Re: [Ifeffit] [Ext] Re: Plotting chi(R) from FEFF in XAS Viewer (Larch) with phase correction
Hi Liam:
I agree with Matt. I don't find phase corrected plots to be very useful.
Rather, I try to just identify peak positions without trying to interpret
what the half-path length might be. I leave that for the results of the
fitting. As a secondary, but perhaps more important point, applying the
phase correction in a plot of the Fourier Transform is only an approximate
calculation because the correct phase shift depends on the identity of the
scattering atom and you don't really know that until you have a path model
in the fitting routines. Once the fitting is done, then you could in
principle phase correct both the data and fit but why bother?
Carlo
On Tue, Dec 13, 2022 at 4:53 PM Matt Newville
wrote:
> Hi Liam,
>
> Yes, this is not currently available. It would not be hard to enable,
> but I am not sure it is a great thing to do. I admit that I sort of find
> that phase-correction plots need a lot of explanation, and so are prone to
> causing confusion. They might be useful for Pt metal, but they cannot
> really be correct for multi-atomic systems. Well, I guess "correct" is not
> the only consideration ;).
>
> I guess I would ask if there are suggestions and input from people
> teaching XAFS on whether phase corrections (and probably a handful of other
> "tricks" or analysis variations) are actually useful or just confusing.
>
>
>
>
> On Tue, Dec 13, 2022 at 7:58 AM Liam Nagle-Cocco wrote:
>
>> Dear all,
>>
>> In Artemis it is possible to plot chi(R) for FEFF-fit, with the phase
>> corrected - i.e. bond length corrected for deltaR. This is shown in this
>> screenshot below ("Use this path for phase corrected plotting"). Is this
>> possible in XAS Viewer?
>>
>>
>> Liam Nagle-Cocco *(he/his)*
>>
>> PhD Student in Condensed Matter Physics | Cavendish Laboratory
>>
>> Welfare Officer 2022-2023 | Jesus College MCR
>> ___
>> 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
>>
>
>
> --
> --Matt Newville 630-327-7411
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--
Carlo U. Segre (he/him) -- Duchossois Leadership Professor of Physics
Professor of Materials Science & Engineering
Director, Center for Synchrotron Radiation Research and Instrumentation
Illinois Institute of Technology
Voice: 312.567.3498Fax: 312.567.3494
se...@iit.edu http://phys.iit.edu/~segre se...@debian.org
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Re: [Ifeffit] Ifeffit Digest, Vol 238, Issue 13
Hi Matt,
Thanks for your prompt response and explanation.
Liam Nagle-Cocco (he/his)
PhD Student in Condensed Matter Physics | Cavendish Laboratory
Welfare Officer 2022-2023 | Jesus College MCR
From: Ifeffit on behalf of
ifeffit-requ...@millenia.cars.aps.anl.gov
Sent: 13 December 2022 22:53
To: ifeffit@millenia.cars.aps.anl.gov
Subject: Ifeffit Digest, Vol 238, Issue 13
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Today's Topics:
1. Re: Plotting chi(R) from FEFF in XAS Viewer (Larch) with
phase correction (Matt Newville)
--
Message: 1
Date: Tue, 13 Dec 2022 16:53:03 -0600
From: Matt Newville
To: XAFS Analysis using Ifeffit
Subject: Re: [Ifeffit] Plotting chi(R) from FEFF in XAS Viewer (Larch)
with phase correction
Message-ID:
Content-Type: text/plain; charset="utf-8"
Hi Liam,
Yes, this is not currently available. It would not be hard to enable, but
I am not sure it is a great thing to do. I admit that I sort of find that
phase-correction plots need a lot of explanation, and so are prone to
causing confusion. They might be useful for Pt metal, but they cannot
really be correct for multi-atomic systems. Well, I guess "correct" is not
the only consideration ;).
I guess I would ask if there are suggestions and input from people teaching
XAFS on whether phase corrections (and probably a handful of other "tricks"
or analysis variations) are actually useful or just confusing.
On Tue, Dec 13, 2022 at 7:58 AM Liam Nagle-Cocco wrote:
> Dear all,
>
> In Artemis it is possible to plot chi(R) for FEFF-fit, with the phase
> corrected - i.e. bond length corrected for deltaR. This is shown in this
> screenshot below ("Use this path for phase corrected plotting"). Is this
> possible in XAS Viewer?
>
>
> Liam Nagle-Cocco *(he/his)*
>
> PhD Student in Condensed Matter Physics | Cavendish Laboratory
>
> Welfare Officer 2022-2023 | Jesus College MCR
> ___
> Ifeffit mailing list
> Ifeffit@millenia.cars.aps.anl.gov
> https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmillenia.cars.aps.anl.gov%2Fmailman%2Flistinfo%2Fifeffitdata=05%7C01%7Clavn2%40universityofcambridgecloud.onmicrosoft.com%7C0e2ed3af22244ae0c06508dadd5d5753%7C49a50445bdfa4b79ade3547b4f3986e9%7C1%7C0%7C638065690205490641%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7Csdata=XNTSa1iFEQsi937E2alnIoq%2B5hmBrdlWtSXRendZqjs%3Dreserved=0
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--
--Matt Newville 630-327-7411
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Re: [Ifeffit] Plotting chi(R) from FEFF in XAS Viewer (Larch) with phase correction
Hi Liam,
Yes, this is not currently available. It would not be hard to enable, but
I am not sure it is a great thing to do. I admit that I sort of find that
phase-correction plots need a lot of explanation, and so are prone to
causing confusion. They might be useful for Pt metal, but they cannot
really be correct for multi-atomic systems. Well, I guess "correct" is not
the only consideration ;).
I guess I would ask if there are suggestions and input from people teaching
XAFS on whether phase corrections (and probably a handful of other "tricks"
or analysis variations) are actually useful or just confusing.
On Tue, Dec 13, 2022 at 7:58 AM Liam Nagle-Cocco wrote:
> Dear all,
>
> In Artemis it is possible to plot chi(R) for FEFF-fit, with the phase
> corrected - i.e. bond length corrected for deltaR. This is shown in this
> screenshot below ("Use this path for phase corrected plotting"). Is this
> possible in XAS Viewer?
>
>
> Liam Nagle-Cocco *(he/his)*
>
> PhD Student in Condensed Matter Physics | Cavendish Laboratory
>
> Welfare Officer 2022-2023 | Jesus College MCR
> ___
> 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
>
--
--Matt Newville 630-327-7411
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[Ifeffit] Plotting chi(R) from FEFF in XAS Viewer (Larch) with phase correction
Dear all,
In Artemis it is possible to plot chi(R) for FEFF-fit, with the phase corrected
- i.e. bond length corrected for deltaR. This is shown in this screenshot below
("Use this path for phase corrected plotting"). Is this possible in XAS Viewer?
[cid:b58a0f44-1946-4c60-a12e-c1e0bfa50100]
Liam Nagle-Cocco (he/his)
PhD Student in Condensed Matter Physics | Cavendish Laboratory
Welfare Officer 2022-2023 | Jesus College MCR
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Re: [Ifeffit] Installing Larch without installing Anaconda
Dear Matthew, I thank you very much for your quick reply as well as this of Carlo Segre. I apologize, I did not look at the archived messages and now it is clear. I will try to install Larch as you said and keep you in touch if I have any trouble or success ! Bests, Laurent De: "Matt Newville" À: "XAFS Analysis using Ifeffit" Cc: "TRANCHANT Laurent" Envoyé: Lundi 12 Décembre 2022 19:39:21 Objet: Re: [Ifeffit] Installing Larch without installing Anaconda Hi Laurent, Hopefully, you saw the earlier replies - if not, see the archived messages at [ https://millenia.cars.aps.anl.gov/pipermail/ifeffit/2022-November/thread.html | https://millenia.cars.aps.anl.gov/pipermail/ifeffit/2022-November/thread.html ] The basic answer is that you do not need to use Anaconda to run Larch on macOS. There is a MacPorts port available, for example. In fact, Larch is distributed with PyPI so you should (or at least "may") be able to install it in any Python environment, provided the dependencies are also available. I also agree with Dr. Kumar's response that installing into a system-provided Python may not be the best idea (on any system, but especially macOS). Python does support virtual environments pretty well, which I would highly recommend to anyone wanting to install using a system-provided Python. If you have tried installing Larch and run into trouble, let us know what you tried and what did not work. On Mon, Dec 12, 2022 at 10:14 AM TRANCHANT Laurent < [ mailto:laurent.tranch...@synchrotron-soleil.fr | laurent.tranch...@synchrotron-soleil.fr ] > wrote: Dear Mr or Mrs, I sent you this message about ten days ago but on my side I did not receive any answer. I would like to avoid installing Anaconda during the installation of Larch on my MacOS computer. I would like to know if it is possible or not. I thank you in advance for your help. Best regards, Laurent Tranchant De: "TRANCHANT Laurent" < [ mailto:laurent.tranch...@synchrotron-soleil.fr | laurent.tranch...@synchrotron-soleil.fr ] > À: "ifeffit" < [ mailto:ifeffit@millenia.cars.aps.anl.gov | ifeffit@millenia.cars.aps.anl.gov ] > Envoyé: Mercredi 30 Novembre 2022 13:49:11 Objet: Installing Larch without installing Anaconda Dear Mr or Mrs, I am Laurent Tranchant, post-doctoral researcher working at the IPANEMA laboratory at the SOLEIL synchrotron in France. I would like to install Larch (especially to use XAS Viewer to treat my XAS data) without installing Anaconda on MacOS. Do you know if it is possible or not ? For example by using MacPorts instead of Anaconda... It seems that all the solutions proposed online to install Larch on MacOS require the installation of Anaconda Python environment. I thank you in advance for your help. Best regards, Laurent Tranchant ___ Ifeffit mailing list [ mailto:Ifeffit@millenia.cars.aps.anl.gov | Ifeffit@millenia.cars.aps.anl.gov ] [ http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit | http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ] Unsubscribe: [ http://millenia.cars.aps.anl.gov/mailman/options/ifeffit | http://millenia.cars.aps.anl.gov/mailman/options/ifeffit ] -- --Matt Newville http://cars.uchicago.edu/ | cars.uchicago.edu ] > 630-327-7411 ___ 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
