source: Tutorials/TOF Charge Flipping/Charge Flipping with TOF single crystal data in GSASII.htm @ 2349

Last change on this file since 2349 was 1745, checked in by vondreele, 7 years ago

changes to various tutorials - mostly getting file references correct & removing hyperlinks

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File size: 114.5 KB
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404  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 1"/>
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"/>
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408  <w:LsdException Locked="false" SemiHidden="true" Name="Revision"/>
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413   Name="Intense Quote"/>
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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"/>
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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"/>
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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"/>
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567   Name="Grid Table 7 Colorful Accent 5"/>
568  <w:LsdException Locked="false" Priority="46"
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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"/>
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583  <w:LsdException Locked="false" Priority="51" Name="List Table 6 Colorful"/>
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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"/>
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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"
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1164<div class=WordSection1>
1165
1166<h1><span style='mso-fareast-font-family:"Times New Roman"'>Charge flipping
1167with neutron TOF single crystal data<o:p></o:p></span></h1>
1168
1169<p class=MsoNormal>In this exercise you will use GSAS-II to solve the structure
1170of <span class=SpellE>rubrene</span> (C<sub>42</sub>H<sub>28</sub>) from single
1171crystal neutron data via charge flipping. <span class=SpellE>Rubrene</span> is
1172of interest as a molecular semiconductor. It crystallizes in the space group <span
1173class=SpellE>Cmca</span> with the lattice parameters a=26.798Å, b=7.1618Å,
1174c=14.1942Å, Z=4. Thus, the molecule is sited on a special position with 2/m
1175symmetry. If you have not done so already, start GSAS-II.</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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1212 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image001.png"
1213  o:title=""/>
1214</v:shape><![endif]--><![if !vml]><img 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 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 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 <b style='mso-bidi-font-weight:normal'><span style='font-family:
1276"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1277minor-latin'>exercises/TOF Charge Flipping</span></b> and select the file <span
1278class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1279"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1280minor-latin'>ruberene_orthoC.hkl</span></b></span> (double click the name or
1281press the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1282mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Open</span></b>
1283button after selecting it). A popup box will appear.</p>
1284
1285<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1286 id="Picture_x0020_4" o:spid="_x0000_i1056" type="#_x0000_t75" style='width:357.75pt;
1287 height:265.5pt;visibility:visible;mso-wrap-style:square'>
1288 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image007.png"
1289  o:title=""/>
1290</v:shape><![endif]--><![if !vml]><img width=477 height=354
1291src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image008.gif"
1292v:shapes="Picture_x0020_4"><![endif]></span></p>
1293
1294<p class=MsoNormal>Press <span class=GramE><b style='mso-bidi-font-weight:normal'><span
1295style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1296mso-hansi-theme-font:minor-latin'>Yes</span></b></span>; another popup will
1297appear offering you the chance to change the name. Press <b style='mso-bidi-font-weight:
1298normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1299minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>, a new popup
1300appears.</p>
1301
1302<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1303 id="Picture_x0020_5" o:spid="_x0000_i1055" type="#_x0000_t75" style='width:240pt;
1304 height:232.5pt;visibility:visible;mso-wrap-style:square'>
1305 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image009.png"
1306  o:title=""/>
1307</v:shape><![endif]--><![if !vml]><img width=320 height=310
1308src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image010.gif"
1309v:shapes="Picture_x0020_5"><![endif]></span></p>
1310
1311<p class=MsoNormal>Here you select the phase the data belongs to. There is only
1312<span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1313style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1314mso-hansi-theme-font:minor-latin'>rubrene</span></b></span> so select it and
1315press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1316mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1317The bottom of the data tree is shown, a small data window and the plot shows
1318the l=0 slice of the last reflection set loaded (HKLF rubrene_orthoC.hkl_22).</p>
1319
1320<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1321 id="Picture_x0020_6" o:spid="_x0000_i1054" type="#_x0000_t75" style='width:525pt;
1322 height:450pt;visibility:visible;mso-wrap-style:square'>
1323 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image011.png"
1324  o:title=""/>
1325</v:shape><![endif]--><![if !vml]><img width=700 height=600
1326src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image012.gif"
1327v:shapes="Picture_x0020_6"><![endif]></span></p>
1328
1329<p class=MsoNormal>The <b style='mso-bidi-font-weight:normal'><span
1330style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1331mso-hansi-theme-font:minor-latin'>K</span></b> box control allows you to select
1332other zones &amp; layers to view. The drawing geometry is strictly square (i.e.
1333not in reciprocal space units). If you do <b style='mso-bidi-font-weight:normal'><span
1334style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1335mso-hansi-theme-font:minor-latin'>Commands/Plot 3D HKLs</span></b>, a 3D plot
1336of reciprocal space is shown</p>
1337
1338<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1339 id="Picture_x0020_1" o:spid="_x0000_i1053" type="#_x0000_t75" style='width:446.25pt;
1340 height:381.75pt;visibility:visible;mso-wrap-style:square'>
1341 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image013.png"
1342  o:title="" croptop="13337f" cropbottom="14997f" cropleft="41056f"
1343  cropright="9449f"/>
1344</v:shape><![endif]--><![if !vml]><img width=595 height=509
1345src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image014.jpg"
1346v:shapes="Picture_x0020_1"><![endif]></span></p>
1347
1348<p class=MsoNormal>The size of the green boxes is proportional to the structure
1349factors; the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1350"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1351minor-latin'>save as/key</span></b> pulldown will give you other viewing
1352options. Here is a good place to save the GSAS-II project for <span
1353class=SpellE>rubrene</span>. Do <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'>File/Save project</span></b> from the main
1356GSAS-II data tree window; a file dialog box will appear. Enter a file name (I
1357used <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1358style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1359mso-hansi-theme-font:minor-latin'>rubrene</span></b></span> – no extension).</p>
1360
1361<h2>Step 3. Setup for charge flipping</h2>
1362
1363<p class=MsoNormal>We have two tasks here. One is to select the reflection sets
1364to be used in the calculations and the other is to set some controls. To begin
1365select the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1366style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1367mso-hansi-theme-font:minor-latin'>rubrene</span></b></span> phase entry in the
1368GSAS-II data tree; the General tab will appear in the Phase Data for <span
1369class=SpellE>rubrene</span> window</p>
1370
1371<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1372 id="Picture_x0020_8" o:spid="_x0000_i1052" type="#_x0000_t75" style='width:489pt;
1373 height:375pt;visibility:visible;mso-wrap-style:square'>
1374 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image015.png"
1375  o:title=""/>
1376</v:shape><![endif]--><![if !vml]><img width=652 height=500
1377src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image016.gif"
1378v:shapes="Picture_x0020_8"><![endif]></span></p>
1379
1380<p class=MsoNormal>In the Charge flip controls (about center of the page) press
1381the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1382mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Select
1383reflection sets</span></b> button; a <b style='mso-bidi-font-weight:normal'><span
1384style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1385mso-hansi-theme-font:minor-latin'>Use data</span></b> popup will appear. You
1386will want to use all the HKLF data sets; press <b style='mso-bidi-font-weight:
1387normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1388minor-latin;mso-hansi-theme-font:minor-latin'>Set All</span> </b>and press <b
1389style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1390mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1391The General tab will be refreshed. GSAS-II will use all the data to build a
1392reflection set for charge flipping. For duplicate <span class=SpellE>hkls</span>
1393the last one encountered will be used. Since atoms are essentially point <span
1394class=SpellE>scatterers</span> for neutrons, a charge flip map has very sharp
1395peaks so a better choice for the <b style='mso-bidi-font-weight:normal'><span
1396style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1397mso-hansi-theme-font:minor-latin'>k-factor</span></b> (charge flip level) might
1398be <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1399mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0.5</span></b>,
1400the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1401mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>k-max</span></b>
1402should be larger (say <b style='mso-bidi-font-weight:normal'><span
1403style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1404mso-hansi-theme-font:minor-latin'>50</span></b>) and the map <b
1405style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1406mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Resolution</span></b>
1407should be smaller (say <b style='mso-bidi-font-weight:normal'><span
1408style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1409mso-hansi-theme-font:minor-latin'>0.4</span></b>). Set these three values. In
1410the Fourier map controls, set <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'>Peak cutoff %</span></b> to <b
1413style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1414mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>20</span></b>;
1415this sets the lower limit of the peak search in the charge flip map. When done
1416the General tab should look like</p>
1417
1418<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1419 id="Picture_x0020_9" o:spid="_x0000_i1051" type="#_x0000_t75" style='width:516.75pt;
1420 height:375pt;visibility:visible;mso-wrap-style:square'>
1421 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image017.png"
1422  o:title=""/>
1423</v:shape><![endif]--><![if !vml]><img width=689 height=500
1424src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image018.gif"
1425v:shapes="Picture_x0020_9"><![endif]></span></p>
1426
1427<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1428
1429<h2>Step 4. Charge flipping</h2>
1430
1431<p class=MsoNormal>We are now ready for charge flipping. In the General tab
1432menu do <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1433mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/Charge
1434flipping</span></b>; a Charge flipping progress bar will appear showing the
1435residual and cycle count for the charge flipping calculation. In this case the
1436residual quickly drops to ~38% and stays there. Press <b style='mso-bidi-font-weight:
1437normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1438minor-latin;mso-hansi-theme-font:minor-latin'>Cancel</span></b> to stop the
1439calculation; some information will be printed on the console and after a pause
1440the Phase Data window will show <b style='mso-bidi-font-weight:normal'><span
1441style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1442mso-hansi-theme-font:minor-latin'>Map Peaks</span></b> and the plot window will
1443show a drawing of the obtained structure.</p>
1444
1445<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1446 id="Picture_x0020_10" o:spid="_x0000_i1050" type="#_x0000_t75" style='width:375pt;
1447 height:225pt;visibility:visible;mso-wrap-style:square'>
1448 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image019.png"
1449  o:title=""/>
1450</v:shape><![endif]--><![if !vml]><img width=500 height=300
1451src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image020.gif"
1452v:shapes="Picture_x0020_10"><![endif]></span></p>
1453
1454<p class=MsoNormal>If you scroll down the Map peak list you will find some with
1455negative magnitudes at the end of the list. GSAS-II searches the map for both
1456positive and negative peaks; the former are C-atoms and the latter are H-atoms.
1457</p>
1458
1459<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1460 id="Picture_x0020_11" o:spid="_x0000_i1049" type="#_x0000_t75" style='width:6in;
1461 height:365.25pt;visibility:visible;mso-wrap-style:square'>
1462 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image021.png"
1463  o:title="" croptop="9820f" cropbottom="18705f" cropleft="43453f" cropright="6999f"/>
1464</v:shape><![endif]--><![if !vml]><img width=576 height=487
1465src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image022.jpg"
1466v:shapes="Picture_x0020_11"><![endif]></span></p>
1467
1468<p class=MsoNormal>The plot (which I’ve rotated around a bit) shows white spots
1469for the positive peaks and red ones for the negative ones; bonds are white
1470lines. The case I’ve drawn here shows a problem with this charge flip solution.
1471While the charge flipping run has clearly found all the C-atoms and some of the
1472H-atoms, the molecule is incorrectly placed in the unit cell. To fix this you
1473could simply repeat the charge flipping run and hope it puts the molecule in
1474the right place. GSAS-II uses an algorithm based on how structure factor phases
1475are related for a given space group to reposition the solution; it sometimes
1476fails if the phase set isn’t perfect. Or you can “roll” the map
1477right/left/up/down (<b style='mso-bidi-font-weight:normal'><span
1478style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1479mso-hansi-theme-font:minor-latin'>R/L/U/D</span></b> keys) to put the solution
1480where you want. In this case a few steps with the L-key sufficed to put the
1481molecule on a 2/m site (i.e. the center of the cell indicated the multicolored
1482cross on the central C-C bond).</p>
1483
1484<p class=MsoNormal><!--[if gte vml 1]><v:shapetype id="_x0000_t32" coordsize="21600,21600"
1485 o:spt="32" o:oned="t" path="m,l21600,21600e" filled="f">
1486 <v:path arrowok="t" fillok="f" o:connecttype="none"/>
1487 <o:lock v:ext="edit" shapetype="t"/>
1488</v:shapetype><v:shape id="Straight_x0020_Arrow_x0020_Connector_x0020_38"
1489 o:spid="_x0000_s1027" type="#_x0000_t32" style='position:absolute;
1490 margin-left:205.5pt;margin-top:193.5pt;width:15.75pt;height:29.25pt;flip:y;
1491 z-index:251660288;visibility:visible;mso-wrap-style:square;
1492 mso-width-percent:0;mso-height-percent:0;mso-wrap-distance-left:9pt;
1493 mso-wrap-distance-top:0;mso-wrap-distance-right:9pt;
1494 mso-wrap-distance-bottom:0;mso-position-horizontal:absolute;
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1589
1590<p class=MsoNormal>Notice that as the map is rolled, the Map peak positions are
1591shifted to match the change in positions.</p>
1592
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1600v:shapes="Picture_x0020_13"><![endif]></span></p>
1601
1602<p class=MsoNormal>By carefully looking at the map, you can see the 4-ring <span
1603class=SpellE>tetracene</span> (<span class=SpellE>naphthacene</span>) core of
1604the molecule with four phenyl groups attached to both sides on the center two
1605rings. The unique part consists of 1/4<sup>th</sup> of this group (i.e. half of
1606one side of the <span class=SpellE>tetracene</span> and one phenyl); one C-atom
1607sits on a 2-fold and the rest are in general positions. The molecule extends
1608into the neighboring unit cell so you don’t see the whole thing as one group
1609but has two bits on either side (I’ve marked these with arrows above).</p>
1610
1611<h2>Step 5. Peak selection</h2>
1612
1613<p class=MsoNormal>GSAS-II provides several ways of selecting peak positions
1614from a charge flipping map. One way is to pick them directly from the drawing.
1615Place the cursor on one peak and do a <b style='mso-bidi-font-weight:normal'><span
1616style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1617mso-hansi-theme-font:minor-latin'>Shift left mouse button</span></b>; it will
1618be highlighted on the list and it will turn green on the plot. Do a <b
1619style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1620mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Shift right
1621mouse button</span></b> on the remaining peaks you want to <span class=GramE>pick.</span>
1622All will turn green (you may have to wiggle the plot a bit with the mouse to
1623make them show) and all will be highlighted in the list. Alternatively, you can
1624select the entire list of peaks (double click on upper left empty box of the
1625table), then do <b style='mso-bidi-font-weight:normal'><span style='font-family:
1626"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1627minor-latin'>Map peaks/Unique peaks</span></b>. Better still you can sort the
1628peaks by one of the column headings and then do <b style='mso-bidi-font-weight:
1629normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1630minor-latin;mso-hansi-theme-font:minor-latin'>Map peaks/Unique peaks</span></b>.
1631I’ve chosen to sort the peaks on <span class=SpellE><b style='mso-bidi-font-weight:
1632normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1633minor-latin;mso-hansi-theme-font:minor-latin'>dcent</span></b></span> (distance
1634from center of the cell) beforehand. After a pause while it sorts out the unique
1635peaks, it will highlight them in the table and display the picked ones in green
1636on the plot. In this case they will probably be scattered about the unit cell
1637and not make a continuous molecule, but they are largely clustered around the
1638unit cell center. My plot looked like this when I was done.</p>
1639
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1644  o:title="" croptop="10059f" cropbottom="18635f" cropleft="36901f"
1645  cropright="13675f"/>
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1648v:shapes="Picture_x0020_27"><![endif]></span></p>
1649
1650<p class=MsoNormal>The list has them highlighted (the rest are lower down in my
1651list; all 18 atoms were found in this charge flipping result)</p>
1652
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1660v:shapes="Picture_x0020_15"><![endif]></span></p>
1661
1662<p class=MsoNormal>To add them to the Atom list do <b style='mso-bidi-font-weight:
1663normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1664minor-latin;mso-hansi-theme-font:minor-latin'>Map peaks/Move peaks</span></b>;
1665the drawing will show white balls for them.</p>
1666
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1670 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image033.png"
1671  o:title="" croptop="10579f" cropbottom="17404f" cropleft="37800f"
1672  cropright="12584f"/>
1673</v:shape><![endif]--><![if !vml]><img width=576 height=492
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1675v:shapes="Picture_x0020_16"><![endif]></span></p>
1676
1677<p class=MsoNormal>The atom list will give the magnitudes as ‘M’ names; I found
1678all 11 C-atoms and 7 H-atoms that were expected.</p>
1679
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1687v:shapes="Picture_x0020_17"><![endif]></span></p>
1688
1689<h2>Step 6. Atom identification</h2>
1690
1691<p class=MsoNormal>You can reorder the atoms in the list; do an <b
1692style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1693mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Alt select</span></b>
1694for the atom row you want to move. Then do an <b style='mso-bidi-font-weight:
1695normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1696minor-latin;mso-hansi-theme-font:minor-latin'>Alt select</span></b> on the row
1697where you want the moved atom to precede it. This way you can put the C-atoms
1698first and the H-atoms last in the list instead of mixed up as in the above
1699list. Next select all the positive M peaks (pick the top one and then <b
1700style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1701mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Shift</span></b>
1702pick the last one). Do <b style='mso-bidi-font-weight:normal'><span
1703style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1704mso-hansi-theme-font:minor-latin'>Edit/Modify atom parameters</span></b> from
1705the Atoms menu; a popup will appear. Pick <b style='mso-bidi-font-weight:normal'><span
1706style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1707mso-hansi-theme-font:minor-latin'>Type</span></b> and press <b
1708style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1709mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>;
1710a Periodic Table will appear. Select <b style='mso-bidi-font-weight:normal'><span
1711style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1712mso-hansi-theme-font:minor-latin'>C</span></b> from the C-atom pulldown. All
1713the C-atom names and types will change. You should also move the C-atom with
17142(x) site symmetry to the top of the list.</p>
1715
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1719 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image037.png"
1720  o:title=""/>
1721</v:shape><![endif]--><![if !vml]><img width=700 height=300
1722src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image038.gif"
1723v:shapes="Picture_x0020_18"><![endif]></span></p>
1724
1725<p class=MsoNormal>Do the same with the remaining negative M atoms – make them
1726H atoms. The drawing shows molecular fragments scattered about the unit cell;
1727you’d like to unify them into a single molecule. Select the C-atom with 2(x)
1728site symmetry (although any would do). Do <b style='mso-bidi-font-weight:normal'><span
1729style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1730mso-hansi-theme-font:minor-latin'>Edit/Assemble molecule</span></b> from the
1731Atoms menu; a popup will appear offering choices for Bond radii (&amp; Angle
1732radii – ignored here). Press <b style='mso-bidi-font-weight:normal'><span
1733style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1734mso-hansi-theme-font:minor-latin'>Ok</span></b>; the Atom table will be revised
1735and the plot will show an assembled molecule (the picked starting atom in
1736green). </p>
1737
1738<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1739 id="Picture_x0020_19" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:6in;
1740 height:366pt;visibility:visible;mso-wrap-style:square'>
1741 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image039.png"
1742  o:title="" croptop="11018f" cropbottom="17360f" cropleft="37831f"
1743  cropright="12587f"/>
1744</v:shape><![endif]--><![if !vml]><img width=576 height=488
1745src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image040.jpg"
1746v:shapes="Picture_x0020_19"><![endif]></span></p>
1747
1748<p class=MsoNormal>The molecule building has scrambled the order of the atoms;
1749they were located in order as the molecule was built. </p>
1750
1751<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1752 id="Picture_x0020_20" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:525pt;
1753 height:351.75pt;visibility:visible;mso-wrap-style:square'>
1754 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image041.png"
1755  o:title=""/>
1756</v:shape><![endif]--><![if !vml]><img width=700 height=469
1757src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image042.gif"
1758v:shapes="Picture_x0020_20"><![endif]></span></p>
1759
1760<p class=MsoNormal>You can reorder them to put the H-atoms at the end of the
1761list. Then select all of them and then do <span style='font-family:"Calibri",sans-serif;
1762mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Modify
1763atom parameters</span>. Pick <b style='mso-bidi-font-weight:normal'><span
1764style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1765mso-hansi-theme-font:minor-latin'>Name</span></b> from the pulldown and press <b
1766style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1767mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1768You are asked if you really want to do this, press <span class=GramE><b
1769style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1770mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Yes</span></b></span>.
1771The atoms are then renamed in numeric order.</p>
1772
1773<h2>Step 7. Refinement</h2>
1774
1775<p class=MsoNormal>Since the structure is complete, we can do the full
1776refinement. 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'>Controls</span></b> item from the GSAS-II
1779data tree. Unset the <b style='mso-bidi-font-weight:normal'><span
1780style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1781mso-hansi-theme-font:minor-latin'>Refine HKLF as F^2</span></b> box and enter <b
1782style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1783mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>3.0</span></b>
1784for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1785mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Min <span
1786class=SpellE>obs</span>/sig</span></b>. This makes the least squares refine on <span
1787class=SpellE><span class=GramE>F<sub>o</sub></span></span> with 3&#963; cutoff
1788on <span class=SpellE>F<sub>o</sub></span>. From the main GSAS-II data tree
1789menu do <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1790mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>;
1791this will do the 1<sup>st</sup> least squares refinement varying only the data
1792set scale factors. A progress bar popup will appear showing the residuals as
1793the refinement proceeds. When done, a small popup will appear with the final
1794residual; press <b style='mso-bidi-font-weight:normal'><span style='font-family:
1795"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1796minor-latin'>OK</span></b> to accept it. The final <span class=SpellE>R<sub>w</sub></span>
1797is about 49% Go to the <b style='mso-bidi-font-weight:normal'><span
1798style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1799mso-hansi-theme-font:minor-latin'>Atoms</span></b> tab for the <span
1800class=SpellE>rubrene</span> phase, double click the <b style='mso-bidi-font-weight:
1801normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1802minor-latin;mso-hansi-theme-font:minor-latin'>refine</span></b> column heading;
1803a popup box will appear. Select both <b style='mso-bidi-font-weight:normal'><span
1804style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1805mso-hansi-theme-font:minor-latin'>X - coordinates</span></b> and <b
1806style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1807mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>U – thermal
1808parameters</span></b> and press <b style='mso-bidi-font-weight:normal'><span
1809style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1810mso-hansi-theme-font:minor-latin'>OK</span></b>. The atom table will show
1811refine flags for each atom.</p>
1812
1813<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1814 id="Picture_x0020_21" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:525pt;
1815 height:225pt;visibility:visible;mso-wrap-style:square'>
1816 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image043.png"
1817  o:title=""/>
1818</v:shape><![endif]--><![if !vml]><img width=700 height=300
1819src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image044.gif"
1820v:shapes="Picture_x0020_21"><![endif]></span></p>
1821
1822<p class=MsoNormal>Then repeat the <b style='mso-bidi-font-weight:normal'><span
1823style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1824mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> command in the
1825main menu. The final residual will be much better <span class=SpellE>R<sub>w</sub></span>
1826~10%. Next, convert all the atoms from isotropic thermal parameters to
1827anisotropic ones. Double click <span class=GramE>the <b style='mso-bidi-font-weight:
1828normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1829minor-latin;mso-hansi-theme-font:minor-latin'>I</span></b></span><b
1830style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1831mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>/A</span></b>
1832column heading and select <b style='mso-bidi-font-weight:normal'><span
1833style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1834mso-hansi-theme-font:minor-latin'>Anisotropic</span></b> and press <b
1835style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1836mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1837Then repeat <b style='mso-bidi-font-weight:normal'><span style='font-family:
1838"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1839minor-latin'>Calculate/Refine</span></b> (perhaps twice); the final <span
1840class=SpellE>R<sub>w</sub></span> ~6.06% which is quite nice.</p>
1841
1842<h2>Step 8. Further work</h2>
1843
1844<p class=MsoNormal>Since this is TOF neutron single crystal diffraction, a
1845relatively large crystal was used and the neutron wavelength covered a fairly
1846wide range of values. Hence, it is likely that the strong reflection
1847intensities suffered from some level of extinction. To find these parameters
1848select the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1849"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1850minor-latin'>Data</span></b> tab in the Phase Data window; all that will show
1851is a list of a data set names with a <b style='mso-bidi-font-weight:normal'><span
1852style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1853mso-hansi-theme-font:minor-latin'>Show</span></b> box for each. To see what is
1854there select the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1855"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1856minor-latin'>Show</span></b> box; alternatively to see all of them do <b
1857style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1858mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Show/Hide</span></b>
1859all the window will look something like</p>
1860
1861<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1862 id="Picture_x0020_22" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:319.5pt;
1863 height:378pt;visibility:visible;mso-wrap-style:square'>
1864 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image045.png"
1865  o:title=""/>
1866</v:shape><![endif]--><![if !vml]><img width=426 height=504
1867src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image046.gif"
1868v:shapes="Picture_x0020_22"><![endif]></span></p>
1869
1870<p class=MsoNormal>This is a very long display with entries for 23 data sets
1871(NB: in alphabetical order not numeric order!). The Scale factors were selected
1872for refinement by default (box checked). Here you want to select <b
1873style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1874mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Primary</span></b>
1875for the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1876mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Extinction
1877type</span></b> (later you can try the other models) for the 1<sup>st</sup>
1878data set. The window will be repainted with a new line in the data display.
1879Select the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1880"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1881minor-latin'>Ep</span></b> check box so it will be refined. To set all the rest
1882press the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1883mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Copy flags?</span></b>
1884<span class=GramE>button</span> for that data set (not one of the others!). A
1885popup will appear giving the list of data sets; press the <span class=SpellE><b
1886style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1887mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>SetAll</span></b></span>
1888button and then <b style='mso-bidi-font-weight:normal'><span style='font-family:
1889"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1890minor-latin'>OK</span></b>. The data window will be repainted with all the
1891Extinction types set to Primary and Ep set to refine. You could then do <b
1892style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1893mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>
1894but it might be better to constrain all the Ep values to be the same. To do
1895this select <b style='mso-bidi-font-weight:normal'><span style='font-family:
1896"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1897minor-latin'>Constraints</span></b> from the GSASII data tree. A blank window
1898with tabs will appear.</p>
1899
1900<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1901 id="Picture_x0020_23" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:225pt;
1902 height:352.5pt;visibility:visible;mso-wrap-style:square'>
1903 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image047.png"
1904  o:title=""/>
1905</v:shape><![endif]--><![if !vml]><img width=300 height=470
1906src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image048.gif"
1907v:shapes="Picture_x0020_23"><![endif]></span></p>
1908
1909<p class=MsoNormal>Select the <b style='mso-bidi-font-weight:normal'><span
1910style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1911mso-hansi-theme-font:minor-latin'>Histogram/Phase</span></b> constraints tab;
1912the window is still blank but that tab is now highlighted. Next do <b
1913style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1914mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Add
1915equivalence</span></b>; a popup will appear asking for a parameter name to be
1916constrained.</p>
1917
1918<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1919 id="Picture_x0020_24" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:468.75pt;
1920 height:300pt;visibility:visible;mso-wrap-style:square'>
1921 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image049.png"
1922  o:title=""/>
1923</v:shape><![endif]--><![if !vml]><img width=625 height=400
1924src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image050.gif"
1925v:shapes="Picture_x0020_24"><![endif]></span></p>
1926
1927<p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span
1928style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1929mso-hansi-theme-font:minor-latin'>0:0<span class=GramE>:Ep</span></span></b>,
1930that is the primary extinction parameter for the 1<sup>st</sup> dataset and the
1931<span class=SpellE>rubrene</span> phase. Press <b style='mso-bidi-font-weight:
1932normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1933minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.</p>
1934
1935<p class=MsoNormal>The popup is replaced with a new list of all compatible
1936parameters that <b style='mso-bidi-font-weight:normal'><span style='font-family:
1937"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1938minor-latin'>0:0<span class=GramE>:Ep</span></span></b> is to be made
1939equivalent to. Scroll down and find <b style='mso-bidi-font-weight:normal'><span
1940style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1941mso-hansi-theme-font:minor-latin'>0<span class=GramE>:all:Ep</span></span></b>
1942and pick that; the Constraint window will change to</p>
1943
1944<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1945 id="Picture_x0020_25" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:481.5pt;
1946 height:352.5pt;visibility:visible;mso-wrap-style:square'>
1947 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image051.png"
1948  o:title=""/>
1949</v:shape><![endif]--><![if !vml]><img width=642 height=470
1950src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image052.gif"
1951v:shapes="Picture_x0020_25"><![endif]></span></p>
1952
1953<p class=MsoNormal>This shows the constraint making Ep for all 23 data sets
1954equivalent to a single variable. Do <b style='mso-bidi-font-weight:normal'><span
1955style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1956mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; my <span
1957class=SpellE>R<sub>w</sub></span> was 5.907% only a slight improvement. You may
1958wish to try the other extinction models. Do remember to delete the unused
1959constraint before adding a new one for the different extinction parameter.
1960Finally you can draw the molecule; go to <b style='mso-bidi-font-weight:normal'><span
1961style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1962mso-hansi-theme-font:minor-latin'>Atoms</span></b> and do <b style='mso-bidi-font-weight:
1963normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1964minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Reload draw atoms</span></b>.
1965That will put the newest atom parameters into the Draw Atoms table. Select <b
1966style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1967mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Draw Atoms</span></b>.
1968Select the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1969"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1970minor-latin'>Style</span></b> column heading; a popup will appear</p>
1971
1972<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1973 id="Picture_x0020_26" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:259.5pt;
1974 height:252pt;visibility:visible;mso-wrap-style:square'>
1975 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image053.png"
1976  o:title=""/>
1977</v:shape><![endif]--><![if !vml]><img width=346 height=336
1978src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image054.gif"
1979v:shapes="Picture_x0020_26"><![endif]></span></p>
1980
1981<p class=MsoNormal>Notice the first line is blank, if you select that all the
1982atoms will vanish! Select <b style='mso-bidi-font-weight:normal'><span
1983style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1984mso-hansi-theme-font:minor-latin'>ellipsoids</span></b> and press <b
1985style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1986mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1987The plot will change, but it is pretty cluttered.</p>
1988
1989<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1990 id="Picture_x0020_28" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:465.75pt;
1991 height:395.25pt;visibility:visible;mso-wrap-style:square'>
1992 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image055.png"
1993  o:title="" croptop="11745f" cropbottom="16560f" cropleft="43690f"
1994  cropright="6723f"/>
1995</v:shape><![endif]--><![if !vml]><img width=621 height=527
1996src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image056.jpg"
1997v:shapes="Picture_x0020_28"><![endif]></span></p>
1998
1999<p class=MsoNormal>You can remove the Map peaks atoms; go to the <b
2000style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2001mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map peaks</span></b>
2002tab and do <b style='mso-bidi-font-weight:normal'><span style='font-family:
2003"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2004minor-latin'>Map peaks/clear peaks</span></b> from the menu. The list will be
2005erased and the plot will just show the molecule. You can also remove the unit
2006cell edges, go to <b style='mso-bidi-font-weight:normal'><span
2007style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2008mso-hansi-theme-font:minor-latin'>Draw Options</span></b> and uncheck the <b
2009style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2010mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Show unit
2011cell?</span></b> <span class=GramE>box</span>. Finally, you can remove the charge
2012flipping map; go to <b style='mso-bidi-font-weight:normal'><span
2013style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2014mso-hansi-theme-font:minor-latin'>General</span></b> and do <b
2015style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2016mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/Clear
2017map</span></b>. That deletes the scattering density map and the drawing will be
2018free of any clutter.</p>
2019
2020<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2021 id="Picture_x0020_29" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:429.75pt;
2022 height:366pt;visibility:visible;mso-wrap-style:square'>
2023 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image057.png"
2024  o:title="" croptop="8339f" cropbottom="19928f" cropleft="44139f" cropright="6324f"/>
2025</v:shape><![endif]--><![if !vml]><img width=573 height=488
2026src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image058.jpg"
2027v:shapes="Picture_x0020_29"><![endif]></span></p>
2028
2029<p class=MsoNormal>Remember that this is only 1/4<sup>th</sup> of the molecule,
2030we’d like to see the whole thing. First go to the <b style='mso-bidi-font-weight:
2031normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2032minor-latin;mso-hansi-theme-font:minor-latin'>Atoms</span></b> tab and select
2033the C-atom that is in a special position 2(x). The do <b style='mso-bidi-font-weight:
2034normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2035minor-latin;mso-hansi-theme-font:minor-latin'>Compute/Show Distances &amp;
2036Angles</span></b> and respond <b style='mso-bidi-font-weight:normal'><span
2037style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2038mso-hansi-theme-font:minor-latin'>OK</span></b> to the popup. The important
2039result is on the console</p>
2040
2041<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2042 id="Picture_x0020_30" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:609.75pt;
2043 height:278.25pt;visibility:visible;mso-wrap-style:square'>
2044 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image059.png"
2045  o:title=""/>
2046</v:shape><![endif]--><![if !vml]><img width=813 height=371
2047src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image060.gif"
2048v:shapes="Picture_x0020_30"><![endif]></span></p>
2049
2050<p class=MsoNormal>This gives the bond distances and angles about the <span
2051class=GramE>C(</span>1) atom. Particularly note the cell<span class=GramE>+(</span>sym.
2052Op.) information; we will use this to build the drawing. Go to the <b
2053style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2054mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Draw Atoms</span></b>
2055tab and select all the atoms (double click on the upper left box). You should
2056see all atoms selected</p>
2057
2058<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2059 id="Picture_x0020_31" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:450pt;
2060 height:225pt;visibility:visible;mso-wrap-style:square'>
2061 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image061.png"
2062  o:title=""/>
2063</v:shape><![endif]--><![if !vml]><img width=600 height=300
2064src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image062.gif"
2065v:shapes="Picture_x0020_31"><![endif]></span></p>
2066
2067<p class=MsoNormal>Then do <b style='mso-bidi-font-weight:normal'><span
2068style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2069mso-hansi-theme-font:minor-latin'>Edit/Add atoms</span></b>; a popup will
2070appear</p>
2071
2072<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2073 id="Picture_x0020_32" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:179.25pt;
2074 height:246.75pt;visibility:visible;mso-wrap-style:square'>
2075 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image063.png"
2076  o:title=""/>
2077</v:shape><![endif]--><![if !vml]><img width=239 height=329
2078src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image064.gif"
2079v:shapes="Picture_x0020_32"><![endif]></span></p>
2080
2081<p class=MsoNormal>Based on the 1<sup>st</sup> entry in the bond distance table
2082‘<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2083mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>[1 0 0<span
2084class=GramE>]<span style='mso-spacerun:yes'>  </span>+</span>(<span
2085style='mso-spacerun:yes'>  </span>2)</span></b>’, select the controls for the 2<sup>nd</sup>
2086operator and increment the 1<sup>st</sup> unit cell</p>
2087
2088<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2089 id="Picture_x0020_33" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:179.25pt;
2090 height:246.75pt;visibility:visible;mso-wrap-style:square'>
2091 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image065.png"
2092  o:title=""/>
2093</v:shape><![endif]--><![if !vml]><img width=239 height=329
2094src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image066.gif"
2095v:shapes="Picture_x0020_33"><![endif]></span></p>
2096
2097<p class=MsoNormal>Press OK. The plot now shows œ the molecule.</p>
2098
2099<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2100 id="Picture_x0020_34" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:429.75pt;
2101 height:372pt;visibility:visible;mso-wrap-style:square'>
2102 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image067.png"
2103  o:title="" croptop="11786f" cropbottom="16031f" cropleft="46740f"
2104  cropright="3791f"/>
2105</v:shape><![endif]--><![if !vml]><img width=573 height=496
2106src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image068.jpg"
2107v:shapes="Picture_x0020_34"><![endif]></span></p>
2108
2109<p class=MsoNormal>Next select all the Draw atoms again and do <b
2110style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2111mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Add
2112atoms</span></b>; the selection popup will appear. This time use the other
2113nonidentity entry in the bond distance table ‘<b style='mso-bidi-font-weight:
2114normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2115minor-latin;mso-hansi-theme-font:minor-latin'>[0 1 1] + (-2)</span></b>’. The
2116‘-2’ indicates both the inversion and the 2<sup>nd</sup> operator need to be
2117applied; check both and increment the 2<sup>nd</sup> and 3<sup>rd</sup> unit
2118cell entries. </p>
2119
2120<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2121 id="Picture_x0020_36" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:179.25pt;
2122 height:246.75pt;visibility:visible;mso-wrap-style:square'>
2123 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image069.png"
2124  o:title=""/>
2125</v:shape><![endif]--><![if !vml]><img width=239 height=329
2126src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image070.gif"
2127v:shapes="Picture_x0020_36"><![endif]></span></p>
2128
2129<p class=MsoNormal>Press <b style='mso-bidi-font-weight:normal'><span
2130style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2131mso-hansi-theme-font:minor-latin'>OK</span></b>; the entire molecule is drawn.</p>
2132
2133<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2134 id="Picture_x0020_35" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:429.75pt;
2135 height:364.5pt;visibility:visible;mso-wrap-style:square'>
2136 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image071.png"
2137  o:title="" croptop="10221f" cropbottom="18166f" cropleft="42114f"
2138  cropright="8322f"/>
2139</v:shape><![endif]--><![if !vml]><img width=573 height=486
2140src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image072.jpg"
2141v:shapes="Picture_x0020_35"><![endif]></span><span
2142style='mso-spacerun:yes'> </span></p>
2143
2144<p class=MsoNormal>Looks really nice. This ends the tutorial. You can save the
2145project if you wish. All the changes (<span class=SpellE>i.e</span> deleting
2146Map peaks &amp; clearing the map) will be saved.</p>
2147
2148</div>
2149
2150</body>
2151
2152</html>
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