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Timestamp:
May 22, 2015 1:07:32 PM (7 years ago)
Author:
vondreele
Message:

complete TOF Single Crystal Refinement tutorial.

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Tutorials
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5 edited

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

    r1849 r1865  
    2525  <o:Author>vondreele</o:Author>
    2626  <o:LastAuthor>Von Dreele</o:LastAuthor>
    27   <o:Revision>7</o:Revision>
    28   <o:TotalTime>716</o:TotalTime>
     27  <o:Revision>11</o:Revision>
     28  <o:TotalTime>1030</o:TotalTime>
    2929  <o:Created>2015-02-17T16:18:00Z</o:Created>
    30   <o:LastSaved>2015-03-20T13:44:00Z</o:LastSaved>
     30  <o:LastSaved>2015-05-22T18:02:00Z</o:LastSaved>
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     33  <o:Characters>11757</o:Characters>
    3434  <o:Company>Argonne National Laboratory</o:Company>
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    4949 <w:WordDocument>
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    653         mso-font-charset:1;
     652        mso-font-charset:0;
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    12171215
    12181216<p class=MsoNormal>In these exercises you will use GSAS-II to refine the
    1219 structure of sapphire (really corundum, Al<sub>2</sub>O<sub>3</sub>) from single
    1220 crystal diffraction data collected at the SNS on the TOPAZ instrument at room
    1221 temperature. The data consists of a suite of exposures with the crystal in 31
    1222 different orientations. If you have not done so already, start GSAS-II.</p>
     1217structure of sapphire (really corundum, Al<sub>2</sub>O<sub>3</sub>) from
     1218single crystal diffraction data collected at the SNS on the TOPAZ instrument at
     1219room temperature. The data consists of a suite of exposures with the crystal in
     122031 different orientations all within a single data file. Note that menu entries
     1221and user input are shown in bold face below as <b style='mso-bidi-font-weight:
     1222normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1223minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1224mso-bidi-theme-font:minor-latin'>Help/About GSAS-II</span></b>, which lists
     1225first the name of the menu (here <b style='mso-bidi-font-weight:normal'><span
     1226style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1227mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1228minor-latin'>Help</span></b>) and second the name of the entry in the menu
     1229(here <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1230mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1231Calibri;mso-bidi-theme-font:minor-latin'>About GSAS-II</span></b>). If you have
     1232not done so already, start GSAS-II.</p>
    12231233
    12241234<h2>Step 1. Setup the phase information for sapphire</h2>
     
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    12681278src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image002.gif"
    1269 v:shapes="Picture_x0020_28"><![endif]></span></p>
     1279v:shapes="_x0000_i1050"><![endif]></span></p>
    12701280
    12711281<p class=MsoListParagraph><o:p>&nbsp;</o:p></p>
     
    12761286<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    12771287mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>R -3 c</span></b>
    1278 (don’t forget the spaces between axial fields) &amp; press Return. A Space Group
     1288(don’t forget the spaces between axial fields) &amp; press <b style='mso-bidi-font-weight:
     1289normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1290minor-latin;mso-hansi-theme-font:minor-latin'>Return</span></b>. A Space Group
    12791291Information popup window will appear; press <b style='mso-bidi-font-weight:
    12801292normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     
    12841296
    12851297<p class=MsoListParagraph><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
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    12871299 height:375pt;visibility:visible;mso-wrap-style:square'>
    12881300 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image003.png"
     
    13171329
    13181330<p class=MsoListParagraph><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
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    13201332 height:225pt;visibility:visible;mso-wrap-style:square'>
    13211333 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image005.png"
     
    13281340style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>5.<span
    13291341style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Double
    1330 click the first entry under Type (H); a periodic table will appear. Select Al.
    1331 Do the same for the second one and pick O. The Atom list should look like</p>
     1342click the first entry under Type (H); a periodic table will appear. Select <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'>Al</span></b>.
     1345Do the same for the second one and pick <b style='mso-bidi-font-weight:normal'><span
     1346style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1347mso-hansi-theme-font:minor-latin'>O</span></b>. The Atom list should look like</p>
    13321348
    13331349<p class=MsoListParagraph><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1334  id="Picture_x0020_32" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:525pt;
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    13351351 height:225pt;visibility:visible;mso-wrap-style:square'>
    13361352 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image007.png"
     
    13431359style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>6.<span
    13441360style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Change
    1345 the <span class=GramE>Al(</span>z) to 0. 352, the O(x) to -0.306 and the <span
    1346 class=GramE>O(</span>z) to Œ (it will be changed to 0.2500). Site symmetries
    1347 and multiplicities will automatically change for these positions.</p>
     1361the <span class=GramE>Al(</span>z) to <b style='mso-bidi-font-weight:normal'><span
     1362style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1363mso-hansi-theme-font:minor-latin'>0. 352</span></b>, the O(x) to <b
     1364style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1365mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>-0.306</span></b>
     1366and the <span class=GramE>O(</span>z) to <b style='mso-bidi-font-weight:normal'><span
     1367style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1368mso-hansi-theme-font:minor-latin'>Œ</span></b> (it will be changed to 0.2500).
     1369Site symmetries and multiplicities will automatically change for these
     1370positions.</p>
    13481371
    13491372<p class=MsoListParagraph><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1350  id="Picture_x0020_34" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:525pt;
     1373 id="Picture_x0020_34" o:spid="_x0000_i1046" type="#_x0000_t75" style='width:525pt;
    13511374 height:225pt;visibility:visible;mso-wrap-style:square'>
    13521375 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image009.png"
     
    13831406mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Import/Structure
    13841407Factor/from Neutron TOF HKL F<sup>2 </sup>file</span></b>; a file dialog box
    1385 will appear. Change the directory to the location of this exercise (e<b
    1386 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1387 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>xercises/TOF
     1408will appear. Change the directory to the location of this exercise (<b
     1409style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1410mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>exercises/TOF
    13881411Single Crystal Refinement</span></b> – yours might be different), select <span
    13891412class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
     
    14031426
    14041427<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1405  id="Picture_x0020_35" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:240pt;
     1428 id="Picture_x0020_35" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:240pt;
    14061429 height:232.5pt;visibility:visible;mso-wrap-style:square'>
    14071430 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image011.png"
     
    14121435
    14131436<p class=MsoNormal>This makes the connection between the data you just read and
    1414 the phase (sapphire) you entered in Step 1. Select it (or <b style='mso-bidi-font-weight:
    1415 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1416 minor-latin;mso-hansi-theme-font:minor-latin'>Set All</span></b>) and press OK.
     1437the phase (<b style='mso-bidi-font-weight:normal'><span style='font-family:
     1438"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1439minor-latin'>sapphire</span></b>) you entered in Step 1. Select it (or <b
     1440style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1441mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Set All</span></b>)
     1442and press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1443mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
    14171444The GSAS-II data tree window will show all the new histograms, expanding the
    14181445last one.</p>
    14191446
    14201447<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1421  id="Picture_x0020_36" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:300pt;
     1448 id="Picture_x0020_36" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:300pt;
    14221449 height:187.5pt;visibility:visible;mso-wrap-style:square'>
    14231450 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image013.png"
     
    14281455
    14291456<p class=MsoNormal>The plot window shows a not very interesting 2D view of the
    1430 l=0 layer of reciprocal space for the last data set. If you select <b
    1431 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1457l=0 layer of reciprocal space for the last data set. If you select the 1<sup>st</sup>
     1458HKLF entry (<b style='mso-bidi-font-weight:normal'><span style='font-family:
     1459"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1460minor-latin'>HKLF <span class=SpellE>sapphire_sphere.hkl</span></span></b>) the
     1461plot is a bit more interesting.</p>
     1462
     1463<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1464 id="Picture_x0020_10" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:525pt;
     1465 height:450pt;visibility:visible;mso-wrap-style:square'>
     1466 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image015.png"
     1467  o:title=""/>
     1468</v:shape><![endif]--><![if !vml]><img width=700 height=600
     1469src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image016.gif"
     1470v:shapes="Picture_x0020_10"><![endif]></span></p>
     1471
     1472<p class=MsoNormal>Green circles are drawn representing the magnitude of 4
     1473structure factors on the l=0 layer. The positions are strictly on a square
     1474grid; you can “tab” through the layers on l with <span class=GramE>the <b
     1475style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1476mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>+/-</span></b></span>
     1477keys. Find other commands in the “K” box in the tools part of the plot. If you
     1478select <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    14321479mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Commands/Plot
    1433 3D HKLs</span></b> from the data window you’ll see a 3D view of the reflection
     14803D HKLs</span></b> from the data window you’ll see a 3D view of this reflection
    14341481set; press <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
    14351482style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     
    14401487
    14411488<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1442  id="Picture_x0020_1" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:432.75pt;
    1443  height:373.5pt;visibility:visible;mso-wrap-style:square'>
    1444  <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image015.png"
    1445   o:title="" croptop="10203f" cropbottom="17848f" cropleft="40194f"
    1446   cropright="10376f"/>
    1447 </v:shape><![endif]--><![if !vml]><img width=577 height=498
    1448 src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image016.jpg"
    1449 v:shapes="Picture_x0020_1"><![endif]></span></p>
    1450 
    1451 <p class=MsoNormal>The save as/key commands give you control on the appearance
    1452 of the plot; the plot responds to zoom/rotate commands from the mouse. Left
    1453 mouse button to rotate, right mouse button to translate, center wheel to rotate
    1454 about view direction and the wheel to zoom in or out. One cursor is the view
    1455 point and the other is the 000 reciprocal space origin. </p>
     1489 id="Picture_x0020_11" o:spid="_x0000_i1042" type="#_x0000_t75" style='width:363pt;
     1490 height:311.25pt;visibility:visible;mso-wrap-style:square'>
     1491 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image017.png"
     1492  o:title="" croptop="11818f" cropbottom="16324f" cropleft="40001f"
     1493  cropright="10518f"/>
     1494</v:shape><![endif]--><![if !vml]><img width=484 height=415
     1495src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image018.jpg"
     1496v:shapes="Picture_x0020_11"><![endif]></span></p>
     1497
     1498<p class=MsoNormal>Here the plot has the correct representation for reciprocal
     1499space as sampled by this crystal orientation on TOPAZ. The <b style='mso-bidi-font-weight:
     1500normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1501minor-latin;mso-hansi-theme-font:minor-latin'>save as/key</span></b> commands
     1502give you control on the appearance of the plot; the plot responds to
     1503zoom/rotate commands from the mouse. Left mouse button to rotate, right mouse
     1504button to translate, center wheel to rotate about view direction and the wheel
     1505to zoom in or out. One cursor is the view point and the other is the 000
     1506reciprocal space origin. </p>
     1507
     1508<p class=MsoNormal>If you want to see the entire data set plotted together do <b
     1509style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1510mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Commands/Plot
     1511all 3D HKLs</span></b>; a data selection popup window will appear. Do <b
     1512style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1513mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Set Al</span></b>l
     1514and then <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1515mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>
     1516to select all the data; the plot will be redrawn (I’ve pressed the ‘<span
     1517class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
     1518"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1519minor-latin'>i</span></b></span>’ key as before)</p>
     1520
     1521<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1522 id="Picture_x0020_12" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:365.25pt;
     1523 height:310.5pt;visibility:visible;mso-wrap-style:square'>
     1524 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image019.png"
     1525  o:title="" croptop="12098f" cropbottom="16193f" cropleft="40187f"
     1526  cropright="10237f"/>
     1527</v:shape><![endif]--><![if !vml]><img width=487 height=414
     1528src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image020.jpg"
     1529v:shapes="Picture_x0020_12"><![endif]></span></p>
     1530
     1531<p class=MsoNormal>I’ve rotated the drawing around to show an obvious gap in
     1532the coverage.</p>
     1533
     1534<p class=MsoNormal>We’re now ready to do the refinement.</p>
    14561535
    14571536<h2>Step 3. Initial least squares refinement</h2>
    14581537
    1459 <p class=MsoNormal>By default the scale factors for all 31 data set are set to be
    1460 refined so you can immediately do a refinement. Select Calculate/Refine from
    1461 the main GSAS-II data tree window menu. This will do an F2 refinement by
    1462 default; probably better is an F refinement. Select Controls from the tree</p>
     1538<p class=MsoNormal>By default the scale factors for all 31 data set are set to
     1539be refined so you can immediately do a refinement. Select <b style='mso-bidi-font-weight:
     1540normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1541minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> from
     1542the main GSAS-II data tree window menu. This will do an F refinement by
     1543default. A progress bar will appear to show you the residuals as the histograms
     1544are processed. When it finishes and you have accepted the result a plot will
     1545show the l=0 layer for the 1<sup>st</sup> data set.</p>
    14631546
    14641547<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1465  id="Picture_x0020_38" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:348.75pt;
    1466  height:173.25pt;visibility:visible;mso-wrap-style:square'>
    1467  <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image017.png"
     1548 id="_x0000_i1040" type="#_x0000_t75" style='width:525pt;height:450pt;
     1549 visibility:visible;mso-wrap-style:square'>
     1550 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image021.png"
    14681551  o:title=""/>
    1469 </v:shape><![endif]--><![if !vml]><img width=465 height=231
    1470 src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image018.gif"
    1471 v:shapes="Picture_x0020_38"><![endif]></span></p>
    1472 
    1473 <p class=MsoNormal>Uncheck the Refine HKLF as F^2? Box and set the Min <span
    1474 class=SpellE>obs</span>/sig to 1.0.</p>
     1552</v:shape><![endif]--><![if !vml]><img width=700 height=600
     1553src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image022.gif"
     1554v:shapes="_x0000_i1040"><![endif]></span></p>
     1555
     1556<p class=MsoNormal>Green rings are the observed magnitude, blue rings are the
     1557calculated ones and the solid disk is the difference (green for positive &amp;
     1558red for negative <span class=SpellE>F<sub>o</sub></span>-F<sub>c</sub>). You
     1559can see the whole scope of the fit by doing <b style='mso-bidi-font-weight:
     1560normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1561minor-latin;mso-hansi-theme-font:minor-latin'>Commands/Plot all 3D HKLs</span></b>
     1562and selecting all the HKLF entries; press the “<b style='mso-bidi-font-weight:
     1563normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1564minor-latin;mso-hansi-theme-font:minor-latin'>w</span></b>” key to show the
     1565weighted &#916;F points.</p>
     1566
     1567<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1568 id="_x0000_i1039" type="#_x0000_t75" style='width:369pt;height:310.5pt;
     1569 visibility:visible;mso-wrap-style:square'>
     1570 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image023.png"
     1571  o:title="" croptop="9828f" cropbottom="18427f" cropleft="38257f" cropright="12033f"/>
     1572</v:shape><![endif]--><![if !vml]><img width=492 height=414
     1573src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image024.jpg"
     1574v:shapes="_x0000_i1039"><![endif]></span></p>
     1575
     1576<p class=MsoNormal>The size of the squares is proportional to the magnitude of <span
     1577class=SpellE>w&#916;F</span>. The cluster of negative <span class=SpellE>w&#916;F</span>
     1578points around the reciprocal space origin is pretty clearly a consequence of
     1579extinction so we’ll have to include that in the refinement model. One should
     1580not be tempted to refine coordinates and thermal parameters until extinction is
     1581accounted for in the refinement.</p>
     1582
     1583<h2>Step 3. Extinction model selection and refinement</h2>
     1584
     1585<p class=MsoNormal>GSAS-II has a number of extinction models available for
     1586single crystal data. These include Primary, Secondary types I and II with
     1587either Gaussian or Lorentzian distributions. To select one find the <b
     1588style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1589mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sapphire</span></b>
     1590entry in the GSAS-II data tree and select its <b style='mso-bidi-font-weight:
     1591normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1592minor-latin;mso-hansi-theme-font:minor-latin'>Data</span></b> tab.</p>
     1593
     1594<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1595 id="Picture_x0020_16" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:300pt;
     1596 height:303pt;visibility:visible;mso-wrap-style:square'>
     1597 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image025.png"
     1598  o:title=""/>
     1599</v:shape><![endif]--><![if !vml]><img width=400 height=404
     1600src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image026.gif"
     1601v:shapes="Picture_x0020_16"><![endif]></span></p>
     1602
     1603<p class=MsoNormal>We can cut to the chase here – select <b style='mso-bidi-font-weight:
     1604normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1605minor-latin;mso-hansi-theme-font:minor-latin'>Secondary Type I</span></b> from
     1606the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1607mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Extinction
     1608type</span></b> pull down list (the tab will be redrawn) and check the <span
     1609class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
     1610"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1611minor-latin'>Eg</span></b></span> box; leave the <span class=SpellE><b
     1612style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1613mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Approx</span></b></span>
     1614selection as <b style='mso-bidi-font-weight:normal'><span style='font-family:
     1615"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1616minor-latin'>Lorentzian</span></b>. Later on after you’ve finished the
     1617tutorial, you can try the other models and see how they compare. Next do <b
     1618style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1619mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Copy
     1620selected data</span></b>, pick <b style='mso-bidi-font-weight:normal'><span
     1621style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1622mso-hansi-theme-font:minor-latin'>Extinction</span></b> from the list of
     1623parameters and press <b style='mso-bidi-font-weight:normal'><span
     1624style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1625mso-hansi-theme-font:minor-latin'>OK</span></b>. Then do <b style='mso-bidi-font-weight:
     1626normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1627minor-latin;mso-hansi-theme-font:minor-latin'>Set All</span></b> and press <b
     1628style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1629mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>
     1630from the next popup; this will copy the extinction model to all HKLF data sets.</p>
     1631
     1632<p class=MsoNormal>Because all of these extinction models are needed for one crystal,
     1633it makes sense to tie them together into a single parameter. Select <b
     1634style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1635mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Constraints</span></b>
     1636from the main GSAS-II data tree and pick the <b style='mso-bidi-font-weight:
     1637normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1638minor-latin;mso-hansi-theme-font:minor-latin'>Histogram/Phase constraints</span></b>
     1639tab; it will be empty. Do <b style='mso-bidi-font-weight:normal'><span
     1640style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1641mso-hansi-theme-font:minor-latin'>Edit/Add equivalence</span></b>; the
     1642following popup will appear</p>
     1643
     1644<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1645 id="Picture_x0020_17" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:468.75pt;
     1646 height:300pt;visibility:visible;mso-wrap-style:square'>
     1647 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image027.png"
     1648  o:title=""/>
     1649</v:shape><![endif]--><![if !vml]><img width=625 height=400
     1650src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image028.gif"
     1651v:shapes="Picture_x0020_17"><![endif]></span></p>
     1652
     1653<p class=MsoNormal>Select the line beginning with ‘<b style='mso-bidi-font-weight:
     1654normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1655minor-latin;mso-hansi-theme-font:minor-latin'>0:0<span class=GramE>:Eg<span
     1656style='font-family:"Times New Roman",serif;font-weight:normal'>’</span></span></span></b>
     1657(the Secondary type I parameter you just set to vary) and press <b
     1658style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1659mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
     1660A new popup will appear; you’ll want to see the bottom of the list</p>
     1661
     1662<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1663 id="Picture_x0020_18" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:468.75pt;
     1664 height:300pt;visibility:visible;mso-wrap-style:square'>
     1665 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image029.png"
     1666  o:title=""/>
     1667</v:shape><![endif]--><![if !vml]><img width=625 height=400
     1668src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image030.gif"
     1669v:shapes="Picture_x0020_18"><![endif]></span></p>
     1670
     1671<p class=MsoNormal>Pick either <b style='mso-bidi-font-weight:normal'><span
     1672style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1673mso-hansi-theme-font:minor-latin'>0<span class=GramE>:all:Eg</span></span></b>
     1674or <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1675mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0:all=<span
     1676class=SpellE>SNT:Eg</span></span></b> and press <b style='mso-bidi-font-weight:
     1677normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1678minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>. The equivalence
     1679making <span class=SpellE>Eg</span> for all histograms the same parameter will
     1680be shown</p>
     1681
     1682<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1683 id="Picture_x0020_20" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:481.5pt;
     1684 height:184.5pt;visibility:visible;mso-wrap-style:square'>
     1685 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image031.png"
     1686  o:title=""/>
     1687</v:shape><![endif]--><![if !vml]><img width=642 height=246
     1688src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image032.gif"
     1689v:shapes="Picture_x0020_20"><![endif]></span></p>
     1690
     1691<p class=MsoNormal>Now do <b style='mso-bidi-font-weight:normal'><span
     1692style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1693mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> from the main
     1694GSAS-II data tree menu. You may have to repeat this twice to get convergence (<span
     1695class=SpellE>Rw</span> ~14%); note the console output – value of Delta
     1696indicates closeness to convergence. Select one of the HKLF data sets and view
     1697the 3D Structure Factors plot for it alone</p>
     1698
     1699<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1700 id="_x0000_i1034" type="#_x0000_t75" style='width:362.25pt;height:311.25pt;
     1701 visibility:visible;mso-wrap-style:square'>
     1702 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image033.png"
     1703  o:title="" croptop="15476f" cropbottom="12688f" cropleft="40744f"
     1704  cropright="9798f"/>
     1705</v:shape><![endif]--><![if !vml]><img width=483 height=415
     1706src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image034.jpg"
     1707v:shapes="_x0000_i1034"><![endif]></span></p>
     1708
     1709<p class=MsoNormal>The <span class=SpellE>wDF</span> is positive close to 0<span
     1710class=GramE>,0,0</span> then negative for an inner shell around the positive
     1711core and finally positive for the outer shell. This is a thermal
     1712parameter/extinction effect. So both have to be now refined. However, as a
     1713matter of course we may expect that the extinction corrections are less
     1714accurate when <span class=SpellE><span class=GramE>Fo</span></span>&lt;&lt; Fc.
     1715In addition some reflections were poorly measured. We want to reject
     1716reflections where <span class=SpellE>Fo</span>/Fc &lt; 0.5 and Fo2/<span
     1717class=GramE>s(</span>Fo2) &lt; 3. These can be applied on the <b
     1718style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1719mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Controls</span></b>
     1720page. After setting these my Controls were</p>
     1721
     1722<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1723 id="_x0000_i1033" type="#_x0000_t75" style='width:366pt;height:212.25pt;
     1724 visibility:visible;mso-wrap-style:square'>
     1725 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image035.png"
     1726  o:title=""/>
     1727</v:shape><![endif]--><![if !vml]><img width=488 height=283
     1728src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image036.gif"
     1729v:shapes="_x0000_i1033"><![endif]></span></p>
     1730
     1731<p class=MsoNormal>Finally we can add the atom parameters for sapphire. Select
     1732the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1733mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Atoms</span></b>
     1734tab for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1735mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phase/sapphire</span></b></p>
     1736
     1737<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1738 id="Picture_x0020_21" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:525pt;
     1739 height:225pt;visibility:visible;mso-wrap-style:square'>
     1740 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image009.png"
     1741  o:title=""/>
     1742</v:shape><![endif]--><![if !vml]><img width=700 height=300
     1743src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image010.gif"
     1744v:shapes="Picture_x0020_21"><![endif]></span></p>
     1745
     1746<p class=MsoNormal>Double (right) click 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'>Refine</span></b> column heading;
     1749a popup will appear</p>
     1750
     1751<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1752 id="Picture_x0020_22" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:259.5pt;
     1753 height:252pt;visibility:visible;mso-wrap-style:square'>
     1754 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image037.png"
     1755  o:title=""/>
     1756</v:shape><![endif]--><![if !vml]><img width=346 height=336
     1757src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image038.gif"
     1758v:shapes="Picture_x0020_22"><![endif]></span></p>
     1759
     1760<p class=MsoNormal>Choose both <b style='mso-bidi-font-weight:normal'><span
     1761style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1762mso-hansi-theme-font:minor-latin'>X</span></b> and <b style='mso-bidi-font-weight:
     1763normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1764minor-latin;mso-hansi-theme-font:minor-latin'>U</span></b> and press <b
     1765style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1766mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>;
     1767the Atoms tab will be redrawn</p>
     1768
     1769<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1770 id="Picture_x0020_23" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:525pt;
     1771 height:225pt;visibility:visible;mso-wrap-style:square'>
     1772 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image039.png"
     1773  o:title=""/>
     1774</v:shape><![endif]--><![if !vml]><img width=700 height=300
     1775src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image040.gif"
     1776v:shapes="Picture_x0020_23"><![endif]></span></p>
     1777
     1778<p class=MsoNormal>Showing the refine flags for both atoms. GSAS-II will sort
     1779out the special position rules for the two sites.</p>
     1780
     1781<p class=MsoNormal>Now do <b style='mso-bidi-font-weight:normal'><span
     1782style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1783mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> (twice to get
     1784convergence). My <span class=SpellE>Rw</span> = 5.91%, GOF = 2.4; find these on
     1785the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1786mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Covariance</span></b>
     1787data window. Now get a new 3D plot of all the reflections; select any HKLF
     1788entry, then do <b style='mso-bidi-font-weight:normal'><span style='font-family:
     1789"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1790minor-latin'>Commands/Plot all 3D HKLs</span></b>. Press <b style='mso-bidi-font-weight:
     1791normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1792minor-latin;mso-hansi-theme-font:minor-latin'>w</span></b> key.</p>
     1793
     1794<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1795 id="Picture_x0020_24" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:363pt;
     1796 height:312.75pt;visibility:visible;mso-wrap-style:square'>
     1797 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image041.png"
     1798  o:title="" croptop="10627f" cropbottom="17360f" cropleft="40646f"
     1799  cropright="9847f"/>
     1800</v:shape><![endif]--><![if !vml]><img width=484 height=417
     1801src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image042.jpg"
     1802v:shapes="Picture_x0020_24"><![endif]></span></p>
     1803
     1804<p class=MsoNormal>It’s pretty obvious that there is one really bad reflection
     1805and (a bit more subtly) it is messing up one TOPAS data set. To find it first
     1806look through the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
     1807style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1808mso-hansi-theme-font:minor-latin'>sapphire.lst</span></b></span> file; that
     1809will give fitting information for all the histograms (near bottom of the
     1810listing). Open it with your favorite text editor; I’ve shown an interesting bit
     1811of it here showing results for histograms 22-24.</p>
     1812
     1813<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1814
     1815<p class=MsoNormal>Phase:<span style='mso-spacerun:yes'>  </span><span
     1816class=GramE>sapphire<span style='mso-spacerun:yes'>  </span>in</span>
     1817histogram:<span style='mso-spacerun:yes'>  </span>HKLF
     1818sapphire_sphere.hkl_22<span
     1819style='mso-spacerun:yes'>                                         </span><o:p></o:p></p>
     1820
     1821<p class=MsoNormal>------------------------------------------------------------------------------------------------------<o:p></o:p></p>
     1822
     1823<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Final refinement RF,
     1824RF^2 = 4.64%, 8.41% on 134 reflections (3 user rejected, 9 <span class=SpellE>sp.gp.extinct</span>)<span
     1825style='mso-spacerun:yes'>       </span><o:p></o:p></p>
     1826
     1827<p class=MsoNormal><span style='mso-spacerun:yes'> </span>HKLF histogram weight
     1828factor <span class=GramE>=<span style='mso-spacerun:yes'>  </span>1.000</span><span
     1829style='mso-spacerun:yes'>                                                               
     1830</span><o:p></o:p></p>
     1831
     1832<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Scale <span
     1833class=GramE>factor :</span><span style='mso-spacerun:yes'>    </span>66.8623,
     1834sig<span style='mso-spacerun:yes'>     </span>0.8144<span
     1835style='mso-spacerun:yes'>        </span><span
     1836style='mso-spacerun:yes'>                                                    </span><o:p></o:p></p>
     1837
     1838<p class=MsoNormal><span
     1839style='mso-spacerun:yes'>                                                                                                     
     1840</span><o:p></o:p></p>
     1841
     1842<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Single crystal
     1843extinction: Type:<span style='mso-spacerun:yes'>  </span><span class=GramE>Lorentzian<span
     1844style='mso-spacerun:yes'>  </span><span class=SpellE>Approx</span></span>:<span
     1845style='mso-spacerun:yes'>  </span>Secondary Type I<span
     1846style='mso-spacerun:yes'>                            </span><span
     1847style='mso-spacerun:yes'>  </span><o:p></o:p></p>
     1848
     1849<p class=MsoNormal><span style='mso-spacerun:yes'>       </span><span
     1850class=SpellE>Eg</span>:<span style='mso-spacerun:yes'>     </span>5.58e-04
     1851sig:<span style='mso-spacerun:yes'>     </span>1.28e-05<span
     1852style='mso-spacerun:yes'>                                                            
     1853</span><o:p></o:p></p>
     1854
     1855<p class=MsoNormal><span
     1856style='mso-spacerun:yes'>                                                                                                     
     1857</span><o:p></o:p></p>
     1858
     1859<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Phase:<span
     1860style='mso-spacerun:yes'>  </span><span class=GramE>sapphire<span
     1861style='mso-spacerun:yes'>  </span>in</span> histogram:<span
     1862style='mso-spacerun:yes'>  </span>HKLF sapphire_sphere.hkl_23<span
     1863style='mso-spacerun:yes'>                                         </span><o:p></o:p></p>
     1864
     1865<p class=MsoNormal>------------------------------------------------------------------------------------------------------<o:p></o:p></p>
     1866
     1867<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Final refinement RF,
     1868RF^2 = 21.69%, 38.49% on 148 reflections (5 user rejected, 6 <span
     1869class=SpellE>sp.gp.extinct</span>)<span style='mso-spacerun:yes'>     </span><o:p></o:p></p>
     1870
     1871<p class=MsoNormal><span style='mso-spacerun:yes'> </span>HKLF histogram weight
     1872factor <span class=GramE>=<span style='mso-spacerun:yes'>  </span>1.000</span><span
     1873style='mso-spacerun:yes'>                                                               
     1874</span><o:p></o:p></p>
     1875
     1876<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Scale <span
     1877class=GramE>factor :</span><span style='mso-spacerun:yes'>    </span>43.2084,
     1878sig<span style='mso-spacerun:yes'>     </span>0.6507<span
     1879style='mso-spacerun:yes'>                                                           
     1880</span><o:p></o:p></p>
     1881
     1882<p class=MsoNormal><span
     1883style='mso-spacerun:yes'>                                            </span><span
     1884style='mso-spacerun:yes'>                                                          </span><o:p></o:p></p>
     1885
     1886<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Single crystal
     1887extinction: Type:<span style='mso-spacerun:yes'>  </span><span class=GramE>Lorentzian<span
     1888style='mso-spacerun:yes'>  </span><span class=SpellE>Approx</span></span>:<span
     1889style='mso-spacerun:yes'>  </span>Secondary Type I<span
     1890style='mso-spacerun:yes'>                              </span><o:p></o:p></p>
     1891
     1892<p class=MsoNormal><span style='mso-spacerun:yes'>       </span><span
     1893class=SpellE>Eg</span>:<span style='mso-spacerun:yes'>     </span>5.58e-04
     1894sig:<span style='mso-spacerun:yes'>     </span>1.28e-05<span
     1895style='mso-spacerun:yes'>                                                    
     1896</span><span style='mso-spacerun:yes'>        </span><o:p></o:p></p>
     1897
     1898<p class=MsoNormal><span
     1899style='mso-spacerun:yes'>                                                                                                     
     1900</span><o:p></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<span
     1906style='mso-spacerun:yes'>                                         </span><o:p></o:p></p>
     1907
     1908<p class=MsoNormal>------------------------------------------------------------------------------------------------------<o:p></o:p></p>
     1909
     1910<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Final refinement RF,
     1911RF^2 = 3.86%, 6.70% on 160 reflections (11 user rejected, 1 <span class=SpellE>sp.gp.extinct</span>)<span
     1912style='mso-spacerun:yes'>      </span><o:p></o:p></p>
     1913
     1914<p class=MsoNormal><span style='mso-spacerun:yes'> </span>HKLF histogram weight
     1915factor <span class=GramE>=<span style='mso-spacerun:yes'>  </span>1.000</span><span
     1916style='mso-spacerun:yes'>                                                    
     1917</span><span style='mso-spacerun:yes'>           </span><o:p></o:p></p>
     1918
     1919<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Scale <span
     1920class=GramE>factor :</span><span style='mso-spacerun:yes'>    </span>66.6296,
     1921sig<span style='mso-spacerun:yes'>     </span>0.7816<span
     1922style='mso-spacerun:yes'>                                                           
     1923</span><o:p></o:p></p>
     1924
     1925<p class=MsoNormal><span
     1926style='mso-spacerun:yes'>                                                                                                     
     1927</span><o:p></o:p></p>
     1928
     1929<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Single crystal
     1930extinction: Type:<span style='mso-spacerun:yes'>  </span><span class=GramE>Lorentzian<span
     1931style='mso-spacerun:yes'>  </span><span class=SpellE>Approx</span></span>:<span
     1932style='mso-spacerun:yes'>  </span>Secondary Type I<span
     1933style='mso-spacerun:yes'>                              </span><o:p></o:p></p>
     1934
     1935<p class=MsoNormal><span style='mso-spacerun:yes'>       </span><span
     1936class=SpellE>Eg</span>:<span style='mso-spacerun:yes'>     </span>5.58e-04
     1937sig:<span style='mso-spacerun:yes'>     </span>1.28e-05<span
     1938style='mso-spacerun:yes'>                                                            
     1939</span><o:p></o:p></p>
     1940
     1941<p class=MsoNormal><span
     1942style='mso-spacerun:yes'>                                                                                       
     1943</span><span style='mso-spacerun:yes'>              </span></p>
     1944
     1945<p class=MsoNormal>There is obviously something wrong with #23 (high residual
     1946&amp; funny scale factor compared to the others). Find <b style='mso-bidi-font-weight:
     1947normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1948minor-latin;mso-hansi-theme-font:minor-latin'>HKLF sapphire_sphere.hkl_23</span></b>
     1949in the GSAS-II data tree &amp; select it. The 3D plot of just that data set
     1950will show the problem reflection.</p>
     1951
     1952<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1953 id="Picture_x0020_25" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:365.25pt;
     1954 height:315pt;visibility:visible;mso-wrap-style:square'>
     1955 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image043.png"
     1956  o:title="" croptop="9290f" cropbottom="18441f" cropleft="38576f" cropright="11843f"/>
     1957</v:shape><![endif]--><![if !vml]><img width=487 height=420
     1958src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image044.jpg"
     1959v:shapes="Picture_x0020_25"><![endif]></span></p>
     1960
     1961<p class=MsoNormal>By zooming in and rotating the plot around a bit, you can identify
     1962the reflection with the cursor. It seems to be the <b style='mso-bidi-font-weight:
     1963normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1964minor-latin;mso-hansi-theme-font:minor-latin'>541</span></b> reflection; select
     1965the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1966mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Reflection
     1967List</span></b> and look for it (unfortunately the reflections are produced in
     1968a somewhat random order by the TOPAZ data acquisition system). It is very near
     1969the bottom of the list (#<b style='mso-bidi-font-weight:normal'><span
     1970style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1971mso-hansi-theme-font:minor-latin'>153</span></b>).</p>
     1972
     1973<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1974 id="Picture_x0020_26" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:585pt;
     1975 height:244.5pt;visibility:visible;mso-wrap-style:square'>
     1976 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image045.png"
     1977  o:title=""/>
     1978</v:shape><![endif]--><![if !vml]><img width=780 height=326
     1979src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image046.gif"
     1980v:shapes="Picture_x0020_26"><![endif]></span></p>
     1981
     1982<p class=MsoNormal>The <span class=SpellE>Fcsq</span> (F<sub>c</sub><sup>2</sup>)
     1983is very much larger than <span class=SpellE>Fosq</span> (F<sub>o</sub><sup>2</sup>)
     1984so that |&#916;F<sup>2</sup>|/<span class=GramE>&#963;(</span>F<sub>o</sub><sup>2</sup>)
     1985&gt; 80! It was obviously poorly measured (e.g. on the edge of the detector,
     1986etc.). We’d like to eliminate it, but perhaps we might be better setting a
     1987lower cutoff on |&#916;F<sup>2</sup>|/<span class=GramE>&#963;(</span>F<sub>o</sub><sup>2</sup>)
     1988to eliminate other similar problem reflections. Go to the <b style='mso-bidi-font-weight:
     1989normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1990minor-latin;mso-hansi-theme-font:minor-latin'>Controls</span></b> entry in the
     1991GSAS-II data tree</p>
     1992
     1993<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1994 id="Picture_x0020_27" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:391.5pt;
     1995 height:225.75pt;visibility:visible;mso-wrap-style:square'>
     1996 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image047.png"
     1997  o:title=""/>
     1998</v:shape><![endif]--><![if !vml]><img width=522 height=301
     1999src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image048.gif"
     2000v:shapes="Picture_x0020_27"><![endif]></span></p>
     2001
     2002<p class=MsoNormal>Change the value of <b style='mso-bidi-font-weight:normal'><span
     2003style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2004mso-hansi-theme-font:minor-latin'>Max <span class=SpellE>delt</span>-F/sig</span></b>
     2005to 20; that will certainly eliminate the bad 541 reflection &amp; perhaps a few
     2006others. Repeat <b style='mso-bidi-font-weight:normal'><span style='font-family:
     2007"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     2008minor-latin'>Calculate/Refine</span></b>; my residual dropped considerably (<span
     2009class=SpellE>Rw</span> ~4.5%) and the 3D plot shows no really bad reflections</p>
     2010
     2011<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     2012 id="Picture_x0020_28" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:363pt;
     2013 height:309.75pt;visibility:visible;mso-wrap-style:square'>
     2014 <v:imagedata src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image049.png"
     2015  o:title="" croptop="8876f" cropbottom="19515f" cropleft="39851f" cropright="10631f"/>
     2016</v:shape><![endif]--><![if !vml]><img width=484 height=413
     2017src="TOF%20single%20crystal%20refinement%20in%20GSAS_files/image050.jpg"
     2018v:shapes="Picture_x0020_28"><![endif]></span></p>
     2019
     2020<p class=MsoNormal>Looking the <span class=SpellE><b style='mso-bidi-font-weight:
     2021normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     2022minor-latin;mso-hansi-theme-font:minor-latin'>sapphire.lst</span></b></span><b
     2023style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2024mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> </span></b>file
     2025shows that HKLF #23 is now more in line with the other ones (RF = 4.35% &amp;
     2026scale = 67.41). To finish the refinement make the two sapphire atoms have
     2027anisotropic thermal parameters. Select <b style='mso-bidi-font-weight:normal'><span
     2028style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2029mso-hansi-theme-font:minor-latin'>Phases/sapphire</span></b> and the <b
     2030style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2031mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Atoms</span></b>
     2032tab; then double click <span class=GramE>the <b style='mso-bidi-font-weight:
     2033normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     2034minor-latin;mso-hansi-theme-font:minor-latin'>I</span></b></span><b
     2035style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2036mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>/A</span></b>
     2037column heading. A popup will appear; select <b style='mso-bidi-font-weight:
     2038normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     2039minor-latin;mso-hansi-theme-font:minor-latin'>Anisotropic</span></b> and press <b
     2040style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2041mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
     2042The atom <span class=SpellE>Uijs</span> will appear and <span class=SpellE>Uiso</span>
     2043will be greyed out. Then do <b style='mso-bidi-font-weight:normal'><span
     2044style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2045mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> again. My final
     2046residual was <span class=SpellE>Rw</span>=5.06%. </p>
     2047
     2048<p class=MsoNormal>This completes the tutorial. You can explore the other
     2049extinction models and try different cutoff values for <b style='mso-bidi-font-weight:
     2050normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     2051minor-latin;mso-hansi-theme-font:minor-latin'>Max <span class=SpellE>delt</span>-F/sig</span></b>.
     2052<b style='mso-bidi-font-weight:normal'><u>NB: this should never be set before
     2053the refinement is complete as it can reject large portions of the data
     2054prematurely.<o:p></o:p></u></b></p>
    14752055
    14762056</div>
  • Tutorials/TOF Single Crystal Refinement/TOF single crystal refinement in GSAS_files/filelist.xml

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