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Hi Allan,<br>
<br>
I'm not entirely sure why the difference between observed
(experimentally measured) and calculated (using your script below)
amplitudes of structure factors surprises you..<br>
<br>
Also:<br>
<br>
- your script computes structure factors and prints out amplitudes
(not intensities);<br>
- you do not set the B-factor. By default scatterer object is
constructed with u_iso=0.<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 8/24/15 15:01, Allan Lyckegaard
wrote:<br>
</div>
<blockquote
cite="mid:CACZSzUC43q-z8aOmn6XV8vX5GLyNg-paAHc=V+S87md+bWkkTQ@mail.gmail.com"
type="cite">
<div dir="ltr">Dear CCTBX-list
<div><br>
</div>
<div>I am trying to reproduce the (scaled) intensities for Si
reported here:�<a moz-do-not-send="true"
href="http://rruff.geo.arizona.edu/AMS/xtal_data/DIFfiles/15285.txt">http://rruff.geo.arizona.edu/AMS/xtal_data/DIFfiles/15285.txt</a>
based on this information:�<a moz-do-not-send="true"
href="http://rruff.geo.arizona.edu/AMS/CIF_text_files/15285_cif.txt">http://rruff.geo.arizona.edu/AMS/CIF_text_files/15285_cif.txt</a></div>
<div><br>
</div>
<div>I am using CCTBX in Python:</div>
<div><br>
</div>
<div>
<p style="margin:0px">from cctbx.array_family import flex </p>
<p style="margin:0px">from cctbx import sgtbx, crystal,
miller, xray</p>
<p style="margin:0px">sgnum = 227</p>
<p style="margin:0px">sg =
sgtbx.space_group_info(sgnum).group()</p>
<p style="margin:0px">latticepar = [5.43070, 5.43070, 5.43070,
90, 90, 90]</p>
<p style="margin:0px">dmin = 1.0</p>
<p style="margin:0px">atompos = [['Si',(0.0, 0.0, 0.0)]]</p>
<p style="margin:0px">scatterers = flex.xray_scatterer()</p>
<p style="margin:0px">scatterers.append(xray.scatterer(label=atompos[0][0],
site=atompos[0][1]))</p>
<p style="margin:0px">pg = sg.build_derived_point_group()</p>
<p style="margin:0px">sym =
crystal.symmetry(space_group=sg,unit_cell=latticepar)</p>
<p style="margin:0px">sps =
crystal.special_position_settings(crystal_symmetry=sym)</p>
<p style="margin:0px">structure =
xray.structure(special_position_settings=sps,scatterers=scatterers)</p>
<p style="margin:0px">F =
structure.structure_factors(d_min=dmin,algorithm='direct').f_calc()</p>
<p style="margin:0px">list(F.amplitudes())</p>
<p style="margin:0px"><br>
</p>
<p style="margin:0px">This gives:</p>
<p style="margin:0px">[((0, 2, 2), 0.0),</p>
<p style="margin:0px">�((0, 4, 0), 120.21765812638594),</p>
<p style="margin:0px">�((1, 1, 1), 84.18849550806966),</p>
<p style="margin:0px">�((1, 3, 1), 65.48371727205928),</p>
<p style="margin:0px">�((1, 3, 3), 57.45438308324155),</p>
<p style="margin:0px">�((1, 5, 1), 51.48759686950681),</p>
<p style="margin:0px">�((2, 2, 2), 128.54540698861973),</p>
<p style="margin:0px">�((2, 4, 2), 0.0),</p>
<p style="margin:0px">�((3, 3, 3), 51.48759686950681)]</p>
</div>
<div><br>
</div>
<div>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?</div>
<div><br>
</div>
<div>Cheers,</div>
<div>/Allan</div>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
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</blockquote>
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