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source: Tutorials/TOF Charge Flipping/Charge Flipping with TOF single crystal data in GSASII.htm @ 1741

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1159	</head>
1160
1161	<body lang=EN-US link=blue vlink=purple style='tab-interval:.5in'>
1162
1163	<div class=WordSection1>
1164
1165	<h1><span style='mso-fareast-font-family:"Times New Roman"'>Charge flipping
1166	with neutron TOF single crystal data<o:p></o:p></span></h1>
1167
1168	<p class=MsoNormal>In this exercise you will use GSAS-II to solve the structure
1169	of <span class=SpellE>rubrene</span> (C<sub>42</sub>H<sub>28</sub>) from single
1170	crystal neutron data via charge flipping. <span class=SpellE>Rubrene</span> is of
1171	interest as a molecular semiconductor. It crystallizes in the space group <span
1172	class=SpellE>Cmca</span> with the lattice parameters a=26.798Å, b=7.1618Å,
1173	c=14.1942Å, Z=4. Thus, the molecule is sited on a special position with 2/m
1174	symmetry. If you have not done so already, <a href="Starting%20GSAS.htm">start
1175	GSAS-II</a>.</p>
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 border=0 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 border=0 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 border=0 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 <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1276	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1277	mso-hansi-theme-font:minor-latin'>GSASIIexercises</span></b></span><b
1278	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1279	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>/TOF Charge
1280	Flipping</span></b> and select the file <span class=SpellE><b style='mso-bidi-font-weight:
1281	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1282	minor-latin;mso-hansi-theme-font:minor-latin'>ruberene_orthoC.hkl</span></b></span>
1283	(double click the name or press the <b style='mso-bidi-font-weight:normal'><span
1284	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1285	mso-hansi-theme-font:minor-latin'>Open</span></b> button after selecting it). A
1286	popup box will appear.</p>
1287
1288	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1289	id="Picture_x0020_4" o:spid="_x0000_i1056" type="#_x0000_t75" style='width:357.75pt;
1290	height:265.5pt;visibility:visible;mso-wrap-style:square'>
1291	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image007.png"
1292	o:title=""/>
1293	</v:shape><![endif]--><![if !vml]><img border=0 width=477 height=354
1294	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image008.gif"
1295	v:shapes="Picture_x0020_4"><![endif]></span></p>
1296
1297	<p class=MsoNormal>Press <span class=GramE><b style='mso-bidi-font-weight:normal'><span
1298	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1299	mso-hansi-theme-font:minor-latin'>Yes</span></b></span>; another popup will
1300	appear offering you the chance to change the name. Press <b style='mso-bidi-font-weight:
1301	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1302	minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>, a new popup
1303	appears.</p>
1304
1305	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1306	id="Picture_x0020_5" o:spid="_x0000_i1055" type="#_x0000_t75" style='width:240pt;
1307	height:232.5pt;visibility:visible;mso-wrap-style:square'>
1308	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image009.png"
1309	o:title=""/>
1310	</v:shape><![endif]--><![if !vml]><img border=0 width=320 height=310
1311	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image010.gif"
1312	v:shapes="Picture_x0020_5"><![endif]></span></p>
1313
1314	<p class=MsoNormal>Here you select the phase the data belongs to. There is only
1315	<span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1316	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1317	mso-hansi-theme-font:minor-latin'>rubrene</span></b></span> so select it and
1318	press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1319	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1320	The bottom of the data tree is shown, a small data window and the plot shows
1321	the l=0 slice of the last reflection set loaded (HKLF rubrene_orthoC.hkl_22).</p>
1322
1323	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1324	id="Picture_x0020_6" o:spid="_x0000_i1054" type="#_x0000_t75" style='width:525pt;
1325	height:450pt;visibility:visible;mso-wrap-style:square'>
1326	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image011.png"
1327	o:title=""/>
1328	</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1329	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image012.gif"
1330	v:shapes="Picture_x0020_6"><![endif]></span></p>
1331
1332	<p class=MsoNormal>The <b style='mso-bidi-font-weight:normal'><span
1333	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1334	mso-hansi-theme-font:minor-latin'>K</span></b> box control allows you to select
1335	other zones & layers to view. The drawing geometry is strictly square (i.e.
1336	not in reciprocal space units). If you do <b style='mso-bidi-font-weight:normal'><span
1337	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1338	mso-hansi-theme-font:minor-latin'>Commands/Plot 3D HKLs</span></b>, a 3D plot
1339	of reciprocal space is shown</p>
1340
1341	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1342	id="Picture_x0020_1" o:spid="_x0000_i1053" type="#_x0000_t75" style='width:446.25pt;
1343	height:381.75pt;visibility:visible;mso-wrap-style:square'>
1344	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image013.png"
1345	o:title="" croptop="13337f" cropbottom="14997f" cropleft="41056f"
1346	cropright="9449f"/>
1347	</v:shape><![endif]--><![if !vml]><img border=0 width=595 height=509
1348	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image014.jpg"
1349	v:shapes="Picture_x0020_1"><![endif]></span></p>
1350
1351	<p class=MsoNormal>The size of the green boxes is proportional to the structure
1352	factors; the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1353	"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1354	minor-latin'>save as/key</span></b> pulldown will give you other viewing
1355	options. Here is a good place to save the GSAS-II project for <span
1356	class=SpellE>rubrene</span>. Do <b style='mso-bidi-font-weight:normal'><span
1357	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1358	mso-hansi-theme-font:minor-latin'>File/Save project</span></b> from the main
1359	GSAS-II data tree window; a file dialog box will appear. Enter a file name (I
1360	used <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1361	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1362	mso-hansi-theme-font:minor-latin'>rubrene</span></b></span> no extension).</p>
1363
1364	<h2>Step 3. Setup for charge flipping</h2>
1365
1366	<p class=MsoNormal>We have two tasks here. One is to select the reflection sets
1367	to be used in the calculations and the other is to set some controls. To begin
1368	select the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1369	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1370	mso-hansi-theme-font:minor-latin'>rubrene</span></b></span> phase entry in the
1371	GSAS-II data tree; the General tab will appear in the Phase Data for <span
1372	class=SpellE>rubrene</span> window</p>
1373
1374	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1375	id="Picture_x0020_8" o:spid="_x0000_i1052" type="#_x0000_t75" style='width:489pt;
1376	height:375pt;visibility:visible;mso-wrap-style:square'>
1377	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image015.png"
1378	o:title=""/>
1379	</v:shape><![endif]--><![if !vml]><img border=0 width=652 height=500
1380	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image016.gif"
1381	v:shapes="Picture_x0020_8"><![endif]></span></p>
1382
1383	<p class=MsoNormal>In the Charge flip controls (about center of the page) press
1384	the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1385	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Select
1386	reflection sets</span></b> button; a <b style='mso-bidi-font-weight:normal'><span
1387	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1388	mso-hansi-theme-font:minor-latin'>Use data</span></b> popup will appear. You
1389	will want to use all the HKLF data sets; press <b style='mso-bidi-font-weight:
1390	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1391	minor-latin;mso-hansi-theme-font:minor-latin'>Set All</span> </b>and press <b
1392	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1393	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1394	The General tab will be refreshed. GSAS-II will use all the data to build a
1395	reflection set for charge flipping. For duplicate <span class=SpellE>hkls</span>
1396	the last one encountered will be used. Since atoms are essentially point <span
1397	class=SpellE>scatterers</span> for neutrons, a charge flip map has very sharp
1398	peaks so a better choice for the <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'>k-factor</span></b> (charge flip level) might
1401	be <b 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'>0.5</span></b>,
1403	the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1404	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>k-max</span></b>
1405	should be larger (say <b style='mso-bidi-font-weight:normal'><span
1406	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1407	mso-hansi-theme-font:minor-latin'>50</span></b>) and the map <b
1408	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1409	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Resolution</span></b>
1410	should be smaller (say <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'>0.4</span></b>). Set these three values. In
1413	the Fourier map controls, set <b style='mso-bidi-font-weight:normal'><span
1414	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1415	mso-hansi-theme-font:minor-latin'>Peak cutoff %</span></b> to <b
1416	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1417	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>20</span></b>;
1418	this sets the lower limit of the peak search in the charge flip map. When done
1419	the General tab should look like</p>
1420
1421	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1422	id="_x0000_i1051" type="#_x0000_t75" style='width:516.75pt;height:375pt;
1423	visibility:visible;mso-wrap-style:square'>
1424	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image017.png"
1425	o:title=""/>
1426	</v:shape><![endif]--><![if !vml]><img border=0 width=689 height=500
1427	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image018.gif"
1428	v:shapes="_x0000_i1051"><![endif]></span></p>
1429
1430	<p class=MsoNormal><o:p> </o:p></p>
1431
1432	<h2>Step 4. Charge flipping</h2>
1433
1434	<p class=MsoNormal>We are now ready for charge flipping. In the General tab
1435	menu do <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1436	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/Charge
1437	flipping</span></b>; a Charge flipping progress bar will appear showing the
1438	residual and cycle count for the charge flipping calculation. In this case the
1439	residual quickly drops to ~38% and stays there. Press <b style='mso-bidi-font-weight:
1440	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1441	minor-latin;mso-hansi-theme-font:minor-latin'>Cancel</span></b> to stop the
1442	calculation; some information will be printed on the console and after a pause
1443	the Phase Data window will show <b style='mso-bidi-font-weight:normal'><span
1444	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1445	mso-hansi-theme-font:minor-latin'>Map Peaks</span></b> and the plot window will
1446	show a drawing of the obtained structure.</p>
1447
1448	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1449	id="_x0000_i1050" type="#_x0000_t75" style='width:375pt;height:225pt;
1450	visibility:visible;mso-wrap-style:square'>
1451	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image019.png"
1452	o:title=""/>
1453	</v:shape><![endif]--><![if !vml]><img border=0 width=500 height=300
1454	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image020.gif"
1455	v:shapes="_x0000_i1050"><![endif]></span></p>
1456
1457	<p class=MsoNormal>If you scroll down the Map peak list you will find some with
1458	negative magnitudes at the end of the list. GSAS-II searches the map for both
1459	positive and negative peaks; the former are C-atoms and the latter are H-atoms.
1460	</p>
1461
1462	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1463	id="Picture_x0020_11" o:spid="_x0000_i1049" type="#_x0000_t75" style='width:6in;
1464	height:365.25pt;visibility:visible;mso-wrap-style:square'>
1465	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image021.png"
1466	o:title="" croptop="9820f" cropbottom="18705f" cropleft="43453f" cropright="6999f"/>
1467	</v:shape><![endif]--><![if !vml]><img border=0 width=576 height=487
1468	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image022.jpg"
1469	v:shapes="Picture_x0020_11"><![endif]></span></p>
1470
1471	<p class=MsoNormal>The plot (which Ive rotated around a bit) shows white spots
1472	for the positive peaks and red ones for the negative ones; bonds are white
1473	lines. The case Ive drawn here shows a problem with this charge flip solution.
1474	While the charge flipping run has clearly found all the C-atoms and some of the
1475	H-atoms, the molecule is incorrectly placed in the unit cell. To fix this you
1476	could simply repeat the charge flipping run and hope it puts the molecule in
1477	the right place. GSAS-II uses an algorithm based on how structure factor phases
1478	are related for a given space group to reposition the solution; it sometimes fails
1479	if the phase set isnt perfect. Or you can roll the map right/left/up/down (<b
1480	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1481	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>R/L/U/D</span></b>
1482	keys) to put the solution where you want. In this case a few steps with the
1483	L-key sufficed to put the molecule on a 2/m site (i.e. the center of the cell
1484	indicated the multicolored cross on the central C-C bond).</p>
1485
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1495	mso-wrap-distance-top:0;mso-wrap-distance-right:9pt;
1496	mso-wrap-distance-bottom:0;mso-position-horizontal:absolute;
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1579	absolute;z-index:251659264;margin-left:292px;margin-top:203px;width:40px;
1580	height:27px'><img width=40 height=27
1581	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image024.gif"
1582	v:shapes="Straight_x0020_Arrow_x0020_Connector_x0020_37"></span><![endif]><span
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1586	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image025.png"
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1590	v:shapes="Picture_x0020_12"><![endif]></span></p>
1591
1592	<p class=MsoNormal>Notice that as the map is rolled, the Map peak positions are
1593	shifted to match the change in positions.</p>
1594
1595	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1596	id="_x0000_i1047" type="#_x0000_t75" style='width:375pt;height:225pt;
1597	visibility:visible;mso-wrap-style:square'>
1598	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image027.png"
1599	o:title=""/>
1600	</v:shape><![endif]--><![if !vml]><img border=0 width=500 height=300
1601	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image028.gif"
1602	v:shapes="_x0000_i1047"><![endif]></span></p>
1603
1604	<p class=MsoNormal>By carefully looking at the map, you can see the 4-ring <span
1605	class=SpellE>tetracene</span> (<span class=SpellE>naphthacene</span>) core of
1606	the molecule with four phenyl groups attached to both sides on the center two rings.
1607	The unique part consists of 1/4<sup>th</sup> of this group (i.e. half of one
1608	side of the <span class=SpellE>tetracene</span> and one phenyl); one C-atom
1609	sits on a 2-fold and the rest are in general positions. The molecule extends
1610	into the neighboring unit cell so you dont see the whole thing as one group
1611	but has two bits on either side (Ive marked these with arrows above).</p>
1612
1613	<h2>Step 5. Peak selection</h2>
1614
1615	<p class=MsoNormal>GSAS-II provides several ways of selecting peak positions
1616	from a charge flipping map. One way is to pick them directly from the drawing.
1617	Place the cursor on one peak and do a <b style='mso-bidi-font-weight:normal'><span
1618	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1619	mso-hansi-theme-font:minor-latin'>Shift left mouse button</span></b>; it will
1620	be highlighted on the list and it will turn green on the plot. Do a <b
1621	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1622	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Shift right
1623	mouse button</span></b> on the remaining peaks you want to <span class=GramE>pick.</span>
1624	All will turn green (you may have to wiggle the plot a bit with the mouse to
1625	make them show) and all will be highlighted in the list. Alternatively, you can
1626	select the entire list of peaks (double click on upper left empty box of the
1627	table), then do <b style='mso-bidi-font-weight:normal'><span style='font-family:
1628	"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1629	minor-latin'>Map peaks/Unique peaks</span></b>. Better still you can sort the
1630	peaks by one of the column headings and then do <b style='mso-bidi-font-weight:
1631	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1632	minor-latin;mso-hansi-theme-font:minor-latin'>Map peaks/Unique peaks</span></b>.
1633	Ive chosen to sort the peaks on <span class=SpellE><b style='mso-bidi-font-weight:
1634	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1635	minor-latin;mso-hansi-theme-font:minor-latin'>dcent</span></b></span> (distance
1636	from center of the cell) beforehand. After a pause while it sorts out the
1637	unique peaks, it will highlight them in the table and display the picked ones
1638	in green on the plot. In this case they will probably be scattered about the
1639	unit cell and not make a continuous molecule, but they are largely clustered
1640	around the unit cell center. My plot looked like this when I was done.</p>
1641
1642	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1643	id="Picture_x0020_27" o:spid="_x0000_i1046" type="#_x0000_t75" style='width:429.75pt;
1644	height:364.5pt;visibility:visible;mso-wrap-style:square'>
1645	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image029.png"
1646	o:title="" croptop="10059f" cropbottom="18635f" cropleft="36901f"
1647	cropright="13675f"/>
1648	</v:shape><![endif]--><![if !vml]><img border=0 width=573 height=486
1649	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image030.jpg"
1650	v:shapes="Picture_x0020_27"><![endif]></span></p>
1651
1652	<p class=MsoNormal>The list has them highlighted (the rest are lower down in my
1653	list; all 18 atoms were found in this charge flipping result)</p>
1654
1655	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1656	id="_x0000_i1045" type="#_x0000_t75" style='width:375pt;height:435.75pt;
1657	visibility:visible;mso-wrap-style:square'>
1658	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image031.png"
1659	o:title=""/>
1660	</v:shape><![endif]--><![if !vml]><img border=0 width=500 height=581
1661	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image032.gif"
1662	v:shapes="_x0000_i1045"><![endif]></span></p>
1663
1664	<p class=MsoNormal>To add them to the Atom list do <b style='mso-bidi-font-weight:
1665	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1666	minor-latin;mso-hansi-theme-font:minor-latin'>Map peaks/Move peaks</span></b>;
1667	the drawing will show white balls for them.</p>
1668
1669	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1670	id="_x0000_i1044" type="#_x0000_t75" style='width:6in;height:369pt;
1671	visibility:visible;mso-wrap-style:square'>
1672	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image033.png"
1673	o:title="" croptop="10579f" cropbottom="17404f" cropleft="37800f"
1674	cropright="12584f"/>
1675	</v:shape><![endif]--><![if !vml]><img border=0 width=576 height=492
1676	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image034.jpg"
1677	v:shapes="_x0000_i1044"><![endif]></span></p>
1678
1679	<p class=MsoNormal>The atom list will give the magnitudes as M names; I found
1680	all 11 C-atoms and 7 H-atoms that were expected.</p>
1681
1682	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1683	id="_x0000_i1043" type="#_x0000_t75" style='width:525pt;height:351.75pt;
1684	visibility:visible;mso-wrap-style:square'>
1685	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image035.png"
1686	o:title=""/>
1687	</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=469
1688	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image036.gif"
1689	v:shapes="_x0000_i1043"><![endif]></span></p>
1690
1691	<h2>Step 6. Atom identification</h2>
1692
1693	<p class=MsoNormal>You can reorder the atoms in the list; do an <b
1694	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1695	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Alt select</span></b>
1696	for the atom row you want to move. Then do an <b style='mso-bidi-font-weight:
1697	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1698	minor-latin;mso-hansi-theme-font:minor-latin'>Alt select</span></b> on the row
1699	where you want the moved atom to precede it. This way you can put the C-atoms
1700	first and the H-atoms last in the list instead of mixed up as in the above
1701	list. Next select all the positive M peaks (pick the top one and then <b
1702	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1703	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Shift</span></b>
1704	pick the last one). Do <b style='mso-bidi-font-weight:normal'><span
1705	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1706	mso-hansi-theme-font:minor-latin'>Edit/Modify atom parameters</span></b> from
1707	the Atoms menu; a popup will appear. Pick <b style='mso-bidi-font-weight:normal'><span
1708	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1709	mso-hansi-theme-font:minor-latin'>Type</span></b> and press <b
1710	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1711	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>;
1712	a Periodic Table will appear. Select <b style='mso-bidi-font-weight:normal'><span
1713	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1714	mso-hansi-theme-font:minor-latin'>C</span></b> from the C-atom pulldown. All
1715	the C-atom names and types will change. You should also move the C-atom with
1716	2(x) site symmetry to the top of the list.</p>
1717
1718	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1719	id="_x0000_i1042" type="#_x0000_t75" style='width:525pt;height:225pt;
1720	visibility:visible;mso-wrap-style:square'>
1721	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image037.png"
1722	o:title=""/>
1723	</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=300
1724	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image038.gif"
1725	v:shapes="_x0000_i1042"><![endif]></span></p>
1726
1727	<p class=MsoNormal>Do the same with the remaining negative M atoms make them
1728	H atoms. The drawing shows molecular fragments scattered about the unit cell;
1729	youd like to unify them into a single molecule. Select the C-atom with 2(x)
1730	site symmetry (although any would do). Do <b style='mso-bidi-font-weight:normal'><span
1731	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1732	mso-hansi-theme-font:minor-latin'>Edit/Assemble molecule</span></b> from the
1733	Atoms menu; a popup will appear offering choices for Bond radii (& Angle
1734	radii ignored here). Press <b style='mso-bidi-font-weight:normal'><span
1735	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1736	mso-hansi-theme-font:minor-latin'>Ok</span></b>; the Atom table will be revised
1737	and the plot will show an assembled molecule (the picked starting atom in
1738	green). </p>
1739
1740	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1741	id="_x0000_i1041" type="#_x0000_t75" style='width:6in;height:366pt;
1742	visibility:visible;mso-wrap-style:square'>
1743	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image039.png"
1744	o:title="" croptop="11018f" cropbottom="17360f" cropleft="37831f"
1745	cropright="12587f"/>
1746	</v:shape><![endif]--><![if !vml]><img border=0 width=576 height=488
1747	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image040.jpg"
1748	v:shapes="_x0000_i1041"><![endif]></span></p>
1749
1750	<p class=MsoNormal>The molecule building has scrambled the order of the atoms;
1751	they were located in order as the molecule was built. </p>
1752
1753	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1754	id="_x0000_i1040" type="#_x0000_t75" style='width:525pt;height:351.75pt;
1755	visibility:visible;mso-wrap-style:square'>
1756	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image041.png"
1757	o:title=""/>
1758	</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=469
1759	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image042.gif"
1760	v:shapes="_x0000_i1040"><![endif]></span></p>
1761
1762	<p class=MsoNormal>You can reorder them to put the H-atoms at the end of the list.
1763	Then select all of them and then do <span style='font-family:"Calibri",sans-serif;
1764	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Modify
1765	atom parameters</span>. Pick <b style='mso-bidi-font-weight:normal'><span
1766	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1767	mso-hansi-theme-font:minor-latin'>Name</span></b> from the pulldown and press <b
1768	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1769	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1770	You are asked if you really want to do this, press <span class=GramE><b
1771	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1772	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Yes</span></b></span>.
1773	The atoms are then renamed in numeric order.</p>
1774
1775	<h2>Step 7. Refinement</h2>
1776
1777	<p class=MsoNormal>Since the structure is complete, we can do the full
1778	refinement. Select the <b style='mso-bidi-font-weight:normal'><span
1779	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1780	mso-hansi-theme-font:minor-latin'>Controls</span></b> item from the GSAS-II
1781	data tree. Unset the <b style='mso-bidi-font-weight:normal'><span
1782	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1783	mso-hansi-theme-font:minor-latin'>Refine HKLF as F^2</span></b> box and enter <b
1784	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'>3.0</span></b>
1786	for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1787	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Min <span
1788	class=SpellE>obs</span>/sig</span></b>. This makes the least squares refine on <span
1789	class=SpellE><span class=GramE>F<sub>o</sub></span></span> with 3σ cutoff
1790	on <span class=SpellE>F<sub>o</sub></span>. From the main GSAS-II data tree menu
1791	do <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1792	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>;
1793	this will do the 1<sup>st</sup> least squares refinement varying only the data
1794	set scale factors. A progress bar popup will appear showing the residuals as
1795	the refinement proceeds. When done, a small popup will appear with the final
1796	residual; press <b style='mso-bidi-font-weight:normal'><span style='font-family:
1797	"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1798	minor-latin'>OK</span></b> to accept it. The final <span class=SpellE>R<sub>w</sub></span>
1799	is about 49% Go to the <b style='mso-bidi-font-weight:normal'><span
1800	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1801	mso-hansi-theme-font:minor-latin'>Atoms</span></b> tab for the <span
1802	class=SpellE>rubrene</span> phase, double click the <b style='mso-bidi-font-weight:
1803	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1804	minor-latin;mso-hansi-theme-font:minor-latin'>refine</span></b> column heading;
1805	a popup box will appear. Select both <b style='mso-bidi-font-weight:normal'><span
1806	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1807	mso-hansi-theme-font:minor-latin'>X - coordinates</span></b> and <b
1808	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1809	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>U thermal
1810	parameters</span></b> and press <b style='mso-bidi-font-weight:normal'><span
1811	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1812	mso-hansi-theme-font:minor-latin'>OK</span></b>. The atom table will show refine
1813	flags for each atom.</p>
1814
1815	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1816	id="_x0000_i1039" type="#_x0000_t75" style='width:525pt;height:225pt;
1817	visibility:visible;mso-wrap-style:square'>
1818	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image043.png"
1819	o:title=""/>
1820	</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=300
1821	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image044.gif"
1822	v:shapes="_x0000_i1039"><![endif]></span></p>
1823
1824	<p class=MsoNormal>Then repeat the <b style='mso-bidi-font-weight:normal'><span
1825	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1826	mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> command in the
1827	main menu. The final residual will be much better <span class=SpellE>R<sub>w</sub></span>
1828	~10%. Next, convert all the atoms from isotropic thermal parameters to
1829	anisotropic ones. Double click <span class=GramE>the <b style='mso-bidi-font-weight:
1830	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1831	minor-latin;mso-hansi-theme-font:minor-latin'>I</span></b></span><b
1832	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1833	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>/A</span></b>
1834	column heading and select <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'>Anisotropic</span></b> and press <b
1837	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1838	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1839	Then repeat <b style='mso-bidi-font-weight:normal'><span style='font-family:
1840	"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1841	minor-latin'>Calculate/Refine</span></b> (perhaps twice); the final <span
1842	class=SpellE>R<sub>w</sub></span> ~6.06% which is quite nice.</p>
1843
1844	<h2>Step 8. Further work</h2>
1845
1846	<p class=MsoNormal>Since this is TOF neutron single crystal diffraction, a
1847	relatively large crystal was used and the neutron wavelength covered a fairly
1848	wide range of values. Hence, it is likely that the strong reflection intensities
1849	suffered from some level of extinction. To find these parameters select the <b
1850	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1851	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Data</span></b>
1852	tab in the Phase Data window; all that will show is a list of a data set names
1853	with a <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1854	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Show</span></b>
1855	box for each. To see what is there select the <b style='mso-bidi-font-weight:
1856	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1857	minor-latin;mso-hansi-theme-font:minor-latin'>Show</span></b> box; alternatively
1858	to see all of them do <b style='mso-bidi-font-weight:normal'><span
1859	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1860	mso-hansi-theme-font:minor-latin'>Edit/Show/Hide</span></b> all the window will
1861	look something like</p>
1862
1863	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1864	id="Picture_x0020_22" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:319.5pt;
1865	height:378pt;visibility:visible;mso-wrap-style:square'>
1866	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image045.png"
1867	o:title=""/>
1868	</v:shape><![endif]--><![if !vml]><img border=0 width=426 height=504
1869	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image046.gif"
1870	v:shapes="Picture_x0020_22"><![endif]></span></p>
1871
1872	<p class=MsoNormal>This is a very long display with entries for 23 data sets
1873	(NB: in alphabetical order not numeric order!). The Scale factors were selected
1874	for refinement by default (box checked). Here you want to select <b
1875	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'>Primary</span></b>
1877	for the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1878	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Extinction
1879	type</span></b> (later you can try the other models) for the 1<sup>st</sup>
1880	data set. The window will be repainted with a new line in the data display. Select
1881	the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1882	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Ep</span></b>
1883	check box so it will be refined. To set all the rest press the <b
1884	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1885	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Copy flags?</span></b>
1886	<span class=GramE>button</span> for that data set (not one of the others!). A
1887	popup will appear giving the list of data sets; press the <span class=SpellE><b
1888	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1889	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>SetAll</span></b></span>
1890	button and then <b style='mso-bidi-font-weight:normal'><span style='font-family:
1891	"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1892	minor-latin'>OK</span></b>. The data window will be repainted with all the
1893	Extinction types set to Primary and Ep set to refine. You could then do <b
1894	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1895	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>
1896	but it might be better to constrain all the Ep values to be the same. To do
1897	this select <b style='mso-bidi-font-weight:normal'><span style='font-family:
1898	"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1899	minor-latin'>Constraints</span></b> from the GSASII data tree. A blank window
1900	with tabs will appear.</p>
1901
1902	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1903	id="Picture_x0020_23" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:225pt;
1904	height:352.5pt;visibility:visible;mso-wrap-style:square'>
1905	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image047.png"
1906	o:title=""/>
1907	</v:shape><![endif]--><![if !vml]><img border=0 width=300 height=470
1908	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image048.gif"
1909	v:shapes="Picture_x0020_23"><![endif]></span></p>
1910
1911	<p class=MsoNormal>Select the <b style='mso-bidi-font-weight:normal'><span
1912	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1913	mso-hansi-theme-font:minor-latin'>Histogram/Phase</span></b> constraints tab; the
1914	window is still blank but that tab is now highlighted. Next do <b
1915	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1916	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Add
1917	equivalence</span></b>; a popup will appear asking for a parameter name to be
1918	constrained.</p>
1919
1920	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1921	id="Picture_x0020_24" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:468.75pt;
1922	height:300pt;visibility:visible;mso-wrap-style:square'>
1923	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image049.png"
1924	o:title=""/>
1925	</v:shape><![endif]--><![if !vml]><img border=0 width=625 height=400
1926	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image050.gif"
1927	v:shapes="Picture_x0020_24"><![endif]></span></p>
1928
1929	<p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span
1930	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1931	mso-hansi-theme-font:minor-latin'>0:0<span class=GramE>:Ep</span></span></b>,
1932	that is the primary extinction parameter for the 1<sup>st</sup> dataset and the
1933	<span class=SpellE>rubrene</span> phase. Press <b style='mso-bidi-font-weight:
1934	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1935	minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.</p>
1936
1937	<p class=MsoNormal>The popup is replaced with a new list of all compatible
1938	parameters that <b style='mso-bidi-font-weight:normal'><span style='font-family:
1939	"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1940	minor-latin'>0:0<span class=GramE>:Ep</span></span></b> is to be made
1941	equivalent to. Scroll down and find <b style='mso-bidi-font-weight:normal'><span
1942	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1943	mso-hansi-theme-font:minor-latin'>0<span class=GramE>:all:Ep</span></span></b>
1944	and pick that; the Constraint window will change to</p>
1945
1946	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1947	id="Picture_x0020_25" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:481.5pt;
1948	height:352.5pt;visibility:visible;mso-wrap-style:square'>
1949	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image051.png"
1950	o:title=""/>
1951	</v:shape><![endif]--><![if !vml]><img border=0 width=642 height=470
1952	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image052.gif"
1953	v:shapes="Picture_x0020_25"><![endif]></span></p>
1954
1955	<p class=MsoNormal>This shows the constraint making Ep for all 23 data sets
1956	equivalent to a single variable. Do <b style='mso-bidi-font-weight:normal'><span
1957	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1958	mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; my <span
1959	class=SpellE>R<sub>w</sub></span> was 5.907% only a slight improvement. You may
1960	wish to try the other extinction models. Do remember to delete the unused
1961	constraint before adding a new one for the different extinction parameter.
1962	Finally you can draw the molecule; go to <b style='mso-bidi-font-weight:normal'><span
1963	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1964	mso-hansi-theme-font:minor-latin'>Atoms</span></b> and do <b style='mso-bidi-font-weight:
1965	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1966	minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Reload draw atoms</span></b>.
1967	That will put the newest atom parameters into the Draw Atoms table. Select <b
1968	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1969	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Draw Atoms</span></b>.
1970	Select the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1971	"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1972	minor-latin'>Style</span></b> column heading; a popup will appear</p>
1973
1974	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1975	id="Picture_x0020_26" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:259.5pt;
1976	height:252pt;visibility:visible;mso-wrap-style:square'>
1977	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image053.png"
1978	o:title=""/>
1979	</v:shape><![endif]--><![if !vml]><img border=0 width=346 height=336
1980	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image054.gif"
1981	v:shapes="Picture_x0020_26"><![endif]></span></p>
1982
1983	<p class=MsoNormal>Notice the first line is blank, if you select that all the
1984	atoms will vanish! Select <b style='mso-bidi-font-weight:normal'><span
1985	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1986	mso-hansi-theme-font:minor-latin'>ellipsoids</span></b> and press <b
1987	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1988	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1989	The plot will change, but it is pretty cluttered.</p>
1990
1991	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1992	id="Picture_x0020_28" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:465.75pt;
1993	height:395.25pt;visibility:visible;mso-wrap-style:square'>
1994	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image055.png"
1995	o:title="" croptop="11745f" cropbottom="16560f" cropleft="43690f"
1996	cropright="6723f"/>
1997	</v:shape><![endif]--><![if !vml]><img border=0 width=621 height=527
1998	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image056.jpg"
1999	v:shapes="Picture_x0020_28"><![endif]></span></p>
2000
2001	<p class=MsoNormal>You can remove the Map peaks atoms; go to the <b
2002	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2003	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map peaks</span></b>
2004	tab and do <b style='mso-bidi-font-weight:normal'><span style='font-family:
2005	"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2006	minor-latin'>Map peaks/clear peaks</span></b> from the menu. The list will be
2007	erased and the plot will just show the molecule. You can also remove the unit
2008	cell edges, go to <b style='mso-bidi-font-weight:normal'><span
2009	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2010	mso-hansi-theme-font:minor-latin'>Draw Options</span></b> and uncheck the <b
2011	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2012	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Show unit
2013	cell?</span></b> <span class=GramE>box</span>. Finally, you can remove the
2014	charge flipping map; go to <b style='mso-bidi-font-weight:normal'><span
2015	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2016	mso-hansi-theme-font:minor-latin'>General</span></b> and do <b
2017	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2018	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/Clear
2019	map</span></b>. That deletes the scattering density map and the drawing will be
2020	free of any clutter.</p>
2021
2022	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2023	id="Picture_x0020_29" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:429.75pt;
2024	height:366pt;visibility:visible;mso-wrap-style:square'>
2025	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image057.png"
2026	o:title="" croptop="8339f" cropbottom="19928f" cropleft="44139f" cropright="6324f"/>
2027	</v:shape><![endif]--><![if !vml]><img border=0 width=573 height=488
2028	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image058.jpg"
2029	v:shapes="Picture_x0020_29"><![endif]></span></p>
2030
2031	<p class=MsoNormal>Remember that this is only 1/4<sup>th</sup> of the molecule,
2032	wed like to see the whole thing. First go to the <b style='mso-bidi-font-weight:
2033	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2034	minor-latin;mso-hansi-theme-font:minor-latin'>Atoms</span></b> tab and select the
2035	C-atom that is in a special position 2(x). The do <b style='mso-bidi-font-weight:
2036	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2037	minor-latin;mso-hansi-theme-font:minor-latin'>Compute/Show Distances &
2038	Angles</span></b> and respond <b style='mso-bidi-font-weight:normal'><span
2039	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2040	mso-hansi-theme-font:minor-latin'>OK</span></b> to the popup. The important
2041	result is on the console</p>
2042
2043	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2044	id="Picture_x0020_30" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:609.75pt;
2045	height:278.25pt;visibility:visible;mso-wrap-style:square'>
2046	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image059.png"
2047	o:title=""/>
2048	</v:shape><![endif]--><![if !vml]><img border=0 width=813 height=371
2049	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image060.gif"
2050	v:shapes="Picture_x0020_30"><![endif]></span></p>
2051
2052	<p class=MsoNormal>This gives the bond distances and angles about the <span
2053	class=GramE>C(</span>1) atom. Particularly note the cell<span class=GramE>+(</span>sym.
2054	Op.) information; we will use this to build the drawing. Go to the <b
2055	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2056	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Draw Atoms</span></b>
2057	tab and select all the atoms (double click on the upper left box). You should
2058	see all atoms selected</p>
2059
2060	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2061	id="Picture_x0020_31" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:450pt;
2062	height:225pt;visibility:visible;mso-wrap-style:square'>
2063	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image061.png"
2064	o:title=""/>
2065	</v:shape><![endif]--><![if !vml]><img border=0 width=600 height=300
2066	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image062.gif"
2067	v:shapes="Picture_x0020_31"><![endif]></span></p>
2068
2069	<p class=MsoNormal>Then do <b style='mso-bidi-font-weight:normal'><span
2070	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2071	mso-hansi-theme-font:minor-latin'>Edit/Add atoms</span></b>; a popup will
2072	appear</p>
2073
2074	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2075	id="Picture_x0020_32" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:179.25pt;
2076	height:246.75pt;visibility:visible;mso-wrap-style:square'>
2077	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image063.png"
2078	o:title=""/>
2079	</v:shape><![endif]--><![if !vml]><img border=0 width=239 height=329
2080	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image064.gif"
2081	v:shapes="Picture_x0020_32"><![endif]></span></p>
2082
2083	<p class=MsoNormal>Based on the 1<sup>st</sup> entry in the bond distance table
2084	<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2085	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>[1 0 0<span
2086	class=GramE>]<span style='mso-spacerun:yes'> </span>+</span>(<span
2087	style='mso-spacerun:yes'> </span>2)</span></b>, select the controls for the 2<sup>nd</sup>
2088	operator and increment the 1<sup>st</sup> unit cell</p>
2089
2090	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2091	id="Picture_x0020_33" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:179.25pt;
2092	height:246.75pt;visibility:visible;mso-wrap-style:square'>
2093	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image065.png"
2094	o:title=""/>
2095	</v:shape><![endif]--><![if !vml]><img border=0 width=239 height=329
2096	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image066.gif"
2097	v:shapes="Picture_x0020_33"><![endif]></span></p>
2098
2099	<p class=MsoNormal>Press OK. The plot now shows œ the molecule.</p>
2100
2101	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2102	id="Picture_x0020_34" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:429.75pt;
2103	height:372pt;visibility:visible;mso-wrap-style:square'>
2104	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image067.png"
2105	o:title="" croptop="11786f" cropbottom="16031f" cropleft="46740f"
2106	cropright="3791f"/>
2107	</v:shape><![endif]--><![if !vml]><img border=0 width=573 height=496
2108	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image068.jpg"
2109	v:shapes="Picture_x0020_34"><![endif]></span></p>
2110
2111	<p class=MsoNormal>Next select all the Draw atoms again and do <b
2112	style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2113	mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Add
2114	atoms</span></b>; the selection popup will appear. This time use the other
2115	nonidentity entry in the bond distance table <b style='mso-bidi-font-weight:
2116	normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2117	minor-latin;mso-hansi-theme-font:minor-latin'>[0 1 1] + (-2)</span></b>. The -2
2118	indicates both the inversion and the 2<sup>nd</sup> operator need to be applied;
2119	check both and increment the 2<sup>nd</sup> and 3<sup>rd</sup> unit cell
2120	entries. </p>
2121
2122	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2123	id="Picture_x0020_36" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:179.25pt;
2124	height:246.75pt;visibility:visible;mso-wrap-style:square'>
2125	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image069.png"
2126	o:title=""/>
2127	</v:shape><![endif]--><![if !vml]><img border=0 width=239 height=329
2128	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image070.gif"
2129	v:shapes="Picture_x0020_36"><![endif]></span></p>
2130
2131	<p class=MsoNormal>Press <b style='mso-bidi-font-weight:normal'><span
2132	style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2133	mso-hansi-theme-font:minor-latin'>OK</span></b>; the entire molecule is drawn.</p>
2134
2135	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2136	id="Picture_x0020_35" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:429.75pt;
2137	height:364.5pt;visibility:visible;mso-wrap-style:square'>
2138	<v:imagedata src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image071.png"
2139	o:title="" croptop="10221f" cropbottom="18166f" cropleft="42114f"
2140	cropright="8322f"/>
2141	</v:shape><![endif]--><![if !vml]><img border=0 width=573 height=486
2142	src="Charge%20Flipping%20with%20TOF%20single%20crystal%20data%20in%20GSASII_files/image072.jpg"
2143	v:shapes="Picture_x0020_35"><![endif]></span><span
2144	style='mso-spacerun:yes'> </span></p>
2145
2146	<p class=MsoNormal>Looks really nice. This ends the tutorial. You can save the
2147	project if you wish. All the changes (<span class=SpellE>i.e</span> deleting
2148	Map peaks & clearing the map) will be saved.</p>
2149
2150	</div>
2151
2152	</body>
2153
2154	</html>

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