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<body class='hmmessage'><div dir='ltr'>Hi Graeme,<div><br></div><div>indeed, by setting d_min you modify the miller set which is used to calculate the structure factors,</div><div><br></div><div>Cheers,</div><div><br></div><div>o<br><br><div><div id="SkyDrivePlaceholder"></div><hr id="stopSpelling">From: Graeme.Winter@diamond.ac.uk<br>To: cctbxbb@phenix-online.org<br>Date: Fri, 7 Dec 2012 15:36:42 +0000<br>Subject: [cctbxbb] Structure factor calculation weirdness<br><br>
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<p class="ecxMsoNormal">Hi Folks,</p>
<p class="ecxMsoNormal"> </p>
<p class="ecxMsoNormal">Some confusion here at diamond � it seems that the amplitude of F(hkl) depends on dmin</p>
<p class="ecxMsoNormal"> </p>
<p class="ecxMsoNormal">----------------</p>
<p class="ecxMsoNormal"> </p>
<p class="ecxMsoNormal">from cctbx import xray</p>
<p class="ecxMsoNormal">from cctbx import crystal</p>
<p class="ecxMsoNormal">from cctbx.array_family import flex</p>
<p class="ecxMsoNormal"> </p>
<p class="ecxMsoNormal"># 14keV</p>
<p class="ecxMsoNormal"> </p>
<p class="ecxMsoNormal">wavelength = 12.3984 / 14.0</p>
<p class="ecxMsoNormal"> </p>
<p class="ecxMsoNormal">spgroup = 'Fd-3m'</p>
<p class="ecxMsoNormal">latt = (5.4309, 5.4309, 5.4309, 90, 90, 90)</p>
<p class="ecxMsoNormal">atoms = [('Si', 0.125, 0.125, 0.125)]</p>
<p class="ecxMsoNormal"> </p>
<p class="ecxMsoNormal">allscatterers=[]</p>
<p class="ecxMsoNormal">for atom in atoms:</p>
<p class="ecxMsoNormal"> allscatterers.append(xray.scatterer(</p>
<p class="ecxMsoNormal"> label = atom[0],</p>
<p class="ecxMsoNormal"> site = (atom[1], atom[2], atom[3]), u = 0))</p>
<p class="ecxMsoNormal"> </p>
<p class="ecxMsoNormal">structure = xray.structure(</p>
<p class="ecxMsoNormal"> special_position_settings = crystal.special_position_settings(</p>
<p class="ecxMsoNormal"> crystal_symmetry = crystal.symmetry(</p>
<p class="ecxMsoNormal"> unit_cell = latt,</p>
<p class="ecxMsoNormal"> space_group_symbol = spgroup)),</p>
<p class="ecxMsoNormal"> scatterers = flex.xray_scatterer(allscatterers)).expand_to_p1()
</p>
<p class="ecxMsoNormal"> </p>
<p class="ecxMsoNormal">for dmin in 5.0, 2.5, 1.7:</p>
<p class="ecxMsoNormal"> </p>
<p class="ecxMsoNormal"> print dmin</p>
<p class="ecxMsoNormal"> f_calculations = structure.structure_factors(</p>
<p class="ecxMsoNormal"> d_min = dmin).f_calc().amplitudes().show_array()</p>
<p class="ecxMsoNormal"> </p>
<p class="ecxMsoNormal">---------------</p>
<p class="ecxMsoNormal"> </p>
<p class="ecxMsoNormal">Chopped out only 001, 010, 100 from this�</p>
<p class="ecxMsoNormal"> </p>
<p class="ecxMsoNormal">5.0</p>
<p class="ecxMsoNormal">(0, 0, 1) 0.290277589693</p>
<p class="ecxMsoNormal">(0, 1, 0) 0.290277589693</p>
<p class="ecxMsoNormal">(1, 0, 0) 0.290277589693</p>
<p class="ecxMsoNormal">2.5</p>
<p class="ecxMsoNormal">(0, 0, 1) 0.0</p>
<p class="ecxMsoNormal">(0, 1, 0) 0.0</p>
<p class="ecxMsoNormal">(1, 0, 0) 0.0</p>
<p class="ecxMsoNormal"><snip></p>
<p class="ecxMsoNormal">1.7</p>
<p class="ecxMsoNormal">(0, 0, 1) 0.278378587828</p>
<p class="ecxMsoNormal">(0, 1, 0) 0.278378587828</p>
<p class="ecxMsoNormal">(1, 0, 0) 0.278378587828</p>
<p class="ecxMsoNormal"><snip></p>
<p class="ecxMsoNormal"> </p>
<p class="ecxMsoNormal">Have we misunderstood something?</p>
<p class="ecxMsoNormal"> </p>
<p class="ecxMsoNormal">Thanks,</p>
<p class="ecxMsoNormal"> </p>
<p class="ecxMsoNormal">Graeme</p>
<p class="ecxMsoNormal"> </p>
<p class="ecxMsoNormal"><span style="font-size:10.0pt;font-family:"Arial","sans-serif"">Dr. Graeme Winter</span></p>
<p class="ecxMsoNormal"><span style="font-size:10.0pt;font-family:"Arial","sans-serif"">Senior Software Scientist</span></p>
<p class="ecxMsoNormal"><span style="font-size:10.0pt;font-family:"Arial","sans-serif"">Diamond Light Source</span></p>
<p class="ecxMsoNormal"> </p>
<p class="ecxMsoNormal"><span style="font-size:10.0pt;font-family:"Arial","sans-serif"">+44 1235 778091 (work)</span></p>
<p class="ecxMsoNormal"><span style="font-size:10.0pt;font-family:"Arial","sans-serif"">+44 7786 662784 (work mobile)</span></p>
<p class="ecxMsoNormal"> </p>
<p class="ecxMsoNormal"> </p>
</div>
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