source: Tutorials/TOF Charge Flipping/Charge Flipping with TOF single crystal data in GSASII.htm @ 3692

Last change on this file since 3692 was 3071, checked in by vondreele, 4 years ago

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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
1178<p class=MsoNormal>In this exercise you will use GSAS-II to solve the structure
1179of <span class=SpellE>rubrene</span> (C<sub>42</sub>H<sub>28</sub>) from single
1180crystal neutron data via charge flipping. <span class=SpellE>Rubrene</span> is of
1181interest as a molecular semiconductor. It crystallizes in the space group <span
1182class=SpellE>Cmca</span> with the lattice parameters a=26.798Å, b=7.1618Å,
1183c=14.1942Å, Z=4. Thus, the molecule is sited on a special position with 2/m
1184symmetry. If you have not done so already, start GSAS-II.</p>
1185
1186<h2>Step 1. Set the phase information</h2>
1187
1188<p class=MsoNormal>To begin this tutorial, do <b style='mso-bidi-font-weight:
1189normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1190minor-latin;mso-hansi-theme-font:minor-latin'>Data/Add new phase</span></b> in
1191the main GSAS-II data tree menu. A popup window will appear asking for a phase
1192name; I used <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1193style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1194mso-hansi-theme-font:minor-latin'>rubrene</span></b></span>. The General tab
1195for this phase will be shown</p>
1196
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1217</v:shapetype><v:shape id="Picture_x0020_1" o:spid="_x0000_i1056" type="#_x0000_t75"
1218 style='width:468pt;height:210pt;visibility:visible;mso-wrap-style:square'>
1219 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image002.png"
1220  o:title=""/>
1221</v:shape><![endif]--><![if !vml]><img width=624 height=280
1222src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image001.gif"
1223v:shapes="Picture_x0020_1"><![endif]></span></p>
1224
1225<p class=MsoNormal>Enter the space group (<b style='mso-bidi-font-weight:normal'><span
1226style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1227mso-hansi-theme-font:minor-latin'>C m c a</span></b> – don’t forget the spaces)
1228and press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1229mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Enter</span></b>.
1230A popup with Space group information will appear</p>
1231
1232<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1233 id="_x0000_i1055" type="#_x0000_t75" style='width:275.25pt;height:207pt;
1234 visibility:visible;mso-wrap-style:square'>
1235 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image006.png"
1236  o:title=""/>
1237</v:shape><![endif]--><![if !vml]><img width=367 height=276
1238src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image003.gif"
1239v:shapes="_x0000_i1055"><![endif]></span></p>
1240
1241<p class=MsoNormal>Press <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'>OK</span></b>; the General tab will be
1244repainted with defaults for the orthorhombic lattice parameters. Enter <b
1245style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1246mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>26.798</span></b>
1247for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1248mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>a</span></b>,
1249<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1250mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>7.1618</span></b>
1251for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1252mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>b</span></b>
1253and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1254mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>14.1942</span></b>
1255for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1256mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>c</span></b>.
1257Press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1258mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Enter</span></b>,
1259the unit cell volume (2724.178) will be updated.</p>
1260
1261<h2>Step 2. Import the data</h2>
1262
1263<p class=MsoNormal>The <span class=SpellE>rubrene</span> data were collected on
1264the TOPAZ instrument at the SNS Facility, Oak Ridge National Laboratory with 23
1265different crystal orientations; the local instrument data processing software
1266has applied corrections and combined them into a single multicolumn <span
1267class=SpellE>hkl</span> file. To import this do <b style='mso-bidi-font-weight:
1268normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1269minor-latin;mso-hansi-theme-font:minor-latin'>Import/Structure Factor/from
1270Neutron TOF HKL F<sup>2</sup> file</span></b>; a directory dialog box will
1271appear. Go to the directory <b style='mso-bidi-font-weight:normal'><span
1272style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1273mso-hansi-theme-font:minor-latin'>TOF Charge Flipping/data</span></b> and
1274select the file <span class=SpellE><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'>ruberene_orthoC.hkl</span></b></span> (double
1277click the name or press the <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'>Open</span></b> button after selecting it). A
1280popup box will appear.</p>
1281
1282<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1283 id="_x0000_i1054" type="#_x0000_t75" style='width:307.5pt;height:147.75pt;
1284 visibility:visible;mso-wrap-style:square'>
1285 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image010.png"
1286  o:title=""/>
1287</v:shape><![endif]--><![if !vml]><img width=410 height=197
1288src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image005.gif"
1289v:shapes="_x0000_i1054"><![endif]></span></p>
1290
1291<p class=MsoNormal>Press <span class=GramE><b style='mso-bidi-font-weight:normal'><span
1292style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1293mso-hansi-theme-font:minor-latin'>Yes</span></b></span>; another popup will
1294appear offering you the chance to change the name. Press <b style='mso-bidi-font-weight:
1295normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1296minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>, a new popup
1297appears.</p>
1298
1299<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1300 id="_x0000_i1053" type="#_x0000_t75" style='width:233.25pt;height:228.75pt;
1301 visibility:visible;mso-wrap-style:square'>
1302 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image014.png"
1303  o:title=""/>
1304</v:shape><![endif]--><![if !vml]><img width=311 height=305
1305src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image007.gif"
1306v:shapes="_x0000_i1053"><![endif]></span></p>
1307
1308<p class=MsoNormal>Here you select the phase the data belongs to. There is only
1309<span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1310style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1311mso-hansi-theme-font:minor-latin'>rubrene</span></b></span> so select it and
1312press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1313mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1314The bottom of the data tree is shown, a small data window and the plot shows
1315the l=0 slice of the last reflection set loaded (HKLF rubrene_orthoC.hkl_22).</p>
1316
1317<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1318 id="_x0000_i1052" type="#_x0000_t75" style='width:468pt;height:401.25pt;
1319 visibility:visible;mso-wrap-style:square'>
1320 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image018.png"
1321  o:title=""/>
1322</v:shape><![endif]--><![if !vml]><img width=624 height=535
1323src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image009.gif"
1324v:shapes="_x0000_i1052"><![endif]></span></p>
1325
1326<p class=MsoNormal>The <b style='mso-bidi-font-weight:normal'><span
1327style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1328mso-hansi-theme-font:minor-latin'>K</span></b> box control allows you to select
1329other zones &amp; layers to view. The drawing geometry is strictly square (i.e.
1330not in reciprocal space units). If you do <b style='mso-bidi-font-weight:normal'><span
1331style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1332mso-hansi-theme-font:minor-latin'>Commands/Plot 3D HKLs</span></b>, a 3D plot
1333of reciprocal space is shown</p>
1334
1335<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1336 id="_x0000_i1051" type="#_x0000_t75" style='width:468pt;height:403.5pt;
1337 visibility:visible;mso-wrap-style:square'>
1338 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image022.png"
1339  o:title=""/>
1340</v:shape><![endif]--><![if !vml]><img width=624 height=538
1341src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image011.gif"
1342v:shapes="_x0000_i1051"><![endif]></span></p>
1343
1344<p class=MsoNormal>The size of the green boxes is proportional to the structure
1345factors; the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1346"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1347minor-latin'>save as/key</span></b> pulldown will give you other viewing
1348options. Here is a good place to save the GSAS-II project for <span
1349class=SpellE>rubrene</span>. Do <b style='mso-bidi-font-weight:normal'><span
1350style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1351mso-hansi-theme-font:minor-latin'>File/Save project</span></b> from the main
1352GSAS-II data tree window; a file dialog box will appear. Enter a file name (I
1353used <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1354style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1355mso-hansi-theme-font:minor-latin'>rubrene</span></b></span> – no extension).</p>
1356
1357<h2>Step 3. Setup for charge flipping</h2>
1358
1359<p class=MsoNormal>We have two tasks here. One is to select the reflection sets
1360to be used in the calculations and the other is to set some controls. To begin
1361select the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1362style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1363mso-hansi-theme-font:minor-latin'>rubrene</span></b></span> phase entry in the
1364GSAS-II data tree; the General tab will appear in the Phase Data for <span
1365class=SpellE>rubrene</span> window</p>
1366
1367<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1368 id="_x0000_i1050" type="#_x0000_t75" style='width:468pt;height:222.75pt;
1369 visibility:visible;mso-wrap-style:square'>
1370 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image024.png"
1371  o:title=""/>
1372</v:shape><![endif]--><![if !vml]><img width=624 height=297
1373src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image013.gif"
1374v:shapes="_x0000_i1050"><![endif]></span></p>
1375
1376<p class=MsoNormal>In the Charge flip controls (about center of the page) press
1377the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1378mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Select
1379reflection sets</span></b> button; a <b style='mso-bidi-font-weight:normal'><span
1380style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1381mso-hansi-theme-font:minor-latin'>Use data</span></b> popup will appear. You
1382will want to use all the HKLF data sets; press <b style='mso-bidi-font-weight:
1383normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1384minor-latin;mso-hansi-theme-font:minor-latin'>Set All</span> </b>and press <b
1385style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1386mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1387The General tab will be refreshed. GSAS-II will use all the data to build a
1388reflection set for charge flipping. For duplicate <span class=SpellE>hkls</span>
1389the last one encountered will be used. Since atoms are essentially point <span
1390class=SpellE>scatterers</span> for neutrons, a charge flip map has very sharp
1391peaks so a better choice for the <b style='mso-bidi-font-weight:normal'><span
1392style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1393mso-hansi-theme-font:minor-latin'>k-factor</span></b> (charge flip level) might
1394be <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1395mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0.5</span></b>,
1396the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1397mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>k-max</span></b>
1398should be larger (say <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'>50</span></b>) and the map <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'>Resolution</span></b>
1403should be smaller (say <b style='mso-bidi-font-weight:normal'><span
1404style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1405mso-hansi-theme-font:minor-latin'>0.4</span></b>). Set these three values. In
1406the Fourier map controls, set <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'>Peak cutoff %</span></b> to <b
1409style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1410mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>20</span></b>;
1411this sets the lower limit of the peak search in the charge flip map. When done
1412the General tab should look like</p>
1413
1414<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1415 id="_x0000_i1049" type="#_x0000_t75" style='width:468pt;height:222.75pt;
1416 visibility:visible;mso-wrap-style:square'>
1417 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image028.png"
1418  o:title=""/>
1419</v:shape><![endif]--><![if !vml]><img width=624 height=297
1420src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image015.gif"
1421v:shapes="_x0000_i1049"><![endif]></span></p>
1422
1423<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1424
1425<h2>Step 4. Charge flipping</h2>
1426
1427<p class=MsoNormal>We are now ready for charge flipping. In the General tab
1428menu do <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1429mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/Charge
1430flipping</span></b>; a Charge flipping progress bar will appear showing the
1431residual and cycle count for the charge flipping calculation. In this case the
1432residual quickly drops to ~38% and stays there. Press <b style='mso-bidi-font-weight:
1433normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1434minor-latin;mso-hansi-theme-font:minor-latin'>Cancel</span></b> to stop the
1435calculation; some information will be printed on the console and after a pause
1436the Phase Data window will show <b style='mso-bidi-font-weight:normal'><span
1437style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1438mso-hansi-theme-font:minor-latin'>Map Peaks</span></b> and the plot window will
1439show a drawing of the obtained structure.</p>
1440
1441<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1442 id="Picture_x0020_33" o:spid="_x0000_i1048" type="#_x0000_t75" style='width:468pt;
1443 height:315.75pt;visibility:visible;mso-wrap-style:square'>
1444 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image017.png"
1445  o:title=""/>
1446</v:shape><![endif]--><![if !vml]><img width=624 height=421
1447src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image019.gif"
1448v:shapes="Picture_x0020_33"><![endif]></span></p>
1449
1450<p class=MsoNormal>If you scroll down the Map peak list you will find some with
1451negative magnitudes at the end of the list. GSAS-II searches the map for both
1452positive and negative peaks; the former are C-atoms and the latter are H-atoms.
1453</p>
1454
1455<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1456 id="Picture_x0020_34" o:spid="_x0000_i1047" type="#_x0000_t75" style='width:468pt;
1457 height:404.25pt;visibility:visible;mso-wrap-style:square'>
1458 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image021.png"
1459  o:title=""/>
1460</v:shape><![endif]--><![if !vml]><img width=624 height=539
1461src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image025.gif"
1462v:shapes="Picture_x0020_34"><![endif]></span></p>
1463
1464<p class=MsoNormal>The plot (which I’ve rotated around a bit) shows white spots
1465for the positive peaks and red ones for the negative ones; bonds are white lines.
1466Your solution may show a problem with the charge flip solution. While the
1467charge flipping run has clearly found all the C-atoms and some of the H-atoms,
1468the molecule may be incorrectly placed in the unit cell (the multicolored cross
1469should be in the middle of the C-C bond at the center of the molecule). To fix
1470this you could simply repeat the charge flipping run and hope it puts the
1471molecule in the right place. GSAS-II uses an algorithm based on how structure
1472factor phases are related for a given space group to reposition the solution;
1473it sometimes fails if the phase set isn’t perfect. Or you can “roll” the map
1474right/left/up/down (<b style='mso-bidi-font-weight:normal'><span
1475style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1476mso-hansi-theme-font:minor-latin'>R/L/U/D</span></b> keys) to put the solution
1477where you want.<span style='mso-spacerun:yes'>  </span>Notice that as the map
1478is rolled, the Map peak positions are shifted to match the change in positions.</p>
1479
1480<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1481
1482<p class=MsoNormal>By carefully looking at the map, you can see the 4-ring <span
1483class=SpellE>tetracene</span> (<span class=SpellE>naphthacene</span>) core of
1484the molecule with four phenyl groups attached to both sides on the center two
1485rings. The unique part consists of 1/4<sup>th</sup> of this group (i.e. half of
1486one side of the <span class=SpellE>tetracene</span> and one phenyl); one C-atom
1487sits on a 2-fold and the rest are in general positions. The molecule extends
1488into the neighboring unit cell so you don’t see the whole thing as one group
1489but has two bits on either side.</p>
1490
1491<h2>Step 5. Peak selection</h2>
1492
1493<p class=MsoNormal>GSAS-II provides several ways of selecting peak positions
1494from a charge flipping map. One way is to pick them directly from the drawing.
1495Place the cursor on one peak and do a <b style='mso-bidi-font-weight:normal'><span
1496style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1497mso-hansi-theme-font:minor-latin'>Shift left mouse button</span></b>; it will
1498be highlighted on the list and it will turn green on the plot. Do a <b
1499style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1500mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Shift right
1501mouse button</span></b> on the remaining peaks you want to <span class=GramE>pick.</span>
1502All will turn green (you may have to wiggle the plot a bit with the mouse to
1503make them show) and all will be highlighted in the list. Alternatively, you can
1504select the entire list of peaks (double click on upper left empty box of the
1505table), then do <b style='mso-bidi-font-weight:normal'><span style='font-family:
1506"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1507minor-latin'>Map peaks/Unique peaks</span></b>. Better still you can sort the
1508peaks by one of the column headings and then do <b style='mso-bidi-font-weight:
1509normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1510minor-latin;mso-hansi-theme-font:minor-latin'>Map peaks/Unique peaks</span></b>.
1511I’ve chosen to sort the peaks on <span class=SpellE><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'>dcent</span></b></span> (distance
1514from center of the cell) beforehand. After a pause while it sorts out the
1515unique peaks, it will highlight them in the table and display the picked ones
1516in green on the plot. In this case they will probably be scattered about the
1517unit cell and not make a continuous molecule, but they are largely clustered
1518around the unit cell center. My plot looked like this when I was done.</p>
1519
1520<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1521 id="_x0000_i1046" type="#_x0000_t75" style='width:468pt;height:379.5pt;
1522 visibility:visible;mso-wrap-style:square'>
1523 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image040.png"
1524  o:title=""/>
1525</v:shape><![endif]--><![if !vml]><img width=624 height=506
1526src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image027.gif"
1527v:shapes="_x0000_i1046"><![endif]></span></p>
1528
1529<p class=MsoNormal>The list has them highlighted (the rest are lower down in my
1530list; all 18 atoms were found in this charge flipping result)</p>
1531
1532<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1533 id="Picture_x0020_35" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:468pt;
1534 height:394.5pt;visibility:visible;mso-wrap-style:square'>
1535 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image029.png"
1536  o:title=""/>
1537</v:shape><![endif]--><![if !vml]><img width=624 height=526
1538src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image031.gif"
1539v:shapes="Picture_x0020_35"><![endif]></span></p>
1540
1541<p class=MsoNormal>To add them to the Atom list do <b style='mso-bidi-font-weight:
1542normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1543minor-latin;mso-hansi-theme-font:minor-latin'>Map peaks/Move peaks</span></b>;
1544the drawing will show white balls for them.</p>
1545
1546<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1547 id="Picture_x0020_36" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:468pt;
1548 height:404.25pt;visibility:visible;mso-wrap-style:square'>
1549 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image033.png"
1550  o:title=""/>
1551</v:shape><![endif]--><![if !vml]><img width=624 height=539
1552src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image035.gif"
1553v:shapes="Picture_x0020_36"><![endif]></span></p>
1554
1555<p class=MsoNormal>The atom list will give the magnitudes as ‘M’ names; I found
1556all 11 C-atoms and 7 H-atoms that were expected.</p>
1557
1558<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1559 id="Picture_x0020_37" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:468pt;
1560 height:342pt;visibility:visible;mso-wrap-style:square'>
1561 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image073.png"
1562  o:title=""/>
1563</v:shape><![endif]--><![if !vml]><img width=624 height=456
1564src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image074.gif"
1565v:shapes="Picture_x0020_37"><![endif]></span></p>
1566
1567<h2>Step 6. Atom identification</h2>
1568
1569<p class=MsoNormal>You can reorder the atoms in the list; do an <b
1570style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1571mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Alt select</span></b>
1572for the atom row you want to move. Then do an <b style='mso-bidi-font-weight:
1573normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1574minor-latin;mso-hansi-theme-font:minor-latin'>Alt select</span></b> on the row
1575where you want the moved atom to precede it. This way you can put the C-atoms
1576first and the H-atoms last in the list instead of mixed up as in the above
1577list. Next select all the positive M peaks (pick the top one and then <b
1578style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1579mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Shift</span></b>
1580pick the last one). Do <b style='mso-bidi-font-weight:normal'><span
1581style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1582mso-hansi-theme-font:minor-latin'>Edit Atoms/On selected atoms/Modify
1583parameters</span></b> from the Atoms menu; a popup will appear. Pick <b
1584style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1585mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Type</span></b>
1586and press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1587mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>;
1588a Periodic Table will appear. Select <b style='mso-bidi-font-weight:normal'><span
1589style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1590mso-hansi-theme-font:minor-latin'>C</span></b> from the C-atom pulldown. All
1591the C-atom names and types will change and the plot will show dark gray spheres
1592for the C-atoms. You should also move the C-atom with 2(x) site symmetry to the
1593top of the list (if it isn’t there already).</p>
1594
1595<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1596 id="Picture_x0020_38" o:spid="_x0000_i1042" type="#_x0000_t75" style='width:468pt;
1597 height:268.5pt;visibility:visible;mso-wrap-style:square'>
1598 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image075.png"
1599  o:title=""/>
1600</v:shape><![endif]--><![if !vml]><img width=624 height=358
1601src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image076.gif"
1602v:shapes="Picture_x0020_38"><![endif]></span></p>
1603
1604<p class=MsoNormal>Do the same with the remaining negative M atoms – make them
1605H atoms. The drawing shows molecular fragments scattered about the unit cell;
1606you’d like to unify them into a single molecule. Select the C-atom with 2(x)
1607site symmetry (although any would do). Do <b style='mso-bidi-font-weight:normal'><span
1608style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1609mso-hansi-theme-font:minor-latin'>Edit Atoms/Assemble molecule</span></b> from
1610the Atoms menu; a popup will appear offering choices for Bond radii (&amp;
1611Angle radii – ignored here). Press <b style='mso-bidi-font-weight:normal'><span
1612style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1613mso-hansi-theme-font:minor-latin'>Ok</span></b>; the Atom table will be revised
1614and the plot will show an assembled molecule. </p>
1615
1616<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1617 id="Picture_x0020_39" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:468pt;
1618 height:405pt;visibility:visible;mso-wrap-style:square'>
1619 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image077.png"
1620  o:title=""/>
1621</v:shape><![endif]--><![if !vml]><img width=624 height=540
1622src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image078.gif"
1623v:shapes="Picture_x0020_39"><![endif]></span></p>
1624
1625<p class=MsoNormal>The molecule building has scrambled the order of the atoms;
1626they were located in order as the molecule was built. </p>
1627
1628<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1629 id="Picture_x0020_40" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:468pt;
1630 height:268.5pt;visibility:visible;mso-wrap-style:square'>
1631 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image079.png"
1632  o:title=""/>
1633</v:shape><![endif]--><![if !vml]><img width=624 height=358
1634src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image080.gif"
1635v:shapes="Picture_x0020_40"><![endif]></span></p>
1636
1637<p class=MsoNormal>You can reorder them to put the H-atoms at the end of the
1638list (if they weren’t there already). Then select all of them and then do <b
1639style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1640mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1641minor-latin'>Edit Atoms/On Selected atoms…/Modify parameters</span></b>. Pick <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'>Name</span></b>
1644from the pulldown and press <b style='mso-bidi-font-weight:normal'><span
1645style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1646mso-hansi-theme-font:minor-latin'>OK</span></b>. You are asked if you really
1647want to do this, 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'>Yes</span></b>. The atoms are then renamed in
1650numeric order.</p>
1651
1652<h2>Step 7. Refinement</h2>
1653
1654<p class=MsoNormal>Since the structure is complete, we can do the full
1655refinement. Select the <b style='mso-bidi-font-weight:normal'><span
1656style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1657mso-hansi-theme-font:minor-latin'>Controls</span></b> item from the GSAS-II
1658data tree. Unset 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'>Refine HKLF as F^2</span></b> box and enter <b
1661style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1662mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>3.0</span></b>
1663for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1664mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Min <span
1665class=SpellE>obs</span>/sig</span></b>. This makes the least squares refine on <span
1666class=SpellE>F<sub>o</sub></span> with 3&#963; cutoff on <span class=SpellE>F<sub>o</sub></span>.
1667From the main GSAS-II data tree menu do <b style='mso-bidi-font-weight:normal'><span
1668style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1669mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; this will do the
16701<sup>st</sup> least squares refinement varying only the data set scale factors.
1671A progress bar popup will appear showing the residuals as the refinement
1672proceeds. When done, a small popup will appear with the final residual; press <b
1673style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1674mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>
1675to accept it. The final <span class=SpellE>R<sub>w</sub></span> is about 47% Go
1676to the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1677mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Atoms</span></b>
1678tab for the <span class=SpellE>rubrene</span> phase, double click the <b
1679style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1680mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>refine</span></b>
1681column heading; a popup box will appear. Select both <b style='mso-bidi-font-weight:
1682normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1683minor-latin;mso-hansi-theme-font:minor-latin'>X - coordinates</span></b> and <b
1684style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1685mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>U – thermal
1686parameters</span></b> and press <b style='mso-bidi-font-weight:normal'><span
1687style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1688mso-hansi-theme-font:minor-latin'>OK</span></b>. The atom table will show
1689refine flags for each atom.</p>
1690
1691<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1692 id="Picture_x0020_41" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:468pt;
1693 height:199.5pt;visibility:visible;mso-wrap-style:square'>
1694 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image081.png"
1695  o:title=""/>
1696</v:shape><![endif]--><![if !vml]><img width=624 height=266
1697src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image082.gif"
1698v:shapes="Picture_x0020_41"><![endif]></span></p>
1699
1700<p class=MsoNormal>Then repeat the <b style='mso-bidi-font-weight:normal'><span
1701style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1702mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> (twice<span
1703class=GramE>)command</span> in the main menu. The final residual will be much
1704better <span class=SpellE>R<sub>w</sub></span> ~10%. Next, convert all the
1705atoms from isotropic thermal parameters to anisotropic ones. Double click the <b
1706style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1707mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>I/A</span></b>
1708column heading and select <b style='mso-bidi-font-weight:normal'><span
1709style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1710mso-hansi-theme-font:minor-latin'>Anisotropic</span></b> and press <b
1711style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1712mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1713Then repeat <b style='mso-bidi-font-weight:normal'><span style='font-family:
1714"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1715minor-latin'>Calculate/Refine</span></b> (perhaps twice); the final <span
1716class=SpellE>R<sub>w</sub></span> ~5.9% which is quite nice.</p>
1717
1718<h2>Step 8. Further work</h2>
1719
1720<p class=MsoNormal>Since this is TOF neutron single crystal diffraction, a
1721relatively large crystal was used and the neutron wavelength covered a fairly
1722wide range of values. Hence, it is likely that the strong reflection
1723intensities suffered from some level of extinction. To find these parameters
1724select the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1725"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1726minor-latin'>Data</span></b> tab in the Phase Data window; all that will show
1727is a list of a data set names with the 1<sup>st</sup> one highlighted; the
1728window will look something like</p>
1729
1730<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1731 id="Picture_x0020_42" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:468pt;
1732 height:199.5pt;visibility:visible;mso-wrap-style:square'>
1733 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image083.png"
1734  o:title=""/>
1735</v:shape><![endif]--><![if !vml]><img width=624 height=266
1736src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image084.gif"
1737v:shapes="Picture_x0020_42"><![endif]></span></p>
1738
1739<p class=MsoNormal>The Scale factors is selected for refinement by default (box
1740checked). Here you want to select <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'>Primary</span></b> for the <b
1743style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1744mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Extinction
1745type</span></b> (later you can try the other models) for the 1<sup>st</sup>
1746data set. The window will be repainted with a new line in the data display.
1747Select the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1748"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1749minor-latin'>Ep</span></b> check box so it will be refined. To set all the rest
1750do <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1751mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1752minor-latin'>Edit Phase/Copy <span class=SpellE>Flags<span style='font-family:
1753"Times New Roman",serif;font-weight:normal'>A</span></span></span></b> popup
1754will appear giving the list of data sets; press the <b style='mso-bidi-font-weight:
1755normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1756minor-latin;mso-hansi-theme-font:minor-latin'>Set All</span></b> button and
1757then <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1758mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1759You could then do <b style='mso-bidi-font-weight:normal'><span
1760style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1761mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> but it might be
1762better to constrain all the Ep values to be the same. To do this select <b
1763style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1764mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Constraints</span></b>
1765from the GSASII data tree. A blank window with tabs will appear.</p>
1766
1767<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1768 id="Picture_x0020_43" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:468pt;
1769 height:180.75pt;visibility:visible;mso-wrap-style:square'>
1770 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image085.png"
1771  o:title=""/>
1772</v:shape><![endif]--><![if !vml]><img width=624 height=241
1773src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image086.gif"
1774v:shapes="Picture_x0020_43"><![endif]></span></p>
1775
1776<p class=MsoNormal>Select the <b style='mso-bidi-font-weight:normal'><span
1777style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1778mso-hansi-theme-font:minor-latin'>Histogram/Phase</span></b> constraints tab; the
1779window is still blank but that tab is now highlighted. Next do <b
1780style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1781mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit Constr<span
1782class=GramE>./</span>Add equivalence</span></b>; a popup will appear asking for
1783a parameter name to be constrained.</p>
1784
1785<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1786 id="Picture_x0020_44" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:468pt;
1787 height:299.25pt;visibility:visible;mso-wrap-style:square'>
1788 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image087.png"
1789  o:title=""/>
1790</v:shape><![endif]--><![if !vml]><img width=624 height=399
1791src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image088.gif"
1792v:shapes="Picture_x0020_44"><![endif]></span></p>
1793
1794<p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span
1795style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1796mso-hansi-theme-font:minor-latin'>0:0<span class=GramE>:Ep</span></span></b>,
1797that is the primary extinction parameter for the 1<sup>st</sup> dataset and the
1798<span class=SpellE>rubrene</span> phase. Press <b style='mso-bidi-font-weight:
1799normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1800minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.</p>
1801
1802<p class=MsoNormal>The popup is replaced with a new list of all compatible
1803parameters that <b style='mso-bidi-font-weight:normal'><span style='font-family:
1804"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1805minor-latin'>0:0<span class=GramE>:Ep</span></span></b> is to be made
1806equivalent to. Scroll down and find <b style='mso-bidi-font-weight:normal'><span
1807style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1808mso-hansi-theme-font:minor-latin'>0<span class=GramE>:all:Ep</span></span></b>
1809and pick that and press <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;mso-bidi-theme-font:minor-latin'>OK</span></b>;
1812the Constraint window will change to</p>
1813
1814<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1815 id="Picture_x0020_45" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:468pt;
1816 height:156.75pt;visibility:visible;mso-wrap-style:square'>
1817 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image089.png"
1818  o:title=""/>
1819</v:shape><![endif]--><![if !vml]><img width=624 height=209
1820src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image090.gif"
1821v:shapes="Picture_x0020_45"><![endif]></span></p>
1822
1823<p class=MsoNormal>This shows the constraint making Ep for all 23 data sets
1824equivalent to a single variable. Do <b style='mso-bidi-font-weight:normal'><span
1825style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1826mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; my <span
1827class=SpellE>R<sub>w</sub></span> was 5.474% only a slight improvement. You may
1828wish to try the other extinction models. Do remember to delete the unused
1829constraint before adding a new one for the different extinction parameter.
1830Finally you can draw the molecule; go to <b style='mso-bidi-font-weight:normal'><span
1831style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1832mso-hansi-theme-font:minor-latin'>Atoms</span></b> and do <b style='mso-bidi-font-weight:
1833normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1834minor-latin;mso-hansi-theme-font:minor-latin'>Edit Atoms/Reload draw atoms</span></b>.
1835That will put the newest atom parameters into the Draw Atoms table. Select <b
1836style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1837mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Draw Atoms</span></b>.
1838Select the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1839"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1840minor-latin'>Style</span></b> column heading; a popup will appear</p>
1841
1842<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1843 id="Picture_x0020_46" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:171pt;
1844 height:190.5pt;visibility:visible;mso-wrap-style:square'>
1845 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image091.png"
1846  o:title=""/>
1847</v:shape><![endif]--><![if !vml]><img width=228 height=254
1848src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image092.gif"
1849v:shapes="Picture_x0020_46"><![endif]></span></p>
1850
1851<p class=MsoNormal>Notice the first line is blank, if you select that all the
1852atoms will vanish! Select <b style='mso-bidi-font-weight:normal'><span
1853style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1854mso-hansi-theme-font:minor-latin'>ellipsoids</span></b> and press <b
1855style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1856mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1857I also set the ellipsoid probability to 99% (slider on the <b style='mso-bidi-font-weight:
1858normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1859minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Draw
1860Options</span></b> tab). The plot will change, but it is pretty cluttered.</p>
1861
1862<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1863 id="Picture_x0020_47" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:468pt;
1864 height:403.5pt;visibility:visible;mso-wrap-style:square'>
1865 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image093.png"
1866  o:title=""/>
1867</v:shape><![endif]--><![if !vml]><img width=624 height=538
1868src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image094.gif"
1869v:shapes="Picture_x0020_47"><![endif]></span></p>
1870
1871<p class=MsoNormal>You can remove the Map peaks atoms; go to the <b
1872style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1873mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map peaks</span></b>
1874tab and do <b style='mso-bidi-font-weight:normal'><span style='font-family:
1875"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1876minor-latin'>Map peaks/clear peaks</span></b> from the menu. The list will be
1877erased and the plot will just show the molecule. You can also remove the unit
1878cell edges, go to <b style='mso-bidi-font-weight:normal'><span
1879style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1880mso-hansi-theme-font:minor-latin'>Draw Options</span></b> and uncheck the <b
1881style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1882mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Show unit
1883cell?</span></b> box. Finally, you can remove the charge flipping map; go to <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'>General</span></b>
1886and do <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1887mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/Clear
1888map</span></b>. That deletes the scattering density map and the drawing will be
1889free of any clutter.</p>
1890
1891<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1892 id="Picture_x0020_48" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:468pt;
1893 height:404.25pt;visibility:visible;mso-wrap-style:square'>
1894 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image095.png"
1895  o:title=""/>
1896</v:shape><![endif]--><![if !vml]><img width=624 height=539
1897src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image096.gif"
1898v:shapes="Picture_x0020_48"><![endif]></span></p>
1899
1900<p class=MsoNormal>Remember that this is only 1/4<sup>th</sup> of the molecule,
1901we’d like to see the whole thing. First go to the <b style='mso-bidi-font-weight:
1902normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1903minor-latin;mso-hansi-theme-font:minor-latin'>Atoms</span></b> tab and select
1904the C-atom that is in a special position 2(x). The do <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'>Compute/Show Distances &amp;
1907Angles</span></b> and respond <b style='mso-bidi-font-weight:normal'><span
1908style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1909mso-hansi-theme-font:minor-latin'>OK</span></b> to the popup. The important
1910result is on the console</p>
1911
1912<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1913 id="Picture_x0020_49" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:468pt;
1914 height:272.25pt;visibility:visible;mso-wrap-style:square'>
1915 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image097.png"
1916  o:title=""/>
1917</v:shape><![endif]--><![if !vml]><img width=624 height=363
1918src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image098.gif"
1919v:shapes="Picture_x0020_49"><![endif]></span></p>
1920
1921<p class=MsoNormal>This gives the bond distances and angles about the <span
1922class=GramE>C(</span>1) atom. Particularly note the cell<span class=GramE>+(</span>sym.
1923Op.) information; we will use this to build the drawing. Go to the <b
1924style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1925mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Draw Atoms</span></b>
1926tab and select all the atoms (double click on the upper left box). You should
1927see all atoms selected</p>
1928
1929<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1930 id="Picture_x0020_50" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:468pt;
1931 height:208.5pt;visibility:visible;mso-wrap-style:square'>
1932 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image099.png"
1933  o:title=""/>
1934</v:shape><![endif]--><![if !vml]><img width=624 height=278
1935src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image100.gif"
1936v:shapes="Picture_x0020_50"><![endif]></span></p>
1937
1938<p class=MsoNormal>Then do <b style='mso-bidi-font-weight:normal'><span
1939style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1940mso-hansi-theme-font:minor-latin'>Edit Figure/Add atoms</span></b>; a popup
1941will appear</p>
1942
1943<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1944 id="Picture_x0020_51" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:189pt;
1945 height:264pt;visibility:visible;mso-wrap-style:square'>
1946 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image101.png"
1947  o:title=""/>
1948</v:shape><![endif]--><![if !vml]><img width=252 height=352
1949src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image102.gif"
1950v:shapes="Picture_x0020_51"><![endif]></span></p>
1951
1952<p class=MsoNormal>Based on the 1<sup>st</sup> entry in the bond distance table
1953‘<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1954mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>[1 0 0<span
1955class=GramE>]<span style='mso-spacerun:yes'>  </span>+</span>(<span
1956style='mso-spacerun:yes'>  </span>2)</span></b>’, select the controls for the 2<sup>nd</sup>
1957operator and increment the 1<sup>st</sup> unit cell</p>
1958
1959<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1960 id="Picture_x0020_52" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:189pt;
1961 height:264pt;visibility:visible;mso-wrap-style:square'>
1962 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image103.png"
1963  o:title=""/>
1964</v:shape><![endif]--><![if !vml]><img width=252 height=352
1965src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image104.gif"
1966v:shapes="Picture_x0020_52"><![endif]></span></p>
1967
1968<p class=MsoNormal>Press <b style='mso-bidi-font-weight:normal'><span
1969style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1970mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>OK</span></b>.
1971The plot now shows œ the molecule.</p>
1972
1973<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1974 id="Picture_x0020_53" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:468pt;
1975 height:403.5pt;visibility:visible;mso-wrap-style:square'>
1976 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image105.png"
1977  o:title=""/>
1978</v:shape><![endif]--><![if !vml]><img width=624 height=538
1979src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image106.gif"
1980v:shapes="Picture_x0020_53"><![endif]></span></p>
1981
1982<p class=MsoNormal>Next select all the Draw atoms again and do <b
1983style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1984mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit Figure/Add
1985atoms</span></b>; the selection popup will appear. This time use the other
1986nonidentity entry in the bond distance table ‘<b style='mso-bidi-font-weight:
1987normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1988minor-latin;mso-hansi-theme-font:minor-latin'>[0 1 1] + (-2)</span></b>’. The
1989‘-2’ indicates both the inversion and the 2<sup>nd</sup> operator need to be
1990applied; check both and increment the 2<sup>nd</sup> and 3<sup>rd</sup> unit
1991cell entries. </p>
1992
1993<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1994 id="Picture_x0020_54" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:189pt;
1995 height:264pt;visibility:visible;mso-wrap-style:square'>
1996 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image107.png"
1997  o:title=""/>
1998</v:shape><![endif]--><![if !vml]><img width=252 height=352
1999src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image108.gif"
2000v:shapes="Picture_x0020_54"><![endif]></span></p>
2001
2002<p class=MsoNormal>Press <b style='mso-bidi-font-weight:normal'><span
2003style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2004mso-hansi-theme-font:minor-latin'>OK</span></b>; the entire molecule is drawn.</p>
2005
2006<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2007 id="Picture_x0020_55" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:468pt;
2008 height:403.5pt;visibility:visible;mso-wrap-style:square'>
2009 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image109.png"
2010  o:title=""/>
2011</v:shape><![endif]--><![if !vml]><img width=624 height=538
2012src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image119.gif"
2013v:shapes="Picture_x0020_55"><![endif]></span><span
2014style='mso-spacerun:yes'> </span></p>
2015
2016<p class=MsoNormal>Looks really nice. This ends the tutorial. You can save the
2017project if you wish. All the changes (<span class=SpellE>i.e</span> deleting
2018Map peaks &amp; clearing the map) will be saved.</p>
2019
2020</div>
2021
2022</body>
2023
2024</html>
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