Ignore:
Timestamp:
Mar 20, 2015 8:49:59 AM (7 years ago)
Author:
vondreele
Message:

changes to various tutorials - mostly getting file references correct & removing hyperlinks

Location:
Tutorials/TOF Charge Flipping
Files:
2 edited

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  • Tutorials/TOF Charge Flipping/Charge Flipping with TOF single crystal data in GSASII.htm

    r1687 r1745  
    2525  <o:Author>vondreele</o:Author>
    2626  <o:LastAuthor>Von Dreele</o:LastAuthor>
    27   <o:Revision>7</o:Revision>
    28   <o:TotalTime>611</o:TotalTime>
     27  <o:Revision>8</o:Revision>
     28  <o:TotalTime>612</o:TotalTime>
    2929  <o:Created>2015-02-20T14:49:00Z</o:Created>
    30   <o:LastSaved>2015-02-24T22:39:00Z</o:LastSaved>
     30  <o:LastSaved>2015-03-20T13:41:00Z</o:LastSaved>
    3131  <o:Pages>1</o:Pages>
    32   <o:Words>2192</o:Words>
    33   <o:Characters>12499</o:Characters>
     32  <o:Words>2186</o:Words>
     33  <o:Characters>12463</o:Characters>
    3434  <o:Company>Argonne National Laboratory</o:Company>
    35   <o:Lines>104</o:Lines>
     35  <o:Lines>103</o:Lines>
    3636  <o:Paragraphs>29</o:Paragraphs>
    37   <o:CharactersWithSpaces>14662</o:CharactersWithSpaces>
     37  <o:CharactersWithSpaces>14620</o:CharactersWithSpaces>
    3838  <o:Version>15.00</o:Version>
    3939 </o:DocumentProperties>
     
    4848<!--[if gte mso 9]><xml>
    4949 <w:WordDocument>
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    653         mso-font-charset:0;
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    11681169<p class=MsoNormal>In this exercise you will use GSAS-II to solve the structure
    11691170of <span class=SpellE>rubrene</span> (C<sub>42</sub>H<sub>28</sub>) from single
    1170 crystal neutron data via charge flipping. <span class=SpellE>Rubrene</span> is of
    1171 interest as a molecular semiconductor. It crystallizes in the space group <span
     1171crystal neutron data via charge flipping. <span class=SpellE>Rubrene</span> is
     1172of interest as a molecular semiconductor. It crystallizes in the space group <span
    11721173class=SpellE>Cmca</span> with the lattice parameters a=26.798Å, b=7.1618Å,
    11731174c=14.1942Å, Z=4. Thus, the molecule is sited on a special position with 2/m
    1174 symmetry. If you have not done so already, <a href="Starting%20GSAS.htm">start
    1175 GSAS-II</a>.</p>
     1175symmetry. If you have not done so already, start GSAS-II.</p>
    11761176
    11771177<h2>Step 1. Set the phase information</h2>
     
    12121212 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image001.png"
    12131213  o:title=""/>
    1214 </v:shape><![endif]--><![if !vml]><img border=0 width=400 height=250
     1214</v:shape><![endif]--><![if !vml]><img width=400 height=250
    12151215src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image002.gif"
    12161216v:shapes="_x0000_i1059"><![endif]></span></p>
     
    12231223 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image003.png"
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     1225</v:shape><![endif]--><![if !vml]><img width=854 height=500
    12261226src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image004.gif"
    12271227v:shapes="Picture_x0020_2"><![endif]></span></p>
     
    12391239 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image005.png"
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    1241 </v:shape><![endif]--><![if !vml]><img border=0 width=334 height=237
     1241</v:shape><![endif]--><![if !vml]><img width=334 height=237
    12421242src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image006.gif"
    12431243v:shapes="Picture_x0020_3"><![endif]></span></p>
     
    12731273minor-latin;mso-hansi-theme-font:minor-latin'>Import/Structure Factor/from
    12741274Neutron TOF HKL F2 file</span></b>; a directory dialog box will appear. Go to
    1275 the directory <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
    1276 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1277 mso-hansi-theme-font:minor-latin'>GSASIIexercises</span></b></span><b
    1278 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1279 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>/TOF Charge
    1280 Flipping</span></b> and select the file <span class=SpellE><b style='mso-bidi-font-weight:
    1281 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1282 minor-latin;mso-hansi-theme-font:minor-latin'>ruberene_orthoC.hkl</span></b></span>
    1283 (double click the name or press the <b style='mso-bidi-font-weight:normal'><span
    1284 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1285 mso-hansi-theme-font:minor-latin'>Open</span></b> button after selecting it). A
    1286 popup box will appear.</p>
     1275the directory <b style='mso-bidi-font-weight:normal'><span style='font-family:
     1276"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1277minor-latin'>exercises/TOF Charge Flipping</span></b> and select the file <span
     1278class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
     1279"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1280minor-latin'>ruberene_orthoC.hkl</span></b></span> (double click the name or
     1281press the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1282mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Open</span></b>
     1283button after selecting it). A popup box will appear.</p>
    12871284
    12881285<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    12911288 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image007.png"
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    1293 </v:shape><![endif]--><![if !vml]><img border=0 width=477 height=354
     1290</v:shape><![endif]--><![if !vml]><img width=477 height=354
    12941291src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image008.gif"
    12951292v:shapes="Picture_x0020_4"><![endif]></span></p>
     
    13081305 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image009.png"
    13091306  o:title=""/>
    1310 </v:shape><![endif]--><![if !vml]><img border=0 width=320 height=310
     1307</v:shape><![endif]--><![if !vml]><img width=320 height=310
    13111308src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image010.gif"
    13121309v:shapes="Picture_x0020_5"><![endif]></span></p>
     
    13261323 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image011.png"
    13271324  o:title=""/>
    1328 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
     1325</v:shape><![endif]--><![if !vml]><img width=700 height=600
    13291326src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image012.gif"
    13301327v:shapes="Picture_x0020_6"><![endif]></span></p>
     
    13451342  o:title="" croptop="13337f" cropbottom="14997f" cropleft="41056f"
    13461343  cropright="9449f"/>
    1347 </v:shape><![endif]--><![if !vml]><img border=0 width=595 height=509
     1344</v:shape><![endif]--><![if !vml]><img width=595 height=509
    13481345src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image014.jpg"
    13491346v:shapes="Picture_x0020_1"><![endif]></span></p>
     
    13771374 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image015.png"
    13781375  o:title=""/>
    1379 </v:shape><![endif]--><![if !vml]><img border=0 width=652 height=500
     1376</v:shape><![endif]--><![if !vml]><img width=652 height=500
    13801377src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image016.gif"
    13811378v:shapes="Picture_x0020_8"><![endif]></span></p>
     
    14201417
    14211418<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1422  id="_x0000_i1051" type="#_x0000_t75" style='width:516.75pt;height:375pt;
    1423  visibility:visible;mso-wrap-style:square'>
     1419 id="Picture_x0020_9" o:spid="_x0000_i1051" type="#_x0000_t75" style='width:516.75pt;
     1420 height:375pt;visibility:visible;mso-wrap-style:square'>
    14241421 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image017.png"
    14251422  o:title=""/>
    1426 </v:shape><![endif]--><![if !vml]><img border=0 width=689 height=500
     1423</v:shape><![endif]--><![if !vml]><img width=689 height=500
    14271424src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image018.gif"
    1428 v:shapes="_x0000_i1051"><![endif]></span></p>
     1425v:shapes="Picture_x0020_9"><![endif]></span></p>
    14291426
    14301427<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    14471444
    14481445<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1449  id="_x0000_i1050" type="#_x0000_t75" style='width:375pt;height:225pt;
    1450  visibility:visible;mso-wrap-style:square'>
     1446 id="Picture_x0020_10" o:spid="_x0000_i1050" type="#_x0000_t75" style='width:375pt;
     1447 height:225pt;visibility:visible;mso-wrap-style:square'>
    14511448 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image019.png"
    14521449  o:title=""/>
    1453 </v:shape><![endif]--><![if !vml]><img border=0 width=500 height=300
     1450</v:shape><![endif]--><![if !vml]><img width=500 height=300
    14541451src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image020.gif"
    1455 v:shapes="_x0000_i1050"><![endif]></span></p>
     1452v:shapes="Picture_x0020_10"><![endif]></span></p>
    14561453
    14571454<p class=MsoNormal>If you scroll down the Map peak list you will find some with
     
    14651462 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image021.png"
    14661463  o:title="" croptop="9820f" cropbottom="18705f" cropleft="43453f" cropright="6999f"/>
    1467 </v:shape><![endif]--><![if !vml]><img border=0 width=576 height=487
     1464</v:shape><![endif]--><![if !vml]><img width=576 height=487
    14681465src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image022.jpg"
    14691466v:shapes="Picture_x0020_11"><![endif]></span></p>
     
    14761473could simply repeat the charge flipping run and hope it puts the molecule in
    14771474the right place. GSAS-II uses an algorithm based on how structure factor phases
    1478 are related for a given space group to reposition the solution; it sometimes fails
    1479 if the phase set isn’t perfect. Or you can “roll” the map right/left/up/down (<b
    1480 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1481 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>R/L/U/D</span></b>
    1482 keys) to put the solution where you want. In this case a few steps with the
    1483 L-key sufficed to put the molecule on a 2/m site (i.e. the center of the cell
    1484 indicated the multicolored cross on the central C-C bond).</p>
     1475are related for a given space group to reposition the solution; it sometimes
     1476fails if the phase set isn’t perfect. Or you can “roll” the map
     1477right/left/up/down (<b style='mso-bidi-font-weight:normal'><span
     1478style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1479mso-hansi-theme-font:minor-latin'>R/L/U/D</span></b> keys) to put the solution
     1480where you want. In this case a few steps with the L-key sufficed to put the
     1481molecule on a 2/m site (i.e. the center of the cell indicated the multicolored
     1482cross on the central C-C bond).</p>
    14851483
    14861484<p class=MsoNormal><!--[if gte vml 1]><v:shapetype id="_x0000_t32" coordsize="21600,21600"
     
    15861584 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image025.png"
    15871585  o:title="" croptop="2195f" cropbottom="27669f" cropleft="17163f" cropright="33289f"/>
    1588 </v:shape><![endif]--><![if !vml]><img border=0 width=573 height=466
     1586</v:shape><![endif]--><![if !vml]><img width=573 height=466
    15891587src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image026.jpg"
    15901588v:shapes="Picture_x0020_12"><![endif]></span></p>
     
    15941592
    15951593<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1596  id="_x0000_i1047" type="#_x0000_t75" style='width:375pt;height:225pt;
    1597  visibility:visible;mso-wrap-style:square'>
     1594 id="Picture_x0020_13" o:spid="_x0000_i1047" type="#_x0000_t75" style='width:375pt;
     1595 height:225pt;visibility:visible;mso-wrap-style:square'>
    15981596 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image027.png"
    15991597  o:title=""/>
    1600 </v:shape><![endif]--><![if !vml]><img border=0 width=500 height=300
     1598</v:shape><![endif]--><![if !vml]><img width=500 height=300
    16011599src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image028.gif"
    1602 v:shapes="_x0000_i1047"><![endif]></span></p>
     1600v:shapes="Picture_x0020_13"><![endif]></span></p>
    16031601
    16041602<p class=MsoNormal>By carefully looking at the map, you can see the 4-ring <span
    16051603class=SpellE>tetracene</span> (<span class=SpellE>naphthacene</span>) core of
    1606 the molecule with four phenyl groups attached to both sides on the center two rings.
    1607 The unique part consists of 1/4<sup>th</sup> of this group (i.e. half of one
    1608 side of the <span class=SpellE>tetracene</span> and one phenyl); one C-atom
     1604the molecule with four phenyl groups attached to both sides on the center two
     1605rings. The unique part consists of 1/4<sup>th</sup> of this group (i.e. half of
     1606one side of the <span class=SpellE>tetracene</span> and one phenyl); one C-atom
    16091607sits on a 2-fold and the rest are in general positions. The molecule extends
    16101608into the neighboring unit cell so you don’t see the whole thing as one group
     
    16341632normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    16351633minor-latin;mso-hansi-theme-font:minor-latin'>dcent</span></b></span> (distance
    1636 from center of the cell) beforehand. After a pause while it sorts out the
    1637 unique peaks, it will highlight them in the table and display the picked ones
    1638 in green on the plot. In this case they will probably be scattered about the
    1639 unit cell and not make a continuous molecule, but they are largely clustered
    1640 around the unit cell center. My plot looked like this when I was done.</p>
     1634from center of the cell) beforehand. After a pause while it sorts out the unique
     1635peaks, it will highlight them in the table and display the picked ones in green
     1636on the plot. In this case they will probably be scattered about the unit cell
     1637and not make a continuous molecule, but they are largely clustered around the
     1638unit cell center. My plot looked like this when I was done.</p>
    16411639
    16421640<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    16461644  o:title="" croptop="10059f" cropbottom="18635f" cropleft="36901f"
    16471645  cropright="13675f"/>
    1648 </v:shape><![endif]--><![if !vml]><img border=0 width=573 height=486
     1646</v:shape><![endif]--><![if !vml]><img width=573 height=486
    16491647src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image030.jpg"
    16501648v:shapes="Picture_x0020_27"><![endif]></span></p>
     
    16541652
    16551653<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1656  id="_x0000_i1045" type="#_x0000_t75" style='width:375pt;height:435.75pt;
    1657  visibility:visible;mso-wrap-style:square'>
     1654 id="Picture_x0020_15" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:375pt;
     1655 height:435.75pt;visibility:visible;mso-wrap-style:square'>
    16581656 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image031.png"
    16591657  o:title=""/>
    1660 </v:shape><![endif]--><![if !vml]><img border=0 width=500 height=581
     1658</v:shape><![endif]--><![if !vml]><img width=500 height=581
    16611659src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image032.gif"
    1662 v:shapes="_x0000_i1045"><![endif]></span></p>
     1660v:shapes="Picture_x0020_15"><![endif]></span></p>
    16631661
    16641662<p class=MsoNormal>To add them to the Atom list do <b style='mso-bidi-font-weight:
     
    16681666
    16691667<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1670  id="_x0000_i1044" type="#_x0000_t75" style='width:6in;height:369pt;
    1671  visibility:visible;mso-wrap-style:square'>
     1668 id="Picture_x0020_16" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:6in;
     1669 height:369pt;visibility:visible;mso-wrap-style:square'>
    16721670 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image033.png"
    16731671  o:title="" croptop="10579f" cropbottom="17404f" cropleft="37800f"
    16741672  cropright="12584f"/>
    1675 </v:shape><![endif]--><![if !vml]><img border=0 width=576 height=492
     1673</v:shape><![endif]--><![if !vml]><img width=576 height=492
    16761674src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image034.jpg"
    1677 v:shapes="_x0000_i1044"><![endif]></span></p>
     1675v:shapes="Picture_x0020_16"><![endif]></span></p>
    16781676
    16791677<p class=MsoNormal>The atom list will give the magnitudes as ‘M’ names; I found
     
    16811679
    16821680<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1683  id="_x0000_i1043" type="#_x0000_t75" style='width:525pt;height:351.75pt;
    1684  visibility:visible;mso-wrap-style:square'>
     1681 id="Picture_x0020_17" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:525pt;
     1682 height:351.75pt;visibility:visible;mso-wrap-style:square'>
    16851683 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image035.png"
    16861684  o:title=""/>
    1687 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=469
     1685</v:shape><![endif]--><![if !vml]><img width=700 height=469
    16881686src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image036.gif"
    1689 v:shapes="_x0000_i1043"><![endif]></span></p>
     1687v:shapes="Picture_x0020_17"><![endif]></span></p>
    16901688
    16911689<h2>Step 6. Atom identification</h2>
     
    17171715
    17181716<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1719  id="_x0000_i1042" type="#_x0000_t75" style='width:525pt;height:225pt;
    1720  visibility:visible;mso-wrap-style:square'>
     1717 id="Picture_x0020_18" o:spid="_x0000_i1042" type="#_x0000_t75" style='width:525pt;
     1718 height:225pt;visibility:visible;mso-wrap-style:square'>
    17211719 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image037.png"
    17221720  o:title=""/>
    1723 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=300
     1721</v:shape><![endif]--><![if !vml]><img width=700 height=300
    17241722src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image038.gif"
    1725 v:shapes="_x0000_i1042"><![endif]></span></p>
     1723v:shapes="Picture_x0020_18"><![endif]></span></p>
    17261724
    17271725<p class=MsoNormal>Do the same with the remaining negative M atoms – make them
     
    17391737
    17401738<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1741  id="_x0000_i1041" type="#_x0000_t75" style='width:6in;height:366pt;
    1742  visibility:visible;mso-wrap-style:square'>
     1739 id="Picture_x0020_19" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:6in;
     1740 height:366pt;visibility:visible;mso-wrap-style:square'>
    17431741 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image039.png"
    17441742  o:title="" croptop="11018f" cropbottom="17360f" cropleft="37831f"
    17451743  cropright="12587f"/>
    1746 </v:shape><![endif]--><![if !vml]><img border=0 width=576 height=488
     1744</v:shape><![endif]--><![if !vml]><img width=576 height=488
    17471745src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image040.jpg"
    1748 v:shapes="_x0000_i1041"><![endif]></span></p>
     1746v:shapes="Picture_x0020_19"><![endif]></span></p>
    17491747
    17501748<p class=MsoNormal>The molecule building has scrambled the order of the atoms;
     
    17521750
    17531751<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1754  id="_x0000_i1040" type="#_x0000_t75" style='width:525pt;height:351.75pt;
    1755  visibility:visible;mso-wrap-style:square'>
     1752 id="Picture_x0020_20" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:525pt;
     1753 height:351.75pt;visibility:visible;mso-wrap-style:square'>
    17561754 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image041.png"
    17571755  o:title=""/>
    1758 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=469
     1756</v:shape><![endif]--><![if !vml]><img width=700 height=469
    17591757src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image042.gif"
    1760 v:shapes="_x0000_i1040"><![endif]></span></p>
    1761 
    1762 <p class=MsoNormal>You can reorder them to put the H-atoms at the end of the list.
    1763 Then select all of them and then do <span style='font-family:"Calibri",sans-serif;
     1758v:shapes="Picture_x0020_20"><![endif]></span></p>
     1759
     1760<p class=MsoNormal>You can reorder them to put the H-atoms at the end of the
     1761list. Then select all of them and then do <span style='font-family:"Calibri",sans-serif;
    17641762mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Modify
    17651763atom parameters</span>. Pick <b style='mso-bidi-font-weight:normal'><span
     
    17881786class=SpellE>obs</span>/sig</span></b>. This makes the least squares refine on <span
    17891787class=SpellE><span class=GramE>F<sub>o</sub></span></span> with 3&#963; cutoff
    1790 on <span class=SpellE>F<sub>o</sub></span>. From the main GSAS-II data tree menu
    1791 do <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1788on <span class=SpellE>F<sub>o</sub></span>. From the main GSAS-II data tree
     1789menu do <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    17921790mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>;
    17931791this will do the 1<sup>st</sup> least squares refinement varying only the data
     
    18101808parameters</span></b> and press <b style='mso-bidi-font-weight:normal'><span
    18111809style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1812 mso-hansi-theme-font:minor-latin'>OK</span></b>. The atom table will show refine
    1813 flags for each atom.</p>
    1814 
    1815 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1816  id="_x0000_i1039" type="#_x0000_t75" style='width:525pt;height:225pt;
    1817  visibility:visible;mso-wrap-style:square'>
     1810mso-hansi-theme-font:minor-latin'>OK</span></b>. The atom table will show
     1811refine flags for each atom.</p>
     1812
     1813<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1814 id="Picture_x0020_21" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:525pt;
     1815 height:225pt;visibility:visible;mso-wrap-style:square'>
    18181816 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image043.png"
    18191817  o:title=""/>
    1820 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=300
     1818</v:shape><![endif]--><![if !vml]><img width=700 height=300
    18211819src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image044.gif"
    1822 v:shapes="_x0000_i1039"><![endif]></span></p>
     1820v:shapes="Picture_x0020_21"><![endif]></span></p>
    18231821
    18241822<p class=MsoNormal>Then repeat the <b style='mso-bidi-font-weight:normal'><span
     
    18461844<p class=MsoNormal>Since this is TOF neutron single crystal diffraction, a
    18471845relatively large crystal was used and the neutron wavelength covered a fairly
    1848 wide range of values. Hence, it is likely that the strong reflection intensities
    1849 suffered from some level of extinction. To find these parameters select the <b
    1850 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1851 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Data</span></b>
    1852 tab in the Phase Data window; all that will show is a list of a data set names
    1853 with a <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1854 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Show</span></b>
    1855 box for each. To see what is there select the <b style='mso-bidi-font-weight:
    1856 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1857 minor-latin;mso-hansi-theme-font:minor-latin'>Show</span></b> box; alternatively
    1858 to see all of them do <b style='mso-bidi-font-weight:normal'><span
    1859 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1860 mso-hansi-theme-font:minor-latin'>Edit/Show/Hide</span></b> all the window will
    1861 look something like</p>
     1846wide range of values. Hence, it is likely that the strong reflection
     1847intensities suffered from some level of extinction. To find these parameters
     1848select the <b style='mso-bidi-font-weight:normal'><span style='font-family:
     1849"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1850minor-latin'>Data</span></b> tab in the Phase Data window; all that will show
     1851is a list of a data set names with a <b style='mso-bidi-font-weight:normal'><span
     1852style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1853mso-hansi-theme-font:minor-latin'>Show</span></b> box for each. To see what is
     1854there select the <b style='mso-bidi-font-weight:normal'><span style='font-family:
     1855"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1856minor-latin'>Show</span></b> box; alternatively to see all of them do <b
     1857style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1858mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Show/Hide</span></b>
     1859all the window will look something like</p>
    18621860
    18631861<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    18661864 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image045.png"
    18671865  o:title=""/>
    1868 </v:shape><![endif]--><![if !vml]><img border=0 width=426 height=504
     1866</v:shape><![endif]--><![if !vml]><img width=426 height=504
    18691867src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image046.gif"
    18701868v:shapes="Picture_x0020_22"><![endif]></span></p>
     
    18781876mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Extinction
    18791877type</span></b> (later you can try the other models) for the 1<sup>st</sup>
    1880 data set. The window will be repainted with a new line in the data display. Select
    1881 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1882 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Ep</span></b>
    1883 check box so it will be refined. To set all the rest press the <b
    1884 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1878data set. The window will be repainted with a new line in the data display.
     1879Select the <b style='mso-bidi-font-weight:normal'><span style='font-family:
     1880"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1881minor-latin'>Ep</span></b> check box so it will be refined. To set all the rest
     1882press the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    18851883mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Copy flags?</span></b>
    18861884<span class=GramE>button</span> for that data set (not one of the others!). A
     
    19051903 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image047.png"
    19061904  o:title=""/>
    1907 </v:shape><![endif]--><![if !vml]><img border=0 width=300 height=470
     1905</v:shape><![endif]--><![if !vml]><img width=300 height=470
    19081906src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image048.gif"
    19091907v:shapes="Picture_x0020_23"><![endif]></span></p>
     
    19111909<p class=MsoNormal>Select the <b style='mso-bidi-font-weight:normal'><span
    19121910style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1913 mso-hansi-theme-font:minor-latin'>Histogram/Phase</span></b> constraints tab; the
    1914 window is still blank but that tab is now highlighted. Next do <b
     1911mso-hansi-theme-font:minor-latin'>Histogram/Phase</span></b> constraints tab;
     1912the window is still blank but that tab is now highlighted. Next do <b
    19151913style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    19161914mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Add
     
    19231921 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image049.png"
    19241922  o:title=""/>
    1925 </v:shape><![endif]--><![if !vml]><img border=0 width=625 height=400
     1923</v:shape><![endif]--><![if !vml]><img width=625 height=400
    19261924src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image050.gif"
    19271925v:shapes="Picture_x0020_24"><![endif]></span></p>
     
    19491947 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image051.png"
    19501948  o:title=""/>
    1951 </v:shape><![endif]--><![if !vml]><img border=0 width=642 height=470
     1949</v:shape><![endif]--><![if !vml]><img width=642 height=470
    19521950src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image052.gif"
    19531951v:shapes="Picture_x0020_25"><![endif]></span></p>
     
    19771975 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image053.png"
    19781976  o:title=""/>
    1979 </v:shape><![endif]--><![if !vml]><img border=0 width=346 height=336
     1977</v:shape><![endif]--><![if !vml]><img width=346 height=336
    19801978src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image054.gif"
    19811979v:shapes="Picture_x0020_26"><![endif]></span></p>
     
    19951993  o:title="" croptop="11745f" cropbottom="16560f" cropleft="43690f"
    19961994  cropright="6723f"/>
    1997 </v:shape><![endif]--><![if !vml]><img border=0 width=621 height=527
     1995</v:shape><![endif]--><![if !vml]><img width=621 height=527
    19981996src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image056.jpg"
    19991997v:shapes="Picture_x0020_28"><![endif]></span></p>
     
    20112009style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    20122010mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Show unit
    2013 cell?</span></b> <span class=GramE>box</span>. Finally, you can remove the
    2014 charge flipping map; go to <b style='mso-bidi-font-weight:normal'><span
     2011cell?</span></b> <span class=GramE>box</span>. Finally, you can remove the charge
     2012flipping map; go to <b style='mso-bidi-font-weight:normal'><span
    20152013style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    20162014mso-hansi-theme-font:minor-latin'>General</span></b> and do <b
     
    20252023 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image057.png"
    20262024  o:title="" croptop="8339f" cropbottom="19928f" cropleft="44139f" cropright="6324f"/>
    2027 </v:shape><![endif]--><![if !vml]><img border=0 width=573 height=488
     2025</v:shape><![endif]--><![if !vml]><img width=573 height=488
    20282026src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image058.jpg"
    20292027v:shapes="Picture_x0020_29"><![endif]></span></p>
     
    20322030we’d like to see the whole thing. First go to the <b style='mso-bidi-font-weight:
    20332031normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    2034 minor-latin;mso-hansi-theme-font:minor-latin'>Atoms</span></b> tab and select the
    2035 C-atom that is in a special position 2(x). The do <b style='mso-bidi-font-weight:
     2032minor-latin;mso-hansi-theme-font:minor-latin'>Atoms</span></b> tab and select
     2033the C-atom that is in a special position 2(x). The do <b style='mso-bidi-font-weight:
    20362034normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    20372035minor-latin;mso-hansi-theme-font:minor-latin'>Compute/Show Distances &amp;
     
    20462044 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image059.png"
    20472045  o:title=""/>
    2048 </v:shape><![endif]--><![if !vml]><img border=0 width=813 height=371
     2046</v:shape><![endif]--><![if !vml]><img width=813 height=371
    20492047src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image060.gif"
    20502048v:shapes="Picture_x0020_30"><![endif]></span></p>
     
    20632061 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image061.png"
    20642062  o:title=""/>
    2065 </v:shape><![endif]--><![if !vml]><img border=0 width=600 height=300
     2063</v:shape><![endif]--><![if !vml]><img width=600 height=300
    20662064src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image062.gif"
    20672065v:shapes="Picture_x0020_31"><![endif]></span></p>
     
    20772075 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image063.png"
    20782076  o:title=""/>
    2079 </v:shape><![endif]--><![if !vml]><img border=0 width=239 height=329
     2077</v:shape><![endif]--><![if !vml]><img width=239 height=329
    20802078src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image064.gif"
    20812079v:shapes="Picture_x0020_32"><![endif]></span></p>
     
    20932091 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image065.png"
    20942092  o:title=""/>
    2095 </v:shape><![endif]--><![if !vml]><img border=0 width=239 height=329
     2093</v:shape><![endif]--><![if !vml]><img width=239 height=329
    20962094src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image066.gif"
    20972095v:shapes="Picture_x0020_33"><![endif]></span></p>
     
    21052103  o:title="" croptop="11786f" cropbottom="16031f" cropleft="46740f"
    21062104  cropright="3791f"/>
    2107 </v:shape><![endif]--><![if !vml]><img border=0 width=573 height=496
     2105</v:shape><![endif]--><![if !vml]><img width=573 height=496
    21082106src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image068.jpg"
    21092107v:shapes="Picture_x0020_34"><![endif]></span></p>
     
    21152113nonidentity entry in the bond distance table ‘<b style='mso-bidi-font-weight:
    21162114normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    2117 minor-latin;mso-hansi-theme-font:minor-latin'>[0 1 1] + (-2)</span></b>’. The ‘-2’
    2118 indicates both the inversion and the 2<sup>nd</sup> operator need to be applied;
    2119 check both and increment the 2<sup>nd</sup> and 3<sup>rd</sup> unit cell
    2120 entries. </p>
     2115minor-latin;mso-hansi-theme-font:minor-latin'>[0 1 1] + (-2)</span></b>’. The
     2116‘-2’ indicates both the inversion and the 2<sup>nd</sup> operator need to be
     2117applied; check both and increment the 2<sup>nd</sup> and 3<sup>rd</sup> unit
     2118cell entries. </p>
    21212119
    21222120<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    21252123 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image069.png"
    21262124  o:title=""/>
    2127 </v:shape><![endif]--><![if !vml]><img border=0 width=239 height=329
     2125</v:shape><![endif]--><![if !vml]><img width=239 height=329
    21282126src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image070.gif"
    21292127v:shapes="Picture_x0020_36"><![endif]></span></p>
     
    21392137  o:title="" croptop="10221f" cropbottom="18166f" cropleft="42114f"
    21402138  cropright="8322f"/>
    2141 </v:shape><![endif]--><![if !vml]><img border=0 width=573 height=486
     2139</v:shape><![endif]--><![if !vml]><img width=573 height=486
    21422140src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image072.jpg"
    21432141v:shapes="Picture_x0020_35"><![endif]></span><span
  • Tutorials/TOF Charge Flipping/Charge Flipping with TOF single crystal data in GSASII_files/props079.xml

    r1670 r1745  
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