Re: [Ifeffit] difference spectra- Ifeffit Digest, Vol 159, Issue 23

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:

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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)

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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:

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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)

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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

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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/

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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

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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/

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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 -------

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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/

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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/

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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

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