[cctbxbb] Structure factor calculation for Si

[Peter Zwart]

Hi,

There are two standard space group settings for F d -3 m (namely 1 and 2)
and I am not sure what the literature uses.
It is a puzzle indeed, in one setting (2,2,0) is absent, in another it
isn't. I guess the difference is space group settings, but the choice
between setting 1 and 2 still doesn't reproduce the table you send, which
by chance isn't in the paper listed in the link you send.

P








On 24 August 2015 at 15:55, Pavel Afonine <pafonine at lbl.gov> wrote:

> Hi Allan,
>
> I'm not entirely sure why the difference between observed (experimentally
> measured) and calculated (using your script below) amplitudes of structure
> factors surprises you..
>
> Also:
>
> - your script computes structure factors and prints out amplitudes (not
> intensities);
> - you do not set the B-factor. By default scatterer object is constructed
> with u_iso=0.
>
> Pavel
>
>
> On 8/24/15 15:01, Allan Lyckegaard wrote:
>
> Dear CCTBX-list
>
> I am trying to reproduce the (scaled) intensities for Si reported here:
> http://rruff.geo.arizona.edu/AMS/xtal_data/DIFfiles/15285.txt based on
> this information:
> http://rruff.geo.arizona.edu/AMS/CIF_text_files/15285_cif.txt
>
> I am using CCTBX in Python:
>
> from cctbx.array_family import flex
>
> from cctbx import sgtbx, crystal, miller, xray
>
> sgnum = 227
>
> sg = sgtbx.space_group_info(sgnum).group()
>
> latticepar = [5.43070, 5.43070, 5.43070, 90, 90, 90]
>
> dmin = 1.0
>
> atompos = [['Si',(0.0, 0.0, 0.0)]]
>
> scatterers = flex.xray_scatterer()
>
> scatterers.append(xray.scatterer(label=atompos[0][0], site=atompos[0][1]))
>
> pg = sg.build_derived_point_group()
>
> sym = crystal.symmetry(space_group=sg,unit_cell=latticepar)
>
> sps = crystal.special_position_settings(crystal_symmetry=sym)
>
> structure =
> xray.structure(special_position_settings=sps,scatterers=scatterers)
>
> F = structure.structure_factors(d_min=dmin,algorithm='direct').f_calc()
>
> list(F.amplitudes())
>
>
> This gives:
>
> [((0, 2, 2), 0.0),
>
>  ((0, 4, 0), 120.21765812638594),
>
>  ((1, 1, 1), 84.18849550806966),
>
>  ((1, 3, 1), 65.48371727205928),
>
>  ((1, 3, 3), 57.45438308324155),
>
>  ((1, 5, 1), 51.48759686950681),
>
>  ((2, 2, 2), 128.54540698861973),
>
>  ((2, 4, 2), 0.0),
>
>  ((3, 3, 3), 51.48759686950681)]
>
> How come CCTBX give an amplitude of 0.0 for (0,2,2) and (2,4,2)? The
> measured intensities in the DIFfile above does not show this. Am I missing
> something?
>
> Cheers,
> /Allan
>
>
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>
>
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-- 
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P.H. Zwart
Staff Scientist
Berkeley Center for Structural Biology, Science lead
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
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