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- 4114 discussions
Hi Karla,
These are excellent questions for the mailing list, so I am taking the
liberty of CCing my answers to the list. That way, other people can
have a chance to answer your excellent questions.
On Thursday 31 March 2005 14:10, you wrote:
> Hello,
> I am fairly new to EXAFS data analysis. I am currently working on
> data that I collected from 10-ID at the APS.
Aha! My new home! I just collected my first spectra from that
beamline a couple of weeks ago. ;-)
> I have a couple of questions. First, in Artemis, when I click on
> the "x" buttons to select my k- and r-ranges, the window never seems
> to correspond to where I clicked. Is this a bug?
Probably not. The default in Artemis is use a Kaiser-Bessel window.
The various strange words to describe FT windows ("Kaiser-Bessel",
"Hanning", "Welch", and so on) refer to different functional forms for
the window. None of the functional forms will be 0 at the specified
boundary -- instead they all have window sills that extend a bit below
the boundary. Thus, if you use the Kaiser-Bessel window, set kmin=2,
and dk=1, the window will become non-zero at about 1.5.
In short, it's not a bug. It's an unexpected (for you, at least ;-)
feature of the functional form of the window.
Try setting dk or dr to 0 then replotting. The FT may not look good,
but the window plotted by Artemis will be what I think you were
expecting.
> Second, why does Artemis allow a physical parameter like sigma
> squared to be negative?
There are a few ways I could answer this question. I could talk about
how Artemis allows arbitrarily sophisticated fitting models where the
sophisticated user needs complete freedom to specify the fitting
model. But that's a little abstract, so let's consider a slightly
more concrete example.
Suppose that your sample has some kind of oxygen-coordinated iron atom
and you have reason to believe that there is a high level of disorder
in the first coordination shell. So you choose to run Feff using some
model compound that itself has much disorder in the first shell. You
then use the first shell paths that came from the Feff calculation to
model your unknown data. In this case a negative sigma^2 might be
telling you that your unknown has *less* disorder than you model
compound.
In more general terms, the negative sigma^2 is probably trying to tell
you something. You should remember that sigma^2 is correlated to
other terms in the fit, most importantly to the various amplitude
terms, such as coordination number and S02. If sigma^2 is negative,
then the fitten value for amplitude is probably to small. A negative
sigma^2 will puff up the signal to compensate for the amplitude term
being rather too small. If Artemis did not allow sigma^2 to go
negative, you might never know about this kind of problem.
So I would say that this too is a feature of the program and not a bug.
> Lastly, I have had a hard time figuring out these math expressions
> despite reading over the mailing lists. Can you use the ">" sign so
> that sigma squared is always greater than 0? How else can I write a
> math expression so that the fitting never gives me a sigma squared
> that is less than 0? Any help would be greatly appreciated!
Using ">" won't work. ">" is not a symbol in Ifeffit's math parser.
This is a topic that has come up many times over the past few years on
the mailing list. In fact, I think that someone should write a FAQ
entry on this topic.
Here are a few suggestions:
1. Guess a parameter like this: "guess ss 0.003", then use it on
the sigma^2 line of the path page like this: "abs(ss)".
2. A very similar approach is to use the max function. In the
sigma^2 line of the path page, say this: "min(ss, 0)". This can
be improved slightly. Doing this: "min(ss, 0.001)" constrains the
sigma^2 for the path to be no smaller than 0.001.
3. If you start reading the mailing list archives here:
http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2005-February/001650.html
you will find a conversation between Matt and Scott about a way to
impose a penalty for a sigma^2 being too small rather than forcing
to be above a hard boundary. Matt's scheme is kind of involved...
If you use any of these approaches, I would encourage you to do so
with hesitation. As I mentioned above, the negative sigma^2 is not a
short coming of Ifeffit or Artemis. Much more likely, it is useful
information that you should heed and use to figure out what
shortcoming in your fitting model is leading that to happen.
HTH,
B
--
Bruce Ravel ----------------------------------- bravel(a)anl.gov -or-
ravel(a)phys.washington.edu
Environmental Research Division, Building 203, Room E-165
Argonne National Laboratory phone and voice mail: (1) 630 252 5033
Argonne IL 60439, USA fax: (1) 630 252 9793
My homepage: http://feff.phys.washington.edu/~ravel
EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/
9
16
Hello,all
We finally succeeded in installing horae-048 in Fedora 2! It took us a long time
to figure out why Tk could not be detected, but it turned out that the right
version of Tk is the key. We found Tk-804.027 working in our Fedora2 system.
The right order of installation is also important. We had to restart everything
in installing horae after we set up Tk.If you are using this Tk-804.027, you
don't need to look for unix folder as said on some web,just simply
gunzip
tar -xvf finename.tar
(enter the new folder Tk-804.027)
make
make install(after this,you can make test if you want)
And then the installation of horae will jsut go fluently following the
instructions! To use athena or artemis, you need to enter the fold where
athena.pl and artemis.pl are,and then "perl athena.pl".
cheers
Yanan
----------------------------------------------------------------
This message was sent using IMP, the Internet Messaging Program.
4
5
Ok Matt,
I thought you might have a general idea for how I could
gather more info for you about the problem. I did mention previously
this weekend to you that I am using windows XP. I also had thought
I'd posted a file, but I'd just sent it to Adam. From now on I will
send a file every time I have a problem. This is with athena version
8.034. Matts theory that there is not enough of a Mu(E) range sounds
good to me so far.
--Dan
3
3
Hi,
I looked at the file. But as with your first file, I have no trouble saving
chi files. I used athena 0.8.34 on Windows 2000. You should not have any
trouble with XP. BTW the file you sent says it was created with Athena
0.8.30. I think it should still work but it might indicate a problem with
your installation. You could try unistalling and re-install and get the
updates when the updater runs.
I hope this helps,
Adam
> Ok Matt,
>
> I thought you might have a general idea for how I could
> gather more info for you about the problem. I did mention previously
> this weekend to you that I am using windows XP. I also had thought
> I'd posted a file, but I'd just sent it to Adam. From now on I will
> send a file every time I have a problem. This is with athena version
> 8.034. Matts theory that there is not enough of a Mu(E) range sounds
> good to me so far.
>
> --Dan
------------------------------------------------------
M. Adam Webb
Ph.D., MCIC
Alberta Synchrotron Institute (http://www.asi-cls.ca/)
8308 - 114 Street, Suite 2080
Edmonton, Alberta, T6G 2E1, Canada
Phone: (780)492-5464 Fax: (780)492-6160
Email: adam.webb(a)asi-cls.ca
1
0
Bruce, Matt, Adam, others,
I'm still having this problem with Athena where I try to
save data as a chi file and the file is created, but empty. The chi
files should be several killobytes large, but mine are 0 KB. I've
just upgraded to the newest version of Athena 8.037. I wonder, is it
my data or my operating system? No one else seems to be having these
sorts of problems.
--Dan
2
1
Hi Bruce,
I found a difference in functionality in Athena when I tried to use
"open file" or "open many files" in the main menu .
When using the many files option I found this message:
Athena trapped a warning!
The following message was trapped by Athena:
Athena0.8.034warnC:\Program
Files\Ifeffit\horae\stash\ATHENA.TRAPCODE(0x21a5d800
) at athena line 1363
main::__ANON__('Tk::Error: Can\'t call method "lower" without a
package
or objec...') called at blib\lib\Tk.pm (autosplit into
blib\lib\auto\Tk\Error.al
) line 402
Tk::Error('MainWindow=HASH(0x21072a84)', 'Can\'t call method
"lower" wit
hout a package or object reference...', '[\&main::read_file,1]', '(menu
invoke)'
) called at /PerlApp/Tk.pm line 340
eval {...} called at /PerlApp/Tk.pm line 340
Tk::MainLoop() called at athena line 1419
When I opened the same file alone using the "open file" option , Athena
says the file is not monotonically sorted and it cannot be opened. So,
that's the problem with the file.
Then, Athena offers to sort the data and continue loading the file. Why
this message is not shown when I opened multiple files?
I tried to open only one file (the one that is not monotonically
sorted) using the "open many files" option and the message was the same
as the "open file"option.
When using the "many files" option with many files, Athena does not show
that message window and stays partially inactive (menu options are
active but plot options are not active).
A few sample file are atached.
Thanks,
Raul
--
Raul Barrea, Ph.D.
Assistant Research Professor of Physics,
Associate Director Biophysics Collaborative Access Team (BioCAT)
CSRRI, Dept. BCPS, Illinois Institute of Technology
BioCAT/APS/435B/Sector 18
Argonne National Laboratory
9700 South Cass Avenue,
Argonne, IL 60439
Tel.: (630) 252-0541
Fax: (630) 252-0545
Email: barrea(a)bio.aps.anl.gov
Email: barrea(a)iit.edu
pager: barrea-pager(a)bio.aps.anl.gov
# File header:
# Date and time: Sun Feb 20 23:25:41 2005
# Original name of the file: whiteCuscan.154
# Beamline: 18ID
# User's Comments: User's comments 1
# User's Comments: User's comments 2
# Scan type, mode: EXAFS Continuous Scan, Fixed-Time Mode
# Monochromator type: Si_111, mono 1
# Int. Motor 1 name: energy_MO1_1m
# Start, end, step: 8.7790 , 9.2790 , 0.0010
# Int. Motor 2 name: theta_MO1
# Start, end, step: 13.0183 , 12.3054 , 0.0014
# Scan time: 60.00
# Number of scans: 1
# Undulator linked, offset: 0.1000
# Ext. Motor 1 name: stepper19
# Start, end, step: -71.0000 , -75.0000 , -0.1000
# Ext. Motor 1 position: -74.0000
# Ext. Motor 2 name: stepper20
# Start, end, step: 5.9000 , 8.5000 , 0.1000
# Ext. Motor 2 position: 6.2000
# Scaler channel_number/column_name/dark_current:
# ch#6/I0/1951 ch#7/I1/2611 ch#15/CuKalfa/0
# Dark current last measurement: Sun Feb 20 20:17:51 2005
#
#
#
#
#
#
#
#
#
# Energy I0, I1, CuKalfa
#
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# File header:
# Date and time: Sun Feb 20 23:22:02 2005
# Original name of the file: whiteCuscan.151
# Beamline: 18ID
# User's Comments: User's comments 1
# User's Comments: User's comments 2
# Scan type, mode: EXAFS Continuous Scan, Fixed-Time Mode
# Monochromator type: Si_111, mono 1
# Int. Motor 1 name: energy_MO1_1m
# Start, end, step: 8.7790 , 9.2790 , 0.0010
# Int. Motor 2 name: theta_MO1
# Start, end, step: 13.0183 , 12.3054 , 0.0014
# Scan time: 60.00
# Number of scans: 1
# Undulator linked, offset: 0.1000
# Ext. Motor 1 name: stepper19
# Start, end, step: -71.0000 , -75.0000 , -0.1000
# Ext. Motor 1 position: -73.7000
# Ext. Motor 2 name: stepper20
# Start, end, step: 5.9000 , 8.5000 , 0.1000
# Ext. Motor 2 position: 6.2000
# Scaler channel_number/column_name/dark_current:
# ch#6/I0/1951 ch#7/I1/2611 ch#15/CuKalfa/0
# Dark current last measurement: Sun Feb 20 20:17:51 2005
#
#
#
#
#
#
#
#
#
# Energy I0, I1, CuKalfa
#
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# File header:
# Date and time: Sun Feb 20 23:23:15 2005
# Original name of the file: whiteCuscan.152
# Beamline: 18ID
# User's Comments: User's comments 1
# User's Comments: User's comments 2
# Scan type, mode: EXAFS Continuous Scan, Fixed-Time Mode
# Monochromator type: Si_111, mono 1
# Int. Motor 1 name: energy_MO1_1m
# Start, end, step: 8.7790 , 9.2790 , 0.0010
# Int. Motor 2 name: theta_MO1
# Start, end, step: 13.0183 , 12.3054 , 0.0014
# Scan time: 60.00
# Number of scans: 1
# Undulator linked, offset: 0.1000
# Ext. Motor 1 name: stepper19
# Start, end, step: -71.0000 , -75.0000 , -0.1000
# Ext. Motor 1 position: -73.8000
# Ext. Motor 2 name: stepper20
# Start, end, step: 5.9000 , 8.5000 , 0.1000
# Ext. Motor 2 position: 6.2000
# Scaler channel_number/column_name/dark_current:
# ch#6/I0/1951 ch#7/I1/2611 ch#15/CuKalfa/0
# Dark current last measurement: Sun Feb 20 20:17:51 2005
#
#
#
#
#
#
#
#
#
# Energy I0, I1, CuKalfa
#
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# File header:
# Date and time: Sun Feb 20 23:24:28 2005
# Original name of the file: whiteCuscan.153
# Beamline: 18ID
# User's Comments: User's comments 1
# User's Comments: User's comments 2
# Scan type, mode: EXAFS Continuous Scan, Fixed-Time Mode
# Monochromator type: Si_111, mono 1
# Int. Motor 1 name: energy_MO1_1m
# Start, end, step: 8.7790 , 9.2790 , 0.0010
# Int. Motor 2 name: theta_MO1
# Start, end, step: 13.0183 , 12.3054 , 0.0014
# Scan time: 60.00
# Number of scans: 1
# Undulator linked, offset: 0.1000
# Ext. Motor 1 name: stepper19
# Start, end, step: -71.0000 , -75.0000 , -0.1000
# Ext. Motor 1 position: -73.9000
# Ext. Motor 2 name: stepper20
# Start, end, step: 5.9000 , 8.5000 , 0.1000
# Ext. Motor 2 position: 6.2000
# Scaler channel_number/column_name/dark_current:
# ch#6/I0/1951 ch#7/I1/2611 ch#15/CuKalfa/0
# Dark current last measurement: Sun Feb 20 20:17:51 2005
#
#
#
#
#
#
#
#
#
# Energy I0, I1, CuKalfa
#
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# File header:
# Date and time: Sun Feb 20 23:20:49 2005
# Original name of the file: whiteCuscan.150
# Beamline: 18ID
# User's Comments: User's comments 1
# User's Comments: User's comments 2
# Scan type, mode: EXAFS Continuous Scan, Fixed-Time Mode
# Monochromator type: Si_111, mono 1
# Int. Motor 1 name: energy_MO1_1m
# Start, end, step: 8.7790 , 9.2790 , 0.0010
# Int. Motor 2 name: theta_MO1
# Start, end, step: 13.0183 , 12.3054 , 0.0014
# Scan time: 60.00
# Number of scans: 1
# Undulator linked, offset: 0.1000
# Ext. Motor 1 name: stepper19
# Start, end, step: -71.0000 , -75.0000 , -0.1000
# Ext. Motor 1 position: -73.6000
# Ext. Motor 2 name: stepper20
# Start, end, step: 5.9000 , 8.5000 , 0.1000
# Ext. Motor 2 position: 6.2000
# Scaler channel_number/column_name/dark_current:
# ch#6/I0/1951 ch#7/I1/2611 ch#15/CuKalfa/0
# Dark current last measurement: Sun Feb 20 20:17:51 2005
#
#
#
#
#
#
#
#
#
# Energy I0, I1, CuKalfa
#
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2
1
Hi,
Is there anyone who can tell me how to view the residual in Artemis? Every
time I checked the residual, only got the data curve.
Best,
Ye
4
5
Hi everyone!
I am back from vacation and (on March 7th) started my new position here in
Argonne's Environmental Research Division. I had a splendid vacation and am
very excited about my new position. For those of you who are APS users, I'll
be spending a good fraction of my time at sector 10 (MR-CAT). Stop by and
say hi -- especially those of you that I have met in person!
I have to confess that I have not been following the discussions on the
mailing list very closely in the last several weeks, but I see that there
have been a number of bug reports and other problems that people have
encountered with the software. I am still settling into my new job and my
new home, but I hope to get back to work on the codes real soon. And I will
certainly resume active participation in the discussions on the list.
Regards,
Bruce
--
Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu
Environmental Research Division, Bldg 203, Room E165
Argonne National Laboratory phone: (1) 630 252 5033
Argonne IL 60439, USA fax: (1) 630 252 9793
My homepage: http://feff.phys.washington.edu/~ravel
EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/
3
2
Dan,
I think the problem was when you first imported the data. When you import the
data, Athena tries to figure out what type it is. In your case the first file
is very short and Athena probably selected XANES data. This disables the k,q
etc since they don't apply. Re-import your data but be sure to select mu(E)
as the Data Type in the import window.
The rest of your problems should go away.
Cheers,
Adam
> Dear mailing list --
>
> I'm having difficulty creating a chi file. First off I cannot
> plot my data files in k, q , etc. The files can only be plotted in E
> or merged and plotted in k, q, etc.
>
> Second, when I go to the file menu to create a chi(k) from the
> marked original text file, Athena won't let me. That is to say the
> only option is create to Save Mu(E) and when I do that a file is
> created with nothing in it.
>
> When I merge 2 data files and create a chi(k) file from that,
> again, a file is created and named, but nothing is there. Is there
> something wrong with my data files? I don't see any error messages.
> Let me know if you need more info.
>
> I'll also attach my athena file.
>
> Thanks, Dan
------------------------------------------------------
M. Adam Webb
Ph.D., MCIC
Alberta Synchrotron Institute (http://www.asi-cls.ca/)
8308 - 114 Street, Suite 2080
Edmonton, Alberta, T6G 2E1, Canada
Phone: (780)492-5464 Fax: (780)492-6160
Email: adam.webb(a)asi-cls.ca
2
1
Dear mailing list --
I'm having difficulty creating a chi file. First off I cannot
plot my data files in k, q , etc. The files can only be plotted in E
or merged and plotted in k, q, etc.
Second, when I go to the file menu to create a chi(k) from the
marked original text file, Athena won't let me. That is to say the
only option is create to Save Mu(E) and when I do that a file is
created with nothing in it.
When I merge 2 data files and create a chi(k) file from that,
again, a file is created and named, but nothing is there. Is there
something wrong with my data files? I don't see any error messages.
Let me know if you need more info.
I'll also attach my athena file.
Thanks, Dan
1
0