Re: [Ifeffit] Difference spectra- Ifeffit Digest, Vol 159, Issue 21

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 ****************************************