Changeset 3071


Ignore:
Timestamp:
Sep 13, 2017 10:13:54 AM (4 years ago)
Author:
vondreele
Message:

update to 2 frame

Location:
Tutorials/TOF Charge Flipping
Files:
48 added
73 deleted
20 edited

Legend:

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

    r2390 r3071  
    2424 <o:DocumentProperties>
    2525  <o:Author>vondreele</o:Author>
    26   <o:LastAuthor>Von Dreele</o:LastAuthor>
    27   <o:Revision>9</o:Revision>
    28   <o:TotalTime>613</o:TotalTime>
     26  <o:LastAuthor>vondreele</o:LastAuthor>
     27  <o:Revision>11</o:Revision>
     28  <o:TotalTime>729</o:TotalTime>
    2929  <o:Created>2015-02-20T14:49:00Z</o:Created>
    30   <o:LastSaved>2016-07-28T18:56:00Z</o:LastSaved>
    31   <o:Pages>1</o:Pages>
    32   <o:Words>2185</o:Words>
    33   <o:Characters>12459</o:Characters>
     30  <o:LastSaved>2017-09-13T15:11:00Z</o:LastSaved>
     31  <o:Pages>25</o:Pages>
     32  <o:Words>2147</o:Words>
     33  <o:Characters>12238</o:Characters>
    3434  <o:Company>Argonne National Laboratory</o:Company>
    35   <o:Lines>103</o:Lines>
    36   <o:Paragraphs>29</o:Paragraphs>
    37   <o:CharactersWithSpaces>14615</o:CharactersWithSpaces>
     35  <o:Lines>101</o:Lines>
     36  <o:Paragraphs>28</o:Paragraphs>
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    3838  <o:Version>16.00</o:Version>
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    4040</xml><![endif]-->
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     43target="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/props071.xml">
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    1118         mso-bidi-font-family:Calibri;}
     1119        mso-fareast-theme-font:minor-fareast;}
    11191120span.SpellE
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    1169    <o:r id="V:Rule2" type="connector" idref="#Straight_x0020_Arrow_x0020_Connector_x0020_38"/>
    1170   </o:rules>
    11711168 </o:shapelayout></xml><![endif]-->
    11721169</head>
     
    11911188<p class=MsoNormal>To begin this tutorial, do <b style='mso-bidi-font-weight:
    11921189normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1193 minor-latin;mso-hansi-theme-font:minor-latin'>Data/Add phase</span></b> in the
    1194 main GSAS-II data tree menu. A popup window will appear asking for a phase
     1190minor-latin;mso-hansi-theme-font:minor-latin'>Data/Add new phase</span></b> in
     1191the main GSAS-II data tree menu. A popup window will appear asking for a phase
    11951192name; I used <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
    11961193style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1197 mso-hansi-theme-font:minor-latin'>rubrene</span></b></span>. Then select <span
    1198 class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
    1199 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1200 minor-latin'>rubrene</span></b></span> from the data tree</p>
     1194mso-hansi-theme-font:minor-latin'>rubrene</span></b></span>. The General tab
     1195for this phase will be shown</p>
    12011196
    12021197<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
     
    12201215 <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
    12211216 <o:lock v:ext="edit" aspectratio="t"/>
    1222 </v:shapetype><v:shape id="_x0000_i1059" type="#_x0000_t75" style='width:300pt;
    1223  height:187.5pt;visibility:visible;mso-wrap-style:square'>
    1224  <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image001.png"
    1225   o:title=""/>
    1226 </v:shape><![endif]--><![if !vml]><img width=400 height=250
    1227 src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image073.gif"
    1228 v:shapes="_x0000_i1059"><![endif]></span></p>
    1229 
    1230 <p class=MsoNormal>The General tab for this phase will be shown</p>
    1231 
    1232 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1233  id="Picture_x0020_2" o:spid="_x0000_i1058" type="#_x0000_t75" style='width:640.5pt;
    1234  height:375pt;visibility:visible;mso-wrap-style:square'>
    1235  <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image003.png"
    1236   o:title=""/>
    1237 </v:shape><![endif]--><![if !vml]><img width=854 height=500
    1238 src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image074.gif"
    1239 v:shapes="Picture_x0020_2"><![endif]></span></p>
     1217</v:shapetype><v:shape id="Picture_x0020_1" o:spid="_x0000_i1056" type="#_x0000_t75"
     1218 style='width:468pt;height:210pt;visibility:visible;mso-wrap-style:square'>
     1219 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image002.png"
     1220  o:title=""/>
     1221</v:shape><![endif]--><![if !vml]><img width=624 height=280
     1222src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image001.gif"
     1223v:shapes="Picture_x0020_1"><![endif]></span></p>
    12401224
    12411225<p class=MsoNormal>Enter the space group (<b style='mso-bidi-font-weight:normal'><span
     
    12471231
    12481232<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1249  id="Picture_x0020_3" o:spid="_x0000_i1057" type="#_x0000_t75" style='width:250.5pt;
    1250  height:177.75pt;visibility:visible;mso-wrap-style:square'>
    1251  <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image005.png"
    1252   o:title=""/>
    1253 </v:shape><![endif]--><![if !vml]><img width=334 height=237
    1254 src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image075.gif"
    1255 v:shapes="Picture_x0020_3"><![endif]></span></p>
     1233 id="_x0000_i1055" type="#_x0000_t75" style='width:275.25pt;height:207pt;
     1234 visibility:visible;mso-wrap-style:square'>
     1235 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image006.png"
     1236  o:title=""/>
     1237</v:shape><![endif]--><![if !vml]><img width=367 height=276
     1238src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image003.gif"
     1239v:shapes="_x0000_i1055"><![endif]></span></p>
    12561240
    12571241<p class=MsoNormal>Press <b style='mso-bidi-font-weight:normal'><span
     
    12841268normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    12851269minor-latin;mso-hansi-theme-font:minor-latin'>Import/Structure Factor/from
    1286 Neutron TOF HKL F2 file</span></b>; a directory dialog box will appear. Go to
    1287 the directory <b style='mso-bidi-font-weight:normal'><span style='font-family:
    1288 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1289 minor-latin'>TOF Charge Flipping/data</span></b> and select the file <span
    1290 class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
    1291 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1292 minor-latin'>ruberene_orthoC.hkl</span></b></span> (double click the name or
    1293 press the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1294 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Open</span></b>
    1295 button after selecting it). A popup box will appear.</p>
    1296 
    1297 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1298  id="Picture_x0020_4" o:spid="_x0000_i1056" type="#_x0000_t75" style='width:357.75pt;
    1299  height:265.5pt;visibility:visible;mso-wrap-style:square'>
    1300  <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image007.png"
    1301   o:title=""/>
    1302 </v:shape><![endif]--><![if !vml]><img width=477 height=354
    1303 src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image076.gif"
    1304 v:shapes="Picture_x0020_4"><![endif]></span></p>
    1305 
    1306 <p class=MsoNormal>Press <b style='mso-bidi-font-weight:normal'><span
    1307 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1308 mso-hansi-theme-font:minor-latin'>Yes</span></b>; another popup will appear
    1309 offering you the chance to change the name. Press <b style='mso-bidi-font-weight:
     1270Neutron TOF HKL F<sup>2</sup> file</span></b>; a directory dialog box will
     1271appear. Go to the directory <b style='mso-bidi-font-weight:normal'><span
     1272style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1273mso-hansi-theme-font:minor-latin'>TOF Charge Flipping/data</span></b> and
     1274select the file <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
     1275style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1276mso-hansi-theme-font:minor-latin'>ruberene_orthoC.hkl</span></b></span> (double
     1277click the name or press the <b style='mso-bidi-font-weight:normal'><span
     1278style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1279mso-hansi-theme-font:minor-latin'>Open</span></b> button after selecting it). A
     1280popup box will appear.</p>
     1281
     1282<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1283 id="_x0000_i1054" type="#_x0000_t75" style='width:307.5pt;height:147.75pt;
     1284 visibility:visible;mso-wrap-style:square'>
     1285 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image010.png"
     1286  o:title=""/>
     1287</v:shape><![endif]--><![if !vml]><img width=410 height=197
     1288src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image005.gif"
     1289v:shapes="_x0000_i1054"><![endif]></span></p>
     1290
     1291<p class=MsoNormal>Press <span class=GramE><b style='mso-bidi-font-weight:normal'><span
     1292style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1293mso-hansi-theme-font:minor-latin'>Yes</span></b></span>; another popup will
     1294appear offering you the chance to change the name. Press <b style='mso-bidi-font-weight:
    13101295normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    13111296minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>, a new popup
     
    13131298
    13141299<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1315  id="Picture_x0020_5" o:spid="_x0000_i1055" type="#_x0000_t75" style='width:240pt;
    1316  height:232.5pt;visibility:visible;mso-wrap-style:square'>
    1317  <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image009.png"
    1318   o:title=""/>
    1319 </v:shape><![endif]--><![if !vml]><img width=320 height=310
    1320 src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image077.gif"
    1321 v:shapes="Picture_x0020_5"><![endif]></span></p>
     1300 id="_x0000_i1053" type="#_x0000_t75" style='width:233.25pt;height:228.75pt;
     1301 visibility:visible;mso-wrap-style:square'>
     1302 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image014.png"
     1303  o:title=""/>
     1304</v:shape><![endif]--><![if !vml]><img width=311 height=305
     1305src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image007.gif"
     1306v:shapes="_x0000_i1053"><![endif]></span></p>
    13221307
    13231308<p class=MsoNormal>Here you select the phase the data belongs to. There is only
     
    13311316
    13321317<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1333  id="Picture_x0020_6" o:spid="_x0000_i1054" type="#_x0000_t75" style='width:525pt;
    1334  height:450pt;visibility:visible;mso-wrap-style:square'>
    1335  <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image011.png"
    1336   o:title=""/>
    1337 </v:shape><![endif]--><![if !vml]><img width=700 height=600
    1338 src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image078.gif"
    1339 v:shapes="Picture_x0020_6"><![endif]></span></p>
     1318 id="_x0000_i1052" type="#_x0000_t75" style='width:468pt;height:401.25pt;
     1319 visibility:visible;mso-wrap-style:square'>
     1320 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image018.png"
     1321  o:title=""/>
     1322</v:shape><![endif]--><![if !vml]><img width=624 height=535
     1323src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image009.gif"
     1324v:shapes="_x0000_i1052"><![endif]></span></p>
    13401325
    13411326<p class=MsoNormal>The <b style='mso-bidi-font-weight:normal'><span
     
    13491334
    13501335<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1351  id="Picture_x0020_1" o:spid="_x0000_i1053" type="#_x0000_t75" style='width:446.25pt;
    1352  height:381.75pt;visibility:visible;mso-wrap-style:square'>
    1353  <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image013.png"
    1354   o:title="" croptop="13337f" cropbottom="14997f" cropleft="41056f"
    1355   cropright="9449f"/>
    1356 </v:shape><![endif]--><![if !vml]><img width=595 height=509
    1357 src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image079.jpg"
    1358 v:shapes="Picture_x0020_1"><![endif]></span></p>
     1336 id="_x0000_i1051" type="#_x0000_t75" style='width:468pt;height:403.5pt;
     1337 visibility:visible;mso-wrap-style:square'>
     1338 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image022.png"
     1339  o:title=""/>
     1340</v:shape><![endif]--><![if !vml]><img width=624 height=538
     1341src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image011.gif"
     1342v:shapes="_x0000_i1051"><![endif]></span></p>
    13591343
    13601344<p class=MsoNormal>The size of the green boxes is proportional to the structure
     
    13821366
    13831367<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1384  id="Picture_x0020_8" o:spid="_x0000_i1052" type="#_x0000_t75" style='width:489pt;
    1385  height:375pt;visibility:visible;mso-wrap-style:square'>
    1386  <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image015.png"
    1387   o:title=""/>
    1388 </v:shape><![endif]--><![if !vml]><img width=652 height=500
    1389 src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image080.gif"
    1390 v:shapes="Picture_x0020_8"><![endif]></span></p>
     1368 id="_x0000_i1050" type="#_x0000_t75" style='width:468pt;height:222.75pt;
     1369 visibility:visible;mso-wrap-style:square'>
     1370 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image024.png"
     1371  o:title=""/>
     1372</v:shape><![endif]--><![if !vml]><img width=624 height=297
     1373src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image013.gif"
     1374v:shapes="_x0000_i1050"><![endif]></span></p>
    13911375
    13921376<p class=MsoNormal>In the Charge flip controls (about center of the page) press
     
    13951379reflection sets</span></b> button; a <b style='mso-bidi-font-weight:normal'><span
    13961380style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1397 mso-hansi-theme-font:minor-latin'>Use data</span></b> popup will appear. You will
    1398 want to use all the HKLF data sets; press <b style='mso-bidi-font-weight:normal'><span
    1399 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1400 mso-hansi-theme-font:minor-latin'>Set All</span> </b>and press <b
     1381mso-hansi-theme-font:minor-latin'>Use data</span></b> popup will appear. You
     1382will want to use all the HKLF data sets; press <b style='mso-bidi-font-weight:
     1383normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1384minor-latin;mso-hansi-theme-font:minor-latin'>Set All</span> </b>and press <b
    14011385style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    14021386mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
     
    14291413
    14301414<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
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    14651449
    14661450<p class=MsoNormal>If you scroll down the Map peak list you will find some with
     
    14701454
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    14791463
    14801464<p class=MsoNormal>The plot (which I’ve rotated around a bit) shows white spots
    1481 for the positive peaks and red ones for the negative ones; bonds are white
    1482 lines. The case I’ve drawn here shows a problem with this charge flip solution.
    1483 While the charge flipping run has clearly found all the C-atoms and some of the
    1484 H-atoms, the molecule is incorrectly placed in the unit cell. To fix this you
    1485 could simply repeat the charge flipping run and hope it puts the molecule in
    1486 the right place. GSAS-II uses an algorithm based on how structure factor phases
    1487 are related for a given space group to reposition the solution; it sometimes
    1488 fails if the phase set isn’t perfect. Or you can “roll” the map
     1465for the positive peaks and red ones for the negative ones; bonds are white lines.
     1466Your solution may show a problem with the charge flip solution. While the
     1467charge flipping run has clearly found all the C-atoms and some of the H-atoms,
     1468the molecule may be incorrectly placed in the unit cell (the multicolored cross
     1469should be in the middle of the C-C bond at the center of the molecule). To fix
     1470this you could simply repeat the charge flipping run and hope it puts the
     1471molecule in the right place. GSAS-II uses an algorithm based on how structure
     1472factor phases are related for a given space group to reposition the solution;
     1473it sometimes fails if the phase set isn’t perfect. Or you can “roll” the map
    14891474right/left/up/down (<b style='mso-bidi-font-weight:normal'><span
    14901475style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    14911476mso-hansi-theme-font:minor-latin'>R/L/U/D</span></b> keys) to put the solution
    1492 where you want. In this case a few steps with the L-key sufficed to put the
    1493 molecule on a 2/m site (i.e. the center of the cell indicated the multicolored
    1494 cross on the central C-C bond).</p>
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    1601 
    1602 <p class=MsoNormal>Notice that as the map is rolled, the Map peak positions are
    1603 shifted to match the change in positions.</p>
    1604 
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     1477where you want.<span style='mso-spacerun:yes'>  </span>Notice that as the map
     1478is rolled, the Map peak positions are shifted to match the change in positions.</p>
     1479
     1480<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    16131481
    16141482<p class=MsoNormal>By carefully looking at the map, you can see the 4-ring <span
     
    16191487sits on a 2-fold and the rest are in general positions. The molecule extends
    16201488into the neighboring unit cell so you don’t see the whole thing as one group
    1621 but has two bits on either side (I’ve marked these with arrows above).</p>
     1489but has two bits on either side.</p>
    16221490
    16231491<h2>Step 5. Peak selection</h2>
     
    16511519
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    1659 src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image088.jpg"
    1660 v:shapes="Picture_x0020_27"><![endif]></span></p>
     1521 id="_x0000_i1046" type="#_x0000_t75" style='width:468pt;height:379.5pt;
     1522 visibility:visible;mso-wrap-style:square'>
     1523 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image040.png"
     1524  o:title=""/>
     1525</v:shape><![endif]--><![if !vml]><img width=624 height=506
     1526src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image027.gif"
     1527v:shapes="_x0000_i1046"><![endif]></span></p>
    16611528
    16621529<p class=MsoNormal>The list has them highlighted (the rest are lower down in my
     
    16641531
    16651532<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1666  id="Picture_x0020_15" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:375pt;
    1667  height:435.75pt;visibility:visible;mso-wrap-style:square'>
    1668  <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image031.png"
    1669   o:title=""/>
    1670 </v:shape><![endif]--><![if !vml]><img width=500 height=581
    1671 src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image089.gif"
    1672 v:shapes="Picture_x0020_15"><![endif]></span></p>
     1533 id="Picture_x0020_35" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:468pt;
     1534 height:394.5pt;visibility:visible;mso-wrap-style:square'>
     1535 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image029.png"
     1536  o:title=""/>
     1537</v:shape><![endif]--><![if !vml]><img width=624 height=526
     1538src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image031.gif"
     1539v:shapes="Picture_x0020_35"><![endif]></span></p>
    16731540
    16741541<p class=MsoNormal>To add them to the Atom list do <b style='mso-bidi-font-weight:
     
    16781545
    16791546<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1680  id="Picture_x0020_16" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:6in;
    1681  height:369pt;visibility:visible;mso-wrap-style:square'>
     1547 id="Picture_x0020_36" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:468pt;
     1548 height:404.25pt;visibility:visible;mso-wrap-style:square'>
    16821549 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image033.png"
    1683   o:title="" croptop="10579f" cropbottom="17404f" cropleft="37800f"
    1684   cropright="12584f"/>
    1685 </v:shape><![endif]--><![if !vml]><img width=576 height=492
    1686 src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image090.jpg"
    1687 v:shapes="Picture_x0020_16"><![endif]></span></p>
     1550  o:title=""/>
     1551</v:shape><![endif]--><![if !vml]><img width=624 height=539
     1552src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image035.gif"
     1553v:shapes="Picture_x0020_36"><![endif]></span></p>
    16881554
    16891555<p class=MsoNormal>The atom list will give the magnitudes as ‘M’ names; I found
     
    16911557
    16921558<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1693  id="Picture_x0020_17" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:525pt;
    1694  height:351.75pt;visibility:visible;mso-wrap-style:square'>
    1695  <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image035.png"
    1696   o:title=""/>
    1697 </v:shape><![endif]--><![if !vml]><img width=700 height=469
    1698 src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image091.gif"
    1699 v:shapes="Picture_x0020_17"><![endif]></span></p>
     1559 id="Picture_x0020_37" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:468pt;
     1560 height:342pt;visibility:visible;mso-wrap-style:square'>
     1561 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image073.png"
     1562  o:title=""/>
     1563</v:shape><![endif]--><![if !vml]><img width=624 height=456
     1564src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image074.gif"
     1565v:shapes="Picture_x0020_37"><![endif]></span></p>
    17001566
    17011567<h2>Step 6. Atom identification</h2>
     
    17141580pick the last one). Do <b style='mso-bidi-font-weight:normal'><span
    17151581style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1716 mso-hansi-theme-font:minor-latin'>Edit/Modify atom parameters</span></b> from
    1717 the Atoms menu; a popup will appear. Pick <b style='mso-bidi-font-weight:normal'><span
    1718 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1719 mso-hansi-theme-font:minor-latin'>Type</span></b> and press <b
    1720 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1582mso-hansi-theme-font:minor-latin'>Edit Atoms/On selected atoms/Modify
     1583parameters</span></b> from the Atoms menu; a popup will appear. Pick <b
     1584style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1585mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Type</span></b>
     1586and press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    17211587mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>;
    17221588a Periodic Table will appear. Select <b style='mso-bidi-font-weight:normal'><span
    17231589style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    17241590mso-hansi-theme-font:minor-latin'>C</span></b> from the C-atom pulldown. All
    1725 the C-atom names and types will change. You should also move the C-atom with
    1726 2(x) site symmetry to the top of the list.</p>
    1727 
    1728 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1729  id="Picture_x0020_18" o:spid="_x0000_i1042" type="#_x0000_t75" style='width:525pt;
    1730  height:225pt;visibility:visible;mso-wrap-style:square'>
    1731  <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image037.png"
    1732   o:title=""/>
    1733 </v:shape><![endif]--><![if !vml]><img width=700 height=300
    1734 src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image092.gif"
    1735 v:shapes="Picture_x0020_18"><![endif]></span></p>
     1591the C-atom names and types will change and the plot will show dark gray spheres
     1592for the C-atoms. You should also move the C-atom with 2(x) site symmetry to the
     1593top of the list (if it isn’t there already).</p>
     1594
     1595<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1596 id="Picture_x0020_38" o:spid="_x0000_i1042" type="#_x0000_t75" style='width:468pt;
     1597 height:268.5pt;visibility:visible;mso-wrap-style:square'>
     1598 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image075.png"
     1599  o:title=""/>
     1600</v:shape><![endif]--><![if !vml]><img width=624 height=358
     1601src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image076.gif"
     1602v:shapes="Picture_x0020_38"><![endif]></span></p>
    17361603
    17371604<p class=MsoNormal>Do the same with the remaining negative M atoms – make them
     
    17401607site symmetry (although any would do). Do <b style='mso-bidi-font-weight:normal'><span
    17411608style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1742 mso-hansi-theme-font:minor-latin'>Edit/Assemble molecule</span></b> from the
    1743 Atoms menu; a popup will appear offering choices for Bond radii (&amp; Angle
    1744 radii – ignored here). Press <b style='mso-bidi-font-weight:normal'><span
     1609mso-hansi-theme-font:minor-latin'>Edit Atoms/Assemble molecule</span></b> from
     1610the Atoms menu; a popup will appear offering choices for Bond radii (&amp;
     1611Angle radii – ignored here). Press <b style='mso-bidi-font-weight:normal'><span
    17451612style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    17461613mso-hansi-theme-font:minor-latin'>Ok</span></b>; the Atom table will be revised
    1747 and the plot will show an assembled molecule (the picked starting atom in
    1748 green). </p>
    1749 
    1750 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1751  id="Picture_x0020_19" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:6in;
    1752  height:366pt;visibility:visible;mso-wrap-style:square'>
    1753  <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image039.png"
    1754   o:title="" croptop="11018f" cropbottom="17360f" cropleft="37831f"
    1755   cropright="12587f"/>
    1756 </v:shape><![endif]--><![if !vml]><img width=576 height=488
    1757 src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image093.jpg"
    1758 v:shapes="Picture_x0020_19"><![endif]></span></p>
     1614and the plot will show an assembled molecule. </p>
     1615
     1616<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1617 id="Picture_x0020_39" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:468pt;
     1618 height:405pt;visibility:visible;mso-wrap-style:square'>
     1619 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image077.png"
     1620  o:title=""/>
     1621</v:shape><![endif]--><![if !vml]><img width=624 height=540
     1622src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image078.gif"
     1623v:shapes="Picture_x0020_39"><![endif]></span></p>
    17591624
    17601625<p class=MsoNormal>The molecule building has scrambled the order of the atoms;
     
    17621627
    17631628<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1764  id="Picture_x0020_20" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:525pt;
    1765  height:351.75pt;visibility:visible;mso-wrap-style:square'>
    1766  <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image041.png"
    1767   o:title=""/>
    1768 </v:shape><![endif]--><![if !vml]><img width=700 height=469
    1769 src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image094.gif"
    1770 v:shapes="Picture_x0020_20"><![endif]></span></p>
     1629 id="Picture_x0020_40" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:468pt;
     1630 height:268.5pt;visibility:visible;mso-wrap-style:square'>
     1631 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image079.png"
     1632  o:title=""/>
     1633</v:shape><![endif]--><![if !vml]><img width=624 height=358
     1634src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image080.gif"
     1635v:shapes="Picture_x0020_40"><![endif]></span></p>
    17711636
    17721637<p class=MsoNormal>You can reorder them to put the H-atoms at the end of the
    1773 list. Then select all of them and then do <span style='font-family:"Calibri",sans-serif;
    1774 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Modify
    1775 atom parameters</span>. Pick <b style='mso-bidi-font-weight:normal'><span
    1776 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1777 mso-hansi-theme-font:minor-latin'>Name</span></b> from the pulldown and press <b
    1778 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1779 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
    1780 You are asked if you really want to do this, press <b style='mso-bidi-font-weight:
     1638list (if they weren’t there already). Then select all of them and then do <b
     1639style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1640mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1641minor-latin'>Edit Atoms/On Selected atoms
     1642/Modify parameters</span></b>. Pick <b
     1643style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1644mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Name</span></b>
     1645from the pulldown and press <b style='mso-bidi-font-weight:normal'><span
     1646style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1647mso-hansi-theme-font:minor-latin'>OK</span></b>. You are asked if you really
     1648want to do this, press <b style='mso-bidi-font-weight:normal'><span
     1649style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1650mso-hansi-theme-font:minor-latin'>Yes</span></b>. The atoms are then renamed in
     1651numeric order.</p>
     1652
     1653<h2>Step 7. Refinement</h2>
     1654
     1655<p class=MsoNormal>Since the structure is complete, we can do the full
     1656refinement. Select the <b style='mso-bidi-font-weight:normal'><span
     1657style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1658mso-hansi-theme-font:minor-latin'>Controls</span></b> item from the GSAS-II
     1659data tree. Unset the <b style='mso-bidi-font-weight:normal'><span
     1660style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1661mso-hansi-theme-font:minor-latin'>Refine HKLF as F^2</span></b> box and enter <b
     1662style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1663mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>3.0</span></b>
     1664for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1665mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Min <span
     1666class=SpellE>obs</span>/sig</span></b>. This makes the least squares refine on <span
     1667class=SpellE>F<sub>o</sub></span> with 3&#963; cutoff on <span class=SpellE>F<sub>o</sub></span>.
     1668From the main GSAS-II data tree menu do <b style='mso-bidi-font-weight:normal'><span
     1669style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1670mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; this will do the
     16711<sup>st</sup> least squares refinement varying only the data set scale factors.
     1672A progress bar popup will appear showing the residuals as the refinement
     1673proceeds. When done, a small popup will appear with the final residual; press <b
     1674style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1675mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>
     1676to accept it. The final <span class=SpellE>R<sub>w</sub></span> is about 47% Go
     1677to the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1678mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Atoms</span></b>
     1679tab for the <span class=SpellE>rubrene</span> phase, double click the <b
     1680style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1681mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>refine</span></b>
     1682column heading; a popup box will appear. Select both <b style='mso-bidi-font-weight:
    17811683normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1782 minor-latin;mso-hansi-theme-font:minor-latin'>Yes</span></b>. The atoms are
    1783 then renamed in numeric order.</p>
    1784 
    1785 <h2>Step 7. Refinement</h2>
    1786 
    1787 <p class=MsoNormal>Since the structure is complete, we can do the full refinement.
    1788 Select the <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:
    1790 minor-latin'>Controls</span></b> item from the GSAS-II data tree. Unset the <b
    1791 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1792 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Refine HKLF
    1793 as F^2</span></b> box and enter <b style='mso-bidi-font-weight:normal'><span
    1794 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1795 mso-hansi-theme-font:minor-latin'>3.0</span></b> for <b style='mso-bidi-font-weight:
    1796 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1797 minor-latin;mso-hansi-theme-font:minor-latin'>Min <span class=SpellE>obs</span>/sig</span></b>.
    1798 This makes the least squares refine on <span class=SpellE>F<sub>o</sub></span>
    1799 with 3&#963; cutoff on <span class=SpellE>F<sub>o</sub></span>. From the main
    1800 GSAS-II data tree menu do <b style='mso-bidi-font-weight:normal'><span
    1801 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1802 mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; this will do the
    1803 1<sup>st</sup> least squares refinement varying only the data set scale
    1804 factors. A progress bar popup will appear showing the residuals as the
    1805 refinement proceeds. When done, a small popup will appear with the final
    1806 residual; press <b style='mso-bidi-font-weight:normal'><span style='font-family:
    1807 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1808 minor-latin'>OK</span></b> to accept it. The final <span class=SpellE>R<sub>w</sub></span>
    1809 is about 49% Go to the <b style='mso-bidi-font-weight:normal'><span
    1810 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1811 mso-hansi-theme-font:minor-latin'>Atoms</span></b> tab for the <span
    1812 class=SpellE>rubrene</span> phase, double click the <b style='mso-bidi-font-weight:
    1813 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1814 minor-latin;mso-hansi-theme-font:minor-latin'>refine</span></b> column heading;
    1815 a popup box will appear. Select both <b style='mso-bidi-font-weight:normal'><span
    1816 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1817 mso-hansi-theme-font:minor-latin'>X - coordinates</span></b> and <b
     1684minor-latin;mso-hansi-theme-font:minor-latin'>X - coordinates</span></b> and <b
    18181685style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    18191686mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>U – thermal
     
    18241691
    18251692<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1826  id="Picture_x0020_21" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:525pt;
    1827  height:225pt;visibility:visible;mso-wrap-style:square'>
    1828  <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image043.png"
    1829   o:title=""/>
    1830 </v:shape><![endif]--><![if !vml]><img width=700 height=300
    1831 src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image095.gif"
    1832 v:shapes="Picture_x0020_21"><![endif]></span></p>
     1693 id="Picture_x0020_41" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:468pt;
     1694 height:199.5pt;visibility:visible;mso-wrap-style:square'>
     1695 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image081.png"
     1696  o:title=""/>
     1697</v:shape><![endif]--><![if !vml]><img width=624 height=266
     1698src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image082.gif"
     1699v:shapes="Picture_x0020_41"><![endif]></span></p>
    18331700
    18341701<p class=MsoNormal>Then repeat the <b style='mso-bidi-font-weight:normal'><span
    18351702style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1836 mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> command in the
    1837 main menu. The final residual will be much better <span class=SpellE>R<sub>w</sub></span>
    1838 ~10%. Next, convert all the atoms from isotropic thermal parameters to
    1839 anisotropic ones. Double click the <b style='mso-bidi-font-weight:normal'><span
    1840 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1841 mso-hansi-theme-font:minor-latin'>I/A</span></b> column heading and select <b
    1842 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1843 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Anisotropic</span></b>
    1844 and press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1703mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> (twice<span
     1704class=GramE>)command</span> in the main menu. The final residual will be much
     1705better <span class=SpellE>R<sub>w</sub></span> ~10%. Next, convert all the
     1706atoms from isotropic thermal parameters to anisotropic ones. Double click the <b
     1707style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1708mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>I/A</span></b>
     1709column heading and select <b style='mso-bidi-font-weight:normal'><span
     1710style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1711mso-hansi-theme-font:minor-latin'>Anisotropic</span></b> and press <b
     1712style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    18451713mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
    18461714Then repeat <b style='mso-bidi-font-weight:normal'><span style='font-family:
    18471715"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    18481716minor-latin'>Calculate/Refine</span></b> (perhaps twice); the final <span
    1849 class=SpellE>R<sub>w</sub></span> ~6.06% which is quite nice.</p>
     1717class=SpellE>R<sub>w</sub></span> ~5.9% which is quite nice.</p>
    18501718
    18511719<h2>Step 8. Further work</h2>
    18521720
    18531721<p class=MsoNormal>Since this is TOF neutron single crystal diffraction, a
    1854 relatively large crystal was used and the neutron wavelength covered a fairly wide
    1855 range of values. Hence, it is likely that the strong reflection intensities
    1856 suffered from some level of extinction. To find these parameters select the <b
    1857 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1858 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Data</span></b>
    1859 tab in the Phase Data window; all that will show is a list of a data set names
    1860 with a <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1861 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Show</span></b>
    1862 box for each. To see what is there select the <b style='mso-bidi-font-weight:
    1863 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1864 minor-latin;mso-hansi-theme-font:minor-latin'>Show</span></b> box;
    1865 alternatively to see all of them do <b style='mso-bidi-font-weight:normal'><span
    1866 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1867 mso-hansi-theme-font:minor-latin'>Edit/Show/Hide</span></b> all the window will
    1868 look something like</p>
    1869 
    1870 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1871  id="Picture_x0020_22" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:319.5pt;
    1872  height:378pt;visibility:visible;mso-wrap-style:square'>
    1873  <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image045.png"
    1874   o:title=""/>
    1875 </v:shape><![endif]--><![if !vml]><img width=426 height=504
    1876 src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image096.gif"
    1877 v:shapes="Picture_x0020_22"><![endif]></span></p>
    1878 
    1879 <p class=MsoNormal>This is a very long display with entries for 23 data sets
    1880 (NB: in alphabetical order not numeric order!). The Scale factors were selected
    1881 for refinement by default (box checked). Here you want to select <b
    1882 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1883 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Primary</span></b>
    1884 for the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1722relatively large crystal was used and the neutron wavelength covered a fairly
     1723wide range of values. Hence, it is likely that the strong reflection
     1724intensities suffered from some level of extinction. To find these parameters
     1725select the <b style='mso-bidi-font-weight:normal'><span style='font-family:
     1726"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1727minor-latin'>Data</span></b> tab in the Phase Data window; all that will show
     1728is a list of a data set names with the 1<sup>st</sup> one highlighted; the
     1729window will look something like</p>
     1730
     1731<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1732 id="Picture_x0020_42" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:468pt;
     1733 height:199.5pt;visibility:visible;mso-wrap-style:square'>
     1734 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image083.png"
     1735  o:title=""/>
     1736</v:shape><![endif]--><![if !vml]><img width=624 height=266
     1737src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image084.gif"
     1738v:shapes="Picture_x0020_42"><![endif]></span></p>
     1739
     1740<p class=MsoNormal>The Scale factors is selected for refinement by default (box
     1741checked). Here you want to select <b style='mso-bidi-font-weight:normal'><span
     1742style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1743mso-hansi-theme-font:minor-latin'>Primary</span></b> for the <b
     1744style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    18851745mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Extinction
    18861746type</span></b> (later you can try the other models) for the 1<sup>st</sup>
     
    18891749"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    18901750minor-latin'>Ep</span></b> check box so it will be refined. To set all the rest
    1891 press the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1892 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Copy flags?</span></b>
    1893 button for that data set (not one of the others!). A popup will appear giving
    1894 the list of data sets; press the <span class=SpellE><b style='mso-bidi-font-weight:
     1751do <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1752mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1753minor-latin'>Edit Phase/Copy <span class=SpellE>Flags<span style='font-family:
     1754"Times New Roman",serif;font-weight:normal'>A</span></span></span></b> popup
     1755will appear giving the list of data sets; press the <b style='mso-bidi-font-weight:
    18951756normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1896 minor-latin;mso-hansi-theme-font:minor-latin'>SetAll</span></b></span> button
    1897 and then <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1757minor-latin;mso-hansi-theme-font:minor-latin'>Set All</span></b> button and
     1758then <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    18981759mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
    1899 The data window will be repainted with all the Extinction types set to Primary
    1900 and Ep set to refine. You could then do <b style='mso-bidi-font-weight:normal'><span
     1760You could then do <b style='mso-bidi-font-weight:normal'><span
    19011761style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    19021762mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> but it might be
     
    19071767
    19081768<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1909  id="Picture_x0020_23" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:225pt;
    1910  height:352.5pt;visibility:visible;mso-wrap-style:square'>
    1911  <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image047.png"
    1912   o:title=""/>
    1913 </v:shape><![endif]--><![if !vml]><img width=300 height=470
    1914 src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image097.gif"
    1915 v:shapes="Picture_x0020_23"><![endif]></span></p>
     1769 id="Picture_x0020_43" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:468pt;
     1770 height:180.75pt;visibility:visible;mso-wrap-style:square'>
     1771 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image085.png"
     1772  o:title=""/>
     1773</v:shape><![endif]--><![if !vml]><img width=624 height=241
     1774src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image086.gif"
     1775v:shapes="Picture_x0020_43"><![endif]></span></p>
    19161776
    19171777<p class=MsoNormal>Select the <b style='mso-bidi-font-weight:normal'><span
    19181778style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1919 mso-hansi-theme-font:minor-latin'>Histogram/Phase</span></b> constraints tab;
    1920 the window is still blank but that tab is now highlighted. Next do <b
    1921 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1922 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Add
    1923 equivalence</span></b>; a popup will appear asking for a parameter name to be
    1924 constrained.</p>
    1925 
    1926 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1927  id="Picture_x0020_24" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:468.75pt;
    1928  height:300pt;visibility:visible;mso-wrap-style:square'>
    1929  <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image049.png"
    1930   o:title=""/>
    1931 </v:shape><![endif]--><![if !vml]><img width=625 height=400
    1932 src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image098.gif"
    1933 v:shapes="Picture_x0020_24"><![endif]></span></p>
    1934 
    1935 <p class=MsoNormal>Select <span class=GramE><b style='mso-bidi-font-weight:
     1779mso-hansi-theme-font:minor-latin'>Histogram/Phase</span></b> constraints tab; the
     1780window is still blank but that tab is now highlighted. Next do <b
     1781style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1782mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit Constr<span
     1783class=GramE>./</span>Add equivalence</span></b>; a popup will appear asking for
     1784a parameter name to be constrained.</p>
     1785
     1786<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1787 id="Picture_x0020_44" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:468pt;
     1788 height:299.25pt;visibility:visible;mso-wrap-style:square'>
     1789 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image087.png"
     1790  o:title=""/>
     1791</v:shape><![endif]--><![if !vml]><img width=624 height=399
     1792src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image088.gif"
     1793v:shapes="Picture_x0020_44"><![endif]></span></p>
     1794
     1795<p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span
     1796style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1797mso-hansi-theme-font:minor-latin'>0:0<span class=GramE>:Ep</span></span></b>,
     1798that is the primary extinction parameter for the 1<sup>st</sup> dataset and the
     1799<span class=SpellE>rubrene</span> phase. Press <b style='mso-bidi-font-weight:
    19361800normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1937 minor-latin;mso-hansi-theme-font:minor-latin'>0:0:Ep</span></b></span>, that is
    1938 the primary extinction parameter for the 1<sup>st</sup> dataset and the <span
    1939 class=SpellE>rubrene</span> phase. Press <b style='mso-bidi-font-weight:normal'><span
    1940 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1941 mso-hansi-theme-font:minor-latin'>OK</span></b>.</p>
     1801minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.</p>
    19421802
    19431803<p class=MsoNormal>The popup is replaced with a new list of all compatible
    1944 parameters that <span class=GramE><b style='mso-bidi-font-weight:normal'><span
    1945 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1946 mso-hansi-theme-font:minor-latin'>0:0:Ep</span></b></span> is to be made
    1947 equivalent to. Scroll down and find <span class=GramE><b style='mso-bidi-font-weight:
    1948 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1949 minor-latin;mso-hansi-theme-font:minor-latin'>0:all</span></b></span><b
    1950 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1951 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>:Ep</span></b>
    1952 and pick that; the Constraint window will change to</p>
    1953 
    1954 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1955  id="Picture_x0020_25" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:481.5pt;
    1956  height:352.5pt;visibility:visible;mso-wrap-style:square'>
    1957  <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image051.png"
    1958   o:title=""/>
    1959 </v:shape><![endif]--><![if !vml]><img width=642 height=470
    1960 src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image099.gif"
    1961 v:shapes="Picture_x0020_25"><![endif]></span></p>
     1804parameters that <b style='mso-bidi-font-weight:normal'><span style='font-family:
     1805"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1806minor-latin'>0:0<span class=GramE>:Ep</span></span></b> is to be made
     1807equivalent to. Scroll down and find <b style='mso-bidi-font-weight:normal'><span
     1808style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1809mso-hansi-theme-font:minor-latin'>0<span class=GramE>:all:Ep</span></span></b>
     1810and pick that and press <b style='mso-bidi-font-weight:normal'><span
     1811style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1812mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>OK</span></b>;
     1813the Constraint window will change to</p>
     1814
     1815<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1816 id="Picture_x0020_45" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:468pt;
     1817 height:156.75pt;visibility:visible;mso-wrap-style:square'>
     1818 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image089.png"
     1819  o:title=""/>
     1820</v:shape><![endif]--><![if !vml]><img width=624 height=209
     1821src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image090.gif"
     1822v:shapes="Picture_x0020_45"><![endif]></span></p>
    19621823
    19631824<p class=MsoNormal>This shows the constraint making Ep for all 23 data sets
     
    19651826style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    19661827mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; my <span
    1967 class=SpellE>R<sub>w</sub></span> was 5.907% only a slight improvement. You may
     1828class=SpellE>R<sub>w</sub></span> was 5.474% only a slight improvement. You may
    19681829wish to try the other extinction models. Do remember to delete the unused
    19691830constraint before adding a new one for the different extinction parameter.
     
    19721833mso-hansi-theme-font:minor-latin'>Atoms</span></b> and do <b style='mso-bidi-font-weight:
    19731834normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1974 minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Reload draw atoms</span></b>.
     1835minor-latin;mso-hansi-theme-font:minor-latin'>Edit Atoms/Reload draw atoms</span></b>.
    19751836That will put the newest atom parameters into the Draw Atoms table. Select <b
    19761837style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     
    19811842
    19821843<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1983  id="Picture_x0020_26" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:259.5pt;
    1984  height:252pt;visibility:visible;mso-wrap-style:square'>
    1985  <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image053.png"
    1986   o:title=""/>
    1987 </v:shape><![endif]--><![if !vml]><img width=346 height=336
    1988 src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image100.gif"
    1989 v:shapes="Picture_x0020_26"><![endif]></span></p>
     1844 id="Picture_x0020_46" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:171pt;
     1845 height:190.5pt;visibility:visible;mso-wrap-style:square'>
     1846 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image091.png"
     1847  o:title=""/>
     1848</v:shape><![endif]--><![if !vml]><img width=228 height=254
     1849src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image092.gif"
     1850v:shapes="Picture_x0020_46"><![endif]></span></p>
    19901851
    19911852<p class=MsoNormal>Notice the first line is blank, if you select that all the
     
    19951856style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    19961857mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
    1997 The plot will change, but it is pretty cluttered.</p>
    1998 
    1999 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2000  id="Picture_x0020_28" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:465.75pt;
    2001  height:395.25pt;visibility:visible;mso-wrap-style:square'>
    2002  <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image055.png"
    2003   o:title="" croptop="11745f" cropbottom="16560f" cropleft="43690f"
    2004   cropright="6723f"/>
    2005 </v:shape><![endif]--><![if !vml]><img width=621 height=527
    2006 src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image101.jpg"
    2007 v:shapes="Picture_x0020_28"><![endif]></span></p>
     1858I also set the ellipsoid probability to 99% (slider on the <b style='mso-bidi-font-weight:
     1859normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1860minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Draw
     1861Options</span></b> tab). The plot will change, but it is pretty cluttered.</p>
     1862
     1863<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1864 id="Picture_x0020_47" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:468pt;
     1865 height:403.5pt;visibility:visible;mso-wrap-style:square'>
     1866 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image093.png"
     1867  o:title=""/>
     1868</v:shape><![endif]--><![if !vml]><img width=624 height=538
     1869src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image094.gif"
     1870v:shapes="Picture_x0020_47"><![endif]></span></p>
    20081871
    20091872<p class=MsoNormal>You can remove the Map peaks atoms; go to the <b
     
    20281891
    20291892<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2030  id="Picture_x0020_29" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:429.75pt;
    2031  height:366pt;visibility:visible;mso-wrap-style:square'>
    2032  <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image057.png"
    2033   o:title="" croptop="8339f" cropbottom="19928f" cropleft="44139f" cropright="6324f"/>
    2034 </v:shape><![endif]--><![if !vml]><img width=573 height=488
    2035 src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image102.jpg"
    2036 v:shapes="Picture_x0020_29"><![endif]></span></p>
     1893 id="Picture_x0020_48" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:468pt;
     1894 height:404.25pt;visibility:visible;mso-wrap-style:square'>
     1895 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image095.png"
     1896  o:title=""/>
     1897</v:shape><![endif]--><![if !vml]><img width=624 height=539
     1898src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image096.gif"
     1899v:shapes="Picture_x0020_48"><![endif]></span></p>
    20371900
    20381901<p class=MsoNormal>Remember that this is only 1/4<sup>th</sup> of the molecule,
     
    20491912
    20501913<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2051  id="Picture_x0020_30" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:609.75pt;
    2052  height:278.25pt;visibility:visible;mso-wrap-style:square'>
    2053  <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image059.png"
    2054   o:title=""/>
    2055 </v:shape><![endif]--><![if !vml]><img width=813 height=371
    2056 src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image103.gif"
    2057 v:shapes="Picture_x0020_30"><![endif]></span></p>
     1914 id="Picture_x0020_49" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:468pt;
     1915 height:272.25pt;visibility:visible;mso-wrap-style:square'>
     1916 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image097.png"
     1917  o:title=""/>
     1918</v:shape><![endif]--><![if !vml]><img width=624 height=363
     1919src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image098.gif"
     1920v:shapes="Picture_x0020_49"><![endif]></span></p>
    20581921
    20591922<p class=MsoNormal>This gives the bond distances and angles about the <span
     
    20661929
    20671930<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2068  id="Picture_x0020_31" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:450pt;
    2069  height:225pt;visibility:visible;mso-wrap-style:square'>
    2070  <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image061.png"
    2071   o:title=""/>
    2072 </v:shape><![endif]--><![if !vml]><img width=600 height=300
    2073 src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image104.gif"
    2074 v:shapes="Picture_x0020_31"><![endif]></span></p>
     1931 id="Picture_x0020_50" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:468pt;
     1932 height:208.5pt;visibility:visible;mso-wrap-style:square'>
     1933 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image099.png"
     1934  o:title=""/>
     1935</v:shape><![endif]--><![if !vml]><img width=624 height=278
     1936src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image100.gif"
     1937v:shapes="Picture_x0020_50"><![endif]></span></p>
    20751938
    20761939<p class=MsoNormal>Then do <b style='mso-bidi-font-weight:normal'><span
    20771940style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2078 mso-hansi-theme-font:minor-latin'>Edit/Add atoms</span></b>; a popup will
    2079 appear</p>
    2080 
    2081 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2082  id="Picture_x0020_32" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:179.25pt;
    2083  height:246.75pt;visibility:visible;mso-wrap-style:square'>
    2084  <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image063.png"
    2085   o:title=""/>
    2086 </v:shape><![endif]--><![if !vml]><img width=239 height=329
    2087 src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image105.gif"
    2088 v:shapes="Picture_x0020_32"><![endif]></span></p>
     1941mso-hansi-theme-font:minor-latin'>Edit Figure/Add atoms</span></b>; a popup
     1942will appear</p>
     1943
     1944<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1945 id="Picture_x0020_51" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:189pt;
     1946 height:264pt;visibility:visible;mso-wrap-style:square'>
     1947 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image101.png"
     1948  o:title=""/>
     1949</v:shape><![endif]--><![if !vml]><img width=252 height=352
     1950src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image102.gif"
     1951v:shapes="Picture_x0020_51"><![endif]></span></p>
    20891952
    20901953<p class=MsoNormal>Based on the 1<sup>st</sup> entry in the bond distance table
    20911954‘<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    20921955mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>[1 0 0<span
    2093 class=GramE>]<span style='mso-spacerun:yes'>  </span>+(</span><span
     1956class=GramE>]<span style='mso-spacerun:yes'>  </span>+</span>(<span
    20941957style='mso-spacerun:yes'>  </span>2)</span></b>’, select the controls for the 2<sup>nd</sup>
    20951958operator and increment the 1<sup>st</sup> unit cell</p>
    20961959
    20971960<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2098  id="Picture_x0020_33" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:179.25pt;
    2099  height:246.75pt;visibility:visible;mso-wrap-style:square'>
    2100  <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image065.png"
    2101   o:title=""/>
    2102 </v:shape><![endif]--><![if !vml]><img width=239 height=329
     1961 id="Picture_x0020_52" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:189pt;
     1962 height:264pt;visibility:visible;mso-wrap-style:square'>
     1963 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image103.png"
     1964  o:title=""/>
     1965</v:shape><![endif]--><![if !vml]><img width=252 height=352
     1966src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image104.gif"
     1967v:shapes="Picture_x0020_52"><![endif]></span></p>
     1968
     1969<p class=MsoNormal>Press <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;mso-bidi-theme-font:minor-latin'>OK</span></b>.
     1972The plot now shows œ the molecule.</p>
     1973
     1974<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1975 id="Picture_x0020_53" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:468pt;
     1976 height:403.5pt;visibility:visible;mso-wrap-style:square'>
     1977 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image105.png"
     1978  o:title=""/>
     1979</v:shape><![endif]--><![if !vml]><img width=624 height=538
    21031980src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image106.gif"
    2104 v:shapes="Picture_x0020_33"><![endif]></span></p>
    2105 
    2106 <p class=MsoNormal>Press OK. The plot now shows œ the molecule.</p>
    2107 
    2108 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2109  id="Picture_x0020_34" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:429.75pt;
    2110  height:372pt;visibility:visible;mso-wrap-style:square'>
    2111  <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image067.png"
    2112   o:title="" croptop="11786f" cropbottom="16031f" cropleft="46740f"
    2113   cropright="3791f"/>
    2114 </v:shape><![endif]--><![if !vml]><img width=573 height=496
    2115 src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image107.jpg"
    2116 v:shapes="Picture_x0020_34"><![endif]></span></p>
     1981v:shapes="Picture_x0020_53"><![endif]></span></p>
    21171982
    21181983<p class=MsoNormal>Next select all the Draw atoms again and do <b
    21191984style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2120 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Add
     1985mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit Figure/Add
    21211986atoms</span></b>; the selection popup will appear. This time use the other
    21221987nonidentity entry in the bond distance table ‘<b style='mso-bidi-font-weight:
     
    21281993
    21291994<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2130  id="Picture_x0020_36" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:179.25pt;
    2131  height:246.75pt;visibility:visible;mso-wrap-style:square'>
    2132  <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image069.png"
    2133   o:title=""/>
    2134 </v:shape><![endif]--><![if !vml]><img width=239 height=329
     1995 id="Picture_x0020_54" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:189pt;
     1996 height:264pt;visibility:visible;mso-wrap-style:square'>
     1997 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image107.png"
     1998  o:title=""/>
     1999</v:shape><![endif]--><![if !vml]><img width=252 height=352
    21352000src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image108.gif"
    2136 v:shapes="Picture_x0020_36"><![endif]></span></p>
     2001v:shapes="Picture_x0020_54"><![endif]></span></p>
    21372002
    21382003<p class=MsoNormal>Press <b style='mso-bidi-font-weight:normal'><span
     
    21412006
    21422007<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2143  id="Picture_x0020_35" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:429.75pt;
    2144  height:364.5pt;visibility:visible;mso-wrap-style:square'>
    2145  <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image071.png"
    2146   o:title="" croptop="10221f" cropbottom="18166f" cropleft="42114f"
    2147   cropright="8322f"/>
    2148 </v:shape><![endif]--><![if !vml]><img width=573 height=486
    2149 src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image109.jpg"
    2150 v:shapes="Picture_x0020_35"><![endif]></span><span
     2008 id="Picture_x0020_55" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:468pt;
     2009 height:403.5pt;visibility:visible;mso-wrap-style:square'>
     2010 <v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image109.png"
     2011  o:title=""/>
     2012</v:shape><![endif]--><![if !vml]><img width=624 height=538
     2013src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image119.gif"
     2014v:shapes="Picture_x0020_55"><![endif]></span><span
    21512015style='mso-spacerun:yes'> </span></p>
    21522016
  • Tutorials/TOF Charge Flipping/Charge Flipping with TOF single crystal data in GSASII_files/filelist.xml

    r2390 r3071  
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    66  <o:File HRef="image059.png"/>
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