source: Tutorials/TOF Single Crystal Refinement/TOF single crystal refinement in GSAS.htm @ 1865

Last change on this file since 1865 was 1865, checked in by vondreele, 8 years ago

complete TOF Single Crystal Refinement tutorial.
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407  <w:LsdException Locked="false" SemiHidden="true" Name="Revision"/>
408  <w:LsdException Locked="false" Priority="34" QFormat="true"
409   Name="List Paragraph"/>
410  <w:LsdException Locked="false" Priority="29" QFormat="true" Name="Quote"/>
411  <w:LsdException Locked="false" Priority="30" QFormat="true"
412   Name="Intense Quote"/>
413  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 1"/>
414  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 1"/>
415  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 1"/>
416  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 1"/>
417  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 1"/>
418  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 1"/>
419  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 1"/>
420  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 1"/>
421  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 2"/>
422  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 2"/>
423  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 2"/>
424  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 2"/>
425  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 2"/>
426  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 2"/>
427  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 2"/>
428  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 2"/>
429  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 2"/>
430  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 2"/>
431  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 2"/>
432  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 2"/>
433  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 2"/>
434  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 2"/>
435  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 3"/>
436  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 3"/>
437  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 3"/>
438  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 3"/>
439  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 3"/>
440  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 3"/>
441  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 3"/>
442  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 3"/>
443  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 3"/>
444  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 3"/>
445  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 3"/>
446  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 3"/>
447  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 3"/>
448  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 3"/>
449  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 4"/>
450  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 4"/>
451  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 4"/>
452  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 4"/>
453  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 4"/>
454  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 4"/>
455  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 4"/>
456  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 4"/>
457  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 4"/>
458  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 4"/>
459  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 4"/>
460  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 4"/>
461  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 4"/>
462  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 4"/>
463  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 5"/>
464  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 5"/>
465  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 5"/>
466  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 5"/>
467  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 5"/>
468  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 5"/>
469  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 5"/>
470  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 5"/>
471  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 5"/>
472  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 5"/>
473  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 5"/>
474  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 5"/>
475  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 5"/>
476  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 5"/>
477  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 6"/>
478  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 6"/>
479  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 6"/>
480  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 6"/>
481  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 6"/>
482  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 6"/>
483  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 6"/>
484  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 6"/>
485  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 6"/>
486  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 6"/>
487  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 6"/>
488  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 6"/>
489  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 6"/>
490  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 6"/>
491  <w:LsdException Locked="false" Priority="19" QFormat="true"
492   Name="Subtle Emphasis"/>
493  <w:LsdException Locked="false" Priority="21" QFormat="true"
494   Name="Intense Emphasis"/>
495  <w:LsdException Locked="false" Priority="31" QFormat="true"
496   Name="Subtle Reference"/>
497  <w:LsdException Locked="false" Priority="32" QFormat="true"
498   Name="Intense Reference"/>
499  <w:LsdException Locked="false" Priority="33" QFormat="true" Name="Book Title"/>
500  <w:LsdException Locked="false" Priority="37" SemiHidden="true"
501   UnhideWhenUsed="true" Name="Bibliography"/>
502  <w:LsdException Locked="false" Priority="39" SemiHidden="true"
503   UnhideWhenUsed="true" QFormat="true" Name="TOC Heading"/>
504  <w:LsdException Locked="false" Priority="41" Name="Plain Table 1"/>
505  <w:LsdException Locked="false" Priority="42" Name="Plain Table 2"/>
506  <w:LsdException Locked="false" Priority="43" Name="Plain Table 3"/>
507  <w:LsdException Locked="false" Priority="44" Name="Plain Table 4"/>
508  <w:LsdException Locked="false" Priority="45" Name="Plain Table 5"/>
509  <w:LsdException Locked="false" Priority="40" Name="Grid Table Light"/>
510  <w:LsdException Locked="false" Priority="46" Name="Grid Table 1 Light"/>
511  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2"/>
512  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3"/>
513  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4"/>
514  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark"/>
515  <w:LsdException Locked="false" Priority="51" Name="Grid Table 6 Colorful"/>
516  <w:LsdException Locked="false" Priority="52" Name="Grid Table 7 Colorful"/>
517  <w:LsdException Locked="false" Priority="46"
518   Name="Grid Table 1 Light Accent 1"/>
519  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 1"/>
520  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 1"/>
521  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 1"/>
522  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 1"/>
523  <w:LsdException Locked="false" Priority="51"
524   Name="Grid Table 6 Colorful Accent 1"/>
525  <w:LsdException Locked="false" Priority="52"
526   Name="Grid Table 7 Colorful Accent 1"/>
527  <w:LsdException Locked="false" Priority="46"
528   Name="Grid Table 1 Light Accent 2"/>
529  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 2"/>
530  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 2"/>
531  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 2"/>
532  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 2"/>
533  <w:LsdException Locked="false" Priority="51"
534   Name="Grid Table 6 Colorful Accent 2"/>
535  <w:LsdException Locked="false" Priority="52"
536   Name="Grid Table 7 Colorful Accent 2"/>
537  <w:LsdException Locked="false" Priority="46"
538   Name="Grid Table 1 Light Accent 3"/>
539  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 3"/>
540  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 3"/>
541  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 3"/>
542  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 3"/>
543  <w:LsdException Locked="false" Priority="51"
544   Name="Grid Table 6 Colorful Accent 3"/>
545  <w:LsdException Locked="false" Priority="52"
546   Name="Grid Table 7 Colorful Accent 3"/>
547  <w:LsdException Locked="false" Priority="46"
548   Name="Grid Table 1 Light Accent 4"/>
549  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 4"/>
550  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 4"/>
551  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 4"/>
552  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 4"/>
553  <w:LsdException Locked="false" Priority="51"
554   Name="Grid Table 6 Colorful Accent 4"/>
555  <w:LsdException Locked="false" Priority="52"
556   Name="Grid Table 7 Colorful Accent 4"/>
557  <w:LsdException Locked="false" Priority="46"
558   Name="Grid Table 1 Light Accent 5"/>
559  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 5"/>
560  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 5"/>
561  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 5"/>
562  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 5"/>
563  <w:LsdException Locked="false" Priority="51"
564   Name="Grid Table 6 Colorful Accent 5"/>
565  <w:LsdException Locked="false" Priority="52"
566   Name="Grid Table 7 Colorful Accent 5"/>
567  <w:LsdException Locked="false" Priority="46"
568   Name="Grid Table 1 Light Accent 6"/>
569  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 6"/>
570  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 6"/>
571  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 6"/>
572  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 6"/>
573  <w:LsdException Locked="false" Priority="51"
574   Name="Grid Table 6 Colorful Accent 6"/>
575  <w:LsdException Locked="false" Priority="52"
576   Name="Grid Table 7 Colorful Accent 6"/>
577  <w:LsdException Locked="false" Priority="46" Name="List Table 1 Light"/>
578  <w:LsdException Locked="false" Priority="47" Name="List Table 2"/>
579  <w:LsdException Locked="false" Priority="48" Name="List Table 3"/>
580  <w:LsdException Locked="false" Priority="49" Name="List Table 4"/>
581  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark"/>
582  <w:LsdException Locked="false" Priority="51" Name="List Table 6 Colorful"/>
583  <w:LsdException Locked="false" Priority="52" Name="List Table 7 Colorful"/>
584  <w:LsdException Locked="false" Priority="46"
585   Name="List Table 1 Light Accent 1"/>
586  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 1"/>
587  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 1"/>
588  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 1"/>
589  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 1"/>
590  <w:LsdException Locked="false" Priority="51"
591   Name="List Table 6 Colorful Accent 1"/>
592  <w:LsdException Locked="false" Priority="52"
593   Name="List Table 7 Colorful Accent 1"/>
594  <w:LsdException Locked="false" Priority="46"
595   Name="List Table 1 Light Accent 2"/>
596  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 2"/>
597  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 2"/>
598  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 2"/>
599  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 2"/>
600  <w:LsdException Locked="false" Priority="51"
601   Name="List Table 6 Colorful Accent 2"/>
602  <w:LsdException Locked="false" Priority="52"
603   Name="List Table 7 Colorful Accent 2"/>
604  <w:LsdException Locked="false" Priority="46"
605   Name="List Table 1 Light Accent 3"/>
606  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 3"/>
607  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 3"/>
608  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 3"/>
609  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 3"/>
610  <w:LsdException Locked="false" Priority="51"
611   Name="List Table 6 Colorful Accent 3"/>
612  <w:LsdException Locked="false" Priority="52"
613   Name="List Table 7 Colorful Accent 3"/>
614  <w:LsdException Locked="false" Priority="46"
615   Name="List Table 1 Light Accent 4"/>
616  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 4"/>
617  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 4"/>
618  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 4"/>
619  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 4"/>
620  <w:LsdException Locked="false" Priority="51"
621   Name="List Table 6 Colorful Accent 4"/>
622  <w:LsdException Locked="false" Priority="52"
623   Name="List Table 7 Colorful Accent 4"/>
624  <w:LsdException Locked="false" Priority="46"
625   Name="List Table 1 Light Accent 5"/>
626  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 5"/>
627  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 5"/>
628  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 5"/>
629  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 5"/>
630  <w:LsdException Locked="false" Priority="51"
631   Name="List Table 6 Colorful Accent 5"/>
632  <w:LsdException Locked="false" Priority="52"
633   Name="List Table 7 Colorful Accent 5"/>
634  <w:LsdException Locked="false" Priority="46"
635   Name="List Table 1 Light Accent 6"/>
636  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 6"/>
637  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 6"/>
638  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 6"/>
639  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 6"/>
640  <w:LsdException Locked="false" Priority="51"
641   Name="List Table 6 Colorful Accent 6"/>
642  <w:LsdException Locked="false" Priority="52"
643   Name="List Table 7 Colorful Accent 6"/>
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1182<!--[if gte mso 10]>
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1199<![endif]--><!--[if gte mso 9]><xml>
1200 <o:shapedefaults v:ext="edit" spidmax="1026"/>
1201</xml><![endif]--><!--[if gte mso 9]><xml>
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1205</head>
1206
1207<body lang=EN-US link=blue vlink=purple style='tab-interval:.5in'>
1208
1209<div class=WordSection1>
1210
1211<h1><span style='mso-fareast-font-family:"Times New Roman"'>Single crystal
1212structure refinement with TOF data in GSAS-II<o:p></o:p></span></h1>
1213
1214<h2><span style='mso-fareast-font-family:"Times New Roman"'>Introduction: <o:p></o:p></span></h2>
1215
1216<p class=MsoNormal>In these exercises you will use GSAS-II to refine the
1217structure of sapphire (really corundum, Al<sub>2</sub>O<sub>3</sub>) from
1218single crystal diffraction data collected at the SNS on the TOPAZ instrument at
1219room temperature. The data consists of a suite of exposures with the crystal in
122031 different orientations all within a single data file. Note that menu entries
1221and user input are shown in bold face below as <b style='mso-bidi-font-weight:
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1223minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1224mso-bidi-theme-font:minor-latin'>Help/About GSAS-II</span></b>, which lists
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1228minor-latin'>Help</span></b>) and second the name of the entry in the menu
1229(here <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1230mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1231Calibri;mso-bidi-theme-font:minor-latin'>About GSAS-II</span></b>). If you have
1232not done so already, start GSAS-II.</p>
1233
1234<h2>Step 1. Setup the phase information for sapphire</h2>
1235
1236<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1237style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
1238style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Use
1239the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1240mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1241Calibri;mso-bidi-theme-font:minor-latin'>Data/Add phase</span></b> menu item
1242add a new phase into the current GSAS-II project. A popup window will appear
1243asking for a phase name; I entered <b style='mso-bidi-font-weight:normal'><span
1244style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1245mso-hansi-theme-font:minor-latin'>sapphire</span></b>; press <b
1246style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1247mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>
1248when done. Select <b style='mso-bidi-font-weight:normal'><span
1249style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1250mso-hansi-theme-font:minor-latin'>Loaded Data/Phases/sapphire</span></b> from
1251the GSAS-II Data tree window. The General tab for Phase Data will appear.</p>
1252
1253<p class=MsoListParagraph><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
1254 id="_x0000_t75" coordsize="21600,21600" o:spt="75" o:preferrelative="t"
1255 path="m@4@5l@4@11@9@11@9@5xe" filled="f" stroked="f">
1256 <v:stroke joinstyle="miter"/>
1257 <v:formulas>
1258  <v:f eqn="if lineDrawn pixelLineWidth 0"/>
1259  <v:f eqn="sum @0 1 0"/>
1260  <v:f eqn="sum 0 0 @1"/>
1261  <v:f eqn="prod @2 1 2"/>
1262  <v:f eqn="prod @3 21600 pixelWidth"/>
1263  <v:f eqn="prod @3 21600 pixelHeight"/>
1264  <v:f eqn="sum @0 0 1"/>
1265  <v:f eqn="prod @6 1 2"/>
1266  <v:f eqn="prod @7 21600 pixelWidth"/>
1267  <v:f eqn="sum @8 21600 0"/>
1268  <v:f eqn="prod @7 21600 pixelHeight"/>
1269  <v:f eqn="sum @10 21600 0"/>
1270 </v:formulas>
1271 <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
1272 <o:lock v:ext="edit" aspectratio="t"/>
1273</v:shapetype><v:shape id="_x0000_i1050" type="#_x0000_t75" style='width:640.5pt;
1274 height:375pt;visibility:visible;mso-wrap-style:square'>
1275 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image001.png"
1276  o:title=""/>
1277</v:shape><![endif]--><![if !vml]><img width=854 height=500
1278src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image002.gif"
1279v:shapes="_x0000_i1050"><![endif]></span></p>
1280
1281<p class=MsoListParagraph><o:p>&nbsp;</o:p></p>
1282
1283<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1284style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
1285style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Enter
1286<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1287mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>R -3 c</span></b>
1288(don’t forget the spaces between axial fields) &amp; press <b style='mso-bidi-font-weight:
1289normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1290minor-latin;mso-hansi-theme-font:minor-latin'>Return</span></b>. A Space Group
1291Information popup window will appear; press <b style='mso-bidi-font-weight:
1292normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1293minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>. The General window
1294will be refreshed showing only the needed lattice <span style='mso-no-proof:
1295yes'>parameters for R -3 c. </span></p>
1296
1297<p class=MsoListParagraph><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1298 id="Picture_x0020_29" o:spid="_x0000_i1049" type="#_x0000_t75" style='width:487.5pt;
1299 height:375pt;visibility:visible;mso-wrap-style:square'>
1300 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image003.png"
1301  o:title=""/>
1302</v:shape><![endif]--><![if !vml]><img width=650 height=500
1303src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image004.gif"
1304v:shapes="Picture_x0020_29"><![endif]></span></p>
1305
1306<p class=MsoListParagraph><o:p>&nbsp;</o:p></p>
1307
1308<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1309style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1310style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Enter
1311<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1312mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>4.7613</span></b>
1313for <span class=GramE>a and</span> <b style='mso-bidi-font-weight:normal'><span
1314style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1315mso-hansi-theme-font:minor-latin'>12.9846</span></b> for c; a new cell volume
1316will be calculated. </p>
1317
1318<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1319style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
1320style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1321the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1322mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Atoms</span></b>
1323tab; it will be empty. Do <b style='mso-bidi-font-weight:normal'><span
1324style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1325mso-hansi-theme-font:minor-latin'>Edit/Append atom</span></b> from the <b
1326style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1327mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phase Data
1328for sapphire</span></b> menu twice. There will be two UNK entries in the table.</p>
1329
1330<p class=MsoListParagraph><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1331 id="Picture_x0020_31" o:spid="_x0000_i1048" type="#_x0000_t75" style='width:525pt;
1332 height:225pt;visibility:visible;mso-wrap-style:square'>
1333 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image005.png"
1334  o:title=""/>
1335</v:shape><![endif]--><![if !vml]><img width=700 height=300
1336src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image006.gif"
1337v:shapes="Picture_x0020_31"><![endif]></span></p>
1338
1339<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1340style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>5.<span
1341style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Double
1342click the first entry under Type (H); a periodic table will appear. Select <b
1343style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1344mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Al</span></b>.
1345Do the same for the second one and pick <b style='mso-bidi-font-weight:normal'><span
1346style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1347mso-hansi-theme-font:minor-latin'>O</span></b>. The Atom list should look like</p>
1348
1349<p class=MsoListParagraph><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1350 id="Picture_x0020_32" o:spid="_x0000_i1047" type="#_x0000_t75" style='width:525pt;
1351 height:225pt;visibility:visible;mso-wrap-style:square'>
1352 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image007.png"
1353  o:title=""/>
1354</v:shape><![endif]--><![if !vml]><img width=700 height=300
1355src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image008.gif"
1356v:shapes="Picture_x0020_32"><![endif]></span></p>
1357
1358<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1359style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>6.<span
1360style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Change
1361the <span class=GramE>Al(</span>z) to <b style='mso-bidi-font-weight:normal'><span
1362style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1363mso-hansi-theme-font:minor-latin'>0. 352</span></b>, the O(x) to <b
1364style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1365mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>-0.306</span></b>
1366and the <span class=GramE>O(</span>z) to <b style='mso-bidi-font-weight:normal'><span
1367style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1368mso-hansi-theme-font:minor-latin'>Œ</span></b> (it will be changed to 0.2500).
1369Site symmetries and multiplicities will automatically change for these
1370positions.</p>
1371
1372<p class=MsoListParagraph><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1373 id="Picture_x0020_34" o:spid="_x0000_i1046" type="#_x0000_t75" style='width:525pt;
1374 height:225pt;visibility:visible;mso-wrap-style:square'>
1375 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image009.png"
1376  o:title=""/>
1377</v:shape><![endif]--><![if !vml]><img width=700 height=300
1378src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image010.gif"
1379v:shapes="Picture_x0020_34"><![endif]></span></p>
1380
1381<p class=MsoListParagraph><o:p>&nbsp;</o:p></p>
1382
1383<p class=MsoListParagraph>This completes the initial phase setup for sapphire.
1384An alternative would be to read the phase information from another GSAS-II <span
1385class=SpellE>gpx</span> file, a <span class=SpellE>cif</span> file or an old
1386GSAS <span class=SpellE>exp</span> file; these are all accessed from the <b
1387style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1388mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Import/Phase</span></b>
1389menu item on the main GSAS-II Data tree window. It may be useful to save your
1390project at this point; select <b style='mso-bidi-font-weight:normal'><span
1391style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1392mso-hansi-theme-font:minor-latin'>File/Save project as…</span></b> from the
1393main GSAS-II Data tree window menu. A file dialog box will appear; select the
1394directory and give a file name (no extension – I chose <b style='mso-bidi-font-weight:
1395normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1396minor-latin;mso-hansi-theme-font:minor-latin'>sapphire</span></b>).</p>
1397
1398<h2>Step 2. Import the diffraction data</h2>
1399
1400<p class=MsoNormal>The diffraction data collected on TOPAZ has been processed
1401(absorption corrections, wavelength and geometric corrections) to give a single
1402file with 31 embedded histograms as a space delimited multicolumn text file (<span
1403class=SpellE>sapphire_sphere.hkl</span>). To read this file select <b
1404style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1405mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Import/Structure
1406Factor/from Neutron TOF HKL F<sup>2 </sup>file</span></b>; a file dialog box
1407will appear. Change the directory to the location of this exercise (<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'>exercises/TOF
1410Single Crystal Refinement</span></b> – yours might be different), select <span
1411class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1412"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1413minor-latin'>sapphire_sphere.hkl</span></b></span> and press <b
1414style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1415mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Open</span></b>.
1416A popup will show a bit of the file and ask if you want to read this file;
1417press <span class=GramE><b style='mso-bidi-font-weight:normal'><span
1418style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1419mso-hansi-theme-font:minor-latin'>Yes</span></b></span>. Another popup will
1420appear with a suggested name for the data; this will be used for the GSAS-II
1421Data tree. Press <b style='mso-bidi-font-weight:normal'><span style='font-family:
1422"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1423minor-latin'>OK</span></b>. The console will show messages as each histogram is
1424read; when done a new popup will appear</p>
1425
1426<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1427 id="Picture_x0020_35" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:240pt;
1428 height:232.5pt;visibility:visible;mso-wrap-style:square'>
1429 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image011.png"
1430  o:title=""/>
1431</v:shape><![endif]--><![if !vml]><img width=320 height=310
1432src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image012.gif"
1433v:shapes="Picture_x0020_35"><![endif]></span></p>
1434
1435<p class=MsoNormal>This makes the connection between the data you just read and
1436the phase (<b style='mso-bidi-font-weight:normal'><span style='font-family:
1437"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1438minor-latin'>sapphire</span></b>) you entered in Step 1. Select it (or <b
1439style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1440mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Set All</span></b>)
1441and press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1442mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1443The GSAS-II data tree window will show all the new histograms, expanding the
1444last one.</p>
1445
1446<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1447 id="Picture_x0020_36" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:300pt;
1448 height:187.5pt;visibility:visible;mso-wrap-style:square'>
1449 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image013.png"
1450  o:title=""/>
1451</v:shape><![endif]--><![if !vml]><img width=400 height=250
1452src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image014.gif"
1453v:shapes="Picture_x0020_36"><![endif]></span></p>
1454
1455<p class=MsoNormal>The plot window shows a not very interesting 2D view of the
1456l=0 layer of reciprocal space for the last data set. If you select the 1<sup>st</sup>
1457HKLF entry (<b style='mso-bidi-font-weight:normal'><span style='font-family:
1458"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1459minor-latin'>HKLF <span class=SpellE>sapphire_sphere.hkl</span></span></b>) the
1460plot is a bit more interesting.</p>
1461
1462<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1463 id="Picture_x0020_10" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:525pt;
1464 height:450pt;visibility:visible;mso-wrap-style:square'>
1465 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image015.png"
1466  o:title=""/>
1467</v:shape><![endif]--><![if !vml]><img width=700 height=600
1468src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image016.gif"
1469v:shapes="Picture_x0020_10"><![endif]></span></p>
1470
1471<p class=MsoNormal>Green circles are drawn representing the magnitude of 4
1472structure factors on the l=0 layer. The positions are strictly on a square
1473grid; you can “tab” through the layers on l with <span class=GramE>the <b
1474style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1475mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>+/-</span></b></span>
1476keys. Find other commands in the “K” box in the tools part of the plot. If you
1477select <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1478mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Commands/Plot
14793D HKLs</span></b> from the data window you’ll see a 3D view of this reflection
1480set; press <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1481style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1482mso-hansi-theme-font:minor-latin'>i</span></b></span> after selecting the plot
1483(I’ve zoomed in a bit)</p>
1484
1485<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1486
1487<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1488 id="Picture_x0020_11" o:spid="_x0000_i1042" type="#_x0000_t75" style='width:363pt;
1489 height:311.25pt;visibility:visible;mso-wrap-style:square'>
1490 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image017.png"
1491  o:title="" croptop="11818f" cropbottom="16324f" cropleft="40001f"
1492  cropright="10518f"/>
1493</v:shape><![endif]--><![if !vml]><img width=484 height=415
1494src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image018.jpg"
1495v:shapes="Picture_x0020_11"><![endif]></span></p>
1496
1497<p class=MsoNormal>Here the plot has the correct representation for reciprocal
1498space as sampled by this crystal orientation on TOPAZ. The <b style='mso-bidi-font-weight:
1499normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1500minor-latin;mso-hansi-theme-font:minor-latin'>save as/key</span></b> commands
1501give you control on the appearance of the plot; the plot responds to
1502zoom/rotate commands from the mouse. Left mouse button to rotate, right mouse
1503button to translate, center wheel to rotate about view direction and the wheel
1504to zoom in or out. One cursor is the view point and the other is the 000
1505reciprocal space origin. </p>
1506
1507<p class=MsoNormal>If you want to see the entire data set plotted together do <b
1508style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1509mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Commands/Plot
1510all 3D HKLs</span></b>; a data selection popup window will appear. Do <b
1511style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1512mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Set Al</span></b>l
1513and then <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1514mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>
1515to select all the data; the plot will be redrawn (I’ve pressed the ‘<span
1516class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1517"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1518minor-latin'>i</span></b></span>’ key as before)</p>
1519
1520<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1521 id="Picture_x0020_12" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:365.25pt;
1522 height:310.5pt;visibility:visible;mso-wrap-style:square'>
1523 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image019.png"
1524  o:title="" croptop="12098f" cropbottom="16193f" cropleft="40187f"
1525  cropright="10237f"/>
1526</v:shape><![endif]--><![if !vml]><img width=487 height=414
1527src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image020.jpg"
1528v:shapes="Picture_x0020_12"><![endif]></span></p>
1529
1530<p class=MsoNormal>I’ve rotated the drawing around to show an obvious gap in
1531the coverage.</p>
1532
1533<p class=MsoNormal>We’re now ready to do the refinement.</p>
1534
1535<h2>Step 3. Initial least squares refinement</h2>
1536
1537<p class=MsoNormal>By default the scale factors for all 31 data set are set to
1538be refined so you can immediately do a refinement. Select <b style='mso-bidi-font-weight:
1539normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1540minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> from
1541the main GSAS-II data tree window menu. This will do an F refinement by
1542default. A progress bar will appear to show you the residuals as the histograms
1543are processed. When it finishes and you have accepted the result a plot will
1544show the l=0 layer for the 1<sup>st</sup> data set.</p>
1545
1546<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1547 id="_x0000_i1040" type="#_x0000_t75" style='width:525pt;height:450pt;
1548 visibility:visible;mso-wrap-style:square'>
1549 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image021.png"
1550  o:title=""/>
1551</v:shape><![endif]--><![if !vml]><img width=700 height=600
1552src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image022.gif"
1553v:shapes="_x0000_i1040"><![endif]></span></p>
1554
1555<p class=MsoNormal>Green rings are the observed magnitude, blue rings are the
1556calculated ones and the solid disk is the difference (green for positive &amp;
1557red for negative <span class=SpellE>F<sub>o</sub></span>-F<sub>c</sub>). You
1558can see the whole scope of the fit by doing <b style='mso-bidi-font-weight:
1559normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1560minor-latin;mso-hansi-theme-font:minor-latin'>Commands/Plot all 3D HKLs</span></b>
1561and selecting all the HKLF entries; press the “<b style='mso-bidi-font-weight:
1562normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1563minor-latin;mso-hansi-theme-font:minor-latin'>w</span></b>” key to show the
1564weighted &#916;F points.</p>
1565
1566<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1567 id="_x0000_i1039" type="#_x0000_t75" style='width:369pt;height:310.5pt;
1568 visibility:visible;mso-wrap-style:square'>
1569 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image023.png"
1570  o:title="" croptop="9828f" cropbottom="18427f" cropleft="38257f" cropright="12033f"/>
1571</v:shape><![endif]--><![if !vml]><img width=492 height=414
1572src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image024.jpg"
1573v:shapes="_x0000_i1039"><![endif]></span></p>
1574
1575<p class=MsoNormal>The size of the squares is proportional to the magnitude of <span
1576class=SpellE>w&#916;F</span>. The cluster of negative <span class=SpellE>w&#916;F</span>
1577points around the reciprocal space origin is pretty clearly a consequence of
1578extinction so we’ll have to include that in the refinement model. One should
1579not be tempted to refine coordinates and thermal parameters until extinction is
1580accounted for in the refinement.</p>
1581
1582<h2>Step 3. Extinction model selection and refinement</h2>
1583
1584<p class=MsoNormal>GSAS-II has a number of extinction models available for
1585single crystal data. These include Primary, Secondary types I and II with
1586either Gaussian or Lorentzian distributions. To select one find the <b
1587style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1588mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sapphire</span></b>
1589entry in the GSAS-II data tree and select its <b style='mso-bidi-font-weight:
1590normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1591minor-latin;mso-hansi-theme-font:minor-latin'>Data</span></b> tab.</p>
1592
1593<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1594 id="Picture_x0020_16" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:300pt;
1595 height:303pt;visibility:visible;mso-wrap-style:square'>
1596 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image025.png"
1597  o:title=""/>
1598</v:shape><![endif]--><![if !vml]><img width=400 height=404
1599src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image026.gif"
1600v:shapes="Picture_x0020_16"><![endif]></span></p>
1601
1602<p class=MsoNormal>We can cut to the chase here – select <b style='mso-bidi-font-weight:
1603normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1604minor-latin;mso-hansi-theme-font:minor-latin'>Secondary Type I</span></b> from
1605the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1606mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Extinction
1607type</span></b> pull down list (the tab will be redrawn) and check the <span
1608class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1609"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1610minor-latin'>Eg</span></b></span> box; leave the <span class=SpellE><b
1611style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1612mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Approx</span></b></span>
1613selection as <b style='mso-bidi-font-weight:normal'><span style='font-family:
1614"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1615minor-latin'>Lorentzian</span></b>. Later on after you’ve finished the
1616tutorial, you can try the other models and see how they compare. Next do <b
1617style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1618mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Copy
1619selected data</span></b>, pick <b style='mso-bidi-font-weight:normal'><span
1620style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1621mso-hansi-theme-font:minor-latin'>Extinction</span></b> from the list of
1622parameters and press <b style='mso-bidi-font-weight:normal'><span
1623style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1624mso-hansi-theme-font:minor-latin'>OK</span></b>. Then do <b style='mso-bidi-font-weight:
1625normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1626minor-latin;mso-hansi-theme-font:minor-latin'>Set All</span></b> and press <b
1627style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1628mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>
1629from the next popup; this will copy the extinction model to all HKLF data sets.</p>
1630
1631<p class=MsoNormal>Because all of these extinction models are needed for one crystal,
1632it makes sense to tie them together into a single parameter. Select <b
1633style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1634mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Constraints</span></b>
1635from the main GSAS-II data tree and pick the <b style='mso-bidi-font-weight:
1636normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1637minor-latin;mso-hansi-theme-font:minor-latin'>Histogram/Phase constraints</span></b>
1638tab; it will be empty. Do <b style='mso-bidi-font-weight:normal'><span
1639style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1640mso-hansi-theme-font:minor-latin'>Edit/Add equivalence</span></b>; the
1641following popup will appear</p>
1642
1643<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1644 id="Picture_x0020_17" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:468.75pt;
1645 height:300pt;visibility:visible;mso-wrap-style:square'>
1646 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image027.png"
1647  o:title=""/>
1648</v:shape><![endif]--><![if !vml]><img width=625 height=400
1649src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image028.gif"
1650v:shapes="Picture_x0020_17"><![endif]></span></p>
1651
1652<p class=MsoNormal>Select the line beginning with ‘<b style='mso-bidi-font-weight:
1653normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1654minor-latin;mso-hansi-theme-font:minor-latin'>0:0<span class=GramE>:Eg<span
1655style='font-family:"Times New Roman",serif;font-weight:normal'>’</span></span></span></b>
1656(the Secondary type I parameter you just set to vary) and press <b
1657style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1658mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1659A new popup will appear; you’ll want to see the bottom of the list</p>
1660
1661<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1662 id="Picture_x0020_18" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:468.75pt;
1663 height:300pt;visibility:visible;mso-wrap-style:square'>
1664 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image029.png"
1665  o:title=""/>
1666</v:shape><![endif]--><![if !vml]><img width=625 height=400
1667src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image030.gif"
1668v:shapes="Picture_x0020_18"><![endif]></span></p>
1669
1670<p class=MsoNormal>Pick either <b style='mso-bidi-font-weight:normal'><span
1671style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1672mso-hansi-theme-font:minor-latin'>0<span class=GramE>:all:Eg</span></span></b>
1673or <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1674mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0:all=<span
1675class=SpellE>SNT:Eg</span></span></b> and press <b style='mso-bidi-font-weight:
1676normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1677minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>. The equivalence
1678making <span class=SpellE>Eg</span> for all histograms the same parameter will
1679be shown</p>
1680
1681<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1682 id="Picture_x0020_20" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:481.5pt;
1683 height:184.5pt;visibility:visible;mso-wrap-style:square'>
1684 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image031.png"
1685  o:title=""/>
1686</v:shape><![endif]--><![if !vml]><img width=642 height=246
1687src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image032.gif"
1688v:shapes="Picture_x0020_20"><![endif]></span></p>
1689
1690<p class=MsoNormal>Now do <b style='mso-bidi-font-weight:normal'><span
1691style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1692mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> from the main
1693GSAS-II data tree menu. You may have to repeat this twice to get convergence (<span
1694class=SpellE>Rw</span> ~14%); note the console output – value of Delta
1695indicates closeness to convergence. Select one of the HKLF data sets and view
1696the 3D Structure Factors plot for it alone</p>
1697
1698<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1699 id="_x0000_i1034" type="#_x0000_t75" style='width:362.25pt;height:311.25pt;
1700 visibility:visible;mso-wrap-style:square'>
1701 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image033.png"
1702  o:title="" croptop="15476f" cropbottom="12688f" cropleft="40744f"
1703  cropright="9798f"/>
1704</v:shape><![endif]--><![if !vml]><img width=483 height=415
1705src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image034.jpg"
1706v:shapes="_x0000_i1034"><![endif]></span></p>
1707
1708<p class=MsoNormal>The <span class=SpellE>wDF</span> is positive close to 0<span
1709class=GramE>,0,0</span> then negative for an inner shell around the positive
1710core and finally positive for the outer shell. This is a thermal
1711parameter/extinction effect. So both have to be now refined. However, as a
1712matter of course we may expect that the extinction corrections are less
1713accurate when <span class=SpellE><span class=GramE>Fo</span></span>&lt;&lt; Fc.
1714In addition some reflections were poorly measured. We want to reject
1715reflections where <span class=SpellE>Fo</span>/Fc &lt; 0.5 and Fo2/<span
1716class=GramE>s(</span>Fo2) &lt; 3. These can be applied on the <b
1717style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1718mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Controls</span></b>
1719page. After setting these my Controls were</p>
1720
1721<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1722 id="_x0000_i1033" type="#_x0000_t75" style='width:366pt;height:212.25pt;
1723 visibility:visible;mso-wrap-style:square'>
1724 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image035.png"
1725  o:title=""/>
1726</v:shape><![endif]--><![if !vml]><img width=488 height=283
1727src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image036.gif"
1728v:shapes="_x0000_i1033"><![endif]></span></p>
1729
1730<p class=MsoNormal>Finally we can add the atom parameters for sapphire. Select
1731the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1732mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Atoms</span></b>
1733tab for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1734mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phase/sapphire</span></b></p>
1735
1736<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1737 id="Picture_x0020_21" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:525pt;
1738 height:225pt;visibility:visible;mso-wrap-style:square'>
1739 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image009.png"
1740  o:title=""/>
1741</v:shape><![endif]--><![if !vml]><img width=700 height=300
1742src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image010.gif"
1743v:shapes="Picture_x0020_21"><![endif]></span></p>
1744
1745<p class=MsoNormal>Double (right) click the <b style='mso-bidi-font-weight:
1746normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1747minor-latin;mso-hansi-theme-font:minor-latin'>Refine</span></b> column heading;
1748a popup will appear</p>
1749
1750<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1751 id="Picture_x0020_22" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:259.5pt;
1752 height:252pt;visibility:visible;mso-wrap-style:square'>
1753 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image037.png"
1754  o:title=""/>
1755</v:shape><![endif]--><![if !vml]><img width=346 height=336
1756src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image038.gif"
1757v:shapes="Picture_x0020_22"><![endif]></span></p>
1758
1759<p class=MsoNormal>Choose both <b style='mso-bidi-font-weight:normal'><span
1760style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1761mso-hansi-theme-font:minor-latin'>X</span></b> and <b style='mso-bidi-font-weight:
1762normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1763minor-latin;mso-hansi-theme-font:minor-latin'>U</span></b> and press <b
1764style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1765mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>;
1766the Atoms tab will be redrawn</p>
1767
1768<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1769 id="Picture_x0020_23" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:525pt;
1770 height:225pt;visibility:visible;mso-wrap-style:square'>
1771 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image039.png"
1772  o:title=""/>
1773</v:shape><![endif]--><![if !vml]><img width=700 height=300
1774src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image040.gif"
1775v:shapes="Picture_x0020_23"><![endif]></span></p>
1776
1777<p class=MsoNormal>Showing the refine flags for both atoms. GSAS-II will sort
1778out the special position rules for the two sites.</p>
1779
1780<p class=MsoNormal>Now do <b style='mso-bidi-font-weight:normal'><span
1781style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1782mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> (twice to get
1783convergence). My <span class=SpellE>Rw</span> = 5.91%, GOF = 2.4; find these on
1784the <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'>Covariance</span></b>
1786data window. Now get a new 3D plot of all the reflections; select any HKLF
1787entry, then do <b style='mso-bidi-font-weight:normal'><span style='font-family:
1788"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1789minor-latin'>Commands/Plot all 3D HKLs</span></b>. Press <b style='mso-bidi-font-weight:
1790normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1791minor-latin;mso-hansi-theme-font:minor-latin'>w</span></b> key.</p>
1792
1793<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1794 id="Picture_x0020_24" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:363pt;
1795 height:312.75pt;visibility:visible;mso-wrap-style:square'>
1796 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image041.png"
1797  o:title="" croptop="10627f" cropbottom="17360f" cropleft="40646f"
1798  cropright="9847f"/>
1799</v:shape><![endif]--><![if !vml]><img width=484 height=417
1800src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image042.jpg"
1801v:shapes="Picture_x0020_24"><![endif]></span></p>
1802
1803<p class=MsoNormal>It’s pretty obvious that there is one really bad reflection
1804and (a bit more subtly) it is messing up one TOPAS data set. To find it first
1805look through the <span class=SpellE><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'>sapphire.lst</span></b></span> file; that
1808will give fitting information for all the histograms (near bottom of the
1809listing). Open it with your favorite text editor; I’ve shown an interesting bit
1810of it here showing results for histograms 22-24.</p>
1811
1812<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1813
1814<p class=MsoNormal>Phase:<span style='mso-spacerun:yes'>  </span><span
1815class=GramE>sapphire<span style='mso-spacerun:yes'>  </span>in</span>
1816histogram:<span style='mso-spacerun:yes'>  </span>HKLF
1817sapphire_sphere.hkl_22<span
1818style='mso-spacerun:yes'>                                         </span><o:p></o:p></p>
1819
1820<p class=MsoNormal>------------------------------------------------------------------------------------------------------<o:p></o:p></p>
1821
1822<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Final refinement RF,
1823RF^2 = 4.64%, 8.41% on 134 reflections (3 user rejected, 9 <span class=SpellE>sp.gp.extinct</span>)<span
1824style='mso-spacerun:yes'>       </span><o:p></o:p></p>
1825
1826<p class=MsoNormal><span style='mso-spacerun:yes'> </span>HKLF histogram weight
1827factor <span class=GramE>=<span style='mso-spacerun:yes'>  </span>1.000</span><span
1828style='mso-spacerun:yes'>                                                               
1829</span><o:p></o:p></p>
1830
1831<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Scale <span
1832class=GramE>factor :</span><span style='mso-spacerun:yes'>    </span>66.8623,
1833sig<span style='mso-spacerun:yes'>     </span>0.8144<span
1834style='mso-spacerun:yes'>        </span><span
1835style='mso-spacerun:yes'>                                                    </span><o:p></o:p></p>
1836
1837<p class=MsoNormal><span
1838style='mso-spacerun:yes'>                                                                                                     
1839</span><o:p></o:p></p>
1840
1841<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Single crystal
1842extinction: Type:<span style='mso-spacerun:yes'>  </span><span class=GramE>Lorentzian<span
1843style='mso-spacerun:yes'>  </span><span class=SpellE>Approx</span></span>:<span
1844style='mso-spacerun:yes'>  </span>Secondary Type I<span
1845style='mso-spacerun:yes'>                            </span><span
1846style='mso-spacerun:yes'>  </span><o:p></o:p></p>
1847
1848<p class=MsoNormal><span style='mso-spacerun:yes'>       </span><span
1849class=SpellE>Eg</span>:<span style='mso-spacerun:yes'>     </span>5.58e-04
1850sig:<span style='mso-spacerun:yes'>     </span>1.28e-05<span
1851style='mso-spacerun:yes'>                                                            
1852</span><o:p></o:p></p>
1853
1854<p class=MsoNormal><span
1855style='mso-spacerun:yes'>                                                                                                     
1856</span><o:p></o:p></p>
1857
1858<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Phase:<span
1859style='mso-spacerun:yes'>  </span><span class=GramE>sapphire<span
1860style='mso-spacerun:yes'>  </span>in</span> histogram:<span
1861style='mso-spacerun:yes'>  </span>HKLF sapphire_sphere.hkl_23<span
1862style='mso-spacerun:yes'>                                         </span><o:p></o:p></p>
1863
1864<p class=MsoNormal>------------------------------------------------------------------------------------------------------<o:p></o:p></p>
1865
1866<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Final refinement RF,
1867RF^2 = 21.69%, 38.49% on 148 reflections (5 user rejected, 6 <span
1868class=SpellE>sp.gp.extinct</span>)<span style='mso-spacerun:yes'>     </span><o:p></o:p></p>
1869
1870<p class=MsoNormal><span style='mso-spacerun:yes'> </span>HKLF histogram weight
1871factor <span class=GramE>=<span style='mso-spacerun:yes'>  </span>1.000</span><span
1872style='mso-spacerun:yes'>                                                               
1873</span><o:p></o:p></p>
1874
1875<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Scale <span
1876class=GramE>factor :</span><span style='mso-spacerun:yes'>    </span>43.2084,
1877sig<span style='mso-spacerun:yes'>     </span>0.6507<span
1878style='mso-spacerun:yes'>                                                           
1879</span><o:p></o:p></p>
1880
1881<p class=MsoNormal><span
1882style='mso-spacerun:yes'>                                            </span><span
1883style='mso-spacerun:yes'>                                                          </span><o:p></o:p></p>
1884
1885<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Single crystal
1886extinction: Type:<span style='mso-spacerun:yes'>  </span><span class=GramE>Lorentzian<span
1887style='mso-spacerun:yes'>  </span><span class=SpellE>Approx</span></span>:<span
1888style='mso-spacerun:yes'>  </span>Secondary Type I<span
1889style='mso-spacerun:yes'>                              </span><o:p></o:p></p>
1890
1891<p class=MsoNormal><span style='mso-spacerun:yes'>       </span><span
1892class=SpellE>Eg</span>:<span style='mso-spacerun:yes'>     </span>5.58e-04
1893sig:<span style='mso-spacerun:yes'>     </span>1.28e-05<span
1894style='mso-spacerun:yes'>                                                    
1895</span><span style='mso-spacerun:yes'>        </span><o:p></o:p></p>
1896
1897<p class=MsoNormal><span
1898style='mso-spacerun:yes'>                                                                                                     
1899</span><o:p></o:p></p>
1900
1901<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Phase:<span
1902style='mso-spacerun:yes'>  </span><span class=GramE>sapphire<span
1903style='mso-spacerun:yes'>  </span>in</span> histogram:<span
1904style='mso-spacerun:yes'>  </span>HKLF sapphire_sphere.hkl_24<span
1905style='mso-spacerun:yes'>                                         </span><o:p></o:p></p>
1906
1907<p class=MsoNormal>------------------------------------------------------------------------------------------------------<o:p></o:p></p>
1908
1909<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Final refinement RF,
1910RF^2 = 3.86%, 6.70% on 160 reflections (11 user rejected, 1 <span class=SpellE>sp.gp.extinct</span>)<span
1911style='mso-spacerun:yes'>      </span><o:p></o:p></p>
1912
1913<p class=MsoNormal><span style='mso-spacerun:yes'> </span>HKLF histogram weight
1914factor <span class=GramE>=<span style='mso-spacerun:yes'>  </span>1.000</span><span
1915style='mso-spacerun:yes'>                                                    
1916</span><span style='mso-spacerun:yes'>           </span><o:p></o:p></p>
1917
1918<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Scale <span
1919class=GramE>factor :</span><span style='mso-spacerun:yes'>    </span>66.6296,
1920sig<span style='mso-spacerun:yes'>     </span>0.7816<span
1921style='mso-spacerun:yes'>                                                           
1922</span><o:p></o:p></p>
1923
1924<p class=MsoNormal><span
1925style='mso-spacerun:yes'>                                                                                                     
1926</span><o:p></o:p></p>
1927
1928<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Single crystal
1929extinction: Type:<span style='mso-spacerun:yes'>  </span><span class=GramE>Lorentzian<span
1930style='mso-spacerun:yes'>  </span><span class=SpellE>Approx</span></span>:<span
1931style='mso-spacerun:yes'>  </span>Secondary Type I<span
1932style='mso-spacerun:yes'>                              </span><o:p></o:p></p>
1933
1934<p class=MsoNormal><span style='mso-spacerun:yes'>       </span><span
1935class=SpellE>Eg</span>:<span style='mso-spacerun:yes'>     </span>5.58e-04
1936sig:<span style='mso-spacerun:yes'>     </span>1.28e-05<span
1937style='mso-spacerun:yes'>                                                            
1938</span><o:p></o:p></p>
1939
1940<p class=MsoNormal><span
1941style='mso-spacerun:yes'>                                                                                       
1942</span><span style='mso-spacerun:yes'>              </span></p>
1943
1944<p class=MsoNormal>There is obviously something wrong with #23 (high residual
1945&amp; funny scale factor compared to the others). Find <b style='mso-bidi-font-weight:
1946normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1947minor-latin;mso-hansi-theme-font:minor-latin'>HKLF sapphire_sphere.hkl_23</span></b>
1948in the GSAS-II data tree &amp; select it. The 3D plot of just that data set
1949will show the problem reflection.</p>
1950
1951<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1952 id="Picture_x0020_25" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:365.25pt;
1953 height:315pt;visibility:visible;mso-wrap-style:square'>
1954 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image043.png"
1955  o:title="" croptop="9290f" cropbottom="18441f" cropleft="38576f" cropright="11843f"/>
1956</v:shape><![endif]--><![if !vml]><img width=487 height=420
1957src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image044.jpg"
1958v:shapes="Picture_x0020_25"><![endif]></span></p>
1959
1960<p class=MsoNormal>By zooming in and rotating the plot around a bit, you can identify
1961the reflection with the cursor. It seems to be the <b style='mso-bidi-font-weight:
1962normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1963minor-latin;mso-hansi-theme-font:minor-latin'>541</span></b> reflection; select
1964the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1965mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Reflection
1966List</span></b> and look for it (unfortunately the reflections are produced in
1967a somewhat random order by the TOPAZ data acquisition system). It is very near
1968the bottom of the list (#<b style='mso-bidi-font-weight:normal'><span
1969style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1970mso-hansi-theme-font:minor-latin'>153</span></b>).</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_i1027" type="#_x0000_t75" style='width:585pt;
1974 height:244.5pt;visibility:visible;mso-wrap-style:square'>
1975 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image045.png"
1976  o:title=""/>
1977</v:shape><![endif]--><![if !vml]><img width=780 height=326
1978src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image046.gif"
1979v:shapes="Picture_x0020_26"><![endif]></span></p>
1980
1981<p class=MsoNormal>The <span class=SpellE>Fcsq</span> (F<sub>c</sub><sup>2</sup>)
1982is very much larger than <span class=SpellE>Fosq</span> (F<sub>o</sub><sup>2</sup>)
1983so that |&#916;F<sup>2</sup>|/<span class=GramE>&#963;(</span>F<sub>o</sub><sup>2</sup>)
1984&gt; 80! It was obviously poorly measured (e.g. on the edge of the detector,
1985etc.). We’d like to eliminate it, but perhaps we might be better setting a
1986lower cutoff on |&#916;F<sup>2</sup>|/<span class=GramE>&#963;(</span>F<sub>o</sub><sup>2</sup>)
1987to eliminate other similar problem reflections. Go to the <b style='mso-bidi-font-weight:
1988normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1989minor-latin;mso-hansi-theme-font:minor-latin'>Controls</span></b> entry in the
1990GSAS-II data tree</p>
1991
1992<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1993 id="Picture_x0020_27" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:391.5pt;
1994 height:225.75pt;visibility:visible;mso-wrap-style:square'>
1995 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image047.png"
1996  o:title=""/>
1997</v:shape><![endif]--><![if !vml]><img width=522 height=301
1998src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image048.gif"
1999v:shapes="Picture_x0020_27"><![endif]></span></p>
2000
2001<p class=MsoNormal>Change the value of <b style='mso-bidi-font-weight:normal'><span
2002style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2003mso-hansi-theme-font:minor-latin'>Max <span class=SpellE>delt</span>-F/sig</span></b>
2004to 20; that will certainly eliminate the bad 541 reflection &amp; perhaps a few
2005others. Repeat <b style='mso-bidi-font-weight:normal'><span style='font-family:
2006"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2007minor-latin'>Calculate/Refine</span></b>; my residual dropped considerably (<span
2008class=SpellE>Rw</span> ~4.5%) and the 3D plot shows no really bad reflections</p>
2009
2010<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2011 id="Picture_x0020_28" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:363pt;
2012 height:309.75pt;visibility:visible;mso-wrap-style:square'>
2013 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image049.png"
2014  o:title="" croptop="8876f" cropbottom="19515f" cropleft="39851f" cropright="10631f"/>
2015</v:shape><![endif]--><![if !vml]><img width=484 height=413
2016src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image050.jpg"
2017v:shapes="Picture_x0020_28"><![endif]></span></p>
2018
2019<p class=MsoNormal>Looking the <span class=SpellE><b style='mso-bidi-font-weight:
2020normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2021minor-latin;mso-hansi-theme-font:minor-latin'>sapphire.lst</span></b></span><b
2022style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2023mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> </span></b>file
2024shows that HKLF #23 is now more in line with the other ones (RF = 4.35% &amp;
2025scale = 67.41). To finish the refinement make the two sapphire atoms have
2026anisotropic thermal parameters. Select <b style='mso-bidi-font-weight:normal'><span
2027style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2028mso-hansi-theme-font:minor-latin'>Phases/sapphire</span></b> and the <b
2029style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2030mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Atoms</span></b>
2031tab; then double click <span class=GramE>the <b style='mso-bidi-font-weight:
2032normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2033minor-latin;mso-hansi-theme-font:minor-latin'>I</span></b></span><b
2034style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2035mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>/A</span></b>
2036column heading. A popup will appear; select <b style='mso-bidi-font-weight:
2037normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2038minor-latin;mso-hansi-theme-font:minor-latin'>Anisotropic</span></b> and press <b
2039style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2040mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
2041The atom <span class=SpellE>Uijs</span> will appear and <span class=SpellE>Uiso</span>
2042will be greyed out. Then do <b style='mso-bidi-font-weight:normal'><span
2043style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2044mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> again. My final
2045residual was <span class=SpellE>Rw</span>=5.06%. </p>
2046
2047<p class=MsoNormal>This completes the tutorial. You can explore the other
2048extinction models and try different cutoff values for <b style='mso-bidi-font-weight:
2049normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2050minor-latin;mso-hansi-theme-font:minor-latin'>Max <span class=SpellE>delt</span>-F/sig</span></b>.
2051<b style='mso-bidi-font-weight:normal'><u>NB: this should never be set before
2052the refinement is complete as it can reject large portions of the data
2053prematurely.<o:p></o:p></u></b></p>
2054
2055</div>
2056
2057</body>
2058
2059</html>
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