[mcstas-users] Ordering of reflections in single crystal hkl file
Erik Bergbäck Knudsen
erkn at risoe.dtu.dk
Wed Nov 23 13:34:14 CET 2011
Dear Leighton and others
It is indeed correct that Single_crystal assumes that the reflection
list is sorted in terms of tau (low-to high) and does terminate the
search when Tau gets too large. If this is not clear in the
documentation then this should be remedied at once - i.e. I'll do
something about this ASAP.
The reason for this is that the reflection list has to be traversed
at least once for each neutron and hence performance is an issue.
I too have encountered the problem with Crystallographica and am
actively pursuing a practical way around it - f.i. by
ways of cctbx - beacuse I myself want to use Single_crystal with large
molecules. As such it is not necessarily designed to deal with large
molecules but there is no formal problem with it. It just takes a while
to run through long lists of reflections.
Since we are experiencing similar problems, I'd be happy to work
with you to find a practical solution.
cheers
Erik
On Tue, 22 Nov 2011 22:39:25 +0100
"Coates, Leighton" <coatesl at ornl.gov> wrote:
> Hi All
>
> After rerunning several simulations with McStas last week I think we
> (me and Franz Gallmeier) stumbled on something relating to
> simulating diffraction from Large molecules (lots of reflections)
> from what we can tell it makes a big difference how the input hkl
> file is ordered for the single Crystal component.
>
> We are thinking that the Single crystal component searches through
> the text file of Bragg reflexes and terminates when 2*wavevector <
> Tau, because then the Bragg condition cannot be satisfied at any
> angle.
>
> However if the Bragg reflexes are ordered from high to low Tau or not
> ordered well this happens much faster than if the list of reflexes is
> ordered from low Tau to high Tau.
>
> Thus to make things work properly the hkl file should be ordered from
> low to high Tau. Has anyone seen this before and Peter does this make
> sense or is it something else?
>
> I checked out the example file YBaCuO.lau (see below) from the
> example data and it looks formatted that way. The Crystallographica
> program cannot handle large molecules so its not possible To use it I
> guess we are using the single crystal component for things it was
> never designed to handle !
>
>
> YBaCuO: cubic
> 2 # a=b=3.8186, c=11.6777; 90 deg
> 3 #
> 4 # Format parameters: Crystallographica format
> 5 # column_j 4 multiplicity 'j'
> 6 # column_d 5 d-spacing 'd' in [Angs]
> 7 # column_F2 7 norm of scattering factor |F|^2 in [fm^2]
> 8 # column_h 1
> 9 # column_k 2
> 10 # column_l 3
> 11 #
> 12 # h k l Mult. d-space 2Theta F-squared
> 13 0 0 1 2 11.6777 7.57041 76.2348
> 14 0 0 -1 2 11.6777 7.57041 76.2348
> 15 0 0 2 2 5.83885 15.1741 397.027
> 16 0 0 -2 2 5.83885 15.1741 397.027
> 17 0 0 3 2 3.89257 22.8458 2084.26
> 18 0 0 -3 2 3.89257 22.8458 2084.26
> 19 0 1 0 2 3.8843 22.895 2310.15
> 20 0 -1 0 2 3.8843 22.895 2310.15
> 21 1 0 0 2 3.8186 23.2944 1590.25
> 22 -1 0 0 2 3.8186 23.2944 1590.25
> 23 0 1 -1 4 3.68575 24.1465 79.9977
> 24 0 -1 1 4 3.68575 24.1465 79.9977
> 25 0 1 1 4 3.68575 24.1465 79.9976
> 26 0 -1 -1 4 3.68575 24.1465 79.9976
> 27 1 0 1 4 3.62948 24.5266 21.5105
> 28 1 0 -1 4 3.62948 24.5266 21.5105
> 29 -1 0 1 4 3.62948 24.5266 21.5105
> 30 -1 0 -1 4 3.62948 24.5266 21.5105
> 31 0 1 2 4 3.23404 27.5814 891.25
> 32 0 -1 -2 4 3.23404 27.5814 891.25
> 33 0 1 -2 4 3.23404 27.5814 891.25
> 34 0 -1 2 4 3.23404 27.5814 891.25
> 35 1 0 -2 4 3.19583 27.9179 1402.22
> 36 -1 0 2 4 3.19583 27.9179 1402.22
> 37 1 0 2 4 3.19583 27.9179 1402.22
> 38 -1 0 -2 4 3.19583 27.9179 1402.22
> 39 0 1 3 4 2.74953 32.566 20895.5
> 40 0 -1 -3 4 2.74953 32.566 20895.5
> 41 0 1 -3 4 2.74953 32.566 20895.5
> 42 0 -1 3 4 2.74953 32.566 20895.5
> 43 1 0 3 4 2.72593 32.8559 22705.3
> 44 1 0 -3 4 2.72593 32.8559 22705.3
> 45 -1 0 3 4 2.72593 32.8559 22705.3
> 46 -1 0 -3 4 2.72593 32.8559 22705.3
> 47 1 1 0 4 2.72309 32.8911 22369.7
> 48 1 -1 0 4 2.72309 32.8911 22369.7
> 49 -1 1 0 4 2.72309 32.8911 22369.7
> 50 -1 -1 0 4 2.72309 32.8911 22369.7
> 51 1 -1 -1 8 2.65194 33.7997 265.48
> 52 -1 1 1 8 2.65194 33.7997 265.48
> 53 1 1 1 8 2.65194 33.7997 265.48
> 54 1 1 -1 8 2.65194 33.7997 265.48
> 55 -1 -1 1 8 2.65194 33.7997 265.48
> 56 -1 -1 -1 8 2.65194 33.7997 265.48
> 57 1 -1 1 8 2.65194 33.7997 265.479
> 58 -1 1 -1 8 2.65194 33.7997 265.479
>
>
> Best Wishes
>
> Leighton
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--
Erik Bergbäck Knudsen, Scientist | morituri
AFM / Risø DTU, Po. Box. 49, DK-4000 Roskilde, Denmark | te
phone: (+45) 4677 5795, mobile: (+45) 2132 6655 | salutant
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