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

sb2c08 at gmail.com sb2c08 at gmail.com
Tue May 31 14:34:31 CDT 2016


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 at millenia.cars.aps.anl.gov wrote:
> 
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> Today's Topics:
> 
>   1. Re: Difference spectra- Ifeffit Digest, Vol 159, Issue 21
>      (sb2c08 at 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 at gmail.com
> To: ifeffit at millenia.cars.aps.anl.gov
> Subject: Re: [Ifeffit] Difference spectra- Ifeffit Digest, Vol 159,
>    Issue 21
> Message-ID: <A5D4B2A5-A353-4813-BFC0-A31105BE4B21 at gmail.com>
> 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 at millenia.cars.aps.anl.gov wrote:
>> 
>> Send Ifeffit mailing list submissions to
>>   ifeffit at millenia.cars.aps.anl.gov
>> 
>> To subscribe or unsubscribe via the World Wide Web, visit
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>> or, via email, send a message with subject or body 'help' to
>>   ifeffit-request at millenia.cars.aps.anl.gov
>> 
>> You can reach the person managing the list at
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>> 
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of Ifeffit digest..."
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>> 
>> Today's Topics:
>> 
>>  1. Difference spectra (sb2c08 at 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 at gmail.com
>> To: ifeffit at millenia.cars.aps.anl.gov
>> Subject: [Ifeffit] Difference spectra
>> Message-ID: <A460A00C-45B0-4ED5-969C-6FB3BF0C67A2 at gmail.com>
>> 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 <bravel at bnl.gov>
>> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
>> Subject: Re: [Ifeffit] Difference spectra
>> Message-ID: <574D8142.8060001 at bnl.gov>
>> Content-Type: text/plain; charset=windows-1252; format=flowed
>> 
>>> On 05/30/2016 01:25 PM, sb2c08 at 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 at 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 <bravel at bnl.gov>
>> To: mazhar iqbal <mazharphy_05 at yahoo.com>, XAFS Analysis using Ifeffit
>>   <ifeffit at millenia.cars.aps.anl.gov>
>> Subject: Re: [Ifeffit] Regarding time resolved XAS
>> Message-ID: <574D8223.3080109 at 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 at 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" <alessandro.longo at cnr.it>
>> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
>> Subject: [Ifeffit] Atoms on the WEB
>> Message-ID: <20160531124332.M60406 at 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 at cnr.it
>> phone: 00390916809359
>> fax  : 00390916809399
>> 
>> Open WebMail Project (http://openwebmail.org)
>> 
>> 
>> ---------- Original Message -----------
>> From: Bruce Ravel <bravel at bnl.gov>
>> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
>> Sent: Tue, 31 May 2016 08:19:14 -0400
>> Subject: Re: [Ifeffit] Difference spectra
>> 
>>>> On 05/30/2016 01:25 PM, sb2c08 at 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 at 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 at 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 <bravel at bnl.gov>
>> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
>> Subject: Re: [Ifeffit] Atoms on the WEB
>> Message-ID: <574D8C27.4090907 at 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 at 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 at 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 <bravel at bnl.gov>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] Difference spectra- Ifeffit Digest, Vol 159,
>    Issue 21
> Message-ID: <574DCD6C.6080800 at bnl.gov>
> Content-Type: text/plain; charset=windows-1252; format=flowed
> 
>> On 05/31/2016 01:23 PM, sb2c08 at 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 at 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 <afrenke2 at yu.edu>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] Difference spectra- Ifeffit Digest, Vol 159,
>    Issue 21
> Message-ID:
>    <545F89325F51764C902D37B42C9F4D530210471863 at 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 at bnl.gov
> 
> ________________________________________
> From: Ifeffit [ifeffit-bounces at millenia.cars.aps.anl.gov] on behalf of Bruce Ravel [bravel at 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 at 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 at 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 at 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 at 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
> ****************************************



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