source: Tutorials/TOF Single Crystal Refinement/TOF single crystal refinement in GSAS.htm @ 3073

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408  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 1"/>
409  <w:LsdException Locked="false" SemiHidden="true" Name="Revision"/>
410  <w:LsdException Locked="false" Priority="34" QFormat="true"
411   Name="List Paragraph"/>
412  <w:LsdException Locked="false" Priority="29" QFormat="true" Name="Quote"/>
413  <w:LsdException Locked="false" Priority="30" QFormat="true"
414   Name="Intense Quote"/>
415  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 1"/>
416  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 1"/>
417  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 1"/>
418  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 1"/>
419  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 1"/>
420  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 1"/>
421  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 1"/>
422  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 1"/>
423  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 2"/>
424  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 2"/>
425  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 2"/>
426  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 2"/>
427  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 2"/>
428  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 2"/>
429  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 2"/>
430  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 2"/>
431  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 2"/>
432  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 2"/>
433  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 2"/>
434  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 2"/>
435  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 2"/>
436  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 2"/>
437  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 3"/>
438  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 3"/>
439  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 3"/>
440  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 3"/>
441  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 3"/>
442  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 3"/>
443  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 3"/>
444  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 3"/>
445  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 3"/>
446  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 3"/>
447  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 3"/>
448  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 3"/>
449  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 3"/>
450  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 3"/>
451  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 4"/>
452  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 4"/>
453  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 4"/>
454  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 4"/>
455  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 4"/>
456  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 4"/>
457  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 4"/>
458  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 4"/>
459  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 4"/>
460  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 4"/>
461  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 4"/>
462  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 4"/>
463  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 4"/>
464  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 4"/>
465  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 5"/>
466  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 5"/>
467  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 5"/>
468  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 5"/>
469  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 5"/>
470  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 5"/>
471  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 5"/>
472  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 5"/>
473  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 5"/>
474  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 5"/>
475  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 5"/>
476  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 5"/>
477  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 5"/>
478  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 5"/>
479  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 6"/>
480  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 6"/>
481  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 6"/>
482  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 6"/>
483  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 6"/>
484  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 6"/>
485  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 6"/>
486  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 6"/>
487  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 6"/>
488  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 6"/>
489  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 6"/>
490  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 6"/>
491  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 6"/>
492  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 6"/>
493  <w:LsdException Locked="false" Priority="19" QFormat="true"
494   Name="Subtle Emphasis"/>
495  <w:LsdException Locked="false" Priority="21" QFormat="true"
496   Name="Intense Emphasis"/>
497  <w:LsdException Locked="false" Priority="31" QFormat="true"
498   Name="Subtle Reference"/>
499  <w:LsdException Locked="false" Priority="32" QFormat="true"
500   Name="Intense Reference"/>
501  <w:LsdException Locked="false" Priority="33" QFormat="true" Name="Book Title"/>
502  <w:LsdException Locked="false" Priority="37" SemiHidden="true"
503   UnhideWhenUsed="true" Name="Bibliography"/>
504  <w:LsdException Locked="false" Priority="39" SemiHidden="true"
505   UnhideWhenUsed="true" QFormat="true" Name="TOC Heading"/>
506  <w:LsdException Locked="false" Priority="41" Name="Plain Table 1"/>
507  <w:LsdException Locked="false" Priority="42" Name="Plain Table 2"/>
508  <w:LsdException Locked="false" Priority="43" Name="Plain Table 3"/>
509  <w:LsdException Locked="false" Priority="44" Name="Plain Table 4"/>
510  <w:LsdException Locked="false" Priority="45" Name="Plain Table 5"/>
511  <w:LsdException Locked="false" Priority="40" Name="Grid Table Light"/>
512  <w:LsdException Locked="false" Priority="46" Name="Grid Table 1 Light"/>
513  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2"/>
514  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3"/>
515  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4"/>
516  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark"/>
517  <w:LsdException Locked="false" Priority="51" Name="Grid Table 6 Colorful"/>
518  <w:LsdException Locked="false" Priority="52" Name="Grid Table 7 Colorful"/>
519  <w:LsdException Locked="false" Priority="46"
520   Name="Grid Table 1 Light Accent 1"/>
521  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 1"/>
522  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 1"/>
523  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 1"/>
524  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 1"/>
525  <w:LsdException Locked="false" Priority="51"
526   Name="Grid Table 6 Colorful Accent 1"/>
527  <w:LsdException Locked="false" Priority="52"
528   Name="Grid Table 7 Colorful Accent 1"/>
529  <w:LsdException Locked="false" Priority="46"
530   Name="Grid Table 1 Light Accent 2"/>
531  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 2"/>
532  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 2"/>
533  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 2"/>
534  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 2"/>
535  <w:LsdException Locked="false" Priority="51"
536   Name="Grid Table 6 Colorful Accent 2"/>
537  <w:LsdException Locked="false" Priority="52"
538   Name="Grid Table 7 Colorful Accent 2"/>
539  <w:LsdException Locked="false" Priority="46"
540   Name="Grid Table 1 Light Accent 3"/>
541  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 3"/>
542  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 3"/>
543  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 3"/>
544  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 3"/>
545  <w:LsdException Locked="false" Priority="51"
546   Name="Grid Table 6 Colorful Accent 3"/>
547  <w:LsdException Locked="false" Priority="52"
548   Name="Grid Table 7 Colorful Accent 3"/>
549  <w:LsdException Locked="false" Priority="46"
550   Name="Grid Table 1 Light Accent 4"/>
551  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 4"/>
552  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 4"/>
553  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 4"/>
554  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 4"/>
555  <w:LsdException Locked="false" Priority="51"
556   Name="Grid Table 6 Colorful Accent 4"/>
557  <w:LsdException Locked="false" Priority="52"
558   Name="Grid Table 7 Colorful Accent 4"/>
559  <w:LsdException Locked="false" Priority="46"
560   Name="Grid Table 1 Light Accent 5"/>
561  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 5"/>
562  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 5"/>
563  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 5"/>
564  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 5"/>
565  <w:LsdException Locked="false" Priority="51"
566   Name="Grid Table 6 Colorful Accent 5"/>
567  <w:LsdException Locked="false" Priority="52"
568   Name="Grid Table 7 Colorful Accent 5"/>
569  <w:LsdException Locked="false" Priority="46"
570   Name="Grid Table 1 Light Accent 6"/>
571  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 6"/>
572  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 6"/>
573  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 6"/>
574  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 6"/>
575  <w:LsdException Locked="false" Priority="51"
576   Name="Grid Table 6 Colorful Accent 6"/>
577  <w:LsdException Locked="false" Priority="52"
578   Name="Grid Table 7 Colorful Accent 6"/>
579  <w:LsdException Locked="false" Priority="46" Name="List Table 1 Light"/>
580  <w:LsdException Locked="false" Priority="47" Name="List Table 2"/>
581  <w:LsdException Locked="false" Priority="48" Name="List Table 3"/>
582  <w:LsdException Locked="false" Priority="49" Name="List Table 4"/>
583  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark"/>
584  <w:LsdException Locked="false" Priority="51" Name="List Table 6 Colorful"/>
585  <w:LsdException Locked="false" Priority="52" Name="List Table 7 Colorful"/>
586  <w:LsdException Locked="false" Priority="46"
587   Name="List Table 1 Light Accent 1"/>
588  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 1"/>
589  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 1"/>
590  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 1"/>
591  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 1"/>
592  <w:LsdException Locked="false" Priority="51"
593   Name="List Table 6 Colorful Accent 1"/>
594  <w:LsdException Locked="false" Priority="52"
595   Name="List Table 7 Colorful Accent 1"/>
596  <w:LsdException Locked="false" Priority="46"
597   Name="List Table 1 Light Accent 2"/>
598  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 2"/>
599  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 2"/>
600  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 2"/>
601  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 2"/>
602  <w:LsdException Locked="false" Priority="51"
603   Name="List Table 6 Colorful Accent 2"/>
604  <w:LsdException Locked="false" Priority="52"
605   Name="List Table 7 Colorful Accent 2"/>
606  <w:LsdException Locked="false" Priority="46"
607   Name="List Table 1 Light Accent 3"/>
608  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 3"/>
609  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 3"/>
610  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 3"/>
611  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 3"/>
612  <w:LsdException Locked="false" Priority="51"
613   Name="List Table 6 Colorful Accent 3"/>
614  <w:LsdException Locked="false" Priority="52"
615   Name="List Table 7 Colorful Accent 3"/>
616  <w:LsdException Locked="false" Priority="46"
617   Name="List Table 1 Light Accent 4"/>
618  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 4"/>
619  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 4"/>
620  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 4"/>
621  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 4"/>
622  <w:LsdException Locked="false" Priority="51"
623   Name="List Table 6 Colorful Accent 4"/>
624  <w:LsdException Locked="false" Priority="52"
625   Name="List Table 7 Colorful Accent 4"/>
626  <w:LsdException Locked="false" Priority="46"
627   Name="List Table 1 Light Accent 5"/>
628  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 5"/>
629  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 5"/>
630  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 5"/>
631  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 5"/>
632  <w:LsdException Locked="false" Priority="51"
633   Name="List Table 6 Colorful Accent 5"/>
634  <w:LsdException Locked="false" Priority="52"
635   Name="List Table 7 Colorful Accent 5"/>
636  <w:LsdException Locked="false" Priority="46"
637   Name="List Table 1 Light Accent 6"/>
638  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 6"/>
639  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 6"/>
640  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 6"/>
641  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 6"/>
642  <w:LsdException Locked="false" Priority="51"
643   Name="List Table 6 Colorful Accent 6"/>
644  <w:LsdException Locked="false" Priority="52"
645   Name="List Table 7 Colorful Accent 6"/>
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1195-->
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1214<![endif]--><!--[if gte mso 9]><xml>
1215 <o:shapedefaults v:ext="edit" spidmax="1026"/>
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1221
1222<body lang=EN-US link=blue vlink=purple style='tab-interval:.5in'>
1223
1224<div class=WordSection1>
1225
1226<h1><span style='mso-fareast-font-family:"Times New Roman"'>Single crystal
1227structure refinement with TOF data in GSAS-II<o:p></o:p></span></h1>
1228
1229<h2><span style='mso-fareast-font-family:"Times New Roman"'>Introduction: <o:p></o:p></span></h2>
1230
1231<p class=MsoNormal>In these exercises you will use GSAS-II to refine the
1232structure of sapphire (really corundum, Al<sub>2</sub>O<sub>3</sub>) from
1233single crystal diffraction data collected at the SNS on the TOPAZ instrument at
1234room temperature. The data consists of a suite of exposures with the crystal in
123531 different orientations all within a single data file. Note that menu entries
1236and user input are shown in bold face below as <b style='mso-bidi-font-weight:
1237normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1238minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Help/About
1239GSAS-II</span></b>, which lists first the name of the menu (here <b
1240style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1241mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1242minor-latin'>Help</span></b>) and second the name of the entry in the menu
1243(here <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1244mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1245minor-latin'>About GSAS-II</span></b>). If you have not done so already, start
1246GSAS-II.</p>
1247
1248<h2>Step 1. Setup the phase information for sapphire</h2>
1249
1250<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1251style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
1252style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Use
1253the <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;mso-bidi-theme-font:
1255minor-latin'>Data/Add new phase</span></b> menu item add a new phase into the
1256current GSAS-II project. A popup window will appear asking for a phase name; I
1257entered <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'>sapphire</span></b>;
1259press <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'>OK</span></b>
1261when done. Select <b style='mso-bidi-font-weight:normal'><span
1262style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1263mso-hansi-theme-font:minor-latin'>Loaded Data/Phases/sapphire</span></b> from
1264the GSAS-II Data tree window. The General tab for Phase Data will appear.</p>
1265
1266<p class=MsoListParagraph><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
1267 id="_x0000_t75" coordsize="21600,21600" o:spt="75" o:preferrelative="t"
1268 path="m@4@5l@4@11@9@11@9@5xe" filled="f" stroked="f">
1269 <v:stroke joinstyle="miter"/>
1270 <v:formulas>
1271  <v:f eqn="if lineDrawn pixelLineWidth 0"/>
1272  <v:f eqn="sum @0 1 0"/>
1273  <v:f eqn="sum 0 0 @1"/>
1274  <v:f eqn="prod @2 1 2"/>
1275  <v:f eqn="prod @3 21600 pixelWidth"/>
1276  <v:f eqn="prod @3 21600 pixelHeight"/>
1277  <v:f eqn="sum @0 0 1"/>
1278  <v:f eqn="prod @6 1 2"/>
1279  <v:f eqn="prod @7 21600 pixelWidth"/>
1280  <v:f eqn="sum @8 21600 0"/>
1281  <v:f eqn="prod @7 21600 pixelHeight"/>
1282  <v:f eqn="sum @10 21600 0"/>
1283 </v:formulas>
1284 <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
1285 <o:lock v:ext="edit" aspectratio="t"/>
1286</v:shapetype><v:shape id="Picture_x0020_27" o:spid="_x0000_i1050" type="#_x0000_t75"
1287 style='width:468pt;height:209.25pt;visibility:visible;mso-wrap-style:square'>
1288 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image001.png"
1289  o:title=""/>
1290</v:shape><![endif]--><![if !vml]><img width=624 height=279
1291src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image002.gif"
1292v:shapes="Picture_x0020_27"><![endif]></span></p>
1293
1294<p class=MsoListParagraph><o:p>&nbsp;</o:p></p>
1295
1296<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1297style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
1298style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Enter
1299<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1300mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>R -3 c</span></b>
1301(don’t forget the spaces between axial fields) &amp; press <b style='mso-bidi-font-weight:
1302normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1303minor-latin;mso-hansi-theme-font:minor-latin'>Return</span></b>. A Space Group
1304Information popup window will appear; press <b style='mso-bidi-font-weight:
1305normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1306minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>. The General window
1307will be refreshed showing only the needed lattice <span style='mso-no-proof:
1308yes'>parameters for R -3 c. </span></p>
1309
1310<p class=MsoListParagraph><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1311 id="Picture_x0020_28" o:spid="_x0000_i1049" type="#_x0000_t75" style='width:468pt;
1312 height:265.5pt;visibility:visible;mso-wrap-style:square'>
1313 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image003.png"
1314  o:title=""/>
1315</v:shape><![endif]--><![if !vml]><img width=624 height=354
1316src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image004.gif"
1317v:shapes="Picture_x0020_28"><![endif]></span></p>
1318
1319<p class=MsoListParagraph><o:p>&nbsp;</o:p></p>
1320
1321<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1322style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1323style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Enter
1324<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1325mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>4.7613</span></b>
1326for <span class=GramE>a and</span> <b style='mso-bidi-font-weight:normal'><span
1327style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1328mso-hansi-theme-font:minor-latin'>12.9846</span></b> for c; a new cell volume
1329will be calculated. </p>
1330
1331<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1332style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
1333style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1334the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1335mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Atoms</span></b>
1336tab; it will be empty. Do <b style='mso-bidi-font-weight:normal'><span
1337style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1338mso-hansi-theme-font:minor-latin'>Edit Atoms/Append atom</span></b> from the <b
1339style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1340mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phase Data
1341for sapphire</span></b> menu twice. There will be two UNK entries in the table.</p>
1342
1343<p class=MsoListParagraph><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1344 id="Picture_x0020_29" o:spid="_x0000_i1048" type="#_x0000_t75" style='width:468pt;
1345 height:153.75pt;visibility:visible;mso-wrap-style:square'>
1346 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image005.png"
1347  o:title=""/>
1348</v:shape><![endif]--><![if !vml]><img width=624 height=205
1349src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image006.gif"
1350v:shapes="Picture_x0020_29"><![endif]></span></p>
1351
1352<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1353style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>5.<span
1354style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Double
1355click the first entry under Type (H); a periodic table will appear. Select <b
1356style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1357mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Al</span></b>.
1358Do the same for the second one and pick <b style='mso-bidi-font-weight:normal'><span
1359style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1360mso-hansi-theme-font:minor-latin'>O</span></b>. The Atom list should look like</p>
1361
1362<p class=MsoListParagraph><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1363 id="Picture_x0020_30" o:spid="_x0000_i1047" type="#_x0000_t75" style='width:468pt;
1364 height:153.75pt;visibility:visible;mso-wrap-style:square'>
1365 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image007.png"
1366  o:title=""/>
1367</v:shape><![endif]--><![if !vml]><img width=624 height=205
1368src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image008.gif"
1369v:shapes="Picture_x0020_30"><![endif]></span></p>
1370
1371<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1372style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>6.<span
1373style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Change
1374the <span class=GramE>Al(</span>z) to <b style='mso-bidi-font-weight:normal'><span
1375style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1376mso-hansi-theme-font:minor-latin'>0. 352</span></b>, the O(x) to <b
1377style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1378mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>-0.306</span></b>
1379and the O(z) to <b style='mso-bidi-font-weight:normal'><span style='font-family:
1380"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1381minor-latin'>Œ</span></b> (it will be changed to 0.2500). Also set both <span
1382class=SpellE>Uiso</span> to <b style='mso-bidi-font-weight:normal'><span
1383style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1384mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>0.005</span></b>.
1385Site symmetries and multiplicities will automatically change for these
1386positions.</p>
1387
1388<p class=MsoListParagraph><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1389 id="Picture_x0020_31" o:spid="_x0000_i1046" type="#_x0000_t75" style='width:468pt;
1390 height:153.75pt;visibility:visible;mso-wrap-style:square'>
1391 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image009.png"
1392  o:title=""/>
1393</v:shape><![endif]--><![if !vml]><img width=624 height=205
1394src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image010.gif"
1395v:shapes="Picture_x0020_31"><![endif]></span></p>
1396
1397<p class=MsoListParagraph><o:p>&nbsp;</o:p></p>
1398
1399<p class=MsoListParagraph>This completes the initial phase setup for sapphire.
1400An alternative would be to read the phase information from another GSAS-II <span
1401class=SpellE>gpx</span> file, a <span class=SpellE>cif</span> file or an old
1402GSAS <span class=SpellE>exp</span> file; these are all accessed from the <b
1403style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1404mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Import/Phase</span></b>
1405menu item on the main GSAS-II Data tree window. It may be useful to save your
1406project at this point; select <b style='mso-bidi-font-weight:normal'><span
1407style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1408mso-hansi-theme-font:minor-latin'>File/Save project as…</span></b> from the
1409main GSAS-II Data tree window menu. A file dialog box will appear; select the
1410directory and give a file name (no extension – I chose <b style='mso-bidi-font-weight:
1411normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1412minor-latin;mso-hansi-theme-font:minor-latin'>sapphire</span></b>).</p>
1413
1414<h2>Step 2. Import the diffraction data</h2>
1415
1416<p class=MsoNormal>The diffraction data collected on TOPAZ has been processed
1417(absorption corrections, wavelength and geometric corrections) to give a single
1418file with 31 embedded histograms as a space delimited multicolumn text file (<span
1419class=SpellE>sapphire_sphere.hkl</span>). To read this file select <b
1420style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1421mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Import/Structure
1422Factor/from Neutron TOF HKL F<sup>2 </sup>file</span></b>; a file dialog box
1423will appear. Change the directory to the location of this exercise (<b
1424style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1425mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>TOF Single
1426Crystal Refinement/data</span></b> – yours might be different), select <span
1427class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1428"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1429minor-latin'>sapphire_sphere.hkl</span></b></span> and press <b
1430style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1431mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Open</span></b>.
1432A popup will show a bit of the file and ask if you want to read this file;
1433press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1434mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Yes</span></b>.
1435Another popup will appear with a suggested name for the data; this will be used
1436for the GSAS-II Data tree. Press <b style='mso-bidi-font-weight:normal'><span
1437style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1438mso-hansi-theme-font:minor-latin'>OK</span></b>. The console will show messages
1439as each histogram is read; when done a new popup will appear</p>
1440
1441<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1442 id="Picture_x0020_32" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:233.25pt;
1443 height:228.75pt;visibility:visible;mso-wrap-style:square'>
1444 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image011.png"
1445  o:title=""/>
1446</v:shape><![endif]--><![if !vml]><img width=311 height=305
1447src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image012.gif"
1448v:shapes="Picture_x0020_32"><![endif]></span></p>
1449
1450<p class=MsoNormal>This makes the connection between the data you just read and
1451the phase (<b style='mso-bidi-font-weight:normal'><span style='font-family:
1452"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1453minor-latin'>sapphire</span></b>) you entered in Step 1. Select it (or <b
1454style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1455mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Set All</span></b>)
1456and press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1457mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1458The GSAS-II data tree window will show all the new histograms, expanding the
1459last one.</p>
1460
1461<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1462 id="Picture_x0020_33" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:468pt;
1463 height:153.75pt;visibility:visible;mso-wrap-style:square'>
1464 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image013.png"
1465  o:title=""/>
1466</v:shape><![endif]--><![if !vml]><img width=624 height=205
1467src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image014.gif"
1468v:shapes="Picture_x0020_33"><![endif]></span></p>
1469
1470<p class=MsoNormal>The plot window shows a not very interesting 2D view of the
1471l=0 layer of reciprocal space for the last data set. If you select the 1<sup>st</sup>
1472HKLF entry (<b style='mso-bidi-font-weight:normal'><span style='font-family:
1473"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1474minor-latin'>HKLF <span class=SpellE>sapphire_sphere.hkl</span></span></b>) the
1475plot is a bit more interesting.</p>
1476
1477<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1478 id="Picture_x0020_34" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:468pt;
1479 height:401.25pt;visibility:visible;mso-wrap-style:square'>
1480 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image015.png"
1481  o:title=""/>
1482</v:shape><![endif]--><![if !vml]><img width=624 height=535
1483src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image016.gif"
1484v:shapes="Picture_x0020_34"><![endif]></span></p>
1485
1486<p class=MsoNormal>Green circles are drawn representing the magnitude of 4
1487structure factors on the l=0 layer. The positions are strictly on a square
1488grid; you can “tab” through the layers on l with the <b style='mso-bidi-font-weight:
1489normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1490minor-latin;mso-hansi-theme-font:minor-latin'>+/-</span></b> keys. Find other
1491commands in the “K” box in the tools part of the plot. If you select <b
1492style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1493mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Commands/Plot
14943D HKLs</span></b> from the data window you’ll see a 3D view of this reflection
1495set; press <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1496style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1497mso-hansi-theme-font:minor-latin'>i</span></b></span> after selecting the plot
1498(I’ve zoomed in a bit)</p>
1499
1500<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1501
1502<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1503 id="Picture_x0020_35" o:spid="_x0000_i1042" type="#_x0000_t75" style='width:468pt;
1504 height:406.5pt;visibility:visible;mso-wrap-style:square'>
1505 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image017.png"
1506  o:title=""/>
1507</v:shape><![endif]--><![if !vml]><img width=624 height=542
1508src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image018.gif"
1509v:shapes="Picture_x0020_35"><![endif]></span></p>
1510
1511<p class=MsoNormal>Here the plot has the correct representation for reciprocal
1512space as sampled by this crystal orientation on TOPAZ; the two branches come
1513from the two detectors on this instrument. The <b style='mso-bidi-font-weight:
1514normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1515minor-latin;mso-hansi-theme-font:minor-latin'>save as/key</span></b> commands
1516give you control on the appearance of the plot; the plot responds to
1517zoom/rotate commands from the mouse. Left mouse button to rotate, right mouse
1518button to translate, center wheel to rotate about view direction and the wheel
1519to zoom in or out. One cursor is the view point and the other is the 000
1520reciprocal space origin. </p>
1521
1522<p class=MsoNormal>If you want to see the entire data set plotted together do <b
1523style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1524mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Commands/Plot
1525all 3D HKLs</span></b>; a data selection popup window will appear. Do <b
1526style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1527mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Set Al</span></b>l
1528and then <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1529mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>
1530to select all the data; the plot will be redrawn (I’ve pressed the ‘<span
1531class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1532"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1533minor-latin'>i</span></b></span>’ key as before)</p>
1534
1535<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1536 id="Picture_x0020_36" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:468pt;
1537 height:402.75pt;visibility:visible;mso-wrap-style:square'>
1538 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image019.png"
1539  o:title=""/>
1540</v:shape><![endif]--><![if !vml]><img width=624 height=537
1541src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image020.gif"
1542v:shapes="Picture_x0020_36"><![endif]></span></p>
1543
1544<p class=MsoNormal>I’ve rotated the drawing around to show an obvious gap in
1545the coverage.</p>
1546
1547<p class=MsoNormal>We’re now ready to do the refinement.</p>
1548
1549<h2>Step 3. Initial least squares refinement</h2>
1550
1551<p class=MsoNormal>By default the scale factors for all 31 data set are set to
1552be refined so you can immediately do a refinement. Select <b style='mso-bidi-font-weight:
1553normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1554minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> from
1555the main GSAS-II data tree window menu. You will need to save a copy of the
1556project first; select an appropriate directory and a name (I used ‘sapphire’). This
1557will do an F refinement by default. A progress bar will appear to show you the
1558residuals as the histograms are processed. When it finishes and you have
1559accepted the result a plot will show the l=0 layer for the 1<sup>st</sup> data
1560set.</p>
1561
1562<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1563 id="Picture_x0020_43" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:468pt;
1564 height:401.25pt;visibility:visible;mso-wrap-style:square'>
1565 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image021.png"
1566  o:title=""/>
1567</v:shape><![endif]--><![if !vml]><img width=624 height=535
1568src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image022.gif"
1569v:shapes="Picture_x0020_43"><![endif]></span></p>
1570
1571<p class=MsoNormal>Green rings are the observed magnitude, blue rings are the
1572calculated ones and the solid disk is the difference (green for positive &amp;
1573red for negative <span class=SpellE>F<sub>o</sub></span>-F<sub>c</sub>). You
1574can see the whole scope of the fit by doing <b style='mso-bidi-font-weight:
1575normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1576minor-latin;mso-hansi-theme-font:minor-latin'>Commands/Plot all 3D HKLs</span></b>
1577and selecting all the HKLF entries; press the “<b style='mso-bidi-font-weight:
1578normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1579minor-latin;mso-hansi-theme-font:minor-latin'>w</span></b>” key to show the
1580weighted &#916;F points.</p>
1581
1582<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1583 id="Picture_x0020_44" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:468pt;
1584 height:404.25pt;visibility:visible;mso-wrap-style:square'>
1585 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image023.png"
1586  o:title=""/>
1587</v:shape><![endif]--><![if !vml]><img width=624 height=539
1588src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image024.gif"
1589v:shapes="Picture_x0020_44"><![endif]></span></p>
1590
1591<p class=MsoNormal>The size of the squares is proportional to the magnitude of <span
1592class=SpellE>w&#916;F</span>. The cluster of negative <span class=SpellE>w&#916;F</span>
1593points around the reciprocal space origin is pretty clearly a consequence of
1594extinction so we’ll have to include that in the refinement model. One should
1595not be tempted to refine coordinates and thermal parameters until extinction is
1596accounted for in the refinement.</p>
1597
1598<h2>Step 3. Extinction model selection and refinement</h2>
1599
1600<p class=MsoNormal>GSAS-II has a number of extinction models available for
1601single crystal data. These include Primary, Secondary types I and II with
1602either Gaussian or Lorentzian distributions. To select one find the <b
1603style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1604mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sapphire</span></b>
1605entry in the GSAS-II data tree and select its <b style='mso-bidi-font-weight:
1606normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1607minor-latin;mso-hansi-theme-font:minor-latin'>Data</span></b> tab.</p>
1608
1609<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1610 id="Picture_x0020_39" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:468pt;
1611 height:265.5pt;visibility:visible;mso-wrap-style:square'>
1612 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image025.png"
1613  o:title=""/>
1614</v:shape><![endif]--><![if !vml]><img width=624 height=354
1615src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image026.gif"
1616v:shapes="Picture_x0020_39"><![endif]></span></p>
1617
1618<p class=MsoNormal>We can cut to the chase here – select <b style='mso-bidi-font-weight:
1619normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1620minor-latin;mso-hansi-theme-font:minor-latin'>Secondary Type I</span></b> from
1621the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1622mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Extinction
1623type</span></b> pull down list (the tab will be redrawn) and check the <span
1624class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1625"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1626minor-latin'>Eg</span></b></span> box; leave the <span class=SpellE><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'>Approx</span></b></span>
1629selection as <b style='mso-bidi-font-weight:normal'><span style='font-family:
1630"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1631minor-latin'>Lorentzian</span></b>. Later on after you’ve finished the
1632tutorial, you can try the other models and see how they compare. Next do <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'>Edit Phase/Copy
1635selected data</span></b>, pick <b style='mso-bidi-font-weight:normal'><span
1636style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1637mso-hansi-theme-font:minor-latin'>Extinction</span></b> from the list of
1638parameters and press <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'>OK</span></b>. Then do <b style='mso-bidi-font-weight:
1641normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1642minor-latin;mso-hansi-theme-font:minor-latin'>Set All</span></b> and press <b
1643style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1644mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>
1645from the next popup; this will copy the extinction model to all HKLF data sets.</p>
1646
1647<p class=MsoNormal>Because all of these extinction models are needed for one
1648crystal, it makes sense to tie them together into a single parameter. Select <b
1649style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1650mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Constraints</span></b>
1651from the main GSAS-II data tree and pick the <b style='mso-bidi-font-weight:
1652normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1653minor-latin;mso-hansi-theme-font:minor-latin'>Histogram/Phase constraints</span></b>
1654tab; it will be empty. Do <b style='mso-bidi-font-weight:normal'><span
1655style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1656mso-hansi-theme-font:minor-latin'>Edit Constr<span class=GramE>./</span>Add
1657equivalence</span></b>; the following popup will appear</p>
1658
1659<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1660 id="Picture_x0020_40" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:468pt;
1661 height:299.25pt;visibility:visible;mso-wrap-style:square'>
1662 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image027.png"
1663  o:title=""/>
1664</v:shape><![endif]--><![if !vml]><img width=624 height=399
1665src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image028.gif"
1666v:shapes="Picture_x0020_40"><![endif]></span></p>
1667
1668<p class=MsoNormal>Select the line beginning with ‘<b style='mso-bidi-font-weight:
1669normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1670minor-latin;mso-hansi-theme-font:minor-latin'>0:0<span class=GramE>:Eg<span
1671style='font-family:"Times New Roman",serif;font-weight:normal'>’</span></span></span></b>
1672(the Secondary type I parameter you just set to vary) and press <b
1673style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1674mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1675A new popup will appear; you’ll want to see the bottom of the list</p>
1676
1677<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1678 id="Picture_x0020_41" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:468pt;
1679 height:237.75pt;visibility:visible;mso-wrap-style:square'>
1680 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image029.png"
1681  o:title=""/>
1682</v:shape><![endif]--><![if !vml]><img width=624 height=317
1683src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image030.gif"
1684v:shapes="Picture_x0020_41"><![endif]></span></p>
1685
1686<p class=MsoNormal>Pick either <b style='mso-bidi-font-weight:normal'><span
1687style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1688mso-hansi-theme-font:minor-latin'>0<span class=GramE>:all:Eg</span></span></b>
1689or <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1690mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0:all=<span
1691class=SpellE>SNT:Eg</span></span></b> and press <b style='mso-bidi-font-weight:
1692normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1693minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>. The equivalence
1694making <span class=SpellE>Eg</span> for all histograms the same parameter will
1695be shown</p>
1696
1697<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1698 id="Picture_x0020_42" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:468pt;
1699 height:184.5pt;visibility:visible;mso-wrap-style:square'>
1700 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image031.png"
1701  o:title=""/>
1702</v:shape><![endif]--><![if !vml]><img width=624 height=246
1703src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image032.gif"
1704v:shapes="Picture_x0020_42"><![endif]></span></p>
1705
1706<p class=MsoNormal>Now do <b style='mso-bidi-font-weight:normal'><span
1707style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1708mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> from the main
1709GSAS-II data tree menu. You may have to repeat this twice to get convergence (<span
1710class=SpellE>Rw</span> ~6.8%); note the console output – value of Delta indicates
1711closeness to convergence. Select one of the HKLF data sets and view the 3D
1712Structure Factors plot for it alone</p>
1713
1714<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1715 id="Picture_x0020_45" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:468pt;
1716 height:403.5pt;visibility:visible;mso-wrap-style:square'>
1717 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image033.png"
1718  o:title=""/>
1719</v:shape><![endif]--><![if !vml]><img width=624 height=538
1720src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image034.gif"
1721v:shapes="Picture_x0020_45"><![endif]></span></p>
1722
1723<p class=MsoNormal>The <span class=SpellE>wDF</span> is positive close to 0<span
1724class=GramE>,0,0</span> then negative for an inner shell around the positive
1725core and finally positive for the outer shell. This is a thermal
1726parameter/extinction effect. So both have to be now refined. However, as a
1727matter of course we may expect that the extinction corrections are less
1728accurate when <span class=SpellE>Fo</span>&lt;&lt; Fc. In addition some
1729reflections were poorly measured. We want to reject reflections where <b
1730style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1731mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1732minor-latin'>Min extinct.</span></b> = <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;mso-bidi-theme-font:minor-latin'>0.5</span></b>
1735and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1736mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1737minor-latin'>Min <span class=SpellE>obs</span>/sig</span></b> = <b
1738style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1739mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1740minor-latin'>3</span></b>. These can be applied on the <b style='mso-bidi-font-weight:
1741normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1742minor-latin;mso-hansi-theme-font:minor-latin'>Controls</span></b> page. After
1743setting these my Controls were</p>
1744
1745<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1746 id="Picture_x0020_46" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:468pt;
1747 height:215.25pt;visibility:visible;mso-wrap-style:square'>
1748 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image035.png"
1749  o:title=""/>
1750</v:shape><![endif]--><![if !vml]><img width=624 height=287
1751src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image036.gif"
1752v:shapes="Picture_x0020_46"><![endif]></span></p>
1753
1754<p class=MsoNormal>Finally we can add the atom parameters for sapphire. Select
1755the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1756mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Atoms</span></b>
1757tab for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1758mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phase/sapphire</span></b></p>
1759
1760<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1761 id="Picture_x0020_47" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:468pt;
1762 height:117.75pt;visibility:visible;mso-wrap-style:square'>
1763 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image037.png"
1764  o:title=""/>
1765</v:shape><![endif]--><![if !vml]><img width=624 height=157
1766src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image038.gif"
1767v:shapes="Picture_x0020_47"><![endif]></span></p>
1768
1769<p class=MsoNormal>Double (right) click the <b style='mso-bidi-font-weight:
1770normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1771minor-latin;mso-hansi-theme-font:minor-latin'>Refine</span></b> column heading;
1772a popup will appear</p>
1773
1774<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1775 id="Picture_x0020_48" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:171.75pt;
1776 height:150pt;visibility:visible;mso-wrap-style:square'>
1777 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image039.png"
1778  o:title=""/>
1779</v:shape><![endif]--><![if !vml]><img width=229 height=200
1780src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image040.gif"
1781v:shapes="Picture_x0020_48"><![endif]></span></p>
1782
1783<p class=MsoNormal>Choose both <b style='mso-bidi-font-weight:normal'><span
1784style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1785mso-hansi-theme-font:minor-latin'>X</span></b> and <b style='mso-bidi-font-weight:
1786normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1787minor-latin;mso-hansi-theme-font:minor-latin'>U</span></b> and press <b
1788style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1789mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>;
1790the Atoms tab will be redrawn</p>
1791
1792<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1793 id="Picture_x0020_49" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:468pt;
1794 height:117.75pt;visibility:visible;mso-wrap-style:square'>
1795 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image041.png"
1796  o:title=""/>
1797</v:shape><![endif]--><![if !vml]><img width=624 height=157
1798src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image042.gif"
1799v:shapes="Picture_x0020_49"><![endif]></span></p>
1800
1801<p class=MsoNormal>Showing the refine flags for both atoms. GSAS-II will sort
1802out the special position rules for the two sites.</p>
1803
1804<p class=MsoNormal>Now do <b style='mso-bidi-font-weight:normal'><span
1805style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1806mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> (twice to get convergence).
1807My <span class=SpellE>Rw</span> = 4.705%, GOF = 1.91; find these on the <b
1808style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1809mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Covariance</span></b>
1810data window. Now get a new 3D plot of all the reflections; select any HKLF
1811entry, then do <b style='mso-bidi-font-weight:normal'><span style='font-family:
1812"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1813minor-latin'>Commands/Plot all 3D HKLs</span></b>. Press <b style='mso-bidi-font-weight:
1814normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1815minor-latin;mso-hansi-theme-font:minor-latin'>w</span></b> key.</p>
1816
1817<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1818 id="Picture_x0020_50" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:468pt;
1819 height:405pt;visibility:visible;mso-wrap-style:square'>
1820 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image043.png"
1821  o:title=""/>
1822</v:shape><![endif]--><![if !vml]><img width=624 height=540
1823src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image044.gif"
1824v:shapes="Picture_x0020_50"><![endif]></span></p>
1825
1826<p class=MsoNormal>It’s pretty obvious that there is one really bad reflection
1827and (a bit more subtly) it is messing up one TOPAS data set. To find it first
1828look through the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1829style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1830mso-hansi-theme-font:minor-latin'>sapphire.lst</span></b></span> file; that
1831will give fitting information for all the histograms (near bottom of the
1832listing). Open it with your favorite text editor; I’ve shown an interesting bit
1833of it here showing results for histograms 22-24.</p>
1834
1835<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1836
1837<p class=MsoNormal>Phase:<span style='mso-spacerun:yes'>  </span><span
1838class=GramE>sapphire<span style='mso-spacerun:yes'>  </span>in</span>
1839histogram:<span style='mso-spacerun:yes'>  </span>HKLF sapphire_sphere.hkl_22<o:p></o:p></p>
1840
1841<p class=MsoNormal>=====================================================================<o:p></o:p></p>
1842
1843<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Final refinement RF,
1844RF^2 = 4.66%, 8.45% on 134 reflections (3 user rejected, 9 <span class=SpellE>sp.gp.extinct</span>)<o:p></o:p></p>
1845
1846<p class=MsoNormal><span style='mso-spacerun:yes'> </span>HKLF histogram weight
1847factor <span class=GramE>=<span style='mso-spacerun:yes'>  </span>1.000</span><o:p></o:p></p>
1848
1849<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Scale <span
1850class=GramE>factor :</span><span style='mso-spacerun:yes'>    </span>66.5252,
1851sig<span style='mso-spacerun:yes'>     </span>0.7222<o:p></o:p></p>
1852
1853<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1854
1855<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Single crystal
1856extinction: Type:<span style='mso-spacerun:yes'>  </span><span class=GramE>Lorentzian<span
1857style='mso-spacerun:yes'>  </span><span class=SpellE>Approx</span></span>:<span
1858style='mso-spacerun:yes'>  </span>Secondary Type I<o:p></o:p></p>
1859
1860<p class=MsoNormal><span style='mso-spacerun:yes'>       </span><span
1861class=SpellE>Eg</span>:<span style='mso-spacerun:yes'>     </span>5.71e-04
1862sig:<span style='mso-spacerun:yes'>     </span>7.44e-06<o:p></o:p></p>
1863
1864<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1865
1866<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Phase:<span
1867style='mso-spacerun:yes'>  </span><span class=GramE>sapphire<span
1868style='mso-spacerun:yes'>  </span>in</span> histogram:<span
1869style='mso-spacerun:yes'>  </span>HKLF sapphire_sphere.hkl_23<o:p></o:p></p>
1870
1871<p class=MsoNormal>=====================================================================<o:p></o:p></p>
1872
1873<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Final refinement RF,
1874RF^2 = 6.10%, 11.18% on 147 reflections (6 user rejected, 6 <span class=SpellE>sp.gp.extinct</span>)<o:p></o:p></p>
1875
1876<p class=MsoNormal><span style='mso-spacerun:yes'> </span>HKLF histogram weight
1877factor <span class=GramE>=<span style='mso-spacerun:yes'>  </span>1.000</span><o:p></o:p></p>
1878
1879<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Scale <span
1880class=GramE>factor :</span><span style='mso-spacerun:yes'>    </span>63.2155,
1881sig<span style='mso-spacerun:yes'>     </span>0.6834<o:p></o:p></p>
1882
1883<p class=MsoNormal><o:p>&nbsp;</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<o:p></o:p></p>
1889
1890<p class=MsoNormal><span style='mso-spacerun:yes'>       </span><span
1891class=SpellE>Eg</span>:<span style='mso-spacerun:yes'>     </span>5.71e-04
1892sig:<span style='mso-spacerun:yes'>     </span>7.44e-06<o:p></o:p></p>
1893
1894<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1895
1896<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Phase:<span
1897style='mso-spacerun:yes'>  </span><span class=GramE>sapphire<span
1898style='mso-spacerun:yes'>  </span>in</span> histogram:<span
1899style='mso-spacerun:yes'>  </span>HKLF sapphire_sphere.hkl_24<o:p></o:p></p>
1900
1901<p class=MsoNormal>=====================================================================<o:p></o:p></p>
1902
1903<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Final refinement RF,
1904RF^2 = 3.77%, 6.60% on 160 reflections (11 user rejected, 1 <span class=SpellE>sp.gp.extinct</span>)<o:p></o:p></p>
1905
1906<p class=MsoNormal><span style='mso-spacerun:yes'> </span>HKLF histogram weight
1907factor <span class=GramE>=<span style='mso-spacerun:yes'>  </span>1.000</span><o:p></o:p></p>
1908
1909<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Scale <span
1910class=GramE>factor :</span><span style='mso-spacerun:yes'>    </span>66.4019,
1911sig<span style='mso-spacerun:yes'>     </span>0.6817<o:p></o:p></p>
1912
1913<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1914
1915<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Single crystal
1916extinction: Type:<span style='mso-spacerun:yes'>  </span><span class=GramE>Lorentzian<span
1917style='mso-spacerun:yes'>  </span><span class=SpellE>Approx</span></span>:<span
1918style='mso-spacerun:yes'>  </span>Secondary Type I<o:p></o:p></p>
1919
1920<p class=MsoNormal><span style='mso-spacerun:yes'>       </span><span
1921class=SpellE>Eg</span>:<span style='mso-spacerun:yes'>     </span>5.71e-04
1922sig:<span style='mso-spacerun:yes'>     </span>7.44e-06<o:p></o:p></p>
1923
1924<p class=MsoNormal><span style='mso-spacerun:yes'> </span><span
1925style='mso-spacerun:yes'>                                                                  
1926</span><span style='mso-spacerun:yes'>                                  </span></p>
1927
1928<p class=MsoNormal>There is obviously something wrong with #23 (high residual
1929&amp; funny scale factor compared to the others). Find <b style='mso-bidi-font-weight:
1930normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1931minor-latin;mso-hansi-theme-font:minor-latin'>HKLF sapphire_sphere.hkl_23</span></b>
1932in the GSAS-II data tree &amp; select it. The 3D plot of just that data set
1933will show the problem reflection.</p>
1934
1935<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1936 id="Picture_x0020_51" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:468pt;
1937 height:405pt;visibility:visible;mso-wrap-style:square'>
1938 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image045.png"
1939  o:title=""/>
1940</v:shape><![endif]--><![if !vml]><img width=624 height=540
1941src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image046.gif"
1942v:shapes="Picture_x0020_51"><![endif]></span></p>
1943
1944<p class=MsoNormal>By zooming in and rotating the plot around a bit, you can
1945identify the reflection with the cursor. It seems to be the <b
1946style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1947mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>342</span></b>
1948reflection; select the <b style='mso-bidi-font-weight:normal'><span
1949style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1950mso-hansi-theme-font:minor-latin'>Reflection List</span></b> and look for it
1951(unfortunately the reflections are produced in a somewhat random order by the
1952TOPAZ data acquisition system). It is very near the bottom of the list (#<b
1953style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1954mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>147</span></b>).</p>
1955
1956<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1957 id="Picture_x0020_26" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:585pt;
1958 height:244.5pt;visibility:visible;mso-wrap-style:square'>
1959 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image047.png"
1960  o:title=""/>
1961</v:shape><![endif]--><![if !vml]><img width=780 height=326
1962src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image048.gif"
1963v:shapes="Picture_x0020_26"><![endif]></span></p>
1964
1965<p class=MsoNormal>The <span class=SpellE>Fcsq</span> (F<sub>c</sub><sup>2</sup>)
1966is very much larger than <span class=SpellE>Fosq</span> (F<sub>o</sub><sup>2</sup>)
1967so that |&#916;F<sup>2</sup>|/&#963;(F<sub>o</sub><sup>2</sup>) &gt; 80! It was
1968obviously poorly measured (e.g. on the edge of the detector, etc.). We’d like
1969to eliminate it, but perhaps we might be better setting a lower cutoff on
1970|&#916;F<sup>2</sup>|/&#963;(F<sub>o</sub><sup>2</sup>) to eliminate other
1971similar problem reflections. Go to the <b style='mso-bidi-font-weight:normal'><span
1972style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1973mso-hansi-theme-font:minor-latin'>Controls</span></b> entry in the GSAS-II data
1974tree</p>
1975
1976<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1977 id="Picture_x0020_52" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:468pt;
1978 height:200.25pt;visibility:visible;mso-wrap-style:square'>
1979 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image049.png"
1980  o:title=""/>
1981</v:shape><![endif]--><![if !vml]><img width=624 height=267
1982src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image050.gif"
1983v:shapes="Picture_x0020_52"><![endif]></span></p>
1984
1985<p class=MsoNormal>Change the value of <b style='mso-bidi-font-weight:normal'><span
1986style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1987mso-hansi-theme-font:minor-latin'>Max <span class=SpellE>delt</span>-F/sig</span></b>
1988to 20; that will certainly eliminate the bad 342 reflection &amp; perhaps a few
1989others. Repeat <b style='mso-bidi-font-weight:normal'><span style='font-family:
1990"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1991minor-latin'>Calculate/Refine</span></b>; my residual dropped considerably (<span
1992class=SpellE>Rw</span> ~4.5%) and the 3D plot shows no really bad reflections</p>
1993
1994<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1995 id="Picture_x0020_53" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:468pt;
1996 height:404.25pt;visibility:visible;mso-wrap-style:square'>
1997 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image051.png"
1998  o:title=""/>
1999</v:shape><![endif]--><![if !vml]><img width=624 height=539
2000src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image052.gif"
2001v:shapes="Picture_x0020_53"><![endif]></span></p>
2002
2003<p class=MsoNormal>Looking the <span class=SpellE><b style='mso-bidi-font-weight:
2004normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2005minor-latin;mso-hansi-theme-font:minor-latin'>sapphire.lst</span></b></span><b
2006style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2007mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> </span></b>file
2008shows that HKLF #23 is now more in line with the other ones (RF = 4.35% &amp;
2009scale = 67.41). To finish the refinement make the two sapphire atoms have
2010anisotropic thermal parameters. Select <b style='mso-bidi-font-weight:normal'><span
2011style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2012mso-hansi-theme-font:minor-latin'>Phases/sapphire</span></b> and the <b
2013style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2014mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Atoms</span></b>
2015tab; then double click the <b style='mso-bidi-font-weight:normal'><span
2016style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2017mso-hansi-theme-font:minor-latin'>I/A</span></b> column heading. A popup will
2018appear; select <b style='mso-bidi-font-weight:normal'><span style='font-family:
2019"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2020minor-latin'>Anisotropic</span></b> and press <b style='mso-bidi-font-weight:
2021normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2022minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>. The atom <span
2023class=SpellE>Uijs</span> will appear and <span class=SpellE>Uiso</span> will be
2024greyed out. Then do <b style='mso-bidi-font-weight:normal'><span
2025style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2026mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> again. My final
2027residual was <span class=SpellE>Rw</span>=4.20%. </p>
2028
2029<p class=MsoNormal>This completes the tutorial. You can explore the other
2030extinction models and try different cutoff values for <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'>Max <span class=SpellE>delt</span>-F/sig</span></b>.
2033<b style='mso-bidi-font-weight:normal'><u>NB: this should never be set before
2034the refinement is complete as it can reject large portions of the data
2035prematurely.<o:p></o:p></u></b></p>
2036
2037</div>
2038
2039</body>
2040
2041</html>
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