source: Tutorials/TOF Single Crystal Refinement/TOF single crystal refinement in GSAS.htm @ 4891

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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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1214<![endif]--><!--[if gte mso 9]><xml>
1215 <o:shapedefaults v:ext="edit" spidmax="1026"/>
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1220</head>
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<BL>
1230<LI>Exercise files are found <A href="./data/" target="_blank">here</a>
1231</BL>
1232
1233<h2><span style='mso-fareast-font-family:"Times New Roman"'>Introduction: <o:p></o:p></span></h2>
1234
1235<p class=MsoNormal>In these exercises you will use GSAS-II to refine the
1236structure of sapphire (really corundum, Al<sub>2</sub>O<sub>3</sub>) from single
1237crystal diffraction data collected at the SNS on the TOPAZ instrument at room
1238temperature. The data consists of a suite of exposures with the crystal in 31
1239different orientations all within a single data file. Note that menu entries
1240and user input are shown in bold face below as <b style='mso-bidi-font-weight:
1241normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1242minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Help/About
1243GSAS-II</span></b>, which lists first the name of the menu (here <b
1244style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1245mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1246minor-latin'>Help</span></b>) and second the name of the entry in the menu
1247(here <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1248mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1249minor-latin'>About GSAS-II</span></b>). If you have not done so already, start
1250GSAS-II.</p>
1251
1252<h2>Step 1. Setup the phase information for sapphire</h2>
1253
1254<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1255style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
1256style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Use
1257the <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;mso-bidi-theme-font:
1259minor-latin'>Data/Add new phase</span></b> menu item add a new phase into the
1260current GSAS-II project. A popup window will appear asking for a phase name; I
1261entered <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1262mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>sapphire</span></b>;
1263press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1264mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>
1265when done. Select <b style='mso-bidi-font-weight:normal'><span
1266style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1267mso-hansi-theme-font:minor-latin'>Loaded Data/Phases/sapphire</span></b> from
1268the GSAS-II Data tree window. The General tab for Phase Data will appear.</p>
1269
1270<p class=MsoListParagraph><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
1271 id="_x0000_t75" coordsize="21600,21600" o:spt="75" o:preferrelative="t"
1272 path="m@4@5l@4@11@9@11@9@5xe" filled="f" stroked="f">
1273 <v:stroke joinstyle="miter"/>
1274 <v:formulas>
1275  <v:f eqn="if lineDrawn pixelLineWidth 0"/>
1276  <v:f eqn="sum @0 1 0"/>
1277  <v:f eqn="sum 0 0 @1"/>
1278  <v:f eqn="prod @2 1 2"/>
1279  <v:f eqn="prod @3 21600 pixelWidth"/>
1280  <v:f eqn="prod @3 21600 pixelHeight"/>
1281  <v:f eqn="sum @0 0 1"/>
1282  <v:f eqn="prod @6 1 2"/>
1283  <v:f eqn="prod @7 21600 pixelWidth"/>
1284  <v:f eqn="sum @8 21600 0"/>
1285  <v:f eqn="prod @7 21600 pixelHeight"/>
1286  <v:f eqn="sum @10 21600 0"/>
1287 </v:formulas>
1288 <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
1289 <o:lock v:ext="edit" aspectratio="t"/>
1290</v:shapetype><v:shape id="Picture_x0020_27" o:spid="_x0000_i1050" type="#_x0000_t75"
1291 style='width:468pt;height:209.25pt;visibility:visible;mso-wrap-style:square'>
1292 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image001.png"
1293  o:title=""/>
1294</v:shape><![endif]--><![if !vml]><img width=624 height=279
1295src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image053.gif"
1296v:shapes="Picture_x0020_27"><![endif]></span></p>
1297
1298<p class=MsoListParagraph><o:p>&nbsp;</o:p></p>
1299
1300<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1301style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
1302style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Enter
1303<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1304mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>R -3 c</span></b>
1305for the space group (don’t forget the spaces between axial fields) &amp; press <b
1306style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1307mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Return</span></b>.
1308A Space Group Information popup window will appear; press <b style='mso-bidi-font-weight:
1309normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1310minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>. The General window
1311will be refreshed showing only the needed lattice <span style='mso-no-proof:
1312yes'>parameters for R -3 c. </span></p>
1313
1314<p class=MsoListParagraph><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1315 id="Picture_x0020_28" o:spid="_x0000_i1049" type="#_x0000_t75" style='width:468pt;
1316 height:265.5pt;visibility:visible;mso-wrap-style:square'>
1317 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image003.png"
1318  o:title=""/>
1319</v:shape><![endif]--><![if !vml]><img width=624 height=354
1320src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image054.gif"
1321v:shapes="Picture_x0020_28"><![endif]></span></p>
1322
1323<p class=MsoListParagraph><o:p>&nbsp;</o:p></p>
1324
1325<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1326style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1327style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Enter
1328<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1329mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>4.7613</span></b>
1330for <span class=GramE>a and</span> <b style='mso-bidi-font-weight:normal'><span
1331style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1332mso-hansi-theme-font:minor-latin'>12.9846</span></b> for c; a new cell volume
1333will be calculated. </p>
1334
1335<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1336style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
1337style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1338the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1339mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Atoms</span></b>
1340tab; it will be empty. Do <b style='mso-bidi-font-weight:normal'><span
1341style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1342mso-hansi-theme-font:minor-latin'>Edit Atoms/Append atom</span></b> from the <b
1343style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1344mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phase Data
1345for sapphire</span></b> menu twice. There will be two UNK entries in the table.</p>
1346
1347<p class=MsoListParagraph><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1348 id="Picture_x0020_29" o:spid="_x0000_i1048" type="#_x0000_t75" style='width:468pt;
1349 height:153.75pt;visibility:visible;mso-wrap-style:square'>
1350 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image005.png"
1351  o:title=""/>
1352</v:shape><![endif]--><![if !vml]><img width=624 height=205
1353src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image055.gif"
1354v:shapes="Picture_x0020_29"><![endif]></span></p>
1355
1356<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1357style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>5.<span
1358style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Double
1359click the first entry under Type (H); a periodic table will appear. Select <b
1360style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1361mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Al</span></b>.
1362Do the same for the second one and pick <b style='mso-bidi-font-weight:normal'><span
1363style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1364mso-hansi-theme-font:minor-latin'>O</span></b>. The Atom list should look like</p>
1365
1366<p class=MsoListParagraph><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1367 id="Picture_x0020_30" o:spid="_x0000_i1047" type="#_x0000_t75" style='width:468pt;
1368 height:153.75pt;visibility:visible;mso-wrap-style:square'>
1369 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image007.png"
1370  o:title=""/>
1371</v:shape><![endif]--><![if !vml]><img width=624 height=205
1372src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image056.gif"
1373v:shapes="Picture_x0020_30"><![endif]></span></p>
1374
1375<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1376style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>6.<span
1377style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Change
1378the <span class=GramE>Al(</span>z) to <b style='mso-bidi-font-weight:normal'><span
1379style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1380mso-hansi-theme-font:minor-latin'>0. 352</span></b>, the O(x) to <b
1381style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1382mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>-0.306</span></b>
1383and the O(z) to <b style='mso-bidi-font-weight:normal'><span style='font-family:
1384"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1385minor-latin'>Œ</span></b> (it will be changed to 0.2500). Also set both <span
1386class=SpellE>Uiso</span> to <b style='mso-bidi-font-weight:normal'><span
1387style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1388mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>0.005</span></b>.
1389Site symmetries and multiplicities will automatically change for these
1390positions.</p>
1391
1392<p class=MsoListParagraph><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1393 id="Picture_x0020_31" o:spid="_x0000_i1046" type="#_x0000_t75" style='width:468pt;
1394 height:153.75pt;visibility:visible;mso-wrap-style:square'>
1395 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image009.png"
1396  o:title=""/>
1397</v:shape><![endif]--><![if !vml]><img width=624 height=205
1398src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image057.gif"
1399v:shapes="Picture_x0020_31"><![endif]></span></p>
1400
1401<p class=MsoListParagraph><o:p>&nbsp;</o:p></p>
1402
1403<p class=MsoListParagraph>This completes the initial phase setup for sapphire.
1404An alternative would be to read the phase information from another GSAS-II <span
1405class=SpellE>gpx</span> file, a <span class=SpellE>cif</span> file or an old
1406GSAS <span class=SpellE>exp</span> file; these are all accessed from the <b
1407style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1408mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Import/Phase</span></b>
1409menu item on the main GSAS-II Data tree window. It may be useful to save your
1410project at this point; select <b style='mso-bidi-font-weight:normal'><span
1411style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1412mso-hansi-theme-font:minor-latin'>File/Save project as…</span></b> from the
1413main GSAS-II Data tree window menu. A file dialog box will appear; select the
1414directory and give a file name (no extension – I chose <b style='mso-bidi-font-weight:
1415normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1416minor-latin;mso-hansi-theme-font:minor-latin'>sapphire</span></b>).</p>
1417
1418<h2>Step 2. Import the diffraction data</h2>
1419
1420<p class=MsoNormal>The diffraction data collected on TOPAZ has been processed
1421(absorption corrections, wavelength and geometric corrections) to give a single
1422file with 31 embedded histograms as a space delimited multicolumn text file (<span
1423class=SpellE>sapphire_sphere.hkl</span>). To read this file select <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'>Import/Structure
1426Factor/from Neutron SNS TOF HKL F<sup>2 </sup>file</span></b>; a file dialog
1427box will appear. Change the directory to the location of this exercise (<b
1428style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1429mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>TOF Single
1430Crystal Refinement/data</span></b> – yours might be different), select <span
1431class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1432"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1433minor-latin'>sapphire_sphere.hkl</span></b></span> and press <b
1434style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1435mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Open</span></b>.
1436A popup will show a bit of the file and ask if you want to read this file;
1437press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1438mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Yes</span></b>.
1439Another popup will appear with a suggested name for the data; this will be used
1440for the GSAS-II Data tree. Press <b style='mso-bidi-font-weight:normal'><span
1441style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1442mso-hansi-theme-font:minor-latin'>OK</span></b>. The console will show messages
1443as each histogram is read; when done a new popup will appear</p>
1444
1445<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1446 id="Picture_x0020_32" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:233.25pt;
1447 height:228.75pt;visibility:visible;mso-wrap-style:square'>
1448 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image011.png"
1449  o:title=""/>
1450</v:shape><![endif]--><![if !vml]><img width=311 height=305
1451src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image058.gif"
1452v:shapes="Picture_x0020_32"><![endif]></span></p>
1453
1454<p class=MsoNormal>This makes the connection between the data you just read and
1455the phase (<b style='mso-bidi-font-weight:normal'><span style='font-family:
1456"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1457minor-latin'>sapphire</span></b>) you entered in Step 1. Select it (or <b
1458style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1459mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Set All</span></b>)
1460and press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1461mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1462The GSAS-II data tree window will show all the new histograms, expanding the
1463last one.</p>
1464
1465<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1466 id="Picture_x0020_33" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:468pt;
1467 height:153.75pt;visibility:visible;mso-wrap-style:square'>
1468 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image013.png"
1469  o:title=""/>
1470</v:shape><![endif]--><![if !vml]><img width=624 height=205
1471src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image059.gif"
1472v:shapes="Picture_x0020_33"><![endif]></span></p>
1473
1474<p class=MsoNormal>The plot window shows a not very interesting 2D view of the
1475l=0 layer of reciprocal space for the last data set. If you select the 1<sup>st</sup>
1476HKLF entry (<b style='mso-bidi-font-weight:normal'><span style='font-family:
1477"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1478minor-latin'>HKLF <span class=SpellE>sapphire_sphere.hkl</span></span></b>) the
1479plot is a bit more interesting.</p>
1480
1481<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1482 id="Picture_x0020_34" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:468pt;
1483 height:401.25pt;visibility:visible;mso-wrap-style:square'>
1484 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image015.png"
1485  o:title=""/>
1486</v:shape><![endif]--><![if !vml]><img width=624 height=535
1487src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image060.gif"
1488v:shapes="Picture_x0020_34"><![endif]></span></p>
1489
1490<p class=MsoNormal>Green circles are drawn representing the magnitude of 4
1491structure factors on the l=0 layer. The positions are strictly on a square
1492grid; you can “tab” through the layers on l with the <b style='mso-bidi-font-weight:
1493normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1494minor-latin;mso-hansi-theme-font:minor-latin'>+/-</span></b> keys. Find other
1495commands in the “K” box in the tools part of the plot. If you select <b
1496style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1497mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Commands/Plot
14983D HKLs</span></b> from the data window you’ll see a 3D view of this reflection
1499set; press <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1500style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1501mso-hansi-theme-font:minor-latin'>i</span></b></span> after selecting the plot
1502(I’ve zoomed in a bit)</p>
1503
1504<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1505
1506<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1507 id="Picture_x0020_35" o:spid="_x0000_i1042" type="#_x0000_t75" style='width:468pt;
1508 height:406.5pt;visibility:visible;mso-wrap-style:square'>
1509 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image017.png"
1510  o:title=""/>
1511</v:shape><![endif]--><![if !vml]><img width=624 height=542
1512src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image061.gif"
1513v:shapes="Picture_x0020_35"><![endif]></span></p>
1514
1515<p class=MsoNormal>Here the plot has the correct representation for reciprocal
1516space as sampled by this crystal orientation on TOPAZ; the two branches come from
1517the two detectors on this instrument. The <b style='mso-bidi-font-weight:normal'><span
1518style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1519mso-hansi-theme-font:minor-latin'>save as/key</span></b> commands give you
1520control on the appearance of the plot; the plot responds to zoom/rotate
1521commands from the mouse. Left mouse button to rotate, right mouse button to
1522translate, center wheel to rotate about view direction and the wheel to zoom in
1523or out. One cursor is the view point and the other is the 000 reciprocal space
1524origin. </p>
1525
1526<p class=MsoNormal>If you want to see the entire data set plotted together do <b
1527style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1528mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Commands/Plot
1529all 3D HKLs</span></b>; a data selection popup window will appear. Do <b
1530style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1531mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Set Al</span></b>l
1532and then <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1533mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>
1534to select all the data; the plot will be redrawn (I’ve pressed the ‘<span
1535class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1536"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1537minor-latin'>i</span></b></span>’ key as before)</p>
1538
1539<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1540 id="Picture_x0020_36" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:468pt;
1541 height:402.75pt;visibility:visible;mso-wrap-style:square'>
1542 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image019.png"
1543  o:title=""/>
1544</v:shape><![endif]--><![if !vml]><img width=624 height=537
1545src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image062.gif"
1546v:shapes="Picture_x0020_36"><![endif]></span></p>
1547
1548<p class=MsoNormal>I’ve rotated the drawing around to show an obvious gap in
1549the coverage.</p>
1550
1551<p class=MsoNormal>We’re now ready to do the refinement.</p>
1552
1553<h2>Step 3. Initial least squares refinement</h2>
1554
1555<p class=MsoNormal>By default the scale factors for all 31 data set are set to
1556be refined so you can immediately do a refinement. Select <b style='mso-bidi-font-weight:
1557normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1558minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> from
1559the main GSAS-II data tree window menu. You will need to save a copy of the
1560project first; select an appropriate directory and a name (I used ‘<b
1561style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1562mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1563minor-latin'>sapphire’</span></b>). This will do an F refinement by default. A
1564progress bar will appear to show you the residuals as the histograms are
1565processed. When it finishes and you have accepted the result a plot will show
1566the l=0 layer for the 1<sup>st</sup> data set.</p>
1567
1568<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1569 id="Picture_x0020_43" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:468pt;
1570 height:401.25pt;visibility:visible;mso-wrap-style:square'>
1571 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image021.png"
1572  o:title=""/>
1573</v:shape><![endif]--><![if !vml]><img width=624 height=535
1574src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image063.gif"
1575v:shapes="Picture_x0020_43"><![endif]></span></p>
1576
1577<p class=MsoNormal>Green rings are the observed magnitude, blue rings are the
1578calculated ones and the solid disk is the difference (green for positive &amp;
1579red for negative <span class=SpellE>F<sub>o</sub></span>-F<sub>c</sub>). You
1580can see the whole scope of the fit by doing <b style='mso-bidi-font-weight:
1581normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1582minor-latin;mso-hansi-theme-font:minor-latin'>Commands/Plot all 3D HKLs</span></b>
1583and selecting all the HKLF entries; press the “<b style='mso-bidi-font-weight:
1584normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1585minor-latin;mso-hansi-theme-font:minor-latin'>w</span></b>” key to show the
1586weighted &#916;F points.</p>
1587
1588<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1589 id="Picture_x0020_44" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:468pt;
1590 height:404.25pt;visibility:visible;mso-wrap-style:square'>
1591 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image023.png"
1592  o:title=""/>
1593</v:shape><![endif]--><![if !vml]><img width=624 height=539
1594src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image064.gif"
1595v:shapes="Picture_x0020_44"><![endif]></span></p>
1596
1597<p class=MsoNormal>The size of the squares is proportional to the magnitude of <span
1598class=SpellE>w&#916;F</span>. The cluster of negative <span class=SpellE>w&#916;F</span>
1599points around the reciprocal space origin is pretty clearly a consequence of
1600extinction so we’ll have to include that in the refinement model. One should
1601not be tempted to refine coordinates and thermal parameters until extinction is
1602accounted for in the refinement.</p>
1603
1604<h2>Step 3. Extinction model selection and refinement</h2>
1605
1606<p class=MsoNormal>GSAS-II has a number of extinction models available for
1607single crystal data. These include Primary, Secondary types I and II with
1608either Gaussian or Lorentzian distributions. To select one find the <b
1609style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1610mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sapphire</span></b>
1611entry in the GSAS-II data tree and select its <b style='mso-bidi-font-weight:
1612normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1613minor-latin;mso-hansi-theme-font:minor-latin'>Data</span></b> tab.</p>
1614
1615<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1616 id="Picture_x0020_39" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:468pt;
1617 height:265.5pt;visibility:visible;mso-wrap-style:square'>
1618 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image025.png"
1619  o:title=""/>
1620</v:shape><![endif]--><![if !vml]><img width=624 height=354
1621src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image065.gif"
1622v:shapes="Picture_x0020_39"><![endif]></span></p>
1623
1624<p class=MsoNormal>We can cut to the chase here – select <b style='mso-bidi-font-weight:
1625normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1626minor-latin;mso-hansi-theme-font:minor-latin'>Secondary Type I</span></b> from
1627the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1628mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Extinction
1629type</span></b> pull down list (the tab will be redrawn) and check the <span
1630class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1631"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1632minor-latin'>Eg</span></b></span> box; leave the <span class=SpellE><b
1633style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1634mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Approx</span></b></span>
1635selection as <b style='mso-bidi-font-weight:normal'><span style='font-family:
1636"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1637minor-latin'>Lorentzian</span></b>. Later on after you’ve finished the
1638tutorial, you can try the other models and see how they compare. Next do <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'>Edit
1641Phase/Copy selected data</span></b>, pick <b style='mso-bidi-font-weight:normal'><span
1642style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1643mso-hansi-theme-font:minor-latin'>Extinction</span></b> from the list of
1644parameters and press <b style='mso-bidi-font-weight:normal'><span
1645style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1646mso-hansi-theme-font:minor-latin'>OK</span></b>. Then do <b style='mso-bidi-font-weight:
1647normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1648minor-latin;mso-hansi-theme-font:minor-latin'>Set All</span></b> and press <b
1649style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1650mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>
1651from the next popup; this will copy the extinction model to all HKLF data sets.</p>
1652
1653<p class=MsoNormal>Because all of these extinction models are needed for one
1654crystal, it makes sense to tie them together into a single parameter. Select <b
1655style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1656mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Constraints</span></b>
1657from the main GSAS-II data tree and pick the <b style='mso-bidi-font-weight:
1658normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1659minor-latin;mso-hansi-theme-font:minor-latin'>Histogram/Phase constraints</span></b>
1660tab; it will be empty. Do <b style='mso-bidi-font-weight:normal'><span
1661style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1662mso-hansi-theme-font:minor-latin'>Edit Constr<span class=GramE>./</span>Add
1663equivalence</span></b>; the following popup will appear</p>
1664
1665<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1666 id="Picture_x0020_40" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:468pt;
1667 height:299.25pt;visibility:visible;mso-wrap-style:square'>
1668 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image027.png"
1669  o:title=""/>
1670</v:shape><![endif]--><![if !vml]><img width=624 height=399
1671src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image066.gif"
1672v:shapes="Picture_x0020_40"><![endif]></span></p>
1673
1674<p class=MsoNormal>Select the line beginning with ‘<b style='mso-bidi-font-weight:
1675normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1676minor-latin;mso-hansi-theme-font:minor-latin'>0:0<span class=GramE>:Eg<span
1677style='font-family:"Times New Roman",serif;font-weight:normal'>’</span></span></span></b>
1678(the Secondary type I parameter you just set to vary) and press <b
1679style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1680mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1681A new popup will appear; you’ll want to see the bottom of the list</p>
1682
1683<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1684 id="Picture_x0020_41" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:468pt;
1685 height:237.75pt;visibility:visible;mso-wrap-style:square'>
1686 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image029.png"
1687  o:title=""/>
1688</v:shape><![endif]--><![if !vml]><img width=624 height=317
1689src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image067.gif"
1690v:shapes="Picture_x0020_41"><![endif]></span></p>
1691
1692<p class=MsoNormal>Pick either <b style='mso-bidi-font-weight:normal'><span
1693style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1694mso-hansi-theme-font:minor-latin'>0<span class=GramE>:all:Eg</span></span></b>
1695or <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1696mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0:all=<span
1697class=SpellE>SNT:Eg</span></span></b> and press <b style='mso-bidi-font-weight:
1698normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1699minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>. The equivalence
1700making <span class=SpellE>Eg</span> for all histograms the same parameter will
1701be shown</p>
1702
1703<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1704 id="Picture_x0020_42" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:468pt;
1705 height:184.5pt;visibility:visible;mso-wrap-style:square'>
1706 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image031.png"
1707  o:title=""/>
1708</v:shape><![endif]--><![if !vml]><img width=624 height=246
1709src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image068.gif"
1710v:shapes="Picture_x0020_42"><![endif]></span></p>
1711
1712<p class=MsoNormal>Now do <b style='mso-bidi-font-weight:normal'><span
1713style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1714mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> from the main
1715GSAS-II data tree menu. You may have to repeat this twice to get convergence (<span
1716class=SpellE>Rw</span> ~6.8%); note the console output – value of Delta
1717indicates closeness to convergence. Select one of the HKLF data sets and view
1718the 3D Structure Factors plot for it alone</p>
1719
1720<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1721 id="Picture_x0020_45" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:468pt;
1722 height:403.5pt;visibility:visible;mso-wrap-style:square'>
1723 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image033.png"
1724  o:title=""/>
1725</v:shape><![endif]--><![if !vml]><img width=624 height=538
1726src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image069.gif"
1727v:shapes="Picture_x0020_45"><![endif]></span></p>
1728
1729<p class=MsoNormal>The <span class=SpellE>wDF</span> is positive close to 0<span
1730class=GramE>,0,0</span> then negative for an inner shell around the positive
1731core and finally positive for the outer shell. This is a thermal
1732parameter/extinction effect. So both have to be now refined. However, as a
1733matter of course we may expect that the extinction corrections are less
1734accurate when <span class=SpellE>Fo</span>&lt;&lt; Fc. In addition some
1735reflections were poorly measured. We want to reject reflections where <b
1736style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1737mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1738minor-latin'>Min extinct.</span></b> = <b style='mso-bidi-font-weight:normal'><span
1739style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1740mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>0.5</span></b>
1741and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1742mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1743minor-latin'>Min <span class=SpellE>obs</span>/sig</span></b> = <b
1744style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1745mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1746minor-latin'>3</span></b>. These can be applied on the <b style='mso-bidi-font-weight:
1747normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1748minor-latin;mso-hansi-theme-font:minor-latin'>Controls</span></b> page. After
1749setting these my Controls were</p>
1750
1751<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1752 id="Picture_x0020_46" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:468pt;
1753 height:215.25pt;visibility:visible;mso-wrap-style:square'>
1754 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image035.png"
1755  o:title=""/>
1756</v:shape><![endif]--><![if !vml]><img width=624 height=287
1757src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image070.gif"
1758v:shapes="Picture_x0020_46"><![endif]></span></p>
1759
1760<p class=MsoNormal>Finally we can add the atom parameters for sapphire. Select
1761the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1762mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Atoms</span></b>
1763tab for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1764mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phase/sapphire</span></b></p>
1765
1766<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1767 id="Picture_x0020_47" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:468pt;
1768 height:117.75pt;visibility:visible;mso-wrap-style:square'>
1769 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image037.png"
1770  o:title=""/>
1771</v:shape><![endif]--><![if !vml]><img width=624 height=157
1772src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image071.gif"
1773v:shapes="Picture_x0020_47"><![endif]></span></p>
1774
1775<p class=MsoNormal>Double (right) click the <b style='mso-bidi-font-weight:
1776normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1777minor-latin;mso-hansi-theme-font:minor-latin'>Refine</span></b> column heading;
1778a popup will appear</p>
1779
1780<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1781 id="Picture_x0020_48" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:171.75pt;
1782 height:150pt;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=229 height=200
1786src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image072.gif"
1787v:shapes="Picture_x0020_48"><![endif]></span></p>
1788
1789<p class=MsoNormal>Choose both <b style='mso-bidi-font-weight:normal'><span
1790style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1791mso-hansi-theme-font:minor-latin'>X</span></b> and <b style='mso-bidi-font-weight:
1792normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1793minor-latin;mso-hansi-theme-font:minor-latin'>U</span></b> and press <b
1794style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1795mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>;
1796the Atoms tab will be redrawn</p>
1797
1798<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1799 id="Picture_x0020_49" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:468pt;
1800 height:117.75pt;visibility:visible;mso-wrap-style:square'>
1801 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image041.png"
1802  o:title=""/>
1803</v:shape><![endif]--><![if !vml]><img width=624 height=157
1804src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image073.gif"
1805v:shapes="Picture_x0020_49"><![endif]></span></p>
1806
1807<p class=MsoNormal>Showing the refine flags for both atoms. GSAS-II will sort
1808out the special position rules for the two sites.</p>
1809
1810<p class=MsoNormal>Now do <b style='mso-bidi-font-weight:normal'><span
1811style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1812mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> (twice to get
1813convergence). My <span class=SpellE>Rw</span> = 4.705%, GOF = 1.91; find these
1814on the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1815mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Covariance</span></b>
1816data window. Now get a new 3D plot of all the reflections; select any HKLF
1817entry, then do <b style='mso-bidi-font-weight:normal'><span style='font-family:
1818"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1819minor-latin'>Commands/Plot all 3D HKLs</span></b>. Press <b style='mso-bidi-font-weight:
1820normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1821minor-latin;mso-hansi-theme-font:minor-latin'>w</span></b> key.</p>
1822
1823<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1824 id="Picture_x0020_50" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:468pt;
1825 height:405pt;visibility:visible;mso-wrap-style:square'>
1826 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image043.png"
1827  o:title=""/>
1828</v:shape><![endif]--><![if !vml]><img width=624 height=540
1829src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image074.gif"
1830v:shapes="Picture_x0020_50"><![endif]></span></p>
1831
1832<p class=MsoNormal>It’s pretty obvious that there is one really bad reflection
1833and (a bit more subtly) it is messing up one TOPAS data set. To find it first
1834look through the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1835style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1836mso-hansi-theme-font:minor-latin'>sapphire.lst</span></b></span> file; that
1837will give fitting information for all the histograms (near bottom of the
1838listing). Open it with your favorite text editor; I’ve shown an interesting bit
1839of it here showing results for histograms 22-24.</p>
1840
1841<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1842
1843<p class=MsoNormal>Phase:<span style='mso-spacerun:yes'>  </span><span
1844class=GramE>sapphire<span style='mso-spacerun:yes'>  </span>in</span>
1845histogram:<span style='mso-spacerun:yes'>  </span>HKLF sapphire_sphere.hkl_22</p>
1846
1847<p class=MsoNormal>=====================================================================</p>
1848
1849<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Final refinement RF,
1850RF^2 = 4.66%, 8.45% on 134 reflections (3 user rejected, 9 <span class=SpellE>sp.gp.extinct</span>)</p>
1851
1852<p class=MsoNormal><span style='mso-spacerun:yes'> </span>HKLF histogram weight
1853factor <span class=GramE>=<span style='mso-spacerun:yes'>  </span>1.000</span></p>
1854
1855<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Scale <span
1856class=GramE>factor :</span><span style='mso-spacerun:yes'>    </span>66.5252,
1857sig<span style='mso-spacerun:yes'>     </span>0.7222</p>
1858
1859<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1860
1861<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Single crystal
1862extinction: Type:<span style='mso-spacerun:yes'>  </span><span class=GramE>Lorentzian<span
1863style='mso-spacerun:yes'>  </span><span class=SpellE>Approx</span></span>:<span
1864style='mso-spacerun:yes'>  </span>Secondary Type I</p>
1865
1866<p class=MsoNormal><span style='mso-spacerun:yes'>       </span><span
1867class=SpellE>Eg</span>:<span style='mso-spacerun:yes'>     </span>5.71e-04 sig:<span
1868style='mso-spacerun:yes'>     </span>7.44e-06</p>
1869
1870<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1871
1872<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Phase:<span
1873style='mso-spacerun:yes'>  </span><span class=GramE>sapphire<span
1874style='mso-spacerun:yes'>  </span>in</span> histogram:<span
1875style='mso-spacerun:yes'>  </span>HKLF sapphire_sphere.hkl_23</p>
1876
1877<p class=MsoNormal>=====================================================================</p>
1878
1879<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Final refinement RF,
1880RF^2 = 6.10%, 11.18% on 147 reflections (6 user rejected, 6 <span class=SpellE>sp.gp.extinct</span>)</p>
1881
1882<p class=MsoNormal><span style='mso-spacerun:yes'> </span>HKLF histogram weight
1883factor <span class=GramE>=<span style='mso-spacerun:yes'>  </span>1.000</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>63.2155,
1887sig<span style='mso-spacerun:yes'>     </span>0.6834</p>
1888
1889<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1890
1891<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Single crystal
1892extinction: Type:<span style='mso-spacerun:yes'>  </span><span class=GramE>Lorentzian<span
1893style='mso-spacerun:yes'>  </span><span class=SpellE>Approx</span></span>:<span
1894style='mso-spacerun:yes'>  </span>Secondary Type I</p>
1895
1896<p class=MsoNormal><span style='mso-spacerun:yes'>       </span><span
1897class=SpellE>Eg</span>:<span style='mso-spacerun:yes'>     </span>5.71e-04
1898sig:<span style='mso-spacerun:yes'>     </span>7.44e-06</p>
1899
1900<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1901
1902<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Phase:<span
1903style='mso-spacerun:yes'>  </span><span class=GramE>sapphire<span
1904style='mso-spacerun:yes'>  </span>in</span> histogram:<span
1905style='mso-spacerun:yes'>  </span>HKLF sapphire_sphere.hkl_24</p>
1906
1907<p class=MsoNormal>=====================================================================</p>
1908
1909<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Final refinement RF,
1910RF^2 = 3.77%, 6.60% on 160 reflections (11 user rejected, 1 <span class=SpellE>sp.gp.extinct</span>)</p>
1911
1912<p class=MsoNormal><span style='mso-spacerun:yes'> </span>HKLF histogram weight
1913factor <span class=GramE>=<span style='mso-spacerun:yes'>  </span>1.000</span></p>
1914
1915<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Scale <span
1916class=GramE>factor :</span><span style='mso-spacerun:yes'>    </span>66.4019,
1917sig<span style='mso-spacerun:yes'>     </span>0.6817</p>
1918
1919<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1920
1921<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Single crystal
1922extinction: Type:<span style='mso-spacerun:yes'>  </span><span class=GramE>Lorentzian<span
1923style='mso-spacerun:yes'>  </span><span class=SpellE>Approx</span></span>:<span
1924style='mso-spacerun:yes'>  </span>Secondary Type I</p>
1925
1926<p class=MsoNormal><span style='mso-spacerun:yes'>       </span><span
1927class=SpellE>Eg</span>:<span style='mso-spacerun:yes'>     </span>5.71e-04
1928sig:<span style='mso-spacerun:yes'>     </span>7.44e-06</p>
1929
1930<p class=MsoNormal><span
1931style='mso-spacerun:yes'>                                                                                                     
1932</span></p>
1933
1934<p class=MsoNormal>There is obviously something wrong with #23 (high residual
1935&amp; funny scale factor compared to the others). Find <b style='mso-bidi-font-weight:
1936normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1937minor-latin;mso-hansi-theme-font:minor-latin'>HKLF sapphire_sphere.hkl_23</span></b>
1938in the GSAS-II data tree &amp; select it. The 3D plot of just that data set
1939will show the problem reflection.</p>
1940
1941<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1942 id="Picture_x0020_51" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:468pt;
1943 height:405pt;visibility:visible;mso-wrap-style:square'>
1944 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image045.png"
1945  o:title=""/>
1946</v:shape><![endif]--><![if !vml]><img width=624 height=540
1947src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image075.gif"
1948v:shapes="Picture_x0020_51"><![endif]></span></p>
1949
1950<p class=MsoNormal>By zooming in and rotating the plot around a bit, you can
1951identify the reflection with the cursor. It seems to be the <b
1952style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1953mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>342</span></b>
1954reflection; select the <b style='mso-bidi-font-weight:normal'><span
1955style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1956mso-hansi-theme-font:minor-latin'>Reflection List</span></b> and look for it
1957(unfortunately the reflections are produced in a somewhat random order by the
1958TOPAZ data acquisition system). It is very near the bottom of the list (#<b
1959style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1960mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>147</span></b>).</p>
1961
1962<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1963 id="Picture_x0020_26" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:585pt;
1964 height:244.5pt;visibility:visible;mso-wrap-style:square'>
1965 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image047.png"
1966  o:title=""/>
1967</v:shape><![endif]--><![if !vml]><img width=780 height=326
1968src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image076.gif"
1969v:shapes="Picture_x0020_26"><![endif]></span></p>
1970
1971<p class=MsoNormal>The <span class=SpellE>Fcsq</span> (F<sub>c</sub><sup>2</sup>)
1972is very much larger than <span class=SpellE>Fosq</span> (F<sub>o</sub><sup>2</sup>)
1973so that |&#916;F<sup>2</sup>|/&#963;(F<sub>o</sub><sup>2</sup>) &gt; 80! It was
1974obviously poorly measured (e.g. on the edge of the detector, etc.). We’d like
1975to eliminate it, but perhaps we might be better setting a lower cutoff on
1976|&#916;F<sup>2</sup>|/&#963;(F<sub>o</sub><sup>2</sup>) to eliminate other
1977similar problem reflections. Go to the <b style='mso-bidi-font-weight:normal'><span
1978style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1979mso-hansi-theme-font:minor-latin'>Controls</span></b> entry in the GSAS-II data
1980tree</p>
1981
1982<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1983 id="Picture_x0020_52" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:468pt;
1984 height:200.25pt;visibility:visible;mso-wrap-style:square'>
1985 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image049.png"
1986  o:title=""/>
1987</v:shape><![endif]--><![if !vml]><img width=624 height=267
1988src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image077.gif"
1989v:shapes="Picture_x0020_52"><![endif]></span></p>
1990
1991<p class=MsoNormal>Change the value of <b style='mso-bidi-font-weight:normal'><span
1992style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1993mso-hansi-theme-font:minor-latin'>Max <span class=SpellE>delt</span>-F/sig</span></b>
1994to 20; that will certainly eliminate the bad 342 reflection &amp; perhaps a few
1995others. Repeat <b style='mso-bidi-font-weight:normal'><span style='font-family:
1996"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1997minor-latin'>Calculate/Refine</span></b>; my residual dropped considerably (<span
1998class=SpellE>Rw</span> ~4.5%) and the 3D plot shows no really bad reflections</p>
1999
2000<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2001 id="Picture_x0020_53" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:468pt;
2002 height:404.25pt;visibility:visible;mso-wrap-style:square'>
2003 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image051.png"
2004  o:title=""/>
2005</v:shape><![endif]--><![if !vml]><img width=624 height=539
2006src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image078.gif"
2007v:shapes="Picture_x0020_53"><![endif]></span></p>
2008
2009<p class=MsoNormal>Looking the <span class=SpellE><b style='mso-bidi-font-weight:
2010normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2011minor-latin;mso-hansi-theme-font:minor-latin'>sapphire.lst</span></b></span><b
2012style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2013mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> </span></b>file
2014shows that HKLF #23 is now more in line with the other ones (RF = 4.35% &amp;
2015scale = 67.41). To finish the refinement make the two sapphire atoms have
2016anisotropic thermal parameters. Select <b style='mso-bidi-font-weight:normal'><span
2017style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2018mso-hansi-theme-font:minor-latin'>Phases/sapphire</span></b> and the <b
2019style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2020mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Atoms</span></b>
2021tab; then double click the <b style='mso-bidi-font-weight:normal'><span
2022style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2023mso-hansi-theme-font:minor-latin'>I/A</span></b> column heading. A popup will
2024appear; select <b style='mso-bidi-font-weight:normal'><span style='font-family:
2025"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2026minor-latin'>Anisotropic</span></b> and press <b style='mso-bidi-font-weight:
2027normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2028minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>. The atom <span
2029class=SpellE>Uijs</span> will appear and <span class=SpellE>Uiso</span> will be
2030greyed out. Then do <b style='mso-bidi-font-weight:normal'><span
2031style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2032mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> again. My final
2033residual was <span class=SpellE>Rw</span>=4.20%. </p>
2034
2035<p class=MsoNormal>This completes the tutorial. You can explore the other
2036extinction models and try different cutoff values for <b style='mso-bidi-font-weight:
2037normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2038minor-latin;mso-hansi-theme-font:minor-latin'>Max <span class=SpellE>delt</span>-F/sig</span></b>.
2039<b style='mso-bidi-font-weight:normal'><u>NB: this should never be set before
2040the refinement is complete as it can reject large portions of the data
2041prematurely.<o:p></o:p></u></b></p>
2042
2043</div>
2044
2045</body>
2046
2047</html>
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