Thanks Raul. I am familiar with the instructions in the Demeter video series but there seems no option in Artemis that allows summing the paths generated from atoms. I think Larch would be more capable than Artemis here. Best regards, Kate On 19 March 2018 at 17:49, Acevedo-Esteves, Raul wrote:

Hello

I think this is what you are looking for, in Artemis:

https://vimeo.com/8954845

https://player.vimeo.com/video/8957754

https://vimeo.com/channels/exafs/9469738

https://player.vimeo.com/video/9473249

https://vimeo.com/channels/exafs/9628956

Regards,

Raul Acevedo-Esteves, PhD Post-Doctoral Research Associate/ 8-ID (ISS) beamline NSLS-II, Bldg. 743 C08U Brookhaven National Laboratory Upton, NY 11973-5000 631 344 4181 <(631)%20344-4181>

787 940 4023 <(787)%20940-4023> racevedo@bnl.gov

*From: *Ifeffit on behalf of Katy Smith *Reply-To: *XAFS Analysis using Ifeffit

...

*Date: *ADMonday, March 19, 2018 at 1:39 PM *To: *"ifeffit@millenia.cars.aps.anl.gov" *Subject: *[Ifeffit] synthesis of EXAFS via larch

Dear Colleagues,

I am aiming to use Larch to synthesise EXAFS spectra for metal oxides and I wonder if that would be the right way. I can synthesise the paths in Demeter/Artemis but I have no idea how to sum them in order to obtain a single EXAFS spectrum. Hence, the interest in Larch hoping that it can do what I am looking for.

Best regards,

Kate

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Thank you so much, Matt. These examples seems a good starting point, I'll try it soon. Best wishes, Kate On 19 March 2018 at 18:53, Matt Newville wrote:

Hi Katy,

On Mon, Mar 19, 2018 at 12:39 PM, Katy Smith wrote:

...

Dear Colleagues,

I am aiming to use Larch to synthesise EXAFS spectra for metal oxides and I wonder if that would be the right way. I can synthesise the paths in Demeter/Artemis but I have no idea how to sum them in order to obtain a single EXAFS spectrum. Hence, the interest in Larch hoping that it can do what I am looking for.

You might find the examples at http://xraypy.github.io/xraylarch/xafs/feffpaths.html

helpful. In particular, http://xraypy.github.io/xraylarch/xafs/feffpaths.html# example-adding-feff-files

shows how to sum paths together. The Artemis GUI can help you do this, but being able to do this at the scripting level (aka "the hard way") is really not that hard, and can give you much more power.

--Matt Newville

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I seem to be able to make some progress in using Larch, thanks to the developers. I wish to produce a plot in R rather than k, what would be the equivalent commands to ff2chi, path.k etc as per the /examples/feffit/doc_feffdat3.lar? Thanks, K On 19 March 2018 at 18:53, Matt Newville wrote:

Hi Katy,

On Mon, Mar 19, 2018 at 12:39 PM, Katy Smith wrote:

...

Dear Colleagues,

I am aiming to use Larch to synthesise EXAFS spectra for metal oxides and I wonder if that would be the right way. I can synthesise the paths in Demeter/Artemis but I have no idea how to sum them in order to obtain a single EXAFS spectrum. Hence, the interest in Larch hoping that it can do what I am looking for.

You might find the examples at http://xraypy.github.io/xraylarch/xafs/feffpaths.html

helpful. In particular, http://xraypy.github.io/xraylarch/xafs/feffpaths.html# example-adding-feff-files

shows how to sum paths together. The Artemis GUI can help you do this, but being able to do this at the scripting level (aka "the hard way") is really not that hard, and can give you much more power.

--Matt Newville

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That's Fantastic. Thanks for swift reply, Matt. Best regards, Kate On 20 March 2018 at 18:35, Matt Newville wrote:

Hi Katy,

On Tue, Mar 20, 2018 at 11:34 AM, Katy Smith wrote:

...

I seem to be able to make some progress in using Larch, thanks to the developers. I wish to produce a plot in R rather than k, what would be the equivalent commands to ff2chi, path.k etc as per the /examples/feffit/doc_feffdat3.lar?

The sum with `ff2chi` only sums in k-space. But the output is ready to do a Fourier transform with `xftf` (short for "XAFS Fourier Transform Forward"). So, building on doc_feffdat3.lar, you could do

# sum of paths (assumed to be defined already), writing chi(k) to "mysum": ff2chi([path1, path2, path3, path4, path5], group=mysum)

# now do an XAFS Fourier transform on that group to go from k to R space: xftf(mysum, kweight=2, kmin=3, kmax=15, window='kaiser', dk=4)

# plot of |chir(R)| for this sum plot(mysum.r, mysum.chir_mag, label='sum of paths', xlabel=r'$R \rm\,(\AA)$',ylabel=r'$|\chi(R)| \rm\,(\AA^{-3})$')

We're working to release the next version of Larch very soon, which includes common xafs plotting commands so that the last line there could be written as "plot_chir(mysum, label='sum of paths')".

--Matt

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