[cctbxbb] strange silicon

Marc Gailhanou marc.gailhanou at wanadoo.fr
Mon Oct 17 14:25:01 PDT 2005


Hello,
I have some trouble with cctbx, I try to understand why and I do not succeed. 
I need your help !
I replaced quartz with silicon in the "beach in the box" example/tutorial. 
This is the resulting code :

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

silicon_structure = xray.structure(
  special_position_settings=crystal.special_position_settings(
    crystal_symmetry=crystal.symmetry(
      unit_cell=(5.4307,5.4307,5.4307,90,90,90),
      space_group_symbol="Fd3m")),
  scatterers=flex.xray_scatterer([
    xray.scatterer(
      label="Si",
      site=(0.,0.,0.),
      u=0) ]))

silicon_structure.show_summary().show_scatterers()

for scatterer in silicon_structure.scatterers():
  print "%s:" % scatterer.label, "%8.4f %8.4f %8.4f" % scatterer.site
  site_symmetry = silicon_structure.site_symmetry(scatterer.site)
  print "  point group type:", site_symmetry.point_group_type()
  print "  special position operator:",  site_symmetry.special_op()

f_calc = silicon_structure.structure_factors(d_min=1).f_calc()
f_calc.show_summary().show_array()


and running the script gives the following result result :

Number of scatterers: 1
At special positions: 1
Unit cell: (5.4307, 5.4307, 5.4307, 90, 90, 90)
Space group: F d -3 m :2 (No. 227)
Label, Scattering, Multiplicity, Coordinates, Occupancy, Uiso
Si   Si    16 ( 0.0000  0.0000  0.0000) 1.00 0.0000
Si:   0.0000   0.0000   0.0000
  point group type: -3m
  special position operator: 0,0,0
Miller array info: None
Observation type: None
Type of data: complex_double, size=9
Type of sigmas: None
Number of Miller indices: 9
Anomalous flag: False
Unit cell: (5.4307, 5.4307, 5.4307, 90, 90, 90)
Space group: F d -3 m :2 (No. 227)
(0, 2, 2) 0j
(0, 4, 0) (120.217658126+0j)
(1, 1, 1) (-84.1884955081+0j)
(1, 3, 1) (65.4837172721+0j)
(1, 3, 3) (57.4543830832+0j)
(1, 5, 1) (-51.4875968695+0j)
(2, 2, 2) (128.545406989+0j)
(2, 4, 2) 0j
(3, 3, 3) (-51.4875968695+0j)


The 220 structure factor, at least, does  not look correct . I do not 
understand the 16 multiplicity either. Is there something I miss ?

Best regards
Marc




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