Re: [Ifeffit] synthesis of EXAFS via larch
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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Re: [Ifeffit] synthesis of EXAFS via larch
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 > > ___ > 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 > > ___ 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
Re: [Ifeffit] synthesis of EXAFS via larch
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 > > ___ > 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 > > ___ 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
Re: [Ifeffit] synthesis of EXAFS via larch
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> > racev...@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" 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 > > ___ > 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 > > ___ 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
[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 ___ 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
