source: Tutorials/TOF Charge Flipping/Charge Flipping with TOF single crystal data in GSASII.htm @ 4933

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405  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 1"/>
406  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 1"/>
407  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 1"/>
408  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 1"/>
409  <w:LsdException Locked="false" SemiHidden="true" Name="Revision"/>
410  <w:LsdException Locked="false" Priority="34" QFormat="true"
411   Name="List Paragraph"/>
412  <w:LsdException Locked="false" Priority="29" QFormat="true" Name="Quote"/>
413  <w:LsdException Locked="false" Priority="30" QFormat="true"
414   Name="Intense Quote"/>
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417  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 1"/>
418  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 1"/>
419  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 1"/>
420  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 1"/>
421  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 1"/>
422  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 1"/>
423  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 2"/>
424  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 2"/>
425  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 2"/>
426  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 2"/>
427  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 2"/>
428  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 2"/>
429  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 2"/>
430  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 2"/>
431  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 2"/>
432  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 2"/>
433  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 2"/>
434  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 2"/>
435  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 2"/>
436  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 2"/>
437  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 3"/>
438  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 3"/>
439  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 3"/>
440  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 3"/>
441  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 3"/>
442  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 3"/>
443  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 3"/>
444  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 3"/>
445  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 3"/>
446  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 3"/>
447  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 3"/>
448  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 3"/>
449  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 3"/>
450  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 3"/>
451  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 4"/>
452  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 4"/>
453  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 4"/>
454  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 4"/>
455  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 4"/>
456  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 4"/>
457  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 4"/>
458  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 4"/>
459  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 4"/>
460  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 4"/>
461  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 4"/>
462  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 4"/>
463  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 4"/>
464  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 4"/>
465  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 5"/>
466  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 5"/>
467  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 5"/>
468  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 5"/>
469  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 5"/>
470  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 5"/>
471  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 5"/>
472  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 5"/>
473  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 5"/>
474  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 5"/>
475  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 5"/>
476  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 5"/>
477  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 5"/>
478  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 5"/>
479  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 6"/>
480  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 6"/>
481  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 6"/>
482  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 6"/>
483  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 6"/>
484  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 6"/>
485  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 6"/>
486  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 6"/>
487  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 6"/>
488  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 6"/>
489  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 6"/>
490  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 6"/>
491  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 6"/>
492  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 6"/>
493  <w:LsdException Locked="false" Priority="19" QFormat="true"
494   Name="Subtle Emphasis"/>
495  <w:LsdException Locked="false" Priority="21" QFormat="true"
496   Name="Intense Emphasis"/>
497  <w:LsdException Locked="false" Priority="31" QFormat="true"
498   Name="Subtle Reference"/>
499  <w:LsdException Locked="false" Priority="32" QFormat="true"
500   Name="Intense Reference"/>
501  <w:LsdException Locked="false" Priority="33" QFormat="true" Name="Book Title"/>
502  <w:LsdException Locked="false" Priority="37" SemiHidden="true"
503   UnhideWhenUsed="true" Name="Bibliography"/>
504  <w:LsdException Locked="false" Priority="39" SemiHidden="true"
505   UnhideWhenUsed="true" QFormat="true" Name="TOC Heading"/>
506  <w:LsdException Locked="false" Priority="41" Name="Plain Table 1"/>
507  <w:LsdException Locked="false" Priority="42" Name="Plain Table 2"/>
508  <w:LsdException Locked="false" Priority="43" Name="Plain Table 3"/>
509  <w:LsdException Locked="false" Priority="44" Name="Plain Table 4"/>
510  <w:LsdException Locked="false" Priority="45" Name="Plain Table 5"/>
511  <w:LsdException Locked="false" Priority="40" Name="Grid Table Light"/>
512  <w:LsdException Locked="false" Priority="46" Name="Grid Table 1 Light"/>
513  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2"/>
514  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3"/>
515  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4"/>
516  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark"/>
517  <w:LsdException Locked="false" Priority="51" Name="Grid Table 6 Colorful"/>
518  <w:LsdException Locked="false" Priority="52" Name="Grid Table 7 Colorful"/>
519  <w:LsdException Locked="false" Priority="46"
520   Name="Grid Table 1 Light Accent 1"/>
521  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 1"/>
522  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 1"/>
523  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 1"/>
524  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 1"/>
525  <w:LsdException Locked="false" Priority="51"
526   Name="Grid Table 6 Colorful Accent 1"/>
527  <w:LsdException Locked="false" Priority="52"
528   Name="Grid Table 7 Colorful Accent 1"/>
529  <w:LsdException Locked="false" Priority="46"
530   Name="Grid Table 1 Light Accent 2"/>
531  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 2"/>
532  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 2"/>
533  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 2"/>
534  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 2"/>
535  <w:LsdException Locked="false" Priority="51"
536   Name="Grid Table 6 Colorful Accent 2"/>
537  <w:LsdException Locked="false" Priority="52"
538   Name="Grid Table 7 Colorful Accent 2"/>
539  <w:LsdException Locked="false" Priority="46"
540   Name="Grid Table 1 Light Accent 3"/>
541  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 3"/>
542  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 3"/>
543  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 3"/>
544  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 3"/>
545  <w:LsdException Locked="false" Priority="51"
546   Name="Grid Table 6 Colorful Accent 3"/>
547  <w:LsdException Locked="false" Priority="52"
548   Name="Grid Table 7 Colorful Accent 3"/>
549  <w:LsdException Locked="false" Priority="46"
550   Name="Grid Table 1 Light Accent 4"/>
551  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 4"/>
552  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 4"/>
553  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 4"/>
554  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 4"/>
555  <w:LsdException Locked="false" Priority="51"
556   Name="Grid Table 6 Colorful Accent 4"/>
557  <w:LsdException Locked="false" Priority="52"
558   Name="Grid Table 7 Colorful Accent 4"/>
559  <w:LsdException Locked="false" Priority="46"
560   Name="Grid Table 1 Light Accent 5"/>
561  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 5"/>
562  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 5"/>
563  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 5"/>
564  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 5"/>
565  <w:LsdException Locked="false" Priority="51"
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567  <w:LsdException Locked="false" Priority="52"
568   Name="Grid Table 7 Colorful Accent 5"/>
569  <w:LsdException Locked="false" Priority="46"
570   Name="Grid Table 1 Light Accent 6"/>
571  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 6"/>
572  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 6"/>
573  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 6"/>
574  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 6"/>
575  <w:LsdException Locked="false" Priority="51"
576   Name="Grid Table 6 Colorful Accent 6"/>
577  <w:LsdException Locked="false" Priority="52"
578   Name="Grid Table 7 Colorful Accent 6"/>
579  <w:LsdException Locked="false" Priority="46" Name="List Table 1 Light"/>
580  <w:LsdException Locked="false" Priority="47" Name="List Table 2"/>
581  <w:LsdException Locked="false" Priority="48" Name="List Table 3"/>
582  <w:LsdException Locked="false" Priority="49" Name="List Table 4"/>
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584  <w:LsdException Locked="false" Priority="51" Name="List Table 6 Colorful"/>
585  <w:LsdException Locked="false" Priority="52" Name="List Table 7 Colorful"/>
586  <w:LsdException Locked="false" Priority="46"
587   Name="List Table 1 Light Accent 1"/>
588  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 1"/>
589  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 1"/>
590  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 1"/>
591  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 1"/>
592  <w:LsdException Locked="false" Priority="51"
593   Name="List Table 6 Colorful Accent 1"/>
594  <w:LsdException Locked="false" Priority="52"
595   Name="List Table 7 Colorful Accent 1"/>
596  <w:LsdException Locked="false" Priority="46"
597   Name="List Table 1 Light Accent 2"/>
598  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 2"/>
599  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 2"/>
600  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 2"/>
601  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 2"/>
602  <w:LsdException Locked="false" Priority="51"
603   Name="List Table 6 Colorful Accent 2"/>
604  <w:LsdException Locked="false" Priority="52"
605   Name="List Table 7 Colorful Accent 2"/>
606  <w:LsdException Locked="false" Priority="46"
607   Name="List Table 1 Light Accent 3"/>
608  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 3"/>
609  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 3"/>
610  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 3"/>
611  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 3"/>
612  <w:LsdException Locked="false" Priority="51"
613   Name="List Table 6 Colorful Accent 3"/>
614  <w:LsdException Locked="false" Priority="52"
615   Name="List Table 7 Colorful Accent 3"/>
616  <w:LsdException Locked="false" Priority="46"
617   Name="List Table 1 Light Accent 4"/>
618  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 4"/>
619  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 4"/>
620  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 4"/>
621  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 4"/>
622  <w:LsdException Locked="false" Priority="51"
623   Name="List Table 6 Colorful Accent 4"/>
624  <w:LsdException Locked="false" Priority="52"
625   Name="List Table 7 Colorful Accent 4"/>
626  <w:LsdException Locked="false" Priority="46"
627   Name="List Table 1 Light Accent 5"/>
628  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 5"/>
629  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 5"/>
630  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 5"/>
631  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 5"/>
632  <w:LsdException Locked="false" Priority="51"
633   Name="List Table 6 Colorful Accent 5"/>
634  <w:LsdException Locked="false" Priority="52"
635   Name="List Table 7 Colorful Accent 5"/>
636  <w:LsdException Locked="false" Priority="46"
637   Name="List Table 1 Light Accent 6"/>
638  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 6"/>
639  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 6"/>
640  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 6"/>
641  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 6"/>
642  <w:LsdException Locked="false" Priority="51"
643   Name="List Table 6 Colorful Accent 6"/>
644  <w:LsdException Locked="false" Priority="52"
645   Name="List Table 7 Colorful Accent 6"/>
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1173<div class=WordSection1>
1174
1175<h1><span style='mso-fareast-font-family:"Times New Roman"'>Charge flipping
1176with neutron TOF single crystal data<o:p></o:p></span></h1>
1177<P><BL>
1178  <LI>Exercise files are found <A href="./data/" target="_blank">here</a>
1179</BL></P><P></P>
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 new phase</span></b> in
1194the main 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>. The General tab
1198for this phase will be shown</p>
1199
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1219 <o:lock v:ext="edit" aspectratio="t"/>
1220</v:shapetype><v:shape id="Picture_x0020_1" o:spid="_x0000_i1056" type="#_x0000_t75"
1221 style='width:468pt;height:210pt;visibility:visible;mso-wrap-style:square'>
1222 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image002.png"
1223  o:title=""/>
1224</v:shape><![endif]--><![if !vml]><img width=624 height=280
1225src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image001.gif"
1226v:shapes="Picture_x0020_1"><![endif]></span></p>
1227
1228<p class=MsoNormal>Enter the space group (<b style='mso-bidi-font-weight:normal'><span
1229style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1230mso-hansi-theme-font:minor-latin'>C m c a</span></b> – don’t forget the spaces)
1231and press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1232mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Enter</span></b>.
1233A popup with Space group information will appear</p>
1234
1235<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1236 id="_x0000_i1055" type="#_x0000_t75" style='width:275.25pt;height:207pt;
1237 visibility:visible;mso-wrap-style:square'>
1238 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image006.png"
1239  o:title=""/>
1240</v:shape><![endif]--><![if !vml]><img width=367 height=276
1241src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image003.gif"
1242v:shapes="_x0000_i1055"><![endif]></span></p>
1243
1244<p class=MsoNormal>Press <b style='mso-bidi-font-weight:normal'><span
1245style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1246mso-hansi-theme-font:minor-latin'>OK</span></b>; the General tab will be
1247repainted with defaults for the orthorhombic lattice parameters. Enter <b
1248style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1249mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>26.798</span></b>
1250for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1251mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>a</span></b>,
1252<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1253mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>7.1618</span></b>
1254for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1255mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>b</span></b>
1256and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1257mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>14.1942</span></b>
1258for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1259mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>c</span></b>.
1260Press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1261mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Enter</span></b>,
1262the unit cell volume (2724.178) will be updated.</p>
1263
1264<h2>Step 2. Import the data</h2>
1265
1266<p class=MsoNormal>The <span class=SpellE>rubrene</span> data were collected on
1267the TOPAZ instrument at the SNS Facility, Oak Ridge National Laboratory with 23
1268different crystal orientations; the local instrument data processing software
1269has applied corrections and combined them into a single multicolumn <span
1270class=SpellE>hkl</span> file. To import this do <b style='mso-bidi-font-weight:
1271normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1272minor-latin;mso-hansi-theme-font:minor-latin'>Import/Structure Factor/from
1273Neutron TOF HKL F<sup>2</sup> file</span></b>; a directory dialog box will
1274appear. Go to the directory <b style='mso-bidi-font-weight:normal'><span
1275style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1276mso-hansi-theme-font:minor-latin'>TOF Charge Flipping/data</span></b> and
1277select the file <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1278style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1279mso-hansi-theme-font:minor-latin'>ruberene_orthoC.hkl</span></b></span> (double
1280click the name or press the <b style='mso-bidi-font-weight:normal'><span
1281style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1282mso-hansi-theme-font:minor-latin'>Open</span></b> button after selecting it). A
1283popup box will appear.</p>
1284
1285<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1286 id="_x0000_i1054" type="#_x0000_t75" style='width:307.5pt;height:147.75pt;
1287 visibility:visible;mso-wrap-style:square'>
1288 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image010.png"
1289  o:title=""/>
1290</v:shape><![endif]--><![if !vml]><img width=410 height=197
1291src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image005.gif"
1292v:shapes="_x0000_i1054"><![endif]></span></p>
1293
1294<p class=MsoNormal>Press <span class=GramE><b style='mso-bidi-font-weight:normal'><span
1295style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1296mso-hansi-theme-font:minor-latin'>Yes</span></b></span>; another popup will
1297appear offering you the chance to change the name. Press <b style='mso-bidi-font-weight:
1298normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1299minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>, a new popup
1300appears.</p>
1301
1302<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1303 id="_x0000_i1053" type="#_x0000_t75" style='width:233.25pt;height:228.75pt;
1304 visibility:visible;mso-wrap-style:square'>
1305 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image014.png"
1306  o:title=""/>
1307</v:shape><![endif]--><![if !vml]><img width=311 height=305
1308src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image007.gif"
1309v:shapes="_x0000_i1053"><![endif]></span></p>
1310
1311<p class=MsoNormal>Here you select the phase the data belongs to. There is only
1312<span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1313style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1314mso-hansi-theme-font:minor-latin'>rubrene</span></b></span> so select it and
1315press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1316mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1317The bottom of the data tree is shown, a small data window and the plot shows
1318the l=0 slice of the last reflection set loaded (HKLF rubrene_orthoC.hkl_22).</p>
1319
1320<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1321 id="_x0000_i1052" type="#_x0000_t75" style='width:468pt;height:401.25pt;
1322 visibility:visible;mso-wrap-style:square'>
1323 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image018.png"
1324  o:title=""/>
1325</v:shape><![endif]--><![if !vml]><img width=624 height=535
1326src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image009.gif"
1327v:shapes="_x0000_i1052"><![endif]></span></p>
1328
1329<p class=MsoNormal>The <b style='mso-bidi-font-weight:normal'><span
1330style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1331mso-hansi-theme-font:minor-latin'>K</span></b> box control allows you to select
1332other zones &amp; layers to view. The drawing geometry is strictly square (i.e.
1333not in reciprocal space units). If you do <b style='mso-bidi-font-weight:normal'><span
1334style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1335mso-hansi-theme-font:minor-latin'>Commands/Plot 3D HKLs</span></b>, a 3D plot
1336of reciprocal space is shown</p>
1337
1338<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1339 id="_x0000_i1051" type="#_x0000_t75" style='width:468pt;height:403.5pt;
1340 visibility:visible;mso-wrap-style:square'>
1341 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image022.png"
1342  o:title=""/>
1343</v:shape><![endif]--><![if !vml]><img width=624 height=538
1344src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image011.gif"
1345v:shapes="_x0000_i1051"><![endif]></span></p>
1346
1347<p class=MsoNormal>The size of the green boxes is proportional to the structure
1348factors; the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1349"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1350minor-latin'>save as/key</span></b> pulldown will give you other viewing
1351options. Here is a good place to save the GSAS-II project for <span
1352class=SpellE>rubrene</span>. Do <b style='mso-bidi-font-weight:normal'><span
1353style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1354mso-hansi-theme-font:minor-latin'>File/Save project</span></b> from the main
1355GSAS-II data tree window; a file dialog box will appear. Enter a file name (I
1356used <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1357style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1358mso-hansi-theme-font:minor-latin'>rubrene</span></b></span> – no extension).</p>
1359
1360<h2>Step 3. Setup for charge flipping</h2>
1361
1362<p class=MsoNormal>We have two tasks here. One is to select the reflection sets
1363to be used in the calculations and the other is to set some controls. To begin
1364select the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1365style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1366mso-hansi-theme-font:minor-latin'>rubrene</span></b></span> phase entry in the
1367GSAS-II data tree; the General tab will appear in the Phase Data for <span
1368class=SpellE>rubrene</span> window</p>
1369
1370<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1371 id="_x0000_i1050" type="#_x0000_t75" style='width:468pt;height:222.75pt;
1372 visibility:visible;mso-wrap-style:square'>
1373 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image024.png"
1374  o:title=""/>
1375</v:shape><![endif]--><![if !vml]><img width=624 height=297
1376src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image013.gif"
1377v:shapes="_x0000_i1050"><![endif]></span></p>
1378
1379<p class=MsoNormal>In the Charge flip controls (about center of the page) press
1380the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1381mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Select
1382reflection sets</span></b> button; a <b style='mso-bidi-font-weight:normal'><span
1383style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1384mso-hansi-theme-font:minor-latin'>Use data</span></b> popup will appear. You
1385will want to use all the HKLF data sets; press <b style='mso-bidi-font-weight:
1386normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1387minor-latin;mso-hansi-theme-font:minor-latin'>Set All</span> </b>and press <b
1388style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1389mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1390The General tab will be refreshed. GSAS-II will use all the data to build a
1391reflection set for charge flipping. For duplicate <span class=SpellE>hkls</span>
1392the last one encountered will be used. Since atoms are essentially point <span
1393class=SpellE>scatterers</span> for neutrons, a charge flip map has very sharp
1394peaks so a better choice for the <b style='mso-bidi-font-weight:normal'><span
1395style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1396mso-hansi-theme-font:minor-latin'>k-factor</span></b> (charge flip level) might
1397be <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1398mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0.5</span></b>,
1399the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1400mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>k-max</span></b>
1401should be larger (say <b style='mso-bidi-font-weight:normal'><span
1402style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1403mso-hansi-theme-font:minor-latin'>50</span></b>) and the map <b
1404style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1405mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Resolution</span></b>
1406should be smaller (say <b style='mso-bidi-font-weight:normal'><span
1407style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1408mso-hansi-theme-font:minor-latin'>0.4</span></b>). Set these three values. In
1409the Fourier map controls, set <b style='mso-bidi-font-weight:normal'><span
1410style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1411mso-hansi-theme-font:minor-latin'>Peak cutoff %</span></b> to <b
1412style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1413mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>20</span></b>;
1414this sets the lower limit of the peak search in the charge flip map. When done
1415the General tab should look like</p>
1416
1417<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1418 id="_x0000_i1049" type="#_x0000_t75" style='width:468pt;height:222.75pt;
1419 visibility:visible;mso-wrap-style:square'>
1420 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image028.png"
1421  o:title=""/>
1422</v:shape><![endif]--><![if !vml]><img width=624 height=297
1423src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image015.gif"
1424v:shapes="_x0000_i1049"><![endif]></span></p>
1425
1426<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1427
1428<h2>Step 4. Charge flipping</h2>
1429
1430<p class=MsoNormal>We are now ready for charge flipping. In the General tab
1431menu do <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1432mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/Charge
1433flipping</span></b>; a Charge flipping progress bar will appear showing the
1434residual and cycle count for the charge flipping calculation. In this case the
1435residual quickly drops to ~38% and stays there. Press <b style='mso-bidi-font-weight:
1436normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1437minor-latin;mso-hansi-theme-font:minor-latin'>Cancel</span></b> to stop the
1438calculation; some information will be printed on the console and after a pause
1439the Phase Data window will show <b style='mso-bidi-font-weight:normal'><span
1440style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1441mso-hansi-theme-font:minor-latin'>Map Peaks</span></b> and the plot window will
1442show a drawing of the obtained structure.</p>
1443
1444<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1445 id="Picture_x0020_33" o:spid="_x0000_i1048" type="#_x0000_t75" style='width:468pt;
1446 height:315.75pt;visibility:visible;mso-wrap-style:square'>
1447 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image017.png"
1448  o:title=""/>
1449</v:shape><![endif]--><![if !vml]><img width=624 height=421
1450src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image019.gif"
1451v:shapes="Picture_x0020_33"><![endif]></span></p>
1452
1453<p class=MsoNormal>If you scroll down the Map peak list you will find some with
1454negative magnitudes at the end of the list. GSAS-II searches the map for both
1455positive and negative peaks; the former are C-atoms and the latter are H-atoms.
1456</p>
1457
1458<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1459 id="Picture_x0020_34" o:spid="_x0000_i1047" type="#_x0000_t75" style='width:468pt;
1460 height:404.25pt;visibility:visible;mso-wrap-style:square'>
1461 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image021.png"
1462  o:title=""/>
1463</v:shape><![endif]--><![if !vml]><img width=624 height=539
1464src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image025.gif"
1465v:shapes="Picture_x0020_34"><![endif]></span></p>
1466
1467<p class=MsoNormal>The plot (which I’ve rotated around a bit) shows white spots
1468for the positive peaks and red ones for the negative ones; bonds are white lines.
1469Your solution may show a problem with the charge flip solution. While the
1470charge flipping run has clearly found all the C-atoms and some of the H-atoms,
1471the molecule may be incorrectly placed in the unit cell (the multicolored cross
1472should be in the middle of the C-C bond at the center of the molecule). To fix
1473this you could simply repeat the charge flipping run and hope it puts the
1474molecule in the right place. GSAS-II uses an algorithm based on how structure
1475factor phases are related for a given space group to reposition the solution;
1476it sometimes fails if the phase set isn’t perfect. Or you can “roll” the map
1477right/left/up/down (<b style='mso-bidi-font-weight:normal'><span
1478style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1479mso-hansi-theme-font:minor-latin'>R/L/U/D</span></b> keys) to put the solution
1480where you want.<span style='mso-spacerun:yes'>  </span>Notice that as the map
1481is rolled, the Map peak positions are shifted to match the change in positions.</p>
1482
1483<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1484
1485<p class=MsoNormal>By carefully looking at the map, you can see the 4-ring <span
1486class=SpellE>tetracene</span> (<span class=SpellE>naphthacene</span>) core of
1487the molecule with four phenyl groups attached to both sides on the center two
1488rings. The unique part consists of 1/4<sup>th</sup> of this group (i.e. half of
1489one side of the <span class=SpellE>tetracene</span> and one phenyl); one C-atom
1490sits on a 2-fold and the rest are in general positions. The molecule extends
1491into the neighboring unit cell so you don’t see the whole thing as one group
1492but has two bits on either side.</p>
1493
1494<h2>Step 5. Peak selection</h2>
1495
1496<p class=MsoNormal>GSAS-II provides several ways of selecting peak positions
1497from a charge flipping map. One way is to pick them directly from the drawing.
1498Place the cursor on one peak and do a <b style='mso-bidi-font-weight:normal'><span
1499style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1500mso-hansi-theme-font:minor-latin'>Shift left mouse button</span></b>; it will
1501be highlighted on the list and it will turn green on the plot. Do a <b
1502style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1503mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Shift right
1504mouse button</span></b> on the remaining peaks you want to <span class=GramE>pick.</span>
1505All will turn green (you may have to wiggle the plot a bit with the mouse to
1506make them show) and all will be highlighted in the list. Alternatively, you can
1507select the entire list of peaks (double click on upper left empty box of the
1508table), then do <b style='mso-bidi-font-weight:normal'><span style='font-family:
1509"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1510minor-latin'>Map peaks/Unique peaks</span></b>. Better still you can sort the
1511peaks by one of the column headings and then do <b style='mso-bidi-font-weight:
1512normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1513minor-latin;mso-hansi-theme-font:minor-latin'>Map peaks/Unique peaks</span></b>.
1514I’ve chosen to sort the peaks on <span class=SpellE><b style='mso-bidi-font-weight:
1515normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1516minor-latin;mso-hansi-theme-font:minor-latin'>dcent</span></b></span> (distance
1517from center of the cell) beforehand. After a pause while it sorts out the
1518unique peaks, it will highlight them in the table and display the picked ones
1519in green on the plot. In this case they will probably be scattered about the
1520unit cell and not make a continuous molecule, but they are largely clustered
1521around the unit cell center. My plot looked like this when I was done.</p>
1522
1523<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1524 id="_x0000_i1046" type="#_x0000_t75" style='width:468pt;height:379.5pt;
1525 visibility:visible;mso-wrap-style:square'>
1526 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image040.png"
1527  o:title=""/>
1528</v:shape><![endif]--><![if !vml]><img width=624 height=506
1529src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image027.gif"
1530v:shapes="_x0000_i1046"><![endif]></span></p>
1531
1532<p class=MsoNormal>The list has them highlighted (the rest are lower down in my
1533list; all 18 atoms were found in this charge flipping result)</p>
1534
1535<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1536 id="Picture_x0020_35" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:468pt;
1537 height:394.5pt;visibility:visible;mso-wrap-style:square'>
1538 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image029.png"
1539  o:title=""/>
1540</v:shape><![endif]--><![if !vml]><img width=624 height=526
1541src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image031.gif"
1542v:shapes="Picture_x0020_35"><![endif]></span></p>
1543
1544<p class=MsoNormal>To add them to the Atom list do <b style='mso-bidi-font-weight:
1545normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1546minor-latin;mso-hansi-theme-font:minor-latin'>Map peaks/Move peaks</span></b>;
1547the drawing will show white balls for them.</p>
1548
1549<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1550 id="Picture_x0020_36" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:468pt;
1551 height:404.25pt;visibility:visible;mso-wrap-style:square'>
1552 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image033.png"
1553  o:title=""/>
1554</v:shape><![endif]--><![if !vml]><img width=624 height=539
1555src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image035.gif"
1556v:shapes="Picture_x0020_36"><![endif]></span></p>
1557
1558<p class=MsoNormal>The atom list will give the magnitudes as ‘M’ names; I found
1559all 11 C-atoms and 7 H-atoms that were expected.</p>
1560
1561<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1562 id="Picture_x0020_37" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:468pt;
1563 height:342pt;visibility:visible;mso-wrap-style:square'>
1564 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image073.png"
1565  o:title=""/>
1566</v:shape><![endif]--><![if !vml]><img width=624 height=456
1567src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image074.gif"
1568v:shapes="Picture_x0020_37"><![endif]></span></p>
1569
1570<h2>Step 6. Atom identification</h2>
1571
1572<p class=MsoNormal>You can reorder the atoms in the list; do an <b
1573style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1574mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Alt select</span></b>
1575for the atom row you want to move. Then do an <b style='mso-bidi-font-weight:
1576normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1577minor-latin;mso-hansi-theme-font:minor-latin'>Alt select</span></b> on the row
1578where you want the moved atom to precede it. This way you can put the C-atoms
1579first and the H-atoms last in the list instead of mixed up as in the above
1580list. Next select all the positive M peaks (pick the top one and then <b
1581style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1582mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Shift</span></b>
1583pick the last one). Do <b style='mso-bidi-font-weight:normal'><span
1584style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1585mso-hansi-theme-font:minor-latin'>Edit Atoms/On selected atoms/Modify
1586parameters</span></b> from the Atoms menu; a popup will appear. Pick <b
1587style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1588mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Type</span></b>
1589and press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1590mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>;
1591a Periodic Table will appear. Select <b style='mso-bidi-font-weight:normal'><span
1592style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1593mso-hansi-theme-font:minor-latin'>C</span></b> from the C-atom pulldown. All
1594the C-atom names and types will change and the plot will show dark gray spheres
1595for the C-atoms. You should also move the C-atom with 2(x) site symmetry to the
1596top of the list (if it isn’t there already).</p>
1597
1598<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1599 id="Picture_x0020_38" o:spid="_x0000_i1042" type="#_x0000_t75" style='width:468pt;
1600 height:268.5pt;visibility:visible;mso-wrap-style:square'>
1601 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image075.png"
1602  o:title=""/>
1603</v:shape><![endif]--><![if !vml]><img width=624 height=358
1604src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image076.gif"
1605v:shapes="Picture_x0020_38"><![endif]></span></p>
1606
1607<p class=MsoNormal>Do the same with the remaining negative M atoms – make them
1608H atoms. The drawing shows molecular fragments scattered about the unit cell;
1609you’d like to unify them into a single molecule. Select the C-atom with 2(x)
1610site symmetry (although any would do). Do <b style='mso-bidi-font-weight:normal'><span
1611style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1612mso-hansi-theme-font:minor-latin'>Edit Atoms/Assemble molecule</span></b> from
1613the Atoms menu; a popup will appear offering choices for Bond radii (&amp;
1614Angle radii – ignored here). Press <b style='mso-bidi-font-weight:normal'><span
1615style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1616mso-hansi-theme-font:minor-latin'>Ok</span></b>; the Atom table will be revised
1617and the plot will show an assembled molecule. </p>
1618
1619<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1620 id="Picture_x0020_39" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:468pt;
1621 height:405pt;visibility:visible;mso-wrap-style:square'>
1622 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image077.png"
1623  o:title=""/>
1624</v:shape><![endif]--><![if !vml]><img width=624 height=540
1625src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image078.gif"
1626v:shapes="Picture_x0020_39"><![endif]></span></p>
1627
1628<p class=MsoNormal>The molecule building has scrambled the order of the atoms;
1629they were located in order as the molecule was built. </p>
1630
1631<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1632 id="Picture_x0020_40" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:468pt;
1633 height:268.5pt;visibility:visible;mso-wrap-style:square'>
1634 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image079.png"
1635  o:title=""/>
1636</v:shape><![endif]--><![if !vml]><img width=624 height=358
1637src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image080.gif"
1638v:shapes="Picture_x0020_40"><![endif]></span></p>
1639
1640<p class=MsoNormal>You can reorder them to put the H-atoms at the end of the
1641list (if they weren’t there already). Then select all of them and then do <b
1642style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1643mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1644minor-latin'>Edit Atoms/On Selected atoms…/Modify parameters</span></b>. Pick <b
1645style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1646mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Name</span></b>
1647from the pulldown and press <b style='mso-bidi-font-weight:normal'><span
1648style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1649mso-hansi-theme-font:minor-latin'>OK</span></b>. You are asked if you really
1650want to do this, press <b style='mso-bidi-font-weight:normal'><span
1651style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1652mso-hansi-theme-font:minor-latin'>Yes</span></b>. The atoms are then renamed in
1653numeric order.</p>
1654
1655<h2>Step 7. Refinement</h2>
1656
1657<p class=MsoNormal>Since the structure is complete, we can do the full
1658refinement. Select the <b style='mso-bidi-font-weight:normal'><span
1659style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1660mso-hansi-theme-font:minor-latin'>Controls</span></b> item from the GSAS-II
1661data tree. Unset the <b style='mso-bidi-font-weight:normal'><span
1662style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1663mso-hansi-theme-font:minor-latin'>Refine HKLF as F^2</span></b> box and enter <b
1664style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1665mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>3.0</span></b>
1666for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1667mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Min <span
1668class=SpellE>obs</span>/sig</span></b>. This makes the least squares refine on <span
1669class=SpellE>F<sub>o</sub></span> with 3&#963; cutoff on <span class=SpellE>F<sub>o</sub></span>.
1670From the main GSAS-II data tree menu do <b style='mso-bidi-font-weight:normal'><span
1671style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1672mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; this will do the
16731<sup>st</sup> least squares refinement varying only the data set scale factors.
1674A progress bar popup will appear showing the residuals as the refinement
1675proceeds. When done, a small popup will appear with the final residual; press <b
1676style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1677mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>
1678to accept it. The final <span class=SpellE>R<sub>w</sub></span> is about 47% Go
1679to the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1680mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Atoms</span></b>
1681tab for the <span class=SpellE>rubrene</span> phase, double click the <b
1682style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1683mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>refine</span></b>
1684column heading; a popup box will appear. Select both <b style='mso-bidi-font-weight:
1685normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1686minor-latin;mso-hansi-theme-font:minor-latin'>X - coordinates</span></b> and <b
1687style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1688mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>U – thermal
1689parameters</span></b> and press <b style='mso-bidi-font-weight:normal'><span
1690style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1691mso-hansi-theme-font:minor-latin'>OK</span></b>. The atom table will show
1692refine flags for each atom.</p>
1693
1694<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1695 id="Picture_x0020_41" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:468pt;
1696 height:199.5pt;visibility:visible;mso-wrap-style:square'>
1697 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image081.png"
1698  o:title=""/>
1699</v:shape><![endif]--><![if !vml]><img width=624 height=266
1700src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image082.gif"
1701v:shapes="Picture_x0020_41"><![endif]></span></p>
1702
1703<p class=MsoNormal>Then repeat the <b style='mso-bidi-font-weight:normal'><span
1704style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1705mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> (twice<span
1706class=GramE>)command</span> in the main menu. The final residual will be much
1707better <span class=SpellE>R<sub>w</sub></span> ~10%. Next, convert all the
1708atoms from isotropic thermal parameters to anisotropic ones. Double click the <b
1709style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1710mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>I/A</span></b>
1711column heading and select <b style='mso-bidi-font-weight:normal'><span
1712style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1713mso-hansi-theme-font:minor-latin'>Anisotropic</span></b> and press <b
1714style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1715mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1716Then repeat <b style='mso-bidi-font-weight:normal'><span style='font-family:
1717"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1718minor-latin'>Calculate/Refine</span></b> (perhaps twice); the final <span
1719class=SpellE>R<sub>w</sub></span> ~5.9% which is quite nice.</p>
1720
1721<h2>Step 8. Further work</h2>
1722
1723<p class=MsoNormal>Since this is TOF neutron single crystal diffraction, a
1724relatively large crystal was used and the neutron wavelength covered a fairly
1725wide range of values. Hence, it is likely that the strong reflection
1726intensities suffered from some level of extinction. To find these parameters
1727select the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1728"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1729minor-latin'>Data</span></b> tab in the Phase Data window; all that will show
1730is a list of a data set names with the 1<sup>st</sup> one highlighted; the
1731window will look something like</p>
1732
1733<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1734 id="Picture_x0020_42" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:468pt;
1735 height:199.5pt;visibility:visible;mso-wrap-style:square'>
1736 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image083.png"
1737  o:title=""/>
1738</v:shape><![endif]--><![if !vml]><img width=624 height=266
1739src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image084.gif"
1740v:shapes="Picture_x0020_42"><![endif]></span></p>
1741
1742<p class=MsoNormal>The Scale factors is selected for refinement by default (box
1743checked). Here you want to select <b style='mso-bidi-font-weight:normal'><span
1744style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1745mso-hansi-theme-font:minor-latin'>Primary</span></b> for the <b
1746style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1747mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Extinction
1748type</span></b> (later you can try the other models) for the 1<sup>st</sup>
1749data set. The window will be repainted with a new line in the data display.
1750Select the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1751"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1752minor-latin'>Ep</span></b> check box so it will be refined. To set all the rest
1753do <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1754mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1755minor-latin'>Edit Phase/Copy <span class=SpellE>Flags<span style='font-family:
1756"Times New Roman",serif;font-weight:normal'>A</span></span></span></b> popup
1757will appear giving the list of data sets; press the <b style='mso-bidi-font-weight:
1758normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1759minor-latin;mso-hansi-theme-font:minor-latin'>Set All</span></b> button and
1760then <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1761mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1762You could then do <b style='mso-bidi-font-weight:normal'><span
1763style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1764mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> but it might be
1765better to constrain all the Ep values to be the same. To do this select <b
1766style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1767mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Constraints</span></b>
1768from the GSASII data tree. A blank window with tabs will appear.</p>
1769
1770<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1771 id="Picture_x0020_43" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:468pt;
1772 height:180.75pt;visibility:visible;mso-wrap-style:square'>
1773 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image085.png"
1774  o:title=""/>
1775</v:shape><![endif]--><![if !vml]><img width=624 height=241
1776src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image086.gif"
1777v:shapes="Picture_x0020_43"><![endif]></span></p>
1778
1779<p class=MsoNormal>Select the <b style='mso-bidi-font-weight:normal'><span
1780style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1781mso-hansi-theme-font:minor-latin'>Histogram/Phase</span></b> constraints tab; the
1782window is still blank but that tab is now highlighted. Next do <b
1783style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1784mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit Constr<span
1785class=GramE>./</span>Add equivalence</span></b>; a popup will appear asking for
1786a parameter name to be constrained.</p>
1787
1788<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1789 id="Picture_x0020_44" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:468pt;
1790 height:299.25pt;visibility:visible;mso-wrap-style:square'>
1791 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image087.png"
1792  o:title=""/>
1793</v:shape><![endif]--><![if !vml]><img width=624 height=399
1794src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image088.gif"
1795v:shapes="Picture_x0020_44"><![endif]></span></p>
1796
1797<p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span
1798style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1799mso-hansi-theme-font:minor-latin'>0:0<span class=GramE>:Ep</span></span></b>,
1800that is the primary extinction parameter for the 1<sup>st</sup> dataset and the
1801<span class=SpellE>rubrene</span> phase. Press <b style='mso-bidi-font-weight:
1802normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1803minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.</p>
1804
1805<p class=MsoNormal>The popup is replaced with a new list of all compatible
1806parameters that <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'>0:0<span class=GramE>:Ep</span></span></b> is to be made
1809equivalent to. Scroll down and find <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'>0<span class=GramE>:all:Ep</span></span></b>
1812and pick that and press <b style='mso-bidi-font-weight:normal'><span
1813style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1814mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>OK</span></b>;
1815the Constraint window will change to</p>
1816
1817<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1818 id="Picture_x0020_45" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:468pt;
1819 height:156.75pt;visibility:visible;mso-wrap-style:square'>
1820 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image089.png"
1821  o:title=""/>
1822</v:shape><![endif]--><![if !vml]><img width=624 height=209
1823src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image090.gif"
1824v:shapes="Picture_x0020_45"><![endif]></span></p>
1825
1826<p class=MsoNormal>This shows the constraint making Ep for all 23 data sets
1827equivalent to a single variable. Do <b style='mso-bidi-font-weight:normal'><span
1828style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1829mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; my <span
1830class=SpellE>R<sub>w</sub></span> was 5.474% only a slight improvement. You may
1831wish to try the other extinction models. Do remember to delete the unused
1832constraint before adding a new one for the different extinction parameter.
1833Finally you can draw the molecule; go to <b style='mso-bidi-font-weight:normal'><span
1834style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1835mso-hansi-theme-font:minor-latin'>Atoms</span></b> and do <b style='mso-bidi-font-weight:
1836normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1837minor-latin;mso-hansi-theme-font:minor-latin'>Edit Atoms/Reload draw atoms</span></b>.
1838That will put the newest atom parameters into the Draw Atoms table. Select <b
1839style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1840mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Draw Atoms</span></b>.
1841Select the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1842"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1843minor-latin'>Style</span></b> column heading; a popup will appear</p>
1844
1845<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1846 id="Picture_x0020_46" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:171pt;
1847 height:190.5pt;visibility:visible;mso-wrap-style:square'>
1848 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image091.png"
1849  o:title=""/>
1850</v:shape><![endif]--><![if !vml]><img width=228 height=254
1851src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image092.gif"
1852v:shapes="Picture_x0020_46"><![endif]></span></p>
1853
1854<p class=MsoNormal>Notice the first line is blank, if you select that all the
1855atoms will vanish! Select <b style='mso-bidi-font-weight:normal'><span
1856style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1857mso-hansi-theme-font:minor-latin'>ellipsoids</span></b> and press <b
1858style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1859mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1860I also set the ellipsoid probability to 99% (slider on the <b style='mso-bidi-font-weight:
1861normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1862minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Draw
1863Options</span></b> tab). The plot will change, but it is pretty cluttered.</p>
1864
1865<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1866 id="Picture_x0020_47" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:468pt;
1867 height:403.5pt;visibility:visible;mso-wrap-style:square'>
1868 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image093.png"
1869  o:title=""/>
1870</v:shape><![endif]--><![if !vml]><img width=624 height=538
1871src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image094.gif"
1872v:shapes="Picture_x0020_47"><![endif]></span></p>
1873
1874<p class=MsoNormal>You can remove the Map peaks atoms; go to the <b
1875style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1876mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map peaks</span></b>
1877tab and do <b style='mso-bidi-font-weight:normal'><span style='font-family:
1878"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1879minor-latin'>Map peaks/clear peaks</span></b> from the menu. The list will be
1880erased and the plot will just show the molecule. You can also remove the unit
1881cell edges, go to <b style='mso-bidi-font-weight:normal'><span
1882style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1883mso-hansi-theme-font:minor-latin'>Draw Options</span></b> and uncheck the <b
1884style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1885mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Show unit
1886cell?</span></b> box. Finally, you can remove the charge flipping map; go to <b
1887style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1888mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
1889and do <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1890mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/Clear
1891map</span></b>. That deletes the scattering density map and the drawing will be
1892free of any clutter.</p>
1893
1894<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1895 id="Picture_x0020_48" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:468pt;
1896 height:404.25pt;visibility:visible;mso-wrap-style:square'>
1897 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image095.png"
1898  o:title=""/>
1899</v:shape><![endif]--><![if !vml]><img width=624 height=539
1900src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image096.gif"
1901v:shapes="Picture_x0020_48"><![endif]></span></p>
1902
1903<p class=MsoNormal>Remember that this is only 1/4<sup>th</sup> of the molecule,
1904we’d like to see the whole thing. First go to the <b style='mso-bidi-font-weight:
1905normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1906minor-latin;mso-hansi-theme-font:minor-latin'>Atoms</span></b> tab and select
1907the C-atom that is in a special position 2(x). The do <b style='mso-bidi-font-weight:
1908normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1909minor-latin;mso-hansi-theme-font:minor-latin'>Compute/Show Distances &amp;
1910Angles</span></b> and respond <b style='mso-bidi-font-weight:normal'><span
1911style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1912mso-hansi-theme-font:minor-latin'>OK</span></b> to the popup. The important
1913result is on the console</p>
1914
1915<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1916 id="Picture_x0020_49" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:468pt;
1917 height:272.25pt;visibility:visible;mso-wrap-style:square'>
1918 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image097.png"
1919  o:title=""/>
1920</v:shape><![endif]--><![if !vml]><img width=624 height=363
1921src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image098.gif"
1922v:shapes="Picture_x0020_49"><![endif]></span></p>
1923
1924<p class=MsoNormal>This gives the bond distances and angles about the <span
1925class=GramE>C(</span>1) atom. Particularly note the cell<span class=GramE>+(</span>sym.
1926Op.) information; we will use this to build the drawing. Go to the <b
1927style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1928mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Draw Atoms</span></b>
1929tab and select all the atoms (double click on the upper left box). You should
1930see all atoms selected</p>
1931
1932<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1933 id="Picture_x0020_50" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:468pt;
1934 height:208.5pt;visibility:visible;mso-wrap-style:square'>
1935 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image099.png"
1936  o:title=""/>
1937</v:shape><![endif]--><![if !vml]><img width=624 height=278
1938src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image100.gif"
1939v:shapes="Picture_x0020_50"><![endif]></span></p>
1940
1941<p class=MsoNormal>Then do <b style='mso-bidi-font-weight:normal'><span
1942style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1943mso-hansi-theme-font:minor-latin'>Edit Figure/Add atoms</span></b>; a popup
1944will appear</p>
1945
1946<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1947 id="Picture_x0020_51" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:189pt;
1948 height:264pt;visibility:visible;mso-wrap-style:square'>
1949 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image101.png"
1950  o:title=""/>
1951</v:shape><![endif]--><![if !vml]><img width=252 height=352
1952src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image102.gif"
1953v:shapes="Picture_x0020_51"><![endif]></span></p>
1954
1955<p class=MsoNormal>Based on the 1<sup>st</sup> entry in the bond distance table
1956‘<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1957mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>[1 0 0<span
1958class=GramE>]<span style='mso-spacerun:yes'>  </span>+</span>(<span
1959style='mso-spacerun:yes'>  </span>2)</span></b>’, select the controls for the 2<sup>nd</sup>
1960operator and increment the 1<sup>st</sup> unit cell</p>
1961
1962<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1963 id="Picture_x0020_52" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:189pt;
1964 height:264pt;visibility:visible;mso-wrap-style:square'>
1965 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image103.png"
1966  o:title=""/>
1967</v:shape><![endif]--><![if !vml]><img width=252 height=352
1968src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image104.gif"
1969v:shapes="Picture_x0020_52"><![endif]></span></p>
1970
1971<p class=MsoNormal>Press <b style='mso-bidi-font-weight:normal'><span
1972style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1973mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>OK</span></b>.
1974The plot now shows œ the molecule.</p>
1975
1976<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1977 id="Picture_x0020_53" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:468pt;
1978 height:403.5pt;visibility:visible;mso-wrap-style:square'>
1979 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image105.png"
1980  o:title=""/>
1981</v:shape><![endif]--><![if !vml]><img width=624 height=538
1982src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image106.gif"
1983v:shapes="Picture_x0020_53"><![endif]></span></p>
1984
1985<p class=MsoNormal>Next select all the Draw atoms again and do <b
1986style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1987mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit Figure/Add
1988atoms</span></b>; the selection popup will appear. This time use the other
1989nonidentity entry in the bond distance table ‘<b style='mso-bidi-font-weight:
1990normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1991minor-latin;mso-hansi-theme-font:minor-latin'>[0 1 1] + (-2)</span></b>’. The
1992‘-2’ indicates both the inversion and the 2<sup>nd</sup> operator need to be
1993applied; check both and increment the 2<sup>nd</sup> and 3<sup>rd</sup> unit
1994cell entries. </p>
1995
1996<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1997 id="Picture_x0020_54" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:189pt;
1998 height:264pt;visibility:visible;mso-wrap-style:square'>
1999 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image107.png"
2000  o:title=""/>
2001</v:shape><![endif]--><![if !vml]><img width=252 height=352
2002src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image108.gif"
2003v:shapes="Picture_x0020_54"><![endif]></span></p>
2004
2005<p class=MsoNormal>Press <b style='mso-bidi-font-weight:normal'><span
2006style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2007mso-hansi-theme-font:minor-latin'>OK</span></b>; the entire molecule is drawn.</p>
2008
2009<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2010 id="Picture_x0020_55" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:468pt;
2011 height:403.5pt;visibility:visible;mso-wrap-style:square'>
2012 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image109.png"
2013  o:title=""/>
2014</v:shape><![endif]--><![if !vml]><img width=624 height=538
2015src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image119.gif"
2016v:shapes="Picture_x0020_55"><![endif]></span><span
2017style='mso-spacerun:yes'> </span></p>
2018
2019<p class=MsoNormal>Looks really nice. This ends the tutorial. You can save the
2020project if you wish. All the changes (<span class=SpellE>i.e</span> deleting
2021Map peaks &amp; clearing the map) will be saved.</p>
2022
2023</div>
2024
2025</body>
2026
2027</html>
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