[Ifeffit] Ifeffit Digest, Vol 67, Issue 12
Khalid, Syed
khalid at bnl.gov
Tue Sep 9 09:08:18 CDT 2008
That is correct: It is a QEXAFS scan of Ni foil as a
function of time.
Please see the data attached as a .txt file.
The first column is time, second I0, and third It.
I can plot this in Athena, time appears at energy axis.
I can set the first derivative to 8333.0 eV ( changing X-axis from
time to energy ). If I have another known energy point of Ni scan
( which is not a problem ) then I can convert the time axis to
correct energy axis and proceed with normal analysis.
Is that possible?
-----Original Message-----
From: ifeffit-bounces at millenia.cars.aps.anl.gov
[mailto:ifeffit-bounces at millenia.cars.aps.anl.gov]On Behalf Of
ifeffit-request at millenia.cars.aps.anl.gov
Sent: Tuesday, September 09, 2008 9:23 AM
To: ifeffit at millenia.cars.aps.anl.gov
Subject: Ifeffit Digest, Vol 67, Issue 12
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Today's Topics:
1. Re: ODP: enrgy-axis-expansion (Bruce Ravel)
2. Re: ODP: enrgy-axis-expansion (Matt Newville)
3. Re: Bugs in Athena under Windows (Matt Newville)
4. Noise level in XANES spectrum (Pushan Shah)
5. Re: ODP: enrgy-axis-expansion (Zajac, Dariusz)
6. Re: Noise level in XANES spectrum (Zajac, Dariusz)
7. Re: Ifeffit Digest, Vol 67, Issue 11 (Khalid, Syed)
----------------------------------------------------------------------
Message: 1
Date: Mon, 8 Sep 2008 16:59:08 -0400
From: Bruce Ravel <bravel at bnl.gov>
Subject: Re: [Ifeffit] ODP: enrgy-axis-expansion
To: "XAFS Analysis using Ifeffit" <ifeffit at millenia.cars.aps.anl.gov>
Message-ID: <200809081659.08948.bravel at bnl.gov>
Content-Type: text/plain; charset="utf-8"
On Monday 08 September 2008 16:40:47 Zajac, Dariusz wrote:
> I do not clearly understood what you mean. could you explain it more
> precisely? do you want to replace the x scale from energy to time? if you
> want only set the edge energy use E0
Apparently (and Khalid or Anatoly should correct me if I am wrong), they
are collecting data as a function of time in quick scan mode. They
then have the problem of converting time to energy. If the mono speed
is recorded somehow incorrectly, then there is an accordian effect
throughout the data. I think that Khalid wants to be able to adjust
this accordian effect to correct the energy scale of teh data.
B
--
Bruce Ravel ------------------------------------ bravel at 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/
------------------------------
Message: 2
Date: Mon, 8 Sep 2008 16:18:55 -0500
From: "Matt Newville" <newville at cars.uchicago.edu>
Subject: Re: [Ifeffit] ODP: enrgy-axis-expansion
To: "XAFS Analysis using Ifeffit" <ifeffit at millenia.cars.aps.anl.gov>
Message-ID:
<b8522e3d0809081418h564560d4n2fed4de0223e227 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Hi Khalid,
I agree with Dariusz: I do not understand the question. I have a hard
time believing it is "the beamline cannot provide data as a function
of energy, can Athena do this for me automatically?" (if it is, the
answer is definitely 'No!'). Could you explain what you're trying
to do?
--Matt
------------------------------
Message: 3
Date: Mon, 8 Sep 2008 16:24:45 -0500
From: "Matt Newville" <newville at cars.uchicago.edu>
Subject: Re: [Ifeffit] Bugs in Athena under Windows
To: "XAFS Analysis using Ifeffit" <ifeffit at millenia.cars.aps.anl.gov>
Message-ID:
<b8522e3d0809081424x5a6135dfk3aefb0e4a13c3bce at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Timna,
Posting a project would definitely help here, as would clarify "since
the last two versions ..." to say explicitly which versions do and do
not work. My suspicion is that this related to the bug noted last
week (and possibly another recent vague report of "not working") that
is due to the latest version of athena -for-windows being hard-linked
to pre-final-release of the ifeffit dll which is making athena's
ifeffit session get stuck in an unresponsive state.
I believe the only cure is a new version of athena. Again, if you
could post a project that demonstrates the problem, that would be most
helpful.
--Matt
------------------------------
Message: 4
Date: Tue, 09 Sep 2008 15:48:51 +1000
From: "Pushan Shah" <pshah at gse.mq.edu.au>
Subject: [Ifeffit] Noise level in XANES spectrum
To: <ifeffit at millenia.cars.aps.anl.gov>
Message-ID: <48C69AE2.0BBD.0060.0 at gse.mq.edu.au>
Content-Type: text/plain; charset=US-ASCII
Hello Everyone,
I have a general question regarding noise level of XANES spectrum. I have collected XANES data for an element which is present in ppm level in my samples.
Some samples are exhibiting varying degree of noise in XANES spectrum.
Is the noise level of XANES spectrum would be proportional or consistent with the concentration of the sample? As XANES spectra for some of my samples with relatively higher concentration of this element are exhibiting greater level of noise than those with relatively lower concentrations. Will sample matrix play any role in the noise level?
Thanks and I appreciate your help.
regards,
Pushan
------------------------------
Message: 5
Date: Tue, 9 Sep 2008 10:03:46 +0200
From: "Zajac, Dariusz" <dariusz.zajac at desy.de>
Subject: Re: [Ifeffit] ODP: enrgy-axis-expansion
To: "Bruce Ravel" <bravel at bnl.gov>, "XAFS Analysis using Ifeffit"
<ifeffit at millenia.cars.aps.anl.gov>
Message-ID: <35E004AD6290A7438FCA34BBF325F4161148AA at ADXV2.win.desy.de>
Content-Type: text/plain; charset="us-ascii"
hi
so, I think, in case of converting time scale to energy - this should be
supported by beamline (beamline scientist) somehow...
if there is any nonlinearity of the converion factor (Anatoly - what
whould happened if D parameter is time/energy dependent?) I think only
reference spectra can help - do you have it Syed?
if you have all needed parameters the calibration can be relatively
quickly done in some other programs, also in macro (for many files)
but that's my speculations
kicaj
>-----Original Message-----
>From: ifeffit-bounces at millenia.cars.aps.anl.gov
>[mailto:ifeffit-bounces at millenia.cars.aps.anl.gov] On Behalf
>Of Bruce Ravel
>Sent: Monday, September 08, 2008 10:59 PM
>To: XAFS Analysis using Ifeffit
>Subject: Re: [Ifeffit] ODP: enrgy-axis-expansion
>
>
>On Monday 08 September 2008 16:40:47 Zajac, Dariusz wrote:
>> I do not clearly understood what you mean. could you explain it more
>> precisely? do you want to replace the x scale from energy to
>time? if
>> you want only set the edge energy use E0
>
>
>Apparently (and Khalid or Anatoly should correct me if I am
>wrong), they are collecting data as a function of time in
>quick scan mode. They then have the problem of converting
>time to energy. If the mono speed is recorded somehow
>incorrectly, then there is an accordian effect throughout the
>data. I think that Khalid wants to be able to adjust this
>accordian effect to correct the energy scale of teh data.
>
>B
>
>
>--
> Bruce Ravel ------------------------------------ bravel at 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 at millenia.cars.aps.anl.gov
>http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>
------------------------------
Message: 6
Date: Tue, 9 Sep 2008 10:12:42 +0200
From: "Zajac, Dariusz" <dariusz.zajac at desy.de>
Subject: Re: [Ifeffit] Noise level in XANES spectrum
To: "XAFS Analysis using Ifeffit" <ifeffit at millenia.cars.aps.anl.gov>
Message-ID: <35E004AD6290A7438FCA34BBF325F4161148AB at ADXV2.win.desy.de>
Content-Type: text/plain; charset="us-ascii"
Hi Pushan,
can you tell more about the experiment and the way of data collecting?
how did you measure your samples? which method did you use? what kind of
samples do you have?
the answer of your question is not stricted, but generaly I would say
that the noise level should be independent of the samples, did you
change something on the beamline or program between
samples/measurements? e.g. sample time, no. of repeats, you moved in
/out detector, amplification gain, etc....
kicaj
>-----Original Message-----
>From: ifeffit-bounces at millenia.cars.aps.anl.gov
>[mailto:ifeffit-bounces at millenia.cars.aps.anl.gov] On Behalf
>Of Pushan Shah
>Sent: Tuesday, September 09, 2008 7:49 AM
>To: ifeffit at millenia.cars.aps.anl.gov
>Subject: [Ifeffit] Noise level in XANES spectrum
>
>
>Hello Everyone,
>
>I have a general question regarding noise level of XANES
>spectrum. I have collected XANES data for an element which is
>present in ppm level in my samples.
>
>Some samples are exhibiting varying degree of noise in XANES
>spectrum.
>
>Is the noise level of XANES spectrum would be proportional or
>consistent with the concentration of the sample? As XANES
>spectra for some of my samples with relatively higher
>concentration of this element are exhibiting greater level of
>noise than those with relatively lower concentrations. Will
>sample matrix play any role in the noise level?
>
>Thanks and I appreciate your help.
>
>regards,
>Pushan
>
>
>
>_______________________________________________
>Ifeffit mailing list
>Ifeffit at millenia.cars.aps.anl.gov
>http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>
------------------------------
Message: 7
Date: Tue, 9 Sep 2008 09:22:14 -0400
From: "Khalid, Syed" <khalid at bnl.gov>
Subject: Re: [Ifeffit] Ifeffit Digest, Vol 67, Issue 11
To: <ifeffit at millenia.cars.aps.anl.gov>
Message-ID:
<55C249AA18FE564E86564FEB2412D45BEFD18B at exchangemb1.bnl.gov>
Content-Type: text/plain; charset="iso-8859-1"
Anatoly: I will try your approach:
Same problem I can address in a different way.
Suppose the energy is not linear in case of a Pt-L3 scan.
We can set Pt-L3 edge at known 11564 eV. Scanning all the way to
L2 edge and say we find it 200 eV off (exaggerating), can we set
in Athena the L2 edge at known 13273 eV, while the L3 edge is still
at 11564 eV?
-----Original Message-----
From: ifeffit-bounces at millenia.cars.aps.anl.gov
[mailto:ifeffit-bounces at millenia.cars.aps.anl.gov]On Behalf Of
ifeffit-request at millenia.cars.aps.anl.gov
Sent: Monday, September 08, 2008 4:44 PM
To: ifeffit at millenia.cars.aps.anl.gov
Subject: Ifeffit Digest, Vol 67, Issue 11
Send Ifeffit mailing list submissions to
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When replying, please edit your Subject line so it is more specific
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Today's Topics:
1. FW: enrgy-axis-expansion (Khalid, Syed)
2. Re: enrgy-axis-expansion (Bruce Ravel)
3. Re: enrgy-axis-expansion (Anatoly Frenkel)
4. Re: enrgy-axis-expansion (Bruce Ravel)
5. ODP: enrgy-axis-expansion (Zajac, Dariusz)
----------------------------------------------------------------------
Message: 1
Date: Mon, 8 Sep 2008 13:46:47 -0400
From: "Khalid, Syed" <khalid at bnl.gov>
Subject: [Ifeffit] FW: enrgy-axis-expansion
To: <ifeffit at millenia.cars.aps.anl.gov>
Message-ID:
<55C249AA18FE564E86564FEB2412D45BEFD187 at exchangemb1.bnl.gov>
Content-Type: text/plain; charset="iso-8859-1"
-----Original Message-----
From: Khalid, Syed
Sent: Monday, September 08, 2008 12:21 PM
To: 'ifeffit at millenia.cars.aps.anl.gov'
Subject: enrgy-axis-expansion
It is X-axis, sorry my typo. How to expand or shrink
in an EXAFS spectrum, using Athena.
Syed Khalid
725D, National Synchrotron Light Source
Brookhaven National Laboratory
Upton, NY 11973
Ph: 631-344-7496
FAX: 631-344-3238
e-mail: khalid at bnl.gov
------------------------------
Message: 2
Date: Mon, 8 Sep 2008 13:51:12 -0400
From: Bruce Ravel <bravel at bnl.gov>
Subject: Re: [Ifeffit] enrgy-axis-expansion
To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
Message-ID: <200809081351.12614.bravel at bnl.gov>
Content-Type: text/plain; charset="iso-8859-1"
On Monday 08 September 2008 12:20:47 Khalid, Syed wrote:
> Is it possible in Athena to change the y-axis (energy
> scale) at two different energy points of an EXAFS scan?
>
> I have a Ni foil spectrum as a function of time.
> The edge can be set at 8333.0 eV, and I want to
> to assign higher energy to a known feature in the Ni scan.
I am not 100% certain I understand the question, but I think the
question is about the calibration dialog. That is, you want to assign
an energy shift, but not referenced to the edge energy position.
Why can't you just set the energy shift by hand on Athena's main page?
B
--
Bruce Ravel ------------------------------------ bravel at 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/
------------------------------
Message: 3
Date: Mon, 8 Sep 2008 13:59:42 -0400
From: "Anatoly Frenkel" <frenkel at bnl.gov>
Subject: Re: [Ifeffit] enrgy-axis-expansion
To: "'XAFS Analysis using Ifeffit'"
<ifeffit at millenia.cars.aps.anl.gov>
Message-ID: <20080908175744.9B7E429C12 at fe6.prod.mis.yu.edu>
Content-Type: text/plain; charset="us-ascii"
Khalid, what you can do is to note how much the higher energy (at energy E1)
feature is shifted from what you think it should be (let's say by the amount
of D eV), provided that you fixed the lower energy point to what you wanted
(say, E0). Then, you should transfer the data into a spreadsheet and apply
linear scaling:
E --> E0 + (E-E0)*D
It will ensure that in the range between E0 and E1 the data are linearly
stretched or compressed, depending on the sign of D.
Anatoly
=
_____
From: Khalid, Syed [mailto:khalid at bnl.gov]
Sent: Monday, September 08, 2008 12:21 PM
To: ifeffit at millenia.cars.aps.anl.gov
Subject: [Ifeffit] enrgy-axis-expansion
Is it possible in Athena to change the y-axis (energy
scale) at two different energy points of an EXAFS scan?
I have a Ni foil spectrum as a function of time.
The edge can be set at 8333.0 eV, and I want to
to assign higher energy to a known feature in the Ni scan.
Syed Khalid
725D, National Synchrotron Light Source
Brookhaven National Laboratory
Upton, NY 11973
Ph: 631-344-7496
FAX: 631-344-3238
e-mail: khalid at bnl.gov
_______________________________________________
Ifeffit mailing list
Ifeffit at millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
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Message: 4
Date: Mon, 8 Sep 2008 14:13:37 -0400
From: Bruce Ravel <bravel at bnl.gov>
Subject: Re: [Ifeffit] enrgy-axis-expansion
To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
Message-ID: <200809081413.37559.bravel at bnl.gov>
Content-Type: text/plain; charset="utf-8"
On Monday 08 September 2008 14:03:05 Carlo Segre wrote:
> It sounds to me like the question is a bit more complex than that. I
> believe that with their continuous scan electronics, they get absorption
> as a function of time, not energy. If I am not mistaken, he is asking to
> have a conversion to energy built in somehow.
>From this, I finally understand the question.
Athena does not currently provide a mechanism for expanding the energy
axis. I could be convinced to code that up, but I would need a
clearer statement of what you actually want done and several clear
examples of how to process the data correctly.
B
On Monday 08 September 2008 13:59:42 Anatoly Frenkel wrote:
> Khalid, what you can do is to note how much the higher energy (at energy
> E1) feature is shifted from what you think it should be (let's say by the
> amount of D eV), provided that you fixed the lower energy point to what you
> wanted (say, E0). Then, you should transfer the data into a spreadsheet and
> apply linear scaling:
>
>
>
> E --> E0 + (E-E0)*D
>
>
>
> It will ensure that in the range between E0 and E1 the data are linearly
> stretched or compressed, depending on the sign of D.
>
>
>
> Anatoly
>
>
>
> =
>
> _____
>
> From: Khalid, Syed [mailto:khalid at bnl.gov]
> Sent: Monday, September 08, 2008 12:21 PM
> To: ifeffit at millenia.cars.aps.anl.gov
> Subject: [Ifeffit] enrgy-axis-expansion
>
>
>
> Is it possible in Athena to change the y-axis (energy
> scale) at two different energy points of an EXAFS scan?
>
> I have a Ni foil spectrum as a function of time.
> The edge can be set at 8333.0 eV, and I want to
> to assign higher energy to a known feature in the Ni scan.
>
>
> Syed Khalid
> 725D, National Synchrotron Light Source
> Brookhaven National Laboratory
> Upton, NY 11973
>
> Ph: 631-344-7496
> FAX: 631-344-3238
> e-mail: khalid at bnl.gov
>
> _______________________________________________
> Ifeffit mailing list
> Ifeffit at millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
--
Bruce Ravel ------------------------------------ bravel at 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/
------------------------------
Message: 5
Date: Mon, 8 Sep 2008 22:40:47 +0200
From: "Zajac, Dariusz" <dariusz.zajac at desy.de>
Subject: [Ifeffit] ODP: enrgy-axis-expansion
To: "XAFS Analysis using Ifeffit" <ifeffit at millenia.cars.aps.anl.gov>
Message-ID: <35E004AD6290A7438FCA34BBF325F4160C56CB at ADXV2.win.desy.de>
Content-Type: text/plain; charset="iso-8859-2"
I do not clearly understood what you mean. could you explain it more precisely? do you want to replace the x scale from energy to time?
if you want only set the edge energy use E0
kicaj
________________________________
Od: ifeffit-bounces at millenia.cars.aps.anl.gov w imieniu Khalid, Syed
Wys?ano: Pn 2008-09-08 18:20
Do: ifeffit at millenia.cars.aps.anl.gov
Temat: [Ifeffit] enrgy-axis-expansion
Is it possible in Athena to change the y-axis (energy
scale) at two different energy points of an EXAFS scan?
I have a Ni foil spectrum as a function of time.
The edge can be set at 8333.0 eV, and I want to
to assign higher energy to a known feature in the Ni scan.
Syed Khalid
725D, National Synchrotron Light Source
Brookhaven National Laboratory
Upton, NY 11973
Ph: 631-344-7496
FAX: 631-344-3238
e-mail: khalid at bnl.gov
_______________________________________________
Ifeffit mailing list
Ifeffit at millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
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