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1172	</head>
1173
1174	<body lang=EN-US link=blue vlink=purple style='tab-interval:.5in'>
1175
1176	<div class=WordSection1>
1177
1178	<h1><span style='mso-fareast-font-family:"Times New Roman"'>Charge flipping
1179	with neutron TOF single crystal data<o:p></o:p></span></h1>
1180
1181	<p class=MsoNormal>In this exercise you will use GSAS-II to solve the structure
1182	of <span class=SpellE>rubrene</span> (C<sub>42</sub>H<sub>28</sub>) from single
1183	crystal neutron data via charge flipping. <span class=SpellE>Rubrene</span> is of
1184	interest as a molecular semiconductor. It crystallizes in the space group <span
1185	class=SpellE>Cmca</span> with the lattice parameters a=26.798Å, b=7.1618Å,
1186	c=14.1942Å, Z=4. Thus, the molecule is sited on a special position with 2/m
1187	symmetry. If you have not done so already, start GSAS-II.</p>
1188
1189	<h2>Step 1. Set the phase information</h2>
1190
1191	<p class=MsoNormal>To begin this tutorial, do <b style='mso-bidi-font-weight:
1192	normal'><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
1195	name; I used <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1196	style='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>
1201
1202	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
1203	id="_x0000_t75" coordsize="21600,21600" o:spt="75" o:preferrelative="t"
1204	path="m@4@5l@4@11@9@11@9@5xe" filled="f" stroked="f">
1205	<v:stroke joinstyle="miter"/>
1206	<v:formulas>
1207	<v:f eqn="if lineDrawn pixelLineWidth 0"/>
1208	<v:f eqn="sum @0 1 0"/>
1209	<v:f eqn="sum 0 0 @1"/>
1210	<v:f eqn="prod @2 1 2"/>
1211	<v:f eqn="prod @3 21600 pixelWidth"/>
1212	<v:f eqn="prod @3 21600 pixelHeight"/>
1213	<v:f eqn="sum @0 0 1"/>
1214	<v:f eqn="prod @6 1 2"/>
1215	<v:f eqn="prod @7 21600 pixelWidth"/>
1216	<v:f eqn="sum @8 21600 0"/>
1217	<v:f eqn="prod @7 21600 pixelHeight"/>
1218	<v:f eqn="sum @10 21600 0"/>
1219	</v:formulas>
1220	<v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
1221	<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>
1240
1241	<p class=MsoNormal>Enter the space group (<b style='mso-bidi-font-weight:normal'><span
1242	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1243	mso-hansi-theme-font:minor-latin'>C m c a</span></b> dont forget the spaces)
1244	and press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1245	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Enter</span></b>.
1246	A popup with Space group information will appear</p>
1247
1248	<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>
1256
1257	<p class=MsoNormal>Press <b style='mso-bidi-font-weight:normal'><span
1258	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1259	mso-hansi-theme-font:minor-latin'>OK</span></b>; the General tab will be
1260	repainted with defaults for the orthorhombic lattice parameters. Enter <b
1261	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'>26.798</span></b>
1263	for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1264	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>a</span></b>,
1265	<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1266	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>7.1618</span></b>
1267	for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1268	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>b</span></b>
1269	and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1270	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>14.1942</span></b>
1271	for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1272	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>c</span></b>.
1273	Press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1274	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Enter</span></b>,
1275	the unit cell volume (2724.178) will be updated.</p>
1276
1277	<h2>Step 2. Import the data</h2>
1278
1279	<p class=MsoNormal>The <span class=SpellE>rubrene</span> data were collected on
1280	the TOPAZ instrument at the SNS Facility, Oak Ridge National Laboratory with 23
1281	different crystal orientations; the local instrument data processing software
1282	has applied corrections and combined them into a single multicolumn <span
1283	class=SpellE>hkl</span> file. To import this do <b style='mso-bidi-font-weight:
1284	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1285	minor-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:
1310	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1311	minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>, a new popup
1312	appears.</p>
1313
1314	<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>
1322
1323	<p class=MsoNormal>Here you select the phase the data belongs to. There is only
1324	<span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1325	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1326	mso-hansi-theme-font:minor-latin'>rubrene</span></b></span> so select it and
1327	press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1328	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1329	The bottom of the data tree is shown, a small data window and the plot shows
1330	the l=0 slice of the last reflection set loaded (HKLF rubrene_orthoC.hkl_22).</p>
1331
1332	<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>
1340
1341	<p class=MsoNormal>The <b style='mso-bidi-font-weight:normal'><span
1342	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1343	mso-hansi-theme-font:minor-latin'>K</span></b> box control allows you to select
1344	other zones & layers to view. The drawing geometry is strictly square (i.e.
1345	not in reciprocal space units). If you do <b style='mso-bidi-font-weight:normal'><span
1346	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1347	mso-hansi-theme-font:minor-latin'>Commands/Plot 3D HKLs</span></b>, a 3D plot
1348	of reciprocal space is shown</p>
1349
1350	<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>
1359
1360	<p class=MsoNormal>The size of the green boxes is proportional to the structure
1361	factors; the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1362	"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1363	minor-latin'>save as/key</span></b> pulldown will give you other viewing
1364	options. Here is a good place to save the GSAS-II project for <span
1365	class=SpellE>rubrene</span>. Do <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'>File/Save project</span></b> from the main
1368	GSAS-II data tree window; a file dialog box will appear. Enter a file name (I
1369	used <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1370	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1371	mso-hansi-theme-font:minor-latin'>rubrene</span></b></span> no extension).</p>
1372
1373	<h2>Step 3. Setup for charge flipping</h2>
1374
1375	<p class=MsoNormal>We have two tasks here. One is to select the reflection sets
1376	to be used in the calculations and the other is to set some controls. To begin
1377	select the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1378	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1379	mso-hansi-theme-font:minor-latin'>rubrene</span></b></span> phase entry in the
1380	GSAS-II data tree; the General tab will appear in the Phase Data for <span
1381	class=SpellE>rubrene</span> window</p>
1382
1383	<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>
1391
1392	<p class=MsoNormal>In the Charge flip controls (about center of the page) press
1393	the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1394	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Select
1395	reflection sets</span></b> button; a <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'>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
1401	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1402	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1403	The General tab will be refreshed. GSAS-II will use all the data to build a
1404	reflection set for charge flipping. For duplicate <span class=SpellE>hkls</span>
1405	the last one encountered will be used. Since atoms are essentially point <span
1406	class=SpellE>scatterers</span> for neutrons, a charge flip map has very sharp
1407	peaks so a better choice for the <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'>k-factor</span></b> (charge flip level) might
1410	be <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1411	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0.5</span></b>,
1412	the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1413	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>k-max</span></b>
1414	should be larger (say <b style='mso-bidi-font-weight:normal'><span
1415	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1416	mso-hansi-theme-font:minor-latin'>50</span></b>) and the map <b
1417	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1418	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Resolution</span></b>
1419	should be smaller (say <b style='mso-bidi-font-weight:normal'><span
1420	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1421	mso-hansi-theme-font:minor-latin'>0.4</span></b>). Set these three values. In
1422	the Fourier map controls, set <b style='mso-bidi-font-weight:normal'><span
1423	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1424	mso-hansi-theme-font:minor-latin'>Peak cutoff %</span></b> to <b
1425	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1426	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>20</span></b>;
1427	this sets the lower limit of the peak search in the charge flip map. When done
1428	the General tab should look like</p>
1429
1430	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1431	id="Picture_x0020_9" o:spid="_x0000_i1051" type="#_x0000_t75" style='width:516.75pt;
1432	height:375pt;visibility:visible;mso-wrap-style:square'>
1433	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image017.png"
1434	o:title=""/>
1435	</v:shape><![endif]--><![if !vml]><img width=689 height=500
1436	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image081.gif"
1437	v:shapes="Picture_x0020_9"><![endif]></span></p>
1438
1439	<p class=MsoNormal><o:p> </o:p></p>
1440
1441	<h2>Step 4. Charge flipping</h2>
1442
1443	<p class=MsoNormal>We are now ready for charge flipping. In the General tab
1444	menu do <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1445	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/Charge
1446	flipping</span></b>; a Charge flipping progress bar will appear showing the
1447	residual and cycle count for the charge flipping calculation. In this case the
1448	residual quickly drops to ~38% and stays there. Press <b style='mso-bidi-font-weight:
1449	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1450	minor-latin;mso-hansi-theme-font:minor-latin'>Cancel</span></b> to stop the
1451	calculation; some information will be printed on the console and after a pause
1452	the Phase Data window will show <b style='mso-bidi-font-weight:normal'><span
1453	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1454	mso-hansi-theme-font:minor-latin'>Map Peaks</span></b> and the plot window will
1455	show a drawing of the obtained structure.</p>
1456
1457	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1458	id="Picture_x0020_10" o:spid="_x0000_i1050" type="#_x0000_t75" style='width:375pt;
1459	height:225pt;visibility:visible;mso-wrap-style:square'>
1460	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image019.png"
1461	o:title=""/>
1462	</v:shape><![endif]--><![if !vml]><img width=500 height=300
1463	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image082.gif"
1464	v:shapes="Picture_x0020_10"><![endif]></span></p>
1465
1466	<p class=MsoNormal>If you scroll down the Map peak list you will find some with
1467	negative magnitudes at the end of the list. GSAS-II searches the map for both
1468	positive and negative peaks; the former are C-atoms and the latter are H-atoms.
1469	</p>
1470
1471	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1472	id="Picture_x0020_11" o:spid="_x0000_i1049" type="#_x0000_t75" style='width:6in;
1473	height:365.25pt;visibility:visible;mso-wrap-style:square'>
1474	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image021.png"
1475	o:title="" croptop="9820f" cropbottom="18705f" cropleft="43453f" cropright="6999f"/>
1476	</v:shape><![endif]--><![if !vml]><img width=576 height=487
1477	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image083.jpg"
1478	v:shapes="Picture_x0020_11"><![endif]></span></p>
1479
1480	<p class=MsoNormal>The plot (which Ive 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 Ive 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 isnt perfect. Or you can roll the map
1489	right/left/up/down (<b style='mso-bidi-font-weight:normal'><span
1490	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1491	mso-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>
1495
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1600	v:shapes="Picture_x0020_12"><![endif]></span></p>
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
1605	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
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1608	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image027.png"
1609	o:title=""/>
1610	</v:shape><![endif]--><![if !vml]><img width=500 height=300
1611	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image087.gif"
1612	v:shapes="Picture_x0020_13"><![endif]></span></p>
1613
1614	<p class=MsoNormal>By carefully looking at the map, you can see the 4-ring <span
1615	class=SpellE>tetracene</span> (<span class=SpellE>naphthacene</span>) core of
1616	the molecule with four phenyl groups attached to both sides on the center two
1617	rings. The unique part consists of 1/4<sup>th</sup> of this group (i.e. half of
1618	one side of the <span class=SpellE>tetracene</span> and one phenyl); one C-atom
1619	sits on a 2-fold and the rest are in general positions. The molecule extends
1620	into the neighboring unit cell so you dont see the whole thing as one group
1621	but has two bits on either side (Ive marked these with arrows above).</p>
1622
1623	<h2>Step 5. Peak selection</h2>
1624
1625	<p class=MsoNormal>GSAS-II provides several ways of selecting peak positions
1626	from a charge flipping map. One way is to pick them directly from the drawing.
1627	Place the cursor on one peak and do a <b style='mso-bidi-font-weight:normal'><span
1628	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1629	mso-hansi-theme-font:minor-latin'>Shift left mouse button</span></b>; it will
1630	be highlighted on the list and it will turn green on the plot. Do a <b
1631	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1632	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Shift right
1633	mouse button</span></b> on the remaining peaks you want to <span class=GramE>pick.</span>
1634	All will turn green (you may have to wiggle the plot a bit with the mouse to
1635	make them show) and all will be highlighted in the list. Alternatively, you can
1636	select the entire list of peaks (double click on upper left empty box of the
1637	table), then do <b style='mso-bidi-font-weight:normal'><span style='font-family:
1638	"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1639	minor-latin'>Map peaks/Unique peaks</span></b>. Better still you can sort the
1640	peaks by one of the column headings and then do <b style='mso-bidi-font-weight:
1641	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1642	minor-latin;mso-hansi-theme-font:minor-latin'>Map peaks/Unique peaks</span></b>.
1643	Ive chosen to sort the peaks on <span class=SpellE><b style='mso-bidi-font-weight:
1644	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1645	minor-latin;mso-hansi-theme-font:minor-latin'>dcent</span></b></span> (distance
1646	from center of the cell) beforehand. After a pause while it sorts out the
1647	unique peaks, it will highlight them in the table and display the picked ones
1648	in green on the plot. In this case they will probably be scattered about the
1649	unit cell and not make a continuous molecule, but they are largely clustered
1650	around the unit cell center. My plot looked like this when I was done.</p>
1651
1652	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1653	id="Picture_x0020_27" o:spid="_x0000_i1046" type="#_x0000_t75" style='width:429.75pt;
1654	height:364.5pt;visibility:visible;mso-wrap-style:square'>
1655	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image029.png"
1656	o:title="" croptop="10059f" cropbottom="18635f" cropleft="36901f"
1657	cropright="13675f"/>
1658	</v:shape><![endif]--><![if !vml]><img width=573 height=486
1659	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image088.jpg"
1660	v:shapes="Picture_x0020_27"><![endif]></span></p>
1661
1662	<p class=MsoNormal>The list has them highlighted (the rest are lower down in my
1663	list; all 18 atoms were found in this charge flipping result)</p>
1664
1665	<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>
1673
1674	<p class=MsoNormal>To add them to the Atom list do <b style='mso-bidi-font-weight:
1675	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1676	minor-latin;mso-hansi-theme-font:minor-latin'>Map peaks/Move peaks</span></b>;
1677	the drawing will show white balls for them.</p>
1678
1679	<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'>
1682	<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>
1688
1689	<p class=MsoNormal>The atom list will give the magnitudes as M names; I found
1690	all 11 C-atoms and 7 H-atoms that were expected.</p>
1691
1692	<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>
1700
1701	<h2>Step 6. Atom identification</h2>
1702
1703	<p class=MsoNormal>You can reorder the atoms in the list; do an <b
1704	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1705	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Alt select</span></b>
1706	for the atom row you want to move. Then do an <b style='mso-bidi-font-weight:
1707	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1708	minor-latin;mso-hansi-theme-font:minor-latin'>Alt select</span></b> on the row
1709	where you want the moved atom to precede it. This way you can put the C-atoms
1710	first and the H-atoms last in the list instead of mixed up as in the above
1711	list. Next select all the positive M peaks (pick the top one and then <b
1712	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1713	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Shift</span></b>
1714	pick the last one). Do <b style='mso-bidi-font-weight:normal'><span
1715	style='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;
1721	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>;
1722	a Periodic Table will appear. Select <b style='mso-bidi-font-weight:normal'><span
1723	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1724	mso-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
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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>
1736
1737	<p class=MsoNormal>Do the same with the remaining negative M atoms make them
1738	H atoms. The drawing shows molecular fragments scattered about the unit cell;
1739	youd like to unify them into a single molecule. Select the C-atom with 2(x)
1740	site symmetry (although any would do). Do <b style='mso-bidi-font-weight:normal'><span
1741	style='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 (& Angle
1744	radii ignored here). Press <b style='mso-bidi-font-weight:normal'><span
1745	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1746	mso-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>
1759
1760	<p class=MsoNormal>The molecule building has scrambled the order of the atoms;
1761	they were located in order as the molecule was built. </p>
1762
1763	<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>
1771
1772	<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:
1781	normal'><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 3σ 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
1818	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1819	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>U thermal
1820	parameters</span></b> and press <b style='mso-bidi-font-weight:normal'><span
1821	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1822	mso-hansi-theme-font:minor-latin'>OK</span></b>. The atom table will show
1823	refine flags for each atom.</p>
1824
1825	<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>
1833
1834	<p class=MsoNormal>Then repeat the <b style='mso-bidi-font-weight:normal'><span
1835	style='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;
1845	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1846	Then repeat <b style='mso-bidi-font-weight:normal'><span style='font-family:
1847	"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1848	minor-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>
1850
1851	<h2>Step 8. Further work</h2>
1852
1853	<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;
1885	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Extinction
1886	type</span></b> (later you can try the other models) for the 1<sup>st</sup>
1887	data set. The window will be repainted with a new line in the data display.
1888	Select the <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'>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:
1895	normal'><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;
1898	mso-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
1901	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1902	mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> but it might be
1903	better to constrain all the Ep values to be the same. To do this select <b
1904	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1905	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Constraints</span></b>
1906	from the GSASII data tree. A blank window with tabs will appear.</p>
1907
1908	<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>
1916
1917	<p class=MsoNormal>Select the <b style='mso-bidi-font-weight:normal'><span
1918	style='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:
1936	normal'><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>
1942
1943	<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>
1962
1963	<p class=MsoNormal>This shows the constraint making Ep for all 23 data sets
1964	equivalent to a single variable. Do <b style='mso-bidi-font-weight:normal'><span
1965	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1966	mso-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
1968	wish to try the other extinction models. Do remember to delete the unused
1969	constraint before adding a new one for the different extinction parameter.
1970	Finally you can draw the molecule; go to <b style='mso-bidi-font-weight:normal'><span
1971	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1972	mso-hansi-theme-font:minor-latin'>Atoms</span></b> and do <b style='mso-bidi-font-weight:
1973	normal'><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>.
1975	That will put the newest atom parameters into the Draw Atoms table. Select <b
1976	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1977	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Draw Atoms</span></b>.
1978	Select the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1979	"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1980	minor-latin'>Style</span></b> column heading; a popup will appear</p>
1981
1982	<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>
1990
1991	<p class=MsoNormal>Notice the first line is blank, if you select that all the
1992	atoms will vanish! Select <b style='mso-bidi-font-weight:normal'><span
1993	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1994	mso-hansi-theme-font:minor-latin'>ellipsoids</span></b> and press <b
1995	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1996	mso-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>
2008
2009	<p class=MsoNormal>You can remove the Map peaks atoms; go to the <b
2010	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2011	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map peaks</span></b>
2012	tab and do <b style='mso-bidi-font-weight:normal'><span style='font-family:
2013	"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2014	minor-latin'>Map peaks/clear peaks</span></b> from the menu. The list will be
2015	erased and the plot will just show the molecule. You can also remove the unit
2016	cell edges, go to <b style='mso-bidi-font-weight:normal'><span
2017	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2018	mso-hansi-theme-font:minor-latin'>Draw Options</span></b> and uncheck the <b
2019	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2020	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Show unit
2021	cell?</span></b> box. Finally, you can remove the charge flipping map; go to <b
2022	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2023	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
2024	and do <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2025	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/Clear
2026	map</span></b>. That deletes the scattering density map and the drawing will be
2027	free of any clutter.</p>
2028
2029	<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>
2037
2038	<p class=MsoNormal>Remember that this is only 1/4<sup>th</sup> of the molecule,
2039	wed like to see the whole thing. First go to the <b style='mso-bidi-font-weight:
2040	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2041	minor-latin;mso-hansi-theme-font:minor-latin'>Atoms</span></b> tab and select
2042	the C-atom that is in a special position 2(x). The do <b style='mso-bidi-font-weight:
2043	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2044	minor-latin;mso-hansi-theme-font:minor-latin'>Compute/Show Distances &
2045	Angles</span></b> and respond <b style='mso-bidi-font-weight:normal'><span
2046	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2047	mso-hansi-theme-font:minor-latin'>OK</span></b> to the popup. The important
2048	result is on the console</p>
2049
2050	<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>
2058
2059	<p class=MsoNormal>This gives the bond distances and angles about the <span
2060	class=GramE>C(</span>1) atom. Particularly note the cell<span class=GramE>+(</span>sym.
2061	Op.) information; we will use this to build the drawing. Go to the <b
2062	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2063	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Draw Atoms</span></b>
2064	tab and select all the atoms (double click on the upper left box). You should
2065	see all atoms selected</p>
2066
2067	<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>
2075
2076	<p class=MsoNormal>Then do <b style='mso-bidi-font-weight:normal'><span
2077	style='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>
2089
2090	<p class=MsoNormal>Based on the 1<sup>st</sup> entry in the bond distance table
2091	<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2092	mso-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
2094	style='mso-spacerun:yes'> </span>2)</span></b>, select the controls for the 2<sup>nd</sup>
2095	operator and increment the 1<sup>st</sup> unit cell</p>
2096
2097	<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
2103	src="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>
2117
2118	<p class=MsoNormal>Next select all the Draw atoms again and do <b
2119	style='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
2121	atoms</span></b>; the selection popup will appear. This time use the other
2122	nonidentity entry in the bond distance table <b style='mso-bidi-font-weight:
2123	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2124	minor-latin;mso-hansi-theme-font:minor-latin'>[0 1 1] + (-2)</span></b>. The
2125	-2 indicates both the inversion and the 2<sup>nd</sup> operator need to be
2126	applied; check both and increment the 2<sup>nd</sup> and 3<sup>rd</sup> unit
2127	cell entries. </p>
2128
2129	<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
2135	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image108.gif"
2136	v:shapes="Picture_x0020_36"><![endif]></span></p>
2137
2138	<p class=MsoNormal>Press <b style='mso-bidi-font-weight:normal'><span
2139	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2140	mso-hansi-theme-font:minor-latin'>OK</span></b>; the entire molecule is drawn.</p>
2141
2142	<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
2151	style='mso-spacerun:yes'> </span></p>
2152
2153	<p class=MsoNormal>Looks really nice. This ends the tutorial. You can save the
2154	project if you wish. All the changes (<span class=SpellE>i.e</span> deleting
2155	Map peaks & clearing the map) will be saved.</p>
2156
2157	</div>
2158
2159	</body>
2160
2161	</html>

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