Very large exafs amplitude in collected data - causeunknown

Matt Newville — 2013-06-05T21:47:49

Hi Dan,

On Wed, Jun 5, 2013 at 1:18 PM, Daniel Olive <dolive-/3juihCSby0< at >public.gmane.org> wrote:

Thanks for that. I think many of would be interested to know what the
file really contains (there must be an I0 in there somewhere, no? but
if you just add channels multiple times, shouldn't that normalize out?
 how would it be k-dependent?).  It would be nice to straighten this
out, if for no other reason than to demonstrate that exceedingly large
and poorly documented data files can cause weird, difficult to
diagnose problem, even for the people who originally collected the
data.

--Matt

Re: Very large exafs amplitude in collected data - causeunknown

Daniel Olive — 2013-06-05T18:18:00

Hi All,

Well, this is certainly interesting. I had a chance to look at the data myself, and although I can't say if the results are meaningful, or useful, or even what you wanted, I don't see large amplitudes like Jason and Bruce report. 

A quick glance at the header of the files showed a list of column heading. Column 1 was energy. No I0, but, there was a counter, and everything else was DXP related so I guessed that was your ion chamber. DXP_Total caught my eye, and I'm guessing it sums the dxp## columns that follow. I loaded column 1 vs. (8/7) in Athena. I had to change all the groups to Au L3 edge, and I fixed the E0 to something sensible like 11923 (it's default position was somewhere after the white line). After changing the pre-edge range so it didn't end so close to the peak (-182 to -90) I merged them. k2 weighted graph attached.

A quick first shell fit in Artemis gave me something like 15 Au neighbors at around the distance predicted in, 
http://prb.aps.org/abstract/PRB/v77/i7/e075432
The plot e

Re: Very large exafs amplitude in collected data - causeunknown

Matt Newville — 2013-06-05T17:06:07

Hi Jason,

I didn't try to use the original data (and, like Bruce's rant, once I
saw that it was a spec file with multiple scans [er file and with 100+
columns, I didn't even try).   But from looking at the spectra Bruce
posted, it's hard to see what the problem might be.   It's hard to say
that the data is clearly wrong.  It does look a lot like Au foil, but
with a much, much lower sigma2, or much higher energy resolution or
mean-free-path or something else to increase the amplitude in a
k-dependent way .    It's hard to see how any measurement problem
would give such an artifact, but we don't know a lot about how the
measurements were made.

Obviously, a clearer data file would be helpful, as would more
information about the sample and measurements.   What values do you
get for sigma2?   You said the values were not sensible, but you
didn't say what that was.  You also said the amplitude was "huge, up
to 80 in some cases".   I have no idea what that means...

Was the sample cold?  Do you have multiple meas

Re: Very large exafs amplitude in collected data - causeunknown

Bruce Ravel — 2013-06-05T14:00:05

Jason,

You replaced one large, unweildy file format with another large,
unwieldy file format.  You should consider yourself fortunate that I
have taken the time to bother with you.

The folks on this mailing list, myself included, are volunteers.  None
of us get anything for offering time to answer these questions other
than a sense of community spirit and community service.  It is
completely unreasonable that you have asked your question in a way
that required lots of work simply to understand the question.  Had you
been a little more thoughtful and a little less unreasonably demanding
of the time of volunteer help, you could have converted your data
files into simple, 2-column files -- energy and mu(E) -- that would
have been trivially easy for your volunteer to examine.  Instead, you
first sent the data in one basically inscrutable format, then in a
second similarly unwieldy format.  Awesome.  Such a good use of my
time.

Please read this:

  http://bruceravel.github.io/demeter/pods/help.pod.html

When

Re: Very large exafs amplitude in collected data - cause unknown

Bruce Ravel — 2013-06-04T14:00:39

Jason,

I think it's interesting that a user of two different software packages 
that do not rely upon Ifeffit turns to the Ifeffit mailing list for 
help.  That's great!  This list obviously fills an important gap.

There are rather a lot of columns (189!) in each of your data files and 
the header is not very clear about what's what.  You might consider 
reducing those large, unwieldy, complex, poorly documented files into a 
more easily digested form.  I have no clue how to turn the contents of 
those files into plottable data.  Given that you are asking someone to 
volunteer their time to help you solve a problem, it seems unkind to 
make it so very difficult for a willing volunteer to understand the 
nature of your problem.

B

Very large exafs amplitude in collected data - causeunknown

Jason F. Alvino — 2013-06-04T04:25:22

Hi,

We have collected fluorescence data of PPh3 protected Au nanoparticles
supported on an anatase surface at the Au L3 edge, which provides some
decent looking exafs and seems to fit a bulk gold model rather well (there
seems to be agglomeration on the surface, even with our low loadings).

We have tried to fit the data using both XFIT and EXAFSPAK, but the strange
thing is that the exafs oscillations have a huge amplitude, up to 80 in
some cases.  Because of this, the only way to fit the data while
maintaining sensible Debye-Waller factors is to allow SO2 to become quite
large, or to allow the coordination numbers to become very large.

We have spoken to a few others in the field and they have yet to be able to
rationalize why there is such a large signal.

I have attached an example of one of the data sets with very large
amplitude, if anyone would be willing to take a look at the data it would
be much appreciated.

Cheers,
Jason

Re: Possible bug - dathena does not work on XP mode

ASAKURA, Hiroyuki — 2013-06-01T06:41:08

Hi Bruce,

I applied the new updater package, but could not open dathena with the same dathena.log output "Can't load Ifeffit.dll".
I wrote what I did on XP mode below.

1. Uninstall Demeter and Install Demeter 0.9.13.1
dathena does not boot.

C:\strawberry\perl\site\lib\auto\Ifeffit\Ifeffit.dll
Size: 746 KB
Timestamp: 2012 Oct 22

2. Update Demeter to 0.9.17 (newly packaged updater, 3.45MB)
dathena does not boot

C:\strawberry\perl\site\lib\auto\Ifeffit\Ifeffit.dll
Size: 746 KB
Timestamp: 2013 May 31

C:\strawberry\c\lib\Ifeffit.dll (new!)
Size: 746 KB
Timestamp: 2013 May 31

I saw three command prompts sequentially appeared in this update process.
This process is too fast to follow messages in each window, but there might be something wrong in the second and third prompt. At least, the third one tried to kick some .bat file (right?), but seems to be "not found".
I am not sure this is related to the present issue because dathena does not boot up before applying 0.9.17 updater.

In addition, I tried to insta

Re: Possible bug - dathena does not work on XP mode

Bruce Ravel — 2013-05-31T18:45:17

Hiroyuki,

While I cannot reproduce this problem here on any of my machines, I
went ahead and rebuilt the updater package -- making sure not to make
the one mistake that I know of that leads to the error message from
your log file.

I successfully tested the rebuilt updater on 3 WinXP machines and 1
Win 7 machine.

  http://bruceravel.github.io/demeter/

If this still does not work (which seems likely, given that you say
that 0.9.13.1 also does not work), then the thing I would like to know
is the time stamp and file size of the file

  C:\strawberry\perl\site\lib\auto\Ifeffit\Ifeffit.dll

it should be time stamped May 31, 2013 and the file size should be 746
kb.

If that is ok on your computer, then I would like you to do a search
for "Ifeffit.dll" and tell me where else that file is found on your
computer.

B

PS: I added links to earlier version of the updater package to the
bottom of the Demeter home page.  Won't help in this case, but it may
be useful in  the future.




On Saturday, June 01, 2013 12:0

Re: Possible bug - dathena does not work on XP mode

Bruce Ravel — 2013-05-31T15:49:10

I think I know what the problem is and the fix will require that I
rebuild the updater package.  I am just about to leave my desk, but I
will try to get the fix posted a few hours from now.

Sorry,
B


On Saturday, June 01, 2013 12:05:24 AM ASAKURA, Hiroyuki wrote:

Possible bug - dathena does not work on XP mode

ASAKURA, Hiroyuki — 2013-05-31T15:05:24

Dear list,

I am trying to use dathena, dartemis and dhephaestus in Demeter 0.9.17 package on Windows XP ("XP mode" on Windows 7), but neither Athena nor Artemis nor Hephaestus works. On Windows 7 (both 32 bit and 64 bit), everything works.
The symptoms are similar to the latest post's, the command prompt and the splash screen appears momentarily, disappears, and then nothing happens. In contrast, (stand-alone) Atoms opens. Reinstallation of Demeter does not solve this booting problem.

I checked MinGW and demeter.mru problems reported on this ML, but there are no other MinGW installation or corrupted detemer.mru.

OS: Windows XP on Virtual PC ("XP mode" on Windows 7 32 bit) (Japanese version) (All updates are applied.)
Demeter: 0.9.17 (on standard path C:\strawberry...) (ver. 0.9.13.1 also does not work.)

In addition, I've heard that this phenomenon happens at least on Windows XP in many other real machines. (not on virtual machines)

Any suggestions would be appreciated.

Best regards,

ASAKURA, Hiroyuki

Re: Bug Report - (D)Athena Doesn't Open

2013-05-29T20:02:40

Hi Roberto,
Since uninstalling and installing didn’t helped, you could give a try by doing a System Restore to the restore point when it was working.
Try to Run as administrator if you haven't tried.
cheers
Atul

From: Rodriguez, Roberto 
Sent: Wednesday, May 29, 2013 7:57 PM
To: ifeffit-yJARRRr6MatTopXEvdbuMochTzHAynqa8htcxDm17Xw< at >public.gmane.org 
Subject: [Ifeffit] Bug Report - (D)Athena Doesn't Open

I’m currently having trouble opening both (D)Athena and (D)Artemis.  When I first installed Demeter a couple months ago, the programs worked properly without any issue until recently.  In both cases, the command prompt and the splash screen appear momentarily, disappears, and then nothing happens - the program never opens. To my knowledge, no settings have been changed that would prevent Athena/Artemis from opening. In contrast, (D)Hephaestus and (D)Atoms open and appear to function properly. I’ve tried uninstalling/reinstalling Demeter 0.9.13.1 in addition to installing the Updater 0.9.17, but I keep

Re: Bug Report - (D)Athena Doesn't Open

Bruce Ravel — 2013-05-29T19:21:07

This turned out to be due to a corrupted %APPDATA%\demeter\demeter.mru
file.

That file is used by A&A to populate the "Recently used" submenu under
the File menu in each program.  Somehow, Roberto's .mru file had
become filled with lots of null characters.  The part of Demeter that
opens and reads the mru file got confused by the corrupted file.

I have no ida how the corruption happened.  If anyone else observes
this, please report so that we can identify the cause and leave a
searchable record here on the mailing list.

Roberto was able to resolve the issue by deleting the .mru file.  The
only loss was the record of recently visited files.

Note that this is the sort of problem that is impossible for me to
diagnose without the log files, which Roberto happily included in his
posting to the mailing list.  So let this be a reminder of the
importance of useful, actionable bug reports.

  http://bruceravel.github.io/demeter/pods/bugs.pod.html

B


On Wednesday, May 29, 2013 05:57:04 PM Rodriguez, Roberto wro