[cctbxbb] Structure factor calculation weirdness

[Graeme.Winter at diamond.ac.uk]

Hi Folks,

Some confusion here at diamond - it seems that the amplitude of F(hkl) depends on dmin

----------------

from cctbx import xray
from cctbx import crystal
from cctbx.array_family import flex

# 14keV

wavelength = 12.3984 / 14.0

spgroup = 'Fd-3m'
latt = (5.4309, 5.4309, 5.4309, 90, 90, 90)
atoms = [('Si', 0.125, 0.125, 0.125)]

allscatterers=[]
for atom in atoms:
    allscatterers.append(xray.scatterer(
        label = atom[0],
        site = (atom[1], atom[2], atom[3]), u = 0))

structure = xray.structure(
    special_position_settings = crystal.special_position_settings(
    crystal_symmetry = crystal.symmetry(
    unit_cell = latt,
    space_group_symbol = spgroup)),
    scatterers = flex.xray_scatterer(allscatterers)).expand_to_p1()

for dmin in 5.0, 2.5, 1.7:

    print dmin
    f_calculations = structure.structure_factors(
        d_min = dmin).f_calc().amplitudes().show_array()

---------------

Chopped out only 001, 010, 100 from this...

5.0
(0, 0, 1) 0.290277589693
(0, 1, 0) 0.290277589693
(1, 0, 0) 0.290277589693
2.5
(0, 0, 1) 0.0
(0, 1, 0) 0.0
(1, 0, 0) 0.0
<snip>
1.7
(0, 0, 1) 0.278378587828
(0, 1, 0) 0.278378587828
(1, 0, 0) 0.278378587828
<snip>

Have we misunderstood something?

Thanks,

Graeme

Dr. Graeme Winter
Senior Software Scientist
Diamond Light Source

+44 1235 778091 (work)
+44 7786 662784 (work mobile)





-- 

This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail.

Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. 

Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message.

Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

 







-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/cctbxbb/attachments/20121207/9506986e/attachment-0001.htm>