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Timestamp:
Sep 13, 2017 11:57:54 AM (8 years ago)
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vondreele
Message:

update to 2 frame

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  • TabularUnified Tutorials/TOF Single Crystal Refinement/TOF single crystal refinement in GSAS.htm

    r2390 r3073  
    2424 <o:DocumentProperties>
    2525  <o:Author>vondreele</o:Author>
    26   <o:LastAuthor>Von Dreele</o:LastAuthor>
    27   <o:Revision>12</o:Revision>
    28   <o:TotalTime>1031</o:TotalTime>
     26  <o:LastAuthor>vondreele</o:LastAuthor>
     27  <o:Revision>14</o:Revision>
     28  <o:TotalTime>1085</o:TotalTime>
    2929  <o:Created>2015-02-17T16:18:00Z</o:Created>
    30   <o:LastSaved>2016-07-28T18:57:00Z</o:LastSaved>
     30  <o:LastSaved>2017-09-13T16:56:00Z</o:LastSaved>
    3131  <o:Pages>1</o:Pages>
    32   <o:Words>2061</o:Words>
    33   <o:Characters>11753</o:Characters>
     32  <o:Words>1889</o:Words>
     33  <o:Characters>10773</o:Characters>
    3434  <o:Company>Argonne National Laboratory</o:Company>
    35   <o:Lines>97</o:Lines>
    36   <o:Paragraphs>27</o:Paragraphs>
    37   <o:CharactersWithSpaces>13787</o:CharactersWithSpaces>
     35  <o:Lines>89</o:Lines>
     36  <o:Paragraphs>25</o:Paragraphs>
     37  <o:CharactersWithSpaces>12637</o:CharactersWithSpaces>
    3838  <o:Version>16.00</o:Version>
    3939 </o:DocumentProperties>
     
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    12291230
    12301231<p class=MsoNormal>In these exercises you will use GSAS-II to refine the
    1231 structure of sapphire (really corundum, Al<sub>2</sub>O<sub>3</sub>) from single
    1232 crystal diffraction data collected at the SNS on the TOPAZ instrument at room
    1233 temperature. The data consists of a suite of exposures with the crystal in 31
    1234 different orientations all within a single data file. Note that menu entries
     1232structure of sapphire (really corundum, Al<sub>2</sub>O<sub>3</sub>) from
     1233single crystal diffraction data collected at the SNS on the TOPAZ instrument at
     1234room temperature. The data consists of a suite of exposures with the crystal in
     123531 different orientations all within a single data file. Note that menu entries
    12351236and user input are shown in bold face below as <b style='mso-bidi-font-weight:
    12361237normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1237 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
    1238 mso-bidi-theme-font:minor-latin'>Help/About GSAS-II</span></b>, which lists
    1239 first the name of the menu (here <b style='mso-bidi-font-weight:normal'><span
    1240 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1241 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1238minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Help/About
     1239GSAS-II</span></b>, which lists first the name of the menu (here <b
     1240style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1241mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    12421242minor-latin'>Help</span></b>) and second the name of the entry in the menu
    12431243(here <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1244 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    1245 Calibri;mso-bidi-theme-font:minor-latin'>About GSAS-II</span></b>). If you have
    1246 not done so already, start GSAS-II.</p>
     1244mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1245minor-latin'>About GSAS-II</span></b>). If you have not done so already, start
     1246GSAS-II.</p>
    12471247
    12481248<h2>Step 1. Setup the phase information for sapphire</h2>
     
    12521252style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Use
    12531253the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1254 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    1255 Calibri;mso-bidi-theme-font:minor-latin'>Data/Add phase</span></b> menu item
    1256 add a new phase into the current GSAS-II project. A popup window will appear
    1257 asking for a phase name; I entered <b style='mso-bidi-font-weight:normal'><span
    1258 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1259 mso-hansi-theme-font:minor-latin'>sapphire</span></b>; press <b
    1260 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1254mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1255minor-latin'>Data/Add new phase</span></b> menu item add a new phase into the
     1256current GSAS-II project. A popup window will appear asking for a phase name; I
     1257entered <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1258mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>sapphire</span></b>;
     1259press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    12611260mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>
    12621261when done. Select <b style='mso-bidi-font-weight:normal'><span
     
    12851284 <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
    12861285 <o:lock v:ext="edit" aspectratio="t"/>
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     1286</v:shapetype><v:shape id="Picture_x0020_27" o:spid="_x0000_i1050" type="#_x0000_t75"
     1287 style='width:468pt;height:209.25pt;visibility:visible;mso-wrap-style:square'>
    12891288 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image001.png"
    12901289  o:title=""/>
    1291 </v:shape><![endif]--><![if !vml]><img width=854 height=500
    1292 src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image051.gif"
    1293 v:shapes="Picture_x0020_1"><![endif]></span></p>
     1290</v:shape><![endif]--><![if !vml]><img width=624 height=279
     1291src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image002.gif"
     1292v:shapes="Picture_x0020_27"><![endif]></span></p>
    12941293
    12951294<p class=MsoListParagraph><o:p>&nbsp;</o:p></p>
     
    13101309
    13111310<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'>
     1311 id="Picture_x0020_28" o:spid="_x0000_i1049" type="#_x0000_t75" style='width:468pt;
     1312 height:265.5pt;visibility:visible;mso-wrap-style:square'>
    13141313 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image003.png"
    13151314  o:title=""/>
    1316 </v:shape><![endif]--><![if !vml]><img width=650 height=500
    1317 src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image052.gif"
    1318 v:shapes="Picture_x0020_29"><![endif]></span></p>
     1315</v:shape><![endif]--><![if !vml]><img width=624 height=354
     1316src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image004.gif"
     1317v:shapes="Picture_x0020_28"><![endif]></span></p>
    13191318
    13201319<p class=MsoListParagraph><o:p>&nbsp;</o:p></p>
     
    13251324<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    13261325mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>4.7613</span></b>
    1327 for <span class=GramE>a</span> and <b style='mso-bidi-font-weight:normal'><span
     1326for <span class=GramE>a and</span> <b style='mso-bidi-font-weight:normal'><span
    13281327style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    13291328mso-hansi-theme-font:minor-latin'>12.9846</span></b> for c; a new cell volume
     
    13371336tab; it will be empty. Do <b style='mso-bidi-font-weight:normal'><span
    13381337style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1339 mso-hansi-theme-font:minor-latin'>Edit/Append atom</span></b> from the <b
     1338mso-hansi-theme-font:minor-latin'>Edit Atoms/Append atom</span></b> from the <b
    13401339style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    13411340mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phase Data
     
    13431342
    13441343<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'>
     1344 id="Picture_x0020_29" o:spid="_x0000_i1048" type="#_x0000_t75" style='width:468pt;
     1345 height:153.75pt;visibility:visible;mso-wrap-style:square'>
    13471346 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image005.png"
    13481347  o:title=""/>
    1349 </v:shape><![endif]--><![if !vml]><img width=700 height=300
    1350 src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image053.gif"
    1351 v:shapes="Picture_x0020_31"><![endif]></span></p>
     1348</v:shape><![endif]--><![if !vml]><img width=624 height=205
     1349src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image006.gif"
     1350v:shapes="Picture_x0020_29"><![endif]></span></p>
    13521351
    13531352<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
     
    13621361
    13631362<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'>
     1363 id="Picture_x0020_30" o:spid="_x0000_i1047" type="#_x0000_t75" style='width:468pt;
     1364 height:153.75pt;visibility:visible;mso-wrap-style:square'>
    13661365 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image007.png"
    13671366  o:title=""/>
    1368 </v:shape><![endif]--><![if !vml]><img width=700 height=300
    1369 src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image054.gif"
    1370 v:shapes="Picture_x0020_32"><![endif]></span></p>
     1367</v:shape><![endif]--><![if !vml]><img width=624 height=205
     1368src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image008.gif"
     1369v:shapes="Picture_x0020_30"><![endif]></span></p>
    13711370
    13721371<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
    13731372style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>6.<span
    13741373style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Change
    1375 the Al(z) to <b style='mso-bidi-font-weight:normal'><span style='font-family:
     1374the <span class=GramE>Al(</span>z) to <b style='mso-bidi-font-weight:normal'><span
     1375style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1376mso-hansi-theme-font:minor-latin'>0. 352</span></b>, the O(x) to <b
     1377style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1378mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>-0.306</span></b>
     1379and the O(z) to <b style='mso-bidi-font-weight:normal'><span style='font-family:
    13761380"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1377 minor-latin'>0. 352</span></b>, the O(x) to <b style='mso-bidi-font-weight:
    1378 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1379 minor-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;
    1381 mso-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
    1383 automatically change for these positions.</p>
     1381minor-latin'>Œ</span></b> (it will be changed to 0.2500). Also set both <span
     1382class=SpellE>Uiso</span> to <b style='mso-bidi-font-weight:normal'><span
     1383style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1384mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>0.005</span></b>.
     1385Site symmetries and multiplicities will automatically change for these
     1386positions.</p>
    13841387
    13851388<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'>
     1389 id="Picture_x0020_31" o:spid="_x0000_i1046" type="#_x0000_t75" style='width:468pt;
     1390 height:153.75pt;visibility:visible;mso-wrap-style:square'>
    13881391 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image009.png"
    13891392  o:title=""/>
    1390 </v:shape><![endif]--><![if !vml]><img width=700 height=300
    1391 src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image055.gif"
    1392 v:shapes="Picture_x0020_34"><![endif]></span></p>
     1393</v:shape><![endif]--><![if !vml]><img width=624 height=205
     1394src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image010.gif"
     1395v:shapes="Picture_x0020_31"><![endif]></span></p>
    13931396
    13941397<p class=MsoListParagraph><o:p>&nbsp;</o:p></p>
     
    14381441
    14391442<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1440  id="Picture_x0020_35" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:240pt;
    1441  height:232.5pt;visibility:visible;mso-wrap-style:square'>
     1443 id="Picture_x0020_32" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:233.25pt;
     1444 height:228.75pt;visibility:visible;mso-wrap-style:square'>
    14421445 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image011.png"
    14431446  o:title=""/>
    1444 </v:shape><![endif]--><![if !vml]><img width=320 height=310
    1445 src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image056.gif"
    1446 v:shapes="Picture_x0020_35"><![endif]></span></p>
     1447</v:shape><![endif]--><![if !vml]><img width=311 height=305
     1448src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image012.gif"
     1449v:shapes="Picture_x0020_32"><![endif]></span></p>
    14471450
    14481451<p class=MsoNormal>This makes the connection between the data you just read and
     
    14581461
    14591462<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1460  id="Picture_x0020_36" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:300pt;
    1461  height:187.5pt;visibility:visible;mso-wrap-style:square'>
     1463 id="Picture_x0020_33" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:468pt;
     1464 height:153.75pt;visibility:visible;mso-wrap-style:square'>
    14621465 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image013.png"
    14631466  o:title=""/>
    1464 </v:shape><![endif]--><![if !vml]><img width=400 height=250
    1465 src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image057.gif"
    1466 v:shapes="Picture_x0020_36"><![endif]></span></p>
    1467 
    1468 <p class=MsoNormal>The plot window shows a not very interesting 2D view of the l=0
    1469 layer of reciprocal space for the last data set. If you select the 1<sup>st</sup>
     1467</v:shape><![endif]--><![if !vml]><img width=624 height=205
     1468src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image014.gif"
     1469v:shapes="Picture_x0020_33"><![endif]></span></p>
     1470
     1471<p class=MsoNormal>The plot window shows a not very interesting 2D view of the
     1472l=0 layer of reciprocal space for the last data set. If you select the 1<sup>st</sup>
    14701473HKLF entry (<b style='mso-bidi-font-weight:normal'><span style='font-family:
    14711474"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     
    14741477
    14751478<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1476  id="Picture_x0020_10" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:525pt;
    1477  height:450pt;visibility:visible;mso-wrap-style:square'>
     1479 id="Picture_x0020_34" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:468pt;
     1480 height:401.25pt;visibility:visible;mso-wrap-style:square'>
    14781481 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image015.png"
    14791482  o:title=""/>
    1480 </v:shape><![endif]--><![if !vml]><img width=700 height=600
    1481 src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image058.gif"
    1482 v:shapes="Picture_x0020_10"><![endif]></span></p>
     1483</v:shape><![endif]--><![if !vml]><img width=624 height=535
     1484src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image016.gif"
     1485v:shapes="Picture_x0020_34"><![endif]></span></p>
    14831486
    14841487<p class=MsoNormal>Green circles are drawn representing the magnitude of 4
     
    14991502
    15001503<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1501  id="_x0000_i1042" type="#_x0000_t75" style='width:363pt;height:311.25pt;
    1502  visibility:visible;mso-wrap-style:square'>
     1504 id="Picture_x0020_35" o:spid="_x0000_i1042" type="#_x0000_t75" style='width:468pt;
     1505 height:406.5pt;visibility:visible;mso-wrap-style:square'>
    15031506 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image017.png"
    1504   o:title="" croptop="11818f" cropbottom="16324f" cropleft="40001f"
    1505   cropright="10518f"/>
    1506 </v:shape><![endif]--><![if !vml]><img width=484 height=415
    1507 src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image059.jpg"
    1508 v:shapes="_x0000_i1042"><![endif]></span></p>
     1507  o:title=""/>
     1508</v:shape><![endif]--><![if !vml]><img width=624 height=542
     1509src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image018.gif"
     1510v:shapes="Picture_x0020_35"><![endif]></span></p>
    15091511
    15101512<p class=MsoNormal>Here the plot has the correct representation for reciprocal
    1511 space as sampled by this crystal orientation on TOPAZ. The <b style='mso-bidi-font-weight:
    1512 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1513 minor-latin;mso-hansi-theme-font:minor-latin'>save as/key</span></b> commands give
    1514 you control on the appearance of the plot; the plot responds to zoom/rotate
    1515 commands from the mouse. Left mouse button to rotate, right mouse button to
    1516 translate, center wheel to rotate about view direction and the wheel to zoom in
    1517 or out. One cursor is the view point and the other is the 000 reciprocal space
    1518 origin. </p>
     1513space as sampled by this crystal orientation on TOPAZ; the two branches come
     1514from the two detectors on this instrument. The <b style='mso-bidi-font-weight:
     1515normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1516minor-latin;mso-hansi-theme-font:minor-latin'>save as/key</span></b> commands
     1517give you control on the appearance of the plot; the plot responds to
     1518zoom/rotate commands from the mouse. Left mouse button to rotate, right mouse
     1519button to translate, center wheel to rotate about view direction and the wheel
     1520to zoom in or out. One cursor is the view point and the other is the 000
     1521reciprocal space origin. </p>
    15191522
    15201523<p class=MsoNormal>If you want to see the entire data set plotted together do <b
     
    15321535
    15331536<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1534  id="_x0000_i1041" type="#_x0000_t75" style='width:365.25pt;height:310.5pt;
    1535  visibility:visible;mso-wrap-style:square'>
     1537 id="Picture_x0020_36" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:468pt;
     1538 height:402.75pt;visibility:visible;mso-wrap-style:square'>
    15361539 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image019.png"
    1537   o:title="" croptop="12098f" cropbottom="16193f" cropleft="40187f"
    1538   cropright="10237f"/>
    1539 </v:shape><![endif]--><![if !vml]><img width=487 height=414
    1540 src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image060.jpg"
    1541 v:shapes="_x0000_i1041"><![endif]></span></p>
     1540  o:title=""/>
     1541</v:shape><![endif]--><![if !vml]><img width=624 height=537
     1542src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image020.gif"
     1543v:shapes="Picture_x0020_36"><![endif]></span></p>
    15421544
    15431545<p class=MsoNormal>I’ve rotated the drawing around to show an obvious gap in
     
    15521554normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    15531555minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> from
    1554 the main GSAS-II data tree window menu. This will do an F refinement by
    1555 default. A progress bar will appear to show you the residuals as the histograms
    1556 are processed. When it finishes and you have accepted the result a plot will
    1557 show the l=0 layer for the 1<sup>st</sup> data set.</p>
     1556the main GSAS-II data tree window menu. You will need to save a copy of the
     1557project first; select an appropriate directory and a name (I used ‘sapphire’). This
     1558will do an F refinement by default. A progress bar will appear to show you the
     1559residuals as the histograms are processed. When it finishes and you have
     1560accepted the result a plot will show the l=0 layer for the 1<sup>st</sup> data
     1561set.</p>
    15581562
    15591563<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1560  id="Picture_x0020_11" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:525pt;
    1561  height:450pt;visibility:visible;mso-wrap-style:square'>
     1564 id="Picture_x0020_43" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:468pt;
     1565 height:401.25pt;visibility:visible;mso-wrap-style:square'>
    15621566 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image021.png"
    15631567  o:title=""/>
    1564 </v:shape><![endif]--><![if !vml]><img width=700 height=600
    1565 src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image061.gif"
    1566 v:shapes="Picture_x0020_11"><![endif]></span></p>
     1568</v:shape><![endif]--><![if !vml]><img width=624 height=535
     1569src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image022.gif"
     1570v:shapes="Picture_x0020_43"><![endif]></span></p>
    15671571
    15681572<p class=MsoNormal>Green rings are the observed magnitude, blue rings are the
     
    15781582
    15791583<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1580  id="Picture_x0020_12" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:369pt;
    1581  height:310.5pt;visibility:visible;mso-wrap-style:square'>
     1584 id="Picture_x0020_44" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:468pt;
     1585 height:404.25pt;visibility:visible;mso-wrap-style:square'>
    15821586 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image023.png"
    1583   o:title="" croptop="9828f" cropbottom="18427f" cropleft="38257f" cropright="12033f"/>
    1584 </v:shape><![endif]--><![if !vml]><img width=492 height=414
    1585 src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image062.jpg"
    1586 v:shapes="Picture_x0020_12"><![endif]></span></p>
     1587  o:title=""/>
     1588</v:shape><![endif]--><![if !vml]><img width=624 height=539
     1589src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image024.gif"
     1590v:shapes="Picture_x0020_44"><![endif]></span></p>
    15871591
    15881592<p class=MsoNormal>The size of the squares is proportional to the magnitude of <span
     
    16051609
    16061610<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1607  id="Picture_x0020_16" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:300pt;
    1608  height:303pt;visibility:visible;mso-wrap-style:square'>
     1611 id="Picture_x0020_39" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:468pt;
     1612 height:265.5pt;visibility:visible;mso-wrap-style:square'>
    16091613 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image025.png"
    16101614  o:title=""/>
    1611 </v:shape><![endif]--><![if !vml]><img width=400 height=404
    1612 src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image063.gif"
    1613 v:shapes="Picture_x0020_16"><![endif]></span></p>
     1615</v:shape><![endif]--><![if !vml]><img width=624 height=354
     1616src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image026.gif"
     1617v:shapes="Picture_x0020_39"><![endif]></span></p>
    16141618
    16151619<p class=MsoNormal>We can cut to the chase here – select <b style='mso-bidi-font-weight:
     
    16291633tutorial, you can try the other models and see how they compare. Next do <b
    16301634style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1631 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Copy
     1635mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit Phase/Copy
    16321636selected data</span></b>, pick <b style='mso-bidi-font-weight:normal'><span
    16331637style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     
    16511655tab; it will be empty. Do <b style='mso-bidi-font-weight:normal'><span
    16521656style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1653 mso-hansi-theme-font:minor-latin'>Edit/Add equivalence</span></b>; the
    1654 following popup will appear</p>
     1657mso-hansi-theme-font:minor-latin'>Edit Constr<span class=GramE>./</span>Add
     1658equivalence</span></b>; the following popup will appear</p>
    16551659
    16561660<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1657  id="_x0000_i1037" type="#_x0000_t75" style='width:468.75pt;height:300pt;
    1658  visibility:visible;mso-wrap-style:square'>
     1661 id="Picture_x0020_40" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:468pt;
     1662 height:299.25pt;visibility:visible;mso-wrap-style:square'>
    16591663 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image027.png"
    16601664  o:title=""/>
    1661 </v:shape><![endif]--><![if !vml]><img width=625 height=400
    1662 src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image064.gif"
    1663 v:shapes="_x0000_i1037"><![endif]></span></p>
    1664 
    1665 <p class=MsoNormal>Select the line beginning with ‘<span class=GramE><b
    1666 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1667 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0:0:Eg</span></b></span>’
     1665</v:shape><![endif]--><![if !vml]><img width=624 height=399
     1666src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image028.gif"
     1667v:shapes="Picture_x0020_40"><![endif]></span></p>
     1668
     1669<p class=MsoNormal>Select the line beginning with ‘<b style='mso-bidi-font-weight:
     1670normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1671minor-latin;mso-hansi-theme-font:minor-latin'>0:0<span class=GramE>:Eg<span
     1672style='font-family:"Times New Roman",serif;font-weight:normal'>’</span></span></span></b>
    16681673(the Secondary type I parameter you just set to vary) and press <b
    16691674style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     
    16721677
    16731678<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1674  id="_x0000_i1036" type="#_x0000_t75" style='width:468.75pt;height:300pt;
    1675  visibility:visible;mso-wrap-style:square'>
     1679 id="Picture_x0020_41" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:468pt;
     1680 height:237.75pt;visibility:visible;mso-wrap-style:square'>
    16761681 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image029.png"
    16771682  o:title=""/>
    1678 </v:shape><![endif]--><![if !vml]><img width=625 height=400
    1679 src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image065.gif"
    1680 v:shapes="_x0000_i1036"><![endif]></span></p>
    1681 
    1682 <p class=MsoNormal>Pick either <span class=GramE><b style='mso-bidi-font-weight:
    1683 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1684 minor-latin;mso-hansi-theme-font:minor-latin'>0:all</span></b></span><b
    1685 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1686 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>:Eg</span></b>
     1683</v:shape><![endif]--><![if !vml]><img width=624 height=317
     1684src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image030.gif"
     1685v:shapes="Picture_x0020_41"><![endif]></span></p>
     1686
     1687<p class=MsoNormal>Pick either <b style='mso-bidi-font-weight:normal'><span
     1688style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1689mso-hansi-theme-font:minor-latin'>0<span class=GramE>:all:Eg</span></span></b>
    16871690or <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    16881691mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0:all=<span
     
    16941697
    16951698<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1696  id="Picture_x0020_20" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:481.5pt;
     1699 id="Picture_x0020_42" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:468pt;
    16971700 height:184.5pt;visibility:visible;mso-wrap-style:square'>
    16981701 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image031.png"
    16991702  o:title=""/>
    1700 </v:shape><![endif]--><![if !vml]><img width=642 height=246
    1701 src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image066.gif"
    1702 v:shapes="Picture_x0020_20"><![endif]></span></p>
     1703</v:shape><![endif]--><![if !vml]><img width=624 height=246
     1704src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image032.gif"
     1705v:shapes="Picture_x0020_42"><![endif]></span></p>
    17031706
    17041707<p class=MsoNormal>Now do <b style='mso-bidi-font-weight:normal'><span
    17051708style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1706 mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> from the main GSAS-II
    1707 data tree menu. You may have to repeat this twice to get convergence (<span
    1708 class=SpellE>Rw</span> ~14%); note the console output – value of Delta
    1709 indicates closeness to convergence. Select one of the HKLF data sets and view
    1710 the 3D Structure Factors plot for it alone</p>
     1709mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> from the main
     1710GSAS-II data tree menu. You may have to repeat this twice to get convergence (<span
     1711class=SpellE>Rw</span> ~6.8%); note the console output – value of Delta indicates
     1712closeness to convergence. Select one of the HKLF data sets and view the 3D
     1713Structure Factors plot for it alone</p>
    17111714
    17121715<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1713  id="Picture_x0020_17" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:362.25pt;
    1714  height:311.25pt;visibility:visible;mso-wrap-style:square'>
     1716 id="Picture_x0020_45" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:468pt;
     1717 height:403.5pt;visibility:visible;mso-wrap-style:square'>
    17151718 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image033.png"
    1716   o:title="" croptop="15476f" cropbottom="12688f" cropleft="40744f"
    1717   cropright="9798f"/>
    1718 </v:shape><![endif]--><![if !vml]><img width=483 height=415
    1719 src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image067.jpg"
    1720 v:shapes="Picture_x0020_17"><![endif]></span></p>
    1721 
    1722 <p class=MsoNormal>The <span class=SpellE>wDF</span> is positive close to 0,0,0
    1723 then negative for an inner shell around the positive core and finally positive
    1724 for the outer shell. This is a thermal parameter/extinction effect. So both
    1725 have to be now refined. However, as a matter of course we may expect that the
    1726 extinction corrections are less accurate when <span class=SpellE>Fo</span>&lt;&lt;
    1727 Fc. In addition some reflections were poorly measured. We want to reject
    1728 reflections where <span class=SpellE>Fo</span>/Fc &lt; 0.5 and Fo2/s(Fo2) &lt;
    1729 3. These can be applied on the <b style='mso-bidi-font-weight:normal'><span
    1730 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1731 mso-hansi-theme-font:minor-latin'>Controls</span></b> page. After setting these
    1732 my Controls were</p>
     1719  o:title=""/>
     1720</v:shape><![endif]--><![if !vml]><img width=624 height=538
     1721src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image034.gif"
     1722v:shapes="Picture_x0020_45"><![endif]></span></p>
     1723
     1724<p class=MsoNormal>The <span class=SpellE>wDF</span> is positive close to 0<span
     1725class=GramE>,0,0</span> then negative for an inner shell around the positive
     1726core and finally positive for the outer shell. This is a thermal
     1727parameter/extinction effect. So both have to be now refined. However, as a
     1728matter of course we may expect that the extinction corrections are less
     1729accurate when <span class=SpellE>Fo</span>&lt;&lt; Fc. In addition some
     1730reflections were poorly measured. We want to reject reflections where <b
     1731style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1732mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1733minor-latin'>Min extinct.</span></b> = <b style='mso-bidi-font-weight:normal'><span
     1734style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1735mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>0.5</span></b>
     1736and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1737mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1738minor-latin'>Min <span class=SpellE>obs</span>/sig</span></b> = <b
     1739style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1740mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1741minor-latin'>3</span></b>. These can be applied on the <b style='mso-bidi-font-weight:
     1742normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1743minor-latin;mso-hansi-theme-font:minor-latin'>Controls</span></b> page. After
     1744setting these my Controls were</p>
    17331745
    17341746<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1735  id="Picture_x0020_18" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:366pt;
    1736  height:212.25pt;visibility:visible;mso-wrap-style:square'>
     1747 id="Picture_x0020_46" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:468pt;
     1748 height:215.25pt;visibility:visible;mso-wrap-style:square'>
    17371749 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image035.png"
    17381750  o:title=""/>
    1739 </v:shape><![endif]--><![if !vml]><img width=488 height=283
    1740 src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image068.gif"
    1741 v:shapes="Picture_x0020_18"><![endif]></span></p>
     1751</v:shape><![endif]--><![if !vml]><img width=624 height=287
     1752src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image036.gif"
     1753v:shapes="Picture_x0020_46"><![endif]></span></p>
    17421754
    17431755<p class=MsoNormal>Finally we can add the atom parameters for sapphire. Select
     
    17481760
    17491761<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1750  id="Picture_x0020_21" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:525pt;
    1751  height:225pt;visibility:visible;mso-wrap-style:square'>
    1752  <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image009.png"
    1753   o:title=""/>
    1754 </v:shape><![endif]--><![if !vml]><img width=700 height=300
    1755 src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image055.gif"
    1756 v:shapes="Picture_x0020_21"><![endif]></span></p>
     1762 id="Picture_x0020_47" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:468pt;
     1763 height:117.75pt;visibility:visible;mso-wrap-style:square'>
     1764 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image037.png"
     1765  o:title=""/>
     1766</v:shape><![endif]--><![if !vml]><img width=624 height=157
     1767src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image038.gif"
     1768v:shapes="Picture_x0020_47"><![endif]></span></p>
    17571769
    17581770<p class=MsoNormal>Double (right) click the <b style='mso-bidi-font-weight:
     
    17621774
    17631775<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1764  id="Picture_x0020_22" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:259.5pt;
    1765  height:252pt;visibility:visible;mso-wrap-style:square'>
    1766  <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image037.png"
    1767   o:title=""/>
    1768 </v:shape><![endif]--><![if !vml]><img width=346 height=336
    1769 src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image069.gif"
    1770 v:shapes="Picture_x0020_22"><![endif]></span></p>
     1776 id="Picture_x0020_48" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:171.75pt;
     1777 height:150pt;visibility:visible;mso-wrap-style:square'>
     1778 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image039.png"
     1779  o:title=""/>
     1780</v:shape><![endif]--><![if !vml]><img width=229 height=200
     1781src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image040.gif"
     1782v:shapes="Picture_x0020_48"><![endif]></span></p>
    17711783
    17721784<p class=MsoNormal>Choose both <b style='mso-bidi-font-weight:normal'><span
     
    17801792
    17811793<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1782  id="Picture_x0020_23" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:525pt;
    1783  height:225pt;visibility:visible;mso-wrap-style:square'>
    1784  <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image039.png"
    1785   o:title=""/>
    1786 </v:shape><![endif]--><![if !vml]><img width=700 height=300
    1787 src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image070.gif"
    1788 v:shapes="Picture_x0020_23"><![endif]></span></p>
     1794 id="Picture_x0020_49" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:468pt;
     1795 height:117.75pt;visibility:visible;mso-wrap-style:square'>
     1796 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image041.png"
     1797  o:title=""/>
     1798</v:shape><![endif]--><![if !vml]><img width=624 height=157
     1799src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image042.gif"
     1800v:shapes="Picture_x0020_49"><![endif]></span></p>
    17891801
    17901802<p class=MsoNormal>Showing the refine flags for both atoms. GSAS-II will sort
     
    17931805<p class=MsoNormal>Now do <b style='mso-bidi-font-weight:normal'><span
    17941806style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1795 mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> (twice to get
    1796 convergence). My <span class=SpellE>Rw</span> = 5.91%, GOF = 2.4; find these on
    1797 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1807mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> (twice to get convergence).
     1808My <span class=SpellE>Rw</span> = 4.705%, GOF = 1.91; find these on the <b
     1809style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    17981810mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Covariance</span></b>
    17991811data window. Now get a new 3D plot of all the reflections; select any HKLF
     
    18051817
    18061818<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1807  id="Picture_x0020_24" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:363pt;
    1808  height:312.75pt;visibility:visible;mso-wrap-style:square'>
    1809  <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image041.png"
    1810   o:title="" croptop="10627f" cropbottom="17360f" cropleft="40646f"
    1811   cropright="9847f"/>
    1812 </v:shape><![endif]--><![if !vml]><img width=484 height=417
    1813 src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image071.jpg"
    1814 v:shapes="Picture_x0020_24"><![endif]></span></p>
     1819 id="Picture_x0020_50" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:468pt;
     1820 height:405pt;visibility:visible;mso-wrap-style:square'>
     1821 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image043.png"
     1822  o:title=""/>
     1823</v:shape><![endif]--><![if !vml]><img width=624 height=540
     1824src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image044.gif"
     1825v:shapes="Picture_x0020_50"><![endif]></span></p>
    18151826
    18161827<p class=MsoNormal>It’s pretty obvious that there is one really bad reflection
     
    18271838<p class=MsoNormal>Phase:<span style='mso-spacerun:yes'>  </span><span
    18281839class=GramE>sapphire<span style='mso-spacerun:yes'>  </span>in</span>
    1829 histogram:<span style='mso-spacerun:yes'>  </span>HKLF sapphire_sphere.hkl_22<span
    1830 style='mso-spacerun:yes'>                                         </span></p>
    1831 
    1832 <p class=MsoNormal>------------------------------------------------------------------------------------------------------</p>
     1840histogram:<span style='mso-spacerun:yes'>  </span>HKLF sapphire_sphere.hkl_22<o:p></o:p></p>
     1841
     1842<p class=MsoNormal>=====================================================================<o:p></o:p></p>
    18331843
    18341844<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Final refinement RF,
    1835 RF^2 = 4.64%, 8.41% on 134 reflections (3 user rejected, 9 <span class=SpellE>sp.gp.extinct</span>)<span
    1836 style='mso-spacerun:yes'>       </span></p>
     1845RF^2 = 4.66%, 8.45% on 134 reflections (3 user rejected, 9 <span class=SpellE>sp.gp.extinct</span>)<o:p></o:p></p>
    18371846
    18381847<p class=MsoNormal><span style='mso-spacerun:yes'> </span>HKLF histogram weight
    1839 factor <span class=GramE>=<span style='mso-spacerun:yes'>  </span>1.000</span><span
    1840 style='mso-spacerun:yes'>                                                               
    1841 </span></p>
     1848factor <span class=GramE>=<span style='mso-spacerun:yes'>  </span>1.000</span><o:p></o:p></p>
    18421849
    18431850<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Scale <span
    1844 class=GramE>factor :</span><span style='mso-spacerun:yes'>    </span>66.8623,
    1845 sig<span style='mso-spacerun:yes'>     </span>0.8144<span
    1846 style='mso-spacerun:yes'>                                                           
    1847 </span></p>
    1848 
    1849 <p class=MsoNormal><span
    1850 style='mso-spacerun:yes'>                                    </span><span
    1851 style='mso-spacerun:yes'>                                                                  </span></p>
     1851class=GramE>factor :</span><span style='mso-spacerun:yes'>    </span>66.5252,
     1852sig<span style='mso-spacerun:yes'>     </span>0.7222<o:p></o:p></p>
     1853
     1854<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    18521855
    18531856<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Single crystal
    18541857extinction: Type:<span style='mso-spacerun:yes'>  </span><span class=GramE>Lorentzian<span
    18551858style='mso-spacerun:yes'>  </span><span class=SpellE>Approx</span></span>:<span
    1856 style='mso-spacerun:yes'>  </span>Secondary Type I<span
    1857 style='mso-spacerun:yes'>                              </span></p>
     1859style='mso-spacerun:yes'>  </span>Secondary Type I<o:p></o:p></p>
    18581860
    18591861<p class=MsoNormal><span style='mso-spacerun:yes'>       </span><span
    1860 class=SpellE>Eg</span>:<span style='mso-spacerun:yes'>     </span>5.58e-04
    1861 sig:<span style='mso-spacerun:yes'>     </span>1.28e-05<span
    1862 style='mso-spacerun:yes'>                                             </span><span
    1863 style='mso-spacerun:yes'>                </span></p>
    1864 
    1865 <p class=MsoNormal><span
    1866 style='mso-spacerun:yes'>                                                                                                     
    1867 </span></p>
     1862class=SpellE>Eg</span>:<span style='mso-spacerun:yes'>     </span>5.71e-04
     1863sig:<span style='mso-spacerun:yes'>     </span>7.44e-06<o:p></o:p></p>
     1864
     1865<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    18681866
    18691867<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Phase:<span
    18701868style='mso-spacerun:yes'>  </span><span class=GramE>sapphire<span
    18711869style='mso-spacerun:yes'>  </span>in</span> histogram:<span
    1872 style='mso-spacerun:yes'>  </span>HKLF sapphire_sphere.hkl_23<span
    1873 style='mso-spacerun:yes'>                                         </span></p>
    1874 
    1875 <p class=MsoNormal>------------------------------------------------------------------------------------------------------</p>
     1870style='mso-spacerun:yes'>  </span>HKLF sapphire_sphere.hkl_23<o:p></o:p></p>
     1871
     1872<p class=MsoNormal>=====================================================================<o:p></o:p></p>
    18761873
    18771874<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Final refinement RF,
    1878 RF^2 = 21.69%, 38.49% on 148 reflections (5 user rejected, 6 <span
    1879 class=SpellE>sp.gp.extinct</span>)<span style='mso-spacerun:yes'>     </span></p>
     1875RF^2 = 6.10%, 11.18% on 147 reflections (6 user rejected, 6 <span class=SpellE>sp.gp.extinct</span>)<o:p></o:p></p>
    18801876
    18811877<p class=MsoNormal><span style='mso-spacerun:yes'> </span>HKLF histogram weight
    1882 factor <span class=GramE>=<span style='mso-spacerun:yes'>  </span>1.000</span><span
    1883 style='mso-spacerun:yes'>                                             </span><span
    1884 style='mso-spacerun:yes'>                   </span></p>
     1878factor <span class=GramE>=<span style='mso-spacerun:yes'>  </span>1.000</span><o:p></o:p></p>
    18851879
    18861880<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Scale <span
    1887 class=GramE>factor :</span><span style='mso-spacerun:yes'>    </span>43.2084,
    1888 sig<span style='mso-spacerun:yes'>     </span>0.6507<span
    1889 style='mso-spacerun:yes'>                                                           
    1890 </span></p>
    1891 
    1892 <p class=MsoNormal><span
    1893 style='mso-spacerun:yes'>                                                                                                     
    1894 </span></p>
     1881class=GramE>factor :</span><span style='mso-spacerun:yes'>    </span>63.2155,
     1882sig<span style='mso-spacerun:yes'>     </span>0.6834<o:p></o:p></p>
     1883
     1884<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    18951885
    18961886<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Single crystal
    18971887extinction: Type:<span style='mso-spacerun:yes'>  </span><span class=GramE>Lorentzian<span
    18981888style='mso-spacerun:yes'>  </span><span class=SpellE>Approx</span></span>:<span
    1899 style='mso-spacerun:yes'>  </span>Secondary Type I<span
    1900 style='mso-spacerun:yes'>                              </span></p>
     1889style='mso-spacerun:yes'>  </span>Secondary Type I<o:p></o:p></p>
    19011890
    19021891<p class=MsoNormal><span style='mso-spacerun:yes'>       </span><span
    1903 class=SpellE>Eg</span>:<span style='mso-spacerun:yes'>     </span>5.58e-04
    1904 sig:<span style='mso-spacerun:yes'>     </span>1.28e-05<span
    1905 style='mso-spacerun:yes'>                                                            
    1906 </span></p>
    1907 
    1908 <p class=MsoNormal><span
    1909 style='mso-spacerun:yes'>                                                                               
    1910 </span><span style='mso-spacerun:yes'>                      </span></p>
     1892class=SpellE>Eg</span>:<span style='mso-spacerun:yes'>     </span>5.71e-04
     1893sig:<span style='mso-spacerun:yes'>     </span>7.44e-06<o:p></o:p></p>
     1894
     1895<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    19111896
    19121897<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Phase:<span
    19131898style='mso-spacerun:yes'>  </span><span class=GramE>sapphire<span
    19141899style='mso-spacerun:yes'>  </span>in</span> histogram:<span
    1915 style='mso-spacerun:yes'>  </span>HKLF sapphire_sphere.hkl_24<span
    1916 style='mso-spacerun:yes'>                                         </span></p>
    1917 
    1918 <p class=MsoNormal>------------------------------------------------------------------------------------------------------</p>
     1900style='mso-spacerun:yes'>  </span>HKLF sapphire_sphere.hkl_24<o:p></o:p></p>
     1901
     1902<p class=MsoNormal>=====================================================================<o:p></o:p></p>
    19191903
    19201904<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Final refinement RF,
    1921 RF^2 = 3.86%, 6.70% on 160 reflections (11 user rejected, 1 <span class=SpellE>sp.gp.extinct</span>)<span
    1922 style='mso-spacerun:yes'>      </span></p>
     1905RF^2 = 3.77%, 6.60% on 160 reflections (11 user rejected, 1 <span class=SpellE>sp.gp.extinct</span>)<o:p></o:p></p>
    19231906
    19241907<p class=MsoNormal><span style='mso-spacerun:yes'> </span>HKLF histogram weight
    1925 factor <span class=GramE>=<span style='mso-spacerun:yes'>  </span>1.000</span><span
    1926 style='mso-spacerun:yes'>                                                               
    1927 </span></p>
     1908factor <span class=GramE>=<span style='mso-spacerun:yes'>  </span>1.000</span><o:p></o:p></p>
    19281909
    19291910<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Scale <span
    1930 class=GramE>factor :</span><span style='mso-spacerun:yes'>    </span>66.6296,
    1931 sig<span style='mso-spacerun:yes'>     </span>0.7816<span
    1932 style='mso-spacerun:yes'>                                   </span><span
    1933 style='mso-spacerun:yes'>                         </span></p>
    1934 
    1935 <p class=MsoNormal><span
    1936 style='mso-spacerun:yes'>                                                                                                     
    1937 </span></p>
     1911class=GramE>factor :</span><span style='mso-spacerun:yes'>    </span>66.4019,
     1912sig<span style='mso-spacerun:yes'>     </span>0.6817<o:p></o:p></p>
     1913
     1914<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    19381915
    19391916<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Single crystal
    19401917extinction: Type:<span style='mso-spacerun:yes'>  </span><span class=GramE>Lorentzian<span
    19411918style='mso-spacerun:yes'>  </span><span class=SpellE>Approx</span></span>:<span
    1942 style='mso-spacerun:yes'>  </span>Secondary Type I<span
    1943 style='mso-spacerun:yes'>                              </span></p>
     1919style='mso-spacerun:yes'>  </span>Secondary Type I<o:p></o:p></p>
    19441920
    19451921<p class=MsoNormal><span style='mso-spacerun:yes'>       </span><span
    1946 class=SpellE>Eg</span>:<span style='mso-spacerun:yes'>     </span>5.58e-04 sig:<span
    1947 style='mso-spacerun:yes'>     </span>1.28e-05<span
    1948 style='mso-spacerun:yes'>                                                            
    1949 </span></p>
    1950 
    1951 <p class=MsoNormal><span
    1952 style='mso-spacerun:yes'>                                                                                                     
    1953 </span></p>
     1922class=SpellE>Eg</span>:<span style='mso-spacerun:yes'>     </span>5.71e-04
     1923sig:<span style='mso-spacerun:yes'>     </span>7.44e-06<o:p></o:p></p>
     1924
     1925<p class=MsoNormal><span style='mso-spacerun:yes'> </span><span
     1926style='mso-spacerun:yes'>                                                                  
     1927</span><span style='mso-spacerun:yes'>                                  </span></p>
    19541928
    19551929<p class=MsoNormal>There is obviously something wrong with #23 (high residual
     
    19611935
    19621936<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1963  id="Picture_x0020_25" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:365.25pt;
    1964  height:315pt;visibility:visible;mso-wrap-style:square'>
    1965  <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image043.png"
    1966   o:title="" croptop="9290f" cropbottom="18441f" cropleft="38576f" cropright="11843f"/>
    1967 </v:shape><![endif]--><![if !vml]><img width=487 height=420
    1968 src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image072.jpg"
    1969 v:shapes="Picture_x0020_25"><![endif]></span></p>
     1937 id="Picture_x0020_51" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:468pt;
     1938 height:405pt;visibility:visible;mso-wrap-style:square'>
     1939 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image045.png"
     1940  o:title=""/>
     1941</v:shape><![endif]--><![if !vml]><img width=624 height=540
     1942src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image046.gif"
     1943v:shapes="Picture_x0020_51"><![endif]></span></p>
    19701944
    19711945<p class=MsoNormal>By zooming in and rotating the plot around a bit, you can
    19721946identify the reflection with the cursor. It seems to be the <b
    19731947style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1974 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>541</span></b>
     1948mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>342</span></b>
    19751949reflection; select the <b style='mso-bidi-font-weight:normal'><span
    19761950style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     
    19791953TOPAZ data acquisition system). It is very near the bottom of the list (#<b
    19801954style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1981 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>153</span></b>).</p>
     1955mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>147</span></b>).</p>
    19821956
    19831957<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    19841958 id="Picture_x0020_26" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:585pt;
    19851959 height:244.5pt;visibility:visible;mso-wrap-style:square'>
    1986  <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image045.png"
     1960 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image047.png"
    19871961  o:title=""/>
    19881962</v:shape><![endif]--><![if !vml]><img width=780 height=326
    1989 src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image073.gif"
     1963src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image048.gif"
    19901964v:shapes="Picture_x0020_26"><![endif]></span></p>
    19911965
     
    20021976
    20031977<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2004  id="Picture_x0020_27" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:391.5pt;
    2005  height:225.75pt;visibility:visible;mso-wrap-style:square'>
    2006  <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image047.png"
    2007   o:title=""/>
    2008 </v:shape><![endif]--><![if !vml]><img width=522 height=301
    2009 src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image074.gif"
    2010 v:shapes="Picture_x0020_27"><![endif]></span></p>
     1978 id="Picture_x0020_52" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:468pt;
     1979 height:200.25pt;visibility:visible;mso-wrap-style:square'>
     1980 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image049.png"
     1981  o:title=""/>
     1982</v:shape><![endif]--><![if !vml]><img width=624 height=267
     1983src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image050.gif"
     1984v:shapes="Picture_x0020_52"><![endif]></span></p>
    20111985
    20121986<p class=MsoNormal>Change the value of <b style='mso-bidi-font-weight:normal'><span
    20131987style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    20141988mso-hansi-theme-font:minor-latin'>Max <span class=SpellE>delt</span>-F/sig</span></b>
    2015 to 20; that will certainly eliminate the bad 541 reflection &amp; perhaps a few
     1989to 20; that will certainly eliminate the bad 342 reflection &amp; perhaps a few
    20161990others. Repeat <b style='mso-bidi-font-weight:normal'><span style='font-family:
    20171991"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     
    20201994
    20211995<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2022  id="Picture_x0020_28" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:363pt;
    2023  height:309.75pt;visibility:visible;mso-wrap-style:square'>
    2024  <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image049.png"
    2025   o:title="" croptop="8876f" cropbottom="19515f" cropleft="39851f" cropright="10631f"/>
    2026 </v:shape><![endif]--><![if !vml]><img width=484 height=413
    2027 src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image075.jpg"
    2028 v:shapes="Picture_x0020_28"><![endif]></span></p>
     1996 id="Picture_x0020_53" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:468pt;
     1997 height:404.25pt;visibility:visible;mso-wrap-style:square'>
     1998 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image051.png"
     1999  o:title=""/>
     2000</v:shape><![endif]--><![if !vml]><img width=624 height=539
     2001src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image052.gif"
     2002v:shapes="Picture_x0020_53"><![endif]></span></p>
    20292003
    20302004<p class=MsoNormal>Looking the <span class=SpellE><b style='mso-bidi-font-weight:
     
    20522026style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    20532027mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> again. My final
    2054 residual was <span class=SpellE>Rw</span>=5.06%. </p>
     2028residual was <span class=SpellE>Rw</span>=4.20%. </p>
    20552029
    20562030<p class=MsoNormal>This completes the tutorial. You can explore the other
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