[Ifeffit] Setting ranges in peak fitting
Adrian Gainar
adrian.gainar at postgrad.manchester.ac.uk
Tue Jul 28 04:59:01 CDT 2015
Hi Ken,
Our work seems pretty similar in terms of peak fitting C K-edge spectra of organic compounds with Athena, as I dealt with this throughout my PhD programme.
The answer is positive, you can do peak fitting restrained only to a certain fitting range that you choose.
So, in order to do this, you can choose the minimum and maximum values of the fit range from the Peak Fitting window in Athena (you can either use the pluck buttons and choose the points on the plots window, or enter them manually).
After you set the fit range that strictly contains the position of the peak you want to fit (preferably it shall not contain other peaks), you just need to tick the parameters that you want to keep fixed for that specific peak (including other peaks you do not want to change the fitting parameters for). For example, if you want to keep fixed the height/amplitude or width of the peak of interest, you need to tick these corresponding boxes and leave un-ticked the box containing the energy position (E0).
Once you are finished with one peak, you can continue the same procedure with the rest of the peaks in your spectrum.
This is a way faster method to fit peaks in an effective way, and it usually works fine - sometimes you still need to make some manual adjustments to the parameters to convince yourself whether the fits can be done better or not.
I hope this helps a bit.
Regards,
Adrian
*******************
Adrian Gainar
PhD student
Office: D37
School of Chemical Engineering and Analytical Science
Jackson's Mill
University of Manchester
Manchester
M13 9PL
UK
e-mail address contact: adrian.gainar at postgrad.manchester.ac.uk
office telephone no.: +44(0)161 306 4362
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From: ifeffit-bounces at millenia.cars.aps.anl.gov [ifeffit-bounces at millenia.cars.aps.anl.gov] on behalf of Kenneth Latham [Kenneth.Latham at uon.edu.au]
Sent: 28 July 2015 05:59
To: ifeffit at millenia.cars.aps.anl.gov
Subject: [Ifeffit] Setting ranges in peak fitting
Hi Bruce,
To clarify this further, I am peak fitting a number of peaks under the carbon edge. For example, I know from the literature that the 1s-p transition for the C=C should be located between 284.5 to 285.5 eV, so I would fit a peak at about 285 eV to start with. I would then move on to fitting additional peaks based on their literature values with what I know about the material/where obvious peaks are in the NEXAFS.
The problem now comes when I tell Athena to fit, it will start to move the peaks all over the place to obtain the best fit, typically placing them in locations where functionalities don't appear under the NEXAFS. In other words, it would move peaks away from where I would expect them to be based on the literature. This can be partially stopped by fixing all but one peak, fitting it and then and applying this procedure to every peak multiple times.
What I was wondering is if Athena has the ability to set a range that each peak is allowed to move, i.e., the C=C center would be restricted to values between 284.5-285.5 eV. Hence I could set up the ranges and fit quickly based on those.
Cheers,
Ken Latham
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From: ifeffit-bounces at millenia.cars.aps.anl.gov <ifeffit-bounces at millenia.cars.aps.anl.gov> on behalf of ifeffit-request at millenia.cars.aps.anl.gov <ifeffit-request at millenia.cars.aps.anl.gov>
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Subject: Ifeffit Digest, Vol 149, Issue 23
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Today's Topics:
1. Setting ranges in peak fitting Athena (Kenneth Latham)
2. Re: Setting ranges in peak fitting Athena (Ravel, Bruce)
3. Re: Setting ranges in peak fitting Athena (Matt Newville)
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Message: 1
Date: Fri, 24 Jul 2015 00:14:18 +0000
From: Kenneth Latham <Kenneth.Latham at uon.edu.au>
To: "ifeffit at millenia.cars.aps.anl.gov"
<ifeffit at millenia.cars.aps.anl.gov>
Subject: [Ifeffit] Setting ranges in peak fitting Athena
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<CY1PR02MB1416E3DBC230406B078F9A07AA810 at CY1PR02MB1416.namprd02.prod.outlook.com>
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Hi Bruce,
Is it possible to set a range of values that the the center (or any other values) can be between for line shapes when peak fitting in Athena? Similar to what you can do in CasaXPS.
If not, do you know of a program that can handle NEXAFS peak fitting and has that feature?
Cheers,
Ken
------------------------------
Message: 2
Date: Fri, 24 Jul 2015 13:14:03 +0000
From: "Ravel, Bruce" <bravel at bnl.gov>
To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] Setting ranges in peak fitting Athena
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Hi Ken,
I'm sorry, but I don't quite understand your question. And I have no idea what casaXPS is, so that reference doesn't help me.
Are you asking whether you can put gaps in the fit range?
B
On July 23, 2015, at 8:16 PM, Kenneth Latham <Kenneth.Latham at uon.edu.au> wrote:
Hi Bruce,
Is it possible to set a range of values that the the center (or any other values) can be between for line shapes when peak fitting in Athena? Similar to what you can do in CasaXPS.
If not, do you know of a program that can handle NEXAFS peak fitting and has that feature?
Cheers,
Ken
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Message: 3
Date: Fri, 24 Jul 2015 11:05:45 -0500
From: Matt Newville <newville at cars.uchicago.edu>
To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] Setting ranges in peak fitting Athena
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<CA+7ESbo5Z27OdFi3a5D0S9rDX8v3x=8E1WtEvEhuthtUHB1ARQ at mail.gmail.com>
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I thought maybe Ken was asking about having box constraints or min/max
constraints on parameter values. But that is kind of a guess.
Hi Ken,
I'm sorry, but I don't quite understand your question. And I have no idea
what casaXPS is, so that reference doesn't help me.
Are you asking whether you can put gaps in the fit range?
B
On July 23, 2015, at 8:16 PM, Kenneth Latham <Kenneth.Latham at uon.edu.au>
wrote:
Hi Bruce,
Is it possible to set a range of values that the the center (or any other
values) can be between for line shapes when peak fitting in Athena? Similar
to what you can do in CasaXPS.
If not, do you know of a program that can handle NEXAFS peak fitting and
has that feature?
Cheers,
Ken
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