source: Tutorials/TOF Single Crystal Refinement/TOF single crystal refinement in GSAS.htm @ 3553

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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
1301-3 c</span></b> for the space group
1302(don’t forget the spaces between axial fields) &amp; press <b style='mso-bidi-font-weight:
1303normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1304minor-latin;mso-hansi-theme-font:minor-latin'>Return</span></b>. A Space Group
1305Information popup window will appear; press <b style='mso-bidi-font-weight:
1306normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1307minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>. The General window
1308will be refreshed showing only the needed lattice <span style='mso-no-proof:
1309yes'>parameters for R -3 c. </span></p>
1310
1311<p class=MsoListParagraph><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1312 id="Picture_x0020_28" o:spid="_x0000_i1049" type="#_x0000_t75" style='width:468pt;
1313 height:265.5pt;visibility:visible;mso-wrap-style:square'>
1314 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image003.png"
1315  o:title=""/>
1316</v:shape><![endif]--><![if !vml]><img width=624 height=354
1317src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image004.gif"
1318v:shapes="Picture_x0020_28"><![endif]></span></p>
1319
1320<p class=MsoListParagraph><o:p>&nbsp;</o:p></p>
1321
1322<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1323style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1324style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Enter
1325<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1326mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>4.7613</span></b>
1327for <span class=GramE>a and</span> <b style='mso-bidi-font-weight:normal'><span
1328style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1329mso-hansi-theme-font:minor-latin'>12.9846</span></b> for c; a new cell volume
1330will be calculated. </p>
1331
1332<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1333style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
1334style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1335the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1336mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Atoms</span></b>
1337tab; it will be empty. Do <b style='mso-bidi-font-weight:normal'><span
1338style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1339mso-hansi-theme-font:minor-latin'>Edit Atoms/Append atom</span></b> from the <b
1340style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1341mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phase Data
1342for sapphire</span></b> menu twice. There will be two UNK entries in the table.</p>
1343
1344<p class=MsoListParagraph><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1345 id="Picture_x0020_29" o:spid="_x0000_i1048" type="#_x0000_t75" style='width:468pt;
1346 height:153.75pt;visibility:visible;mso-wrap-style:square'>
1347 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image005.png"
1348  o:title=""/>
1349</v:shape><![endif]--><![if !vml]><img width=624 height=205
1350src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image006.gif"
1351v:shapes="Picture_x0020_29"><![endif]></span></p>
1352
1353<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1354style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>5.<span
1355style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Double
1356click the first entry under Type (H); a periodic table will appear. Select <b
1357style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1358mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Al</span></b>.
1359Do the same for the second one and pick <b style='mso-bidi-font-weight:normal'><span
1360style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1361mso-hansi-theme-font:minor-latin'>O</span></b>. The Atom list should look like</p>
1362
1363<p class=MsoListParagraph><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1364 id="Picture_x0020_30" o:spid="_x0000_i1047" type="#_x0000_t75" style='width:468pt;
1365 height:153.75pt;visibility:visible;mso-wrap-style:square'>
1366 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image007.png"
1367  o:title=""/>
1368</v:shape><![endif]--><![if !vml]><img width=624 height=205
1369src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image008.gif"
1370v:shapes="Picture_x0020_30"><![endif]></span></p>
1371
1372<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1373style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>6.<span
1374style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Change
1375the <span class=GramE>Al(</span>z) to <b style='mso-bidi-font-weight:normal'><span
1376style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1377mso-hansi-theme-font:minor-latin'>0. 352</span></b>, the O(x) to <b
1378style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1379mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>-0.306</span></b>
1380and the O(z) to <b style='mso-bidi-font-weight:normal'><span style='font-family:
1381"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1382minor-latin'>Œ</span></b> (it will be changed to 0.2500). Also set both <span
1383class=SpellE>Uiso</span> to <b style='mso-bidi-font-weight:normal'><span
1384style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1385mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>0.005</span></b>.
1386Site symmetries and multiplicities will automatically change for these
1387positions.</p>
1388
1389<p class=MsoListParagraph><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1390 id="Picture_x0020_31" o:spid="_x0000_i1046" type="#_x0000_t75" style='width:468pt;
1391 height:153.75pt;visibility:visible;mso-wrap-style:square'>
1392 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image009.png"
1393  o:title=""/>
1394</v:shape><![endif]--><![if !vml]><img width=624 height=205
1395src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image010.gif"
1396v:shapes="Picture_x0020_31"><![endif]></span></p>
1397
1398<p class=MsoListParagraph><o:p>&nbsp;</o:p></p>
1399
1400<p class=MsoListParagraph>This completes the initial phase setup for sapphire.
1401An alternative would be to read the phase information from another GSAS-II <span
1402class=SpellE>gpx</span> file, a <span class=SpellE>cif</span> file or an old
1403GSAS <span class=SpellE>exp</span> file; these are all accessed from the <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/Phase</span></b>
1406menu item on the main GSAS-II Data tree window. It may be useful to save your
1407project at this point; select <b style='mso-bidi-font-weight:normal'><span
1408style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1409mso-hansi-theme-font:minor-latin'>File/Save project as…</span></b> from the
1410main GSAS-II Data tree window menu. A file dialog box will appear; select the
1411directory and give a file name (no extension – I chose <b style='mso-bidi-font-weight:
1412normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1413minor-latin;mso-hansi-theme-font:minor-latin'>sapphire</span></b>).</p>
1414
1415<h2>Step 2. Import the diffraction data</h2>
1416
1417<p class=MsoNormal>The diffraction data collected on TOPAZ has been processed
1418(absorption corrections, wavelength and geometric corrections) to give a single
1419file with 31 embedded histograms as a space delimited multicolumn text file (<span
1420class=SpellE>sapphire_sphere.hkl</span>). To read this file select <b
1421style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1422mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Import/Structure
1423Factor/from Neutron ISIS SXD TOF HKL F<sup>2 </sup>file</span></b>; a file dialog box
1424will appear. Change the directory to the location of this exercise (<b
1425style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1426mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>TOF Single
1427Crystal Refinement/data</span></b> – yours might be different), select <span
1428class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1429"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1430minor-latin'>sapphire_sphere.hkl</span></b></span> and press <b
1431style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1432mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Open</span></b>.
1433A popup will show a bit of the file and ask if you want to read this file;
1434press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1435mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Yes</span></b>.
1436Another popup will appear with a suggested name for the data; this will be used
1437for the GSAS-II Data tree. Press <b style='mso-bidi-font-weight:normal'><span
1438style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1439mso-hansi-theme-font:minor-latin'>OK</span></b>. The console will show messages
1440as each histogram is read; when done a new popup will appear</p>
1441
1442<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1443 id="Picture_x0020_32" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:233.25pt;
1444 height:228.75pt;visibility:visible;mso-wrap-style:square'>
1445 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image011.png"
1446  o:title=""/>
1447</v:shape><![endif]--><![if !vml]><img width=311 height=305
1448src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image012.gif"
1449v:shapes="Picture_x0020_32"><![endif]></span></p>
1450
1451<p class=MsoNormal>This makes the connection between the data you just read and
1452the phase (<b style='mso-bidi-font-weight:normal'><span style='font-family:
1453"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1454minor-latin'>sapphire</span></b>) you entered in Step 1. Select it (or <b
1455style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1456mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Set All</span></b>)
1457and press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1458mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1459The GSAS-II data tree window will show all the new histograms, expanding the
1460last one.</p>
1461
1462<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1463 id="Picture_x0020_33" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:468pt;
1464 height:153.75pt;visibility:visible;mso-wrap-style:square'>
1465 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image013.png"
1466  o:title=""/>
1467</v:shape><![endif]--><![if !vml]><img width=624 height=205
1468src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image014.gif"
1469v:shapes="Picture_x0020_33"><![endif]></span></p>
1470
1471<p class=MsoNormal>The plot window shows a not very interesting 2D view of the
1472l=0 layer of reciprocal space for the last data set. If you select the 1<sup>st</sup>
1473HKLF entry (<b style='mso-bidi-font-weight:normal'><span style='font-family:
1474"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1475minor-latin'>HKLF <span class=SpellE>sapphire_sphere.hkl</span></span></b>) the
1476plot is a bit more interesting.</p>
1477
1478<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1479 id="Picture_x0020_34" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:468pt;
1480 height:401.25pt;visibility:visible;mso-wrap-style:square'>
1481 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image015.png"
1482  o:title=""/>
1483</v:shape><![endif]--><![if !vml]><img width=624 height=535
1484src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image016.gif"
1485v:shapes="Picture_x0020_34"><![endif]></span></p>
1486
1487<p class=MsoNormal>Green circles are drawn representing the magnitude of 4
1488structure factors on the l=0 layer. The positions are strictly on a square
1489grid; you can “tab” through the layers on l with the <b style='mso-bidi-font-weight:
1490normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1491minor-latin;mso-hansi-theme-font:minor-latin'>+/-</span></b> keys. Find other
1492commands in the “K” box in the tools part of the plot. If you select <b
1493style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1494mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Commands/Plot
14953D HKLs</span></b> from the data window you’ll see a 3D view of this reflection
1496set; press <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1497style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1498mso-hansi-theme-font:minor-latin'>i</span></b></span> after selecting the plot
1499(I’ve zoomed in a bit)</p>
1500
1501<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1502
1503<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1504 id="Picture_x0020_35" o:spid="_x0000_i1042" type="#_x0000_t75" style='width:468pt;
1505 height:406.5pt;visibility:visible;mso-wrap-style:square'>
1506 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image017.png"
1507  o:title=""/>
1508</v:shape><![endif]--><![if !vml]><img width=624 height=542
1509src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image018.gif"
1510v:shapes="Picture_x0020_35"><![endif]></span></p>
1511
1512<p class=MsoNormal>Here the plot has the correct representation for reciprocal
1513space as sampled by this crystal orientation on TOPAZ; the two branches come
1514from the two detectors on this instrument. The <b style='mso-bidi-font-weight:
1515normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1516minor-latin;mso-hansi-theme-font:minor-latin'>save as/key</span></b> commands
1517give you control on the appearance of the plot; the plot responds to
1518zoom/rotate commands from the mouse. Left mouse button to rotate, right mouse
1519button to translate, center wheel to rotate about view direction and the wheel
1520to zoom in or out. One cursor is the view point and the other is the 000
1521reciprocal space origin. </p>
1522
1523<p class=MsoNormal>If you want to see the entire data set plotted together do <b
1524style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1525mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Commands/Plot
1526all 3D HKLs</span></b>; a data selection popup window will appear. Do <b
1527style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1528mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Set Al</span></b>l
1529and then <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1530mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>
1531to select all the data; the plot will be redrawn (I’ve pressed the ‘<span
1532class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1533"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1534minor-latin'>i</span></b></span>’ key as before)</p>
1535
1536<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1537 id="Picture_x0020_36" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:468pt;
1538 height:402.75pt;visibility:visible;mso-wrap-style:square'>
1539 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image019.png"
1540  o:title=""/>
1541</v:shape><![endif]--><![if !vml]><img width=624 height=537
1542src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image020.gif"
1543v:shapes="Picture_x0020_36"><![endif]></span></p>
1544
1545<p class=MsoNormal>I’ve rotated the drawing around to show an obvious gap in
1546the coverage.</p>
1547
1548<p class=MsoNormal>We’re now ready to do the refinement.</p>
1549
1550<h2>Step 3. Initial least squares refinement</h2>
1551
1552<p class=MsoNormal>By default the scale factors for all 31 data set are set to
1553be refined so you can immediately do a refinement. Select <b style='mso-bidi-font-weight:
1554normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1555minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> from
1556the main GSAS-II data tree window menu. You will need to save a copy of the
1557project first; select an appropriate directory and a name (I used ‘sapphire’). This
1558will do an F refinement by default. A progress bar will appear to show you the
1559residuals as the histograms are processed. When it finishes and you have
1560accepted the result a plot will show the l=0 layer for the 1<sup>st</sup> data
1561set.</p>
1562
1563<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1564 id="Picture_x0020_43" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:468pt;
1565 height:401.25pt;visibility:visible;mso-wrap-style:square'>
1566 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image021.png"
1567  o:title=""/>
1568</v:shape><![endif]--><![if !vml]><img width=624 height=535
1569src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image022.gif"
1570v:shapes="Picture_x0020_43"><![endif]></span></p>
1571
1572<p class=MsoNormal>Green rings are the observed magnitude, blue rings are the
1573calculated ones and the solid disk is the difference (green for positive &amp;
1574red for negative <span class=SpellE>F<sub>o</sub></span>-F<sub>c</sub>). You
1575can see the whole scope of the fit by doing <b style='mso-bidi-font-weight:
1576normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1577minor-latin;mso-hansi-theme-font:minor-latin'>Commands/Plot all 3D HKLs</span></b>
1578and selecting all the HKLF entries; press the “<b style='mso-bidi-font-weight:
1579normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1580minor-latin;mso-hansi-theme-font:minor-latin'>w</span></b>” key to show the
1581weighted &#916;F points.</p>
1582
1583<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1584 id="Picture_x0020_44" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:468pt;
1585 height:404.25pt;visibility:visible;mso-wrap-style:square'>
1586 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image023.png"
1587  o:title=""/>
1588</v:shape><![endif]--><![if !vml]><img width=624 height=539
1589src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image024.gif"
1590v:shapes="Picture_x0020_44"><![endif]></span></p>
1591
1592<p class=MsoNormal>The size of the squares is proportional to the magnitude of <span
1593class=SpellE>w&#916;F</span>. The cluster of negative <span class=SpellE>w&#916;F</span>
1594points around the reciprocal space origin is pretty clearly a consequence of
1595extinction so we’ll have to include that in the refinement model. One should
1596not be tempted to refine coordinates and thermal parameters until extinction is
1597accounted for in the refinement.</p>
1598
1599<h2>Step 3. Extinction model selection and refinement</h2>
1600
1601<p class=MsoNormal>GSAS-II has a number of extinction models available for
1602single crystal data. These include Primary, Secondary types I and II with
1603either Gaussian or Lorentzian distributions. To select one find the <b
1604style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1605mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sapphire</span></b>
1606entry in the GSAS-II data tree and select its <b style='mso-bidi-font-weight:
1607normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1608minor-latin;mso-hansi-theme-font:minor-latin'>Data</span></b> tab.</p>
1609
1610<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1611 id="Picture_x0020_39" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:468pt;
1612 height:265.5pt;visibility:visible;mso-wrap-style:square'>
1613 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image025.png"
1614  o:title=""/>
1615</v:shape><![endif]--><![if !vml]><img width=624 height=354
1616src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image026.gif"
1617v:shapes="Picture_x0020_39"><![endif]></span></p>
1618
1619<p class=MsoNormal>We can cut to the chase here – select <b style='mso-bidi-font-weight:
1620normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1621minor-latin;mso-hansi-theme-font:minor-latin'>Secondary Type I</span></b> from
1622the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1623mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Extinction
1624type</span></b> pull down list (the tab will be redrawn) and check the <span
1625class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1626"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1627minor-latin'>Eg</span></b></span> box; leave the <span class=SpellE><b
1628style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1629mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Approx</span></b></span>
1630selection as <b style='mso-bidi-font-weight:normal'><span style='font-family:
1631"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1632minor-latin'>Lorentzian</span></b>. Later on after you’ve finished the
1633tutorial, you can try the other models and see how they compare. Next do <b
1634style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1635mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit Phase/Copy
1636selected data</span></b>, pick <b style='mso-bidi-font-weight:normal'><span
1637style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1638mso-hansi-theme-font:minor-latin'>Extinction</span></b> from the list of
1639parameters and press <b style='mso-bidi-font-weight:normal'><span
1640style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1641mso-hansi-theme-font:minor-latin'>OK</span></b>. Then do <b style='mso-bidi-font-weight:
1642normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1643minor-latin;mso-hansi-theme-font:minor-latin'>Set All</span></b> and press <b
1644style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1645mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>
1646from the next popup; this will copy the extinction model to all HKLF data sets.</p>
1647
1648<p class=MsoNormal>Because all of these extinction models are needed for one
1649crystal, it makes sense to tie them together into a single parameter. Select <b
1650style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1651mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Constraints</span></b>
1652from the main GSAS-II data tree and pick the <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'>Histogram/Phase constraints</span></b>
1655tab; it will be empty. Do <b style='mso-bidi-font-weight:normal'><span
1656style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1657mso-hansi-theme-font:minor-latin'>Edit Constr<span class=GramE>./</span>Add
1658equivalence</span></b>; the following popup will appear</p>
1659
1660<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1661 id="Picture_x0020_40" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:468pt;
1662 height:299.25pt;visibility:visible;mso-wrap-style:square'>
1663 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image027.png"
1664  o:title=""/>
1665</v:shape><![endif]--><![if !vml]><img width=624 height=399
1666src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image028.gif"
1667v:shapes="Picture_x0020_40"><![endif]></span></p>
1668
1669<p class=MsoNormal>Select the line beginning with ‘<b style='mso-bidi-font-weight:
1670normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1671minor-latin;mso-hansi-theme-font:minor-latin'>0:0<span class=GramE>:Eg<span
1672style='font-family:"Times New Roman",serif;font-weight:normal'>’</span></span></span></b>
1673(the Secondary type I parameter you just set to vary) and press <b
1674style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1675mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1676A new popup will appear; you’ll want to see the bottom of the list</p>
1677
1678<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1679 id="Picture_x0020_41" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:468pt;
1680 height:237.75pt;visibility:visible;mso-wrap-style:square'>
1681 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image029.png"
1682  o:title=""/>
1683</v:shape><![endif]--><![if !vml]><img width=624 height=317
1684src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image030.gif"
1685v:shapes="Picture_x0020_41"><![endif]></span></p>
1686
1687<p class=MsoNormal>Pick either <b style='mso-bidi-font-weight:normal'><span
1688style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1689mso-hansi-theme-font:minor-latin'>0<span class=GramE>:all:Eg</span></span></b>
1690or <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1691mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0:all=<span
1692class=SpellE>SNT:Eg</span></span></b> and press <b style='mso-bidi-font-weight:
1693normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1694minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>. The equivalence
1695making <span class=SpellE>Eg</span> for all histograms the same parameter will
1696be shown</p>
1697
1698<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1699 id="Picture_x0020_42" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:468pt;
1700 height:184.5pt;visibility:visible;mso-wrap-style:square'>
1701 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image031.png"
1702  o:title=""/>
1703</v:shape><![endif]--><![if !vml]><img width=624 height=246
1704src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image032.gif"
1705v:shapes="Picture_x0020_42"><![endif]></span></p>
1706
1707<p class=MsoNormal>Now do <b style='mso-bidi-font-weight:normal'><span
1708style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1709mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> from the main
1710GSAS-II data tree menu. You may have to repeat this twice to get convergence (<span
1711class=SpellE>Rw</span> ~6.8%); note the console output – value of Delta indicates
1712closeness to convergence. Select one of the HKLF data sets and view the 3D
1713Structure Factors plot for it alone</p>
1714
1715<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1716 id="Picture_x0020_45" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:468pt;
1717 height:403.5pt;visibility:visible;mso-wrap-style:square'>
1718 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image033.png"
1719  o:title=""/>
1720</v:shape><![endif]--><![if !vml]><img width=624 height=538
1721src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image034.gif"
1722v:shapes="Picture_x0020_45"><![endif]></span></p>
1723
1724<p class=MsoNormal>The <span class=SpellE>wDF</span> is positive close to 0<span
1725class=GramE>,0,0</span> then negative for an inner shell around the positive
1726core and finally positive for the outer shell. This is a thermal
1727parameter/extinction effect. So both have to be now refined. However, as a
1728matter of course we may expect that the extinction corrections are less
1729accurate when <span class=SpellE>Fo</span>&lt;&lt; Fc. In addition some
1730reflections were poorly measured. We want to reject reflections where <b
1731style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1732mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1733minor-latin'>Min extinct.</span></b> = <b style='mso-bidi-font-weight:normal'><span
1734style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1735mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>0.5</span></b>
1736and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1737mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1738minor-latin'>Min <span class=SpellE>obs</span>/sig</span></b> = <b
1739style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1740mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1741minor-latin'>3</span></b>. These can be applied on the <b style='mso-bidi-font-weight:
1742normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1743minor-latin;mso-hansi-theme-font:minor-latin'>Controls</span></b> page. After
1744setting these my Controls were</p>
1745
1746<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1747 id="Picture_x0020_46" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:468pt;
1748 height:215.25pt;visibility:visible;mso-wrap-style:square'>
1749 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image035.png"
1750  o:title=""/>
1751</v:shape><![endif]--><![if !vml]><img width=624 height=287
1752src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image036.gif"
1753v:shapes="Picture_x0020_46"><![endif]></span></p>
1754
1755<p class=MsoNormal>Finally we can add the atom parameters for sapphire. Select
1756the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1757mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Atoms</span></b>
1758tab for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1759mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phase/sapphire</span></b></p>
1760
1761<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1762 id="Picture_x0020_47" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:468pt;
1763 height:117.75pt;visibility:visible;mso-wrap-style:square'>
1764 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image037.png"
1765  o:title=""/>
1766</v:shape><![endif]--><![if !vml]><img width=624 height=157
1767src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image038.gif"
1768v:shapes="Picture_x0020_47"><![endif]></span></p>
1769
1770<p class=MsoNormal>Double (right) click the <b style='mso-bidi-font-weight:
1771normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1772minor-latin;mso-hansi-theme-font:minor-latin'>Refine</span></b> column heading;
1773a popup will appear</p>
1774
1775<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1776 id="Picture_x0020_48" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:171.75pt;
1777 height:150pt;visibility:visible;mso-wrap-style:square'>
1778 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image039.png"
1779  o:title=""/>
1780</v:shape><![endif]--><![if !vml]><img width=229 height=200
1781src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image040.gif"
1782v:shapes="Picture_x0020_48"><![endif]></span></p>
1783
1784<p class=MsoNormal>Choose both <b style='mso-bidi-font-weight:normal'><span
1785style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1786mso-hansi-theme-font:minor-latin'>X</span></b> and <b style='mso-bidi-font-weight:
1787normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1788minor-latin;mso-hansi-theme-font:minor-latin'>U</span></b> and press <b
1789style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1790mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>;
1791the Atoms tab will be redrawn</p>
1792
1793<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1794 id="Picture_x0020_49" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:468pt;
1795 height:117.75pt;visibility:visible;mso-wrap-style:square'>
1796 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image041.png"
1797  o:title=""/>
1798</v:shape><![endif]--><![if !vml]><img width=624 height=157
1799src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image042.gif"
1800v:shapes="Picture_x0020_49"><![endif]></span></p>
1801
1802<p class=MsoNormal>Showing the refine flags for both atoms. GSAS-II will sort
1803out the special position rules for the two sites.</p>
1804
1805<p class=MsoNormal>Now do <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'>Calculate/Refine</span></b> (twice to get convergence).
1808My <span class=SpellE>Rw</span> = 4.705%, GOF = 1.91; find these on the <b
1809style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1810mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Covariance</span></b>
1811data window. Now get a new 3D plot of all the reflections; select any HKLF
1812entry, then do <b style='mso-bidi-font-weight:normal'><span style='font-family:
1813"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1814minor-latin'>Commands/Plot all 3D HKLs</span></b>. Press <b style='mso-bidi-font-weight:
1815normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1816minor-latin;mso-hansi-theme-font:minor-latin'>w</span></b> key.</p>
1817
1818<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1819 id="Picture_x0020_50" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:468pt;
1820 height:405pt;visibility:visible;mso-wrap-style:square'>
1821 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image043.png"
1822  o:title=""/>
1823</v:shape><![endif]--><![if !vml]><img width=624 height=540
1824src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image044.gif"
1825v:shapes="Picture_x0020_50"><![endif]></span></p>
1826
1827<p class=MsoNormal>It’s pretty obvious that there is one really bad reflection
1828and (a bit more subtly) it is messing up one TOPAS data set. To find it first
1829look through the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1830style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1831mso-hansi-theme-font:minor-latin'>sapphire.lst</span></b></span> file; that
1832will give fitting information for all the histograms (near bottom of the
1833listing). Open it with your favorite text editor; I’ve shown an interesting bit
1834of it here showing results for histograms 22-24.</p>
1835
1836<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1837
1838<p class=MsoNormal>Phase:<span style='mso-spacerun:yes'>  </span><span
1839class=GramE>sapphire<span style='mso-spacerun:yes'>  </span>in</span>
1840histogram:<span style='mso-spacerun:yes'>  </span>HKLF sapphire_sphere.hkl_22<o:p></o:p></p>
1841
1842<p class=MsoNormal>=====================================================================<o:p></o:p></p>
1843
1844<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Final refinement RF,
1845RF^2 = 4.66%, 8.45% on 134 reflections (3 user rejected, 9 <span class=SpellE>sp.gp.extinct</span>)<o:p></o:p></p>
1846
1847<p class=MsoNormal><span style='mso-spacerun:yes'> </span>HKLF histogram weight
1848factor <span class=GramE>=<span style='mso-spacerun:yes'>  </span>1.000</span><o:p></o:p></p>
1849
1850<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Scale <span
1851class=GramE>factor :</span><span style='mso-spacerun:yes'>    </span>66.5252,
1852sig<span style='mso-spacerun:yes'>     </span>0.7222<o:p></o:p></p>
1853
1854<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1855
1856<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Single crystal
1857extinction: Type:<span style='mso-spacerun:yes'>  </span><span class=GramE>Lorentzian<span
1858style='mso-spacerun:yes'>  </span><span class=SpellE>Approx</span></span>:<span
1859style='mso-spacerun:yes'>  </span>Secondary Type I<o:p></o:p></p>
1860
1861<p class=MsoNormal><span style='mso-spacerun:yes'>       </span><span
1862class=SpellE>Eg</span>:<span style='mso-spacerun:yes'>     </span>5.71e-04
1863sig:<span style='mso-spacerun:yes'>     </span>7.44e-06<o:p></o:p></p>
1864
1865<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1866
1867<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Phase:<span
1868style='mso-spacerun:yes'>  </span><span class=GramE>sapphire<span
1869style='mso-spacerun:yes'>  </span>in</span> histogram:<span
1870style='mso-spacerun:yes'>  </span>HKLF sapphire_sphere.hkl_23<o:p></o:p></p>
1871
1872<p class=MsoNormal>=====================================================================<o:p></o:p></p>
1873
1874<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Final refinement RF,
1875RF^2 = 6.10%, 11.18% on 147 reflections (6 user rejected, 6 <span class=SpellE>sp.gp.extinct</span>)<o:p></o:p></p>
1876
1877<p class=MsoNormal><span style='mso-spacerun:yes'> </span>HKLF histogram weight
1878factor <span class=GramE>=<span style='mso-spacerun:yes'>  </span>1.000</span><o:p></o:p></p>
1879
1880<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Scale <span
1881class=GramE>factor :</span><span style='mso-spacerun:yes'>    </span>63.2155,
1882sig<span style='mso-spacerun:yes'>     </span>0.6834<o:p></o:p></p>
1883
1884<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1885
1886<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Single crystal
1887extinction: Type:<span style='mso-spacerun:yes'>  </span><span class=GramE>Lorentzian<span
1888style='mso-spacerun:yes'>  </span><span class=SpellE>Approx</span></span>:<span
1889style='mso-spacerun:yes'>  </span>Secondary Type I<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>5.71e-04
1893sig:<span style='mso-spacerun:yes'>     </span>7.44e-06<o:p></o:p></p>
1894
1895<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1896
1897<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Phase:<span
1898style='mso-spacerun:yes'>  </span><span class=GramE>sapphire<span
1899style='mso-spacerun:yes'>  </span>in</span> histogram:<span
1900style='mso-spacerun:yes'>  </span>HKLF sapphire_sphere.hkl_24<o:p></o:p></p>
1901
1902<p class=MsoNormal>=====================================================================<o:p></o:p></p>
1903
1904<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Final refinement RF,
1905RF^2 = 3.77%, 6.60% on 160 reflections (11 user rejected, 1 <span class=SpellE>sp.gp.extinct</span>)<o:p></o:p></p>
1906
1907<p class=MsoNormal><span style='mso-spacerun:yes'> </span>HKLF histogram weight
1908factor <span class=GramE>=<span style='mso-spacerun:yes'>  </span>1.000</span><o:p></o:p></p>
1909
1910<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Scale <span
1911class=GramE>factor :</span><span style='mso-spacerun:yes'>    </span>66.4019,
1912sig<span style='mso-spacerun:yes'>     </span>0.6817<o:p></o:p></p>
1913
1914<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1915
1916<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Single crystal
1917extinction: Type:<span style='mso-spacerun:yes'>  </span><span class=GramE>Lorentzian<span
1918style='mso-spacerun:yes'>  </span><span class=SpellE>Approx</span></span>:<span
1919style='mso-spacerun:yes'>  </span>Secondary Type I<o:p></o:p></p>
1920
1921<p class=MsoNormal><span style='mso-spacerun:yes'>       </span><span
1922class=SpellE>Eg</span>:<span style='mso-spacerun:yes'>     </span>5.71e-04
1923sig:<span style='mso-spacerun:yes'>     </span>7.44e-06<o:p></o:p></p>
1924
1925<p class=MsoNormal><span style='mso-spacerun:yes'> </span><span
1926style='mso-spacerun:yes'>                                                                  
1927</span><span style='mso-spacerun:yes'>                                  </span></p>
1928
1929<p class=MsoNormal>There is obviously something wrong with #23 (high residual
1930&amp; funny scale factor compared to the others). Find <b style='mso-bidi-font-weight:
1931normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1932minor-latin;mso-hansi-theme-font:minor-latin'>HKLF sapphire_sphere.hkl_23</span></b>
1933in the GSAS-II data tree &amp; select it. The 3D plot of just that data set
1934will show the problem reflection.</p>
1935
1936<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1937 id="Picture_x0020_51" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:468pt;
1938 height:405pt;visibility:visible;mso-wrap-style:square'>
1939 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image045.png"
1940  o:title=""/>
1941</v:shape><![endif]--><![if !vml]><img width=624 height=540
1942src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image046.gif"
1943v:shapes="Picture_x0020_51"><![endif]></span></p>
1944
1945<p class=MsoNormal>By zooming in and rotating the plot around a bit, you can
1946identify the reflection with the cursor. It seems to be the <b
1947style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1948mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>342</span></b>
1949reflection; select the <b style='mso-bidi-font-weight:normal'><span
1950style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1951mso-hansi-theme-font:minor-latin'>Reflection List</span></b> and look for it
1952(unfortunately the reflections are produced in a somewhat random order by the
1953TOPAZ data acquisition system). It is very near the bottom of the list (#<b
1954style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1955mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>147</span></b>).</p>
1956
1957<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1958 id="Picture_x0020_26" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:585pt;
1959 height:244.5pt;visibility:visible;mso-wrap-style:square'>
1960 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image047.png"
1961  o:title=""/>
1962</v:shape><![endif]--><![if !vml]><img width=780 height=326
1963src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image048.gif"
1964v:shapes="Picture_x0020_26"><![endif]></span></p>
1965
1966<p class=MsoNormal>The <span class=SpellE>Fcsq</span> (F<sub>c</sub><sup>2</sup>)
1967is very much larger than <span class=SpellE>Fosq</span> (F<sub>o</sub><sup>2</sup>)
1968so that |&#916;F<sup>2</sup>|/&#963;(F<sub>o</sub><sup>2</sup>) &gt; 80! It was
1969obviously poorly measured (e.g. on the edge of the detector, etc.). We’d like
1970to eliminate it, but perhaps we might be better setting a lower cutoff on
1971|&#916;F<sup>2</sup>|/&#963;(F<sub>o</sub><sup>2</sup>) to eliminate other
1972similar problem reflections. Go to the <b style='mso-bidi-font-weight:normal'><span
1973style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1974mso-hansi-theme-font:minor-latin'>Controls</span></b> entry in the GSAS-II data
1975tree</p>
1976
1977<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1978 id="Picture_x0020_52" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:468pt;
1979 height:200.25pt;visibility:visible;mso-wrap-style:square'>
1980 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image049.png"
1981  o:title=""/>
1982</v:shape><![endif]--><![if !vml]><img width=624 height=267
1983src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image050.gif"
1984v:shapes="Picture_x0020_52"><![endif]></span></p>
1985
1986<p class=MsoNormal>Change the value of <b style='mso-bidi-font-weight:normal'><span
1987style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1988mso-hansi-theme-font:minor-latin'>Max <span class=SpellE>delt</span>-F/sig</span></b>
1989to 20; that will certainly eliminate the bad 342 reflection &amp; perhaps a few
1990others. Repeat <b style='mso-bidi-font-weight:normal'><span style='font-family:
1991"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1992minor-latin'>Calculate/Refine</span></b>; my residual dropped considerably (<span
1993class=SpellE>Rw</span> ~4.5%) and the 3D plot shows no really bad reflections</p>
1994
1995<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1996 id="Picture_x0020_53" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:468pt;
1997 height:404.25pt;visibility:visible;mso-wrap-style:square'>
1998 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image051.png"
1999  o:title=""/>
2000</v:shape><![endif]--><![if !vml]><img width=624 height=539
2001src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image052.gif"
2002v:shapes="Picture_x0020_53"><![endif]></span></p>
2003
2004<p class=MsoNormal>Looking the <span class=SpellE><b style='mso-bidi-font-weight:
2005normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2006minor-latin;mso-hansi-theme-font:minor-latin'>sapphire.lst</span></b></span><b
2007style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2008mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> </span></b>file
2009shows that HKLF #23 is now more in line with the other ones (RF = 4.35% &amp;
2010scale = 67.41). To finish the refinement make the two sapphire atoms have
2011anisotropic thermal parameters. Select <b style='mso-bidi-font-weight:normal'><span
2012style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2013mso-hansi-theme-font:minor-latin'>Phases/sapphire</span></b> and the <b
2014style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2015mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Atoms</span></b>
2016tab; then double click the <b style='mso-bidi-font-weight:normal'><span
2017style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2018mso-hansi-theme-font:minor-latin'>I/A</span></b> column heading. A popup will
2019appear; select <b style='mso-bidi-font-weight:normal'><span style='font-family:
2020"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2021minor-latin'>Anisotropic</span></b> and press <b style='mso-bidi-font-weight:
2022normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2023minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>. The atom <span
2024class=SpellE>Uijs</span> will appear and <span class=SpellE>Uiso</span> will be
2025greyed out. Then do <b style='mso-bidi-font-weight:normal'><span
2026style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2027mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> again. My final
2028residual was <span class=SpellE>Rw</span>=4.20%. </p>
2029
2030<p class=MsoNormal>This completes the tutorial. You can explore the other
2031extinction models and try different cutoff values for <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'>Max <span class=SpellE>delt</span>-F/sig</span></b>.
2034<b style='mso-bidi-font-weight:normal'><u>NB: this should never be set before
2035the refinement is complete as it can reject large portions of the data
2036prematurely.<o:p></o:p></u></b></p>
2037
2038</div>
2039
2040</body>
2041
2042</html>
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