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source: Tutorials/TOF Charge Flipping/Charge Flipping with TOF single crystal data in GSASII.htm @ 1752

Last change on this file since 1752 was 1745, checked in by vondreele, 8 years ago
changes to various tutorials - mostly getting file references correct & removing hyperlinks
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1160	</head>
1161
1162	<body lang=EN-US link=blue vlink=purple style='tab-interval:.5in'>
1163
1164	<div class=WordSection1>
1165
1166	<h1><span style='mso-fareast-font-family:"Times New Roman"'>Charge flipping
1167	with neutron TOF single crystal data<o:p></o:p></span></h1>
1168
1169	<p class=MsoNormal>In this exercise you will use GSAS-II to solve the structure
1170	of <span class=SpellE>rubrene</span> (C<sub>42</sub>H<sub>28</sub>) from single
1171	crystal neutron data via charge flipping. <span class=SpellE>Rubrene</span> is
1172	of interest as a molecular semiconductor. It crystallizes in the space group <span
1173	class=SpellE>Cmca</span> with the lattice parameters a=26.798Å, b=7.1618Å,
1174	c=14.1942Å, Z=4. Thus, the molecule is sited on a special position with 2/m
1175	symmetry. If you have not done so already, start GSAS-II.</p>
1176
1177	<h2>Step 1. Set the phase information</h2>
1178
1179	<p class=MsoNormal>To begin this tutorial, do <b style='mso-bidi-font-weight:
1180	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1181	minor-latin;mso-hansi-theme-font:minor-latin'>Data/Add phase</span></b> in the
1182	main GSAS-II data tree menu. A popup window will appear asking for a phase
1183	name; I used <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1184	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1185	mso-hansi-theme-font:minor-latin'>rubrene</span></b></span>. Then select <span
1186	class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1187	"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1188	minor-latin'>rubrene</span></b></span> from the data tree</p>
1189
1190	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
1191	id="_x0000_t75" coordsize="21600,21600" o:spt="75" o:preferrelative="t"
1192	path="m@4@5l@4@11@9@11@9@5xe" filled="f" stroked="f">
1193	<v:stroke joinstyle="miter"/>
1194	<v:formulas>
1195	<v:f eqn="if lineDrawn pixelLineWidth 0"/>
1196	<v:f eqn="sum @0 1 0"/>
1197	<v:f eqn="sum 0 0 @1"/>
1198	<v:f eqn="prod @2 1 2"/>
1199	<v:f eqn="prod @3 21600 pixelWidth"/>
1200	<v:f eqn="prod @3 21600 pixelHeight"/>
1201	<v:f eqn="sum @0 0 1"/>
1202	<v:f eqn="prod @6 1 2"/>
1203	<v:f eqn="prod @7 21600 pixelWidth"/>
1204	<v:f eqn="sum @8 21600 0"/>
1205	<v:f eqn="prod @7 21600 pixelHeight"/>
1206	<v:f eqn="sum @10 21600 0"/>
1207	</v:formulas>
1208	<v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
1209	<o:lock v:ext="edit" aspectratio="t"/>
1210	</v:shapetype><v:shape id="_x0000_i1059" type="#_x0000_t75" style='width:300pt;
1211	height:187.5pt;visibility:visible;mso-wrap-style:square'>
1212	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image001.png"
1213	o:title=""/>
1214	</v:shape><![endif]--><![if !vml]><img width=400 height=250
1215	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image002.gif"
1216	v:shapes="_x0000_i1059"><![endif]></span></p>
1217
1218	<p class=MsoNormal>The General tab for this phase will be shown</p>
1219
1220	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1221	id="Picture_x0020_2" o:spid="_x0000_i1058" type="#_x0000_t75" style='width:640.5pt;
1222	height:375pt;visibility:visible;mso-wrap-style:square'>
1223	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image003.png"
1224	o:title=""/>
1225	</v:shape><![endif]--><![if !vml]><img width=854 height=500
1226	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image004.gif"
1227	v:shapes="Picture_x0020_2"><![endif]></span></p>
1228
1229	<p class=MsoNormal>Enter the space group (<b style='mso-bidi-font-weight:normal'><span
1230	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1231	mso-hansi-theme-font:minor-latin'>C m c a</span></b> dont forget the spaces)
1232	and press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1233	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Enter</span></b>.
1234	A popup with Space group information will appear</p>
1235
1236	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1237	id="Picture_x0020_3" o:spid="_x0000_i1057" type="#_x0000_t75" style='width:250.5pt;
1238	height:177.75pt;visibility:visible;mso-wrap-style:square'>
1239	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image005.png"
1240	o:title=""/>
1241	</v:shape><![endif]--><![if !vml]><img width=334 height=237
1242	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image006.gif"
1243	v:shapes="Picture_x0020_3"><![endif]></span></p>
1244
1245	<p class=MsoNormal>Press <b style='mso-bidi-font-weight:normal'><span
1246	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1247	mso-hansi-theme-font:minor-latin'>OK</span></b>; the General tab will be
1248	repainted with defaults for the orthorhombic lattice parameters. Enter <b
1249	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1250	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>26.798</span></b>
1251	for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1252	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>a</span></b>,
1253	<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1254	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>7.1618</span></b>
1255	for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1256	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>b</span></b>
1257	and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1258	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>14.1942</span></b>
1259	for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1260	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>c</span></b>.
1261	Press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1262	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Enter</span></b>,
1263	the unit cell volume (2724.178) will be updated.</p>
1264
1265	<h2>Step 2. Import the data</h2>
1266
1267	<p class=MsoNormal>The <span class=SpellE>rubrene</span> data were collected on
1268	the TOPAZ instrument at the SNS Facility, Oak Ridge National Laboratory with 23
1269	different crystal orientations; the local instrument data processing software
1270	has applied corrections and combined them into a single multicolumn <span
1271	class=SpellE>hkl</span> file. To import this do <b style='mso-bidi-font-weight:
1272	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1273	minor-latin;mso-hansi-theme-font:minor-latin'>Import/Structure Factor/from
1274	Neutron TOF HKL F2 file</span></b>; a directory dialog box will appear. Go to
1275	the 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:
1277	minor-latin'>exercises/TOF Charge Flipping</span></b> and select the file <span
1278	class=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:
1280	minor-latin'>ruberene_orthoC.hkl</span></b></span> (double click the name or
1281	press the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1282	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Open</span></b>
1283	button after selecting it). A popup box will appear.</p>
1284
1285	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1286	id="Picture_x0020_4" o:spid="_x0000_i1056" type="#_x0000_t75" style='width:357.75pt;
1287	height:265.5pt;visibility:visible;mso-wrap-style:square'>
1288	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image007.png"
1289	o:title=""/>
1290	</v:shape><![endif]--><![if !vml]><img width=477 height=354
1291	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image008.gif"
1292	v:shapes="Picture_x0020_4"><![endif]></span></p>
1293
1294	<p class=MsoNormal>Press <span class=GramE><b style='mso-bidi-font-weight:normal'><span
1295	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1296	mso-hansi-theme-font:minor-latin'>Yes</span></b></span>; another popup will
1297	appear offering you the chance to change the name. Press <b style='mso-bidi-font-weight:
1298	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1299	minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>, a new popup
1300	appears.</p>
1301
1302	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1303	id="Picture_x0020_5" o:spid="_x0000_i1055" type="#_x0000_t75" style='width:240pt;
1304	height:232.5pt;visibility:visible;mso-wrap-style:square'>
1305	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image009.png"
1306	o:title=""/>
1307	</v:shape><![endif]--><![if !vml]><img width=320 height=310
1308	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image010.gif"
1309	v:shapes="Picture_x0020_5"><![endif]></span></p>
1310
1311	<p class=MsoNormal>Here you select the phase the data belongs to. There is only
1312	<span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1313	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1314	mso-hansi-theme-font:minor-latin'>rubrene</span></b></span> so select it and
1315	press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1316	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1317	The bottom of the data tree is shown, a small data window and the plot shows
1318	the l=0 slice of the last reflection set loaded (HKLF rubrene_orthoC.hkl_22).</p>
1319
1320	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1321	id="Picture_x0020_6" o:spid="_x0000_i1054" type="#_x0000_t75" style='width:525pt;
1322	height:450pt;visibility:visible;mso-wrap-style:square'>
1323	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image011.png"
1324	o:title=""/>
1325	</v:shape><![endif]--><![if !vml]><img width=700 height=600
1326	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image012.gif"
1327	v:shapes="Picture_x0020_6"><![endif]></span></p>
1328
1329	<p class=MsoNormal>The <b style='mso-bidi-font-weight:normal'><span
1330	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1331	mso-hansi-theme-font:minor-latin'>K</span></b> box control allows you to select
1332	other zones & layers to view. The drawing geometry is strictly square (i.e.
1333	not in reciprocal space units). If you do <b style='mso-bidi-font-weight:normal'><span
1334	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1335	mso-hansi-theme-font:minor-latin'>Commands/Plot 3D HKLs</span></b>, a 3D plot
1336	of reciprocal space is shown</p>
1337
1338	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1339	id="Picture_x0020_1" o:spid="_x0000_i1053" type="#_x0000_t75" style='width:446.25pt;
1340	height:381.75pt;visibility:visible;mso-wrap-style:square'>
1341	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image013.png"
1342	o:title="" croptop="13337f" cropbottom="14997f" cropleft="41056f"
1343	cropright="9449f"/>
1344	</v:shape><![endif]--><![if !vml]><img width=595 height=509
1345	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image014.jpg"
1346	v:shapes="Picture_x0020_1"><![endif]></span></p>
1347
1348	<p class=MsoNormal>The size of the green boxes is proportional to the structure
1349	factors; the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1350	"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1351	minor-latin'>save as/key</span></b> pulldown will give you other viewing
1352	options. Here is a good place to save the GSAS-II project for <span
1353	class=SpellE>rubrene</span>. Do <b style='mso-bidi-font-weight:normal'><span
1354	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1355	mso-hansi-theme-font:minor-latin'>File/Save project</span></b> from the main
1356	GSAS-II data tree window; a file dialog box will appear. Enter a file name (I
1357	used <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1358	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1359	mso-hansi-theme-font:minor-latin'>rubrene</span></b></span> no extension).</p>
1360
1361	<h2>Step 3. Setup for charge flipping</h2>
1362
1363	<p class=MsoNormal>We have two tasks here. One is to select the reflection sets
1364	to be used in the calculations and the other is to set some controls. To begin
1365	select the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1366	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1367	mso-hansi-theme-font:minor-latin'>rubrene</span></b></span> phase entry in the
1368	GSAS-II data tree; the General tab will appear in the Phase Data for <span
1369	class=SpellE>rubrene</span> window</p>
1370
1371	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1372	id="Picture_x0020_8" o:spid="_x0000_i1052" type="#_x0000_t75" style='width:489pt;
1373	height:375pt;visibility:visible;mso-wrap-style:square'>
1374	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image015.png"
1375	o:title=""/>
1376	</v:shape><![endif]--><![if !vml]><img width=652 height=500
1377	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image016.gif"
1378	v:shapes="Picture_x0020_8"><![endif]></span></p>
1379
1380	<p class=MsoNormal>In the Charge flip controls (about center of the page) press
1381	the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1382	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Select
1383	reflection sets</span></b> button; a <b style='mso-bidi-font-weight:normal'><span
1384	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1385	mso-hansi-theme-font:minor-latin'>Use data</span></b> popup will appear. You
1386	will want to use all the HKLF data sets; press <b style='mso-bidi-font-weight:
1387	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1388	minor-latin;mso-hansi-theme-font:minor-latin'>Set All</span> </b>and press <b
1389	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1390	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1391	The General tab will be refreshed. GSAS-II will use all the data to build a
1392	reflection set for charge flipping. For duplicate <span class=SpellE>hkls</span>
1393	the last one encountered will be used. Since atoms are essentially point <span
1394	class=SpellE>scatterers</span> for neutrons, a charge flip map has very sharp
1395	peaks so a better choice for the <b style='mso-bidi-font-weight:normal'><span
1396	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1397	mso-hansi-theme-font:minor-latin'>k-factor</span></b> (charge flip level) might
1398	be <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1399	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0.5</span></b>,
1400	the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1401	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>k-max</span></b>
1402	should be larger (say <b style='mso-bidi-font-weight:normal'><span
1403	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1404	mso-hansi-theme-font:minor-latin'>50</span></b>) and the map <b
1405	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1406	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Resolution</span></b>
1407	should be smaller (say <b style='mso-bidi-font-weight:normal'><span
1408	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1409	mso-hansi-theme-font:minor-latin'>0.4</span></b>). Set these three values. In
1410	the Fourier map controls, set <b style='mso-bidi-font-weight:normal'><span
1411	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1412	mso-hansi-theme-font:minor-latin'>Peak cutoff %</span></b> to <b
1413	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1414	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>20</span></b>;
1415	this sets the lower limit of the peak search in the charge flip map. When done
1416	the General tab should look like</p>
1417
1418	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
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'>
1421	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image017.png"
1422	o:title=""/>
1423	</v:shape><![endif]--><![if !vml]><img width=689 height=500
1424	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image018.gif"
1425	v:shapes="Picture_x0020_9"><![endif]></span></p>
1426
1427	<p class=MsoNormal><o:p> </o:p></p>
1428
1429	<h2>Step 4. Charge flipping</h2>
1430
1431	<p class=MsoNormal>We are now ready for charge flipping. In the General tab
1432	menu do <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1433	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/Charge
1434	flipping</span></b>; a Charge flipping progress bar will appear showing the
1435	residual and cycle count for the charge flipping calculation. In this case the
1436	residual quickly drops to ~38% and stays there. Press <b style='mso-bidi-font-weight:
1437	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1438	minor-latin;mso-hansi-theme-font:minor-latin'>Cancel</span></b> to stop the
1439	calculation; some information will be printed on the console and after a pause
1440	the Phase Data window will show <b style='mso-bidi-font-weight:normal'><span
1441	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1442	mso-hansi-theme-font:minor-latin'>Map Peaks</span></b> and the plot window will
1443	show a drawing of the obtained structure.</p>
1444
1445	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1446	id="Picture_x0020_10" o:spid="_x0000_i1050" type="#_x0000_t75" style='width:375pt;
1447	height:225pt;visibility:visible;mso-wrap-style:square'>
1448	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image019.png"
1449	o:title=""/>
1450	</v:shape><![endif]--><![if !vml]><img width=500 height=300
1451	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image020.gif"
1452	v:shapes="Picture_x0020_10"><![endif]></span></p>
1453
1454	<p class=MsoNormal>If you scroll down the Map peak list you will find some with
1455	negative magnitudes at the end of the list. GSAS-II searches the map for both
1456	positive and negative peaks; the former are C-atoms and the latter are H-atoms.
1457	</p>
1458
1459	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1460	id="Picture_x0020_11" o:spid="_x0000_i1049" type="#_x0000_t75" style='width:6in;
1461	height:365.25pt;visibility:visible;mso-wrap-style:square'>
1462	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image021.png"
1463	o:title="" croptop="9820f" cropbottom="18705f" cropleft="43453f" cropright="6999f"/>
1464	</v:shape><![endif]--><![if !vml]><img width=576 height=487
1465	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image022.jpg"
1466	v:shapes="Picture_x0020_11"><![endif]></span></p>
1467
1468	<p class=MsoNormal>The plot (which Ive rotated around a bit) shows white spots
1469	for the positive peaks and red ones for the negative ones; bonds are white
1470	lines. The case Ive drawn here shows a problem with this charge flip solution.
1471	While the charge flipping run has clearly found all the C-atoms and some of the
1472	H-atoms, the molecule is incorrectly placed in the unit cell. To fix this you
1473	could simply repeat the charge flipping run and hope it puts the molecule in
1474	the right place. GSAS-II uses an algorithm based on how structure factor phases
1475	are related for a given space group to reposition the solution; it sometimes
1476	fails if the phase set isnt perfect. Or you can roll the map
1477	right/left/up/down (<b style='mso-bidi-font-weight:normal'><span
1478	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1479	mso-hansi-theme-font:minor-latin'>R/L/U/D</span></b> keys) to put the solution
1480	where you want. In this case a few steps with the L-key sufficed to put the
1481	molecule on a 2/m site (i.e. the center of the cell indicated the multicolored
1482	cross on the central C-C bond).</p>
1483
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1578	height:27px'><img width=40 height=27
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1580	v:shapes="Straight_x0020_Arrow_x0020_Connector_x0020_37"></span><![endif]><span
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1588	v:shapes="Picture_x0020_12"><![endif]></span></p>
1589
1590	<p class=MsoNormal>Notice that as the map is rolled, the Map peak positions are
1591	shifted to match the change in positions.</p>
1592
1593	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
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1596	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image027.png"
1597	o:title=""/>
1598	</v:shape><![endif]--><![if !vml]><img width=500 height=300
1599	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image028.gif"
1600	v:shapes="Picture_x0020_13"><![endif]></span></p>
1601
1602	<p class=MsoNormal>By carefully looking at the map, you can see the 4-ring <span
1603	class=SpellE>tetracene</span> (<span class=SpellE>naphthacene</span>) core of
1604	the molecule with four phenyl groups attached to both sides on the center two
1605	rings. The unique part consists of 1/4<sup>th</sup> of this group (i.e. half of
1606	one side of the <span class=SpellE>tetracene</span> and one phenyl); one C-atom
1607	sits on a 2-fold and the rest are in general positions. The molecule extends
1608	into the neighboring unit cell so you dont see the whole thing as one group
1609	but has two bits on either side (Ive marked these with arrows above).</p>
1610
1611	<h2>Step 5. Peak selection</h2>
1612
1613	<p class=MsoNormal>GSAS-II provides several ways of selecting peak positions
1614	from a charge flipping map. One way is to pick them directly from the drawing.
1615	Place the cursor on one peak and do a <b style='mso-bidi-font-weight:normal'><span
1616	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1617	mso-hansi-theme-font:minor-latin'>Shift left mouse button</span></b>; it will
1618	be highlighted on the list and it will turn green on the plot. Do a <b
1619	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1620	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Shift right
1621	mouse button</span></b> on the remaining peaks you want to <span class=GramE>pick.</span>
1622	All will turn green (you may have to wiggle the plot a bit with the mouse to
1623	make them show) and all will be highlighted in the list. Alternatively, you can
1624	select the entire list of peaks (double click on upper left empty box of the
1625	table), then do <b style='mso-bidi-font-weight:normal'><span style='font-family:
1626	"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1627	minor-latin'>Map peaks/Unique peaks</span></b>. Better still you can sort the
1628	peaks by one of the column headings and then do <b style='mso-bidi-font-weight:
1629	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1630	minor-latin;mso-hansi-theme-font:minor-latin'>Map peaks/Unique peaks</span></b>.
1631	Ive chosen to sort the peaks on <span class=SpellE><b style='mso-bidi-font-weight:
1632	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1633	minor-latin;mso-hansi-theme-font:minor-latin'>dcent</span></b></span> (distance
1634	from center of the cell) beforehand. After a pause while it sorts out the unique
1635	peaks, it will highlight them in the table and display the picked ones in green
1636	on the plot. In this case they will probably be scattered about the unit cell
1637	and not make a continuous molecule, but they are largely clustered around the
1638	unit cell center. My plot looked like this when I was done.</p>
1639
1640	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1641	id="Picture_x0020_27" o:spid="_x0000_i1046" type="#_x0000_t75" style='width:429.75pt;
1642	height:364.5pt;visibility:visible;mso-wrap-style:square'>
1643	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image029.png"
1644	o:title="" croptop="10059f" cropbottom="18635f" cropleft="36901f"
1645	cropright="13675f"/>
1646	</v:shape><![endif]--><![if !vml]><img width=573 height=486
1647	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image030.jpg"
1648	v:shapes="Picture_x0020_27"><![endif]></span></p>
1649
1650	<p class=MsoNormal>The list has them highlighted (the rest are lower down in my
1651	list; all 18 atoms were found in this charge flipping result)</p>
1652
1653	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
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'>
1656	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image031.png"
1657	o:title=""/>
1658	</v:shape><![endif]--><![if !vml]><img width=500 height=581
1659	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image032.gif"
1660	v:shapes="Picture_x0020_15"><![endif]></span></p>
1661
1662	<p class=MsoNormal>To add them to the Atom list do <b style='mso-bidi-font-weight:
1663	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1664	minor-latin;mso-hansi-theme-font:minor-latin'>Map peaks/Move peaks</span></b>;
1665	the drawing will show white balls for them.</p>
1666
1667	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1668	id="Picture_x0020_16" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:6in;
1669	height:369pt;visibility:visible;mso-wrap-style:square'>
1670	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image033.png"
1671	o:title="" croptop="10579f" cropbottom="17404f" cropleft="37800f"
1672	cropright="12584f"/>
1673	</v:shape><![endif]--><![if !vml]><img width=576 height=492
1674	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image034.jpg"
1675	v:shapes="Picture_x0020_16"><![endif]></span></p>
1676
1677	<p class=MsoNormal>The atom list will give the magnitudes as M names; I found
1678	all 11 C-atoms and 7 H-atoms that were expected.</p>
1679
1680	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
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'>
1683	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image035.png"
1684	o:title=""/>
1685	</v:shape><![endif]--><![if !vml]><img width=700 height=469
1686	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image036.gif"
1687	v:shapes="Picture_x0020_17"><![endif]></span></p>
1688
1689	<h2>Step 6. Atom identification</h2>
1690
1691	<p class=MsoNormal>You can reorder the atoms in the list; do an <b
1692	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1693	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Alt select</span></b>
1694	for the atom row you want to move. Then do an <b style='mso-bidi-font-weight:
1695	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1696	minor-latin;mso-hansi-theme-font:minor-latin'>Alt select</span></b> on the row
1697	where you want the moved atom to precede it. This way you can put the C-atoms
1698	first and the H-atoms last in the list instead of mixed up as in the above
1699	list. Next select all the positive M peaks (pick the top one and then <b
1700	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1701	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Shift</span></b>
1702	pick the last one). Do <b style='mso-bidi-font-weight:normal'><span
1703	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1704	mso-hansi-theme-font:minor-latin'>Edit/Modify atom parameters</span></b> from
1705	the Atoms menu; a popup will appear. Pick <b style='mso-bidi-font-weight:normal'><span
1706	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1707	mso-hansi-theme-font:minor-latin'>Type</span></b> and press <b
1708	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1709	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>;
1710	a Periodic Table will appear. Select <b style='mso-bidi-font-weight:normal'><span
1711	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1712	mso-hansi-theme-font:minor-latin'>C</span></b> from the C-atom pulldown. All
1713	the C-atom names and types will change. You should also move the C-atom with
1714	2(x) site symmetry to the top of the list.</p>
1715
1716	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
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1718	height:225pt;visibility:visible;mso-wrap-style:square'>
1719	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image037.png"
1720	o:title=""/>
1721	</v:shape><![endif]--><![if !vml]><img width=700 height=300
1722	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image038.gif"
1723	v:shapes="Picture_x0020_18"><![endif]></span></p>
1724
1725	<p class=MsoNormal>Do the same with the remaining negative M atoms make them
1726	H atoms. The drawing shows molecular fragments scattered about the unit cell;
1727	youd like to unify them into a single molecule. Select the C-atom with 2(x)
1728	site symmetry (although any would do). Do <b style='mso-bidi-font-weight:normal'><span
1729	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1730	mso-hansi-theme-font:minor-latin'>Edit/Assemble molecule</span></b> from the
1731	Atoms menu; a popup will appear offering choices for Bond radii (& Angle
1732	radii ignored here). Press <b style='mso-bidi-font-weight:normal'><span
1733	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1734	mso-hansi-theme-font:minor-latin'>Ok</span></b>; the Atom table will be revised
1735	and the plot will show an assembled molecule (the picked starting atom in
1736	green). </p>
1737
1738	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1739	id="Picture_x0020_19" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:6in;
1740	height:366pt;visibility:visible;mso-wrap-style:square'>
1741	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image039.png"
1742	o:title="" croptop="11018f" cropbottom="17360f" cropleft="37831f"
1743	cropright="12587f"/>
1744	</v:shape><![endif]--><![if !vml]><img width=576 height=488
1745	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image040.jpg"
1746	v:shapes="Picture_x0020_19"><![endif]></span></p>
1747
1748	<p class=MsoNormal>The molecule building has scrambled the order of the atoms;
1749	they were located in order as the molecule was built. </p>
1750
1751	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
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'>
1754	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image041.png"
1755	o:title=""/>
1756	</v:shape><![endif]--><![if !vml]><img width=700 height=469
1757	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image042.gif"
1758	v: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
1761	list. Then select all of them and then do <span style='font-family:"Calibri",sans-serif;
1762	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Modify
1763	atom parameters</span>. Pick <b style='mso-bidi-font-weight:normal'><span
1764	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1765	mso-hansi-theme-font:minor-latin'>Name</span></b> from the pulldown and press <b
1766	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1767	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1768	You are asked if you really want to do this, press <span class=GramE><b
1769	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1770	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Yes</span></b></span>.
1771	The atoms are then renamed in numeric order.</p>
1772
1773	<h2>Step 7. Refinement</h2>
1774
1775	<p class=MsoNormal>Since the structure is complete, we can do the full
1776	refinement. Select the <b style='mso-bidi-font-weight:normal'><span
1777	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1778	mso-hansi-theme-font:minor-latin'>Controls</span></b> item from the GSAS-II
1779	data tree. Unset the <b style='mso-bidi-font-weight:normal'><span
1780	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1781	mso-hansi-theme-font:minor-latin'>Refine HKLF as F^2</span></b> box and enter <b
1782	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1783	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>3.0</span></b>
1784	for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1785	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Min <span
1786	class=SpellE>obs</span>/sig</span></b>. This makes the least squares refine on <span
1787	class=SpellE><span class=GramE>F<sub>o</sub></span></span> with 3σ cutoff
1788	on <span class=SpellE>F<sub>o</sub></span>. From the main GSAS-II data tree
1789	menu do <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1790	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>;
1791	this will do the 1<sup>st</sup> least squares refinement varying only the data
1792	set scale factors. A progress bar popup will appear showing the residuals as
1793	the refinement proceeds. When done, a small popup will appear with the final
1794	residual; press <b style='mso-bidi-font-weight:normal'><span style='font-family:
1795	"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1796	minor-latin'>OK</span></b> to accept it. The final <span class=SpellE>R<sub>w</sub></span>
1797	is about 49% Go to the <b style='mso-bidi-font-weight:normal'><span
1798	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1799	mso-hansi-theme-font:minor-latin'>Atoms</span></b> tab for the <span
1800	class=SpellE>rubrene</span> phase, double click the <b style='mso-bidi-font-weight:
1801	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1802	minor-latin;mso-hansi-theme-font:minor-latin'>refine</span></b> column heading;
1803	a popup box will appear. Select both <b style='mso-bidi-font-weight:normal'><span
1804	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1805	mso-hansi-theme-font:minor-latin'>X - coordinates</span></b> and <b
1806	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1807	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>U thermal
1808	parameters</span></b> and press <b style='mso-bidi-font-weight:normal'><span
1809	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1810	mso-hansi-theme-font:minor-latin'>OK</span></b>. The atom table will show
1811	refine 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'>
1816	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image043.png"
1817	o:title=""/>
1818	</v:shape><![endif]--><![if !vml]><img width=700 height=300
1819	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image044.gif"
1820	v:shapes="Picture_x0020_21"><![endif]></span></p>
1821
1822	<p class=MsoNormal>Then repeat the <b style='mso-bidi-font-weight:normal'><span
1823	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1824	mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> command in the
1825	main menu. The final residual will be much better <span class=SpellE>R<sub>w</sub></span>
1826	~10%. Next, convert all the atoms from isotropic thermal parameters to
1827	anisotropic ones. Double click <span class=GramE>the <b style='mso-bidi-font-weight:
1828	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1829	minor-latin;mso-hansi-theme-font:minor-latin'>I</span></b></span><b
1830	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1831	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>/A</span></b>
1832	column heading and select <b style='mso-bidi-font-weight:normal'><span
1833	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1834	mso-hansi-theme-font:minor-latin'>Anisotropic</span></b> and press <b
1835	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1836	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1837	Then repeat <b style='mso-bidi-font-weight:normal'><span style='font-family:
1838	"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1839	minor-latin'>Calculate/Refine</span></b> (perhaps twice); the final <span
1840	class=SpellE>R<sub>w</sub></span> ~6.06% which is quite nice.</p>
1841
1842	<h2>Step 8. Further work</h2>
1843
1844	<p class=MsoNormal>Since this is TOF neutron single crystal diffraction, a
1845	relatively large crystal was used and the neutron wavelength covered a fairly
1846	wide range of values. Hence, it is likely that the strong reflection
1847	intensities suffered from some level of extinction. To find these parameters
1848	select 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:
1850	minor-latin'>Data</span></b> tab in the Phase Data window; all that will show
1851	is a list of a data set names with a <b style='mso-bidi-font-weight:normal'><span
1852	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1853	mso-hansi-theme-font:minor-latin'>Show</span></b> box for each. To see what is
1854	there 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:
1856	minor-latin'>Show</span></b> box; alternatively to see all of them do <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'>Edit/Show/Hide</span></b>
1859	all the window will look something like</p>
1860
1861	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1862	id="Picture_x0020_22" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:319.5pt;
1863	height:378pt;visibility:visible;mso-wrap-style:square'>
1864	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image045.png"
1865	o:title=""/>
1866	</v:shape><![endif]--><![if !vml]><img width=426 height=504
1867	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image046.gif"
1868	v:shapes="Picture_x0020_22"><![endif]></span></p>
1869
1870	<p class=MsoNormal>This is a very long display with entries for 23 data sets
1871	(NB: in alphabetical order not numeric order!). The Scale factors were selected
1872	for refinement by default (box checked). Here you want to select <b
1873	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1874	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Primary</span></b>
1875	for the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1876	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Extinction
1877	type</span></b> (later you can try the other models) for the 1<sup>st</sup>
1878	data set. The window will be repainted with a new line in the data display.
1879	Select 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:
1881	minor-latin'>Ep</span></b> check box so it will be refined. To set all the rest
1882	press the <b 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'>Copy flags?</span></b>
1884	<span class=GramE>button</span> for that data set (not one of the others!). A
1885	popup will appear giving the list of data sets; press the <span class=SpellE><b
1886	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1887	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>SetAll</span></b></span>
1888	button and then <b style='mso-bidi-font-weight:normal'><span style='font-family:
1889	"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1890	minor-latin'>OK</span></b>. The data window will be repainted with all the
1891	Extinction types set to Primary and Ep set to refine. You could then do <b
1892	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1893	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>
1894	but it might be better to constrain all the Ep values to be the same. To do
1895	this select <b style='mso-bidi-font-weight:normal'><span style='font-family:
1896	"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1897	minor-latin'>Constraints</span></b> from the GSASII data tree. A blank window
1898	with tabs will appear.</p>
1899
1900	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1901	id="Picture_x0020_23" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:225pt;
1902	height:352.5pt;visibility:visible;mso-wrap-style:square'>
1903	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image047.png"
1904	o:title=""/>
1905	</v:shape><![endif]--><![if !vml]><img width=300 height=470
1906	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image048.gif"
1907	v:shapes="Picture_x0020_23"><![endif]></span></p>
1908
1909	<p class=MsoNormal>Select the <b style='mso-bidi-font-weight:normal'><span
1910	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1911	mso-hansi-theme-font:minor-latin'>Histogram/Phase</span></b> constraints tab;
1912	the window is still blank but that tab is now highlighted. Next do <b
1913	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1914	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Add
1915	equivalence</span></b>; a popup will appear asking for a parameter name to be
1916	constrained.</p>
1917
1918	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1919	id="Picture_x0020_24" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:468.75pt;
1920	height:300pt;visibility:visible;mso-wrap-style:square'>
1921	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image049.png"
1922	o:title=""/>
1923	</v:shape><![endif]--><![if !vml]><img width=625 height=400
1924	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image050.gif"
1925	v:shapes="Picture_x0020_24"><![endif]></span></p>
1926
1927	<p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span
1928	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1929	mso-hansi-theme-font:minor-latin'>0:0<span class=GramE>:Ep</span></span></b>,
1930	that is the primary extinction parameter for the 1<sup>st</sup> dataset and the
1931	<span class=SpellE>rubrene</span> phase. Press <b style='mso-bidi-font-weight:
1932	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1933	minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.</p>
1934
1935	<p class=MsoNormal>The popup is replaced with a new list of all compatible
1936	parameters that <b style='mso-bidi-font-weight:normal'><span style='font-family:
1937	"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1938	minor-latin'>0:0<span class=GramE>:Ep</span></span></b> is to be made
1939	equivalent to. Scroll down and find <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'>0<span class=GramE>:all:Ep</span></span></b>
1942	and pick that; the Constraint window will change to</p>
1943
1944	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1945	id="Picture_x0020_25" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:481.5pt;
1946	height:352.5pt;visibility:visible;mso-wrap-style:square'>
1947	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image051.png"
1948	o:title=""/>
1949	</v:shape><![endif]--><![if !vml]><img width=642 height=470
1950	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image052.gif"
1951	v:shapes="Picture_x0020_25"><![endif]></span></p>
1952
1953	<p class=MsoNormal>This shows the constraint making Ep for all 23 data sets
1954	equivalent to a single variable. Do <b style='mso-bidi-font-weight:normal'><span
1955	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1956	mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; my <span
1957	class=SpellE>R<sub>w</sub></span> was 5.907% only a slight improvement. You may
1958	wish to try the other extinction models. Do remember to delete the unused
1959	constraint before adding a new one for the different extinction parameter.
1960	Finally you can draw the molecule; go to <b style='mso-bidi-font-weight:normal'><span
1961	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1962	mso-hansi-theme-font:minor-latin'>Atoms</span></b> and do <b style='mso-bidi-font-weight:
1963	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1964	minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Reload draw atoms</span></b>.
1965	That will put the newest atom parameters into the Draw Atoms table. Select <b
1966	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1967	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Draw Atoms</span></b>.
1968	Select the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1969	"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1970	minor-latin'>Style</span></b> column heading; a popup will appear</p>
1971
1972	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1973	id="Picture_x0020_26" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:259.5pt;
1974	height:252pt;visibility:visible;mso-wrap-style:square'>
1975	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image053.png"
1976	o:title=""/>
1977	</v:shape><![endif]--><![if !vml]><img width=346 height=336
1978	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image054.gif"
1979	v:shapes="Picture_x0020_26"><![endif]></span></p>
1980
1981	<p class=MsoNormal>Notice the first line is blank, if you select that all the
1982	atoms will vanish! Select <b style='mso-bidi-font-weight:normal'><span
1983	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1984	mso-hansi-theme-font:minor-latin'>ellipsoids</span></b> and press <b
1985	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1986	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1987	The plot will change, but it is pretty cluttered.</p>
1988
1989	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1990	id="Picture_x0020_28" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:465.75pt;
1991	height:395.25pt;visibility:visible;mso-wrap-style:square'>
1992	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image055.png"
1993	o:title="" croptop="11745f" cropbottom="16560f" cropleft="43690f"
1994	cropright="6723f"/>
1995	</v:shape><![endif]--><![if !vml]><img width=621 height=527
1996	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image056.jpg"
1997	v:shapes="Picture_x0020_28"><![endif]></span></p>
1998
1999	<p class=MsoNormal>You can remove the Map peaks atoms; go to the <b
2000	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2001	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map peaks</span></b>
2002	tab and do <b style='mso-bidi-font-weight:normal'><span style='font-family:
2003	"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2004	minor-latin'>Map peaks/clear peaks</span></b> from the menu. The list will be
2005	erased and the plot will just show the molecule. You can also remove the unit
2006	cell edges, go to <b style='mso-bidi-font-weight:normal'><span
2007	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2008	mso-hansi-theme-font:minor-latin'>Draw Options</span></b> and uncheck the <b
2009	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2010	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Show unit
2011	cell?</span></b> <span class=GramE>box</span>. Finally, you can remove the charge
2012	flipping map; go to <b style='mso-bidi-font-weight:normal'><span
2013	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2014	mso-hansi-theme-font:minor-latin'>General</span></b> and do <b
2015	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2016	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/Clear
2017	map</span></b>. That deletes the scattering density map and the drawing will be
2018	free of any clutter.</p>
2019
2020	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2021	id="Picture_x0020_29" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:429.75pt;
2022	height:366pt;visibility:visible;mso-wrap-style:square'>
2023	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image057.png"
2024	o:title="" croptop="8339f" cropbottom="19928f" cropleft="44139f" cropright="6324f"/>
2025	</v:shape><![endif]--><![if !vml]><img width=573 height=488
2026	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image058.jpg"
2027	v:shapes="Picture_x0020_29"><![endif]></span></p>
2028
2029	<p class=MsoNormal>Remember that this is only 1/4<sup>th</sup> of the molecule,
2030	wed like to see the whole thing. First go to the <b style='mso-bidi-font-weight:
2031	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2032	minor-latin;mso-hansi-theme-font:minor-latin'>Atoms</span></b> tab and select
2033	the C-atom that is in a special position 2(x). The do <b style='mso-bidi-font-weight:
2034	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2035	minor-latin;mso-hansi-theme-font:minor-latin'>Compute/Show Distances &
2036	Angles</span></b> and respond <b style='mso-bidi-font-weight:normal'><span
2037	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2038	mso-hansi-theme-font:minor-latin'>OK</span></b> to the popup. The important
2039	result is on the console</p>
2040
2041	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2042	id="Picture_x0020_30" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:609.75pt;
2043	height:278.25pt;visibility:visible;mso-wrap-style:square'>
2044	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image059.png"
2045	o:title=""/>
2046	</v:shape><![endif]--><![if !vml]><img width=813 height=371
2047	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image060.gif"
2048	v:shapes="Picture_x0020_30"><![endif]></span></p>
2049
2050	<p class=MsoNormal>This gives the bond distances and angles about the <span
2051	class=GramE>C(</span>1) atom. Particularly note the cell<span class=GramE>+(</span>sym.
2052	Op.) information; we will use this to build the drawing. Go to the <b
2053	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2054	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Draw Atoms</span></b>
2055	tab and select all the atoms (double click on the upper left box). You should
2056	see all atoms selected</p>
2057
2058	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2059	id="Picture_x0020_31" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:450pt;
2060	height:225pt;visibility:visible;mso-wrap-style:square'>
2061	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image061.png"
2062	o:title=""/>
2063	</v:shape><![endif]--><![if !vml]><img width=600 height=300
2064	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image062.gif"
2065	v:shapes="Picture_x0020_31"><![endif]></span></p>
2066
2067	<p class=MsoNormal>Then do <b style='mso-bidi-font-weight:normal'><span
2068	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2069	mso-hansi-theme-font:minor-latin'>Edit/Add atoms</span></b>; a popup will
2070	appear</p>
2071
2072	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2073	id="Picture_x0020_32" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:179.25pt;
2074	height:246.75pt;visibility:visible;mso-wrap-style:square'>
2075	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image063.png"
2076	o:title=""/>
2077	</v:shape><![endif]--><![if !vml]><img width=239 height=329
2078	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image064.gif"
2079	v:shapes="Picture_x0020_32"><![endif]></span></p>
2080
2081	<p class=MsoNormal>Based on the 1<sup>st</sup> entry in the bond distance table
2082	<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2083	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>[1 0 0<span
2084	class=GramE>]<span style='mso-spacerun:yes'> </span>+</span>(<span
2085	style='mso-spacerun:yes'> </span>2)</span></b>, select the controls for the 2<sup>nd</sup>
2086	operator and increment the 1<sup>st</sup> unit cell</p>
2087
2088	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2089	id="Picture_x0020_33" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:179.25pt;
2090	height:246.75pt;visibility:visible;mso-wrap-style:square'>
2091	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image065.png"
2092	o:title=""/>
2093	</v:shape><![endif]--><![if !vml]><img width=239 height=329
2094	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image066.gif"
2095	v:shapes="Picture_x0020_33"><![endif]></span></p>
2096
2097	<p class=MsoNormal>Press OK. The plot now shows œ the molecule.</p>
2098
2099	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2100	id="Picture_x0020_34" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:429.75pt;
2101	height:372pt;visibility:visible;mso-wrap-style:square'>
2102	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image067.png"
2103	o:title="" croptop="11786f" cropbottom="16031f" cropleft="46740f"
2104	cropright="3791f"/>
2105	</v:shape><![endif]--><![if !vml]><img width=573 height=496
2106	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image068.jpg"
2107	v:shapes="Picture_x0020_34"><![endif]></span></p>
2108
2109	<p class=MsoNormal>Next select all the Draw atoms again and do <b
2110	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2111	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Add
2112	atoms</span></b>; the selection popup will appear. This time use the other
2113	nonidentity entry in the bond distance table <b style='mso-bidi-font-weight:
2114	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2115	minor-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
2117	applied; check both and increment the 2<sup>nd</sup> and 3<sup>rd</sup> unit
2118	cell entries. </p>
2119
2120	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2121	id="Picture_x0020_36" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:179.25pt;
2122	height:246.75pt;visibility:visible;mso-wrap-style:square'>
2123	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image069.png"
2124	o:title=""/>
2125	</v:shape><![endif]--><![if !vml]><img width=239 height=329
2126	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image070.gif"
2127	v:shapes="Picture_x0020_36"><![endif]></span></p>
2128
2129	<p class=MsoNormal>Press <b style='mso-bidi-font-weight:normal'><span
2130	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2131	mso-hansi-theme-font:minor-latin'>OK</span></b>; the entire molecule is drawn.</p>
2132
2133	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2134	id="Picture_x0020_35" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:429.75pt;
2135	height:364.5pt;visibility:visible;mso-wrap-style:square'>
2136	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image071.png"
2137	o:title="" croptop="10221f" cropbottom="18166f" cropleft="42114f"
2138	cropright="8322f"/>
2139	</v:shape><![endif]--><![if !vml]><img width=573 height=486
2140	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image072.jpg"
2141	v:shapes="Picture_x0020_35"><![endif]></span><span
2142	style='mso-spacerun:yes'> </span></p>
2143
2144	<p class=MsoNormal>Looks really nice. This ends the tutorial. You can save the
2145	project if you wish. All the changes (<span class=SpellE>i.e</span> deleting
2146	Map peaks & clearing the map) will be saved.</p>
2147
2148	</div>
2149
2150	</body>
2151
2152	</html>

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