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Timestamp:
May 7, 2012 4:48:24 PM (10 years ago)
Author:
vondreele
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  • trunk/help/Fit Peaks.htm

    r591 r602  
    2323  <o:Author>Von Dreele</o:Author>
    2424  <o:LastAuthor>Von Dreele</o:LastAuthor>
    25   <o:Revision>11</o:Revision>
    26   <o:TotalTime>234</o:TotalTime>
     25  <o:Revision>13</o:Revision>
     26  <o:TotalTime>238</o:TotalTime>
    2727  <o:Created>2012-05-05T16:28:00Z</o:Created>
    28   <o:LastSaved>2012-05-06T20:12:00Z</o:LastSaved>
     28  <o:LastSaved>2012-05-07T21:46:00Z</o:LastSaved>
    2929  <o:Pages>9</o:Pages>
    30   <o:Words>1797</o:Words>
    31   <o:Characters>10243</o:Characters>
     30  <o:Words>1789</o:Words>
     31  <o:Characters>10202</o:Characters>
    3232  <o:Company>Argonne National Laboratory</o:Company>
    3333  <o:Lines>85</o:Lines>
    34   <o:Paragraphs>24</o:Paragraphs>
    35   <o:CharactersWithSpaces>12016</o:CharactersWithSpaces>
     34  <o:Paragraphs>23</o:Paragraphs>
     35  <o:CharactersWithSpaces>11968</o:CharactersWithSpaces>
    3636  <o:Version>14.00</o:Version>
    3737 </o:DocumentProperties>
     
    11331133be done.</p>
    11341134
    1135 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    1136 
    11371135<p class=MsoNormal>If you have not done so already, <a
    11381136href="Starting%20GSAS.htm">start GSAS-II</a>.</p>
     
    11451143the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    11461144mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1147 minor-latin'>Data/Read powder data</span></b> menu item to read the data file
    1148 into the current GSAS-II project. This read option is set to read any of the
    1149 powder data formats (except neutron TOF time map files) defined for GSAS
    1150 (angles in <span class=SpellE>centidegrees</span>). It will also read the <span
    1151 class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
    1152 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1153 minor-latin;mso-bidi-theme-font:minor-latin'>xye</span></b></span> format
    1154 (angles in degrees) used by <span class=SpellE>Topas</span>, etc.<span
    1155 style='mso-spacerun:yes'>  </span>Change the file directory to <b
     1145minor-latin'>Data/Read powder data</span></b> menu item to read the data file into
     1146the current GSAS-II project. This read option is set to read any of the powder
     1147data formats (except neutron TOF time map files) defined for GSAS (angles in <span
     1148class=SpellE>centidegrees</span>). It will also read the <span class=SpellE><b
    11561149style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    11571150mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1158 minor-latin'>Exercises/LaB6</span></b><span style='font-family:"Calibri","sans-serif";
    1159 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1160 minor-latin'> to find the file; you may need to change the file type to <b
    1161 style='mso-bidi-font-weight:normal'>All files (*.*)</b> to find the desired
    1162 file.</span></p>
     1151minor-latin'>xye</span></b></span> format (angles in degrees) used by <span
     1152class=SpellE>Topas</span>, etc.<span style='mso-spacerun:yes'>  </span>Change
     1153the file directory to <b style='mso-bidi-font-weight:normal'><span
     1154style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1155mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Exercises/LaB6</span></b><span
     1156style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1157mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'> to find the
     1158file; you may need to change the file type to <b style='mso-bidi-font-weight:
     1159normal'>All files (*.*)</b> to find the desired file.</span></p>
    11631160
    11641161<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
     
    11981195file was created from the 12 detector raw data.</p>
    11991196
    1200 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    1201 
    12021197<p class=MsoNormal>At this point the <b style='mso-bidi-font-weight:normal'><span
    12031198style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    12041199mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II data
    12051200tree</span></b> window will have several entries </p>
    1206 
    1207 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    12081201
    12091202<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
     
    12331226src="Fit%20Peaks_files/image001.png" v:shapes="Picture_x0020_1"><![endif]></span></p>
    12341227
    1235 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    1236 
    12371228<p class=MsoNormal><span class=GramE>and</span> the plot window will show the
    12381229powder pattern</p>
    1239 
    1240 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    12411230
    12421231<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    12761265lower limit or a right click on a data point for the upper limit.</p>
    12771266
    1278 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    1279 
    12801267<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    12811268 id="Picture_x0020_4" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:225pt;
     
    12871274<h2>Step 3: Determine Peak Positions</h2>
    12881275
    1289 <p class=MsoListParagraph style='margin-left:39.0pt;mso-add-space:auto;
    1290 text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
     1276<p class=MsoListParagraphCxSpFirst style='margin-left:39.0pt;mso-add-space:
     1277auto;text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
    12911278style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
    12921279style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Click
     
    12991286style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    13001287mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1301 minor-latin'>Limits</span></b> window is erased). At this point it is wise to </p>
    1302 
    1303 <p class=MsoNormal><span style='mso-spacerun:yes'> </span><span class=GramE>zoom</span>
    1304 in on the data that will be used for indexing. </p>
    1305 
    1306 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    1307 
    1308 <p class=MsoListParagraph style='margin-left:39.0pt;mso-add-space:auto;
    1309 text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
     1288minor-latin'>Limits</span></b> window is erased). At this point it is wise <span
     1289class=GramE>to<span style='mso-spacerun:yes'>  </span>zoom</span> in on the
     1290data that will be used for indexing. </p>
     1291
     1292<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
     1293auto;text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
    13101294style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
    13111295style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Click
    13121296on the Zoom button, <span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1313  id="Picture_x0020_5" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:21.75pt;
    1314  height:18.75pt;visibility:visible;mso-wrap-style:square'>
     1297 id="_x0000_i1044" type="#_x0000_t75" style='width:21.75pt;height:18.75pt;
     1298 visibility:visible;mso-wrap-style:square'>
    13151299 <v:imagedata src="Fit%20Peaks_files/image004.jpg" o:title="" croptop="1f"
    13161300  cropbottom="-1f" cropleft="35827f" cropright="19224f"/>
    13171301</v:shape><![endif]--><![if !vml]><img border=0 width=29 height=25
    1318 src="Fit%20Peaks_files/image005.jpg" v:shapes="Picture_x0020_5"><![endif]></span>,
     1302src="Fit%20Peaks_files/image005.jpg" v:shapes="_x0000_i1044"><![endif]></span>,
    13191303then press the left mouse in one corner of the region to be used; holding the
    13201304mouse button down, drag over the region to the opposite corner; a box will be
    13211305drawn over the region to be zoomed. </p>
    13221306
    1323 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    1324 
    1325 <p class=MsoListParagraph style='margin-left:39.0pt;mso-add-space:auto;
    1326 text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
     1307<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
     1308auto;text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
    13271309style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
    13281310style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    13291311style='mso-bidi-font-weight:normal'>Important</b>: Click on the Zoom <span
    1330 style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_6"
     1312style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_5"
    13311313 o:spid="_x0000_i1043" type="#_x0000_t75" style='width:23.25pt;height:20.25pt;
    13321314 visibility:visible;mso-wrap-style:square'>
     
    13341316  cropbottom="-1f" cropleft="35827f" cropright="19224f"/>
    13351317</v:shape><![endif]--><![if !vml]><img border=0 width=31 height=27
    1336 src="Fit%20Peaks_files/image006.jpg" v:shapes="Picture_x0020_6"><![endif]></span><span
     1318src="Fit%20Peaks_files/image006.jpg" v:shapes="Picture_x0020_5"><![endif]></span><span
    13371319style='mso-spacerun:yes'> </span>button again to turn off the zoom mode. </p>
    13381320
    1339 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    1340 
    1341 <p class=MsoListParagraphCxSpFirst style='margin-left:39.0pt;mso-add-space:
     1321<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
    13421322auto;text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
    13431323style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
    13441324style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Using
    1345 the left mouse button, click on a data point near the top of each peak to be added
    1346 to the peak list. It is usually best to start at the upper end of the pattern
    1347 as the next peak to pick isn’t obscured by the tool tip. As this is done, a
    1348 vertical blue line is drawn in the plot window<span style='mso-spacerun:yes'> 
    1349 </span>for each peak selected</p>
    1350 
    1351 <p class=MsoListParagraphCxSpMiddle><o:p>&nbsp;</o:p></p>
     1325the left mouse button, click on a data point near the top of each peak to be
     1326added to the peak list. It is usually best to start at the upper end of the
     1327pattern as the next peak to pick isn’t obscured by the tool tip. As this is
     1328done, a vertical blue line is drawn in the plot window<span
     1329style='mso-spacerun:yes'>  </span>for each peak selected</p>
    13521330
    13531331<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="_x0000_i1042"
    1355  type="#_x0000_t75" style='width:525pt;height:450pt;visibility:visible;
    1356  mso-wrap-style:square'>
     1332auto'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_6"
     1333 o:spid="_x0000_i1042" type="#_x0000_t75" style='width:525pt;height:450pt;
     1334 visibility:visible;mso-wrap-style:square'>
    13571335 <v:imagedata src="Fit%20Peaks_files/image007.png" o:title=""/>
    13581336</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
    1359 src="Fit%20Peaks_files/image007.png" v:shapes="_x0000_i1042"><![endif]></span></p>
    1360 
    1361 <p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
    1362 auto'><o:p>&nbsp;</o:p></p>
     1337src="Fit%20Peaks_files/image007.png" v:shapes="Picture_x0020_6"><![endif]></span></p>
    13631338
    13641339<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
     
    13671342minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak
    13681343List</span></b> window in order of increasing 2<span style='font-family:Symbol'>Q</span>.</p>
    1369 
    1370 <p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
    1371 auto'><o:p>&nbsp;</o:p></p>
    13721344
    13731345<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
     
    13801352
    13811353<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
    1382 auto'><o:p>&nbsp;</o:p></p>
    1383 
    1384 <p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
    13851354auto'>Note that if peaks are not being added, you probably have not exited zoom
    13861355mode.</p>
    1387 
    1388 <p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
    1389 auto'><o:p>&nbsp;</o:p></p>
    13901356
    13911357<p class=MsoListParagraphCxSpLast style='margin-left:39.0pt;mso-add-space:auto'>Add
     
    14001366refinement and then adding <span class=GramE>a parameters</span> to complete
    14011367the fitting,</p>
    1402 
    1403 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    14041368
    14051369<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
     
    14301394values and a summary of the refinement is shown on the console window as well.</p>
    14311395
    1432 <p class=MsoListParagraphCxSpMiddle><o:p>&nbsp;</o:p></p>
    1433 
    14341396<p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    14351397 id="Picture_x0020_8" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:525pt;
     
    14391401src="Fit%20Peaks_files/image009.png" v:shapes="Picture_x0020_8"><![endif]></span></p>
    14401402
    1441 <p class=MsoListParagraphCxSpMiddle><o:p>&nbsp;</o:p></p>
    1442 
    1443 <p class=MsoListParagraphCxSpLast><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1403<p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    14441404 id="Picture_x0020_9" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:401.25pt;
    14451405 height:262.5pt;visibility:visible;mso-wrap-style:square'>
     
    14481408src="Fit%20Peaks_files/image010.png" v:shapes="Picture_x0020_9"><![endif]></span></p>
    14491409
    1450 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    1451 
    1452 <p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
     1410<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
    14531411style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
    14541412style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Now
     
    14791437minor-latin'>n</span></b> would turn them off).</p>
    14801438
    1481 <p class=MsoNormal><span style='mso-spacerun:yes'> </span></p>
    1482 
    1483 <p class=MsoListParagraph style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
    1484 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
    1485 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Next,
    1486 repeat the refinement using the <b style='mso-bidi-font-weight:normal'><span
     1439<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Next, repeat the
     1440refinement using the <b style='mso-bidi-font-weight:normal'><span
    14871441style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    14881442mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak
     
    14921446minor-latin'>Peak List</span></b> window.</p>
    14931447
    1494 <p class=MsoNormal><span style='mso-spacerun:yes'> </span></p>
    1495 
    1496 <p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
    1497 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
    1498 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Now,
    1499 select peak widths for refinement. This can be done by refining sigma (Gaussian
    1500 width) and/or gamma (Lorentzian width) for individual peaks, but here we can
    1501 constrain the peaks to follow an instrumental broadening equation. Select the <b
     1448<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Now, select peak
     1449widths for refinement. This can be done by refining sigma (Gaussian width)
     1450and/or gamma (Lorentzian width) for individual peaks, but here we can constrain
     1451the peaks to follow an instrumental broadening equation. Select the <b
    15021452style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    15031453mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    15041454minor-latin'>Instrumental Parameters</span></b> item in the data tree. This
    1505 opens a window for peak profile terms<br>
    1506 <br>
    1507 <span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_10"
    1508  o:spid="_x0000_i1038" type="#_x0000_t75" style='width:422.25pt;height:154.5pt;
    1509  visibility:visible;mso-wrap-style:square'>
     1455opens a window for peak profile terms</p>
     1456
     1457<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1458 id="Picture_x0020_10" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:422.25pt;
     1459 height:154.5pt;visibility:visible;mso-wrap-style:square'>
    15101460 <v:imagedata src="Fit%20Peaks_files/image011.png" o:title=""/>
    15111461</v:shape><![endif]--><![if !vml]><img border=0 width=563 height=206
    15121462src="Fit%20Peaks_files/image011.png" v:shapes="Picture_x0020_10"><![endif]></span></p>
    15131463
    1514 <p class=MsoListParagraphCxSpMiddle><o:p>&nbsp;</o:p></p>
    1515 
    1516 <p class=MsoListParagraphCxSpLast>The plot window shows the resolution curves
     1464<p class=MsoListParagraphCxSpFirst>The plot window shows the resolution curves
    15171465corresponding to the values of the Gaussian U, V, W, Lorentzian X &amp; Y
    15181466coefficients; ‘+’ marks show the individual values based on the sig &amp; gam
     
    15201468U, V, W, and Lorentzian X, Y. </p>
    15211469
    1522 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    1523 
    1524 <p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
    1525 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>5.<span
     1470<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
     1471style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
    15261472style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Then,
    15271473repeat the refinement. First click on the <b style='mso-bidi-font-weight:normal'><span
     
    15351481see </p>
    15361482
    1537 <p class=MsoListParagraphCxSpMiddle><o:p>&nbsp;</o:p></p>
    1538 
    15391483<p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    15401484 id="Picture_x0020_11" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:525pt;
     
    15441488src="Fit%20Peaks_files/image012.png" v:shapes="Picture_x0020_11"><![endif]></span></p>
    15451489
    1546 <p class=MsoListParagraphCxSpMiddle><o:p>&nbsp;</o:p></p>
    1547 
    15481490<p class=MsoListParagraphCxSpLast>The <span class=SpellE>Rwp</span> is ~6% as
    15491491shown on the console window. Again the <b style='mso-bidi-font-weight:normal'><span
     
    15701512minor-latin'>Peak List</span></b>.</p>
    15711513
    1572 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    1573 
    15741514<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    15751515 id="Picture_x0020_12" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:367.5pt;
     
    15791519src="Fit%20Peaks_files/image013.png" v:shapes="Picture_x0020_12"><![endif]></span></p>
    15801520
    1581 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    1582 
    15831521<p class=MsoNormal>Note that by default all peaks are selected to be used. You
    15841522may choose to not use a fitted peak (e.g. if suspected as from a contaminant).</p>
     
    15911529List</span></b> data item. This brings up a window for indexing and cell
    15921530refinement options</p>
    1593 
    1594 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    15951531
    15961532<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    16011537src="Fit%20Peaks_files/image014.png" v:shapes="Picture_x0020_13"><![endif]></span></p>
    16021538
    1603 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    1604 
    16051539<p class=MsoNormal>For the most rapid search (since we know the right answer),
    16061540select <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     
    16161550Cells List</span></b> window</p>
    16171551
    1618 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    1619 
    16201552<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    16211553 id="Picture_x0020_14" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:527.25pt;
     
    16361568first cell in the list (M20=2961.34) with a=5.87864 Å generates very many lines
    16371569with no corresponding peaks</p>
    1638 
    1639 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    16401570
    16411571<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    16471577style='mso-spacerun:yes'> </span></p>
    16481578
    1649 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    1650 
    16511579<p class=MsoNormal><span class=GramE>while</span> the (M20=609.02) cell with
    16521580a=2.93932 Å generates not enough lines to match all the peaks</p>
    1653 
    1654 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    16551581
    16561582<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    16861612offset</span></b> (in this case hardly anything happens!) </p>
    16871613
    1688 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    1689 
    16901614<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    16911615 id="Picture_x0020_17" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:527.25pt;
     
    16951619src="Fit%20Peaks_files/image018.png" v:shapes="Picture_x0020_17"><![endif]></span></p>
    16961620
    1697 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    1698 
    16991621<p class=MsoNormal>Notice that a new entry heads the list in the <b
    17001622style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     
    17081630minor-latin'>Zero offset</span></b> is shown.</p>
    17091631
    1710 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    1711 
    17121632<p class=MsoNormal>(Optional) Finally, use of the <b style='mso-bidi-font-weight:
    17131633normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     
    17231643(if it wasn’t already present). This new phase can be used in future analysis
    17241644(e.g. Rietveld or Pawley refinement).</p>
    1725 
    1726 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    17271645
    17281646<p class=MsoNormal>To continue with the second part of this exercise, <span
     
    17631681file. Load them in &amp; the plot is</p>
    17641682
    1765 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    1766 
    17671683<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    17681684 id="Picture_x0020_18" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:525pt;
     
    17721688src="Fit%20Peaks_files/image019.png" v:shapes="Picture_x0020_18"><![endif]></span></p>
    17731689
    1774 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    1775 
    17761690<p class=MsoNormal>I’ve zoomed in &amp; shifted the plot some to highlight the
    17771691lower part of the pattern.</p>
     
    178717017.81deg. I found 28 peaks (there were a few very weak ones I skipped – they
    17881702might be from a second phase? We’ll see later).</p>
    1789 
    1790 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    17911703
    17921704<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    18421754My result was </p>
    18431755
    1844 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    1845 
    18461756<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    18471757 id="Picture_x0020_20" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:527.25pt;
     
    18511761src="Fit%20Peaks_files/image021.png" v:shapes="Picture_x0020_20"><![endif]></span></p>
    18521762
    1853 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    1854 
    18551763<p class=MsoNormal>Notice an equally good M20 result with twice the volume. The
    18561764plot shows every peak indexed including a couple of weak peaks not selected for
    18571765the peak fitting.</p>
    1858 
    1859 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    18601766
    18611767<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    18661772src="Fit%20Peaks_files/image022.png" v:shapes="Picture_x0020_21"><![endif]></span></p>
    18671773
    1868 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    1869 
    1870 <p class=MsoNormal>Although the weak peak at 2<span style='font-family:Symbol'>Q</span>~7.3
    1871 has a shoulder that wasn’t indexed. I presume that is a contaminant. By sliding
    1872 the cursor over the index lines without any visible peak you can see that the
    1873 missing ones are (010, 100, 001, 110, 030, 111, 20-1, 10-2, 041, 050, 21-2,
    1874 23-1, 22-2, 141, 201,102, 15-1, 112, &amp; 24-1). Many of these are accidental
    1875 but the 0k0; k&#8800;2n and h0l; h+l&#8800;2n ones characterize the space group
    1876 P2<sub>1</sub>/n. Armed with this information you can <b style='mso-bidi-font-weight:
    1877 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1878 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Make
    1879 new phase</span></b> for the indexed cell (I called it ‘kryptonite’) and set
    1880 the space group in the Phase Data for kryptonite window.</p>
    1881 
    1882 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1774<p class=MsoNormal>Although the weak peak at 2<span style='font-family:Symbol;
     1775mso-char-type:symbol;mso-symbol-font-family:Symbol'><span style='mso-char-type:
     1776symbol;mso-symbol-font-family:Symbol'>Q</span></span>~7.3 has a shoulder that
     1777wasn’t indexed. I presume that is a contaminant. By sliding the cursor over the
     1778index lines without any visible peak you can see that the missing ones are
     1779(010, 100, 001, 110, 030, 111, 20-1, 10-2, 041, 050, 21-2, 23-1, 22-2, 141,
     1780201,102, 15-1, 112, &amp; 24-1). Many of these are accidental but the 0k0; k&#8800;2n
     1781and h0l; h+l&#8800;2n ones characterize the space group P2<sub>1</sub>/n. Armed
     1782with this information you can <b style='mso-bidi-font-weight:normal'><span
     1783style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1784mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Make new
     1785phase</span></b> for the indexed cell (I called it ‘kryptonite’) and set the
     1786space group in the Phase Data for kryptonite window.</p>
    18831787
    18841788<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    18891793src="Fit%20Peaks_files/image023.png" v:shapes="Picture_x0020_22"><![endif]></span></p>
    18901794
    1891 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    1892 
    18931795<p class=MsoNormal>Setting the space group will show a window with some
    18941796information. Press <b style='mso-bidi-font-weight:normal'><span
     
    18961798mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>OK</span></b>
    18971799to close it.</p>
    1898 
    1899 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    19001800
    19011801<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    19061806src="Fit%20Peaks_files/image024.png" v:shapes="Picture_x0020_23"><![endif]></span></p>
    19071807
    1908 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    1909 
    19101808<p class=MsoNormal>This concludes this exercise. The features of the Phase Data
    19111809window will be presented in other exercises.</p>
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