source: Tutorials/TOF Single Crystal Refinement/TOF single crystal refinement in GSAS.htm @ 4385

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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 single
1233crystal diffraction data collected at the SNS on the TOPAZ instrument at room
1234temperature. The data consists of a suite of exposures with the crystal in 31
1235different 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/image053.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>
1301for the space group (don’t forget the spaces between axial fields) &amp; press <b
1302style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1303mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Return</span></b>.
1304A Space Group Information 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/image054.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/image055.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/image056.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/image057.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 SNS TOF HKL F<sup>2 </sup>file</span></b>; a file dialog
1423box will 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/image058.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/image059.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/image060.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/image061.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 from
1513the two detectors on this instrument. The <b style='mso-bidi-font-weight:normal'><span
1514style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1515mso-hansi-theme-font:minor-latin'>save as/key</span></b> commands give you
1516control on the appearance of the plot; the plot responds to zoom/rotate
1517commands from the mouse. Left mouse button to rotate, right mouse button to
1518translate, center wheel to rotate about view direction and the wheel to zoom in
1519or out. One cursor is the view point and the other is the 000 reciprocal space
1520origin. </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/image062.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 ‘<b
1557style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1558mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1559minor-latin'>sapphire’</span></b>). This will do an F refinement by default. A
1560progress bar will appear to show you the residuals as the histograms are
1561processed. When it finishes and you have accepted the result a plot will show
1562the l=0 layer for the 1<sup>st</sup> data set.</p>
1563
1564<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1565 id="Picture_x0020_43" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:468pt;
1566 height:401.25pt;visibility:visible;mso-wrap-style:square'>
1567 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image021.png"
1568  o:title=""/>
1569</v:shape><![endif]--><![if !vml]><img width=624 height=535
1570src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image063.gif"
1571v:shapes="Picture_x0020_43"><![endif]></span></p>
1572
1573<p class=MsoNormal>Green rings are the observed magnitude, blue rings are the
1574calculated ones and the solid disk is the difference (green for positive &amp;
1575red for negative <span class=SpellE>F<sub>o</sub></span>-F<sub>c</sub>). You
1576can see the whole scope of the fit by doing <b style='mso-bidi-font-weight:
1577normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1578minor-latin;mso-hansi-theme-font:minor-latin'>Commands/Plot all 3D HKLs</span></b>
1579and selecting all the HKLF entries; press the “<b style='mso-bidi-font-weight:
1580normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1581minor-latin;mso-hansi-theme-font:minor-latin'>w</span></b>” key to show the
1582weighted &#916;F points.</p>
1583
1584<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1585 id="Picture_x0020_44" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:468pt;
1586 height:404.25pt;visibility:visible;mso-wrap-style:square'>
1587 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image023.png"
1588  o:title=""/>
1589</v:shape><![endif]--><![if !vml]><img width=624 height=539
1590src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image064.gif"
1591v:shapes="Picture_x0020_44"><![endif]></span></p>
1592
1593<p class=MsoNormal>The size of the squares is proportional to the magnitude of <span
1594class=SpellE>w&#916;F</span>. The cluster of negative <span class=SpellE>w&#916;F</span>
1595points around the reciprocal space origin is pretty clearly a consequence of
1596extinction so we’ll have to include that in the refinement model. One should
1597not be tempted to refine coordinates and thermal parameters until extinction is
1598accounted for in the refinement.</p>
1599
1600<h2>Step 3. Extinction model selection and refinement</h2>
1601
1602<p class=MsoNormal>GSAS-II has a number of extinction models available for
1603single crystal data. These include Primary, Secondary types I and II with
1604either Gaussian or Lorentzian distributions. To select one find the <b
1605style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1606mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sapphire</span></b>
1607entry in the GSAS-II data tree and select its <b style='mso-bidi-font-weight:
1608normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1609minor-latin;mso-hansi-theme-font:minor-latin'>Data</span></b> tab.</p>
1610
1611<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1612 id="Picture_x0020_39" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:468pt;
1613 height:265.5pt;visibility:visible;mso-wrap-style:square'>
1614 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image025.png"
1615  o:title=""/>
1616</v:shape><![endif]--><![if !vml]><img width=624 height=354
1617src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image065.gif"
1618v:shapes="Picture_x0020_39"><![endif]></span></p>
1619
1620<p class=MsoNormal>We can cut to the chase here – select <b style='mso-bidi-font-weight:
1621normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1622minor-latin;mso-hansi-theme-font:minor-latin'>Secondary Type I</span></b> from
1623the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1624mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Extinction
1625type</span></b> pull down list (the tab will be redrawn) and check the <span
1626class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1627"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1628minor-latin'>Eg</span></b></span> box; leave the <span class=SpellE><b
1629style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1630mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Approx</span></b></span>
1631selection as <b style='mso-bidi-font-weight:normal'><span style='font-family:
1632"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1633minor-latin'>Lorentzian</span></b>. Later on after you’ve finished the
1634tutorial, you can try the other models and see how they compare. Next do <b
1635style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1636mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit
1637Phase/Copy selected data</span></b>, pick <b style='mso-bidi-font-weight:normal'><span
1638style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1639mso-hansi-theme-font:minor-latin'>Extinction</span></b> from the list of
1640parameters and press <b style='mso-bidi-font-weight:normal'><span
1641style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1642mso-hansi-theme-font:minor-latin'>OK</span></b>. Then do <b style='mso-bidi-font-weight:
1643normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1644minor-latin;mso-hansi-theme-font:minor-latin'>Set All</span></b> and press <b
1645style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1646mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>
1647from the next popup; this will copy the extinction model to all HKLF data sets.</p>
1648
1649<p class=MsoNormal>Because all of these extinction models are needed for one
1650crystal, it makes sense to tie them together into a single parameter. Select <b
1651style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1652mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Constraints</span></b>
1653from the main GSAS-II data tree and pick the <b style='mso-bidi-font-weight:
1654normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1655minor-latin;mso-hansi-theme-font:minor-latin'>Histogram/Phase constraints</span></b>
1656tab; it will be empty. Do <b style='mso-bidi-font-weight:normal'><span
1657style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1658mso-hansi-theme-font:minor-latin'>Edit Constr<span class=GramE>./</span>Add
1659equivalence</span></b>; the following popup will appear</p>
1660
1661<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1662 id="Picture_x0020_40" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:468pt;
1663 height:299.25pt;visibility:visible;mso-wrap-style:square'>
1664 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image027.png"
1665  o:title=""/>
1666</v:shape><![endif]--><![if !vml]><img width=624 height=399
1667src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image066.gif"
1668v:shapes="Picture_x0020_40"><![endif]></span></p>
1669
1670<p class=MsoNormal>Select the line beginning with ‘<b style='mso-bidi-font-weight:
1671normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1672minor-latin;mso-hansi-theme-font:minor-latin'>0:0<span class=GramE>:Eg<span
1673style='font-family:"Times New Roman",serif;font-weight:normal'>’</span></span></span></b>
1674(the Secondary type I parameter you just set to vary) and press <b
1675style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1676mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1677A new popup will appear; you’ll want to see the bottom of the list</p>
1678
1679<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1680 id="Picture_x0020_41" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:468pt;
1681 height:237.75pt;visibility:visible;mso-wrap-style:square'>
1682 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image029.png"
1683  o:title=""/>
1684</v:shape><![endif]--><![if !vml]><img width=624 height=317
1685src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image067.gif"
1686v:shapes="Picture_x0020_41"><![endif]></span></p>
1687
1688<p class=MsoNormal>Pick either <b style='mso-bidi-font-weight:normal'><span
1689style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1690mso-hansi-theme-font:minor-latin'>0<span class=GramE>:all:Eg</span></span></b>
1691or <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1692mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0:all=<span
1693class=SpellE>SNT:Eg</span></span></b> and press <b style='mso-bidi-font-weight:
1694normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1695minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>. The equivalence
1696making <span class=SpellE>Eg</span> for all histograms the same parameter will
1697be shown</p>
1698
1699<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1700 id="Picture_x0020_42" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:468pt;
1701 height:184.5pt;visibility:visible;mso-wrap-style:square'>
1702 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image031.png"
1703  o:title=""/>
1704</v:shape><![endif]--><![if !vml]><img width=624 height=246
1705src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image068.gif"
1706v:shapes="Picture_x0020_42"><![endif]></span></p>
1707
1708<p class=MsoNormal>Now do <b style='mso-bidi-font-weight:normal'><span
1709style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1710mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> from the main
1711GSAS-II data tree menu. You may have to repeat this twice to get convergence (<span
1712class=SpellE>Rw</span> ~6.8%); note the console output – value of Delta
1713indicates closeness to convergence. Select one of the HKLF data sets and view
1714the 3D Structure Factors plot for it alone</p>
1715
1716<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1717 id="Picture_x0020_45" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:468pt;
1718 height:403.5pt;visibility:visible;mso-wrap-style:square'>
1719 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image033.png"
1720  o:title=""/>
1721</v:shape><![endif]--><![if !vml]><img width=624 height=538
1722src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image069.gif"
1723v:shapes="Picture_x0020_45"><![endif]></span></p>
1724
1725<p class=MsoNormal>The <span class=SpellE>wDF</span> is positive close to 0<span
1726class=GramE>,0,0</span> then negative for an inner shell around the positive
1727core and finally positive for the outer shell. This is a thermal
1728parameter/extinction effect. So both have to be now refined. However, as a
1729matter of course we may expect that the extinction corrections are less
1730accurate when <span class=SpellE>Fo</span>&lt;&lt; Fc. In addition some
1731reflections were poorly measured. We want to reject reflections where <b
1732style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1733mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1734minor-latin'>Min extinct.</span></b> = <b style='mso-bidi-font-weight:normal'><span
1735style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1736mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>0.5</span></b>
1737and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1738mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1739minor-latin'>Min <span class=SpellE>obs</span>/sig</span></b> = <b
1740style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1741mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1742minor-latin'>3</span></b>. These can be applied on the <b style='mso-bidi-font-weight:
1743normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1744minor-latin;mso-hansi-theme-font:minor-latin'>Controls</span></b> page. After
1745setting these my Controls were</p>
1746
1747<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1748 id="Picture_x0020_46" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:468pt;
1749 height:215.25pt;visibility:visible;mso-wrap-style:square'>
1750 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image035.png"
1751  o:title=""/>
1752</v:shape><![endif]--><![if !vml]><img width=624 height=287
1753src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image070.gif"
1754v:shapes="Picture_x0020_46"><![endif]></span></p>
1755
1756<p class=MsoNormal>Finally we can add the atom parameters for sapphire. Select
1757the <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'>Atoms</span></b>
1759tab for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1760mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phase/sapphire</span></b></p>
1761
1762<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1763 id="Picture_x0020_47" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:468pt;
1764 height:117.75pt;visibility:visible;mso-wrap-style:square'>
1765 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image037.png"
1766  o:title=""/>
1767</v:shape><![endif]--><![if !vml]><img width=624 height=157
1768src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image071.gif"
1769v:shapes="Picture_x0020_47"><![endif]></span></p>
1770
1771<p class=MsoNormal>Double (right) click the <b style='mso-bidi-font-weight:
1772normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1773minor-latin;mso-hansi-theme-font:minor-latin'>Refine</span></b> column heading;
1774a popup will appear</p>
1775
1776<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1777 id="Picture_x0020_48" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:171.75pt;
1778 height:150pt;visibility:visible;mso-wrap-style:square'>
1779 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image039.png"
1780  o:title=""/>
1781</v:shape><![endif]--><![if !vml]><img width=229 height=200
1782src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image072.gif"
1783v:shapes="Picture_x0020_48"><![endif]></span></p>
1784
1785<p class=MsoNormal>Choose both <b style='mso-bidi-font-weight:normal'><span
1786style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1787mso-hansi-theme-font:minor-latin'>X</span></b> and <b style='mso-bidi-font-weight:
1788normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1789minor-latin;mso-hansi-theme-font:minor-latin'>U</span></b> and press <b
1790style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1791mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>;
1792the Atoms tab will be redrawn</p>
1793
1794<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1795 id="Picture_x0020_49" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:468pt;
1796 height:117.75pt;visibility:visible;mso-wrap-style:square'>
1797 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image041.png"
1798  o:title=""/>
1799</v:shape><![endif]--><![if !vml]><img width=624 height=157
1800src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image073.gif"
1801v:shapes="Picture_x0020_49"><![endif]></span></p>
1802
1803<p class=MsoNormal>Showing the refine flags for both atoms. GSAS-II will sort
1804out the special position rules for the two sites.</p>
1805
1806<p class=MsoNormal>Now do <b style='mso-bidi-font-weight:normal'><span
1807style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1808mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> (twice to get
1809convergence). My <span class=SpellE>Rw</span> = 4.705%, GOF = 1.91; find these
1810on the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1811mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Covariance</span></b>
1812data window. Now get a new 3D plot of all the reflections; select any HKLF
1813entry, then do <b style='mso-bidi-font-weight:normal'><span style='font-family:
1814"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1815minor-latin'>Commands/Plot all 3D HKLs</span></b>. Press <b style='mso-bidi-font-weight:
1816normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1817minor-latin;mso-hansi-theme-font:minor-latin'>w</span></b> key.</p>
1818
1819<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1820 id="Picture_x0020_50" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:468pt;
1821 height:405pt;visibility:visible;mso-wrap-style:square'>
1822 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image043.png"
1823  o:title=""/>
1824</v:shape><![endif]--><![if !vml]><img width=624 height=540
1825src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image074.gif"
1826v:shapes="Picture_x0020_50"><![endif]></span></p>
1827
1828<p class=MsoNormal>It’s pretty obvious that there is one really bad reflection
1829and (a bit more subtly) it is messing up one TOPAS data set. To find it first
1830look through the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1831style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1832mso-hansi-theme-font:minor-latin'>sapphire.lst</span></b></span> file; that
1833will give fitting information for all the histograms (near bottom of the
1834listing). Open it with your favorite text editor; I’ve shown an interesting bit
1835of it here showing results for histograms 22-24.</p>
1836
1837<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1838
1839<p class=MsoNormal>Phase:<span style='mso-spacerun:yes'>  </span><span
1840class=GramE>sapphire<span style='mso-spacerun:yes'>  </span>in</span>
1841histogram:<span style='mso-spacerun:yes'>  </span>HKLF sapphire_sphere.hkl_22</p>
1842
1843<p class=MsoNormal>=====================================================================</p>
1844
1845<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Final refinement RF,
1846RF^2 = 4.66%, 8.45% on 134 reflections (3 user rejected, 9 <span class=SpellE>sp.gp.extinct</span>)</p>
1847
1848<p class=MsoNormal><span style='mso-spacerun:yes'> </span>HKLF histogram weight
1849factor <span class=GramE>=<span style='mso-spacerun:yes'>  </span>1.000</span></p>
1850
1851<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Scale <span
1852class=GramE>factor :</span><span style='mso-spacerun:yes'>    </span>66.5252,
1853sig<span style='mso-spacerun:yes'>     </span>0.7222</p>
1854
1855<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1856
1857<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Single crystal
1858extinction: Type:<span style='mso-spacerun:yes'>  </span><span class=GramE>Lorentzian<span
1859style='mso-spacerun:yes'>  </span><span class=SpellE>Approx</span></span>:<span
1860style='mso-spacerun:yes'>  </span>Secondary Type I</p>
1861
1862<p class=MsoNormal><span style='mso-spacerun:yes'>       </span><span
1863class=SpellE>Eg</span>:<span style='mso-spacerun:yes'>     </span>5.71e-04 sig:<span
1864style='mso-spacerun:yes'>     </span>7.44e-06</p>
1865
1866<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1867
1868<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Phase:<span
1869style='mso-spacerun:yes'>  </span><span class=GramE>sapphire<span
1870style='mso-spacerun:yes'>  </span>in</span> histogram:<span
1871style='mso-spacerun:yes'>  </span>HKLF sapphire_sphere.hkl_23</p>
1872
1873<p class=MsoNormal>=====================================================================</p>
1874
1875<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Final refinement RF,
1876RF^2 = 6.10%, 11.18% on 147 reflections (6 user rejected, 6 <span class=SpellE>sp.gp.extinct</span>)</p>
1877
1878<p class=MsoNormal><span style='mso-spacerun:yes'> </span>HKLF histogram weight
1879factor <span class=GramE>=<span style='mso-spacerun:yes'>  </span>1.000</span></p>
1880
1881<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Scale <span
1882class=GramE>factor :</span><span style='mso-spacerun:yes'>    </span>63.2155,
1883sig<span style='mso-spacerun:yes'>     </span>0.6834</p>
1884
1885<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1886
1887<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Single crystal
1888extinction: Type:<span style='mso-spacerun:yes'>  </span><span class=GramE>Lorentzian<span
1889style='mso-spacerun:yes'>  </span><span class=SpellE>Approx</span></span>:<span
1890style='mso-spacerun:yes'>  </span>Secondary Type I</p>
1891
1892<p class=MsoNormal><span style='mso-spacerun:yes'>       </span><span
1893class=SpellE>Eg</span>:<span style='mso-spacerun:yes'>     </span>5.71e-04
1894sig:<span style='mso-spacerun:yes'>     </span>7.44e-06</p>
1895
1896<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1897
1898<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Phase:<span
1899style='mso-spacerun:yes'>  </span><span class=GramE>sapphire<span
1900style='mso-spacerun:yes'>  </span>in</span> histogram:<span
1901style='mso-spacerun:yes'>  </span>HKLF sapphire_sphere.hkl_24</p>
1902
1903<p class=MsoNormal>=====================================================================</p>
1904
1905<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Final refinement RF,
1906RF^2 = 3.77%, 6.60% on 160 reflections (11 user rejected, 1 <span class=SpellE>sp.gp.extinct</span>)</p>
1907
1908<p class=MsoNormal><span style='mso-spacerun:yes'> </span>HKLF histogram weight
1909factor <span class=GramE>=<span style='mso-spacerun:yes'>  </span>1.000</span></p>
1910
1911<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Scale <span
1912class=GramE>factor :</span><span style='mso-spacerun:yes'>    </span>66.4019,
1913sig<span style='mso-spacerun:yes'>     </span>0.6817</p>
1914
1915<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1916
1917<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Single crystal
1918extinction: Type:<span style='mso-spacerun:yes'>  </span><span class=GramE>Lorentzian<span
1919style='mso-spacerun:yes'>  </span><span class=SpellE>Approx</span></span>:<span
1920style='mso-spacerun:yes'>  </span>Secondary Type I</p>
1921
1922<p class=MsoNormal><span style='mso-spacerun:yes'>       </span><span
1923class=SpellE>Eg</span>:<span style='mso-spacerun:yes'>     </span>5.71e-04
1924sig:<span style='mso-spacerun:yes'>     </span>7.44e-06</p>
1925
1926<p class=MsoNormal><span
1927style='mso-spacerun:yes'>                                                                                                     
1928</span></p>
1929
1930<p class=MsoNormal>There is obviously something wrong with #23 (high residual
1931&amp; funny scale factor compared to the others). Find <b style='mso-bidi-font-weight:
1932normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1933minor-latin;mso-hansi-theme-font:minor-latin'>HKLF sapphire_sphere.hkl_23</span></b>
1934in the GSAS-II data tree &amp; select it. The 3D plot of just that data set
1935will show the problem reflection.</p>
1936
1937<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1938 id="Picture_x0020_51" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:468pt;
1939 height:405pt;visibility:visible;mso-wrap-style:square'>
1940 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image045.png"
1941  o:title=""/>
1942</v:shape><![endif]--><![if !vml]><img width=624 height=540
1943src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image075.gif"
1944v:shapes="Picture_x0020_51"><![endif]></span></p>
1945
1946<p class=MsoNormal>By zooming in and rotating the plot around a bit, you can
1947identify the reflection with the cursor. It seems to be the <b
1948style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1949mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>342</span></b>
1950reflection; select the <b style='mso-bidi-font-weight:normal'><span
1951style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1952mso-hansi-theme-font:minor-latin'>Reflection List</span></b> and look for it
1953(unfortunately the reflections are produced in a somewhat random order by the
1954TOPAZ data acquisition system). It is very near the bottom of the list (#<b
1955style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1956mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>147</span></b>).</p>
1957
1958<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1959 id="Picture_x0020_26" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:585pt;
1960 height:244.5pt;visibility:visible;mso-wrap-style:square'>
1961 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image047.png"
1962  o:title=""/>
1963</v:shape><![endif]--><![if !vml]><img width=780 height=326
1964src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image076.gif"
1965v:shapes="Picture_x0020_26"><![endif]></span></p>
1966
1967<p class=MsoNormal>The <span class=SpellE>Fcsq</span> (F<sub>c</sub><sup>2</sup>)
1968is very much larger than <span class=SpellE>Fosq</span> (F<sub>o</sub><sup>2</sup>)
1969so that |&#916;F<sup>2</sup>|/&#963;(F<sub>o</sub><sup>2</sup>) &gt; 80! It was
1970obviously poorly measured (e.g. on the edge of the detector, etc.). We’d like
1971to eliminate it, but perhaps we might be better setting a lower cutoff on
1972|&#916;F<sup>2</sup>|/&#963;(F<sub>o</sub><sup>2</sup>) to eliminate other
1973similar problem reflections. Go to the <b style='mso-bidi-font-weight:normal'><span
1974style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1975mso-hansi-theme-font:minor-latin'>Controls</span></b> entry in the GSAS-II data
1976tree</p>
1977
1978<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1979 id="Picture_x0020_52" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:468pt;
1980 height:200.25pt;visibility:visible;mso-wrap-style:square'>
1981 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image049.png"
1982  o:title=""/>
1983</v:shape><![endif]--><![if !vml]><img width=624 height=267
1984src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image077.gif"
1985v:shapes="Picture_x0020_52"><![endif]></span></p>
1986
1987<p class=MsoNormal>Change the value of <b style='mso-bidi-font-weight:normal'><span
1988style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1989mso-hansi-theme-font:minor-latin'>Max <span class=SpellE>delt</span>-F/sig</span></b>
1990to 20; that will certainly eliminate the bad 342 reflection &amp; perhaps a few
1991others. Repeat <b style='mso-bidi-font-weight:normal'><span style='font-family:
1992"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1993minor-latin'>Calculate/Refine</span></b>; my residual dropped considerably (<span
1994class=SpellE>Rw</span> ~4.5%) and the 3D plot shows no really bad reflections</p>
1995
1996<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1997 id="Picture_x0020_53" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:468pt;
1998 height:404.25pt;visibility:visible;mso-wrap-style:square'>
1999 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image051.png"
2000  o:title=""/>
2001</v:shape><![endif]--><![if !vml]><img width=624 height=539
2002src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image078.gif"
2003v:shapes="Picture_x0020_53"><![endif]></span></p>
2004
2005<p class=MsoNormal>Looking the <span class=SpellE><b style='mso-bidi-font-weight:
2006normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2007minor-latin;mso-hansi-theme-font:minor-latin'>sapphire.lst</span></b></span><b
2008style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2009mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> </span></b>file
2010shows that HKLF #23 is now more in line with the other ones (RF = 4.35% &amp;
2011scale = 67.41). To finish the refinement make the two sapphire atoms have
2012anisotropic thermal parameters. Select <b style='mso-bidi-font-weight:normal'><span
2013style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2014mso-hansi-theme-font:minor-latin'>Phases/sapphire</span></b> and the <b
2015style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2016mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Atoms</span></b>
2017tab; then double click the <b style='mso-bidi-font-weight:normal'><span
2018style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2019mso-hansi-theme-font:minor-latin'>I/A</span></b> column heading. A popup will
2020appear; select <b style='mso-bidi-font-weight:normal'><span style='font-family:
2021"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2022minor-latin'>Anisotropic</span></b> and press <b style='mso-bidi-font-weight:
2023normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2024minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>. The atom <span
2025class=SpellE>Uijs</span> will appear and <span class=SpellE>Uiso</span> will be
2026greyed out. Then do <b style='mso-bidi-font-weight:normal'><span
2027style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2028mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> again. My final
2029residual was <span class=SpellE>Rw</span>=4.20%. </p>
2030
2031<p class=MsoNormal>This completes the tutorial. You can explore the other
2032extinction models and try different cutoff values for <b style='mso-bidi-font-weight:
2033normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2034minor-latin;mso-hansi-theme-font:minor-latin'>Max <span class=SpellE>delt</span>-F/sig</span></b>.
2035<b style='mso-bidi-font-weight:normal'><u>NB: this should never be set before
2036the refinement is complete as it can reject large portions of the data
2037prematurely.<o:p></o:p></u></b></p>
2038
2039</div>
2040
2041</body>
2042
2043</html>
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