Changeset 1725
- Timestamp:
- Mar 17, 2015 10:22:47 AM (9 years ago)
- Location:
- Tutorials/FitPeaks
- Files:
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- 23 edited
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Fit Peaks.htm (modified) (70 diffs)
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Tutorials/FitPeaks/Fit Peaks.htm
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<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 202 Name="List Bullet 3"/> 203 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 204 Name="List Bullet 4"/> 205 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 206 Name="List Bullet 5"/> 207 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 208 Name="List Number 2"/> 209 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 210 Name="List Number 3"/> 211 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 212 Name="List Number 4"/> 213 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 214 Name="List Number 5"/> 215 <w:LsdException Locked="false" Priority="10" QFormat="true" Name="Title"/> 216 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 217 Name="Closing"/> 218 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 219 Name="Signature"/> 220 <w:LsdException Locked="false" Priority="1" SemiHidden="true" 221 UnhideWhenUsed="true" Name="Default Paragraph Font"/> 222 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 223 Name="Body Text"/> 224 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 225 Name="Body Text Indent"/> 226 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 227 Name="List Continue"/> 228 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 229 Name="List Continue 2"/> 230 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 231 Name="List Continue 3"/> 232 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 233 Name="List Continue 4"/> 234 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 235 Name="List Continue 5"/> 236 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 237 Name="Message Header"/> 238 <w:LsdException Locked="false" Priority="11" QFormat="true" Name="Subtitle"/> 239 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 240 Name="Salutation"/> 241 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 242 Name="Date"/> 243 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 244 Name="Body Text First Indent"/> 245 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 246 Name="Body Text First Indent 2"/> 247 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 248 Name="Note Heading"/> 249 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 250 Name="Body Text 2"/> 251 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 252 Name="Body Text 3"/> 253 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 254 Name="Body Text Indent 2"/> 255 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 256 Name="Body Text Indent 3"/> 257 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 258 Name="Block Text"/> 259 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 260 Name="Hyperlink"/> 261 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 262 Name="FollowedHyperlink"/> 263 <w:LsdException Locked="false" Priority="22" QFormat="true" Name="Strong"/> 264 <w:LsdException Locked="false" Priority="20" QFormat="true" Name="Emphasis"/> 265 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 266 Name="Document Map"/> 267 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 268 Name="Plain Text"/> 269 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 270 Name="E-mail Signature"/> 271 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 272 Name="HTML Top of Form"/> 273 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 274 Name="HTML Bottom of Form"/> 275 <w:LsdException Locked="false" SemiHidden="true" 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SemiHidden="true" UnhideWhenUsed="true" 296 Name="HTML Variable"/> 297 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 298 Name="Normal Table"/> 299 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 300 Name="annotation subject"/> 301 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 302 Name="No List"/> 303 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 304 Name="Outline List 1"/> 305 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 306 Name="Outline List 2"/> 307 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 308 Name="Outline List 3"/> 309 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 310 Name="Table Simple 1"/> 311 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 312 Name="Table Simple 2"/> 313 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 314 Name="Table Simple 3"/> 315 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SemiHidden="true" UnhideWhenUsed="true" 354 Name="Table Grid 8"/> 355 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 356 Name="Table List 1"/> 357 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 358 Name="Table List 2"/> 359 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 360 Name="Table List 3"/> 361 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 362 Name="Table List 4"/> 363 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 364 Name="Table List 5"/> 365 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 366 Name="Table List 6"/> 367 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 368 Name="Table List 7"/> 369 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 370 Name="Table List 8"/> 371 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 372 Name="Table 3D effects 1"/> 373 <w:LsdException 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Name="Table Web 3"/> 393 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 394 Name="Balloon Text"/> 395 <w:LsdException Locked="false" Priority="59" Name="Table Grid"/> 396 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 397 Name="Table Theme"/> 398 <w:LsdException Locked="false" SemiHidden="true" Name="Placeholder Text"/> 399 <w:LsdException Locked="false" Priority="1" QFormat="true" Name="No Spacing"/> 400 <w:LsdException Locked="false" Priority="60" Name="Light Shading"/> 401 <w:LsdException Locked="false" Priority="61" Name="Light List"/> 402 <w:LsdException Locked="false" Priority="62" Name="Light Grid"/> 403 <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1"/> 404 <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2"/> 405 <w:LsdException Locked="false" Priority="65" Name="Medium List 1"/> 406 <w:LsdException Locked="false" Priority="66" Name="Medium List 2"/> 407 <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1"/> 408 <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2"/> 409 <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3"/> 410 <w:LsdException Locked="false" Priority="70" Name="Dark List"/> 411 <w:LsdException Locked="false" Priority="71" Name="Colorful Shading"/> 412 <w:LsdException Locked="false" Priority="72" Name="Colorful List"/> 413 <w:LsdException Locked="false" Priority="73" Name="Colorful Grid"/> 414 <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 1"/> 415 <w:LsdException Locked="false" Priority="61" Name="Light List Accent 1"/> 416 <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 1"/> 417 <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 1"/> 418 <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 1"/> 419 <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 1"/> 420 <w:LsdException Locked="false" SemiHidden="true" Name="Revision"/> 421 <w:LsdException Locked="false" Priority="34" QFormat="true" 422 Name="List Paragraph"/> 423 <w:LsdException Locked="false" Priority="29" QFormat="true" Name="Quote"/> 424 <w:LsdException Locked="false" Priority="30" QFormat="true" 425 Name="Intense Quote"/> 426 <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 1"/> 427 <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 1"/> 428 <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 1"/> 429 <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 1"/> 430 <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 1"/> 431 <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 1"/> 432 <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 1"/> 433 <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 1"/> 434 <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 2"/> 435 <w:LsdException Locked="false" Priority="61" Name="Light List Accent 2"/> 436 <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 2"/> 437 <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 2"/> 438 <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 2"/> 439 <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 2"/> 440 <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 2"/> 441 <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 2"/> 442 <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 2"/> 443 <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 2"/> 444 <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 2"/> 445 <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 2"/> 446 <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 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Priority="69" Name="Medium Grid 3 Accent 4"/> 472 <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 4"/> 473 <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 4"/> 474 <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 4"/> 475 <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 4"/> 476 <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 5"/> 477 <w:LsdException Locked="false" Priority="61" Name="Light List Accent 5"/> 478 <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 5"/> 479 <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 5"/> 480 <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 5"/> 481 <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 5"/> 482 <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 5"/> 483 <w:LsdException Locked="false" Priority="67" Name="Medium 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<w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 6"/> 497 <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 6"/> 498 <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 6"/> 499 <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 6"/> 500 <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 6"/> 501 <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 6"/> 502 <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 6"/> 503 <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 6"/> 504 <w:LsdException Locked="false" Priority="19" QFormat="true" 505 Name="Subtle Emphasis"/> 506 <w:LsdException Locked="false" Priority="21" QFormat="true" 507 Name="Intense Emphasis"/> 508 <w:LsdException Locked="false" Priority="31" QFormat="true" 509 Name="Subtle Reference"/> 510 <w:LsdException Locked="false" Priority="32" QFormat="true" 511 Name="Intense Reference"/> 512 <w:LsdException Locked="false" Priority="33" QFormat="true" Name="Book Title"/> 513 <w:LsdException Locked="false" Priority="37" SemiHidden="true" 514 UnhideWhenUsed="true" Name="Bibliography"/> 515 <w:LsdException Locked="false" Priority="39" SemiHidden="true" 516 UnhideWhenUsed="true" QFormat="true" Name="TOC Heading"/> 517 <w:LsdException Locked="false" Priority="41" Name="Plain Table 1"/> 518 <w:LsdException Locked="false" Priority="42" Name="Plain Table 2"/> 519 <w:LsdException Locked="false" Priority="43" Name="Plain Table 3"/> 520 <w:LsdException Locked="false" Priority="44" Name="Plain Table 4"/> 521 <w:LsdException Locked="false" Priority="45" Name="Plain Table 5"/> 522 <w:LsdException Locked="false" Priority="40" Name="Grid Table Light"/> 523 <w:LsdException Locked="false" Priority="46" Name="Grid Table 1 Light"/> 524 <w:LsdException Locked="false" Priority="47" Name="Grid Table 2"/> 525 <w:LsdException Locked="false" Priority="48" Name="Grid 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Name="Grid Table 6 Colorful Accent 3"/> 558 <w:LsdException Locked="false" Priority="52" 559 Name="Grid Table 7 Colorful Accent 3"/> 560 <w:LsdException Locked="false" Priority="46" 561 Name="Grid Table 1 Light Accent 4"/> 562 <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 4"/> 563 <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 4"/> 564 <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 4"/> 565 <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 4"/> 566 <w:LsdException Locked="false" Priority="51" 567 Name="Grid Table 6 Colorful Accent 4"/> 568 <w:LsdException Locked="false" Priority="52" 569 Name="Grid Table 7 Colorful Accent 4"/> 570 <w:LsdException Locked="false" Priority="46" 571 Name="Grid Table 1 Light Accent 5"/> 572 <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 5"/> 573 <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 5"/> 574 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font-family:"Calibri",sans-serif; 917 1236 mso-ascii-font-family:Calibri; 918 1237 mso-ascii-theme-font:minor-latin; … … 1107 1426 mso-pagination:widow-orphan; 1108 1427 font-size:10.0pt; 1109 font-family:"Calibri", "sans-serif";1428 font-family:"Calibri",sans-serif; 1110 1429 mso-ascii-font-family:Calibri; 1111 1430 mso-ascii-theme-font:minor-latin; … … 1132 1451 be done.</p> 1133 1452 1134 <p class=MsoNormal>If you have not done so already, <a 1135 href="Starting%20GSAS.htm">start GSAS-II</a>.</p> 1136 1137 <h2>Step 1: read in the data file</h2> 1453 <p class=MsoNormal>If you have not done so already, start GSAS-II.</p> 1454 1455 <h2>Step 1: Read in the data file</h2> 1138 1456 1139 1457 <p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span 1140 1458 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span 1141 1459 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]>Use 1142 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1143 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 1144 Calibri;mso-bidi-theme-font:minor-latin'>Import/Powder Data/from GSAS powder 1460 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1461 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 1462 Calibri;mso-bidi-theme-font:minor-latin'>Import/Powder Data/from GSAS powder data 1463 file</span></b> menu item to read the data file into the current GSAS-II 1464 project. This read option is set to read any of the powder data formats defined 1465 for GSAS (angles in <span class=SpellE>centidegrees</span>, TOF in µsec). Other 1466 submenu items will read the <span class=SpellE><b style='mso-bidi-font-weight: 1467 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1468 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri; 1469 mso-bidi-theme-font:minor-latin'>cif</span></b></span> format or the <span 1470 class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family: 1471 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1472 minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>xye</span></b></span> 1473 format (angles in degrees) used by <span class=SpellE>Topas</span>, etc.<span 1474 style='mso-spacerun:yes'> </span>In those cases, you would change the file 1475 directory to <b style='mso-bidi-font-weight:normal'><span style='======= 1145 1476 data file</span></b> menu item to read the data file into the current GSAS-II project. 1146 1477 This read option is set to read any of the powder data formats defined for GSAS 1147 1478 (angles in <span class=SpellE>centidegrees</span>, TOF in µsec). Other submenu 1148 items will read the <span class=SpellE><b style=' mso-bidi-font-weight:normal'><span1149 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;1150 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font: 1151 minor-latin'>cif</span></ b></span> format or the <span class=SpellE><b1152 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1479 items will read the <span class=SpellE><b style=' 1480 '><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1481 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font: 1482 minor-latin'>cif</span></span></b> format or the <span class=SpellE><b 1483 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1153 1484 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 1154 1485 Calibri;mso-bidi-theme-font:minor-latin'>xye</span></b></span> format (angles 1155 in degrees) used by <span class=SpellE>Topas</span>, etc. 1156 If you used the 1157 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1158 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 1159 Calibri;mso-bidi-theme-font:minor-latin'>Help/Download tutorial 1160 </span></b> menu entry to open this page and downloaded the exercise 1161 files (recommended), then the Import/... entry will bring you to the location where 1162 the files have been downloaded. (It is also possible to download them manually 1163 from 1164 <A href="https://subversion.xray.aps.anl.gov/pyGSAS/Exercises/FitPeaks/"> 1165 https://subversion.xray.aps.anl.gov/pyGSAS/Exercises/FitPeaks/</a>. In 1166 this case you will need to navigate to the download location 1167 manually.)<BR> 1168 For this tutorial you should see the data files in the file browser, but if 1169 extensions on data files are not the expected ones, you may need to 1170 change the file type to 1171 <b style='mso-bidi-font-weight:normal'>All files (*.*)</style></b> to find the desired 1172 file.</p> 1486 in degrees) used by <span class=SpellE>Topas</span>, etc. to see them. Because 1487 you used <span style='mso-fareast-font-family:Calibri;mso-fareast-theme-font: 1488 minor-latin'>the </span><b style='mso-bidi-font-weight:normal'><span 1489 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1490 mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin;mso-hansi-theme-font: 1491 minor-latin'>Help/Download tutorial</span></b><span style='mso-fareast-font-family: 1492 Calibri;mso-fareast-theme-font:minor-latin'> menu entry to open this page and 1493 downloaded the exercise files (recommended), then the </span><b 1494 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1495 mso-ascii-theme-font:minor-latin;mso-fareast-font-family:Calibri;mso-fareast-theme-font: 1496 minor-latin;mso-hansi-theme-font:minor-latin'>Import/...</span></b><span 1497 style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'> 1498 entry will bring you to the location where the files have been downloaded. (It 1499 is also possible to download them manually from <a 1500 href="https://subversion.xray.aps.anl.gov/pyGSAS/Exercises/FitPeaks/">https://subversion.xray.aps.anl.gov/pyGSAS/Exercises/FitPeaks/</a>. 1501 In this case you will need to navigate to the download location manually.)<br> 1502 For this tutorial you should see the data file in the file browser, but if 1503 extensions on data files are not the expected ones, you may need to change the 1504 file type to <b style='mso-bidi-font-weight:normal'>All files (*.*)</b> to find 1505 the desired file.</span></p> 1173 1506 1174 1507 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span 1175 1508 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span 1176 1509 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]>Select 1177 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1510 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1178 1511 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 1179 1512 Calibri;mso-bidi-theme-font:minor-latin'>11bmb_3844.fxye</span></b><span 1180 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;1513 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1181 1514 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font: 1182 1515 minor-latin'> data</span> file in the first dialog and press <b 1183 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1516 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1184 1517 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 1185 1518 Calibri;mso-bidi-theme-font:minor-latin'>Open</span></b>. There will be a 1186 1519 Dialog box asking <span class=GramE><b style='mso-bidi-font-weight:normal'><span 1187 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;1520 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1188 1521 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font: 1189 1522 minor-latin'>Is</span></b></span><b style='mso-bidi-font-weight:normal'><span 1190 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;1523 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1191 1524 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font: 1192 1525 minor-latin'> this the file you want?</span></b> Press <span class=GramE><b 1193 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1526 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1194 1527 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 1195 1528 Calibri;mso-bidi-theme-font:minor-latin'>Yes</span></b></span> button to … … 1199 1532 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span 1200 1533 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]>The 1201 file <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1534 file <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1202 1535 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 1203 1536 Calibri;mso-bidi-theme-font:minor-latin'>11bmb_3844.prm</span></b> instrument 1204 1537 parameter file is automatically selected; it was produced by 11BM-B instrument 1205 1538 processing software when the corresponding <span class=SpellE><b 1206 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1539 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1207 1540 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 1208 1541 Calibri;mso-bidi-theme-font:minor-latin'>fxye</span></b></span> file was … … 1212 1545 1213 1546 <p class=MsoNormal>At this point the <b style='mso-bidi-font-weight:normal'><span 1214 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;1547 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1215 1548 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font: 1216 1549 minor-latin'>GSAS-II data tree</span></b> window will have several entries </p> … … 1236 1569 <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/> 1237 1570 <o:lock v:ext="edit" aspectratio="t"/> 1238 </v:shapetype><v:shape id="Picture_x0020_1" o:spid="_x0000_i105 2" type="#_x0000_t75"1571 </v:shapetype><v:shape id="Picture_x0020_1" o:spid="_x0000_i1050" type="#_x0000_t75" 1239 1572 style='width:300pt;height:187.5pt;visibility:visible;mso-wrap-style:square'> 1240 1573 <v:imagedata src="Fit%20Peaks_files/image001.png" o:title=""/> … … 1246 1579 1247 1580 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape 1248 id=" Picture_x0020_2" o:spid="_x0000_i1051" type="#_x0000_t75" style='width:525pt;1249 height:450pt;visibility:visible;mso-wrap-style:square'>1581 id="_x0000_i1049" type="#_x0000_t75" style='width:525pt;height:450pt; 1582 visibility:visible;mso-wrap-style:square'> 1250 1583 <v:imagedata src="Fit%20Peaks_files/image002.png" o:title=""/> 1251 1584 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600 1252 src="Fit%20Peaks_files/image002.png" v:shapes=" Picture_x0020_2"><![endif]></span></p>1585 src="Fit%20Peaks_files/image002.png" v:shapes="_x0000_i1049"><![endif]></span></p> 1253 1586 1254 1587 <h2>Step 2: Select Limits </h2> … … 1256 1589 <p class=MsoNormal><span style='mso-spacerun:yes'> </span>This pattern has much 1257 1590 more data than we need, so it is helpful to cut down the range. Click on the <b 1258 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1591 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1259 1592 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 1260 1593 Calibri;mso-bidi-theme-font:minor-latin'>Limits</span></b> item in the <b 1261 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1594 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1262 1595 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 1263 1596 Calibri;mso-bidi-theme-font:minor-latin'>GSAS-II data tree</span></b>. The 1264 1597 small window is repainted. Use the <b style='mso-bidi-font-weight:normal'><span 1265 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;1598 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1266 1599 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font: 1267 1600 minor-latin'>changed</span></b> row of entry boxes to set <span class=SpellE><b 1268 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1601 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1269 1602 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 1270 1603 Calibri;mso-bidi-theme-font:minor-latin'>Tmin</span></b></span> and <span 1271 1604 class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family: 1272 "Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:1605 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1273 1606 minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>Tmax</span></b></span> 1274 to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1607 to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1275 1608 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 1276 1609 Calibri;mso-bidi-theme-font:minor-latin'>4</span></b> and <b style='mso-bidi-font-weight: 1277 normal'><span style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:1610 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1278 1611 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri; 1279 1612 mso-bidi-theme-font:minor-latin'>27.5</span></b>. Notice on the plot that the 1280 1613 limit lines have moved to these positions; the green lower limit is just below 1281 1614 the 1<sup>st</sup> peak and the red upper limit is in a wide gap between peaks. 1282 You may also drag the limit lines to the desired location or place them by a 1283 leftmouse click on a data point for the lower limit or a right click on a data1615 You may also drag the limit lines to the desired location or place them by a left 1616 mouse click on a data point for the lower limit or a right click on a data 1284 1617 point for the upper limit.</p> 1285 1618 1286 1619 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape 1287 id=" _x0000_i1050" type="#_x0000_t75" style='width:226.5pt;height:123.75pt;1288 visibility:visible;mso-wrap-style:square'>1620 id="Picture_x0020_3" o:spid="_x0000_i1048" type="#_x0000_t75" style='width:226.5pt; 1621 height:123.75pt;visibility:visible;mso-wrap-style:square'> 1289 1622 <v:imagedata src="Fit%20Peaks_files/image003.png" o:title=""/> 1290 1623 </v:shape><![endif]--><![if !vml]><img border=0 width=302 height=165 1291 src="Fit%20Peaks_files/image003.png" v:shapes=" _x0000_i1050"><![endif]></span></p>1624 src="Fit%20Peaks_files/image003.png" v:shapes="Picture_x0020_3"><![endif]></span></p> 1292 1625 1293 1626 <h2>Step 3: Determine Peak Positions</h2> … … 1297 1630 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span 1298 1631 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]>Click 1299 on the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1632 on the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1300 1633 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 1301 1634 Calibri;mso-bidi-theme-font:minor-latin'>Peak List</span></b> item in the <b 1302 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1635 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1303 1636 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 1304 1637 Calibri;mso-bidi-theme-font:minor-latin'>GSAS-II data tree</span></b>. This 1305 1638 creates an empty window of peak positions (the <b style='mso-bidi-font-weight: 1306 normal'><span style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:1639 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1307 1640 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri; 1308 mso-bidi-theme-font:minor-latin'>Limits</span></b> window is erased). At this point1309 it is wise to zoom in on the data that will be used for indexing. </p>1641 mso-bidi-theme-font:minor-latin'>Limits</span></b> window is erased). At this 1642 point it is wise to zoom in on the data that will be used for indexing. </p> 1310 1643 1311 1644 <p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space: … … 1313 1646 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span 1314 1647 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]>Click 1315 on the Zoom button, <span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape 1316 id="Picture_x0020_4" o:spid="_x0000_i1049" type="#_x0000_t75" style='width:21.75pt; 1317 height:18.75pt;visibility:visible;mso-wrap-style:square'> 1318 <v:imagedata src="Fit%20Peaks_files/image004.jpg" o:title="" croptop="1f" 1319 cropbottom="-1f" cropleft="35827f" cropright="19224f"/> 1320 </v:shape><![endif]--><![if !vml]><img border=0 width=29 height=25 1321 src="Fit%20Peaks_files/image029.jpg" v:shapes="Picture_x0020_4"><![endif]></span>, 1322 then press the left mouse in one corner of the region to be used; holding the 1323 mouse button down, drag over the region to the opposite corner; a box will be 1324 drawn over the region to be zoomed. </p> 1648 on the Zoom button (5<sup>th</sup> one from the left on the plot toolbar), then 1649 press the left mouse in one corner of the region to be used; holding the mouse 1650 button down, drag over the region to the opposite corner; a box will be drawn 1651 over the region to be zoomed and the plot will be redrawn with the new limits. 1652 The toolbar has a number of buttons to the right of the help button (?) that 1653 can be used to incrementally change the view.</p> 1325 1654 1326 1655 <p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space: … … 1328 1657 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span 1329 1658 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 1330 style='mso-bidi-font-weight:normal'>Important</b>: Click on the Zoom <span 1331 style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_5" 1332 o:spid="_x0000_i1048" type="#_x0000_t75" style='width:23.25pt;height:20.25pt; 1333 visibility:visible;mso-wrap-style:square'> 1334 <v:imagedata src="Fit%20Peaks_files/image004.jpg" o:title="" croptop="1f" 1335 cropbottom="-1f" cropleft="35827f" cropright="19224f"/> 1336 </v:shape><![endif]--><![if !vml]><img border=0 width=31 height=27 1337 src="Fit%20Peaks_files/image030.jpg" v:shapes="Picture_x0020_5"><![endif]></span><span 1338 style='mso-spacerun:yes'> </span>button again to turn off the zoom mode. </p> 1659 style='mso-bidi-font-weight:normal'>Important</b>: Click on the Zoom button 1660 again to turn off the zoom mode. </p> 1339 1661 1340 1662 <p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space: … … 1342 1664 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span 1343 1665 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]>Under 1344 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1666 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1345 1667 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Peak Fitting</span></b> 1346 in the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1668 in the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1347 1669 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Peak List</span></b> 1348 1670 window select <b style='mso-bidi-font-weight:normal'><span style='font-family: 1349 "Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:1671 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1350 1672 minor-latin'>Auto search</span></b>. The plot window will immediately show that 1351 1673 all peaks were picked with a blue vertical line on each one</p> 1352 1674 1353 1675 <p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space: 1354 auto'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id=" Picture_x0020_27"1355 o:spid="_x0000_i1047" type="#_x0000_t75" style='width:525pt;height:450pt;1356 visibility:visible;mso-wrap-style:square'>1357 <v:imagedata src="Fit%20Peaks_files/image00 7.png" o:title=""/>1676 auto'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="_x0000_i1047" 1677 type="#_x0000_t75" style='width:525pt;height:450pt;visibility:visible; 1678 mso-wrap-style:square'> 1679 <v:imagedata src="Fit%20Peaks_files/image004.png" o:title=""/> 1358 1680 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600 1359 src="Fit%20Peaks_files/image00 7.png" v:shapes="Picture_x0020_27"><![endif]></span></p>1681 src="Fit%20Peaks_files/image004.png" v:shapes="_x0000_i1047"><![endif]></span></p> 1360 1682 1361 1683 <p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space: 1362 1684 auto'><span class=GramE>and</span> peaks are shown in the <b style='mso-bidi-font-weight: 1363 normal'><span style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:1685 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1364 1686 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri; 1365 1687 mso-bidi-theme-font:minor-latin'>Peak List</span></b> window in order of … … 1370 1692 o:spid="_x0000_i1046" type="#_x0000_t75" style='width:401.25pt;height:262.5pt; 1371 1693 visibility:visible;mso-wrap-style:square'> 1372 <v:imagedata src="Fit%20Peaks_files/image0 31.png" o:title=""/>1694 <v:imagedata src="Fit%20Peaks_files/image005.png" o:title=""/> 1373 1695 </v:shape><![endif]--><![if !vml]><img border=0 width=535 height=350 1374 src="Fit%20Peaks_files/image0 31.png" v:shapes="Picture_x0020_29"><![endif]></span></p>1696 src="Fit%20Peaks_files/image005.png" v:shapes="Picture_x0020_29"><![endif]></span></p> 1375 1697 1376 1698 <p class=MsoListParagraphCxSpLast style='margin-left:39.0pt;mso-add-space:auto'>There 1377 will be 20 + peaks in this example. You should examine both the list and the1378 plot to be sure the auto search did not pick a peak twice (quite rarely) or 1379 skip a peak or shoulder. You can add a peak to the list by pressing the left 1380 mouse button with the pointer on a data point at the peak top or shoulder; be1381 surethe zoom/shift buttons are off. You may drag a peak position as needed. A1699 will be 20 peaks in this example. You should examine both the list and the plot 1700 to be sure the auto search did not pick a peak twice (quite rarely) or skip a 1701 peak or shoulder. You can add a peak to the list by pressing the left mouse 1702 button with the pointer on a data point at the peak top or shoulder; be sure 1703 the zoom/shift buttons are off. You may drag a peak position as needed. A 1382 1704 position may be deleted with a right click with the mouse on the blue line. You 1383 1705 can also delete a peak by selecting the row in the table; it will be 1384 1706 highlighted in blue. Then press the <b style='mso-bidi-font-weight:normal'><span 1385 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;1707 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1386 1708 mso-hansi-theme-font:minor-latin'>Delete</span></b> key; it will be removed 1387 1709 from the table and the plot. The list will always show the peaks sorted by … … 1398 1720 the peak intensities and the background. These parameters have their refinement 1399 1721 flags turned on by default. Use the menu item <b style='mso-bidi-font-weight: 1400 normal'><span style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:1722 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1401 1723 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri; 1402 mso-bidi-theme-font:minor-latin'>Peak Fitting/ LSQ<span class=SpellE>PeakFit</span>1724 mso-bidi-theme-font:minor-latin'>Peak Fitting/<span class=SpellE>PeakFit</span> 1403 1725 </span></b>on the<b style='mso-bidi-font-weight:normal'><span style='font-family: 1404 "Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:1726 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1405 1727 minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'> Peak 1406 1728 List </span></b>window. Do <b style='mso-bidi-font-weight:normal'>NOT</b> use 1407 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1729 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1408 1730 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 1409 1731 Calibri;mso-bidi-theme-font:minor-latin'>Calculate/Refine</span></b> menu item 1410 in the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1732 in the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1411 1733 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 1412 1734 Calibri;mso-bidi-theme-font:minor-latin'>GSAS-II data tree</span></b> window; 1413 that it to be used for <span class=SpellE>Rietveld</span>/Pawley refinements.1414 You will be asked to save the current project before the fit will proceed; 1415 change directory if desired and provide a suitable name (we assume <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;mso-bidi-font-family:1418 Calibri;mso-bidi-theme-font:minor-latin'>LaB6</span></b>). A window will show 1419 the progress of the refinement and will close when the least-squares fit <span 1420 class=GramE>is</span> complete (usually very fast). The plotis updated with1421 the fit, the peak list window is updated with the new peak values and a summary1422 of the refinement is shown on the consolewindow as well.</p>1735 that it to be used for Rietveld/Pawley refinements. You will be asked to save 1736 the current project before the fit will proceed; change directory if desired 1737 and provide a suitable name (we assume <b style='mso-bidi-font-weight:normal'><span 1738 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1739 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font: 1740 minor-latin'>LaB6</span></b>). A window will show the progress of the 1741 refinement and will close when the least-squares fit is complete (usually very 1742 fast). The plot is updated with the fit, the peak list window is updated with 1743 the new peak values and a summary of the refinement is shown on the console 1744 window as well.</p> 1423 1745 1424 1746 <p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape 1425 id="Picture_x0020_ 8" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:525pt;1747 id="Picture_x0020_31" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:525pt; 1426 1748 height:450pt;visibility:visible;mso-wrap-style:square'> 1427 <v:imagedata src="Fit%20Peaks_files/image00 8.png" o:title=""/>1749 <v:imagedata src="Fit%20Peaks_files/image006.png" o:title=""/> 1428 1750 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600 1429 src="Fit%20Peaks_files/image00 8.png" v:shapes="Picture_x0020_8"><![endif]></span></p>1751 src="Fit%20Peaks_files/image006.png" v:shapes="Picture_x0020_31"><![endif]></span></p> 1430 1752 1431 1753 <p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape 1432 1754 id="Picture_x0020_24" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:401.25pt; 1433 1755 height:262.5pt;visibility:visible;mso-wrap-style:square'> 1434 <v:imagedata src="Fit%20Peaks_files/image00 9.png" o:title=""/>1756 <v:imagedata src="Fit%20Peaks_files/image007.png" o:title=""/> 1435 1757 </v:shape><![endif]--><![if !vml]><img border=0 width=535 height=350 1436 src="Fit%20Peaks_files/image00 9.png" v:shapes="Picture_x0020_24"><![endif]></span></p>1758 src="Fit%20Peaks_files/image007.png" v:shapes="Picture_x0020_24"><![endif]></span></p> 1437 1759 1438 1760 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span … … 1455 1777 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span 1456 1778 class=GramE>single-click</span> on the <b style='mso-bidi-font-weight:normal'><span 1457 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;1779 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1458 1780 mso-hansi-theme-font:minor-latin'>refine</span></b> label above the peak 1459 1781 position check-boxes. The entire column of checkboxes is highlighted in blue. 1460 Press the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1782 Press the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1461 1783 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 1462 1784 Calibri;mso-bidi-theme-font:minor-latin'>y</span></b> key to turn on all 1463 1785 refinement flags (<b style='mso-bidi-font-weight:normal'><span 1464 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;1786 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1465 1787 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font: 1466 1788 minor-latin'>n</span></b> would turn them off).</p> 1467 1789 1468 1790 <p class=MsoNormal style='margin-left:.5in'>Next, repeat the refinement using 1469 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1470 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 1471 Calibri;mso-bidi-theme-font:minor-latin'>Peak Fitting/ LSQ<span class=SpellE>PeakFit</span></span></b>1791 the <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;mso-bidi-font-family: 1793 Calibri;mso-bidi-theme-font:minor-latin'>Peak Fitting/<span class=SpellE>PeakFit</span></span></b> 1472 1794 menu item in the <b style='mso-bidi-font-weight:normal'><span style='font-family: 1473 "Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:1795 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1474 1796 minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>Peak 1475 1797 List</span></b> window.</p> … … 1478 1800 refinement. <span style='mso-fareast-font-family:"Times New Roman"'>This can be 1479 1801 performed in 2 different ways. Method 1: refine sigma (Gaussian 1480 width) and/or gamma (<span class=SpellE>Lorentzian</span> width) for individual 1481 peaks. To do this, click the refinement flags for sigma and/or gamma in 1482 the Peak List window. Method 2: preferably, the 1483 LS refinement of peak widths can be constrained to follow 1484 an instrumental broadening equation as described below. Note - one cannot 1485 refine ALL peak widths using both individual sigma & gamma values 1486 AND instrumental broadening terms at the same time.<b style='mso-bidi-font-weight: 1487 normal'> </b><o:p></o:p></span></p> 1802 width) and/or gamma (Lorentzian width) for individual peaks. To do this, 1803 click the refinement flags for sigma and/or gamma in the Peak List window. 1804 Method 2: preferably, the LS refinement of peak 1805 widths can be constrained to follow an instrumental broadening 1806 equation as described below. Note - one cannot refine ALL peak widths 1807 using both individual sigma & gamma values AND instrumental 1808 broadening terms at the same time.<b style='mso-bidi-font-weight:normal'> </b><o:p></o:p></span></p> 1488 1809 1489 1810 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: 1490 1811 "Times New Roman";mso-bidi-font-weight:bold'>To constrain refined peak widths 1491 1812 to an instrumental broadening equation, first<b> s</b></span>elect the <b 1492 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1813 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1493 1814 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 1494 1815 Calibri;mso-bidi-theme-font:minor-latin'>Instrumental Parameters</span></b> … … 1500 1821 id="Picture_x0020_30" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:419.25pt; 1501 1822 height:183.75pt;visibility:visible;mso-wrap-style:square'> 1502 <v:imagedata src="Fit%20Peaks_files/image0 10.png" o:title=""/>1823 <v:imagedata src="Fit%20Peaks_files/image008.png" o:title=""/> 1503 1824 </v:shape><![endif]--><![if !vml]><img border=0 width=559 height=245 1504 src="Fit%20Peaks_files/image0 10.png" v:shapes="Picture_x0020_30"><![endif]></span></p>1825 src="Fit%20Peaks_files/image008.png" v:shapes="Picture_x0020_30"><![endif]></span></p> 1505 1826 1506 1827 <p class=MsoListParagraphCxSpFirst>The plot window shows the resolution curves 1507 corresponding to the values of the Gaussian U, V, W, <span class=SpellE>Lorentzian</span> 1508 X & Y coefficients; + marks show the individual values based on the sig 1509 & gam values for the peaks in Peak List. Select the refine flag checkbox 1510 for Gaussian <b style='mso-bidi-font-weight:normal'><span style='font-family: 1511 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1512 minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>U</span></b>, 1513 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1514 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 1515 Calibri;mso-bidi-theme-font:minor-latin'>V</span></b>, <b style='mso-bidi-font-weight: 1516 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: 1828 corresponding to the values of the Gaussian U, V, W, Lorentzian X & Y 1829 coefficients; + marks show the individual values based on the sig & gam 1830 values for the peaks in Peak List. Select the refine flag checkbox for Gaussian 1831 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1832 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 1833 Calibri;mso-bidi-theme-font:minor-latin'>U</span></b>, <b style='mso-bidi-font-weight: 1834 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1517 1835 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri; 1518 mso-bidi-theme-font:minor-latin'>W</span></b>, and <span class=SpellE>Lorentzian</span> 1519 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1836 mso-bidi-theme-font:minor-latin'>V</span></b>, <b style='mso-bidi-font-weight: 1837 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1838 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri; 1839 mso-bidi-theme-font:minor-latin'>W</span></b>, and Lorentzian <b 1840 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1520 1841 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 1521 1842 Calibri;mso-bidi-theme-font:minor-latin'>X</span></b>, <b style='mso-bidi-font-weight: 1522 normal'><span style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:1843 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1523 1844 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri; 1524 1845 mso-bidi-theme-font:minor-latin'>Y</span></b>. </p> … … 1528 1849 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]>Then, 1529 1850 repeat the refinement. First click on the <b style='mso-bidi-font-weight:normal'><span 1530 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;1851 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1531 1852 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font: 1532 1853 minor-latin'>Peak List</span></b> item in the data tree and then refine using 1533 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1534 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 1535 Calibri;mso-bidi-theme-font:minor-latin'>Peak Fitting/ LSQ<span class=SpellE>PeakFit</span></span></b>1854 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1855 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 1856 Calibri;mso-bidi-theme-font:minor-latin'>Peak Fitting/<span class=SpellE>PeakFit</span></span></b> 1536 1857 menu item. At this point a good fit should be seen by zooming in on individual 1537 1858 peaks. For example see </p> 1538 1859 1539 1860 <p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape 1540 id="Picture_x0020_ 11" o:spid="_x0000_i1042" type="#_x0000_t75" style='width:525pt;1861 id="Picture_x0020_32" o:spid="_x0000_i1042" type="#_x0000_t75" style='width:525pt; 1541 1862 height:450pt;visibility:visible;mso-wrap-style:square'> 1542 <v:imagedata src="Fit%20Peaks_files/image0 11.png" o:title=""/>1863 <v:imagedata src="Fit%20Peaks_files/image009.png" o:title=""/> 1543 1864 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600 1544 src="Fit%20Peaks_files/image0 11.png" v:shapes="Picture_x0020_11"><![endif]></span></p>1545 1546 <p class=MsoListParagraphCxSpLast>Notice that the peak position is slightly to the1547 right of the peak top. This is a consequence of the peak asymmetry arising from 1548 axial divergence in the <span class=SpellE>diffractometer</span>. The <span 1549 class=SpellE>Rwp</span> is ~6% as shown on the console window. Again the <b 1550 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1551 m so-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:1552 Calibri;mso-bidi-theme-font:minor-latin'>Peak List</span></b> entries are all 1553 updatedwith new values and those in <b style='mso-bidi-font-weight:normal'><span1554 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;1865 src="Fit%20Peaks_files/image009.png" v:shapes="Picture_x0020_32"><![endif]></span></p> 1866 1867 <p class=MsoListParagraphCxSpLast>Notice that the peak position is slightly to 1868 the right of the peak top. This is a consequence of the peak asymmetry arising 1869 from axial divergence in the diffractometer. The <span class=SpellE>Rwp</span> 1870 is ~6% as shown on the console window. Again the <b style='mso-bidi-font-weight: 1871 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1872 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri; 1873 mso-bidi-theme-font:minor-latin'>Peak List</span></b> entries are all updated 1874 with new values and those in <b style='mso-bidi-font-weight:normal'><span 1875 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1555 1876 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font: 1556 1877 minor-latin'>Instrument Parameters</span></b> are also updated.</p> 1557 1878 1558 <h2> <span class=GramE>Step 5.</span>Prepare Indexing Peak List</h2>1879 <h2>Step 5. Prepare Indexing Peak List</h2> 1559 1880 1560 1881 <p class=MsoNormal>A separate list of peaks is kept for use in <span 1561 1882 class=SpellE>autoindexing</span>. It is found in the <b style='mso-bidi-font-weight: 1562 normal'><span style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:1883 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1563 1884 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri; 1564 1885 mso-bidi-theme-font:minor-latin'>Index Peak List</span></b> item in the data 1565 1886 tree. In the initially empty window created by this action, use menu item <b 1566 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1567 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 1568 Calibri;mso-bidi-theme-font:minor-latin'> Index Peaks Operations/Load/Reload</span></b>1569 t o copy the fitted peaks from the <b style='mso-bidi-font-weight:normal'><span1570 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;1887 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1888 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 1889 Calibri;mso-bidi-theme-font:minor-latin'>Operations/Load/Reload</span></b> to copy 1890 the fitted peaks from the <b style='mso-bidi-font-weight:normal'><span 1891 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1571 1892 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font: 1572 1893 minor-latin'>Peak List</span></b>.</p> … … 1575 1896 id="Picture_x0020_26" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:367.5pt; 1576 1897 height:225pt;visibility:visible;mso-wrap-style:square'> 1577 <v:imagedata src="Fit%20Peaks_files/image01 2.png" o:title=""/>1898 <v:imagedata src="Fit%20Peaks_files/image010.png" o:title=""/> 1578 1899 </v:shape><![endif]--><![if !vml]><img border=0 width=490 height=300 1579 src="Fit%20Peaks_files/image01 2.png" v:shapes="Picture_x0020_26"><![endif]></span></p>1900 src="Fit%20Peaks_files/image010.png" v:shapes="Picture_x0020_26"><![endif]></span></p> 1580 1901 1581 1902 <p class=MsoNormal>Note that by default all peaks are selected to be used. You … … 1583 1904 contaminant).</p> 1584 1905 1585 <h2> <span class=GramE>Step 6.</span>Run <span class=SpellE>Autoindexing</span></h2>1906 <h2>Step 6. Run <span class=SpellE>Autoindexing</span></h2> 1586 1907 1587 1908 <p class=MsoNormal>Select the <b style='mso-bidi-font-weight:normal'><span 1588 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;1909 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1589 1910 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font: 1590 1911 minor-latin'>Unit Cells List</span></b> data item. This brings up a window for … … 1592 1913 1593 1914 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape 1594 id="Picture_x0020_ 13" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:527.25pt;1915 id="Picture_x0020_33" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:546pt; 1595 1916 height:204pt;visibility:visible;mso-wrap-style:square'> 1596 <v:imagedata src="Fit%20Peaks_files/image01 3.png" o:title=""/>1597 </v:shape><![endif]--><![if !vml]><img border=0 width=7 03height=2721598 src="Fit%20Peaks_files/image01 3.png" v:shapes="Picture_x0020_13"><![endif]></span></p>1917 <v:imagedata src="Fit%20Peaks_files/image011.png" o:title=""/> 1918 </v:shape><![endif]--><![if !vml]><img border=0 width=728 height=272 1919 src="Fit%20Peaks_files/image011.png" v:shapes="Picture_x0020_33"><![endif]></span></p> 1599 1920 1600 1921 <p class=MsoNormal>For the most rapid search (since we know the right answer), 1601 select <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1922 select <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1602 1923 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 1603 1924 Calibri;mso-bidi-theme-font:minor-latin'>Cubic-P</span></b> and launch the 1604 1925 search using menu item <b style='mso-bidi-font-weight:normal'><span 1605 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;1926 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1606 1927 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font: 1607 1928 minor-latin'>Cell Index/Refine/Index Cell</span></b>. The search then runs and 1608 1929 the console shows a running list of possible cells as they are found; the 1609 1930 sorted by M20 list of possible matching cells is shown in the <b 1610 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1931 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1611 1932 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 1612 1933 Calibri;mso-bidi-theme-font:minor-latin'>Unit Cells List</span></b> window</p> 1613 1934 1614 1935 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape 1615 id="Picture_x0020_ 28" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:527.25pt;1616 height:3 76.5pt;visibility:visible;mso-wrap-style:square'>1617 <v:imagedata src="Fit%20Peaks_files/image01 4.png" o:title=""/>1618 </v:shape><![endif]--><![if !vml]><img border=0 width=7 03 height=5021619 src="Fit%20Peaks_files/image01 4.png" v:shapes="Picture_x0020_28"><![endif]></span></p>1620 1621 <h2> <span class=GramE>Step 7.</span>Review Cell Choices</h2>1936 id="Picture_x0020_34" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:546pt; 1937 height:324pt;visibility:visible;mso-wrap-style:square'> 1938 <v:imagedata src="Fit%20Peaks_files/image012.png" o:title=""/> 1939 </v:shape><![endif]--><![if !vml]><img border=0 width=728 height=432 1940 src="Fit%20Peaks_files/image012.png" v:shapes="Picture_x0020_34"><![endif]></span></p> 1941 1942 <h2>Step 7. Review Cell Choices</h2> 1622 1943 1623 1944 <p class=MsoNormal>Review the list of cells associated with the <b 1624 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1945 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1625 1946 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 1626 1947 Calibri;mso-bidi-theme-font:minor-latin'>Unit Cells List</span></b> data item. … … 1633 1954 1634 1955 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape 1635 id="Picture_x0020_3 8" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:525pt;1956 id="Picture_x0020_35" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:525pt; 1636 1957 height:450pt;visibility:visible;mso-wrap-style:square'> 1637 <v:imagedata src="Fit%20Peaks_files/image01 5.png" o:title=""/>1958 <v:imagedata src="Fit%20Peaks_files/image013.png" o:title=""/> 1638 1959 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600 1639 src="Fit%20Peaks_files/image01 5.png" v:shapes="Picture_x0020_38"><![endif]></span><span1960 src="Fit%20Peaks_files/image013.png" v:shapes="Picture_x0020_35"><![endif]></span><span 1640 1961 style='mso-spacerun:yes'> </span></p> 1641 1962 … … 1644 1965 1645 1966 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape 1646 id="Picture_x0020_3 9" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:525pt;1967 id="Picture_x0020_36" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:525pt; 1647 1968 height:450pt;visibility:visible;mso-wrap-style:square'> 1648 <v:imagedata src="Fit%20Peaks_files/image01 6.png" o:title=""/>1969 <v:imagedata src="Fit%20Peaks_files/image014.png" o:title=""/> 1649 1970 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600 1650 src="Fit%20Peaks_files/image01 6.png" v:shapes="Picture_x0020_39"><![endif]></span></p>1651 1652 <h2> <span class=GramE>Step 8.</span>Select/Refine Cell</h2>1971 src="Fit%20Peaks_files/image014.png" v:shapes="Picture_x0020_36"><![endif]></span></p> 1972 1973 <h2>Step 8. Select/Refine Cell</h2> 1653 1974 1654 1975 <p class=MsoNormal>Select the cell with M20 ~ 2970 with a = 4.15683 Å. This 1655 indexes all peaks with almost a perfect fit to the peak positions (compare dashed1656 red lines to solid blue ones). Import the cell information using the <b1657 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1976 indexes all peaks with almost a perfect fit to the peak positions (compare 1977 dashed red lines to solid blue ones). Import the cell information using the <b 1978 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1658 1979 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 1659 1980 Calibri;mso-bidi-theme-font:minor-latin'>Cell Index/Refine/Copy Cell</span></b> 1660 1981 menu option. Then optimize the cell by refining the lattice parameters and the 1661 two-theta zero: click on the refine checkbox next to the <b style='mso-bidi-font-weight: 1662 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: 1663 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri; 1664 mso-bidi-theme-font:minor-latin'>Zero offset</span></b> value and then the <b 1665 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1666 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 1667 Calibri;mso-bidi-theme-font:minor-latin'>Cell Index/Refine/Refine Cell</span></b> 1668 menu option. The M20 improves to ~3600 and <span class=GramE>the a</span> cell 1669 parameter value shifts from 4.15683 to 4.15691 when zero is refined. (NB: The 1670 certificate value for NIST SRM 660a is 4.15692 Å). Press the <b 1671 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1672 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 1673 Calibri;mso-bidi-theme-font:minor-latin'>Show <span class=SpellE>hkl</span> 1674 positions </span></b>button to update the plot including the refined <b 1675 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1676 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 1677 Calibri;mso-bidi-theme-font:minor-latin'>Zero offset</span></b> (in this case 1678 hardly anything happens!). <span style='mso-spacerun:yes'> </span></p> 1982 two-theta zero: click on the <b style='mso-bidi-font-weight:normal'><span 1983 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1984 mso-hansi-theme-font:minor-latin'>Refine?</span></b> <span class=GramE>checkbox</span> 1985 next to the <b style='mso-bidi-font-weight:normal'><span style='font-family: 1986 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1987 minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>Zero 1988 offset</span></b> value and then the <b style='mso-bidi-font-weight:normal'><span 1989 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1990 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font: 1991 minor-latin'>Cell Index/Refine/Refine Cell</span></b> menu option. The M20 1992 improves to ~3600 and <span class=GramE>the a</span> cell parameter value 1993 shifts from 4.15683 to 4.15691 when zero is refined. (NB: The certificate value 1994 for NIST SRM 660a is 4.15692 Å). Press the <b style='mso-bidi-font-weight:normal'><span 1995 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1996 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font: 1997 minor-latin'>Show <span class=SpellE>hkl</span> positions </span></b>button to 1998 update the plot including the refined <b style='mso-bidi-font-weight:normal'><span 1999 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2000 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font: 2001 minor-latin'>Zero offset</span></b> (in this case hardly anything 2002 happens!).<span style='mso-spacerun:yes'> </span></p> 1679 2003 1680 2004 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape 1681 id="Picture_x0020_ 17" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:527.25pt;1682 height:3 34.5pt;visibility:visible;mso-wrap-style:square'>1683 <v:imagedata src="Fit%20Peaks_files/image01 7.png" o:title=""/>1684 </v:shape><![endif]--><![if !vml]><img border=0 width=7 03 height=4461685 src="Fit%20Peaks_files/image01 7.png" v:shapes="Picture_x0020_17"><![endif]></span></p>2005 id="Picture_x0020_37" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:546pt; 2006 height:309.75pt;visibility:visible;mso-wrap-style:square'> 2007 <v:imagedata src="Fit%20Peaks_files/image015.png" o:title=""/> 2008 </v:shape><![endif]--><![if !vml]><img border=0 width=728 height=413 2009 src="Fit%20Peaks_files/image015.png" v:shapes="Picture_x0020_37"><![endif]></span></p> 1686 2010 1687 2011 <p class=MsoNormal>Notice that a new entry heads the list in the <b 1688 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";2012 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1689 2013 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 1690 2014 Calibri;mso-bidi-theme-font:minor-latin'>Indexing Result</span></b> section of 1691 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1692 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 1693 Calibri;mso-bidi-theme-font:minor-latin'> Cell Index/Refine/Refine</span></b>1694 window with an improved M20(~3600) and a new value for <b style='mso-bidi-font-weight: 1695 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: 1696 m inor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;1697 mso-bidi-theme-font:minor-latin'>Zero offset</span></b> is shown. NB: the <b 1698 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";2015 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 2016 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 2017 Calibri;mso-bidi-theme-font:minor-latin'>Unit Cells List</span></b> window with 2018 an improved <span class=GramE>M20(</span>~3600) and a new value for <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;mso-bidi-font-family: 2021 Calibri;mso-bidi-theme-font:minor-latin'>Zero offset</span></b> is shown. NB: 2022 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1699 2023 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Show <span 1700 2024 class=SpellE>hkl</span> positions</span></b> button has an additional use; you 1701 2025 can enter the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span 1702 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2026 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1703 2027 mso-hansi-theme-font:minor-latin'>Bravais</span></b></span><b style='mso-bidi-font-weight: 1704 normal'><span style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:2028 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1705 2029 minor-latin;mso-hansi-theme-font:minor-latin'> lattice</span></b>, <b 1706 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";2030 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1707 2031 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Space group</span></b> 1708 & <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";2032 & <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1709 2033 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Unit cell</span></b> 1710 2034 for any material. Then pressing <b style='mso-bidi-font-weight:normal'><span 1711 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2035 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1712 2036 mso-hansi-theme-font:minor-latin'>Show <span class=SpellE>hkl</span> positions</span></b> 1713 2037 will use that cell to index the lines in <b style='mso-bidi-font-weight:normal'><span 1714 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2038 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1715 2039 mso-hansi-theme-font:minor-latin'>Index Peak List</span></b>. This might be 1716 2040 useful to identify e.g. a second phase in your pattern.</p> 1717 2041 1718 2042 <p class=MsoNormal>(Optional) Finally, use of the <b style='mso-bidi-font-weight: 1719 normal'><span style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:2043 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1720 2044 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri; 1721 mso-bidi-theme-font:minor-latin'>Cell Index/Refine/ New phase</span></b> menu1722 option allows one to create a phase with these lattice parameters in the data 1723 tree under <b style='mso-bidi-font-weight:normal'><span style='font-family:1724 "Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:2045 mso-bidi-theme-font:minor-latin'>Cell Index/Refine/Make new phase</span></b> 2046 menu option allows one to create a phase with these lattice parameters in the 2047 data tree under <b style='mso-bidi-font-weight:normal'><span style='font-family: 2048 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1725 2049 minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>Phases</span></b>.<span 1726 2050 style='mso-spacerun:yes'> </span>A name for the new phase is requested. This 1727 2051 creates the tree item <b style='mso-bidi-font-weight:normal'><span 1728 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2052 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1729 2053 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font: 1730 2054 minor-latin'>Phases</span></b> (if it wasnt already present). This new phase 1731 can be used in future analysis (e.g. <span class=SpellE>Rietveld</span> or 1732 Pawley refinement).</p> 2055 can be used in future analysis (e.g. Rietveld or Pawley refinement).</p> 1733 2056 1734 2057 <p class=MsoNormal>To continue with the second part of this exercise, select 1735 2058 the menu item <b style='mso-bidi-font-weight:normal'><span style='font-family: 1736 "Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:2059 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1737 2060 minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>File/New 1738 2061 project</span></b> in the <b style='mso-bidi-font-weight:normal'><span 1739 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2062 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1740 2063 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font: 1741 2064 minor-latin'>GSAS-II data tree </span></b>window. You will be asked if you want 1742 2065 the current project saved; if <span class=GramE><b style='mso-bidi-font-weight: 1743 normal'><span style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:2066 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1744 2067 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri; 1745 2068 mso-bidi-theme-font:minor-latin'>Yes</span></b></span> then all the peak 1746 2069 fitting/indexing & cell refinement results will be saved to the <b 1747 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";2070 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1748 2071 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 1749 2072 Calibri;mso-bidi-theme-font:minor-latin'>LaB6.gpx</span></b> file. If <b 1750 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";2073 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1751 2074 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 1752 2075 Calibri;mso-bidi-theme-font:minor-latin'>No</span></b> then the file will … … 1761 2084 (aka <a href="http://en.wikipedia.org/wiki/Kryptonite">kryptonite</a>). The 1762 2085 data were also collected on 11BM-B at APS. The unit cell is monoclinic so it is 1763 a more substantial test of the indexing capability of GSAS-II.</p> 1764 1765 <h2><span class=GramE>Step 1.</span> Read in the data. </h2> 2086 a more substantial test of the indexing capability of GSAS-II. The required 2087 data files should have been downloaded when you downloaded this tutorial. 2088 Otherwise you will need to get them manually from <span style='mso-fareast-font-family: 2089 Calibri;mso-fareast-theme-font:minor-latin'><a 2090 href="https://subversion.xray.aps.anl.gov/pyGSAS/Exercises/FitPeaks/">https://subversion.xray.aps.anl.gov/pyGSAS/Exercises/FitPeaks/</a>. 2091 Be sure to get both </span><b style='mso-bidi-font-weight:normal'><span 2092 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2093 mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin;mso-hansi-theme-font: 2094 minor-latin'>11bmb_6231.fxye</span></b><span style='mso-fareast-font-family: 2095 Calibri;mso-fareast-theme-font:minor-latin'> and </span><b style='mso-bidi-font-weight: 2096 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 2097 minor-latin;mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin; 2098 mso-hansi-theme-font:minor-latin'>11bmb_6231.prm</span></b></p> 2099 2100 <h2>Step 1. Read in the data. </h2> 1766 2101 1767 2102 <p class=MsoNormal>The file is <b style='mso-bidi-font-weight:normal'><span 1768 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;1769 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font: 1770 minor-latin'>\ Exercises\kryptonite\11bmb_6231.fxye</span></b>; it has a1771 corresponding <span class=SpellE><b style='mso-bidi-font-weight:normal'><span1772 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2103 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2104 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font: 2105 minor-latin'>\exercises\<span class=SpellE>FitPeaks</span>\11bmb_6231.fxye</span></b>; 2106 it has a corresponding <span class=SpellE><b style='mso-bidi-font-weight:normal'><span 2107 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1773 2108 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font: 1774 2109 minor-latin'>prm</span></b></span> file. Load them in & the plot is</p> 1775 2110 1776 2111 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape 1777 id="Picture_x0020_ 18" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:525pt;2112 id="Picture_x0020_38" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:525pt; 1778 2113 height:450pt;visibility:visible;mso-wrap-style:square'> 1779 <v:imagedata src="Fit%20Peaks_files/image01 8.png" o:title=""/>2114 <v:imagedata src="Fit%20Peaks_files/image016.png" o:title=""/> 1780 2115 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600 1781 src="Fit%20Peaks_files/image01 8.png" v:shapes="Picture_x0020_18"><![endif]></span></p>2116 src="Fit%20Peaks_files/image016.png" v:shapes="Picture_x0020_38"><![endif]></span></p> 1782 2117 1783 2118 <p class=MsoNormal>Ive zoomed in & shifted the plot some to highlight the … … 1787 2122 1788 2123 <p class=MsoNormal>Set the limits as <b style='mso-bidi-font-weight:normal'><span 1789 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2124 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1790 2125 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font: 1791 2126 minor-latin'>3</span></b> and <b style='mso-bidi-font-weight:normal'><span 1792 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2127 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1793 2128 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font: 1794 2129 minor-latin'>9</span></b>.</p> … … 1798 2133 <p class=MsoNormal>Pick all peaks you can see between the limits (including the 1799 2134 small ones); use <b style='mso-bidi-font-weight:normal'><span style='font-family: 1800 "Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:2135 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1801 2136 minor-latin'>Auto search</span></b> to start and then fill in by hand: Add 1802 2137 peaks by left-clicking on a data point near the top of the peak. Peak positions … … 1808 2143 1809 2144 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape 1810 id="Picture_x0020_ 19" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:525pt;2145 id="Picture_x0020_39" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:525pt; 1811 2146 height:450pt;visibility:visible;mso-wrap-style:square'> 1812 <v:imagedata src="Fit%20Peaks_files/image01 9.png" o:title=""/>2147 <v:imagedata src="Fit%20Peaks_files/image017.png" o:title=""/> 1813 2148 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600 1814 src="Fit%20Peaks_files/image01 9.png" v:shapes="Picture_x0020_19"><![endif]></span><br2149 src="Fit%20Peaks_files/image017.png" v:shapes="Picture_x0020_39"><![endif]></span><br 1815 2150 clear=all style='mso-special-character:line-break'> 1816 2151 </p> 1817 2152 1818 <h2> <span class=GramE>Step 4.</span>Refine peaks</h2>1819 1820 <p class=MsoNormal>Following the steps used in the LaB<sub>6</sub> example above,1821 refine the peaks and the profile shape parameters in <b style='mso-bidi-font-weight: 1822 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: 1823 m inor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;1824 mso-bidi-theme-font:minor-latin'>Instrument Parameters</span></b>. You will be 1825 asked for a project file name at the first refinement (I used <span2153 <h2>Step 4. Refine peaks</h2> 2154 2155 <p class=MsoNormal>Following the steps used in the LaB<sub>6</sub> example 2156 above, refine the peaks and the profile shape parameters in <b 2157 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 2158 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 2159 Calibri;mso-bidi-theme-font:minor-latin'>Instrument Parameters</span></b>. You 2160 will be asked for a project file name at the first refinement (I used <span 1826 2161 class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family: 1827 "Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:2162 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1828 2163 minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>jadarite</span></b></span><b 1829 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";2164 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1830 2165 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 1831 2166 Calibri;mso-bidi-theme-font:minor-latin'></span></b>). In the end my 1832 2167 refinement converged at <span class=SpellE>Rwp</span>=11.41% and some peaks do 1833 2168 show some discrepancy as the sample is more complex than the simple <b 1834 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";2169 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1835 2170 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 1836 2171 Calibri;mso-bidi-theme-font:minor-latin'>U</span></b>, <b style='mso-bidi-font-weight: 1837 normal'><span style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:2172 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1838 2173 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri; 1839 2174 mso-bidi-theme-font:minor-latin'>V</span></b>, <b style='mso-bidi-font-weight: 1840 normal'><span style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:2175 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1841 2176 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri; 1842 2177 mso-bidi-theme-font:minor-latin'>W</span></b>, <b style='mso-bidi-font-weight: 1843 normal'><span style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:2178 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1844 2179 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri; 1845 2180 mso-bidi-theme-font:minor-latin'>X</span></b>, <b style='mso-bidi-font-weight: 1846 normal'><span style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:2181 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1847 2182 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri; 1848 2183 mso-bidi-theme-font:minor-latin'>Y</span></b> model can accommodate. Make sure … … 1850 2185 troublesome). However, this is good enough to proceed.</p> 1851 2186 1852 <h2> <span class=GramE>Step 5.</span>Prepare Indexing Peak List</h2>2187 <h2>Step 5. Prepare Indexing Peak List</h2> 1853 2188 1854 2189 <p class=MsoNormal>As before do <b style='mso-bidi-font-weight:normal'><span 1855 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2190 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1856 2191 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font: 1857 2192 minor-latin'>Operations/Load/Reload</span></b> in the <b style='mso-bidi-font-weight: 1858 normal'><span style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:2193 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1859 2194 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri; 1860 2195 mso-bidi-theme-font:minor-latin'>Index Peak List</span></b> window.</p> 1861 2196 1862 <h2> <span class=GramE>Step 6.</span>Index the cell</h2>2197 <h2>Step 6. Index the cell</h2> 1863 2198 1864 2199 <p class=MsoNormal>Lets assume that we know the cell is primitive monoclinic. … … 1868 2203 1869 2204 <p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span 1870 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2205 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1871 2206 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font: 1872 2207 minor-latin'>Monoclinic-P</span></b> and do <b style='mso-bidi-font-weight: 1873 normal'><span style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:2208 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1874 2209 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri; 1875 2210 mso-bidi-theme-font:minor-latin'>Cell Index/Refine/Index cell</span></b> in the 1876 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";2211 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1877 2212 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 1878 2213 Calibri;mso-bidi-theme-font:minor-latin'>Unit Cells List</span></b> window. … … 1882 2217 console display). Once this is seen (it may take more than one try to get this) 1883 2218 you can stop the indexing search by pressing <b style='mso-bidi-font-weight: 1884 normal'><span style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:2219 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1885 2220 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri; 1886 2221 mso-bidi-theme-font:minor-latin'>Cancel</span></b> on the progress bar window. 1887 2222 Notice the <b style='mso-bidi-font-weight:normal'><span style='font-family: 1888 "Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:2223 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1889 2224 minor-latin'>keep</span></b> column; this allows you to keep some solutions 1890 2225 from one indexing run to the next. It may take more than one press to fully … … 1892 2227 1893 2228 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape 1894 id="Picture_x0020_ 20" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:525pt;2229 id="Picture_x0020_40" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:525pt; 1895 2230 height:450pt;visibility:visible;mso-wrap-style:square'> 1896 <v:imagedata src="Fit%20Peaks_files/image0 20.png" o:title=""/>2231 <v:imagedata src="Fit%20Peaks_files/image018.png" o:title=""/> 1897 2232 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600 1898 src="Fit%20Peaks_files/image0 20.png" v:shapes="Picture_x0020_20"><![endif]><!--[if gte vml 1]><v:shape1899 id="Picture_x0020_ 21" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:527.25pt;1900 height:3 76.5pt;visibility:visible;mso-wrap-style:square'>1901 <v:imagedata src="Fit%20Peaks_files/image0 21.png" o:title=""/>1902 </v:shape><![endif]--><![if !vml]><img border=0 width=7 03 height=5021903 src="Fit%20Peaks_files/image0 21.png" v:shapes="Picture_x0020_21"><![endif]></span></p>1904 1905 <p class=MsoNormal>Notice other equally good M20 results with different1906 volumes; other solutions may be obtained as you keep trying the indexing. Be1907 sure to use <b style='mso-bidi-font-weight:normal'><span style='font-family: 1908 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1909 m inor-latin'>Keep</span></b> to keep good ones as you try new indexing runs.1910 The best solution is the one with the smaller volume and β > 90 deg. 1911 The plot shows every peak indexed including a weak peak not selected for the 1912 peak fitting, although the weak peak at 2<span style='font-family:Symbol; 1913 mso-char-type:symbol;mso-symbol-font-family:Symbol'><span style='mso-char-type: 1914 s ymbol;mso-symbol-font-family:Symbol'>Q</span></span>~7.3 has a shoulder that1915 wasnt indexed. I presume that is a contaminant. Copy the best cell and try to 1916 refine it along with the <b style='mso-bidi-font-weight:normal'><span 1917 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1918 m so-hansi-theme-font:minor-latin'>Zero offset</span></b>. I obtained an1919 improved M20 ~444 and slightly different lattice parameters. Try different 1920 space groups, pressing the <b style='mso-bidi-font-weight:normal'><span1921 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2233 src="Fit%20Peaks_files/image018.png" v:shapes="Picture_x0020_40"><![endif]><!--[if gte vml 1]><v:shape 2234 id="Picture_x0020_41" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:546pt; 2235 height:348.75pt;visibility:visible;mso-wrap-style:square'> 2236 <v:imagedata src="Fit%20Peaks_files/image019.png" o:title=""/> 2237 </v:shape><![endif]--><![if !vml]><img border=0 width=728 height=465 2238 src="Fit%20Peaks_files/image019.png" v:shapes="Picture_x0020_41"><![endif]></span></p> 2239 2240 <p class=MsoNormal>Notice there may be other equally good M20 results with 2241 different volumes; other solutions may be obtained as you keep trying the 2242 indexing. Be sure to use <b style='mso-bidi-font-weight:normal'><span 2243 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2244 mso-hansi-theme-font:minor-latin'>Keep</span></b> to keep good ones as you try 2245 new indexing runs. The best solution is the one with the smaller volume and 2246 β > 90 deg. The plot shows every peak indexed including a weak peak not 2247 selected for the peak fitting, although the weak peak at 2<span 2248 style='font-family:Symbol;mso-char-type:symbol;mso-symbol-font-family:Symbol'><span 2249 style='mso-char-type:symbol;mso-symbol-font-family:Symbol'>Q</span></span>~7.3 2250 has a shoulder that wasnt indexed. I presume that is a contaminant. Copy the 2251 best cell and try to refine it along with the <b style='mso-bidi-font-weight: 2252 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 2253 minor-latin;mso-hansi-theme-font:minor-latin'>Zero offset</span></b>. I 2254 obtained an improved M20 ~444 and slightly different lattice parameters. Try 2255 different space groups, pressing the <b style='mso-bidi-font-weight:normal'><span 2256 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1922 2257 mso-hansi-theme-font:minor-latin'>Show <span class=SpellE>hkl</span> positions</span></b> 1923 2258 each time to see which lines vanish. By sliding the cursor over the index lines … … 1926 2261 accidental but the 0k0; k≠2n and h0l; h+l≠2n ones characterize the 1927 2262 space group P2<sub>1</sub>/n. Armed with this information you can <b 1928 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";2263 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1929 2264 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 1930 2265 Calibri;mso-bidi-theme-font:minor-latin'>Make new phase</span></b> for the 1931 2266 indexed cell (I called it <b style='mso-bidi-font-weight:normal'><span 1932 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2267 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1933 2268 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font: 1934 2269 minor-latin'>kryptonite</span></b>) and select <b style='mso-bidi-font-weight: 1935 normal'><span style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:2270 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1936 2271 minor-latin;mso-hansi-theme-font:minor-latin'>Phases/kryptonite</span></b> from 1937 2272 the GSAS-II data tree.</p> 1938 2273 1939 2274 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape 1940 id="Picture_x0020_ 36" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:542.25pt;1941 height:3 56.25pt;visibility:visible;mso-wrap-style:square'>1942 <v:imagedata src="Fit%20Peaks_files/image02 2.png" o:title=""/>1943 </v:shape><![endif]--><![if !vml]><img border=0 width=723 height= 4751944 src="Fit%20Peaks_files/image02 2.png" v:shapes="Picture_x0020_36"><![endif]></span><span2275 id="Picture_x0020_42" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:542.25pt; 2276 height:375pt;visibility:visible;mso-wrap-style:square'> 2277 <v:imagedata src="Fit%20Peaks_files/image020.png" o:title=""/> 2278 </v:shape><![endif]--><![if !vml]><img border=0 width=723 height=500 2279 src="Fit%20Peaks_files/image020.png" v:shapes="Picture_x0020_42"><![endif]></span><span 1945 2280 style='mso-spacerun:yes'> </span></p> 1946 2281 … … 1949 2284 1950 2285 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape 1951 id="Picture_x0020_ 23" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:333.75pt;1952 height: 209.25pt;visibility:visible;mso-wrap-style:square'>1953 <v:imagedata src="Fit%20Peaks_files/image02 3.png" o:title=""/>1954 </v:shape><![endif]--><![if !vml]><img border=0 width= 445 height=2791955 src="Fit%20Peaks_files/image02 3.png" v:shapes="Picture_x0020_23"><![endif]></span></p>2286 id="Picture_x0020_43" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:228.75pt; 2287 height:168pt;visibility:visible;mso-wrap-style:square'> 2288 <v:imagedata src="Fit%20Peaks_files/image021.png" o:title=""/> 2289 </v:shape><![endif]--><![if !vml]><img border=0 width=305 height=224 2290 src="Fit%20Peaks_files/image021.png" v:shapes="Picture_x0020_43"><![endif]></span></p> 1956 2291 1957 2292 <p class=MsoNormal>This concludes this exercise; <span class=GramE><b 1958 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1959 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 1960 Calibri;mso-bidi-theme-font:minor-latin'>Save</span></b></span> the project file 1961 as it is needed for the <b style='mso-bidi-font-weight:normal'><span 1962 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1963 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font: 1964 minor-latin'><a href="Charge%20Flipping%20in%20GSAS.htm">Charge Flipping</a></span></b> 1965 exercise. The features of the <b style='mso-bidi-font-weight:normal'><span 1966 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1967 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font: 1968 minor-latin'>Phase Data</span></b> window will be presented in other exercises.</p> 2293 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 2294 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 2295 Calibri;mso-bidi-theme-font:minor-latin'>Save</span></b></span> the project 2296 file as it is needed for the <b style='mso-bidi-font-weight:normal'><span 2297 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2298 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font: 2299 minor-latin'>Charge Flipping</span></b> <b style='mso-bidi-font-weight:normal'><span 2300 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2301 mso-hansi-theme-font:minor-latin'>in GSAS</span></b> exercise. The features of 2302 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 2303 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 2304 Calibri;mso-bidi-theme-font:minor-latin'>Phase Data</span></b> window will be 2305 presented in other exercises.</p> 1969 2306 1970 2307 <h1><a name="sucrose_peak_fit"></a>3<sup>rd</sup> Fit Peaks/<span class=SpellE>Autoindexing</span> … … 1974 2311 sucrose in preparation for a charge flipping exercise. If continuing from the 1975 2312 previous indexing example do <b style='mso-bidi-font-weight:normal'><span 1976 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2313 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1977 2314 mso-hansi-theme-font:minor-latin'>File/New project</span></b> from the main 1978 2315 GSAS-II data tree menu; you will be asked if you wish to save the old project. 1979 2316 The data were also collected on 11BM-B at APS. The unit cell is monoclinic so 1980 is a more substantial test of the indexing capability of GSAS-II.</p> 1981 1982 <h2><span class=GramE>Step 1.</span> Read in the data. </h2> 2317 is another more substantial test of the indexing capability of GSAS-II. The 2318 required data files should have been downloaded when you downloaded this 2319 tutorial. Otherwise you will need to get them manually from <span 2320 style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'><a 2321 href="https://subversion.xray.aps.anl.gov/pyGSAS/Exercises/FitPeaks/">https://subversion.xray.aps.anl.gov/pyGSAS/Exercises/FitPeaks/</a>. 2322 Be sure to get </span><b style='mso-bidi-font-weight:normal'><span 2323 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2324 mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin;mso-hansi-theme-font: 2325 minor-latin'>11bmb_8714.fxye<span class=GramE>, <span style='font-family:"Times New Roman",serif; 2326 font-weight:normal'><span style='mso-spacerun:yes'> </span></span>11bmb</span>_8716.fxye</span></b><span 2327 style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'> and 2328 the corresponding .<span class=SpellE>prm</span> files.</span></p> 2329 2330 <h2>Step 1. Read in the data. </h2> 1983 2331 1984 2332 <p class=MsoNormal>The file is <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;mso-bidi-font-family:Calibri;mso-bidi-theme-font: 1987 minor-latin'>\ Exercises\sucrose\11bmb_8716.fxye</span></b>; it has a1988 corresponding <span class=SpellE><b style='mso-bidi-font-weight:normal'><span1989 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2333 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2334 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font: 2335 minor-latin'>\exercises\<span class=SpellE>FitPeaks</span>\11bmb_8716.fxye</span></b>; 2336 it has a corresponding <span class=SpellE><b style='mso-bidi-font-weight:normal'><span 2337 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1990 2338 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font: 1991 2339 minor-latin'>prm</span></b></span> file and is for Domino® sugar ground under 1992 acetone. <span class=GramE>The other <span class=SpellE><b style='mso-bidi-font-weight:1993 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: 1994 m inor-latin;mso-hansi-theme-font:minor-latin'>fxye</span></b></span> file in1995 this directory <b style='mso-bidi-font-weight:normal'><span style='font-family: 1996 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1997 minor-latin'>11bmb_8714.fxye</span></b> is for Domino® 10X powdered sugar used 1998 as is out of the box.</span> Load the <b style='mso-bidi-font-weight:normal'><span 1999 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 2000 mso-hansi-theme-font:minor-latin'>8716</span></b>file in & the plot is</p>2340 acetone. The other <span class=SpellE><b style='mso-bidi-font-weight:normal'><span 2341 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2342 mso-hansi-theme-font:minor-latin'>fxye</span></b></span> file in this directory 2343 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 2344 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>11bmb_8714.fxye</span></b> 2345 is for Domino® 10X powdered sugar used as is out of the box. Load the <b 2346 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 2347 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>8716</span></b> 2348 file in & the plot is</p> 2001 2349 2002 2350 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape 2003 id="Picture_x0020_ 31" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:525pt;2351 id="Picture_x0020_44" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:525pt; 2004 2352 height:450pt;visibility:visible;mso-wrap-style:square'> 2005 <v:imagedata src="Fit%20Peaks_files/image02 4.png" o:title=""/>2353 <v:imagedata src="Fit%20Peaks_files/image022.png" o:title=""/> 2006 2354 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600 2007 src="Fit%20Peaks_files/image02 4.png" v:shapes="Picture_x0020_31"><![endif]></span></p>2355 src="Fit%20Peaks_files/image022.png" v:shapes="Picture_x0020_44"><![endif]></span></p> 2008 2356 2009 2357 <p class=MsoNormal>Ive zoomed in & shifted the plot some to highlight the 2010 lower part of the pattern; Ive also chosen to plot the square root of the 2011 intensity (use <b style='mso-bidi-font-weight:normal'><span style='font-family: 2012 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 2013 minor-latin'>S</span></b>key) as this shows weak peaks better.</p>2358 lower part of the pattern; Ive also chosen to plot the square root of the intensity 2359 (use <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 2360 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>S</span></b> 2361 key) as this shows weak peaks better.</p> 2014 2362 2015 2363 <h2>Step 2 Set limits</h2> 2016 2364 2017 2365 <p class=MsoNormal>Set the limits as <b style='mso-bidi-font-weight:normal'><span 2018 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2366 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2019 2367 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font: 2020 2368 minor-latin'>2</span></b> and <b style='mso-bidi-font-weight:normal'><span 2021 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2369 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2022 2370 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font: 2023 2371 minor-latin'>8</span></b>.</p> … … 2027 2375 <p class=MsoNormal>Pick all peaks you can see between the limits (including the 2028 2376 small ones); use <b style='mso-bidi-font-weight:normal'><span style='font-family: 2029 "Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:2377 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 2030 2378 minor-latin'>Auto search</span></b> to start and then fill in by hand: Add 2031 2379 peaks by left-clicking on a data point near the top of the peak. Peak positions 2032 2380 can be moved by dragging the peak line and peaks can be deleted by 2033 2381 right-clicking on them. This only works when the zoom and reposition modes 2034 (below) are not selected. Also note the shoulder at ~6.3 <span class=SpellE>deg</span> 2035 that should be added to the list. I skipped a couple of very weak peaks; the total 2382 (below) are not selected. An easy to shift the view is to use the < and > 2383 buttons. Also note the shoulder at ~6.3 <span class=SpellE>deg</span> that 2384 should be added to the list. I skipped a couple of very weak peaks; the total 2036 2385 list has >28 peaks.</p> 2037 2386 2038 2387 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape 2039 id="Picture_x0020_ 32" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:525pt;2388 id="Picture_x0020_45" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:525pt; 2040 2389 height:450pt;visibility:visible;mso-wrap-style:square'> 2041 <v:imagedata src="Fit%20Peaks_files/image02 5.png" o:title=""/>2390 <v:imagedata src="Fit%20Peaks_files/image023.png" o:title=""/> 2042 2391 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600 2043 src="Fit%20Peaks_files/image02 5.png" v:shapes="Picture_x0020_32"><![endif]></span><br2392 src="Fit%20Peaks_files/image023.png" v:shapes="Picture_x0020_45"><![endif]></span><br 2044 2393 clear=all style='mso-special-character:line-break'> 2045 2394 </p> 2046 2395 2047 <h2> <span class=GramE>Step 4.</span>Refine peaks</h2>2396 <h2>Step 4. Refine peaks</h2> 2048 2397 2049 2398 <p class=MsoNormal>Following the steps used in the LaB<sub>6</sub> and 2050 2399 kryptonite examples above, refine the peaks and the profile shape parameters in 2051 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";2400 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 2052 2401 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 2053 2402 Calibri;mso-bidi-theme-font:minor-latin'>Instrument Parameters</span></b>. You 2054 2403 will be asked for a project file name at the first refinement (I used <b 2055 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";2404 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 2056 2405 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 2057 2406 Calibri;mso-bidi-theme-font:minor-latin'>sucrose</span></b>). In the end my 2058 refinement converged at <span class=SpellE>Rwp</span>= 7.15% and some peaks do2407 refinement converged at <span class=SpellE>Rwp</span>=6.69% and some peaks do 2059 2408 show some discrepancy as the sample is more complex than the simple <b 2060 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";2409 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 2061 2410 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 2062 2411 Calibri;mso-bidi-theme-font:minor-latin'>U</span></b>, <b style='mso-bidi-font-weight: 2063 normal'><span style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:2412 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 2064 2413 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri; 2065 2414 mso-bidi-theme-font:minor-latin'>V</span></b>, <b style='mso-bidi-font-weight: 2066 normal'><span style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:2415 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 2067 2416 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri; 2068 2417 mso-bidi-theme-font:minor-latin'>W</span></b>, <b style='mso-bidi-font-weight: 2069 normal'><span style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:2418 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 2070 2419 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri; 2071 2420 mso-bidi-theme-font:minor-latin'>X</span></b>, <b style='mso-bidi-font-weight: 2072 normal'><span style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:2421 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 2073 2422 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri; 2074 2423 mso-bidi-theme-font:minor-latin'>Y</span></b> model can accommodate. Make sure 2075 2424 no peaks drift away during refinement. However, this is good enough to proceed.</p> 2076 2425 2077 <h2> <span class=GramE>Step 5.</span>Prepare Indexing Peak List</h2>2426 <h2>Step 5. Prepare Indexing Peak List</h2> 2078 2427 2079 2428 <p class=MsoNormal>As before do <b style='mso-bidi-font-weight:normal'><span 2080 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2429 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2081 2430 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font: 2082 2431 minor-latin'>Operations/Load/Reload</span></b> in the <b style='mso-bidi-font-weight: 2083 normal'><span style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:2432 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 2084 2433 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri; 2085 2434 mso-bidi-theme-font:minor-latin'>Index Peak List</span></b> window.</p> 2086 2435 2087 <h2> <span class=GramE>Step 6.</span>Index the cell</h2>2436 <h2>Step 6. Index the cell</h2> 2088 2437 2089 2438 <p class=MsoNormal>Lets assume that we know the cell in primitive monoclinic. … … 2093 2442 2094 2443 <p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span 2095 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2444 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2096 2445 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font: 2097 2446 minor-latin'>Monoclinic-P</span></b> and do <b style='mso-bidi-font-weight: 2098 normal'><span style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:2447 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 2099 2448 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri; 2100 2449 mso-bidi-theme-font:minor-latin'>Cell Index/Refine/Index cell</span></b> in the 2101 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";2450 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 2102 2451 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 2103 2452 Calibri;mso-bidi-theme-font:minor-latin'>Unit Cells List</span></b> window. … … 2108 2457 Once this is seen (it may take more than one try to get this) you can stop the 2109 2458 indexing search by pressing <b style='mso-bidi-font-weight:normal'><span 2110 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2459 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2111 2460 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font: 2112 2461 minor-latin'>Cancel</span></b> on the progress bar window. Notice the <b … … 2116 2465 2117 2466 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape 2118 id="Picture_x0020_ 33" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:527.25pt;2119 height: 376.5pt;visibility:visible;mso-wrap-style:square'>2120 <v:imagedata src="Fit%20Peaks_files/image02 6.png" o:title=""/>2121 </v:shape><![endif]--><![if !vml]><img border=0 width=7 03 height=5022122 src="Fit%20Peaks_files/image02 6.png" v:shapes="Picture_x0020_33"><![endif]><!--[if gte vml 1]><v:shape2123 id="Picture_x0020_ 34" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:525pt;2467 id="Picture_x0020_46" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:546pt; 2468 height:5in;visibility:visible;mso-wrap-style:square'> 2469 <v:imagedata src="Fit%20Peaks_files/image024.png" o:title=""/> 2470 </v:shape><![endif]--><![if !vml]><img border=0 width=728 height=480 2471 src="Fit%20Peaks_files/image024.png" v:shapes="Picture_x0020_46"><![endif]><!--[if gte vml 1]><v:shape 2472 id="Picture_x0020_47" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:525pt; 2124 2473 height:450pt;visibility:visible;mso-wrap-style:square'> 2125 <v:imagedata src="Fit%20Peaks_files/image02 7.png" o:title=""/>2474 <v:imagedata src="Fit%20Peaks_files/image025.png" o:title=""/> 2126 2475 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600 2127 src="Fit%20Peaks_files/image02 7.png" v:shapes="Picture_x0020_34"><![endif]></span></p>2476 src="Fit%20Peaks_files/image025.png" v:shapes="Picture_x0020_47"><![endif]></span></p> 2128 2477 2129 2478 <p class=MsoNormal>Notice there may be other equally good M20 results with 2130 2479 different volumes; still other solutions may be obtained as you keep trying the 2131 2480 indexing. Be sure to use <b style='mso-bidi-font-weight:normal'><span 2132 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2481 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2133 2482 mso-hansi-theme-font:minor-latin'>Keep</span></b> to keep good ones as you try 2134 2483 new indexing runs. The best solution is the one with the smaller volume and … … 2136 2485 not selected for the peak fitting. Copy the best cell and try to refine it 2137 2486 along with the <b style='mso-bidi-font-weight:normal'><span style='font-family: 2138 "Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:2139 minor-latin'>Zero offset</span></b>. I obtained an improved M20 ~1 257and2487 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 2488 minor-latin'>Zero offset</span></b>. I obtained an improved M20 ~1300 and 2140 2489 slightly different lattice parameters. Try different space groups, pressing the 2141 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";2490 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 2142 2491 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Show <span 2143 2492 class=SpellE>hkl</span> positions</span></b> each time to see which lines 2144 vanish. The correct space group is P2<sub>1</sub>. Armed with this information 2145 you can <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";2493 vanish. The correct space group is P2<sub>1</sub>. Armed with this information you 2494 can <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 2146 2495 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 2147 2496 Calibri;mso-bidi-theme-font:minor-latin'>Make new phase</span></b> for the 2148 2497 indexed cell (I called it <b style='mso-bidi-font-weight:normal'><span 2149 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2498 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2150 2499 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font: 2151 2500 minor-latin'>sucrose</span></b>) and select <b style='mso-bidi-font-weight: 2152 normal'><span style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:2501 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 2153 2502 minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b> from 2154 2503 the GSAS-II data tree.</p> 2155 2504 2156 2505 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape 2157 id="Picture_x0020_ 35" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:542.25pt;2158 height:3 51pt;visibility:visible;mso-wrap-style:square'>2159 <v:imagedata src="Fit%20Peaks_files/image02 8.png" o:title=""/>2160 </v:shape><![endif]--><![if !vml]><img border=0 width=723 height= 4682161 src="Fit%20Peaks_files/image02 8.png" v:shapes="Picture_x0020_35"><![endif]></span><span2506 id="Picture_x0020_48" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:542.25pt; 2507 height:375pt;visibility:visible;mso-wrap-style:square'> 2508 <v:imagedata src="Fit%20Peaks_files/image026.png" o:title=""/> 2509 </v:shape><![endif]--><![if !vml]><img border=0 width=723 height=500 2510 src="Fit%20Peaks_files/image026.png" v:shapes="Picture_x0020_48"><![endif]></span><span 2162 2511 style='mso-spacerun:yes'> </span></p> 2163 2512 2164 2513 <p class=MsoNormal>Notice that the lattice parameters and space group have been 2165 2514 set for you. This concludes this exercise; <b style='mso-bidi-font-weight:normal'><span 2166 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2515 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2167 2516 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font: 2168 2517 minor-latin'>Save</span></b> the project file as it is needed for the sucrose <b 2169 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 2170 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 2171 Calibri;mso-bidi-theme-font:minor-latin'><a 2172 href="Charge%20Flipping%20-%20sucrose.htm">Charge Flipping</a></span></b> 2173 exercise. The features of the <b style='mso-bidi-font-weight:normal'><span 2174 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 2518 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 2519 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 2520 Calibri;mso-bidi-theme-font:minor-latin'>Charge Flipping</span></b> exercise. 2521 The features of the <b style='mso-bidi-font-weight:normal'><span 2522 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2175 2523 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font: 2176 2524 minor-latin'>Phase Data</span></b> window will be presented in other exercises.</p> -
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