Hi, AFIK, in Athena it is not possible - you can do it quickly in other programs, like excel, origin etc... and save/export it in the same format you have in file in Athena you can only choose E0 cheers kicaj

-----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Khalid, Syed Sent: Tuesday, September 09, 2008 4:08 PM To: ifeffit@millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] Ifeffit Digest, Vol 67, Issue 12

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@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov]On Behalf Of ifeffit-request@millenia.cars.aps.anl.gov Sent: Tuesday, September 09, 2008 9:23 AM To: ifeffit@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)

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Message: 1 Date: Mon, 8 Sep 2008 16:59:08 -0400 From: Bruce Ravel Subject: Re: [Ifeffit] ODP: enrgy-axis-expansion To: "XAFS Analysis using Ifeffit" Message-ID: <200809081659.08948.bravel@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@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" Subject: Re: [Ifeffit] ODP: enrgy-axis-expansion To: "XAFS Analysis using Ifeffit" Message-ID: 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

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Message: 3 Date: Mon, 8 Sep 2008 16:24:45 -0500 From: "Matt Newville" Subject: Re: [Ifeffit] Bugs in Athena under Windows To: "XAFS Analysis using Ifeffit" Message-ID: 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

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Message: 4 Date: Tue, 09 Sep 2008 15:48:51 +1000 From: "Pushan Shah" Subject: [Ifeffit] Noise level in XANES spectrum To: Message-ID: <48C69AE2.0BBD.0060.0@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" Subject: Re: [Ifeffit] ODP: enrgy-axis-expansion To: "Bruce Ravel" , "XAFS Analysis using Ifeffit" Message-ID: <35E004AD6290A7438FCA34BBF325F4161148AA@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@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@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@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

------------------------------

Message: 6 Date: Tue, 9 Sep 2008 10:12:42 +0200 From: "Zajac, Dariusz" Subject: Re: [Ifeffit] Noise level in XANES spectrum To: "XAFS Analysis using Ifeffit" Message-ID: <35E004AD6290A7438FCA34BBF325F4161148AB@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@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Pushan Shah Sent: Tuesday, September 09, 2008 7:49 AM To: ifeffit@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@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" Subject: Re: [Ifeffit] Ifeffit Digest, Vol 67, Issue 11 To: Message-ID: <55C249AA18FE564E86564FEB2412D45BEFD18B@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@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov]On Behalf Of ifeffit-request@millenia.cars.aps.anl.gov Sent: Monday, September 08, 2008 4:44 PM To: ifeffit@millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 67, Issue 11

Send Ifeffit mailing list submissions to ifeffit@millenia.cars.aps.anl.gov

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You can reach the person managing the list at ifeffit-owner@millenia.cars.aps.anl.gov

When replying, please edit your Subject line so it is more specific than "Re: Contents of Ifeffit digest..."

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)

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Message: 1 Date: Mon, 8 Sep 2008 13:46:47 -0400 From: "Khalid, Syed" Subject: [Ifeffit] FW: enrgy-axis-expansion To: Message-ID: <55C249AA18FE564E86564FEB2412D45BEFD187@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@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@bnl.gov

------------------------------

Message: 2 Date: Mon, 8 Sep 2008 13:51:12 -0400 From: Bruce Ravel Subject: Re: [Ifeffit] enrgy-axis-expansion To: XAFS Analysis using Ifeffit Message-ID: <200809081351.12614.bravel@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@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" Subject: Re: [Ifeffit] enrgy-axis-expansion To: "'XAFS Analysis using Ifeffit'" Message-ID: <20080908175744.9B7E429C12@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@bnl.gov] Sent: Monday, September 08, 2008 12:21 PM To: ifeffit@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@bnl.gov

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