[RMCProfile-users] [EXTERNAL] Fitting data from SAED

Tue Jun 29 17:09:19 BST 2021

Hi Chris,

For X-ray data, since we have the Q-dependent form factor, therefore during data reduction stage we should already get the data somehow normalized, by doing which hopefully we can get rid of the Q-dependency in the reciprocal space data (this, however, may not be a good assumption in some cases where we have elements whose form factors are quite different from each other). Saying that, in the `XRAY_RECIPROCAL_SPACE_DATA` section, ‘F(Q)’ already indicates normalized data so we don’t need to specify ‘F(Q) normalised’ (as you found, there is probably no such option at all for `XRAY_RECIPROCAL_SPACE_DATA` section).

So if you can manage to get your electron diffraction data somehow into normalized version, I think it should be safe to use ‘F(Q)’ under ` XRAY_RECIPROCAL_SPACE_DATA`.

Please feel free to let me know if any issues with my comments here or if anything I can help with.

Cheers,
Yuanpeng

--

Dr. Yuanpeng Zhang
Neutron Scattering Scientist
Spallation Neutron Source

Oak Ridge National Laboratory
1 bethel valley road, Oak Ridge, TN 37830, US
Mobile: +1(865)-335-4818
Email: zhangy3 at ornl.gov<mailto:zhangy3 at ornl.gov> | Web: https://www.iris2020.net<https://www.iris2020.net/>

From: Stenz, Christian <stenz at physik.rwth-aachen.de>
Date: Tuesday, June 29, 2021 at 11:41 AM
To: Zhang, Yuanpeng <zhangy3 at ornl.gov>, rmcprofile-users at shadow.nd.rl.ac.uk <rmcprofile-users at shadow.nd.rl.ac.uk>
Cc: rmcprofile-users at rmcprofile.org <rmcprofile-users at rmcprofile.org>
Subject: AW: [EXTERNAL] [RMCProfile-users] Fitting data from SAED
Hi Yuanpeng,

Okay it’s good to know of that parametrisation, thanks. It would be no problem for me to transform my normalised F(q) with the electron form factors <f_e(q)>^2 and <f_e(q)^2>. But is the input file F(q) for RMCProfile not supposed to be renormalized with the corresponding x-ray scattering form factors?

So, my idea would be to normalise my electron diffraction data to a function without units, which should then correspond to ‘F(q) normalized’ referring to the RMCProfile manual, and then renormalise with respect to the x-ray form factors to obtain ‘F(q)’, again referring to the RMCProfile manual.

Cheers,
Chris

Von: Zhang, Yuanpeng <zhangy3 at ornl.gov>
Gesendet: Dienstag, 29. Juni 2021 16:20
An: Stenz, Christian <stenz at physik.rwth-aachen.de>; rmcprofile-users at shadow.nd.rl.ac.uk
Cc: rmcprofile-users at rmcprofile.org
Betreff: Re: [EXTERNAL] [RMCProfile-users] Fitting data from SAED

Hi Chris,

Those are the coefficients for the analytical X-ray atomic form factor equation, as you can find in the following paper, https://doi.org/10.1107/S0108767394013292

In Eqn. (1), you can find the expression with 9 coefficients. Moreover, since you have electrons instead of X-ray, I think you may need to do some transformation to get the coefficients for electrons – I am not familiar with this, unfortunately.

Cheers,
Yuanpeng

--

Dr. Yuanpeng Zhang
Neutron Scattering Scientist
Spallation Neutron Source

Oak Ridge National Laboratory
1 bethel valley road, Oak Ridge, TN 37830, US
Mobile: +1(865)-335-4818
Email: zhangy3 at ornl.gov<mailto:zhangy3 at ornl.gov> | Web: https://www.iris2020.net<https://www.iris2020.net/>

From: Stenz, Christian <stenz at physik.rwth-aachen.de<mailto:stenz at physik.rwth-aachen.de>>
Date: Tuesday, June 29, 2021 at 11:08 AM
To: Zhang, Yuanpeng <zhangy3 at ornl.gov<mailto:zhangy3 at ornl.gov>>, rmcprofile-users at shadow.nd.rl.ac.uk<mailto:rmcprofile-users at shadow.nd.rl.ac.uk> <rmcprofile-users at shadow.nd.rl.ac.uk<mailto:rmcprofile-users at shadow.nd.rl.ac.uk>>
Cc: rmcprofile-users at rmcprofile.org<mailto:rmcprofile-users at rmcprofile.org> <rmcprofile-users at rmcprofile.org<mailto:rmcprofile-users at rmcprofile.org>>
Subject: AW: [EXTERNAL] [RMCProfile-users] Fitting data from SAED
Hi Yuanpeng,

Firstly, thanks for the advice.

I have some issues preparing the .xray file by myself as I don’t know how it is set up. If I understood it correctly, the .xray file describes the x-ray atomic form factor with nine parameters per element each.
What do the nine numbers specified behind each element in the .xray file exactly refer to? I can’t seem to find a documentation about this, neither in the manual nor the tutorial.

Cheers,
Chris

Von: Yuanpeng Zhang <zhangy3 at ornl.gov<mailto:zhangy3 at ornl.gov>>
Gesendet: Dienstag, 29. Juni 2021 15:00
An: rmcprofile-users at shadow.nd.rl.ac.uk<mailto:rmcprofile-users at shadow.nd.rl.ac.uk>
Cc: rmcprofile-users at rmcprofile.org<mailto:rmcprofile-users at rmcprofile.org>; Stenz, Christian <stenz at physik.rwth-aachen.de<mailto:stenz at physik.rwth-aachen.de>>
Betreff: Re: [EXTERNAL] [RMCProfile-users] Fitting data from SAED

Hi Christian,

There are several things on top of my head,

  1.  You may want to manually prepare the .xray file to put in the atomic form factors for electron diffraction.

  1.  You can use `XRAY_RECIPROCAL_SPACE_DATA` in this case, given that you transform the input data to allowed format. You can refer to RMCProfile manual for the definition of various formats and I don't think it will be difficult to transform in between those formats. But please feel free to let me know if you have issues with the transformation.

  1.  Also, you may want to read the section of RMCProfile manual about `XRAY_RECIPROCAL_SPACE_DATA` where you can find that we only need to provide the reciprocal space data and RMCProfile can do the Fourier transformation internally and do the fitting in real space automatically if specified to do that. Again, if any issues, please feel free to let me know.

Cheers,
Yuanpeng

--

Dr. Yuanpeng Zhang
Neutron Scattering Scientist
Spallation Neutron Source

Oak Ridge National Laboratory
1 Bethel Valley Rd. Oak Ridge, TN 37830, US
Mobile: +1(865)335-4818
Email: zhangy3 at ornl.gov<https://link.getmailspring.com/link/36835A59-6E0F-489A-994E-5C74EF8FCD20@getmailspring.com/0?redirect=mailto%3Azhangy3%40ornl.gov&recipient=c3RlbnpAcGh5c2lrLnJ3dGgtYWFjaGVuLmRl> | Web: https://www.iris2020.net/<https://link.getmailspring.com/link/36835A59-6E0F-489A-994E-5C74EF8FCD20@getmailspring.com/1?redirect=https%3A%2F%2Fwww.iris2020.net%2F&recipient=c3RlbnpAcGh5c2lrLnJ3dGgtYWFjaGVuLmRl>
On Jun 17 2021, at 6:40 am, Stenz, Christian via rmcprofile-users <rmcprofile-users at shadow.nd.rl.ac.uk<mailto:rmcprofile-users at shadow.nd.rl.ac.uk>> wrote:
Hi all,

I would like to fit my real space and reciprocal space data obtained from TEM selective area electron diffraction (SAED) on amorphous GeTe samples. I don't know much about the backend computations regarding the x-ray/neutron atomic form factors in RMCProfile (of course I had to utilise the electron atomic form factors to calculate F(Q) and D(r)), but should there be any issues when supplying the normalised functions in both real and reciprocal space? I.e.:

XRAY_REAL_SPACE_DATA :: 1

> FILENAME :: GeTe_asd.DrN

> DATA_TYPE :: D(r) normalised

> FIT_TYPE :: D(r) normalised

> START_POINT :: 1

> END_POINT :: 1000

> CONSTANT_OFFSET :: 0.0000

> WEIGHT :: 0.0050

> NO_FITTED_SCALE

NEUTRON_RECIPROCAL_SPACE_DATA :: 1 %% here I declare NEUTRON data instead of XRAY data since one cannot choose the normalised data type in XRAY_RECIPROCAL_SPACE_DATA

> FILENAME :: GeTe_asd.FqN

> DATA_TYPE :: F(Q) normalised

> FIT_TYPE :: F(Q) normalised

> START_POINT :: 1

> END_POINT :: 1341

> CONSTANT_OFFSET :: 0.0000

> WEIGHT :: 0.0050

> NO_FITTED_OFFSET

> NO_FITTED_SCALE

> CONVOLVE ::

Thank you in advance for any kind of feedback!

Best regards,

Christian

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