[Nexus] [nexusformat/definitions] UB matrix in NXsample (#559)

Tue Apr 11 08:39:51 BST 2017

Colleagues

I would also look at

http://mmcif.wwpdb.org/dictionaries/mmcif_std.dic/Items/_diffrn_orient_matrix.UB[2][2].html<http://mmcif.wwpdb.org/dictionaries/mmcif_std.dic/Items/_diffrn_orient_matrix.UB%5B2%5D%5B2%5D.html>

since the CIF wonks have probably defined this to 9dp already…

You do need to be careful w.r.t. definitions - i.e. upper or lower triangular?

Cheers Graeme

On 11 Apr 2017, at 08:31, Tobias Richter <Tobias.Richter at esss.se<mailto:Tobias.Richter at esss.se>> wrote:

Assuming this whole thing checks out to a crystallographer, I’d be in favour of calling the new thing ub_matrix no one refers to it as just “ub” in the emails.
It would go into NXsample_component as [3,3] as well, then.

Cheers,
Tobias

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Date: Tuesday, 11 April 2017 at 08:49
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Subject: Re: [nexusformat/definitions] UB matrix in NXsample (#559)

Hi!

Mixing distances and angles I guess it is something traditional. At least SPEC provides them that way so a lot of people are used to it. For the time being I am going to ask my colleagues to use a "new" sample field named ub with dimensions [n_comp, 3, 3] containing 9 floats. I hope it will be approved.

If the three floats correspond to the angles, the choice is really unfortunate. The actual angle names should have been used because, in addition, they are scanned during measurements and there is more than just four-circle diffractometers.

On the longer term, a better solution is needed. I am not a crystallographer either but I have been dealing with diffractometer geometries and conversion from lab to reciprocal space coordinates based on the diffractometer angles. For that one needs, among others, the UB matrix, the type of diffractometer and geometry. Some classical articles are Busing & Levy 1967, Lohmaier and Vlieg (1992 or 1993 not sure), Ewans-Lutterodt and Tang (1995) and You (1999). I basically support four-circle and six-circle with the same code base. Given that those articles clearly define the different geometries and provide names to the associated angles, an NXdiffractometer class containing the UB matrix, the diffractometertype, mode and angles would be convenient since it would pave the way for conversion to reciprocal space coordinates. One would still some other things like wavelength, detector pixel sizes, distance and coordinates of the hypothetical the point of incidence on the detector if all the diffractometer angles would be at zero. Surface diffraction people, among others, need that type of description.

So, NXdiffractomer inside NXinstrument and eventually linked to from NXsample would be a nice arrangement, but I am going too far. As I said, for the time being I will just put the UB matrix inside NXsample under the name ub.

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