This is very helpful thank you. To give a little bit of context, the reaction is a solution of W(CO)6 irradiated at 266nm, to give W(CO)5*, it would be good to find the overall change of CO distance, especially as the multi scattering dominates the EXAFS. Just as a final point, the difference spectrum is taken from the normalised after and before laser spectra, so supposing the difference is fitted directly in Artemis (and coordination number is known/assumed), the amplitude factor will give an indication of the % change, supposing the Debye-Waller factor is similar to the ground state W(CO)6? But normalisation I find is the first difficult issue.
Thanks Bruce and Anatoly and I will look over the references for some direction.
Stu
On 31 May 2016, at 19:20, ifeffit-request@millenia.cars.aps.anl.gov wrote:
Send Ifeffit mailing list submissions to
ifeffit@millenia.cars.aps.anl.gov
To subscribe or unsubscribe via the World Wide Web, visit
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
or, via email, send a message with subject or body 'help' to
ifeffit-request@millenia.cars.aps.anl.gov
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. Re: Difference spectra- Ifeffit Digest, Vol 159, Issue 21
(sb2c08@gmail.com)
2. Re: Difference spectra- Ifeffit Digest, Vol 159, Issue 21
(Bruce Ravel)
3. Re: Difference spectra- Ifeffit Digest, Vol 159, Issue 21
(Anatoly I Frenkel)
----------------------------------------------------------------------
Message: 1
Date: Tue, 31 May 2016 18:23:42 +0100
From: sb2c08@gmail.com
To: ifeffit@millenia.cars.aps.anl.gov
Subject: Re: [Ifeffit] Difference spectra- Ifeffit Digest, Vol 159,
Issue 21
Message-ID:
Content-Type: text/plain; charset=us-ascii
I am familiar with the software and apologies I did mean Artemis in terms of fitting and understand that there is no pump probe button.
To be clearer, can I make the excited state and ground state models in Artemis, take the data and difference (which can be done in Athena) and use that as a direct comparison, perhaps as you would with XANES data? I understand my data but I do not understand the best method to try get at least a first shell fit from the EXAFS region, collected by taking the difference of the ground state from the excited state, and can this be done in anyway via Artemis through some data analysis.
On 31 May 2016, at 14:07, ifeffit-request@millenia.cars.aps.anl.gov wrote:
Send Ifeffit mailing list submissions to
ifeffit@millenia.cars.aps.anl.gov
To subscribe or unsubscribe via the World Wide Web, visit
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
or, via email, send a message with subject or body 'help' to
ifeffit-request@millenia.cars.aps.anl.gov
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. Difference spectra (sb2c08@gmail.com)
2. Re: Difference spectra (Bruce Ravel)
3. Re: Regarding time resolved XAS (Bruce Ravel)
4. Atoms on the WEB (alessandro longo)
5. Re: Atoms on the WEB (Bruce Ravel)
----------------------------------------------------------------------
Message: 1
Date: Mon, 30 May 2016 18:25:21 +0100
From: sb2c08@gmail.com
To: ifeffit@millenia.cars.aps.anl.gov
Subject: [Ifeffit] Difference spectra
Message-ID:
Content-Type: text/plain; charset=us-ascii
Hi,
We recently collected laser pump-probe XAS data out to k=9. The process to get the excited state is to take the laser off minus the laser on data. I'm a little unsure in terms of trying to fit the difference EXAFS and is it possible via Athena? So far I model the EXAFS of the excited state and take away from the ground state model and compare visually. The only way I can think is to work out the % conversion and add that % of laser off back to the difference data in order to get the real EXAFS of the excited state, which can be fitted through Athena. But this is really difficult and probably inaccurate?
Thanks for any help or suggestions,
Stu
------------------------------
Message: 2
Date: Tue, 31 May 2016 08:19:14 -0400
From: Bruce Ravel
To: XAFS Analysis using Ifeffit
Subject: Re: [Ifeffit] Difference spectra
Message-ID: <574D8142.8060001@bnl.gov>
Content-Type: text/plain; charset=windows-1252; format=flowed
On 05/30/2016 01:25 PM, sb2c08@gmail.com wrote:
We recently collected laser pump-probe XAS data out to k=9. The
process to get the excited state is to take the laser off minus the
laser on data. I'm a little unsure in terms of trying to fit the
difference EXAFS and is it possible via Athena? So far I model the
EXAFS of the excited state and take away from the ground state model
and compare visually. The only way I can think is to work out the %
conversion and add that % of laser off back to the difference data in
order to get the real EXAFS of the excited state, which can be fitted
through Athena. But this is really difficult and probably
inaccurate?
Of course it's not possible to fit and EXAFS spectrum in Athena.
Artemis is the program for fitting the EXAFS.
I am unclear on what you have tried so far, so I am a little unsure what
kind of answer you are looking for. Artemis was not really written with
your sort of experiment in mind. That said, if your problem is fit some
theory from Feff to a measured spectrum with some fitting model -- that
is what Artemis is for. As with any difficult problem, you need to
understand your data and your model and you need to understand Artemis
well enough to implement the fit. But there is no magical, hidden
button that says "fit my pump-probe data."
B
--
Bruce Ravel ------------------------------------ bravel@bnl.gov
National Institute of Standards and Technology
Synchrotron Science Group at NSLS-II
Building 535A
Upton NY, 11973
Homepage: http://bruceravel.github.io/home/
Software: https://github.com/bruceravel
Demeter: http://bruceravel.github.io/demeter/
------------------------------
Message: 3
Date: Tue, 31 May 2016 08:22:59 -0400
From: Bruce Ravel
To: mazhar iqbal , XAFS Analysis using Ifeffit
Subject: Re: [Ifeffit] Regarding time resolved XAS
Message-ID: <574D8223.3080109@bnl.gov>
Content-Type: text/plain; charset=windows-1252; format=flowed
On 05/30/2016 02:20 AM, mazhar iqbal wrote:
I want to ask about the aligning the XAS spectra that is given in
Athena. Can we do the alignment of time resolved spectra? As you know
that the resolved spectra (IR pump X-ray probe) may have edge shift due
to laser pumping. Do you think that the same method of the alignment can
be applied here as well. An additional piece of information is that we
have a reference fluorescence line always on the screen that well behind
the K absorption edge.
Well, you have told us what you have tried nor what problem you are
actually facing. If the question is "does Athena help you align data?"
I think you already know that the answer is yes.
I don't understand the business about a "fluorescence line always on the
screen". How do you propose to use that to align your XAS data?
In the case of a situation where you are purposefully changing the
chemical state of the sample, then you need to have some absolute
reference by which to perform the alignment -- a reference spectrum
measured simultaneously, an encoder reading on the monochromator,
something that allows you to do the chore.
You question is a bit vague and open-ended. Without more information or
a more focused question, I don't know how to help you further.
B
--
Bruce Ravel ------------------------------------ bravel@bnl.gov
National Institute of Standards and Technology
Synchrotron Science Group at NSLS-II
Building 535A
Upton NY, 11973
Homepage: http://bruceravel.github.io/home/
Software: https://github.com/bruceravel
Demeter: http://bruceravel.github.io/demeter/
------------------------------
Message: 4
Date: Tue, 31 May 2016 14:49:50 +0200
From: "alessandro longo"
To: XAFS Analysis using Ifeffit
Subject: [Ifeffit] Atoms on the WEB
Message-ID: <20160531124332.M60406@cnr.it>
Content-Type: text/plain; charset=utf-8
Hi to everyone,
I'm beamline scientist at DUBBLE at ESRF and I was using currently atoms on the web.
I don't want to disturb to much, but I was wondering why now this beatifull tool does't
work anymore. It works only to create the atoms.inp, but it was nice to have the
feff.inp ready from the web application. The main motivation is somtimes the ifeffit
tool is not installed.
Sorry If i took your time and thank you for your answer.
best
Alessandro
--
Ph.D Alessandro Longo
researcher of National Council Research
ISMN-CNR
e-mail: alessandro.longo@cnr.it
phone: 00390916809359
fax : 00390916809399
Open WebMail Project (http://openwebmail.org)
---------- Original Message -----------
From: Bruce Ravel
To: XAFS Analysis using Ifeffit
Sent: Tue, 31 May 2016 08:19:14 -0400
Subject: Re: [Ifeffit] Difference spectra
On 05/30/2016 01:25 PM, sb2c08@gmail.com wrote:
We recently collected laser pump-probe XAS data out to k=9. The
process to get the excited state is to take the laser off minus the
laser on data. I'm a little unsure in terms of trying to fit the
difference EXAFS and is it possible via Athena? So far I model the
EXAFS of the excited state and take away from the ground state model
and compare visually. The only way I can think is to work out the %
conversion and add that % of laser off back to the difference data in
order to get the real EXAFS of the excited state, which can be fitted
through Athena. But this is really difficult and probably
inaccurate?
Of course it's not possible to fit and EXAFS spectrum in Athena.
Artemis is the program for fitting the EXAFS.
I am unclear on what you have tried so far, so I am a little unsure what
kind of answer you are looking for. Artemis was not really written with
your sort of experiment in mind. That said, if your problem is fit some
theory from Feff to a measured spectrum with some fitting model -- that
is what Artemis is for. As with any difficult problem, you need to
understand your data and your model and you need to understand Artemis
well enough to implement the fit. But there is no magical, hidden
button that says "fit my pump-probe data."
B
--
Bruce Ravel ------------------------------------ bravel@bnl.gov
National Institute of Standards and Technology
Synchrotron Science Group at NSLS-II
Building 535A
Upton NY, 11973
Homepage: http://bruceravel.github.io/home/
Software: https://github.com/bruceravel
Demeter: http://bruceravel.github.io/demeter/
_______________________________________________
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
------- End of Original Message -------
------------------------------
Message: 5
Date: Tue, 31 May 2016 09:05:43 -0400
From: Bruce Ravel
To: XAFS Analysis using Ifeffit
Subject: Re: [Ifeffit] Atoms on the WEB
Message-ID: <574D8C27.4090907@bnl.gov>
Content-Type: text/plain; charset=windows-1252; format=flowed
On 05/31/2016 08:49 AM, alessandro longo wrote:
Hi to everyone,
I'm beamline scientist at DUBBLE at ESRF and I was using currently atoms on the web.
I don't want to disturb to much, but I was wondering why now this beatifull tool does't
work anymore. It works only to create the atoms.inp, but it was nice to have the
feff.inp ready from the web application. The main motivation is somtimes the ifeffit
tool is not installed.
Sorry If i took your time and thank you for your answer.
best
Alessandro
It would be nice if you started a new thread for a new question rather
than hijacking an existing thread....
Last December, the computer that hosted the web atoms tool died
dramatically. When Matt rebuilt that server, atoms did not get
restored. The web version of atoms was based on very out date code.
Bottom line is that I need to rewrite the web atoms tool using the
current code base.
It's on my list of things to do.
B
--
Bruce Ravel ------------------------------------ bravel@bnl.gov
National Institute of Standards and Technology
Synchrotron Science Group at NSLS-II
Building 535A
Upton NY, 11973
Homepage: http://bruceravel.github.io/home/
Software: https://github.com/bruceravel
Demeter: http://bruceravel.github.io/demeter/
------------------------------
Subject: Digest Footer
_______________________________________________
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
------------------------------
End of Ifeffit Digest, Vol 159, Issue 21
****************************************
------------------------------
Message: 2
Date: Tue, 31 May 2016 13:44:12 -0400
From: Bruce Ravel
To: XAFS Analysis using Ifeffit
Subject: Re: [Ifeffit] Difference spectra- Ifeffit Digest, Vol 159,
Issue 21
Message-ID: <574DCD6C.6080800@bnl.gov>
Content-Type: text/plain; charset=windows-1252; format=flowed
On 05/31/2016 01:23 PM, sb2c08@gmail.com wrote:
To be clearer, can I make the excited state and ground state models
in Artemis, take the data and difference (which can be done in
Athena) and use that as a direct comparison, perhaps as you would
with XANES data? I understand my data but I do not understand the
best method to try get at least a first shell fit from the EXAFS
region, collected by taking the difference of the ground state from
the excited state, and can this be done in anyway via Artemis through
some data analysis.
While it seems like Artemis specifically wants traditional EXAFS data as
its input, that's not really the case. It just wants something wiggly
that can be Fourier transformed.
While it seems like Artemis wants a full Feff calculation and all the
path files that come from it with all the degeneracies that Feff thinks
it has, that also is not really the case.
I don't know what your data are or what they look like (you haven't told
us), so I will make up a scenario off the top of my head. Hopefully
that will still be instructive.
Suppose that our ground state is a pure metal -- say iron metal. Iron
metal has a near neighbor at about 2.5A. Suppose that our secondary
state includes some iron oxide -- that has a neighbor at about 1.9A and
a correspond peak at a much shorter distance.
Suppose we can guess the amount of pure metal in the secondary state.
Then we could do some simple arithmetic to isolate (approximately!) the
oxide contribution. This will resemble an iron oxide standard, but with
much smaller amplitude.
Seems to me that this difference spectrum could be fit in Artemis by
running Feff on the oxide, parameterizing the fit much like a
conventional spectrum, but giving the model enough freedom to have a
much smaller amplitude. That is, you cannot force the fit to have an
S02 of around 0.9 -- like a normal fit -- and the full coordination
number of the normal oxide. Something in the fitting model must be
introduced to allow the amplitude to be small enough to fit the
difference data properly.
You, then, need to have a way of interpreting this much smaller
amplitude in a way that makes sense for the problem at hand.
To say all that another way ... your difference data has Fourier
components ... Feff provides Fourier components ... you supply a model
(and an interpretation!) that fits Feff's Fourier components to the
Fourier components in your data. If your data can be described by Feff,
Artemis can do the describing.
HTH,
B
--
Bruce Ravel ------------------------------------ bravel@bnl.gov
National Institute of Standards and Technology
Synchrotron Science Group at NSLS-II
Building 535A
Upton NY, 11973
Homepage: http://bruceravel.github.io/home/
Software: https://github.com/bruceravel
Demeter: http://bruceravel.github.io/demeter/
------------------------------
Message: 3
Date: Tue, 31 May 2016 18:20:20 +0000
From: Anatoly I Frenkel
To: XAFS Analysis using Ifeffit
Subject: Re: [Ifeffit] Difference spectra- Ifeffit Digest, Vol 159,
Issue 21
Message-ID:
<545F89325F51764C902D37B42C9F4D530210471863@YUWEXCPM11.yuad.uds.yu.edu>
Content-Type: text/plain; charset="us-ascii"
Hi Stu,
In full agreement with Bruce, what you want to do can be done, and it was done a few times before.
I think the first group that applied conventional EXAFS analysis to differential signals was Pettifer et al in Nature (2005), to analyze EXAFS in magnetrostrictors measured at different values of magnetic field. Then, C. Konig et al did a similar trick for a catalyst under different atmospheres. They also used conventional EXAFS equation to fit the difference because the model allowed them to do so (the changes in the amplitude factors was also an amplitude factor and could be obtained from the fit because the fitting program does not know what the meaning of amplitude factors is, you do.
I want to warn you that normalization of the amplitude of your EXAFS data will be the trickiest part because it depends on how many absorbing species changed structure during the excitation.
In my work we also used this method in a couple of papers, Spanjers et al (for Pd nanoparticles under Ar and inert environment), and Korobko et al, (2015) using electrostrictors with and without applied electric field. The latter example is here:
https://pubweb.bnl.gov/~frenkel/CGO/CGO-modulations.pdf
The references to Pettifer and Konig works are Refs 19 and 20.
Regards,
Anatoly
P.S. If anyone is interested, a postdoctoral position has just opened up in my group, for research of electromechanical materials. Please contact me for further information: frenkel@bnl.gov
________________________________________
From: Ifeffit [ifeffit-bounces@millenia.cars.aps.anl.gov] on behalf of Bruce Ravel [bravel@bnl.gov]
Sent: Tuesday, May 31, 2016 1:44 PM
To: XAFS Analysis using Ifeffit
Subject: Re: [Ifeffit] Difference spectra- Ifeffit Digest, Vol 159, Issue 21
On 05/31/2016 01:23 PM, sb2c08@gmail.com wrote:
To be clearer, can I make the excited state and ground state models
in Artemis, take the data and difference (which can be done in
Athena) and use that as a direct comparison, perhaps as you would
with XANES data? I understand my data but I do not understand the
best method to try get at least a first shell fit from the EXAFS
region, collected by taking the difference of the ground state from
the excited state, and can this be done in anyway via Artemis through
some data analysis.
While it seems like Artemis specifically wants traditional EXAFS data as
its input, that's not really the case. It just wants something wiggly
that can be Fourier transformed.
While it seems like Artemis wants a full Feff calculation and all the
path files that come from it with all the degeneracies that Feff thinks
it has, that also is not really the case.
I don't know what your data are or what they look like (you haven't told
us), so I will make up a scenario off the top of my head. Hopefully
that will still be instructive.
Suppose that our ground state is a pure metal -- say iron metal. Iron
metal has a near neighbor at about 2.5A. Suppose that our secondary
state includes some iron oxide -- that has a neighbor at about 1.9A and
a correspond peak at a much shorter distance.
Suppose we can guess the amount of pure metal in the secondary state.
Then we could do some simple arithmetic to isolate (approximately!) the
oxide contribution. This will resemble an iron oxide standard, but with
much smaller amplitude.
Seems to me that this difference spectrum could be fit in Artemis by
running Feff on the oxide, parameterizing the fit much like a
conventional spectrum, but giving the model enough freedom to have a
much smaller amplitude. That is, you cannot force the fit to have an
S02 of around 0.9 -- like a normal fit -- and the full coordination
number of the normal oxide. Something in the fitting model must be
introduced to allow the amplitude to be small enough to fit the
difference data properly.
You, then, need to have a way of interpreting this much smaller
amplitude in a way that makes sense for the problem at hand.
To say all that another way ... your difference data has Fourier
components ... Feff provides Fourier components ... you supply a model
(and an interpretation!) that fits Feff's Fourier components to the
Fourier components in your data. If your data can be described by Feff,
Artemis can do the describing.
HTH,
B
--
Bruce Ravel ------------------------------------ bravel@bnl.gov
National Institute of Standards and Technology
Synchrotron Science Group at NSLS-II
Building 535A
Upton NY, 11973
Homepage: http://bruceravel.github.io/home/
Software: https://github.com/bruceravel
Demeter: http://bruceravel.github.io/demeter/
_______________________________________________
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
------------------------------
Subject: Digest Footer
_______________________________________________
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
------------------------------
End of Ifeffit Digest, Vol 159, Issue 23
****************************************
Bruce Ravel
sb2c08＠gmail.com