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March 2005
- 14 participants
- 11 discussions
Hi,
There is little discussion over the significance of fitted Debye-Waller factors (ss2) found for
metal centers in metal oxides of heterogeneous catalysts. I am searching for a better way of
determining how reasonable these values are in the fits I get.
1. Are phenomenological models like the correlated Debye model and Einstein model appropriate?
It seems that Debye temperatures are hard to find for oxides.
2. Is there an equivalent value for ss2 in x-ray crystallography data that I can refer to for
comparison in these materials? What should I look for in reviewing published x-ray
crystallographic data?
3. Is the temperature dependence reported for the ss2 for some metals (like Cu and Al) similar to
their respective oxides? For example, in Debye-Waller factor calculations reported for Al metal
by R.C.G Killean (in J.Phys.F: Metal Phys., v. 4, pg. 1908, 1974), the ss2 changes by a factor of
three between 25C and 300C. Would I expect a factor of three increase in crystalline zeolites
(AlO4 structural units).
4. Specific to my work: I have studied Al containing oxides at temperatures between 25 and 300
C. I would like to quantify coordination changes by doing EXAFS fitting of the Al K-edge data.
The EXAFS was taken at temperature and I observe no change in the broadening of the data.
Likewise, the fitting shows no sensitivity in the Debye-Waller factor. It is nearly constant at
0.001 A over the temperatures of interest. Since ss2 and the coordination number (CN) are
correlated, I would like a way to bind the error on the fitted CN by modeling real physical
changes in the Debye-Waller factors. Do you have any suggestions?
Looking forward to your thoughts.
Ian Drake
Graduate Student
UC Berkeley
9
21
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
#
8779.02544 432284.41115 133059.31319 158.33724
8779.18524 434157.03333 132955.96667 241.66667
8779.82756 437123.70000 133730.96667 250.00000
8780.78358 436932.03333 133655.96667 191.66667
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8782.67341 437665.36667 133889.30000 216.66667
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8784.56559 436982.03333 134022.63333 150.00000
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8820.66454 435590.36667 133564.30000 166.66667
8821.61895 435298.70000 133964.30000 233.33333
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8823.52840 437082.03333 134230.96667 200.00000
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8825.43871 436948.70000 134072.63333 250.00000
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8828.30422 435857.03333 133972.63333 175.00000
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8831.17472 438548.70000 134539.30000 200.00000
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8833.08534 437123.70000 134364.30000 133.33333
8834.04251 438107.03333 134439.30000 191.66667
8834.99989 437707.03333 134480.96667 175.00000
8835.95749 437348.70000 134105.96667 100.00000
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8839.78692 437365.36667 133839.30000 133.33333
8840.74558 435240.36667 134172.63333 166.66667
8841.70446 436048.70000 133564.30000 150.00000
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8843.62285 435682.03333 133839.30000 208.33333
8844.58237 433290.36667 133305.96667 108.33333
8845.54209 436407.03333 134264.30000 150.00000
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8850.34240 437498.70000 134339.30000 175.00000
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8854.18619 436873.70000 133939.30000 166.66667
8855.14806 438557.03333 135172.63333 175.00000
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8857.07090 437307.03333 134355.96667 116.66667
8858.03341 437607.03333 134814.30000 191.66667
8858.99614 439115.36667 135114.30000 200.00000
8859.95908 438907.03333 135355.96667 191.66667
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8861.88561 438015.36667 134539.30000 225.00000
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8893.78545 437248.70000 135064.30000 200.00000
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8895.72711 437057.03333 134955.96667 91.66667
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8900.58506 437207.03333 135864.30000 258.33333
8901.55574 437498.70000 135422.63333 133.33333
8902.52820 438007.03333 136089.30000 100.00000
8903.50244 438823.70000 136089.30000 150.00000
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8905.44532 437273.70000 135814.30000 266.66667
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8907.39221 436432.03333 135697.63333 175.00000
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8909.33840 437048.70000 135814.30000 166.66667
8910.31260 436907.03333 135397.63333 183.33333
8911.28703 436998.70000 135614.30000 225.00000
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8914.21162 434898.70000 134814.30000 125.00000
8915.18692 436548.70000 135530.96667 233.33333
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8918.11256 436523.70000 135572.63333 158.33333
8919.08874 436882.03333 135122.63333 175.00000
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8922.01701 435957.03333 134972.63333 141.66667
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8942.57659 434140.36667 133039.30000 150.00000
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8962.24430 432548.70000 133330.96667 175.00000
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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