source: Tutorials/TOF Charge Flipping/Charge Flipping with TOF single crystal data in GSASII.htm @ 1687

Last change on this file since 1687 was 1687, checked in by toby, 7 years ago

set more html svn properties

  • Property svn:mime-type set to text/html
File size: 114.7 KB
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405  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 1"/>
406  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 1"/>
407  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 1"/>
408  <w:LsdException Locked="false" SemiHidden="true" Name="Revision"/>
409  <w:LsdException Locked="false" Priority="34" QFormat="true"
410   Name="List Paragraph"/>
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413   Name="Intense Quote"/>
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416  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 1"/>
417  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 1"/>
418  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 1"/>
419  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 1"/>
420  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 1"/>
421  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 1"/>
422  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 2"/>
423  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 2"/>
424  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 2"/>
425  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 2"/>
426  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 2"/>
427  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 2"/>
428  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 2"/>
429  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 2"/>
430  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 2"/>
431  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 2"/>
432  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 2"/>
433  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 2"/>
434  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 2"/>
435  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 2"/>
436  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 3"/>
437  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 3"/>
438  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 3"/>
439  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 3"/>
440  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 3"/>
441  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 3"/>
442  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 3"/>
443  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 3"/>
444  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 3"/>
445  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 3"/>
446  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 3"/>
447  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 3"/>
448  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 3"/>
449  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 3"/>
450  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 4"/>
451  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 4"/>
452  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 4"/>
453  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 4"/>
454  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 4"/>
455  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 4"/>
456  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 4"/>
457  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 4"/>
458  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 4"/>
459  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 4"/>
460  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 4"/>
461  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 4"/>
462  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 4"/>
463  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 4"/>
464  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 5"/>
465  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 5"/>
466  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 5"/>
467  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 5"/>
468  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 5"/>
469  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 5"/>
470  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 5"/>
471  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 5"/>
472  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 5"/>
473  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 5"/>
474  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 5"/>
475  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 5"/>
476  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 5"/>
477  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 5"/>
478  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 6"/>
479  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 6"/>
480  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 6"/>
481  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 6"/>
482  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 6"/>
483  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 6"/>
484  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 6"/>
485  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 6"/>
486  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 6"/>
487  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 6"/>
488  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 6"/>
489  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 6"/>
490  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 6"/>
491  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 6"/>
492  <w:LsdException Locked="false" Priority="19" QFormat="true"
493   Name="Subtle Emphasis"/>
494  <w:LsdException Locked="false" Priority="21" QFormat="true"
495   Name="Intense Emphasis"/>
496  <w:LsdException Locked="false" Priority="31" QFormat="true"
497   Name="Subtle Reference"/>
498  <w:LsdException Locked="false" Priority="32" QFormat="true"
499   Name="Intense Reference"/>
500  <w:LsdException Locked="false" Priority="33" QFormat="true" Name="Book Title"/>
501  <w:LsdException Locked="false" Priority="37" SemiHidden="true"
502   UnhideWhenUsed="true" Name="Bibliography"/>
503  <w:LsdException Locked="false" Priority="39" SemiHidden="true"
504   UnhideWhenUsed="true" QFormat="true" Name="TOC Heading"/>
505  <w:LsdException Locked="false" Priority="41" Name="Plain Table 1"/>
506  <w:LsdException Locked="false" Priority="42" Name="Plain Table 2"/>
507  <w:LsdException Locked="false" Priority="43" Name="Plain Table 3"/>
508  <w:LsdException Locked="false" Priority="44" Name="Plain Table 4"/>
509  <w:LsdException Locked="false" Priority="45" Name="Plain Table 5"/>
510  <w:LsdException Locked="false" Priority="40" Name="Grid Table Light"/>
511  <w:LsdException Locked="false" Priority="46" Name="Grid Table 1 Light"/>
512  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2"/>
513  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3"/>
514  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4"/>
515  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark"/>
516  <w:LsdException Locked="false" Priority="51" Name="Grid Table 6 Colorful"/>
517  <w:LsdException Locked="false" Priority="52" Name="Grid Table 7 Colorful"/>
518  <w:LsdException Locked="false" Priority="46"
519   Name="Grid Table 1 Light Accent 1"/>
520  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 1"/>
521  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 1"/>
522  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 1"/>
523  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 1"/>
524  <w:LsdException Locked="false" Priority="51"
525   Name="Grid Table 6 Colorful Accent 1"/>
526  <w:LsdException Locked="false" Priority="52"
527   Name="Grid Table 7 Colorful Accent 1"/>
528  <w:LsdException Locked="false" Priority="46"
529   Name="Grid Table 1 Light Accent 2"/>
530  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 2"/>
531  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 2"/>
532  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 2"/>
533  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 2"/>
534  <w:LsdException Locked="false" Priority="51"
535   Name="Grid Table 6 Colorful Accent 2"/>
536  <w:LsdException Locked="false" Priority="52"
537   Name="Grid Table 7 Colorful Accent 2"/>
538  <w:LsdException Locked="false" Priority="46"
539   Name="Grid Table 1 Light Accent 3"/>
540  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 3"/>
541  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 3"/>
542  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 3"/>
543  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 3"/>
544  <w:LsdException Locked="false" Priority="51"
545   Name="Grid Table 6 Colorful Accent 3"/>
546  <w:LsdException Locked="false" Priority="52"
547   Name="Grid Table 7 Colorful Accent 3"/>
548  <w:LsdException Locked="false" Priority="46"
549   Name="Grid Table 1 Light Accent 4"/>
550  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 4"/>
551  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 4"/>
552  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 4"/>
553  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 4"/>
554  <w:LsdException Locked="false" Priority="51"
555   Name="Grid Table 6 Colorful Accent 4"/>
556  <w:LsdException Locked="false" Priority="52"
557   Name="Grid Table 7 Colorful Accent 4"/>
558  <w:LsdException Locked="false" Priority="46"
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561  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 5"/>
562  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 5"/>
563  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 5"/>
564  <w:LsdException Locked="false" Priority="51"
565   Name="Grid Table 6 Colorful Accent 5"/>
566  <w:LsdException Locked="false" Priority="52"
567   Name="Grid Table 7 Colorful Accent 5"/>
568  <w:LsdException Locked="false" Priority="46"
569   Name="Grid Table 1 Light Accent 6"/>
570  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 6"/>
571  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 6"/>
572  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 6"/>
573  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 6"/>
574  <w:LsdException Locked="false" Priority="51"
575   Name="Grid Table 6 Colorful Accent 6"/>
576  <w:LsdException Locked="false" Priority="52"
577   Name="Grid Table 7 Colorful Accent 6"/>
578  <w:LsdException Locked="false" Priority="46" Name="List Table 1 Light"/>
579  <w:LsdException Locked="false" Priority="47" Name="List Table 2"/>
580  <w:LsdException Locked="false" Priority="48" Name="List Table 3"/>
581  <w:LsdException Locked="false" Priority="49" Name="List Table 4"/>
582  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark"/>
583  <w:LsdException Locked="false" Priority="51" Name="List Table 6 Colorful"/>
584  <w:LsdException Locked="false" Priority="52" Name="List Table 7 Colorful"/>
585  <w:LsdException Locked="false" Priority="46"
586   Name="List Table 1 Light Accent 1"/>
587  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 1"/>
588  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 1"/>
589  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 1"/>
590  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 1"/>
591  <w:LsdException Locked="false" Priority="51"
592   Name="List Table 6 Colorful Accent 1"/>
593  <w:LsdException Locked="false" Priority="52"
594   Name="List Table 7 Colorful Accent 1"/>
595  <w:LsdException Locked="false" Priority="46"
596   Name="List Table 1 Light Accent 2"/>
597  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 2"/>
598  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 2"/>
599  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 2"/>
600  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 2"/>
601  <w:LsdException Locked="false" Priority="51"
602   Name="List Table 6 Colorful Accent 2"/>
603  <w:LsdException Locked="false" Priority="52"
604   Name="List Table 7 Colorful Accent 2"/>
605  <w:LsdException Locked="false" Priority="46"
606   Name="List Table 1 Light Accent 3"/>
607  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 3"/>
608  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 3"/>
609  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 3"/>
610  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 3"/>
611  <w:LsdException Locked="false" Priority="51"
612   Name="List Table 6 Colorful Accent 3"/>
613  <w:LsdException Locked="false" Priority="52"
614   Name="List Table 7 Colorful Accent 3"/>
615  <w:LsdException Locked="false" Priority="46"
616   Name="List Table 1 Light Accent 4"/>
617  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 4"/>
618  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 4"/>
619  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 4"/>
620  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 4"/>
621  <w:LsdException Locked="false" Priority="51"
622   Name="List Table 6 Colorful Accent 4"/>
623  <w:LsdException Locked="false" Priority="52"
624   Name="List Table 7 Colorful Accent 4"/>
625  <w:LsdException Locked="false" Priority="46"
626   Name="List Table 1 Light Accent 5"/>
627  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 5"/>
628  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 5"/>
629  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 5"/>
630  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 5"/>
631  <w:LsdException Locked="false" Priority="51"
632   Name="List Table 6 Colorful Accent 5"/>
633  <w:LsdException Locked="false" Priority="52"
634   Name="List Table 7 Colorful Accent 5"/>
635  <w:LsdException Locked="false" Priority="46"
636   Name="List Table 1 Light Accent 6"/>
637  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 6"/>
638  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 6"/>
639  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 6"/>
640  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 6"/>
641  <w:LsdException Locked="false" Priority="51"
642   Name="List Table 6 Colorful Accent 6"/>
643  <w:LsdException Locked="false" Priority="52"
644   Name="List Table 7 Colorful Accent 6"/>
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1163<div class=WordSection1>
1164
1165<h1><span style='mso-fareast-font-family:"Times New Roman"'>Charge flipping
1166with neutron TOF single crystal data<o:p></o:p></span></h1>
1167
1168<p class=MsoNormal>In this exercise you will use GSAS-II to solve the structure
1169of <span class=SpellE>rubrene</span> (C<sub>42</sub>H<sub>28</sub>) from single
1170crystal neutron data via charge flipping. <span class=SpellE>Rubrene</span> is of
1171interest as a molecular semiconductor. It crystallizes in the space group <span
1172class=SpellE>Cmca</span> with the lattice parameters a=26.798Å, b=7.1618Å,
1173c=14.1942Å, Z=4. Thus, the molecule is sited on a special position with 2/m
1174symmetry. If you have not done so already, <a href="Starting%20GSAS.htm">start
1175GSAS-II</a>.</p>
1176
1177<h2>Step 1. Set the phase information</h2>
1178
1179<p class=MsoNormal>To begin this tutorial, do <b style='mso-bidi-font-weight:
1180normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1181minor-latin;mso-hansi-theme-font:minor-latin'>Data/Add phase</span></b> in the
1182main GSAS-II data tree menu. A popup window will appear asking for a phase
1183name; I used <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1184style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1185mso-hansi-theme-font:minor-latin'>rubrene</span></b></span>. Then select <span
1186class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1187"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1188minor-latin'>rubrene</span></b></span> from the data tree</p>
1189
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1213  o:title=""/>
1214</v:shape><![endif]--><![if !vml]><img border=0 width=400 height=250
1215src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image002.gif"
1216v:shapes="_x0000_i1059"><![endif]></span></p>
1217
1218<p class=MsoNormal>The General tab for this phase will be shown</p>
1219
1220<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1221 id="Picture_x0020_2" o:spid="_x0000_i1058" type="#_x0000_t75" style='width:640.5pt;
1222 height:375pt;visibility:visible;mso-wrap-style:square'>
1223 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image003.png"
1224  o:title=""/>
1225</v:shape><![endif]--><![if !vml]><img border=0 width=854 height=500
1226src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image004.gif"
1227v:shapes="Picture_x0020_2"><![endif]></span></p>
1228
1229<p class=MsoNormal>Enter the space group (<b style='mso-bidi-font-weight:normal'><span
1230style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1231mso-hansi-theme-font:minor-latin'>C m c a</span></b> – don’t forget the spaces)
1232and press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1233mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Enter</span></b>.
1234A popup with Space group information will appear</p>
1235
1236<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1237 id="Picture_x0020_3" o:spid="_x0000_i1057" type="#_x0000_t75" style='width:250.5pt;
1238 height:177.75pt;visibility:visible;mso-wrap-style:square'>
1239 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image005.png"
1240  o:title=""/>
1241</v:shape><![endif]--><![if !vml]><img border=0 width=334 height=237
1242src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image006.gif"
1243v:shapes="Picture_x0020_3"><![endif]></span></p>
1244
1245<p class=MsoNormal>Press <b style='mso-bidi-font-weight:normal'><span
1246style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1247mso-hansi-theme-font:minor-latin'>OK</span></b>; the General tab will be
1248repainted with defaults for the orthorhombic lattice parameters. Enter <b
1249style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1250mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>26.798</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'>a</span></b>,
1253<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'>7.1618</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'>b</span></b>
1257and <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'>14.1942</span></b>
1259for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1260mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>c</span></b>.
1261Press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1262mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Enter</span></b>,
1263the unit cell volume (2724.178) will be updated.</p>
1264
1265<h2>Step 2. Import the data</h2>
1266
1267<p class=MsoNormal>The <span class=SpellE>rubrene</span> data were collected on
1268the TOPAZ instrument at the SNS Facility, Oak Ridge National Laboratory with 23
1269different crystal orientations; the local instrument data processing software
1270has applied corrections and combined them into a single multicolumn <span
1271class=SpellE>hkl</span> file. To import this do <b style='mso-bidi-font-weight:
1272normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1273minor-latin;mso-hansi-theme-font:minor-latin'>Import/Structure Factor/from
1274Neutron TOF HKL F2 file</span></b>; a directory dialog box will appear. Go to
1275the directory <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1276style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1277mso-hansi-theme-font:minor-latin'>GSASIIexercises</span></b></span><b
1278style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1279mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>/TOF Charge
1280Flipping</span></b> and select the file <span class=SpellE><b style='mso-bidi-font-weight:
1281normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1282minor-latin;mso-hansi-theme-font:minor-latin'>ruberene_orthoC.hkl</span></b></span>
1283(double click the name or press the <b style='mso-bidi-font-weight:normal'><span
1284style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1285mso-hansi-theme-font:minor-latin'>Open</span></b> button after selecting it). A
1286popup box will appear.</p>
1287
1288<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1289 id="Picture_x0020_4" o:spid="_x0000_i1056" type="#_x0000_t75" style='width:357.75pt;
1290 height:265.5pt;visibility:visible;mso-wrap-style:square'>
1291 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image007.png"
1292  o:title=""/>
1293</v:shape><![endif]--><![if !vml]><img border=0 width=477 height=354
1294src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image008.gif"
1295v:shapes="Picture_x0020_4"><![endif]></span></p>
1296
1297<p class=MsoNormal>Press <span class=GramE><b style='mso-bidi-font-weight:normal'><span
1298style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1299mso-hansi-theme-font:minor-latin'>Yes</span></b></span>; another popup will
1300appear offering you the chance to change the name. Press <b style='mso-bidi-font-weight:
1301normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1302minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>, a new popup
1303appears.</p>
1304
1305<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1306 id="Picture_x0020_5" o:spid="_x0000_i1055" type="#_x0000_t75" style='width:240pt;
1307 height:232.5pt;visibility:visible;mso-wrap-style:square'>
1308 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image009.png"
1309  o:title=""/>
1310</v:shape><![endif]--><![if !vml]><img border=0 width=320 height=310
1311src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image010.gif"
1312v:shapes="Picture_x0020_5"><![endif]></span></p>
1313
1314<p class=MsoNormal>Here you select the phase the data belongs to. There is only
1315<span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1316style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1317mso-hansi-theme-font:minor-latin'>rubrene</span></b></span> so select it and
1318press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1319mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1320The bottom of the data tree is shown, a small data window and the plot shows
1321the l=0 slice of the last reflection set loaded (HKLF rubrene_orthoC.hkl_22).</p>
1322
1323<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1324 id="Picture_x0020_6" o:spid="_x0000_i1054" type="#_x0000_t75" style='width:525pt;
1325 height:450pt;visibility:visible;mso-wrap-style:square'>
1326 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image011.png"
1327  o:title=""/>
1328</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1329src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image012.gif"
1330v:shapes="Picture_x0020_6"><![endif]></span></p>
1331
1332<p class=MsoNormal>The <b style='mso-bidi-font-weight:normal'><span
1333style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1334mso-hansi-theme-font:minor-latin'>K</span></b> box control allows you to select
1335other zones &amp; layers to view. The drawing geometry is strictly square (i.e.
1336not in reciprocal space units). If you do <b style='mso-bidi-font-weight:normal'><span
1337style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1338mso-hansi-theme-font:minor-latin'>Commands/Plot 3D HKLs</span></b>, a 3D plot
1339of reciprocal space is shown</p>
1340
1341<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1342 id="Picture_x0020_1" o:spid="_x0000_i1053" type="#_x0000_t75" style='width:446.25pt;
1343 height:381.75pt;visibility:visible;mso-wrap-style:square'>
1344 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image013.png"
1345  o:title="" croptop="13337f" cropbottom="14997f" cropleft="41056f"
1346  cropright="9449f"/>
1347</v:shape><![endif]--><![if !vml]><img border=0 width=595 height=509
1348src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image014.jpg"
1349v:shapes="Picture_x0020_1"><![endif]></span></p>
1350
1351<p class=MsoNormal>The size of the green boxes is proportional to the structure
1352factors; the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1353"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1354minor-latin'>save as/key</span></b> pulldown will give you other viewing
1355options. Here is a good place to save the GSAS-II project for <span
1356class=SpellE>rubrene</span>. Do <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'>File/Save project</span></b> from the main
1359GSAS-II data tree window; a file dialog box will appear. Enter a file name (I
1360used <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1361style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1362mso-hansi-theme-font:minor-latin'>rubrene</span></b></span> – no extension).</p>
1363
1364<h2>Step 3. Setup for charge flipping</h2>
1365
1366<p class=MsoNormal>We have two tasks here. One is to select the reflection sets
1367to be used in the calculations and the other is to set some controls. To begin
1368select the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1369style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1370mso-hansi-theme-font:minor-latin'>rubrene</span></b></span> phase entry in the
1371GSAS-II data tree; the General tab will appear in the Phase Data for <span
1372class=SpellE>rubrene</span> window</p>
1373
1374<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1375 id="Picture_x0020_8" o:spid="_x0000_i1052" type="#_x0000_t75" style='width:489pt;
1376 height:375pt;visibility:visible;mso-wrap-style:square'>
1377 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image015.png"
1378  o:title=""/>
1379</v:shape><![endif]--><![if !vml]><img border=0 width=652 height=500
1380src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image016.gif"
1381v:shapes="Picture_x0020_8"><![endif]></span></p>
1382
1383<p class=MsoNormal>In the Charge flip controls (about center of the page) press
1384the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1385mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Select
1386reflection sets</span></b> button; a <b style='mso-bidi-font-weight:normal'><span
1387style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1388mso-hansi-theme-font:minor-latin'>Use data</span></b> popup will appear. You
1389will want to use all the HKLF data sets; press <b style='mso-bidi-font-weight:
1390normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1391minor-latin;mso-hansi-theme-font:minor-latin'>Set All</span> </b>and press <b
1392style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1393mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1394The General tab will be refreshed. GSAS-II will use all the data to build a
1395reflection set for charge flipping. For duplicate <span class=SpellE>hkls</span>
1396the last one encountered will be used. Since atoms are essentially point <span
1397class=SpellE>scatterers</span> for neutrons, a charge flip map has very sharp
1398peaks so a better choice for the <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'>k-factor</span></b> (charge flip level) might
1401be <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1402mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0.5</span></b>,
1403the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1404mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>k-max</span></b>
1405should be larger (say <b style='mso-bidi-font-weight:normal'><span
1406style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1407mso-hansi-theme-font:minor-latin'>50</span></b>) and the map <b
1408style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1409mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Resolution</span></b>
1410should be smaller (say <b style='mso-bidi-font-weight:normal'><span
1411style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1412mso-hansi-theme-font:minor-latin'>0.4</span></b>). Set these three values. In
1413the Fourier map controls, set <b style='mso-bidi-font-weight:normal'><span
1414style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1415mso-hansi-theme-font:minor-latin'>Peak cutoff %</span></b> to <b
1416style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1417mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>20</span></b>;
1418this sets the lower limit of the peak search in the charge flip map. When done
1419the General tab should look like</p>
1420
1421<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1422 id="_x0000_i1051" type="#_x0000_t75" style='width:516.75pt;height:375pt;
1423 visibility:visible;mso-wrap-style:square'>
1424 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image017.png"
1425  o:title=""/>
1426</v:shape><![endif]--><![if !vml]><img border=0 width=689 height=500
1427src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image018.gif"
1428v:shapes="_x0000_i1051"><![endif]></span></p>
1429
1430<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1431
1432<h2>Step 4. Charge flipping</h2>
1433
1434<p class=MsoNormal>We are now ready for charge flipping. In the General tab
1435menu do <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1436mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/Charge
1437flipping</span></b>; a Charge flipping progress bar will appear showing the
1438residual and cycle count for the charge flipping calculation. In this case the
1439residual quickly drops to ~38% and stays there. Press <b style='mso-bidi-font-weight:
1440normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1441minor-latin;mso-hansi-theme-font:minor-latin'>Cancel</span></b> to stop the
1442calculation; some information will be printed on the console and after a pause
1443the Phase Data window will show <b style='mso-bidi-font-weight:normal'><span
1444style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1445mso-hansi-theme-font:minor-latin'>Map Peaks</span></b> and the plot window will
1446show a drawing of the obtained structure.</p>
1447
1448<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1449 id="_x0000_i1050" type="#_x0000_t75" style='width:375pt;height:225pt;
1450 visibility:visible;mso-wrap-style:square'>
1451 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image019.png"
1452  o:title=""/>
1453</v:shape><![endif]--><![if !vml]><img border=0 width=500 height=300
1454src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image020.gif"
1455v:shapes="_x0000_i1050"><![endif]></span></p>
1456
1457<p class=MsoNormal>If you scroll down the Map peak list you will find some with
1458negative magnitudes at the end of the list. GSAS-II searches the map for both
1459positive and negative peaks; the former are C-atoms and the latter are H-atoms.
1460</p>
1461
1462<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1463 id="Picture_x0020_11" o:spid="_x0000_i1049" type="#_x0000_t75" style='width:6in;
1464 height:365.25pt;visibility:visible;mso-wrap-style:square'>
1465 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image021.png"
1466  o:title="" croptop="9820f" cropbottom="18705f" cropleft="43453f" cropright="6999f"/>
1467</v:shape><![endif]--><![if !vml]><img border=0 width=576 height=487
1468src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image022.jpg"
1469v:shapes="Picture_x0020_11"><![endif]></span></p>
1470
1471<p class=MsoNormal>The plot (which I’ve rotated around a bit) shows white spots
1472for the positive peaks and red ones for the negative ones; bonds are white
1473lines. The case I’ve drawn here shows a problem with this charge flip solution.
1474While the charge flipping run has clearly found all the C-atoms and some of the
1475H-atoms, the molecule is incorrectly placed in the unit cell. To fix this you
1476could simply repeat the charge flipping run and hope it puts the molecule in
1477the right place. GSAS-II uses an algorithm based on how structure factor phases
1478are related for a given space group to reposition the solution; it sometimes fails
1479if the phase set isn’t perfect. Or you can “roll” the map right/left/up/down (<b
1480style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1481mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>R/L/U/D</span></b>
1482keys) to put the solution where you want. In this case a few steps with the
1483L-key sufficed to put the molecule on a 2/m site (i.e. the center of the cell
1484indicated the multicolored cross on the central C-C bond).</p>
1485
1486<p class=MsoNormal><!--[if gte vml 1]><v:shapetype id="_x0000_t32" coordsize="21600,21600"
1487 o:spt="32" o:oned="t" path="m,l21600,21600e" filled="f">
1488 <v:path arrowok="t" fillok="f" o:connecttype="none"/>
1489 <o:lock v:ext="edit" shapetype="t"/>
1490</v:shapetype><v:shape id="Straight_x0020_Arrow_x0020_Connector_x0020_38"
1491 o:spid="_x0000_s1027" type="#_x0000_t32" style='position:absolute;
1492 margin-left:205.5pt;margin-top:193.5pt;width:15.75pt;height:29.25pt;flip:y;
1493 z-index:251660288;visibility:visible;mso-wrap-style:square;
1494 mso-width-percent:0;mso-height-percent:0;mso-wrap-distance-left:9pt;
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1591
1592<p class=MsoNormal>Notice that as the map is rolled, the Map peak positions are
1593shifted to match the change in positions.</p>
1594
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1603
1604<p class=MsoNormal>By carefully looking at the map, you can see the 4-ring <span
1605class=SpellE>tetracene</span> (<span class=SpellE>naphthacene</span>) core of
1606the molecule with four phenyl groups attached to both sides on the center two rings.
1607The unique part consists of 1/4<sup>th</sup> of this group (i.e. half of one
1608side of the <span class=SpellE>tetracene</span> and one phenyl); one C-atom
1609sits on a 2-fold and the rest are in general positions. The molecule extends
1610into the neighboring unit cell so you don’t see the whole thing as one group
1611but has two bits on either side (I’ve marked these with arrows above).</p>
1612
1613<h2>Step 5. Peak selection</h2>
1614
1615<p class=MsoNormal>GSAS-II provides several ways of selecting peak positions
1616from a charge flipping map. One way is to pick them directly from the drawing.
1617Place the cursor on one peak and do a <b style='mso-bidi-font-weight:normal'><span
1618style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1619mso-hansi-theme-font:minor-latin'>Shift left mouse button</span></b>; it will
1620be highlighted on the list and it will turn green on the plot. Do a <b
1621style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1622mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Shift right
1623mouse button</span></b> on the remaining peaks you want to <span class=GramE>pick.</span>
1624All will turn green (you may have to wiggle the plot a bit with the mouse to
1625make them show) and all will be highlighted in the list. Alternatively, you can
1626select the entire list of peaks (double click on upper left empty box of the
1627table), then do <b style='mso-bidi-font-weight:normal'><span style='font-family:
1628"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1629minor-latin'>Map peaks/Unique peaks</span></b>. Better still you can sort the
1630peaks by one of the column headings and then do <b style='mso-bidi-font-weight:
1631normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1632minor-latin;mso-hansi-theme-font:minor-latin'>Map peaks/Unique peaks</span></b>.
1633I’ve chosen to sort the peaks on <span class=SpellE><b style='mso-bidi-font-weight:
1634normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1635minor-latin;mso-hansi-theme-font:minor-latin'>dcent</span></b></span> (distance
1636from center of the cell) beforehand. After a pause while it sorts out the
1637unique peaks, it will highlight them in the table and display the picked ones
1638in green on the plot. In this case they will probably be scattered about the
1639unit cell and not make a continuous molecule, but they are largely clustered
1640around the unit cell center. My plot looked like this when I was done.</p>
1641
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1651
1652<p class=MsoNormal>The list has them highlighted (the rest are lower down in my
1653list; all 18 atoms were found in this charge flipping result)</p>
1654
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1662v:shapes="_x0000_i1045"><![endif]></span></p>
1663
1664<p class=MsoNormal>To add them to the Atom list do <b style='mso-bidi-font-weight:
1665normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1666minor-latin;mso-hansi-theme-font:minor-latin'>Map peaks/Move peaks</span></b>;
1667the drawing will show white balls for them.</p>
1668
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1670 id="_x0000_i1044" type="#_x0000_t75" style='width:6in;height:369pt;
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1673  o:title="" croptop="10579f" cropbottom="17404f" cropleft="37800f"
1674  cropright="12584f"/>
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1678
1679<p class=MsoNormal>The atom list will give the magnitudes as ‘M’ names; I found
1680all 11 C-atoms and 7 H-atoms that were expected.</p>
1681
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1690
1691<h2>Step 6. Atom identification</h2>
1692
1693<p class=MsoNormal>You can reorder the atoms in the list; do an <b
1694style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1695mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Alt select</span></b>
1696for the atom row you want to move. Then do an <b style='mso-bidi-font-weight:
1697normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1698minor-latin;mso-hansi-theme-font:minor-latin'>Alt select</span></b> on the row
1699where you want the moved atom to precede it. This way you can put the C-atoms
1700first and the H-atoms last in the list instead of mixed up as in the above
1701list. Next select all the positive M peaks (pick the top one and then <b
1702style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1703mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Shift</span></b>
1704pick the last one). Do <b style='mso-bidi-font-weight:normal'><span
1705style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1706mso-hansi-theme-font:minor-latin'>Edit/Modify atom parameters</span></b> from
1707the Atoms menu; a popup will appear. Pick <b style='mso-bidi-font-weight:normal'><span
1708style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1709mso-hansi-theme-font:minor-latin'>Type</span></b> and press <b
1710style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1711mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>;
1712a Periodic Table will appear. Select <b style='mso-bidi-font-weight:normal'><span
1713style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1714mso-hansi-theme-font:minor-latin'>C</span></b> from the C-atom pulldown. All
1715the C-atom names and types will change. You should also move the C-atom with
17162(x) site symmetry to the top of the list.</p>
1717
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1720 visibility:visible;mso-wrap-style:square'>
1721 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image037.png"
1722  o:title=""/>
1723</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=300
1724src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image038.gif"
1725v:shapes="_x0000_i1042"><![endif]></span></p>
1726
1727<p class=MsoNormal>Do the same with the remaining negative M atoms – make them
1728H atoms. The drawing shows molecular fragments scattered about the unit cell;
1729you’d like to unify them into a single molecule. Select the C-atom with 2(x)
1730site symmetry (although any would do). Do <b style='mso-bidi-font-weight:normal'><span
1731style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1732mso-hansi-theme-font:minor-latin'>Edit/Assemble molecule</span></b> from the
1733Atoms menu; a popup will appear offering choices for Bond radii (&amp; Angle
1734radii – ignored here). Press <b style='mso-bidi-font-weight:normal'><span
1735style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1736mso-hansi-theme-font:minor-latin'>Ok</span></b>; the Atom table will be revised
1737and the plot will show an assembled molecule (the picked starting atom in
1738green). </p>
1739
1740<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1741 id="_x0000_i1041" type="#_x0000_t75" style='width:6in;height:366pt;
1742 visibility:visible;mso-wrap-style:square'>
1743 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image039.png"
1744  o:title="" croptop="11018f" cropbottom="17360f" cropleft="37831f"
1745  cropright="12587f"/>
1746</v:shape><![endif]--><![if !vml]><img border=0 width=576 height=488
1747src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image040.jpg"
1748v:shapes="_x0000_i1041"><![endif]></span></p>
1749
1750<p class=MsoNormal>The molecule building has scrambled the order of the atoms;
1751they were located in order as the molecule was built. </p>
1752
1753<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1754 id="_x0000_i1040" type="#_x0000_t75" style='width:525pt;height:351.75pt;
1755 visibility:visible;mso-wrap-style:square'>
1756 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image041.png"
1757  o:title=""/>
1758</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=469
1759src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image042.gif"
1760v:shapes="_x0000_i1040"><![endif]></span></p>
1761
1762<p class=MsoNormal>You can reorder them to put the H-atoms at the end of the list.
1763Then select all of them and then do <span style='font-family:"Calibri",sans-serif;
1764mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Modify
1765atom parameters</span>. Pick <b style='mso-bidi-font-weight:normal'><span
1766style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1767mso-hansi-theme-font:minor-latin'>Name</span></b> from the pulldown and press <b
1768style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1769mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1770You are asked if you really want to do this, press <span class=GramE><b
1771style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1772mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Yes</span></b></span>.
1773The atoms are then renamed in numeric order.</p>
1774
1775<h2>Step 7. Refinement</h2>
1776
1777<p class=MsoNormal>Since the structure is complete, we can do the full
1778refinement. Select the <b style='mso-bidi-font-weight:normal'><span
1779style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1780mso-hansi-theme-font:minor-latin'>Controls</span></b> item from the GSAS-II
1781data tree. Unset the <b style='mso-bidi-font-weight:normal'><span
1782style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1783mso-hansi-theme-font:minor-latin'>Refine HKLF as F^2</span></b> box and enter <b
1784style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1785mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>3.0</span></b>
1786for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1787mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Min <span
1788class=SpellE>obs</span>/sig</span></b>. This makes the least squares refine on <span
1789class=SpellE><span class=GramE>F<sub>o</sub></span></span> with 3&#963; cutoff
1790on <span class=SpellE>F<sub>o</sub></span>. From the main GSAS-II data tree menu
1791do <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1792mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>;
1793this will do the 1<sup>st</sup> least squares refinement varying only the data
1794set scale factors. A progress bar popup will appear showing the residuals as
1795the refinement proceeds. When done, a small popup will appear with the final
1796residual; press <b style='mso-bidi-font-weight:normal'><span style='font-family:
1797"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1798minor-latin'>OK</span></b> to accept it. The final <span class=SpellE>R<sub>w</sub></span>
1799is about 49% Go to the <b style='mso-bidi-font-weight:normal'><span
1800style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1801mso-hansi-theme-font:minor-latin'>Atoms</span></b> tab for the <span
1802class=SpellE>rubrene</span> phase, double click the <b style='mso-bidi-font-weight:
1803normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1804minor-latin;mso-hansi-theme-font:minor-latin'>refine</span></b> column heading;
1805a popup box will appear. Select both <b style='mso-bidi-font-weight:normal'><span
1806style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1807mso-hansi-theme-font:minor-latin'>X - coordinates</span></b> and <b
1808style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1809mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>U – thermal
1810parameters</span></b> and press <b style='mso-bidi-font-weight:normal'><span
1811style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1812mso-hansi-theme-font:minor-latin'>OK</span></b>. The atom table will show refine
1813flags for each atom.</p>
1814
1815<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1816 id="_x0000_i1039" type="#_x0000_t75" style='width:525pt;height:225pt;
1817 visibility:visible;mso-wrap-style:square'>
1818 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image043.png"
1819  o:title=""/>
1820</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=300
1821src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image044.gif"
1822v:shapes="_x0000_i1039"><![endif]></span></p>
1823
1824<p class=MsoNormal>Then repeat the <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> command in the
1827main menu. The final residual will be much better <span class=SpellE>R<sub>w</sub></span>
1828~10%. Next, convert all the atoms from isotropic thermal parameters to
1829anisotropic ones. Double click <span class=GramE>the <b style='mso-bidi-font-weight:
1830normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1831minor-latin;mso-hansi-theme-font:minor-latin'>I</span></b></span><b
1832style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1833mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>/A</span></b>
1834column heading and select <b style='mso-bidi-font-weight:normal'><span
1835style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1836mso-hansi-theme-font:minor-latin'>Anisotropic</span></b> and press <b
1837style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1838mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1839Then repeat <b style='mso-bidi-font-weight:normal'><span style='font-family:
1840"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1841minor-latin'>Calculate/Refine</span></b> (perhaps twice); the final <span
1842class=SpellE>R<sub>w</sub></span> ~6.06% which is quite nice.</p>
1843
1844<h2>Step 8. Further work</h2>
1845
1846<p class=MsoNormal>Since this is TOF neutron single crystal diffraction, a
1847relatively large crystal was used and the neutron wavelength covered a fairly
1848wide range of values. Hence, it is likely that the strong reflection intensities
1849suffered from some level of extinction. To find these parameters select the <b
1850style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1851mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Data</span></b>
1852tab in the Phase Data window; all that will show is a list of a data set names
1853with a <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1854mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Show</span></b>
1855box for each. To see what is there select the <b style='mso-bidi-font-weight:
1856normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1857minor-latin;mso-hansi-theme-font:minor-latin'>Show</span></b> box; alternatively
1858to see all of them do <b style='mso-bidi-font-weight:normal'><span
1859style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1860mso-hansi-theme-font:minor-latin'>Edit/Show/Hide</span></b> all the window will
1861look something like</p>
1862
1863<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1864 id="Picture_x0020_22" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:319.5pt;
1865 height:378pt;visibility:visible;mso-wrap-style:square'>
1866 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image045.png"
1867  o:title=""/>
1868</v:shape><![endif]--><![if !vml]><img border=0 width=426 height=504
1869src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image046.gif"
1870v:shapes="Picture_x0020_22"><![endif]></span></p>
1871
1872<p class=MsoNormal>This is a very long display with entries for 23 data sets
1873(NB: in alphabetical order not numeric order!). The Scale factors were selected
1874for refinement by default (box checked). Here you want to select <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'>Primary</span></b>
1877for the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1878mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Extinction
1879type</span></b> (later you can try the other models) for the 1<sup>st</sup>
1880data set. The window will be repainted with a new line in the data display. Select
1881the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1882mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Ep</span></b>
1883check box so it will be refined. To set all the rest press 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'>Copy flags?</span></b>
1886<span class=GramE>button</span> for that data set (not one of the others!). A
1887popup will appear giving the list of data sets; press the <span class=SpellE><b
1888style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1889mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>SetAll</span></b></span>
1890button and then <b style='mso-bidi-font-weight:normal'><span style='font-family:
1891"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1892minor-latin'>OK</span></b>. The data window will be repainted with all the
1893Extinction types set to Primary and Ep set to refine. You could then do <b
1894style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1895mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>
1896but it might be better to constrain all the Ep values to be the same. To do
1897this select <b style='mso-bidi-font-weight:normal'><span style='font-family:
1898"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1899minor-latin'>Constraints</span></b> from the GSASII data tree. A blank window
1900with tabs will appear.</p>
1901
1902<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1903 id="Picture_x0020_23" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:225pt;
1904 height:352.5pt;visibility:visible;mso-wrap-style:square'>
1905 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image047.png"
1906  o:title=""/>
1907</v:shape><![endif]--><![if !vml]><img border=0 width=300 height=470
1908src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image048.gif"
1909v:shapes="Picture_x0020_23"><![endif]></span></p>
1910
1911<p class=MsoNormal>Select the <b style='mso-bidi-font-weight:normal'><span
1912style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1913mso-hansi-theme-font:minor-latin'>Histogram/Phase</span></b> constraints tab; the
1914window is still blank but that tab is now highlighted. Next do <b
1915style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1916mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Add
1917equivalence</span></b>; a popup will appear asking for a parameter name to be
1918constrained.</p>
1919
1920<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1921 id="Picture_x0020_24" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:468.75pt;
1922 height:300pt;visibility:visible;mso-wrap-style:square'>
1923 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image049.png"
1924  o:title=""/>
1925</v:shape><![endif]--><![if !vml]><img border=0 width=625 height=400
1926src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image050.gif"
1927v:shapes="Picture_x0020_24"><![endif]></span></p>
1928
1929<p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span
1930style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1931mso-hansi-theme-font:minor-latin'>0:0<span class=GramE>:Ep</span></span></b>,
1932that is the primary extinction parameter for the 1<sup>st</sup> dataset and the
1933<span class=SpellE>rubrene</span> phase. Press <b style='mso-bidi-font-weight:
1934normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1935minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.</p>
1936
1937<p class=MsoNormal>The popup is replaced with a new list of all compatible
1938parameters that <b style='mso-bidi-font-weight:normal'><span style='font-family:
1939"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1940minor-latin'>0:0<span class=GramE>:Ep</span></span></b> is to be made
1941equivalent to. Scroll down and find <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'>0<span class=GramE>:all:Ep</span></span></b>
1944and pick that; the Constraint window will change to</p>
1945
1946<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1947 id="Picture_x0020_25" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:481.5pt;
1948 height:352.5pt;visibility:visible;mso-wrap-style:square'>
1949 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image051.png"
1950  o:title=""/>
1951</v:shape><![endif]--><![if !vml]><img border=0 width=642 height=470
1952src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image052.gif"
1953v:shapes="Picture_x0020_25"><![endif]></span></p>
1954
1955<p class=MsoNormal>This shows the constraint making Ep for all 23 data sets
1956equivalent to a single variable. Do <b style='mso-bidi-font-weight:normal'><span
1957style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1958mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; my <span
1959class=SpellE>R<sub>w</sub></span> was 5.907% only a slight improvement. You may
1960wish to try the other extinction models. Do remember to delete the unused
1961constraint before adding a new one for the different extinction parameter.
1962Finally you can draw the molecule; go to <b style='mso-bidi-font-weight:normal'><span
1963style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1964mso-hansi-theme-font:minor-latin'>Atoms</span></b> and do <b style='mso-bidi-font-weight:
1965normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1966minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Reload draw atoms</span></b>.
1967That will put the newest atom parameters into the Draw Atoms table. Select <b
1968style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1969mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Draw Atoms</span></b>.
1970Select the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1971"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1972minor-latin'>Style</span></b> column heading; a popup will appear</p>
1973
1974<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1975 id="Picture_x0020_26" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:259.5pt;
1976 height:252pt;visibility:visible;mso-wrap-style:square'>
1977 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image053.png"
1978  o:title=""/>
1979</v:shape><![endif]--><![if !vml]><img border=0 width=346 height=336
1980src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image054.gif"
1981v:shapes="Picture_x0020_26"><![endif]></span></p>
1982
1983<p class=MsoNormal>Notice the first line is blank, if you select that all the
1984atoms will vanish! Select <b style='mso-bidi-font-weight:normal'><span
1985style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1986mso-hansi-theme-font:minor-latin'>ellipsoids</span></b> and press <b
1987style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1988mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1989The plot will change, but it is pretty cluttered.</p>
1990
1991<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1992 id="Picture_x0020_28" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:465.75pt;
1993 height:395.25pt;visibility:visible;mso-wrap-style:square'>
1994 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image055.png"
1995  o:title="" croptop="11745f" cropbottom="16560f" cropleft="43690f"
1996  cropright="6723f"/>
1997</v:shape><![endif]--><![if !vml]><img border=0 width=621 height=527
1998src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image056.jpg"
1999v:shapes="Picture_x0020_28"><![endif]></span></p>
2000
2001<p class=MsoNormal>You can remove the Map peaks atoms; go to the <b
2002style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2003mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map peaks</span></b>
2004tab and do <b style='mso-bidi-font-weight:normal'><span style='font-family:
2005"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2006minor-latin'>Map peaks/clear peaks</span></b> from the menu. The list will be
2007erased and the plot will just show the molecule. You can also remove the unit
2008cell edges, go to <b style='mso-bidi-font-weight:normal'><span
2009style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2010mso-hansi-theme-font:minor-latin'>Draw Options</span></b> and uncheck the <b
2011style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2012mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Show unit
2013cell?</span></b> <span class=GramE>box</span>. Finally, you can remove the
2014charge flipping map; go to <b style='mso-bidi-font-weight:normal'><span
2015style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2016mso-hansi-theme-font:minor-latin'>General</span></b> and do <b
2017style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2018mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/Clear
2019map</span></b>. That deletes the scattering density map and the drawing will be
2020free of any clutter.</p>
2021
2022<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2023 id="Picture_x0020_29" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:429.75pt;
2024 height:366pt;visibility:visible;mso-wrap-style:square'>
2025 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image057.png"
2026  o:title="" croptop="8339f" cropbottom="19928f" cropleft="44139f" cropright="6324f"/>
2027</v:shape><![endif]--><![if !vml]><img border=0 width=573 height=488
2028src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image058.jpg"
2029v:shapes="Picture_x0020_29"><![endif]></span></p>
2030
2031<p class=MsoNormal>Remember that this is only 1/4<sup>th</sup> of the molecule,
2032we’d like to see the whole thing. First go to the <b style='mso-bidi-font-weight:
2033normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2034minor-latin;mso-hansi-theme-font:minor-latin'>Atoms</span></b> tab and select the
2035C-atom that is in a special position 2(x). The do <b style='mso-bidi-font-weight:
2036normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2037minor-latin;mso-hansi-theme-font:minor-latin'>Compute/Show Distances &amp;
2038Angles</span></b> and respond <b style='mso-bidi-font-weight:normal'><span
2039style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2040mso-hansi-theme-font:minor-latin'>OK</span></b> to the popup. The important
2041result is on the console</p>
2042
2043<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2044 id="Picture_x0020_30" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:609.75pt;
2045 height:278.25pt;visibility:visible;mso-wrap-style:square'>
2046 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image059.png"
2047  o:title=""/>
2048</v:shape><![endif]--><![if !vml]><img border=0 width=813 height=371
2049src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image060.gif"
2050v:shapes="Picture_x0020_30"><![endif]></span></p>
2051
2052<p class=MsoNormal>This gives the bond distances and angles about the <span
2053class=GramE>C(</span>1) atom. Particularly note the cell<span class=GramE>+(</span>sym.
2054Op.) information; we will use this to build the drawing. Go to the <b
2055style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2056mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Draw Atoms</span></b>
2057tab and select all the atoms (double click on the upper left box). You should
2058see all atoms selected</p>
2059
2060<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2061 id="Picture_x0020_31" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:450pt;
2062 height:225pt;visibility:visible;mso-wrap-style:square'>
2063 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image061.png"
2064  o:title=""/>
2065</v:shape><![endif]--><![if !vml]><img border=0 width=600 height=300
2066src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image062.gif"
2067v:shapes="Picture_x0020_31"><![endif]></span></p>
2068
2069<p class=MsoNormal>Then do <b style='mso-bidi-font-weight:normal'><span
2070style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2071mso-hansi-theme-font:minor-latin'>Edit/Add atoms</span></b>; a popup will
2072appear</p>
2073
2074<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2075 id="Picture_x0020_32" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:179.25pt;
2076 height:246.75pt;visibility:visible;mso-wrap-style:square'>
2077 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image063.png"
2078  o:title=""/>
2079</v:shape><![endif]--><![if !vml]><img border=0 width=239 height=329
2080src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image064.gif"
2081v:shapes="Picture_x0020_32"><![endif]></span></p>
2082
2083<p class=MsoNormal>Based on the 1<sup>st</sup> entry in the bond distance table
2084‘<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2085mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>[1 0 0<span
2086class=GramE>]<span style='mso-spacerun:yes'>  </span>+</span>(<span
2087style='mso-spacerun:yes'>  </span>2)</span></b>’, select the controls for the 2<sup>nd</sup>
2088operator and increment the 1<sup>st</sup> unit cell</p>
2089
2090<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2091 id="Picture_x0020_33" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:179.25pt;
2092 height:246.75pt;visibility:visible;mso-wrap-style:square'>
2093 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image065.png"
2094  o:title=""/>
2095</v:shape><![endif]--><![if !vml]><img border=0 width=239 height=329
2096src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image066.gif"
2097v:shapes="Picture_x0020_33"><![endif]></span></p>
2098
2099<p class=MsoNormal>Press OK. The plot now shows œ the molecule.</p>
2100
2101<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2102 id="Picture_x0020_34" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:429.75pt;
2103 height:372pt;visibility:visible;mso-wrap-style:square'>
2104 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image067.png"
2105  o:title="" croptop="11786f" cropbottom="16031f" cropleft="46740f"
2106  cropright="3791f"/>
2107</v:shape><![endif]--><![if !vml]><img border=0 width=573 height=496
2108src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image068.jpg"
2109v:shapes="Picture_x0020_34"><![endif]></span></p>
2110
2111<p class=MsoNormal>Next select all the Draw atoms again and do <b
2112style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2113mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Add
2114atoms</span></b>; the selection popup will appear. This time use the other
2115nonidentity entry in the bond distance table ‘<b style='mso-bidi-font-weight:
2116normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2117minor-latin;mso-hansi-theme-font:minor-latin'>[0 1 1] + (-2)</span></b>’. The ‘-2’
2118indicates both the inversion and the 2<sup>nd</sup> operator need to be applied;
2119check both and increment the 2<sup>nd</sup> and 3<sup>rd</sup> unit cell
2120entries. </p>
2121
2122<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2123 id="Picture_x0020_36" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:179.25pt;
2124 height:246.75pt;visibility:visible;mso-wrap-style:square'>
2125 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image069.png"
2126  o:title=""/>
2127</v:shape><![endif]--><![if !vml]><img border=0 width=239 height=329
2128src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image070.gif"
2129v:shapes="Picture_x0020_36"><![endif]></span></p>
2130
2131<p class=MsoNormal>Press <b style='mso-bidi-font-weight:normal'><span
2132style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2133mso-hansi-theme-font:minor-latin'>OK</span></b>; the entire molecule is drawn.</p>
2134
2135<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2136 id="Picture_x0020_35" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:429.75pt;
2137 height:364.5pt;visibility:visible;mso-wrap-style:square'>
2138 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image071.png"
2139  o:title="" croptop="10221f" cropbottom="18166f" cropleft="42114f"
2140  cropright="8322f"/>
2141</v:shape><![endif]--><![if !vml]><img border=0 width=573 height=486
2142src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image072.jpg"
2143v:shapes="Picture_x0020_35"><![endif]></span><span
2144style='mso-spacerun:yes'> </span></p>
2145
2146<p class=MsoNormal>Looks really nice. This ends the tutorial. You can save the
2147project if you wish. All the changes (<span class=SpellE>i.e</span> deleting
2148Map peaks &amp; clearing the map) will be saved.</p>
2149
2150</div>
2151
2152</body>
2153
2154</html>
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