source: Tutorials/TOF Single Crystal Refinement/TOF single crystal refinement in GSAS.htm @ 2535

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407  <w:LsdException Locked="false" SemiHidden="true" Name="Revision"/>
408  <w:LsdException Locked="false" Priority="34" QFormat="true"
409   Name="List Paragraph"/>
410  <w:LsdException Locked="false" Priority="29" QFormat="true" Name="Quote"/>
411  <w:LsdException Locked="false" Priority="30" QFormat="true"
412   Name="Intense Quote"/>
413  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 1"/>
414  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 1"/>
415  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 1"/>
416  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 1"/>
417  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 1"/>
418  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 1"/>
419  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 1"/>
420  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 1"/>
421  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 2"/>
422  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 2"/>
423  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 2"/>
424  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 2"/>
425  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 2"/>
426  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 2"/>
427  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 2"/>
428  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 2"/>
429  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 2"/>
430  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 2"/>
431  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 2"/>
432  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 2"/>
433  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 2"/>
434  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 2"/>
435  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 3"/>
436  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 3"/>
437  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 3"/>
438  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 3"/>
439  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 3"/>
440  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 3"/>
441  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 3"/>
442  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 3"/>
443  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 3"/>
444  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 3"/>
445  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 3"/>
446  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 3"/>
447  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 3"/>
448  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 3"/>
449  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 4"/>
450  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 4"/>
451  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 4"/>
452  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 4"/>
453  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 4"/>
454  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 4"/>
455  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 4"/>
456  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 4"/>
457  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 4"/>
458  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 4"/>
459  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 4"/>
460  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 4"/>
461  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 4"/>
462  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 4"/>
463  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 5"/>
464  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 5"/>
465  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 5"/>
466  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 5"/>
467  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 5"/>
468  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 5"/>
469  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 5"/>
470  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 5"/>
471  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 5"/>
472  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 5"/>
473  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 5"/>
474  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 5"/>
475  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 5"/>
476  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 5"/>
477  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 6"/>
478  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 6"/>
479  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 6"/>
480  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 6"/>
481  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 6"/>
482  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 6"/>
483  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 6"/>
484  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 6"/>
485  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 6"/>
486  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 6"/>
487  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 6"/>
488  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 6"/>
489  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 6"/>
490  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 6"/>
491  <w:LsdException Locked="false" Priority="19" QFormat="true"
492   Name="Subtle Emphasis"/>
493  <w:LsdException Locked="false" Priority="21" QFormat="true"
494   Name="Intense Emphasis"/>
495  <w:LsdException Locked="false" Priority="31" QFormat="true"
496   Name="Subtle Reference"/>
497  <w:LsdException Locked="false" Priority="32" QFormat="true"
498   Name="Intense Reference"/>
499  <w:LsdException Locked="false" Priority="33" QFormat="true" Name="Book Title"/>
500  <w:LsdException Locked="false" Priority="37" SemiHidden="true"
501   UnhideWhenUsed="true" Name="Bibliography"/>
502  <w:LsdException Locked="false" Priority="39" SemiHidden="true"
503   UnhideWhenUsed="true" QFormat="true" Name="TOC Heading"/>
504  <w:LsdException Locked="false" Priority="41" Name="Plain Table 1"/>
505  <w:LsdException Locked="false" Priority="42" Name="Plain Table 2"/>
506  <w:LsdException Locked="false" Priority="43" Name="Plain Table 3"/>
507  <w:LsdException Locked="false" Priority="44" Name="Plain Table 4"/>
508  <w:LsdException Locked="false" Priority="45" Name="Plain Table 5"/>
509  <w:LsdException Locked="false" Priority="40" Name="Grid Table Light"/>
510  <w:LsdException Locked="false" Priority="46" Name="Grid Table 1 Light"/>
511  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2"/>
512  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3"/>
513  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4"/>
514  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark"/>
515  <w:LsdException Locked="false" Priority="51" Name="Grid Table 6 Colorful"/>
516  <w:LsdException Locked="false" Priority="52" Name="Grid Table 7 Colorful"/>
517  <w:LsdException Locked="false" Priority="46"
518   Name="Grid Table 1 Light Accent 1"/>
519  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 1"/>
520  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 1"/>
521  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 1"/>
522  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 1"/>
523  <w:LsdException Locked="false" Priority="51"
524   Name="Grid Table 6 Colorful Accent 1"/>
525  <w:LsdException Locked="false" Priority="52"
526   Name="Grid Table 7 Colorful Accent 1"/>
527  <w:LsdException Locked="false" Priority="46"
528   Name="Grid Table 1 Light Accent 2"/>
529  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 2"/>
530  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 2"/>
531  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 2"/>
532  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 2"/>
533  <w:LsdException Locked="false" Priority="51"
534   Name="Grid Table 6 Colorful Accent 2"/>
535  <w:LsdException Locked="false" Priority="52"
536   Name="Grid Table 7 Colorful Accent 2"/>
537  <w:LsdException Locked="false" Priority="46"
538   Name="Grid Table 1 Light Accent 3"/>
539  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 3"/>
540  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 3"/>
541  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 3"/>
542  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 3"/>
543  <w:LsdException Locked="false" Priority="51"
544   Name="Grid Table 6 Colorful Accent 3"/>
545  <w:LsdException Locked="false" Priority="52"
546   Name="Grid Table 7 Colorful Accent 3"/>
547  <w:LsdException Locked="false" Priority="46"
548   Name="Grid Table 1 Light Accent 4"/>
549  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 4"/>
550  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 4"/>
551  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 4"/>
552  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 4"/>
553  <w:LsdException Locked="false" Priority="51"
554   Name="Grid Table 6 Colorful Accent 4"/>
555  <w:LsdException Locked="false" Priority="52"
556   Name="Grid Table 7 Colorful Accent 4"/>
557  <w:LsdException Locked="false" Priority="46"
558   Name="Grid Table 1 Light Accent 5"/>
559  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 5"/>
560  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 5"/>
561  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 5"/>
562  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 5"/>
563  <w:LsdException Locked="false" Priority="51"
564   Name="Grid Table 6 Colorful Accent 5"/>
565  <w:LsdException Locked="false" Priority="52"
566   Name="Grid Table 7 Colorful Accent 5"/>
567  <w:LsdException Locked="false" Priority="46"
568   Name="Grid Table 1 Light Accent 6"/>
569  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 6"/>
570  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 6"/>
571  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 6"/>
572  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 6"/>
573  <w:LsdException Locked="false" Priority="51"
574   Name="Grid Table 6 Colorful Accent 6"/>
575  <w:LsdException Locked="false" Priority="52"
576   Name="Grid Table 7 Colorful Accent 6"/>
577  <w:LsdException Locked="false" Priority="46" Name="List Table 1 Light"/>
578  <w:LsdException Locked="false" Priority="47" Name="List Table 2"/>
579  <w:LsdException Locked="false" Priority="48" Name="List Table 3"/>
580  <w:LsdException Locked="false" Priority="49" Name="List Table 4"/>
581  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark"/>
582  <w:LsdException Locked="false" Priority="51" Name="List Table 6 Colorful"/>
583  <w:LsdException Locked="false" Priority="52" Name="List Table 7 Colorful"/>
584  <w:LsdException Locked="false" Priority="46"
585   Name="List Table 1 Light Accent 1"/>
586  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 1"/>
587  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 1"/>
588  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 1"/>
589  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 1"/>
590  <w:LsdException Locked="false" Priority="51"
591   Name="List Table 6 Colorful Accent 1"/>
592  <w:LsdException Locked="false" Priority="52"
593   Name="List Table 7 Colorful Accent 1"/>
594  <w:LsdException Locked="false" Priority="46"
595   Name="List Table 1 Light Accent 2"/>
596  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 2"/>
597  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 2"/>
598  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 2"/>
599  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 2"/>
600  <w:LsdException Locked="false" Priority="51"
601   Name="List Table 6 Colorful Accent 2"/>
602  <w:LsdException Locked="false" Priority="52"
603   Name="List Table 7 Colorful Accent 2"/>
604  <w:LsdException Locked="false" Priority="46"
605   Name="List Table 1 Light Accent 3"/>
606  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 3"/>
607  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 3"/>
608  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 3"/>
609  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 3"/>
610  <w:LsdException Locked="false" Priority="51"
611   Name="List Table 6 Colorful Accent 3"/>
612  <w:LsdException Locked="false" Priority="52"
613   Name="List Table 7 Colorful Accent 3"/>
614  <w:LsdException Locked="false" Priority="46"
615   Name="List Table 1 Light Accent 4"/>
616  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 4"/>
617  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 4"/>
618  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 4"/>
619  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 4"/>
620  <w:LsdException Locked="false" Priority="51"
621   Name="List Table 6 Colorful Accent 4"/>
622  <w:LsdException Locked="false" Priority="52"
623   Name="List Table 7 Colorful Accent 4"/>
624  <w:LsdException Locked="false" Priority="46"
625   Name="List Table 1 Light Accent 5"/>
626  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 5"/>
627  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 5"/>
628  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 5"/>
629  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 5"/>
630  <w:LsdException Locked="false" Priority="51"
631   Name="List Table 6 Colorful Accent 5"/>
632  <w:LsdException Locked="false" Priority="52"
633   Name="List Table 7 Colorful Accent 5"/>
634  <w:LsdException Locked="false" Priority="46"
635   Name="List Table 1 Light Accent 6"/>
636  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 6"/>
637  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 6"/>
638  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 6"/>
639  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 6"/>
640  <w:LsdException Locked="false" Priority="51"
641   Name="List Table 6 Colorful Accent 6"/>
642  <w:LsdException Locked="false" Priority="52"
643   Name="List Table 7 Colorful Accent 6"/>
644 </w:LatentStyles>
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1214 <o:shapedefaults v:ext="edit" spidmax="1026"/>
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1221<body lang=EN-US link=blue vlink=purple style='tab-interval:.5in'>
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1223<div class=WordSection1>
1224
1225<h1><span style='mso-fareast-font-family:"Times New Roman"'>Single crystal
1226structure refinement with TOF data in GSAS-II<o:p></o:p></span></h1>
1227
1228<h2><span style='mso-fareast-font-family:"Times New Roman"'>Introduction: <o:p></o:p></span></h2>
1229
1230<p class=MsoNormal>In these exercises you will use GSAS-II to refine the
1231structure of sapphire (really corundum, Al<sub>2</sub>O<sub>3</sub>) from single
1232crystal diffraction data collected at the SNS on the TOPAZ instrument at room
1233temperature. The data consists of a suite of exposures with the crystal in 31
1234different orientations all within a single data file. Note that menu entries
1235and user input are shown in bold face below as <b style='mso-bidi-font-weight:
1236normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1237minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1238mso-bidi-theme-font:minor-latin'>Help/About GSAS-II</span></b>, which lists
1239first the name of the menu (here <b style='mso-bidi-font-weight:normal'><span
1240style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1241mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;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-font-family:
1245Calibri;mso-bidi-theme-font:minor-latin'>About GSAS-II</span></b>). If you have
1246not done so already, start GSAS-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-font-family:
1255Calibri;mso-bidi-theme-font:minor-latin'>Data/Add phase</span></b> menu item
1256add a new phase into the current GSAS-II project. A popup window will appear
1257asking for a phase name; I entered <b style='mso-bidi-font-weight:normal'><span
1258style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1259mso-hansi-theme-font:minor-latin'>sapphire</span></b>; press <b
1260style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1261mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>
1262when done. Select <b style='mso-bidi-font-weight:normal'><span
1263style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1264mso-hansi-theme-font:minor-latin'>Loaded Data/Phases/sapphire</span></b> from
1265the GSAS-II Data tree window. The General tab for Phase Data will appear.</p>
1266
1267<p class=MsoListParagraph><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
1268 id="_x0000_t75" coordsize="21600,21600" o:spt="75" o:preferrelative="t"
1269 path="m@4@5l@4@11@9@11@9@5xe" filled="f" stroked="f">
1270 <v:stroke joinstyle="miter"/>
1271 <v:formulas>
1272  <v:f eqn="if lineDrawn pixelLineWidth 0"/>
1273  <v:f eqn="sum @0 1 0"/>
1274  <v:f eqn="sum 0 0 @1"/>
1275  <v:f eqn="prod @2 1 2"/>
1276  <v:f eqn="prod @3 21600 pixelWidth"/>
1277  <v:f eqn="prod @3 21600 pixelHeight"/>
1278  <v:f eqn="sum @0 0 1"/>
1279  <v:f eqn="prod @6 1 2"/>
1280  <v:f eqn="prod @7 21600 pixelWidth"/>
1281  <v:f eqn="sum @8 21600 0"/>
1282  <v:f eqn="prod @7 21600 pixelHeight"/>
1283  <v:f eqn="sum @10 21600 0"/>
1284 </v:formulas>
1285 <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
1286 <o:lock v:ext="edit" aspectratio="t"/>
1287</v:shapetype><v:shape id="Picture_x0020_1" o:spid="_x0000_i1050" type="#_x0000_t75"
1288 style='width:640.5pt;height:375pt;visibility:visible;mso-wrap-style:square'>
1289 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image001.png"
1290  o:title=""/>
1291</v:shape><![endif]--><![if !vml]><img width=854 height=500
1292src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image051.gif"
1293v:shapes="Picture_x0020_1"><![endif]></span></p>
1294
1295<p class=MsoListParagraph><o:p>&nbsp;</o:p></p>
1296
1297<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1298style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
1299style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Enter
1300<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1301mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>R -3 c</span></b>
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_29" o:spid="_x0000_i1049" type="#_x0000_t75" style='width:487.5pt;
1313 height:375pt;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=650 height=500
1317src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image052.gif"
1318v:shapes="Picture_x0020_29"><![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</span> and <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/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_31" o:spid="_x0000_i1048" type="#_x0000_t75" style='width:525pt;
1346 height:225pt;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=700 height=300
1350src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image053.gif"
1351v:shapes="Picture_x0020_31"><![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_32" o:spid="_x0000_i1047" type="#_x0000_t75" style='width:525pt;
1365 height:225pt;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=700 height=300
1369src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image054.gif"
1370v:shapes="Picture_x0020_32"><![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 Al(z) to <b style='mso-bidi-font-weight:normal'><span style='font-family:
1376"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1377minor-latin'>0. 352</span></b>, the O(x) to <b style='mso-bidi-font-weight:
1378normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1379minor-latin;mso-hansi-theme-font:minor-latin'>-0.306</span></b> and the O(z) to
1380<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1381mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Œ</span></b>
1382(it will be changed to 0.2500). Site symmetries and multiplicities will
1383automatically change for these positions.</p>
1384
1385<p class=MsoListParagraph><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1386 id="Picture_x0020_34" o:spid="_x0000_i1046" type="#_x0000_t75" style='width:525pt;
1387 height:225pt;visibility:visible;mso-wrap-style:square'>
1388 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image009.png"
1389  o:title=""/>
1390</v:shape><![endif]--><![if !vml]><img width=700 height=300
1391src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image055.gif"
1392v:shapes="Picture_x0020_34"><![endif]></span></p>
1393
1394<p class=MsoListParagraph><o:p>&nbsp;</o:p></p>
1395
1396<p class=MsoListParagraph>This completes the initial phase setup for sapphire.
1397An alternative would be to read the phase information from another GSAS-II <span
1398class=SpellE>gpx</span> file, a <span class=SpellE>cif</span> file or an old
1399GSAS <span class=SpellE>exp</span> file; these are all accessed from the <b
1400style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1401mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Import/Phase</span></b>
1402menu item on the main GSAS-II Data tree window. It may be useful to save your
1403project at this point; select <b style='mso-bidi-font-weight:normal'><span
1404style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1405mso-hansi-theme-font:minor-latin'>File/Save project as…</span></b> from the
1406main GSAS-II Data tree window menu. A file dialog box will appear; select the
1407directory and give a file name (no extension – I chose <b style='mso-bidi-font-weight:
1408normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1409minor-latin;mso-hansi-theme-font:minor-latin'>sapphire</span></b>).</p>
1410
1411<h2>Step 2. Import the diffraction data</h2>
1412
1413<p class=MsoNormal>The diffraction data collected on TOPAZ has been processed
1414(absorption corrections, wavelength and geometric corrections) to give a single
1415file with 31 embedded histograms as a space delimited multicolumn text file (<span
1416class=SpellE>sapphire_sphere.hkl</span>). To read this file select <b
1417style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1418mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Import/Structure
1419Factor/from Neutron TOF HKL F<sup>2 </sup>file</span></b>; a file dialog box
1420will appear. Change the directory to the location of this exercise (<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'>TOF Single
1423Crystal Refinement/data</span></b> – yours might be different), select <span
1424class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1425"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1426minor-latin'>sapphire_sphere.hkl</span></b></span> and press <b
1427style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1428mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Open</span></b>.
1429A popup will show a bit of the file and ask if you want to read this file;
1430press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1431mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Yes</span></b>.
1432Another popup will appear with a suggested name for the data; this will be used
1433for the GSAS-II Data tree. Press <b style='mso-bidi-font-weight:normal'><span
1434style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1435mso-hansi-theme-font:minor-latin'>OK</span></b>. The console will show messages
1436as each histogram is read; when done a new popup will appear</p>
1437
1438<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1439 id="Picture_x0020_35" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:240pt;
1440 height:232.5pt;visibility:visible;mso-wrap-style:square'>
1441 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image011.png"
1442  o:title=""/>
1443</v:shape><![endif]--><![if !vml]><img width=320 height=310
1444src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image056.gif"
1445v:shapes="Picture_x0020_35"><![endif]></span></p>
1446
1447<p class=MsoNormal>This makes the connection between the data you just read and
1448the phase (<b style='mso-bidi-font-weight:normal'><span style='font-family:
1449"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1450minor-latin'>sapphire</span></b>) you entered in Step 1. Select it (or <b
1451style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1452mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Set All</span></b>)
1453and press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1454mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1455The GSAS-II data tree window will show all the new histograms, expanding the
1456last one.</p>
1457
1458<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1459 id="Picture_x0020_36" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:300pt;
1460 height:187.5pt;visibility:visible;mso-wrap-style:square'>
1461 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image013.png"
1462  o:title=""/>
1463</v:shape><![endif]--><![if !vml]><img width=400 height=250
1464src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image057.gif"
1465v:shapes="Picture_x0020_36"><![endif]></span></p>
1466
1467<p class=MsoNormal>The plot window shows a not very interesting 2D view of the l=0
1468layer of reciprocal space for the last data set. If you select the 1<sup>st</sup>
1469HKLF entry (<b style='mso-bidi-font-weight:normal'><span style='font-family:
1470"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1471minor-latin'>HKLF <span class=SpellE>sapphire_sphere.hkl</span></span></b>) the
1472plot is a bit more interesting.</p>
1473
1474<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1475 id="Picture_x0020_10" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:525pt;
1476 height:450pt;visibility:visible;mso-wrap-style:square'>
1477 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image015.png"
1478  o:title=""/>
1479</v:shape><![endif]--><![if !vml]><img width=700 height=600
1480src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image058.gif"
1481v:shapes="Picture_x0020_10"><![endif]></span></p>
1482
1483<p class=MsoNormal>Green circles are drawn representing the magnitude of 4
1484structure factors on the l=0 layer. The positions are strictly on a square
1485grid; you can “tab” through the layers on l with the <b style='mso-bidi-font-weight:
1486normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1487minor-latin;mso-hansi-theme-font:minor-latin'>+/-</span></b> keys. Find other
1488commands in the “K” box in the tools part of the plot. If you select <b
1489style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1490mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Commands/Plot
14913D HKLs</span></b> from the data window you’ll see a 3D view of this reflection
1492set; press <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1493style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1494mso-hansi-theme-font:minor-latin'>i</span></b></span> after selecting the plot
1495(I’ve zoomed in a bit)</p>
1496
1497<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1498
1499<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1500 id="_x0000_i1042" type="#_x0000_t75" style='width:363pt;height:311.25pt;
1501 visibility:visible;mso-wrap-style:square'>
1502 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image017.png"
1503  o:title="" croptop="11818f" cropbottom="16324f" cropleft="40001f"
1504  cropright="10518f"/>
1505</v:shape><![endif]--><![if !vml]><img width=484 height=415
1506src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image059.jpg"
1507v:shapes="_x0000_i1042"><![endif]></span></p>
1508
1509<p class=MsoNormal>Here the plot has the correct representation for reciprocal
1510space as sampled by this crystal orientation on TOPAZ. The <b style='mso-bidi-font-weight:
1511normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1512minor-latin;mso-hansi-theme-font:minor-latin'>save as/key</span></b> commands give
1513you control on the appearance of the plot; the plot responds to zoom/rotate
1514commands from the mouse. Left mouse button to rotate, right mouse button to
1515translate, center wheel to rotate about view direction and the wheel to zoom in
1516or out. One cursor is the view point and the other is the 000 reciprocal space
1517origin. </p>
1518
1519<p class=MsoNormal>If you want to see the entire data set plotted together do <b
1520style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1521mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Commands/Plot
1522all 3D HKLs</span></b>; a data selection popup window will appear. 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'>Set Al</span></b>l
1525and then <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1526mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>
1527to select all the data; the plot will be redrawn (I’ve pressed the ‘<span
1528class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1529"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1530minor-latin'>i</span></b></span>’ key as before)</p>
1531
1532<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1533 id="_x0000_i1041" type="#_x0000_t75" style='width:365.25pt;height:310.5pt;
1534 visibility:visible;mso-wrap-style:square'>
1535 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image019.png"
1536  o:title="" croptop="12098f" cropbottom="16193f" cropleft="40187f"
1537  cropright="10237f"/>
1538</v:shape><![endif]--><![if !vml]><img width=487 height=414
1539src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image060.jpg"
1540v:shapes="_x0000_i1041"><![endif]></span></p>
1541
1542<p class=MsoNormal>I’ve rotated the drawing around to show an obvious gap in
1543the coverage.</p>
1544
1545<p class=MsoNormal>We’re now ready to do the refinement.</p>
1546
1547<h2>Step 3. Initial least squares refinement</h2>
1548
1549<p class=MsoNormal>By default the scale factors for all 31 data set are set to
1550be refined so you can immediately do a refinement. Select <b style='mso-bidi-font-weight:
1551normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1552minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> from
1553the main GSAS-II data tree window menu. This will do an F refinement by
1554default. A progress bar will appear to show you the residuals as the histograms
1555are processed. When it finishes and you have accepted the result a plot will
1556show the l=0 layer for the 1<sup>st</sup> data set.</p>
1557
1558<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1559 id="Picture_x0020_11" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:525pt;
1560 height:450pt;visibility:visible;mso-wrap-style:square'>
1561 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image021.png"
1562  o:title=""/>
1563</v:shape><![endif]--><![if !vml]><img width=700 height=600
1564src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image061.gif"
1565v:shapes="Picture_x0020_11"><![endif]></span></p>
1566
1567<p class=MsoNormal>Green rings are the observed magnitude, blue rings are the
1568calculated ones and the solid disk is the difference (green for positive &amp;
1569red for negative <span class=SpellE>F<sub>o</sub></span>-F<sub>c</sub>). You
1570can see the whole scope of the fit by doing <b style='mso-bidi-font-weight:
1571normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1572minor-latin;mso-hansi-theme-font:minor-latin'>Commands/Plot all 3D HKLs</span></b>
1573and selecting all the HKLF entries; press the “<b style='mso-bidi-font-weight:
1574normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1575minor-latin;mso-hansi-theme-font:minor-latin'>w</span></b>” key to show the
1576weighted &#916;F points.</p>
1577
1578<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1579 id="Picture_x0020_12" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:369pt;
1580 height:310.5pt;visibility:visible;mso-wrap-style:square'>
1581 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image023.png"
1582  o:title="" croptop="9828f" cropbottom="18427f" cropleft="38257f" cropright="12033f"/>
1583</v:shape><![endif]--><![if !vml]><img width=492 height=414
1584src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image062.jpg"
1585v:shapes="Picture_x0020_12"><![endif]></span></p>
1586
1587<p class=MsoNormal>The size of the squares is proportional to the magnitude of <span
1588class=SpellE>w&#916;F</span>. The cluster of negative <span class=SpellE>w&#916;F</span>
1589points around the reciprocal space origin is pretty clearly a consequence of
1590extinction so we’ll have to include that in the refinement model. One should
1591not be tempted to refine coordinates and thermal parameters until extinction is
1592accounted for in the refinement.</p>
1593
1594<h2>Step 3. Extinction model selection and refinement</h2>
1595
1596<p class=MsoNormal>GSAS-II has a number of extinction models available for
1597single crystal data. These include Primary, Secondary types I and II with
1598either Gaussian or Lorentzian distributions. To select one find the <b
1599style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1600mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sapphire</span></b>
1601entry in the GSAS-II data tree and select its <b style='mso-bidi-font-weight:
1602normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1603minor-latin;mso-hansi-theme-font:minor-latin'>Data</span></b> tab.</p>
1604
1605<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1606 id="Picture_x0020_16" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:300pt;
1607 height:303pt;visibility:visible;mso-wrap-style:square'>
1608 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image025.png"
1609  o:title=""/>
1610</v:shape><![endif]--><![if !vml]><img width=400 height=404
1611src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image063.gif"
1612v:shapes="Picture_x0020_16"><![endif]></span></p>
1613
1614<p class=MsoNormal>We can cut to the chase here – select <b style='mso-bidi-font-weight:
1615normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1616minor-latin;mso-hansi-theme-font:minor-latin'>Secondary Type I</span></b> from
1617the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1618mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Extinction
1619type</span></b> pull down list (the tab will be redrawn) and check the <span
1620class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1621"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1622minor-latin'>Eg</span></b></span> box; leave the <span class=SpellE><b
1623style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1624mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Approx</span></b></span>
1625selection as <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'>Lorentzian</span></b>. Later on after you’ve finished the
1628tutorial, you can try the other models and see how they compare. Next do <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'>Edit/Copy
1631selected data</span></b>, pick <b style='mso-bidi-font-weight:normal'><span
1632style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1633mso-hansi-theme-font:minor-latin'>Extinction</span></b> from the list of
1634parameters and press <b style='mso-bidi-font-weight:normal'><span
1635style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1636mso-hansi-theme-font:minor-latin'>OK</span></b>. Then do <b style='mso-bidi-font-weight:
1637normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1638minor-latin;mso-hansi-theme-font:minor-latin'>Set All</span></b> and press <b
1639style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1640mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>
1641from the next popup; this will copy the extinction model to all HKLF data sets.</p>
1642
1643<p class=MsoNormal>Because all of these extinction models are needed for one
1644crystal, it makes sense to tie them together into a single parameter. Select <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'>Constraints</span></b>
1647from the main GSAS-II data tree and pick the <b style='mso-bidi-font-weight:
1648normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1649minor-latin;mso-hansi-theme-font:minor-latin'>Histogram/Phase constraints</span></b>
1650tab; it will be empty. Do <b style='mso-bidi-font-weight:normal'><span
1651style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1652mso-hansi-theme-font:minor-latin'>Edit/Add equivalence</span></b>; the
1653following popup will appear</p>
1654
1655<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1656 id="_x0000_i1037" type="#_x0000_t75" style='width:468.75pt;height:300pt;
1657 visibility:visible;mso-wrap-style:square'>
1658 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image027.png"
1659  o:title=""/>
1660</v:shape><![endif]--><![if !vml]><img width=625 height=400
1661src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image064.gif"
1662v:shapes="_x0000_i1037"><![endif]></span></p>
1663
1664<p class=MsoNormal>Select the line beginning with ‘<span class=GramE><b
1665style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1666mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0:0:Eg</span></b></span>’
1667(the Secondary type I parameter you just set to vary) and press <b
1668style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1669mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1670A new popup will appear; you’ll want to see the bottom of the list</p>
1671
1672<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1673 id="_x0000_i1036" type="#_x0000_t75" style='width:468.75pt;height:300pt;
1674 visibility:visible;mso-wrap-style:square'>
1675 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image029.png"
1676  o:title=""/>
1677</v:shape><![endif]--><![if !vml]><img width=625 height=400
1678src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image065.gif"
1679v:shapes="_x0000_i1036"><![endif]></span></p>
1680
1681<p class=MsoNormal>Pick either <span class=GramE><b style='mso-bidi-font-weight:
1682normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1683minor-latin;mso-hansi-theme-font:minor-latin'>0:all</span></b></span><b
1684style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1685mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>:Eg</span></b>
1686or <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1687mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0:all=<span
1688class=SpellE>SNT:Eg</span></span></b> and press <b style='mso-bidi-font-weight:
1689normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1690minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>. The equivalence
1691making <span class=SpellE>Eg</span> for all histograms the same parameter will
1692be shown</p>
1693
1694<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1695 id="Picture_x0020_20" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:481.5pt;
1696 height:184.5pt;visibility:visible;mso-wrap-style:square'>
1697 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image031.png"
1698  o:title=""/>
1699</v:shape><![endif]--><![if !vml]><img width=642 height=246
1700src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image066.gif"
1701v:shapes="Picture_x0020_20"><![endif]></span></p>
1702
1703<p class=MsoNormal>Now do <b style='mso-bidi-font-weight:normal'><span
1704style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1705mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> from the main GSAS-II
1706data tree menu. You may have to repeat this twice to get convergence (<span
1707class=SpellE>Rw</span> ~14%); note the console output – value of Delta
1708indicates closeness to convergence. Select one of the HKLF data sets and view
1709the 3D Structure Factors plot for it alone</p>
1710
1711<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1712 id="Picture_x0020_17" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:362.25pt;
1713 height:311.25pt;visibility:visible;mso-wrap-style:square'>
1714 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image033.png"
1715  o:title="" croptop="15476f" cropbottom="12688f" cropleft="40744f"
1716  cropright="9798f"/>
1717</v:shape><![endif]--><![if !vml]><img width=483 height=415
1718src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image067.jpg"
1719v:shapes="Picture_x0020_17"><![endif]></span></p>
1720
1721<p class=MsoNormal>The <span class=SpellE>wDF</span> is positive close to 0,0,0
1722then negative for an inner shell around the positive core and finally positive
1723for the outer shell. This is a thermal parameter/extinction effect. So both
1724have to be now refined. However, as a matter of course we may expect that the
1725extinction corrections are less accurate when <span class=SpellE>Fo</span>&lt;&lt;
1726Fc. In addition some reflections were poorly measured. We want to reject
1727reflections where <span class=SpellE>Fo</span>/Fc &lt; 0.5 and Fo2/s(Fo2) &lt;
17283. These can be applied on the <b style='mso-bidi-font-weight:normal'><span
1729style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1730mso-hansi-theme-font:minor-latin'>Controls</span></b> page. After setting these
1731my Controls were</p>
1732
1733<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1734 id="Picture_x0020_18" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:366pt;
1735 height:212.25pt;visibility:visible;mso-wrap-style:square'>
1736 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image035.png"
1737  o:title=""/>
1738</v:shape><![endif]--><![if !vml]><img width=488 height=283
1739src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image068.gif"
1740v:shapes="Picture_x0020_18"><![endif]></span></p>
1741
1742<p class=MsoNormal>Finally we can add the atom parameters for sapphire. Select
1743the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1744mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Atoms</span></b>
1745tab for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1746mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phase/sapphire</span></b></p>
1747
1748<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1749 id="Picture_x0020_21" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:525pt;
1750 height:225pt;visibility:visible;mso-wrap-style:square'>
1751 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image009.png"
1752  o:title=""/>
1753</v:shape><![endif]--><![if !vml]><img width=700 height=300
1754src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image055.gif"
1755v:shapes="Picture_x0020_21"><![endif]></span></p>
1756
1757<p class=MsoNormal>Double (right) click the <b style='mso-bidi-font-weight:
1758normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1759minor-latin;mso-hansi-theme-font:minor-latin'>Refine</span></b> column heading;
1760a popup will appear</p>
1761
1762<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1763 id="Picture_x0020_22" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:259.5pt;
1764 height:252pt;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=346 height=336
1768src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image069.gif"
1769v:shapes="Picture_x0020_22"><![endif]></span></p>
1770
1771<p class=MsoNormal>Choose both <b style='mso-bidi-font-weight:normal'><span
1772style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1773mso-hansi-theme-font:minor-latin'>X</span></b> and <b style='mso-bidi-font-weight:
1774normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1775minor-latin;mso-hansi-theme-font:minor-latin'>U</span></b> and press <b
1776style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1777mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>;
1778the Atoms tab will be redrawn</p>
1779
1780<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1781 id="Picture_x0020_23" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:525pt;
1782 height:225pt;visibility:visible;mso-wrap-style:square'>
1783 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image039.png"
1784  o:title=""/>
1785</v:shape><![endif]--><![if !vml]><img width=700 height=300
1786src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image070.gif"
1787v:shapes="Picture_x0020_23"><![endif]></span></p>
1788
1789<p class=MsoNormal>Showing the refine flags for both atoms. GSAS-II will sort
1790out the special position rules for the two sites.</p>
1791
1792<p class=MsoNormal>Now do <b style='mso-bidi-font-weight:normal'><span
1793style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1794mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> (twice to get
1795convergence). My <span class=SpellE>Rw</span> = 5.91%, GOF = 2.4; find these on
1796the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1797mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Covariance</span></b>
1798data window. Now get a new 3D plot of all the reflections; select any HKLF
1799entry, then do <b style='mso-bidi-font-weight:normal'><span style='font-family:
1800"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1801minor-latin'>Commands/Plot all 3D HKLs</span></b>. Press <b style='mso-bidi-font-weight:
1802normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1803minor-latin;mso-hansi-theme-font:minor-latin'>w</span></b> key.</p>
1804
1805<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1806 id="Picture_x0020_24" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:363pt;
1807 height:312.75pt;visibility:visible;mso-wrap-style:square'>
1808 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image041.png"
1809  o:title="" croptop="10627f" cropbottom="17360f" cropleft="40646f"
1810  cropright="9847f"/>
1811</v:shape><![endif]--><![if !vml]><img width=484 height=417
1812src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image071.jpg"
1813v:shapes="Picture_x0020_24"><![endif]></span></p>
1814
1815<p class=MsoNormal>It’s pretty obvious that there is one really bad reflection
1816and (a bit more subtly) it is messing up one TOPAS data set. To find it first
1817look through the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1818style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1819mso-hansi-theme-font:minor-latin'>sapphire.lst</span></b></span> file; that
1820will give fitting information for all the histograms (near bottom of the
1821listing). Open it with your favorite text editor; I’ve shown an interesting bit
1822of it here showing results for histograms 22-24.</p>
1823
1824<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1825
1826<p class=MsoNormal>Phase:<span style='mso-spacerun:yes'>  </span><span
1827class=GramE>sapphire<span style='mso-spacerun:yes'>  </span>in</span>
1828histogram:<span style='mso-spacerun:yes'>  </span>HKLF sapphire_sphere.hkl_22<span
1829style='mso-spacerun:yes'>                                         </span></p>
1830
1831<p class=MsoNormal>------------------------------------------------------------------------------------------------------</p>
1832
1833<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Final refinement RF,
1834RF^2 = 4.64%, 8.41% on 134 reflections (3 user rejected, 9 <span class=SpellE>sp.gp.extinct</span>)<span
1835style='mso-spacerun:yes'>       </span></p>
1836
1837<p class=MsoNormal><span style='mso-spacerun:yes'> </span>HKLF histogram weight
1838factor <span class=GramE>=<span style='mso-spacerun:yes'>  </span>1.000</span><span
1839style='mso-spacerun:yes'>                                                               
1840</span></p>
1841
1842<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Scale <span
1843class=GramE>factor :</span><span style='mso-spacerun:yes'>    </span>66.8623,
1844sig<span style='mso-spacerun:yes'>     </span>0.8144<span
1845style='mso-spacerun:yes'>                                                           
1846</span></p>
1847
1848<p class=MsoNormal><span
1849style='mso-spacerun:yes'>                                    </span><span
1850style='mso-spacerun:yes'>                                                                  </span></p>
1851
1852<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Single crystal
1853extinction: Type:<span style='mso-spacerun:yes'>  </span><span class=GramE>Lorentzian<span
1854style='mso-spacerun:yes'>  </span><span class=SpellE>Approx</span></span>:<span
1855style='mso-spacerun:yes'>  </span>Secondary Type I<span
1856style='mso-spacerun:yes'>                              </span></p>
1857
1858<p class=MsoNormal><span style='mso-spacerun:yes'>       </span><span
1859class=SpellE>Eg</span>:<span style='mso-spacerun:yes'>     </span>5.58e-04
1860sig:<span style='mso-spacerun:yes'>     </span>1.28e-05<span
1861style='mso-spacerun:yes'>                                             </span><span
1862style='mso-spacerun:yes'>                </span></p>
1863
1864<p class=MsoNormal><span
1865style='mso-spacerun:yes'>                                                                                                     
1866</span></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<span
1872style='mso-spacerun:yes'>                                         </span></p>
1873
1874<p class=MsoNormal>------------------------------------------------------------------------------------------------------</p>
1875
1876<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Final refinement RF,
1877RF^2 = 21.69%, 38.49% on 148 reflections (5 user rejected, 6 <span
1878class=SpellE>sp.gp.extinct</span>)<span style='mso-spacerun:yes'>     </span></p>
1879
1880<p class=MsoNormal><span style='mso-spacerun:yes'> </span>HKLF histogram weight
1881factor <span class=GramE>=<span style='mso-spacerun:yes'>  </span>1.000</span><span
1882style='mso-spacerun:yes'>                                             </span><span
1883style='mso-spacerun:yes'>                   </span></p>
1884
1885<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Scale <span
1886class=GramE>factor :</span><span style='mso-spacerun:yes'>    </span>43.2084,
1887sig<span style='mso-spacerun:yes'>     </span>0.6507<span
1888style='mso-spacerun:yes'>                                                           
1889</span></p>
1890
1891<p class=MsoNormal><span
1892style='mso-spacerun:yes'>                                                                                                     
1893</span></p>
1894
1895<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Single crystal
1896extinction: Type:<span style='mso-spacerun:yes'>  </span><span class=GramE>Lorentzian<span
1897style='mso-spacerun:yes'>  </span><span class=SpellE>Approx</span></span>:<span
1898style='mso-spacerun:yes'>  </span>Secondary Type I<span
1899style='mso-spacerun:yes'>                              </span></p>
1900
1901<p class=MsoNormal><span style='mso-spacerun:yes'>       </span><span
1902class=SpellE>Eg</span>:<span style='mso-spacerun:yes'>     </span>5.58e-04
1903sig:<span style='mso-spacerun:yes'>     </span>1.28e-05<span
1904style='mso-spacerun:yes'>                                                            
1905</span></p>
1906
1907<p class=MsoNormal><span
1908style='mso-spacerun:yes'>                                                                               
1909</span><span style='mso-spacerun:yes'>                      </span></p>
1910
1911<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Phase:<span
1912style='mso-spacerun:yes'>  </span><span class=GramE>sapphire<span
1913style='mso-spacerun:yes'>  </span>in</span> histogram:<span
1914style='mso-spacerun:yes'>  </span>HKLF sapphire_sphere.hkl_24<span
1915style='mso-spacerun:yes'>                                         </span></p>
1916
1917<p class=MsoNormal>------------------------------------------------------------------------------------------------------</p>
1918
1919<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Final refinement RF,
1920RF^2 = 3.86%, 6.70% on 160 reflections (11 user rejected, 1 <span class=SpellE>sp.gp.extinct</span>)<span
1921style='mso-spacerun:yes'>      </span></p>
1922
1923<p class=MsoNormal><span style='mso-spacerun:yes'> </span>HKLF histogram weight
1924factor <span class=GramE>=<span style='mso-spacerun:yes'>  </span>1.000</span><span
1925style='mso-spacerun:yes'>                                                               
1926</span></p>
1927
1928<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Scale <span
1929class=GramE>factor :</span><span style='mso-spacerun:yes'>    </span>66.6296,
1930sig<span style='mso-spacerun:yes'>     </span>0.7816<span
1931style='mso-spacerun:yes'>                                   </span><span
1932style='mso-spacerun:yes'>                         </span></p>
1933
1934<p class=MsoNormal><span
1935style='mso-spacerun:yes'>                                                                                                     
1936</span></p>
1937
1938<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Single crystal
1939extinction: Type:<span style='mso-spacerun:yes'>  </span><span class=GramE>Lorentzian<span
1940style='mso-spacerun:yes'>  </span><span class=SpellE>Approx</span></span>:<span
1941style='mso-spacerun:yes'>  </span>Secondary Type I<span
1942style='mso-spacerun:yes'>                              </span></p>
1943
1944<p class=MsoNormal><span style='mso-spacerun:yes'>       </span><span
1945class=SpellE>Eg</span>:<span style='mso-spacerun:yes'>     </span>5.58e-04 sig:<span
1946style='mso-spacerun:yes'>     </span>1.28e-05<span
1947style='mso-spacerun:yes'>                                                            
1948</span></p>
1949
1950<p class=MsoNormal><span
1951style='mso-spacerun:yes'>                                                                                                     
1952</span></p>
1953
1954<p class=MsoNormal>There is obviously something wrong with #23 (high residual
1955&amp; funny scale factor compared to the others). Find <b style='mso-bidi-font-weight:
1956normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1957minor-latin;mso-hansi-theme-font:minor-latin'>HKLF sapphire_sphere.hkl_23</span></b>
1958in the GSAS-II data tree &amp; select it. The 3D plot of just that data set
1959will show the problem reflection.</p>
1960
1961<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1962 id="Picture_x0020_25" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:365.25pt;
1963 height:315pt;visibility:visible;mso-wrap-style:square'>
1964 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image043.png"
1965  o:title="" croptop="9290f" cropbottom="18441f" cropleft="38576f" cropright="11843f"/>
1966</v:shape><![endif]--><![if !vml]><img width=487 height=420
1967src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image072.jpg"
1968v:shapes="Picture_x0020_25"><![endif]></span></p>
1969
1970<p class=MsoNormal>By zooming in and rotating the plot around a bit, you can
1971identify the reflection with the cursor. It seems to be the <b
1972style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1973mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>541</span></b>
1974reflection; select the <b style='mso-bidi-font-weight:normal'><span
1975style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1976mso-hansi-theme-font:minor-latin'>Reflection List</span></b> and look for it
1977(unfortunately the reflections are produced in a somewhat random order by the
1978TOPAZ data acquisition system). It is very near the bottom of the list (#<b
1979style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1980mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>153</span></b>).</p>
1981
1982<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1983 id="Picture_x0020_26" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:585pt;
1984 height:244.5pt;visibility:visible;mso-wrap-style:square'>
1985 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image045.png"
1986  o:title=""/>
1987</v:shape><![endif]--><![if !vml]><img width=780 height=326
1988src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image073.gif"
1989v:shapes="Picture_x0020_26"><![endif]></span></p>
1990
1991<p class=MsoNormal>The <span class=SpellE>Fcsq</span> (F<sub>c</sub><sup>2</sup>)
1992is very much larger than <span class=SpellE>Fosq</span> (F<sub>o</sub><sup>2</sup>)
1993so that |&#916;F<sup>2</sup>|/&#963;(F<sub>o</sub><sup>2</sup>) &gt; 80! It was
1994obviously poorly measured (e.g. on the edge of the detector, etc.). We’d like
1995to eliminate it, but perhaps we might be better setting a lower cutoff on
1996|&#916;F<sup>2</sup>|/&#963;(F<sub>o</sub><sup>2</sup>) to eliminate other
1997similar problem reflections. Go to the <b style='mso-bidi-font-weight:normal'><span
1998style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1999mso-hansi-theme-font:minor-latin'>Controls</span></b> entry in the GSAS-II data
2000tree</p>
2001
2002<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2003 id="Picture_x0020_27" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:391.5pt;
2004 height:225.75pt;visibility:visible;mso-wrap-style:square'>
2005 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image047.png"
2006  o:title=""/>
2007</v:shape><![endif]--><![if !vml]><img width=522 height=301
2008src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image074.gif"
2009v:shapes="Picture_x0020_27"><![endif]></span></p>
2010
2011<p class=MsoNormal>Change the value of <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'>Max <span class=SpellE>delt</span>-F/sig</span></b>
2014to 20; that will certainly eliminate the bad 541 reflection &amp; perhaps a few
2015others. Repeat <b style='mso-bidi-font-weight:normal'><span style='font-family:
2016"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2017minor-latin'>Calculate/Refine</span></b>; my residual dropped considerably (<span
2018class=SpellE>Rw</span> ~4.5%) and the 3D plot shows no really bad reflections</p>
2019
2020<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2021 id="Picture_x0020_28" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:363pt;
2022 height:309.75pt;visibility:visible;mso-wrap-style:square'>
2023 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image049.png"
2024  o:title="" croptop="8876f" cropbottom="19515f" cropleft="39851f" cropright="10631f"/>
2025</v:shape><![endif]--><![if !vml]><img width=484 height=413
2026src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image075.jpg"
2027v:shapes="Picture_x0020_28"><![endif]></span></p>
2028
2029<p class=MsoNormal>Looking the <span class=SpellE><b style='mso-bidi-font-weight:
2030normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2031minor-latin;mso-hansi-theme-font:minor-latin'>sapphire.lst</span></b></span><b
2032style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2033mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> </span></b>file
2034shows that HKLF #23 is now more in line with the other ones (RF = 4.35% &amp;
2035scale = 67.41). To finish the refinement make the two sapphire atoms have
2036anisotropic thermal parameters. Select <b style='mso-bidi-font-weight:normal'><span
2037style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2038mso-hansi-theme-font:minor-latin'>Phases/sapphire</span></b> and the <b
2039style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2040mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Atoms</span></b>
2041tab; then double click the <b style='mso-bidi-font-weight:normal'><span
2042style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2043mso-hansi-theme-font:minor-latin'>I/A</span></b> column heading. A popup will
2044appear; select <b style='mso-bidi-font-weight:normal'><span style='font-family:
2045"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2046minor-latin'>Anisotropic</span></b> and press <b style='mso-bidi-font-weight:
2047normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2048minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>. The atom <span
2049class=SpellE>Uijs</span> will appear and <span class=SpellE>Uiso</span> will be
2050greyed out. Then do <b style='mso-bidi-font-weight:normal'><span
2051style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2052mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> again. My final
2053residual was <span class=SpellE>Rw</span>=5.06%. </p>
2054
2055<p class=MsoNormal>This completes the tutorial. You can explore the other
2056extinction models and try different cutoff values for <b style='mso-bidi-font-weight:
2057normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2058minor-latin;mso-hansi-theme-font:minor-latin'>Max <span class=SpellE>delt</span>-F/sig</span></b>.
2059<b style='mso-bidi-font-weight:normal'><u>NB: this should never be set before
2060the refinement is complete as it can reject large portions of the data
2061prematurely.<o:p></o:p></u></b></p>
2062
2063</div>
2064
2065</body>
2066
2067</html>
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