source: Tutorials/TOF Charge Flipping/Charge Flipping with TOF single crystal data in GSASII.htm @ 2390

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404  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 1"/>
405  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 1"/>
406  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 1"/>
407  <w:LsdException Locked="false" SemiHidden="true" Name="Revision"/>
408  <w:LsdException Locked="false" Priority="34" QFormat="true"
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411  <w:LsdException Locked="false" Priority="30" QFormat="true"
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415  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 1"/>
416  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 1"/>
417  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 1"/>
418  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 1"/>
419  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 1"/>
420  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 1"/>
421  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 2"/>
422  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 2"/>
423  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 2"/>
424  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 2"/>
425  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 2"/>
426  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 2"/>
427  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 2"/>
428  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 2"/>
429  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 2"/>
430  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 2"/>
431  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 2"/>
432  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 2"/>
433  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 2"/>
434  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 2"/>
435  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 3"/>
436  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 3"/>
437  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 3"/>
438  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 3"/>
439  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 3"/>
440  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 3"/>
441  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 3"/>
442  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 3"/>
443  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 3"/>
444  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 3"/>
445  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 3"/>
446  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 3"/>
447  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 3"/>
448  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 3"/>
449  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 4"/>
450  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 4"/>
451  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 4"/>
452  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 4"/>
453  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 4"/>
454  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 4"/>
455  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 4"/>
456  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 4"/>
457  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 4"/>
458  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 4"/>
459  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 4"/>
460  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 4"/>
461  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 4"/>
462  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 4"/>
463  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 5"/>
464  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 5"/>
465  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 5"/>
466  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 5"/>
467  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 5"/>
468  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 5"/>
469  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 5"/>
470  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 5"/>
471  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 5"/>
472  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 5"/>
473  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 5"/>
474  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 5"/>
475  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 5"/>
476  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 5"/>
477  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 6"/>
478  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 6"/>
479  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 6"/>
480  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 6"/>
481  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 6"/>
482  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 6"/>
483  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 6"/>
484  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 6"/>
485  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 6"/>
486  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 6"/>
487  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 6"/>
488  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 6"/>
489  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 6"/>
490  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 6"/>
491  <w:LsdException Locked="false" Priority="19" QFormat="true"
492   Name="Subtle Emphasis"/>
493  <w:LsdException Locked="false" Priority="21" QFormat="true"
494   Name="Intense Emphasis"/>
495  <w:LsdException Locked="false" Priority="31" QFormat="true"
496   Name="Subtle Reference"/>
497  <w:LsdException Locked="false" Priority="32" QFormat="true"
498   Name="Intense Reference"/>
499  <w:LsdException Locked="false" Priority="33" QFormat="true" Name="Book Title"/>
500  <w:LsdException Locked="false" Priority="37" SemiHidden="true"
501   UnhideWhenUsed="true" Name="Bibliography"/>
502  <w:LsdException Locked="false" Priority="39" SemiHidden="true"
503   UnhideWhenUsed="true" QFormat="true" Name="TOC Heading"/>
504  <w:LsdException Locked="false" Priority="41" Name="Plain Table 1"/>
505  <w:LsdException Locked="false" Priority="42" Name="Plain Table 2"/>
506  <w:LsdException Locked="false" Priority="43" Name="Plain Table 3"/>
507  <w:LsdException Locked="false" Priority="44" Name="Plain Table 4"/>
508  <w:LsdException Locked="false" Priority="45" Name="Plain Table 5"/>
509  <w:LsdException Locked="false" Priority="40" Name="Grid Table Light"/>
510  <w:LsdException Locked="false" Priority="46" Name="Grid Table 1 Light"/>
511  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2"/>
512  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3"/>
513  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4"/>
514  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark"/>
515  <w:LsdException Locked="false" Priority="51" Name="Grid Table 6 Colorful"/>
516  <w:LsdException Locked="false" Priority="52" Name="Grid Table 7 Colorful"/>
517  <w:LsdException Locked="false" Priority="46"
518   Name="Grid Table 1 Light Accent 1"/>
519  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 1"/>
520  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 1"/>
521  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 1"/>
522  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 1"/>
523  <w:LsdException Locked="false" Priority="51"
524   Name="Grid Table 6 Colorful Accent 1"/>
525  <w:LsdException Locked="false" Priority="52"
526   Name="Grid Table 7 Colorful Accent 1"/>
527  <w:LsdException Locked="false" Priority="46"
528   Name="Grid Table 1 Light Accent 2"/>
529  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 2"/>
530  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 2"/>
531  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 2"/>
532  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 2"/>
533  <w:LsdException Locked="false" Priority="51"
534   Name="Grid Table 6 Colorful Accent 2"/>
535  <w:LsdException Locked="false" Priority="52"
536   Name="Grid Table 7 Colorful Accent 2"/>
537  <w:LsdException Locked="false" Priority="46"
538   Name="Grid Table 1 Light Accent 3"/>
539  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 3"/>
540  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 3"/>
541  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 3"/>
542  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 3"/>
543  <w:LsdException Locked="false" Priority="51"
544   Name="Grid Table 6 Colorful Accent 3"/>
545  <w:LsdException Locked="false" Priority="52"
546   Name="Grid Table 7 Colorful Accent 3"/>
547  <w:LsdException Locked="false" Priority="46"
548   Name="Grid Table 1 Light Accent 4"/>
549  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 4"/>
550  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 4"/>
551  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 4"/>
552  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 4"/>
553  <w:LsdException Locked="false" Priority="51"
554   Name="Grid Table 6 Colorful Accent 4"/>
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559  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 5"/>
560  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 5"/>
561  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 5"/>
562  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 5"/>
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564   Name="Grid Table 6 Colorful Accent 5"/>
565  <w:LsdException Locked="false" Priority="52"
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567  <w:LsdException Locked="false" Priority="46"
568   Name="Grid Table 1 Light Accent 6"/>
569  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 6"/>
570  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 6"/>
571  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 6"/>
572  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 6"/>
573  <w:LsdException Locked="false" Priority="51"
574   Name="Grid Table 6 Colorful Accent 6"/>
575  <w:LsdException Locked="false" Priority="52"
576   Name="Grid Table 7 Colorful Accent 6"/>
577  <w:LsdException Locked="false" Priority="46" Name="List Table 1 Light"/>
578  <w:LsdException Locked="false" Priority="47" Name="List Table 2"/>
579  <w:LsdException Locked="false" Priority="48" Name="List Table 3"/>
580  <w:LsdException Locked="false" Priority="49" Name="List Table 4"/>
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582  <w:LsdException Locked="false" Priority="51" Name="List Table 6 Colorful"/>
583  <w:LsdException Locked="false" Priority="52" Name="List Table 7 Colorful"/>
584  <w:LsdException Locked="false" Priority="46"
585   Name="List Table 1 Light Accent 1"/>
586  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 1"/>
587  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 1"/>
588  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 1"/>
589  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 1"/>
590  <w:LsdException Locked="false" Priority="51"
591   Name="List Table 6 Colorful Accent 1"/>
592  <w:LsdException Locked="false" Priority="52"
593   Name="List Table 7 Colorful Accent 1"/>
594  <w:LsdException Locked="false" Priority="46"
595   Name="List Table 1 Light Accent 2"/>
596  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 2"/>
597  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 2"/>
598  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 2"/>
599  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 2"/>
600  <w:LsdException Locked="false" Priority="51"
601   Name="List Table 6 Colorful Accent 2"/>
602  <w:LsdException Locked="false" Priority="52"
603   Name="List Table 7 Colorful Accent 2"/>
604  <w:LsdException Locked="false" Priority="46"
605   Name="List Table 1 Light Accent 3"/>
606  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 3"/>
607  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 3"/>
608  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 3"/>
609  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 3"/>
610  <w:LsdException Locked="false" Priority="51"
611   Name="List Table 6 Colorful Accent 3"/>
612  <w:LsdException Locked="false" Priority="52"
613   Name="List Table 7 Colorful Accent 3"/>
614  <w:LsdException Locked="false" Priority="46"
615   Name="List Table 1 Light Accent 4"/>
616  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 4"/>
617  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 4"/>
618  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 4"/>
619  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 4"/>
620  <w:LsdException Locked="false" Priority="51"
621   Name="List Table 6 Colorful Accent 4"/>
622  <w:LsdException Locked="false" Priority="52"
623   Name="List Table 7 Colorful Accent 4"/>
624  <w:LsdException Locked="false" Priority="46"
625   Name="List Table 1 Light Accent 5"/>
626  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 5"/>
627  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 5"/>
628  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 5"/>
629  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 5"/>
630  <w:LsdException Locked="false" Priority="51"
631   Name="List Table 6 Colorful Accent 5"/>
632  <w:LsdException Locked="false" Priority="52"
633   Name="List Table 7 Colorful Accent 5"/>
634  <w:LsdException Locked="false" Priority="46"
635   Name="List Table 1 Light Accent 6"/>
636  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 6"/>
637  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 6"/>
638  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 6"/>
639  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 6"/>
640  <w:LsdException Locked="false" Priority="51"
641   Name="List Table 6 Colorful Accent 6"/>
642  <w:LsdException Locked="false" Priority="52"
643   Name="List Table 7 Colorful Accent 6"/>
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1173
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1175
1176<div class=WordSection1>
1177
1178<h1><span style='mso-fareast-font-family:"Times New Roman"'>Charge flipping
1179with neutron TOF single crystal data<o:p></o:p></span></h1>
1180
1181<p class=MsoNormal>In this exercise you will use GSAS-II to solve the structure
1182of <span class=SpellE>rubrene</span> (C<sub>42</sub>H<sub>28</sub>) from single
1183crystal neutron data via charge flipping. <span class=SpellE>Rubrene</span> is of
1184interest as a molecular semiconductor. It crystallizes in the space group <span
1185class=SpellE>Cmca</span> with the lattice parameters a=26.798Å, b=7.1618Å,
1186c=14.1942Å, Z=4. Thus, the molecule is sited on a special position with 2/m
1187symmetry. If you have not done so already, start GSAS-II.</p>
1188
1189<h2>Step 1. Set the phase information</h2>
1190
1191<p class=MsoNormal>To begin this tutorial, do <b style='mso-bidi-font-weight:
1192normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1193minor-latin;mso-hansi-theme-font:minor-latin'>Data/Add phase</span></b> in the
1194main GSAS-II data tree menu. A popup window will appear asking for a phase
1195name; I used <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1196style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1197mso-hansi-theme-font:minor-latin'>rubrene</span></b></span>. Then select <span
1198class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1199"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1200minor-latin'>rubrene</span></b></span> from the data tree</p>
1201
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1216  <v:f eqn="sum @8 21600 0"/>
1217  <v:f eqn="prod @7 21600 pixelHeight"/>
1218  <v:f eqn="sum @10 21600 0"/>
1219 </v:formulas>
1220 <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
1221 <o:lock v:ext="edit" aspectratio="t"/>
1222</v:shapetype><v:shape id="_x0000_i1059" type="#_x0000_t75" style='width:300pt;
1223 height:187.5pt;visibility:visible;mso-wrap-style:square'>
1224 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image001.png"
1225  o:title=""/>
1226</v:shape><![endif]--><![if !vml]><img width=400 height=250
1227src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image073.gif"
1228v:shapes="_x0000_i1059"><![endif]></span></p>
1229
1230<p class=MsoNormal>The General tab for this phase will be shown</p>
1231
1232<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1233 id="Picture_x0020_2" o:spid="_x0000_i1058" type="#_x0000_t75" style='width:640.5pt;
1234 height:375pt;visibility:visible;mso-wrap-style:square'>
1235 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image003.png"
1236  o:title=""/>
1237</v:shape><![endif]--><![if !vml]><img width=854 height=500
1238src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image074.gif"
1239v:shapes="Picture_x0020_2"><![endif]></span></p>
1240
1241<p class=MsoNormal>Enter the space group (<b style='mso-bidi-font-weight:normal'><span
1242style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1243mso-hansi-theme-font:minor-latin'>C m c a</span></b> – don’t forget the spaces)
1244and press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1245mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Enter</span></b>.
1246A popup with Space group information will appear</p>
1247
1248<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1249 id="Picture_x0020_3" o:spid="_x0000_i1057" type="#_x0000_t75" style='width:250.5pt;
1250 height:177.75pt;visibility:visible;mso-wrap-style:square'>
1251 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image005.png"
1252  o:title=""/>
1253</v:shape><![endif]--><![if !vml]><img width=334 height=237
1254src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image075.gif"
1255v:shapes="Picture_x0020_3"><![endif]></span></p>
1256
1257<p class=MsoNormal>Press <b style='mso-bidi-font-weight:normal'><span
1258style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1259mso-hansi-theme-font:minor-latin'>OK</span></b>; the General tab will be
1260repainted with defaults for the orthorhombic lattice parameters. Enter <b
1261style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1262mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>26.798</span></b>
1263for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1264mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>a</span></b>,
1265<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1266mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>7.1618</span></b>
1267for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1268mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>b</span></b>
1269and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1270mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>14.1942</span></b>
1271for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1272mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>c</span></b>.
1273Press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1274mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Enter</span></b>,
1275the unit cell volume (2724.178) will be updated.</p>
1276
1277<h2>Step 2. Import the data</h2>
1278
1279<p class=MsoNormal>The <span class=SpellE>rubrene</span> data were collected on
1280the TOPAZ instrument at the SNS Facility, Oak Ridge National Laboratory with 23
1281different crystal orientations; the local instrument data processing software
1282has applied corrections and combined them into a single multicolumn <span
1283class=SpellE>hkl</span> file. To import this do <b style='mso-bidi-font-weight:
1284normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1285minor-latin;mso-hansi-theme-font:minor-latin'>Import/Structure Factor/from
1286Neutron TOF HKL F2 file</span></b>; a directory dialog box will appear. Go to
1287the directory <b style='mso-bidi-font-weight:normal'><span style='font-family:
1288"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1289minor-latin'>TOF Charge Flipping/data</span></b> and select the file <span
1290class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1291"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1292minor-latin'>ruberene_orthoC.hkl</span></b></span> (double click the name or
1293press the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1294mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Open</span></b>
1295button after selecting it). A popup box will appear.</p>
1296
1297<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1298 id="Picture_x0020_4" o:spid="_x0000_i1056" type="#_x0000_t75" style='width:357.75pt;
1299 height:265.5pt;visibility:visible;mso-wrap-style:square'>
1300 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image007.png"
1301  o:title=""/>
1302</v:shape><![endif]--><![if !vml]><img width=477 height=354
1303src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image076.gif"
1304v:shapes="Picture_x0020_4"><![endif]></span></p>
1305
1306<p class=MsoNormal>Press <b style='mso-bidi-font-weight:normal'><span
1307style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1308mso-hansi-theme-font:minor-latin'>Yes</span></b>; another popup will appear
1309offering you the chance to change the name. Press <b style='mso-bidi-font-weight:
1310normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1311minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>, a new popup
1312appears.</p>
1313
1314<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1315 id="Picture_x0020_5" o:spid="_x0000_i1055" type="#_x0000_t75" style='width:240pt;
1316 height:232.5pt;visibility:visible;mso-wrap-style:square'>
1317 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image009.png"
1318  o:title=""/>
1319</v:shape><![endif]--><![if !vml]><img width=320 height=310
1320src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image077.gif"
1321v:shapes="Picture_x0020_5"><![endif]></span></p>
1322
1323<p class=MsoNormal>Here you select the phase the data belongs to. There is only
1324<span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1325style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1326mso-hansi-theme-font:minor-latin'>rubrene</span></b></span> so select it and
1327press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1328mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1329The bottom of the data tree is shown, a small data window and the plot shows
1330the l=0 slice of the last reflection set loaded (HKLF rubrene_orthoC.hkl_22).</p>
1331
1332<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1333 id="Picture_x0020_6" o:spid="_x0000_i1054" type="#_x0000_t75" style='width:525pt;
1334 height:450pt;visibility:visible;mso-wrap-style:square'>
1335 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image011.png"
1336  o:title=""/>
1337</v:shape><![endif]--><![if !vml]><img width=700 height=600
1338src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image078.gif"
1339v:shapes="Picture_x0020_6"><![endif]></span></p>
1340
1341<p class=MsoNormal>The <b style='mso-bidi-font-weight:normal'><span
1342style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1343mso-hansi-theme-font:minor-latin'>K</span></b> box control allows you to select
1344other zones &amp; layers to view. The drawing geometry is strictly square (i.e.
1345not in reciprocal space units). If you do <b style='mso-bidi-font-weight:normal'><span
1346style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1347mso-hansi-theme-font:minor-latin'>Commands/Plot 3D HKLs</span></b>, a 3D plot
1348of reciprocal space is shown</p>
1349
1350<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1351 id="Picture_x0020_1" o:spid="_x0000_i1053" type="#_x0000_t75" style='width:446.25pt;
1352 height:381.75pt;visibility:visible;mso-wrap-style:square'>
1353 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image013.png"
1354  o:title="" croptop="13337f" cropbottom="14997f" cropleft="41056f"
1355  cropright="9449f"/>
1356</v:shape><![endif]--><![if !vml]><img width=595 height=509
1357src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image079.jpg"
1358v:shapes="Picture_x0020_1"><![endif]></span></p>
1359
1360<p class=MsoNormal>The size of the green boxes is proportional to the structure
1361factors; the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1362"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1363minor-latin'>save as/key</span></b> pulldown will give you other viewing
1364options. Here is a good place to save the GSAS-II project for <span
1365class=SpellE>rubrene</span>. Do <b style='mso-bidi-font-weight:normal'><span
1366style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1367mso-hansi-theme-font:minor-latin'>File/Save project</span></b> from the main
1368GSAS-II data tree window; a file dialog box will appear. Enter a file name (I
1369used <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1370style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1371mso-hansi-theme-font:minor-latin'>rubrene</span></b></span> – no extension).</p>
1372
1373<h2>Step 3. Setup for charge flipping</h2>
1374
1375<p class=MsoNormal>We have two tasks here. One is to select the reflection sets
1376to be used in the calculations and the other is to set some controls. To begin
1377select the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1378style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1379mso-hansi-theme-font:minor-latin'>rubrene</span></b></span> phase entry in the
1380GSAS-II data tree; the General tab will appear in the Phase Data for <span
1381class=SpellE>rubrene</span> window</p>
1382
1383<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1384 id="Picture_x0020_8" o:spid="_x0000_i1052" type="#_x0000_t75" style='width:489pt;
1385 height:375pt;visibility:visible;mso-wrap-style:square'>
1386 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image015.png"
1387  o:title=""/>
1388</v:shape><![endif]--><![if !vml]><img width=652 height=500
1389src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image080.gif"
1390v:shapes="Picture_x0020_8"><![endif]></span></p>
1391
1392<p class=MsoNormal>In the Charge flip controls (about center of the page) press
1393the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1394mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Select
1395reflection sets</span></b> button; a <b style='mso-bidi-font-weight:normal'><span
1396style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1397mso-hansi-theme-font:minor-latin'>Use data</span></b> popup will appear. You will
1398want to use all the HKLF data sets; press <b style='mso-bidi-font-weight:normal'><span
1399style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1400mso-hansi-theme-font:minor-latin'>Set All</span> </b>and press <b
1401style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1402mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1403The General tab will be refreshed. GSAS-II will use all the data to build a
1404reflection set for charge flipping. For duplicate <span class=SpellE>hkls</span>
1405the last one encountered will be used. Since atoms are essentially point <span
1406class=SpellE>scatterers</span> for neutrons, a charge flip map has very sharp
1407peaks so a better choice for the <b style='mso-bidi-font-weight:normal'><span
1408style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1409mso-hansi-theme-font:minor-latin'>k-factor</span></b> (charge flip level) might
1410be <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1411mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0.5</span></b>,
1412the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1413mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>k-max</span></b>
1414should be larger (say <b style='mso-bidi-font-weight:normal'><span
1415style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1416mso-hansi-theme-font:minor-latin'>50</span></b>) and the map <b
1417style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1418mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Resolution</span></b>
1419should be smaller (say <b style='mso-bidi-font-weight:normal'><span
1420style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1421mso-hansi-theme-font:minor-latin'>0.4</span></b>). Set these three values. In
1422the Fourier map controls, set <b style='mso-bidi-font-weight:normal'><span
1423style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1424mso-hansi-theme-font:minor-latin'>Peak cutoff %</span></b> to <b
1425style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1426mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>20</span></b>;
1427this sets the lower limit of the peak search in the charge flip map. When done
1428the General tab should look like</p>
1429
1430<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1431 id="Picture_x0020_9" o:spid="_x0000_i1051" type="#_x0000_t75" style='width:516.75pt;
1432 height:375pt;visibility:visible;mso-wrap-style:square'>
1433 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image017.png"
1434  o:title=""/>
1435</v:shape><![endif]--><![if !vml]><img width=689 height=500
1436src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image081.gif"
1437v:shapes="Picture_x0020_9"><![endif]></span></p>
1438
1439<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1440
1441<h2>Step 4. Charge flipping</h2>
1442
1443<p class=MsoNormal>We are now ready for charge flipping. In the General tab
1444menu do <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1445mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/Charge
1446flipping</span></b>; a Charge flipping progress bar will appear showing the
1447residual and cycle count for the charge flipping calculation. In this case the
1448residual quickly drops to ~38% and stays there. Press <b style='mso-bidi-font-weight:
1449normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1450minor-latin;mso-hansi-theme-font:minor-latin'>Cancel</span></b> to stop the
1451calculation; some information will be printed on the console and after a pause
1452the Phase Data window will show <b style='mso-bidi-font-weight:normal'><span
1453style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1454mso-hansi-theme-font:minor-latin'>Map Peaks</span></b> and the plot window will
1455show a drawing of the obtained structure.</p>
1456
1457<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1458 id="Picture_x0020_10" o:spid="_x0000_i1050" type="#_x0000_t75" style='width:375pt;
1459 height:225pt;visibility:visible;mso-wrap-style:square'>
1460 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image019.png"
1461  o:title=""/>
1462</v:shape><![endif]--><![if !vml]><img width=500 height=300
1463src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image082.gif"
1464v:shapes="Picture_x0020_10"><![endif]></span></p>
1465
1466<p class=MsoNormal>If you scroll down the Map peak list you will find some with
1467negative magnitudes at the end of the list. GSAS-II searches the map for both
1468positive and negative peaks; the former are C-atoms and the latter are H-atoms.
1469</p>
1470
1471<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1472 id="Picture_x0020_11" o:spid="_x0000_i1049" type="#_x0000_t75" style='width:6in;
1473 height:365.25pt;visibility:visible;mso-wrap-style:square'>
1474 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image021.png"
1475  o:title="" croptop="9820f" cropbottom="18705f" cropleft="43453f" cropright="6999f"/>
1476</v:shape><![endif]--><![if !vml]><img width=576 height=487
1477src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image083.jpg"
1478v:shapes="Picture_x0020_11"><![endif]></span></p>
1479
1480<p class=MsoNormal>The plot (which I’ve rotated around a bit) shows white spots
1481for the positive peaks and red ones for the negative ones; bonds are white
1482lines. The case I’ve drawn here shows a problem with this charge flip solution.
1483While the charge flipping run has clearly found all the C-atoms and some of the
1484H-atoms, the molecule is incorrectly placed in the unit cell. To fix this you
1485could simply repeat the charge flipping run and hope it puts the molecule in
1486the right place. GSAS-II uses an algorithm based on how structure factor phases
1487are related for a given space group to reposition the solution; it sometimes
1488fails if the phase set isn’t perfect. Or you can “roll” the map
1489right/left/up/down (<b style='mso-bidi-font-weight:normal'><span
1490style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1491mso-hansi-theme-font:minor-latin'>R/L/U/D</span></b> keys) to put the solution
1492where you want. In this case a few steps with the L-key sufficed to put the
1493molecule on a 2/m site (i.e. the center of the cell indicated the multicolored
1494cross on the central C-C bond).</p>
1495
1496<p class=MsoNormal><!--[if gte vml 1]><v:shapetype id="_x0000_t32" coordsize="21600,21600"
1497 o:spt="32" o:oned="t" path="m,l21600,21600e" filled="f">
1498 <v:path arrowok="t" fillok="f" o:connecttype="none"/>
1499 <o:lock v:ext="edit" shapetype="t"/>
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1601
1602<p class=MsoNormal>Notice that as the map is rolled, the Map peak positions are
1603shifted to match the change in positions.</p>
1604
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1613
1614<p class=MsoNormal>By carefully looking at the map, you can see the 4-ring <span
1615class=SpellE>tetracene</span> (<span class=SpellE>naphthacene</span>) core of
1616the molecule with four phenyl groups attached to both sides on the center two
1617rings. The unique part consists of 1/4<sup>th</sup> of this group (i.e. half of
1618one side of the <span class=SpellE>tetracene</span> and one phenyl); one C-atom
1619sits on a 2-fold and the rest are in general positions. The molecule extends
1620into the neighboring unit cell so you don’t see the whole thing as one group
1621but has two bits on either side (I’ve marked these with arrows above).</p>
1622
1623<h2>Step 5. Peak selection</h2>
1624
1625<p class=MsoNormal>GSAS-II provides several ways of selecting peak positions
1626from a charge flipping map. One way is to pick them directly from the drawing.
1627Place the cursor on one peak and do a <b style='mso-bidi-font-weight:normal'><span
1628style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1629mso-hansi-theme-font:minor-latin'>Shift left mouse button</span></b>; it will
1630be highlighted on the list and it will turn green on the plot. Do a <b
1631style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1632mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Shift right
1633mouse button</span></b> on the remaining peaks you want to <span class=GramE>pick.</span>
1634All will turn green (you may have to wiggle the plot a bit with the mouse to
1635make them show) and all will be highlighted in the list. Alternatively, you can
1636select the entire list of peaks (double click on upper left empty box of the
1637table), then do <b style='mso-bidi-font-weight:normal'><span style='font-family:
1638"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1639minor-latin'>Map peaks/Unique peaks</span></b>. Better still you can sort the
1640peaks by one of the column headings and then do <b style='mso-bidi-font-weight:
1641normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1642minor-latin;mso-hansi-theme-font:minor-latin'>Map peaks/Unique peaks</span></b>.
1643I’ve chosen to sort the peaks on <span class=SpellE><b style='mso-bidi-font-weight:
1644normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1645minor-latin;mso-hansi-theme-font:minor-latin'>dcent</span></b></span> (distance
1646from center of the cell) beforehand. After a pause while it sorts out the
1647unique peaks, it will highlight them in the table and display the picked ones
1648in green on the plot. In this case they will probably be scattered about the
1649unit cell and not make a continuous molecule, but they are largely clustered
1650around the unit cell center. My plot looked like this when I was done.</p>
1651
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1661
1662<p class=MsoNormal>The list has them highlighted (the rest are lower down in my
1663list; all 18 atoms were found in this charge flipping result)</p>
1664
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1672v:shapes="Picture_x0020_15"><![endif]></span></p>
1673
1674<p class=MsoNormal>To add them to the Atom list do <b style='mso-bidi-font-weight:
1675normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1676minor-latin;mso-hansi-theme-font:minor-latin'>Map peaks/Move peaks</span></b>;
1677the drawing will show white balls for them.</p>
1678
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1682 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image033.png"
1683  o:title="" croptop="10579f" cropbottom="17404f" cropleft="37800f"
1684  cropright="12584f"/>
1685</v:shape><![endif]--><![if !vml]><img width=576 height=492
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1687v:shapes="Picture_x0020_16"><![endif]></span></p>
1688
1689<p class=MsoNormal>The atom list will give the magnitudes as ‘M’ names; I found
1690all 11 C-atoms and 7 H-atoms that were expected.</p>
1691
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1700
1701<h2>Step 6. Atom identification</h2>
1702
1703<p class=MsoNormal>You can reorder the atoms in the list; do an <b
1704style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1705mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Alt select</span></b>
1706for the atom row you want to move. Then do an <b style='mso-bidi-font-weight:
1707normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1708minor-latin;mso-hansi-theme-font:minor-latin'>Alt select</span></b> on the row
1709where you want the moved atom to precede it. This way you can put the C-atoms
1710first and the H-atoms last in the list instead of mixed up as in the above
1711list. Next select all the positive M peaks (pick the top one and then <b
1712style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1713mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Shift</span></b>
1714pick the last one). Do <b style='mso-bidi-font-weight:normal'><span
1715style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1716mso-hansi-theme-font:minor-latin'>Edit/Modify atom parameters</span></b> from
1717the Atoms menu; a popup will appear. Pick <b style='mso-bidi-font-weight:normal'><span
1718style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1719mso-hansi-theme-font:minor-latin'>Type</span></b> and press <b
1720style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1721mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>;
1722a Periodic Table will appear. Select <b style='mso-bidi-font-weight:normal'><span
1723style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1724mso-hansi-theme-font:minor-latin'>C</span></b> from the C-atom pulldown. All
1725the C-atom names and types will change. You should also move the C-atom with
17262(x) site symmetry to the top of the list.</p>
1727
1728<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1729 id="Picture_x0020_18" o:spid="_x0000_i1042" type="#_x0000_t75" style='width:525pt;
1730 height:225pt;visibility:visible;mso-wrap-style:square'>
1731 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image037.png"
1732  o:title=""/>
1733</v:shape><![endif]--><![if !vml]><img width=700 height=300
1734src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image092.gif"
1735v:shapes="Picture_x0020_18"><![endif]></span></p>
1736
1737<p class=MsoNormal>Do the same with the remaining negative M atoms – make them
1738H atoms. The drawing shows molecular fragments scattered about the unit cell;
1739you’d like to unify them into a single molecule. Select the C-atom with 2(x)
1740site symmetry (although any would do). Do <b style='mso-bidi-font-weight:normal'><span
1741style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1742mso-hansi-theme-font:minor-latin'>Edit/Assemble molecule</span></b> from the
1743Atoms menu; a popup will appear offering choices for Bond radii (&amp; Angle
1744radii – ignored here). Press <b style='mso-bidi-font-weight:normal'><span
1745style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1746mso-hansi-theme-font:minor-latin'>Ok</span></b>; the Atom table will be revised
1747and the plot will show an assembled molecule (the picked starting atom in
1748green). </p>
1749
1750<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1751 id="Picture_x0020_19" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:6in;
1752 height:366pt;visibility:visible;mso-wrap-style:square'>
1753 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image039.png"
1754  o:title="" croptop="11018f" cropbottom="17360f" cropleft="37831f"
1755  cropright="12587f"/>
1756</v:shape><![endif]--><![if !vml]><img width=576 height=488
1757src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image093.jpg"
1758v:shapes="Picture_x0020_19"><![endif]></span></p>
1759
1760<p class=MsoNormal>The molecule building has scrambled the order of the atoms;
1761they were located in order as the molecule was built. </p>
1762
1763<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1764 id="Picture_x0020_20" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:525pt;
1765 height:351.75pt;visibility:visible;mso-wrap-style:square'>
1766 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image041.png"
1767  o:title=""/>
1768</v:shape><![endif]--><![if !vml]><img width=700 height=469
1769src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image094.gif"
1770v:shapes="Picture_x0020_20"><![endif]></span></p>
1771
1772<p class=MsoNormal>You can reorder them to put the H-atoms at the end of the
1773list. Then select all of them and then do <span style='font-family:"Calibri",sans-serif;
1774mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Modify
1775atom parameters</span>. Pick <b style='mso-bidi-font-weight:normal'><span
1776style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1777mso-hansi-theme-font:minor-latin'>Name</span></b> from the pulldown and press <b
1778style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1779mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1780You are asked if you really want to do this, press <b style='mso-bidi-font-weight:
1781normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1782minor-latin;mso-hansi-theme-font:minor-latin'>Yes</span></b>. The atoms are
1783then renamed in numeric order.</p>
1784
1785<h2>Step 7. Refinement</h2>
1786
1787<p class=MsoNormal>Since the structure is complete, we can do the full refinement.
1788Select the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1789"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1790minor-latin'>Controls</span></b> item from the GSAS-II data tree. Unset the <b
1791style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1792mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Refine HKLF
1793as F^2</span></b> box and enter <b style='mso-bidi-font-weight:normal'><span
1794style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1795mso-hansi-theme-font:minor-latin'>3.0</span></b> for <b style='mso-bidi-font-weight:
1796normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1797minor-latin;mso-hansi-theme-font:minor-latin'>Min <span class=SpellE>obs</span>/sig</span></b>.
1798This makes the least squares refine on <span class=SpellE>F<sub>o</sub></span>
1799with 3&#963; cutoff on <span class=SpellE>F<sub>o</sub></span>. From the main
1800GSAS-II data tree menu do <b style='mso-bidi-font-weight:normal'><span
1801style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1802mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; this will do the
18031<sup>st</sup> least squares refinement varying only the data set scale
1804factors. A progress bar popup will appear showing the residuals as the
1805refinement proceeds. When done, a small popup will appear with the final
1806residual; press <b style='mso-bidi-font-weight:normal'><span style='font-family:
1807"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1808minor-latin'>OK</span></b> to accept it. The final <span class=SpellE>R<sub>w</sub></span>
1809is about 49% Go to the <b style='mso-bidi-font-weight:normal'><span
1810style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1811mso-hansi-theme-font:minor-latin'>Atoms</span></b> tab for the <span
1812class=SpellE>rubrene</span> phase, double click the <b style='mso-bidi-font-weight:
1813normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1814minor-latin;mso-hansi-theme-font:minor-latin'>refine</span></b> column heading;
1815a popup box will appear. Select both <b style='mso-bidi-font-weight:normal'><span
1816style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1817mso-hansi-theme-font:minor-latin'>X - coordinates</span></b> and <b
1818style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1819mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>U – thermal
1820parameters</span></b> and press <b style='mso-bidi-font-weight:normal'><span
1821style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1822mso-hansi-theme-font:minor-latin'>OK</span></b>. The atom table will show
1823refine flags for each atom.</p>
1824
1825<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1826 id="Picture_x0020_21" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:525pt;
1827 height:225pt;visibility:visible;mso-wrap-style:square'>
1828 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image043.png"
1829  o:title=""/>
1830</v:shape><![endif]--><![if !vml]><img width=700 height=300
1831src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image095.gif"
1832v:shapes="Picture_x0020_21"><![endif]></span></p>
1833
1834<p class=MsoNormal>Then repeat the <b style='mso-bidi-font-weight:normal'><span
1835style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1836mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> command in the
1837main menu. The final residual will be much better <span class=SpellE>R<sub>w</sub></span>
1838~10%. Next, convert all the atoms from isotropic thermal parameters to
1839anisotropic ones. Double click the <b style='mso-bidi-font-weight:normal'><span
1840style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1841mso-hansi-theme-font:minor-latin'>I/A</span></b> column heading and select <b
1842style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1843mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Anisotropic</span></b>
1844and press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1845mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1846Then repeat <b style='mso-bidi-font-weight:normal'><span style='font-family:
1847"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1848minor-latin'>Calculate/Refine</span></b> (perhaps twice); the final <span
1849class=SpellE>R<sub>w</sub></span> ~6.06% which is quite nice.</p>
1850
1851<h2>Step 8. Further work</h2>
1852
1853<p class=MsoNormal>Since this is TOF neutron single crystal diffraction, a
1854relatively large crystal was used and the neutron wavelength covered a fairly wide
1855range of values. Hence, it is likely that the strong reflection intensities
1856suffered from some level of extinction. To find these parameters select the <b
1857style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1858mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Data</span></b>
1859tab in the Phase Data window; all that will show is a list of a data set names
1860with a <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1861mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Show</span></b>
1862box for each. To see what is there select the <b style='mso-bidi-font-weight:
1863normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1864minor-latin;mso-hansi-theme-font:minor-latin'>Show</span></b> box;
1865alternatively to see all of them do <b style='mso-bidi-font-weight:normal'><span
1866style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1867mso-hansi-theme-font:minor-latin'>Edit/Show/Hide</span></b> all the window will
1868look something like</p>
1869
1870<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1871 id="Picture_x0020_22" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:319.5pt;
1872 height:378pt;visibility:visible;mso-wrap-style:square'>
1873 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image045.png"
1874  o:title=""/>
1875</v:shape><![endif]--><![if !vml]><img width=426 height=504
1876src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image096.gif"
1877v:shapes="Picture_x0020_22"><![endif]></span></p>
1878
1879<p class=MsoNormal>This is a very long display with entries for 23 data sets
1880(NB: in alphabetical order not numeric order!). The Scale factors were selected
1881for refinement by default (box checked). Here you want to select <b
1882style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1883mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Primary</span></b>
1884for the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1885mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Extinction
1886type</span></b> (later you can try the other models) for the 1<sup>st</sup>
1887data set. The window will be repainted with a new line in the data display.
1888Select the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1889"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1890minor-latin'>Ep</span></b> check box so it will be refined. To set all the rest
1891press the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1892mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Copy flags?</span></b>
1893button for that data set (not one of the others!). A popup will appear giving
1894the list of data sets; press the <span class=SpellE><b style='mso-bidi-font-weight:
1895normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1896minor-latin;mso-hansi-theme-font:minor-latin'>SetAll</span></b></span> button
1897and then <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1898mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1899The data window will be repainted with all the Extinction types set to Primary
1900and Ep set to refine. You could then do <b style='mso-bidi-font-weight:normal'><span
1901style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1902mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> but it might be
1903better to constrain all the Ep values to be the same. To do this select <b
1904style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1905mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Constraints</span></b>
1906from the GSASII data tree. A blank window with tabs will appear.</p>
1907
1908<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1909 id="Picture_x0020_23" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:225pt;
1910 height:352.5pt;visibility:visible;mso-wrap-style:square'>
1911 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image047.png"
1912  o:title=""/>
1913</v:shape><![endif]--><![if !vml]><img width=300 height=470
1914src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image097.gif"
1915v:shapes="Picture_x0020_23"><![endif]></span></p>
1916
1917<p class=MsoNormal>Select the <b style='mso-bidi-font-weight:normal'><span
1918style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1919mso-hansi-theme-font:minor-latin'>Histogram/Phase</span></b> constraints tab;
1920the window is still blank but that tab is now highlighted. Next do <b
1921style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1922mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Add
1923equivalence</span></b>; a popup will appear asking for a parameter name to be
1924constrained.</p>
1925
1926<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1927 id="Picture_x0020_24" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:468.75pt;
1928 height:300pt;visibility:visible;mso-wrap-style:square'>
1929 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image049.png"
1930  o:title=""/>
1931</v:shape><![endif]--><![if !vml]><img width=625 height=400
1932src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image098.gif"
1933v:shapes="Picture_x0020_24"><![endif]></span></p>
1934
1935<p class=MsoNormal>Select <span class=GramE><b style='mso-bidi-font-weight:
1936normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1937minor-latin;mso-hansi-theme-font:minor-latin'>0:0:Ep</span></b></span>, that is
1938the primary extinction parameter for the 1<sup>st</sup> dataset and the <span
1939class=SpellE>rubrene</span> phase. Press <b style='mso-bidi-font-weight:normal'><span
1940style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1941mso-hansi-theme-font:minor-latin'>OK</span></b>.</p>
1942
1943<p class=MsoNormal>The popup is replaced with a new list of all compatible
1944parameters that <span class=GramE><b style='mso-bidi-font-weight:normal'><span
1945style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1946mso-hansi-theme-font:minor-latin'>0:0:Ep</span></b></span> is to be made
1947equivalent to. Scroll down and find <span class=GramE><b style='mso-bidi-font-weight:
1948normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1949minor-latin;mso-hansi-theme-font:minor-latin'>0:all</span></b></span><b
1950style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1951mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>:Ep</span></b>
1952and pick that; the Constraint window will change to</p>
1953
1954<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1955 id="Picture_x0020_25" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:481.5pt;
1956 height:352.5pt;visibility:visible;mso-wrap-style:square'>
1957 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image051.png"
1958  o:title=""/>
1959</v:shape><![endif]--><![if !vml]><img width=642 height=470
1960src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image099.gif"
1961v:shapes="Picture_x0020_25"><![endif]></span></p>
1962
1963<p class=MsoNormal>This shows the constraint making Ep for all 23 data sets
1964equivalent to a single variable. Do <b style='mso-bidi-font-weight:normal'><span
1965style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1966mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; my <span
1967class=SpellE>R<sub>w</sub></span> was 5.907% only a slight improvement. You may
1968wish to try the other extinction models. Do remember to delete the unused
1969constraint before adding a new one for the different extinction parameter.
1970Finally you can draw the molecule; go to <b style='mso-bidi-font-weight:normal'><span
1971style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1972mso-hansi-theme-font:minor-latin'>Atoms</span></b> and do <b style='mso-bidi-font-weight:
1973normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1974minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Reload draw atoms</span></b>.
1975That will put the newest atom parameters into the Draw Atoms table. Select <b
1976style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1977mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Draw Atoms</span></b>.
1978Select the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1979"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1980minor-latin'>Style</span></b> column heading; a popup will appear</p>
1981
1982<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1983 id="Picture_x0020_26" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:259.5pt;
1984 height:252pt;visibility:visible;mso-wrap-style:square'>
1985 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image053.png"
1986  o:title=""/>
1987</v:shape><![endif]--><![if !vml]><img width=346 height=336
1988src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image100.gif"
1989v:shapes="Picture_x0020_26"><![endif]></span></p>
1990
1991<p class=MsoNormal>Notice the first line is blank, if you select that all the
1992atoms will vanish! Select <b style='mso-bidi-font-weight:normal'><span
1993style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1994mso-hansi-theme-font:minor-latin'>ellipsoids</span></b> and press <b
1995style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1996mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1997The plot will change, but it is pretty cluttered.</p>
1998
1999<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2000 id="Picture_x0020_28" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:465.75pt;
2001 height:395.25pt;visibility:visible;mso-wrap-style:square'>
2002 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image055.png"
2003  o:title="" croptop="11745f" cropbottom="16560f" cropleft="43690f"
2004  cropright="6723f"/>
2005</v:shape><![endif]--><![if !vml]><img width=621 height=527
2006src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image101.jpg"
2007v:shapes="Picture_x0020_28"><![endif]></span></p>
2008
2009<p class=MsoNormal>You can remove the Map peaks atoms; go to the <b
2010style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2011mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map peaks</span></b>
2012tab and do <b style='mso-bidi-font-weight:normal'><span style='font-family:
2013"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2014minor-latin'>Map peaks/clear peaks</span></b> from the menu. The list will be
2015erased and the plot will just show the molecule. You can also remove the unit
2016cell edges, go to <b style='mso-bidi-font-weight:normal'><span
2017style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2018mso-hansi-theme-font:minor-latin'>Draw Options</span></b> and uncheck the <b
2019style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2020mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Show unit
2021cell?</span></b> box. Finally, you can remove the charge flipping map; go to <b
2022style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2023mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
2024and do <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2025mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/Clear
2026map</span></b>. That deletes the scattering density map and the drawing will be
2027free of any clutter.</p>
2028
2029<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2030 id="Picture_x0020_29" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:429.75pt;
2031 height:366pt;visibility:visible;mso-wrap-style:square'>
2032 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image057.png"
2033  o:title="" croptop="8339f" cropbottom="19928f" cropleft="44139f" cropright="6324f"/>
2034</v:shape><![endif]--><![if !vml]><img width=573 height=488
2035src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image102.jpg"
2036v:shapes="Picture_x0020_29"><![endif]></span></p>
2037
2038<p class=MsoNormal>Remember that this is only 1/4<sup>th</sup> of the molecule,
2039we’d like to see the whole thing. First go to the <b style='mso-bidi-font-weight:
2040normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2041minor-latin;mso-hansi-theme-font:minor-latin'>Atoms</span></b> tab and select
2042the C-atom that is in a special position 2(x). The do <b style='mso-bidi-font-weight:
2043normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2044minor-latin;mso-hansi-theme-font:minor-latin'>Compute/Show Distances &amp;
2045Angles</span></b> and respond <b style='mso-bidi-font-weight:normal'><span
2046style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2047mso-hansi-theme-font:minor-latin'>OK</span></b> to the popup. The important
2048result is on the console</p>
2049
2050<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2051 id="Picture_x0020_30" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:609.75pt;
2052 height:278.25pt;visibility:visible;mso-wrap-style:square'>
2053 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image059.png"
2054  o:title=""/>
2055</v:shape><![endif]--><![if !vml]><img width=813 height=371
2056src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image103.gif"
2057v:shapes="Picture_x0020_30"><![endif]></span></p>
2058
2059<p class=MsoNormal>This gives the bond distances and angles about the <span
2060class=GramE>C(</span>1) atom. Particularly note the cell<span class=GramE>+(</span>sym.
2061Op.) information; we will use this to build the drawing. Go to the <b
2062style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2063mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Draw Atoms</span></b>
2064tab and select all the atoms (double click on the upper left box). You should
2065see all atoms selected</p>
2066
2067<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2068 id="Picture_x0020_31" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:450pt;
2069 height:225pt;visibility:visible;mso-wrap-style:square'>
2070 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image061.png"
2071  o:title=""/>
2072</v:shape><![endif]--><![if !vml]><img width=600 height=300
2073src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image104.gif"
2074v:shapes="Picture_x0020_31"><![endif]></span></p>
2075
2076<p class=MsoNormal>Then do <b style='mso-bidi-font-weight:normal'><span
2077style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2078mso-hansi-theme-font:minor-latin'>Edit/Add atoms</span></b>; a popup will
2079appear</p>
2080
2081<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2082 id="Picture_x0020_32" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:179.25pt;
2083 height:246.75pt;visibility:visible;mso-wrap-style:square'>
2084 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image063.png"
2085  o:title=""/>
2086</v:shape><![endif]--><![if !vml]><img width=239 height=329
2087src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image105.gif"
2088v:shapes="Picture_x0020_32"><![endif]></span></p>
2089
2090<p class=MsoNormal>Based on the 1<sup>st</sup> entry in the bond distance table
2091‘<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2092mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>[1 0 0<span
2093class=GramE>]<span style='mso-spacerun:yes'>  </span>+(</span><span
2094style='mso-spacerun:yes'>  </span>2)</span></b>’, select the controls for the 2<sup>nd</sup>
2095operator and increment the 1<sup>st</sup> unit cell</p>
2096
2097<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2098 id="Picture_x0020_33" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:179.25pt;
2099 height:246.75pt;visibility:visible;mso-wrap-style:square'>
2100 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image065.png"
2101  o:title=""/>
2102</v:shape><![endif]--><![if !vml]><img width=239 height=329
2103src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image106.gif"
2104v:shapes="Picture_x0020_33"><![endif]></span></p>
2105
2106<p class=MsoNormal>Press OK. The plot now shows œ the molecule.</p>
2107
2108<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2109 id="Picture_x0020_34" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:429.75pt;
2110 height:372pt;visibility:visible;mso-wrap-style:square'>
2111 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image067.png"
2112  o:title="" croptop="11786f" cropbottom="16031f" cropleft="46740f"
2113  cropright="3791f"/>
2114</v:shape><![endif]--><![if !vml]><img width=573 height=496
2115src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image107.jpg"
2116v:shapes="Picture_x0020_34"><![endif]></span></p>
2117
2118<p class=MsoNormal>Next select all the Draw atoms again and do <b
2119style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2120mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Add
2121atoms</span></b>; the selection popup will appear. This time use the other
2122nonidentity entry in the bond distance table ‘<b style='mso-bidi-font-weight:
2123normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2124minor-latin;mso-hansi-theme-font:minor-latin'>[0 1 1] + (-2)</span></b>’. The
2125‘-2’ indicates both the inversion and the 2<sup>nd</sup> operator need to be
2126applied; check both and increment the 2<sup>nd</sup> and 3<sup>rd</sup> unit
2127cell entries. </p>
2128
2129<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2130 id="Picture_x0020_36" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:179.25pt;
2131 height:246.75pt;visibility:visible;mso-wrap-style:square'>
2132 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image069.png"
2133  o:title=""/>
2134</v:shape><![endif]--><![if !vml]><img width=239 height=329
2135src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image108.gif"
2136v:shapes="Picture_x0020_36"><![endif]></span></p>
2137
2138<p class=MsoNormal>Press <b style='mso-bidi-font-weight:normal'><span
2139style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2140mso-hansi-theme-font:minor-latin'>OK</span></b>; the entire molecule is drawn.</p>
2141
2142<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2143 id="Picture_x0020_35" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:429.75pt;
2144 height:364.5pt;visibility:visible;mso-wrap-style:square'>
2145 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image071.png"
2146  o:title="" croptop="10221f" cropbottom="18166f" cropleft="42114f"
2147  cropright="8322f"/>
2148</v:shape><![endif]--><![if !vml]><img width=573 height=486
2149src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image109.jpg"
2150v:shapes="Picture_x0020_35"><![endif]></span><span
2151style='mso-spacerun:yes'> </span></p>
2152
2153<p class=MsoNormal>Looks really nice. This ends the tutorial. You can save the
2154project if you wish. All the changes (<span class=SpellE>i.e</span> deleting
2155Map peaks &amp; clearing the map) will be saved.</p>
2156
2157</div>
2158
2159</body>
2160
2161</html>
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