Changeset 864


Ignore:
Timestamp:
Mar 19, 2013 9:33:15 AM (9 years ago)
Author:
vondreele
Message:

fix to mustrain plot scaling - generalized was off by 100X
remove a stray print in GSASIIstruct.py
work on tutorials - add charge flipping

Location:
trunk
Files:
2 added
21 edited

Legend:

Unmodified
Added
Removed
  • trunk/GSASIIplot.py

    r863 r864  
    15041504                        sum = np.sum(np.multiply(Shkl,Strm))
    15051505                        sum = np.where(sum > 0.01,sum,0.01)
    1506                         sum = np.sqrt(sum)*math.pi/0.018      #centidegrees to radians!
     1506                        sum = np.sqrt(sum)*math.pi/1.8      #centidegrees to radians!
    15071507                        return sum*xyz
    15081508                       
  • trunk/GSASIIstruct.py

    r863 r864  
    22652265                    except ValueError:
    22662266                        pass
    2267     print np.sum(pDerv),pDerv.shape
    22682267    return pDerv
    22692268
  • trunk/help/Fit Peaks.htm

    r782 r864  
    2323  <o:Author>Von Dreele</o:Author>
    2424  <o:LastAuthor>Von Dreele</o:LastAuthor>
    25   <o:Revision>22</o:Revision>
    26   <o:TotalTime>429</o:TotalTime>
     25  <o:Revision>29</o:Revision>
     26  <o:TotalTime>717</o:TotalTime>
    2727  <o:Created>2012-05-05T16:28:00Z</o:Created>
    28   <o:LastSaved>2012-10-16T19:18:00Z</o:LastSaved>
    29   <o:Pages>2</o:Pages>
    30   <o:Words>1952</o:Words>
    31   <o:Characters>11133</o:Characters>
     28  <o:LastSaved>2013-03-18T17:01:00Z</o:LastSaved>
     29  <o:Pages>11</o:Pages>
     30  <o:Words>2632</o:Words>
     31  <o:Characters>15009</o:Characters>
    3232  <o:Company>Argonne National Laboratory</o:Company>
    33   <o:Lines>92</o:Lines>
    34   <o:Paragraphs>26</o:Paragraphs>
    35   <o:CharactersWithSpaces>13059</o:CharactersWithSpaces>
     33  <o:Lines>125</o:Lines>
     34  <o:Paragraphs>35</o:Paragraphs>
     35  <o:CharactersWithSpaces>17606</o:CharactersWithSpaces>
    3636  <o:Version>14.00</o:Version>
    3737 </o:DocumentProperties>
     
    4040 </o:OfficeDocumentSettings>
    4141</xml><![endif]-->
    42 <link rel=dataStoreItem href="Fit%20Peaks_files/item0030.xml"
    43 target="Fit%20Peaks_files/props031.xml">
     42<link rel=dataStoreItem href="Fit%20Peaks_files/item0035.xml"
     43target="Fit%20Peaks_files/props036.xml">
    4444<link rel=themeData href="Fit%20Peaks_files/themedata.thmx">
    4545<link rel=colorSchemeMapping href="Fit%20Peaks_files/colorschememapping.xml">
     
    356356        mso-generic-font-family:swiss;
    357357        mso-font-pitch:variable;
    358         mso-font-signature:-520092929 1073786111 9 0 415 0;}
     358        mso-font-signature:-536870145 1073786111 1 0 415 0;}
    359359@font-face
    360360        {font-family:Tahoma;
     
    11131113        mso-ascii-theme-font:minor-latin;
    11141114        mso-hansi-font-family:Calibri;
    1115         mso-hansi-theme-font:minor-latin;
    1116         mso-bidi-font-family:"Times New Roman";
    1117         mso-bidi-theme-font:minor-bidi;}
     1115        mso-hansi-theme-font:minor-latin;}
    11181116</style>
    11191117<![endif]--><!--[if gte mso 9]><xml>
    1120  <o:shapedefaults v:ext="edit" spidmax="1027"/>
     1118 <o:shapedefaults v:ext="edit" spidmax="1026"/>
    11211119</xml><![endif]--><!--[if gte mso 9]><xml>
    11221120 <o:shapelayout v:ext="edit">
     
    11451143style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Use
    11461144the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1147 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1148 minor-latin'>Import/Powder Data/from GSAS file</span></b> menu item to read the
    1149 data file into the current GSAS-II project. This read option is set to read any
    1150 of the powder data formats (except neutron TOF time map files) defined for GSAS
    1151 (angles in <span class=SpellE>centidegrees</span>). Other submenu items will
    1152 read the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
    1153 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1154 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>cif</span></b></span>
    1155 format or the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
    1156 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1157 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>xye</span></b></span>
     1145mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1146Calibri;mso-bidi-theme-font:minor-latin'>Import/Powder Data/from GSAS file</span></b>
     1147menu item to read the data file into the current GSAS-II project. This read
     1148option is set to read any of the powder data formats (except neutron TOF time
     1149map files) defined for GSAS (angles in <span class=SpellE>centidegrees</span>).
     1150Other submenu items will read the <span class=SpellE><b style='mso-bidi-font-weight:
     1151normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1152minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1153mso-bidi-theme-font:minor-latin'>cif</span></b></span> format or the <span
     1154class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
     1155"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1156minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>xye</span></b></span>
    11581157format (angles in degrees) used by <span class=SpellE>Topas</span>, etc.<span
    11591158style='mso-spacerun:yes'>  </span>Change the file directory to <b
    11601159style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1161 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1162 minor-latin'>Exercises/LaB6</span></b><span style='font-family:"Calibri","sans-serif";
    1163 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1160mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1161Calibri;mso-bidi-theme-font:minor-latin'>Exercises/LaB6</span></b><span
     1162style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1163mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    11641164minor-latin'> to find the file; you may need to change the file type to <b
    11651165style='mso-bidi-font-weight:normal'>All files (*.*)</b> to find the desired
     
    11701170style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
    11711171the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1172 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1173 minor-latin'>11bmb_3844.fxye</span></b><span style='font-family:"Calibri","sans-serif";
    1174 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1172mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1173Calibri;mso-bidi-theme-font:minor-latin'>11bmb_3844.fxye</span></b><span
     1174style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1175mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    11751176minor-latin'> data</span> file in the first dialog and press <b
    11761177style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1177 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1178 minor-latin'>Open</span></b>. There will be a Dialog box asking <span
    1179 class=GramE><b style='mso-bidi-font-weight:normal'><span style='font-family:
    1180 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1181 minor-latin;mso-bidi-theme-font:minor-latin'>Is</span></b></span><b
    1182 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1183 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1178mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1179Calibri;mso-bidi-theme-font:minor-latin'>Open</span></b>. There will be a
     1180Dialog box asking <span class=GramE><b style='mso-bidi-font-weight:normal'><span
     1181style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1182mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1183minor-latin'>Is</span></b></span><b style='mso-bidi-font-weight:normal'><span
     1184style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1185mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    11841186minor-latin'> this the file you want?</span></b> Press <span class=GramE><b
    11851187style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1186 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1187 minor-latin'>Yes</span></b></span> button to proceed.</p>
     1188mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1189Calibri;mso-bidi-theme-font:minor-latin'>Yes</span></b></span> button to
     1190proceed.</p>
    11881191
    11891192<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
     
    11911194style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>The
    11921195file <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1193 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1194 minor-latin'>11bmb_3844.prm</span></b> instrument parameter file is
    1195 automatically selected; it was produced by 11BM-B instrument processing
    1196 software when the corresponding <span class=SpellE><b style='mso-bidi-font-weight:
    1197 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1198 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>fxye</span></b></span>
    1199 file was created from the 12 detector raw data. If absent or the name doesn’t
    1200 match the data file name, a file dialog will appear for you to select the
    1201 correct instrument parameter file.</p>
     1196mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1197Calibri;mso-bidi-theme-font:minor-latin'>11bmb_3844.prm</span></b> instrument
     1198parameter file is automatically selected; it was produced by 11BM-B instrument
     1199processing software when the corresponding <span class=SpellE><b
     1200style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1201mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1202Calibri;mso-bidi-theme-font:minor-latin'>fxye</span></b></span> file was
     1203created from the 12 detector raw data. If absent or the name doesn’t match the
     1204data file name, a file dialog will appear for you to select the correct
     1205instrument parameter file.</p>
    12021206
    12031207<p class=MsoNormal>At this point the <b style='mso-bidi-font-weight:normal'><span
    12041208style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1205 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II data
    1206 tree</span></b> window will have several entries </p>
     1209mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1210minor-latin'>GSAS-II data tree</span></b> window will have several entries </p>
    12071211
    12081212<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
     
    12261230 <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
    12271231 <o:lock v:ext="edit" aspectratio="t"/>
    1228 </v:shapetype><v:shape id="Picture_x0020_1" o:spid="_x0000_i1046" type="#_x0000_t75"
     1232</v:shapetype><v:shape id="Picture_x0020_1" o:spid="_x0000_i1052" type="#_x0000_t75"
    12291233 style='width:225pt;height:187.5pt;visibility:visible;mso-wrap-style:square'>
    12301234 <v:imagedata src="Fit%20Peaks_files/image001.png" o:title=""/>
     
    12361240
    12371241<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1238  id="Picture_x0020_2" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:525pt;
     1242 id="Picture_x0020_2" o:spid="_x0000_i1051" type="#_x0000_t75" style='width:525pt;
    12391243 height:450pt;visibility:visible;mso-wrap-style:square'>
    12401244 <v:imagedata src="Fit%20Peaks_files/image002.png" o:title=""/>
     
    12471251more data than we need, so it is helpful to cut down the range. Click on the <b
    12481252style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1249 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1250 minor-latin'>Limits</span></b> item in the <b style='mso-bidi-font-weight:normal'><span
    1251 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1252 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II data
    1253 tree</span></b>. The small window is repainted. Use the <b style='mso-bidi-font-weight:
    1254 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1255 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>changed</span></b>
    1256 row of entry boxes to set <span class=SpellE><b style='mso-bidi-font-weight:
    1257 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1258 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Tmin</span></b></span>
    1259 and <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
    1260 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1261 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Tmax</span></b></span>
     1253mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1254Calibri;mso-bidi-theme-font:minor-latin'>Limits</span></b> item in the <b
     1255style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1256mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1257Calibri;mso-bidi-theme-font:minor-latin'>GSAS-II data tree</span></b>. The
     1258small window is repainted. Use the <b style='mso-bidi-font-weight:normal'><span
     1259style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1260mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1261minor-latin'>changed</span></b> row of entry boxes to set <span class=SpellE><b
     1262style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1263mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1264Calibri;mso-bidi-theme-font:minor-latin'>Tmin</span></b></span> and <span
     1265class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
     1266"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1267minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>Tmax</span></b></span>
    12621268to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1263 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1264 minor-latin'>4</span></b> and <b style='mso-bidi-font-weight:normal'><span
    1265 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1266 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>27.5</span></b>.
    1267 Notice on the plot that the limit lines have moved to these positions; the
    1268 green lower limit is just below the 1<sup>st</sup> peak and the red upper limit
    1269 is in a wide gap between peaks. You may also drag the limit lines to the
    1270 desired location or place them by a left mouse click on a data point for the
    1271 lower limit or a right click on a data point for the upper limit.</p>
     1269mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1270Calibri;mso-bidi-theme-font:minor-latin'>4</span></b> and <b style='mso-bidi-font-weight:
     1271normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1272minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1273mso-bidi-theme-font:minor-latin'>27.5</span></b>. Notice on the plot that the
     1274limit lines have moved to these positions; the green lower limit is just below
     1275the 1<sup>st</sup> peak and the red upper limit is in a wide gap between peaks.
     1276You may also drag the limit lines to the desired location or place them by a
     1277left mouse click on a data point for the lower limit or a right click on a data
     1278point for the upper limit.</p>
    12721279
    12731280<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1274  id="Picture_x0020_3" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:225pt;
     1281 id="Picture_x0020_3" o:spid="_x0000_i1050" type="#_x0000_t75" style='width:225pt;
    12751282 height:120pt;visibility:visible;mso-wrap-style:square'>
    12761283 <v:imagedata src="Fit%20Peaks_files/image003.png" o:title=""/>
     
    12851292style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Click
    12861293on the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1287 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1288 minor-latin'>Peak List</span></b> item in the <b style='mso-bidi-font-weight:
    1289 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1290 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II
    1291 data tree</span></b>. This creates an empty window of peak positions (the <b
    1292 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1293 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1294 minor-latin'>Limits</span></b> window is erased). At this point it is wise <span
    1295 class=GramE>to<span style='mso-spacerun:yes'>  </span>zoom</span> in on the
    1296 data that will be used for indexing. </p>
     1294mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1295Calibri;mso-bidi-theme-font:minor-latin'>Peak List</span></b> item in the <b
     1296style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1297mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1298Calibri;mso-bidi-theme-font:minor-latin'>GSAS-II data tree</span></b>. This
     1299creates an empty window of peak positions (the <b style='mso-bidi-font-weight:
     1300normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1301minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1302mso-bidi-theme-font:minor-latin'>Limits</span></b> window is erased). At this
     1303point it is wise <span class=GramE>to<span style='mso-spacerun:yes'> 
     1304</span>zoom</span> in on the data that will be used for indexing. </p>
    12971305
    12981306<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
     
    13011309style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Click
    13021310on the Zoom button, <span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1303  id="Picture_x0020_4" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:21.75pt;
     1311 id="Picture_x0020_4" o:spid="_x0000_i1049" type="#_x0000_t75" style='width:21.75pt;
    13041312 height:18.75pt;visibility:visible;mso-wrap-style:square'>
    13051313 <v:imagedata src="Fit%20Peaks_files/image004.jpg" o:title="" croptop="1f"
     
    13171325style='mso-bidi-font-weight:normal'>Important</b>: Click on the Zoom <span
    13181326style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_5"
    1319  o:spid="_x0000_i1042" type="#_x0000_t75" style='width:23.25pt;height:20.25pt;
     1327 o:spid="_x0000_i1048" type="#_x0000_t75" style='width:23.25pt;height:20.25pt;
    13201328 visibility:visible;mso-wrap-style:square'>
    13211329 <v:imagedata src="Fit%20Peaks_files/image004.jpg" o:title="" croptop="1f"
     
    13281336auto;text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
    13291337style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
    1330 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Using
    1331 the left mouse button, click on a data point near the top of each peak to be
    1332 added to the peak list. It is usually best to start at the upper end of the
    1333 pattern as the next peak to pick isn’t obscured by the tool tip. As this is
    1334 done, a vertical blue line is drawn in the plot window<span
    1335 style='mso-spacerun:yes'>  </span>for each peak selected</p>
     1338style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Under
     1339<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1340mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Peak Fitting</span></b>
     1341in the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1342mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Peak List</span></b>
     1343window select <b style='mso-bidi-font-weight:normal'><span style='font-family:
     1344"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1345minor-latin'>Auto search</span></b>. The plot window will immediately show that
     1346all peaks were picked with a blue vertical line on each one</p>
    13361347
    13371348<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
    1338 auto'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_6"
    1339  o:spid="_x0000_i1041" type="#_x0000_t75" style='width:525pt;height:450pt;
     1349auto'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_27"
     1350 o:spid="_x0000_i1047" type="#_x0000_t75" style='width:525pt;height:450pt;
    13401351 visibility:visible;mso-wrap-style:square'>
    13411352 <v:imagedata src="Fit%20Peaks_files/image007.png" o:title=""/>
    13421353</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
    1343 src="Fit%20Peaks_files/image007.png" v:shapes="Picture_x0020_6"><![endif]></span></p>
     1354src="Fit%20Peaks_files/image007.png" v:shapes="Picture_x0020_27"><![endif]></span></p>
    13441355
    13451356<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
    1346 auto'><span class=GramE>and</span> peaks are added to the <b style='mso-bidi-font-weight:
    1347 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1348 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak
    1349 List</span></b> window in order of increasing 2<span style='font-family:Symbol'>Q</span>.</p>
     1357auto'><span class=GramE>and</span> peaks are shown in the <b style='mso-bidi-font-weight:
     1358normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1359minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1360mso-bidi-theme-font:minor-latin'>Peak List</span></b> window in order of
     1361increasing 2<span style='font-family:Symbol'>Q</span>.</p>
    13501362
    13511363<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
    13521364auto'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_7"
    1353  o:spid="_x0000_i1040" type="#_x0000_t75" style='width:401.25pt;height:262.5pt;
     1365 o:spid="_x0000_i1046" type="#_x0000_t75" style='width:401.25pt;height:262.5pt;
    13541366 visibility:visible;mso-wrap-style:square'>
    13551367 <v:imagedata src="Fit%20Peaks_files/image008.png" o:title=""/>
     
    13571369src="Fit%20Peaks_files/image008.png" v:shapes="Picture_x0020_7"><![endif]></span></p>
    13581370
    1359 <p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
    1360 auto'>Note that if peaks are not being added, you probably have not exited zoom
    1361 mode.</p>
    1362 
    1363 <p class=MsoListParagraphCxSpLast style='margin-left:39.0pt;mso-add-space:auto'>Add
    1364 approximately 20-25 peaks total to the peak list (there will be 20 in this
    1365 example). Be sure to add the lowest angle peaks that are visible in the plot.
    1366 You may drag a peak position as needed; be sure the zoom/shift buttons are off.
    1367 A position may be deleted with a right click with the mouse on the blue line.</p>
     1371<p class=MsoListParagraphCxSpLast style='margin-left:39.0pt;mso-add-space:auto'>There
     1372will be 23 peaks in this example. You should examine both the list and the plot
     1373to be sure the auto search did not pick a peak twice (there may be three of
     1374these!) or skip a peak or shoulder. You can add a peak to the list by pressing
     1375the left mouse button with the pointer on a data point at the peak top or
     1376shoulder. You may drag a peak position as needed; be sure the zoom/shift
     1377buttons are off. A position may be deleted with a right click with the mouse on
     1378the blue line. You can also delete a peak by selecting the row in the <span
     1379class=GramE>table,</span> it will be highlighted in blue. Then press the Delete
     1380key; it will be removed from the table and the plot. The list will always show
     1381the peaks sorted by position. When done you should have 20 unique peak
     1382positions.</p>
    13681383
    13691384<h2>Step 4: Refine Peak Positions</h2>
    13701385
    13711386<p class=MsoNormal>This refinement proceeds stepwise; first doing the default
    1372 refinement and then adding <span class=GramE>a parameters</span> to complete
    1373 the fitting,</p>
     1387refinement and then adding parameters to complete the fitting,</p>
    13741388
    13751389<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
     
    13791393flags turned on by default. Use the menu item <b style='mso-bidi-font-weight:
    13801394normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1381 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak
    1382 Fitting/LSQ <span class=SpellE>PeakFit</span> </span></b>on the<b
    1383 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1384 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1385 minor-latin'> Peak List </span></b>window. Do <b style='mso-bidi-font-weight:
    1386 normal'>NOT</b> use the <b style='mso-bidi-font-weight:normal'><span
    1387 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1388 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Calculate/Refine</span></b>
    1389 menu item in the <b style='mso-bidi-font-weight:normal'><span style='font-family:
     1395minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1396mso-bidi-theme-font:minor-latin'>Peak Fitting/LSQ <span class=SpellE>PeakFit</span>
     1397</span></b>on the<b style='mso-bidi-font-weight:normal'><span style='font-family:
    13901398"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1391 minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II data tree</span></b>
    1392 window; that it to be used for Rietveld/Pawley refinements. You will be asked
    1393 to save the current project before the fit will proceed; change directory if
    1394 desired and provide a suitable name (we assume <b style='mso-bidi-font-weight:
    1395 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1396 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>LaB6</span></b>).
    1397 A window will show the progress of the refinement and will close when the
    1398 least-squares fit <span class=GramE>is</span> complete (usually very fast). The
    1399 plot is updated with the fit, the peak list window is updated with the new peak
    1400 values and a summary of the refinement is shown on the console window as well.</p>
     1399minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'> Peak
     1400List </span></b>window. Do <b style='mso-bidi-font-weight:normal'>NOT</b> use
     1401the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1402mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1403Calibri;mso-bidi-theme-font:minor-latin'>Calculate/Refine</span></b> menu item
     1404in the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1405mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1406Calibri;mso-bidi-theme-font:minor-latin'>GSAS-II data tree</span></b> window;
     1407that it to be used for Rietveld/Pawley refinements. You will be asked to save
     1408the current project before the fit will proceed; change directory if desired
     1409and provide a suitable name (we assume <b style='mso-bidi-font-weight:normal'><span
     1410style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1411mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1412minor-latin'>LaB6</span></b>). A window will show the progress of the
     1413refinement and will close when the least-squares fit <span class=GramE>is</span>
     1414complete (usually very fast). The plot is updated with the fit, the peak list
     1415window is updated with the new peak values and a summary of the refinement is
     1416shown on the console window as well.</p>
    14011417
    14021418<p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1403  id="Picture_x0020_8" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:525pt;
    1404  height:450pt;visibility:visible;mso-wrap-style:square'>
     1419 id="_x0000_i1045" type="#_x0000_t75" style='width:525pt;height:450pt;
     1420 visibility:visible;mso-wrap-style:square'>
    14051421 <v:imagedata src="Fit%20Peaks_files/image009.png" o:title=""/>
    14061422</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
    1407 src="Fit%20Peaks_files/image009.png" v:shapes="Picture_x0020_8"><![endif]></span></p>
     1423src="Fit%20Peaks_files/image009.png" v:shapes="_x0000_i1045"><![endif]></span></p>
    14081424
    14091425<p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1410  id="Picture_x0020_9" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:401.25pt;
     1426 id="Picture_x0020_24" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:401.25pt;
    14111427 height:262.5pt;visibility:visible;mso-wrap-style:square'>
    14121428 <v:imagedata src="Fit%20Peaks_files/image010.png" o:title=""/>
    14131429</v:shape><![endif]--><![if !vml]><img border=0 width=535 height=350
    1414 src="Fit%20Peaks_files/image010.png" v:shapes="Picture_x0020_9"><![endif]></span></p>
     1430src="Fit%20Peaks_files/image010.png" v:shapes="Picture_x0020_24"><![endif]></span></p>
    14151431
    14161432<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
     
    14351451check-boxes. The entire column of checkboxes is highlighted in blue. Press the <b
    14361452style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1437 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1438 minor-latin'>y</span></b> key to turn on all refinement flags (<b
    1439 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1440 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1453mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1454Calibri;mso-bidi-theme-font:minor-latin'>y</span></b> key to turn on all
     1455refinement flags (<b style='mso-bidi-font-weight:normal'><span
     1456style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1457mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    14411458minor-latin'>n</span></b> would turn them off).</p>
    14421459
    14431460<p class=MsoNormal style='margin-left:.5in'>Next, repeat the refinement using
    14441461the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1445 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1446 minor-latin'>Peak Fitting/LSQ <span class=SpellE>PeakFit</span></span></b> menu
    1447 item in the <b style='mso-bidi-font-weight:normal'><span style='font-family:
     1462mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1463Calibri;mso-bidi-theme-font:minor-latin'>Peak Fitting/LSQ <span class=SpellE>PeakFit</span></span></b>
     1464menu item in the <b style='mso-bidi-font-weight:normal'><span style='font-family:
    14481465"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1449 minor-latin;mso-bidi-theme-font:minor-latin'>Peak List</span></b> window.</p>
    1450 
    1451 <p class=MsoNormal style='margin-left:.5in'><span
    1452 style='mso-spacerun:yes'> </span>Now, select peak widths for refinement. <span
    1453 style='mso-fareast-font-family:"Times New Roman"'>This can be performed in 2
    1454 different ways. &nbsp;Method&nbsp;1:&nbsp;refine sigma (Gaussian width) and/or
    1455 gamma (Lorentzian width) for individual peaks. &nbsp;To do this, click the
    1456 refinement flags for sigma and/or gamma in the Peak List window.
     1466minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>Peak
     1467List</span></b> window.</p>
     1468
     1469<p class=MsoNormal style='margin-left:.5in'>Now, select peak widths for
     1470refinement. <span style='mso-fareast-font-family:"Times New Roman"'>This can be
     1471performed in 2 different ways. &nbsp;Method&nbsp;1:&nbsp;refine sigma (Gaussian
     1472width) and/or gamma (Lorentzian width) for individual peaks. &nbsp;To do this,
     1473click the refinement flags for sigma and/or gamma in the Peak List window.
    14571474&nbsp;&nbsp;Method&nbsp;2: preferably,&nbsp;the LS&nbsp;refinement of&nbsp;peak
    14581475widths can be&nbsp;constrained to&nbsp;follow an instrumental broadening
     
    14651482to an instrumental broadening equation, first<b> s</b></span>elect the <b
    14661483style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1467 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1468 minor-latin'>Instrumental Parameters</span></b> item in the data tree. <span
    1469 class=GramE>This opens a window for peak profile terms<b> </b><span
    1470 style='mso-bidi-font-weight:bold'>and also create</span></span><span
    1471 style='mso-bidi-font-weight:bold'> a new plot window&nbsp;showing the
    1472 instrument profile resolution curve.</span></p>
     1484mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1485Calibri;mso-bidi-theme-font:minor-latin'>Instrumental Parameters</span></b>
     1486item in the data tree. This opens a window for peak profile terms<b> </b><span
     1487style='mso-bidi-font-weight:bold'>and also creates a new plot
     1488window&nbsp;showing the instrument profile resolution curve.</span></p>
    14731489
    14741490<p class=MsoNormal style='margin-left:.5in'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1475  id="Picture_x0020_10" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:422.25pt;
     1491 id="Picture_x0020_10" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:422.25pt;
    14761492 height:154.5pt;visibility:visible;mso-wrap-style:square'>
    14771493 <v:imagedata src="Fit%20Peaks_files/image011.png" o:title=""/>
     
    14841500values for the peaks in Peak List. Select the refine flag checkbox for Gaussian
    14851501<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1486 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1487 minor-latin'>U</span></b>, <b style='mso-bidi-font-weight:normal'><span
    1488 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1489 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>V</span></b>,
    1490 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1491 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1492 minor-latin'>W</span></b>, and Lorentzian <b style='mso-bidi-font-weight:normal'><span
    1493 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1494 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>X</span></b>,
    1495 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1496 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1497 minor-latin'>Y</span></b>. </p>
     1502mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1503Calibri;mso-bidi-theme-font:minor-latin'>U</span></b>, <b style='mso-bidi-font-weight:
     1504normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1505minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1506mso-bidi-theme-font:minor-latin'>V</span></b>, <b style='mso-bidi-font-weight:
     1507normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1508minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1509mso-bidi-theme-font:minor-latin'>W</span></b>, and Lorentzian <b
     1510style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1511mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1512Calibri;mso-bidi-theme-font:minor-latin'>X</span></b>, <b style='mso-bidi-font-weight:
     1513normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1514minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1515mso-bidi-theme-font:minor-latin'>Y</span></b>. </p>
    14981516
    14991517<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
     
    15021520repeat the refinement. First click on the <b style='mso-bidi-font-weight:normal'><span
    15031521style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1504 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak List</span></b>
    1505 item in the data tree and then refine using the <b style='mso-bidi-font-weight:
    1506 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1507 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak
    1508 Fitting/LSQ <span class=SpellE>PeakFit</span></span></b> menu item. At this
    1509 point a good fit should be seen by zooming in on individual peaks. (For example
    1510 see </p>
     1522mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1523minor-latin'>Peak List</span></b> item in the data tree and then refine using
     1524the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1525mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1526Calibri;mso-bidi-theme-font:minor-latin'>Peak Fitting/LSQ <span class=SpellE>PeakFit</span></span></b>
     1527menu item. At this point a good fit should be seen by zooming in on individual
     1528peaks. For example see </p>
    15111529
    15121530<p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1513  id="Picture_x0020_11" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:525pt;
     1531 id="Picture_x0020_11" o:spid="_x0000_i1042" type="#_x0000_t75" style='width:525pt;
    15141532 height:450pt;visibility:visible;mso-wrap-style:square'>
    15151533 <v:imagedata src="Fit%20Peaks_files/image012.png" o:title=""/>
     
    15171535src="Fit%20Peaks_files/image012.png" v:shapes="Picture_x0020_11"><![endif]></span></p>
    15181536
    1519 <p class=MsoListParagraphCxSpLast>The <span class=SpellE>Rwp</span> is ~6% as
    1520 shown on the console window. Again the <b style='mso-bidi-font-weight:normal'><span
    1521 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1522 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak List</span></b>
    1523 entries are all updated with new values and those in <b style='mso-bidi-font-weight:
    1524 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1525 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Instrument
    1526 Parameters</span></b> are also updated.</p>
     1537<p class=MsoListParagraphCxSpLast>Notice that the peak position is slightly to
     1538the right of the peak top. This is a consequence of the peak asymmetry arising
     1539from axial divergence in the diffractometer. The <span class=SpellE>Rwp</span>
     1540is ~6% as shown on the console window. Again the <b style='mso-bidi-font-weight:
     1541normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1542minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1543mso-bidi-theme-font:minor-latin'>Peak List</span></b> entries are all updated
     1544with new values and those in <b style='mso-bidi-font-weight:normal'><span
     1545style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1546mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1547minor-latin'>Instrument Parameters</span></b> are also updated.</p>
    15271548
    15281549<h2><span class=GramE>Step 5.</span> Prepare Indexing Peak List</h2>
     
    15311552class=SpellE>autoindexing</span>. It is found in the <b style='mso-bidi-font-weight:
    15321553normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1533 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Index
    1534 Peak List</span></b> item in the data tree. In the initially empty window
    1535 created by this action, use menu item <b style='mso-bidi-font-weight:normal'><span
    1536 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1537 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Index Peaks
    1538 Operations/Load</span></b> to copy the fitted peaks from the <b
    1539 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1540 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1554minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1555mso-bidi-theme-font:minor-latin'>Index Peak List</span></b> item in the data
     1556tree. In the initially empty window created by this action, use menu item <b
     1557style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1558mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1559Calibri;mso-bidi-theme-font:minor-latin'>Index Peaks Operations/Load</span></b>
     1560to copy the fitted peaks from the <b style='mso-bidi-font-weight:normal'><span
     1561style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1562mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    15411563minor-latin'>Peak List</span></b>.</p>
    15421564
    15431565<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1544  id="Picture_x0020_12" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:367.5pt;
     1566 id="Picture_x0020_26" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:367.5pt;
    15451567 height:225pt;visibility:visible;mso-wrap-style:square'>
    15461568 <v:imagedata src="Fit%20Peaks_files/image013.png" o:title=""/>
    15471569</v:shape><![endif]--><![if !vml]><img border=0 width=490 height=300
    1548 src="Fit%20Peaks_files/image013.png" v:shapes="Picture_x0020_12"><![endif]></span></p>
     1570src="Fit%20Peaks_files/image013.png" v:shapes="Picture_x0020_26"><![endif]></span></p>
    15491571
    15501572<p class=MsoNormal>Note that by default all peaks are selected to be used. You
     
    15561578<p class=MsoNormal>Select the <b style='mso-bidi-font-weight:normal'><span
    15571579style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1558 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Unit Cells
    1559 List</span></b> data item. This brings up a window for indexing and cell refinement
    1560 options</p>
     1580mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1581minor-latin'>Unit Cells List</span></b> data item. This brings up a window for
     1582indexing and cell refinement options</p>
    15611583
    15621584<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1563  id="Picture_x0020_13" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:527.25pt;
     1585 id="Picture_x0020_13" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:527.25pt;
    15641586 height:204pt;visibility:visible;mso-wrap-style:square'>
    15651587 <v:imagedata src="Fit%20Peaks_files/image014.png" o:title=""/>
     
    15691591<p class=MsoNormal>For the most rapid search (since we know the right answer),
    15701592select <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1571 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1572 minor-latin'>Cubic-P</span></b> and launch the search using menu item <b
    1573 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1574 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1575 minor-latin'>Cell Index/Index Cell</span></b>. The search then runs and the console
    1576 shows a running list of possible cells as they are found; the sorted by M20
    1577 list of possible matching cells is shown in the <b style='mso-bidi-font-weight:
    1578 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1579 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Unit
    1580 Cells List</span></b> window</p>
     1593mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1594Calibri;mso-bidi-theme-font:minor-latin'>Cubic-P</span></b> and launch the
     1595search using menu item <b style='mso-bidi-font-weight:normal'><span
     1596style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1597mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1598minor-latin'>Cell Index/Index Cell</span></b>. The search then runs and the
     1599console shows a running list of possible cells as they are found; the sorted by
     1600M20 list of possible matching cells is shown in the <b style='mso-bidi-font-weight:
     1601normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1602minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1603mso-bidi-theme-font:minor-latin'>Unit Cells List</span></b> window</p>
    15811604
    15821605<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1583  id="Picture_x0020_14" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:527.25pt;
     1606 id="Picture_x0020_28" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:527.25pt;
    15841607 height:376.5pt;visibility:visible;mso-wrap-style:square'>
    15851608 <v:imagedata src="Fit%20Peaks_files/image015.png" o:title=""/>
    15861609</v:shape><![endif]--><![if !vml]><img border=0 width=703 height=502
    1587 src="Fit%20Peaks_files/image015.png" v:shapes="Picture_x0020_14"><![endif]></span></p>
     1610src="Fit%20Peaks_files/image015.png" v:shapes="Picture_x0020_28"><![endif]></span></p>
    15881611
    15891612<h2><span class=GramE>Step 7.</span> Review Cell Choices</h2>
     
    15911614<p class=MsoNormal>Review the list of cells associated with the <b
    15921615style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1593 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1594 minor-latin'>Unit Cells List</span></b> data item. Note that as one selects a
    1595 unit cell, the generated reflections for that cell are shown in the plot with
    1596 dashed red lines. Sliding the cursor over these lines shows a small popup
    1597 window with the indexed <span class=SpellE>hkl</span> for them. Note how the
    1598 first cell in the list (M20~3000) with a=5.87864 Å generates very many lines
    1599 with no corresponding peaks (NB: this solution might not always show up!)</p>
     1616mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1617Calibri;mso-bidi-theme-font:minor-latin'>Unit Cells List</span></b> data item.
     1618Note that as one selects a unit cell, the generated reflections for that cell
     1619are shown in the plot with dashed red lines. Sliding the cursor over these
     1620lines shows a small popup window with the indexed <span class=SpellE>hkl</span>
     1621for them. Note how the first cell in the list (M20~2970) with a=5.87864 Å
     1622generates very many lines with no corresponding peaks (NB: this solution might
     1623not always show up!)</p>
    16001624
    16011625<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1602  id="Picture_x0020_15" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:525pt;
     1626 id="Picture_x0020_38" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:525pt;
    16031627 height:450pt;visibility:visible;mso-wrap-style:square'>
    16041628 <v:imagedata src="Fit%20Peaks_files/image016.png" o:title=""/>
    16051629</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
    1606 src="Fit%20Peaks_files/image016.png" v:shapes="Picture_x0020_15"><![endif]></span><span
     1630src="Fit%20Peaks_files/image016.png" v:shapes="Picture_x0020_38"><![endif]></span><span
    16071631style='mso-spacerun:yes'> </span></p>
    16081632
     
    16111635
    16121636<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1613  id="Picture_x0020_16" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:525pt;
     1637 id="Picture_x0020_39" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:525pt;
    16141638 height:450pt;visibility:visible;mso-wrap-style:square'>
    16151639 <v:imagedata src="Fit%20Peaks_files/image017.png" o:title=""/>
    16161640</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
    1617 src="Fit%20Peaks_files/image017.png" v:shapes="Picture_x0020_16"><![endif]></span></p>
     1641src="Fit%20Peaks_files/image017.png" v:shapes="Picture_x0020_39"><![endif]></span></p>
    16181642
    16191643<h2><span class=GramE>Step 8.</span> Select/Refine Cell</h2>
    16201644
    1621 <p class=MsoNormal>Select the cell with M20 ~ 2900 with a = 4.1568 Å. This
     1645<p class=MsoNormal>Select the cell with M20 ~ 2970 with a = 4.15683 Å. This
    16221646indexes all peaks with almost a perfect fit to the peak positions (compare
    16231647dashed red lines to solid blue ones). Import the cell information using the <b
    16241648style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1625 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1626 minor-latin'>Cell Index/Copy Cell</span></b> menu option. Then optimize the
    1627 cell by refining the lattice parameters and the two-theta zero: click on the
    1628 refine checkbox next to the <b style='mso-bidi-font-weight:normal'><span
    1629 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1630 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Zero offset</span></b>
    1631 value and then the <b style='mso-bidi-font-weight:normal'><span
    1632 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1633 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Cell
    1634 Index/Refine Cell</span></b> menu option. <span class=GramE>The a</span> cell
    1635 parameter value shifts from 4.15679 to 4.15684 when zero is refined. Press the <b
    1636 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1637 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1638 minor-latin'>Show refined <span class=SpellE>hkl</span> positions + Zero offset</span></b>
    1639 button to update the plot including the refined <b style='mso-bidi-font-weight:
    1640 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1641 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Zero
    1642 offset</span></b> (in this case hardly anything happens!) </p>
     1649mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1650Calibri;mso-bidi-theme-font:minor-latin'>Cell Index/Copy Cell</span></b> menu
     1651option. Then optimize the cell by refining the lattice parameters and the
     1652two-theta zero: click on the refine checkbox next to the <b style='mso-bidi-font-weight:
     1653normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1654minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1655mso-bidi-theme-font:minor-latin'>Zero offset</span></b> value and then the <b
     1656style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1657mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1658Calibri;mso-bidi-theme-font:minor-latin'>Cell Index/Refine Cell</span></b> menu
     1659option. The M20 improves to ~3600 and <span class=GramE>the a</span> cell
     1660parameter value shifts from 4.15683 to 4.15691 when zero is refined. (NB: The
     1661certificate value for NIST SRM 660a is 4.15692 Å). Press the <b
     1662style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1663mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1664Calibri;mso-bidi-theme-font:minor-latin'>Show refined <span class=SpellE>hkl</span>
     1665positions + Zero offset</span></b> button to update the plot including the
     1666refined <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1667mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1668Calibri;mso-bidi-theme-font:minor-latin'>Zero offset</span></b> (in this case
     1669hardly anything happens!) </p>
    16431670
    16441671<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1645  id="Picture_x0020_17" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:527.25pt;
    1646  height:334.5pt;visibility:visible;mso-wrap-style:square'>
     1672 id="_x0000_i1036" type="#_x0000_t75" style='width:527.25pt;height:334.5pt;
     1673 visibility:visible;mso-wrap-style:square'>
    16471674 <v:imagedata src="Fit%20Peaks_files/image018.png" o:title=""/>
    16481675</v:shape><![endif]--><![if !vml]><img border=0 width=703 height=446
    1649 src="Fit%20Peaks_files/image018.png" v:shapes="Picture_x0020_17"><![endif]></span></p>
     1676src="Fit%20Peaks_files/image018.png" v:shapes="_x0000_i1036"><![endif]></span></p>
    16501677
    16511678<p class=MsoNormal>Notice that a new entry heads the list in the <b
    16521679style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1653 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1654 minor-latin'>Indexing Result</span></b> section of the <b style='mso-bidi-font-weight:
    1655 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1656 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Cell
    1657 Index/Refine</span></b> window with an improved M20(=3614.66) and a new value
    1658 for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1659 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1660 minor-latin'>Zero offset</span></b> is shown.</p>
     1680mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1681Calibri;mso-bidi-theme-font:minor-latin'>Indexing Result</span></b> section of
     1682the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1683mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1684Calibri;mso-bidi-theme-font:minor-latin'>Cell Index/Refine</span></b> window
     1685with an improved M20(=3607.97) and a new value for <b style='mso-bidi-font-weight:
     1686normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1687minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1688mso-bidi-theme-font:minor-latin'>Zero offset</span></b> is shown.</p>
    16611689
    16621690<p class=MsoNormal>(Optional) Finally, use of the <b style='mso-bidi-font-weight:
    16631691normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1664 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Cell
    1665 Index/New phase</span></b> menu option allows one to create a phase with these
    1666 lattice parameters in the data tree under <b style='mso-bidi-font-weight:normal'><span
    1667 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1668 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Phases</span></b>.<span
     1692minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1693mso-bidi-theme-font:minor-latin'>Cell Index/New phase</span></b> menu option
     1694allows one to create a phase with these lattice parameters in the data tree
     1695under <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1696mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1697Calibri;mso-bidi-theme-font:minor-latin'>Phases</span></b>.<span
    16691698style='mso-spacerun:yes'>  </span>A name for the new phase is requested. This
    16701699creates the tree item <b style='mso-bidi-font-weight:normal'><span
    16711700style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1672 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Phases</span></b>
    1673 (if it wasn’t already present). This new phase can be used in future analysis
    1674 (e.g. Rietveld or Pawley refinement).</p>
    1675 
    1676 <p class=MsoNormal>To continue with the second part of this exercise, <span
    1677 class=GramE>do the menu item</span> <b style='mso-bidi-font-weight:normal'><span
    1678 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1679 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>File/Close
     1701mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1702minor-latin'>Phases</span></b> (if it wasn’t already present). This new phase
     1703can be used in future analysis (e.g. Rietveld or Pawley refinement).</p>
     1704
     1705<p class=MsoNormal>To continue with the second part of this exercise, select
     1706the menu item <b style='mso-bidi-font-weight:normal'><span style='font-family:
     1707"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1708minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>File/Close
    16801709project</span></b> in the <b style='mso-bidi-font-weight:normal'><span
    16811710style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1682 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II data
    1683 tree </span></b>window. You will be asked if you want it saved; if <span
    1684 class=GramE><b style='mso-bidi-font-weight:normal'><span style='font-family:
    1685 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1686 minor-latin;mso-bidi-theme-font:minor-latin'>Yes</span></b></span> then all the
    1687 peak fitting/indexing &amp; cell refinement results will be saved to the <b
    1688 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1689 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1690 minor-latin'>LaB6.gpx</span></b> file. If <b style='mso-bidi-font-weight:normal'><span
    1691 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1692 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>No</span></b>
    1693 then the file will remain as it was when created at Step 4 above.</p>
     1711mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1712minor-latin'>GSAS-II data tree </span></b>window. You will be asked if you want
     1713it saved; if <span class=GramE><b style='mso-bidi-font-weight:normal'><span
     1714style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1715mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1716minor-latin'>Yes</span></b></span> then all the peak fitting/indexing &amp;
     1717cell refinement results will be saved to the <b style='mso-bidi-font-weight:
     1718normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1719minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1720mso-bidi-theme-font:minor-latin'>LaB6.gpx</span></b> file. If <b
     1721style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1722mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1723Calibri;mso-bidi-theme-font:minor-latin'>No</span></b> then the file will
     1724remain as it was when created at Step 4 above.</p>
    16941725
    16951726<h1><a name="kryptonite_peak_fit">2<sup>nd</sup> Fit Peaks/</a><span
     
    17001731new mineral <a href="http://en.wikipedia.org/wiki/Jadarite"><span class=SpellE>jadarite</span></a>
    17011732(aka “<a href="http://en.wikipedia.org/wiki/Kryptonite">kryptonite</a>”). The
    1702 data was also collected on 11BM-B at APS. The unit cell is monoclinic so is a
    1703 more substantial test of the indexing capability of GSAS-II.</p>
     1733data was also collected on 11BM-B at APS. The unit cell is monoclinic so is a more
     1734substantial test of the indexing capability of GSAS-II.</p>
    17041735
    17051736<h2><span class=GramE>Step 1.</span> Read in the data. </h2>
     
    17071738<p class=MsoNormal>The file is <b style='mso-bidi-font-weight:normal'><span
    17081739style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1709 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>\Exercises\<span
    1710 class=SpellE>krptonite</span>\11bmb_6231.fxye</span></b>; it has a
     1740mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1741minor-latin'>\Exercises\kryptonite\11bmb_6231.fxye</span></b>; it has a
    17111742corresponding <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
    17121743style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1713 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>prm</span></b></span>
    1714 file. Load them in &amp; the plot is</p>
     1744mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1745minor-latin'>prm</span></b></span> file. Load them in &amp; the plot is</p>
    17151746
    17161747<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1717  id="Picture_x0020_18" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:525pt;
    1718  height:450pt;visibility:visible;mso-wrap-style:square'>
     1748 id="_x0000_i1035" type="#_x0000_t75" style='width:525pt;height:450pt;
     1749 visibility:visible;mso-wrap-style:square'>
    17191750 <v:imagedata src="Fit%20Peaks_files/image019.png" o:title=""/>
    17201751</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
    1721 src="Fit%20Peaks_files/image019.png" v:shapes="Picture_x0020_18"><![endif]></span></p>
     1752src="Fit%20Peaks_files/image019.png" v:shapes="_x0000_i1035"><![endif]></span></p>
    17221753
    17231754<p class=MsoNormal>I’ve zoomed in &amp; shifted the plot some to highlight the
     
    17281759<p class=MsoNormal>Set the limits as <b style='mso-bidi-font-weight:normal'><span
    17291760style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1730 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>3</span></b>
    1731 and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1732 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1733 minor-latin'>10</span></b>.</p>
     1761mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1762minor-latin'>3</span></b> and <b style='mso-bidi-font-weight:normal'><span
     1763style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1764mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1765minor-latin'>9</span></b>.</p>
    17341766
    17351767<h2>Step 3 Pick peaks</h2>
    17361768
    17371769<p class=MsoNormal>Pick all peaks you can see between the limits (including the
    1738 small ones). Note some peaks have shoulders most notably at 5.07, 6.04,
    1739 7.81deg. I found 28 peaks (there were a few very weak ones I skipped – they
    1740 might be from a second phase? We’ll see later).</p>
    1741 
    1742 <p class=MsoNormal><!--[if gte vml 1]><v:shape id="Picture_x0020_19" o:spid="_x0000_s1026"
    1743  type="#_x0000_t75" style='position:absolute;margin-left:0;margin-top:0;
    1744  width:525pt;height:450pt;z-index:251658240;visibility:visible;
    1745  mso-wrap-style:square;mso-width-percent:0;mso-height-percent:0;
    1746  mso-wrap-distance-left:9pt;mso-wrap-distance-top:0;mso-wrap-distance-right:9pt;
    1747  mso-wrap-distance-bottom:0;mso-position-horizontal:left;
    1748  mso-position-horizontal-relative:text;mso-position-vertical:top;
    1749  mso-position-vertical-relative:text;mso-width-percent:0;mso-height-percent:0;
    1750  mso-width-relative:page;mso-height-relative:page'>
     1770small ones); use <b style='mso-bidi-font-weight:normal'><span style='font-family:
     1771"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1772minor-latin'>Auto search</span></b> to start and then fill in by hand. Note
     1773some peaks have shoulders most notably at 5.07, 6.04, 7.81deg. I found 28 peaks
     1774(there was one very weak shoulder at ~7.3 deg. I skipped – it might be from a
     1775second phase? We’ll see later).</p>
     1776
     1777<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1778 id="Picture_x0020_33" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:525pt;
     1779 height:450pt;visibility:visible;mso-wrap-style:square'>
    17511780 <v:imagedata src="Fit%20Peaks_files/image020.png" o:title=""/>
    1752  <w:wrap type="square"/>
    1753 </v:shape><![endif]--><![if !vml]><img width=700 height=600
    1754 src="Fit%20Peaks_files/image020.png" align=left hspace=12 v:shapes="Picture_x0020_19"><![endif]><br
     1781</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
     1782src="Fit%20Peaks_files/image020.png" v:shapes="Picture_x0020_33"><![endif]></span><br
    17551783clear=all style='mso-special-character:line-break'>
    17561784</p>
     
    17581786<h2><span class=GramE>Step 4.</span> Refine peaks</h2>
    17591787
    1760 <p class=MsoNormal>Following the steps above, refine the peaks and the profile
    1761 shape parameters in <b style='mso-bidi-font-weight:normal'><span
    1762 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1763 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Instrument
    1764 Parameters</span></b>. You will be asked for a project file name at the first
    1765 refinement (I used ‘<span class=SpellE><b style='mso-bidi-font-weight:normal'><span
    1766 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1767 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>jadarite</span></b></span><b
    1768 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1769 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1770 minor-latin'>’</span></b>). In the end my refinement converged at <span
    1771 class=SpellE>Rwp</span>=13.18% and some peaks do show some discrepancy as the
    1772 sample is more complex than the simple <b style='mso-bidi-font-weight:normal'><span
    1773 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1774 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>U</span></b>,
    1775 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1776 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1777 minor-latin'>V</span></b>, <b style='mso-bidi-font-weight:normal'><span
    1778 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1779 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>W</span></b>,
    1780 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1781 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1782 minor-latin'>X</span></b>, <b style='mso-bidi-font-weight:normal'><span
    1783 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1784 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Y</span></b>
    1785 model can accommodate. However, this is good enough to proceed.</p>
     1788<p class=MsoNormal>Following the steps used in the LaB<sub>6</sub> example
     1789above, refine the peaks and the profile shape parameters in <b
     1790style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1791mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1792Calibri;mso-bidi-theme-font:minor-latin'>Instrument Parameters</span></b>. You
     1793will be asked for a project file name at the first refinement (I used ‘<span
     1794class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
     1795"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1796minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>jadarite</span></b></span><b
     1797style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1798mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1799Calibri;mso-bidi-theme-font:minor-latin'>’</span></b>). In the end my
     1800refinement converged at <span class=SpellE>Rwp</span>=11.41% and some peaks do
     1801show some discrepancy as the sample is more complex than the simple <b
     1802style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1803mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1804Calibri;mso-bidi-theme-font:minor-latin'>U</span></b>, <b style='mso-bidi-font-weight:
     1805normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1806minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1807mso-bidi-theme-font:minor-latin'>V</span></b>, <b style='mso-bidi-font-weight:
     1808normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1809minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1810mso-bidi-theme-font:minor-latin'>W</span></b>, <b style='mso-bidi-font-weight:
     1811normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1812minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1813mso-bidi-theme-font:minor-latin'>X</span></b>, <b style='mso-bidi-font-weight:
     1814normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1815minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1816mso-bidi-theme-font:minor-latin'>Y</span></b> model can accommodate. Make sure no
     1817peaks drift away during refinement (one weak one at ~6.67 is particularly
     1818troublesome). However, this is good enough to proceed.</p>
    17861819
    17871820<h2><span class=GramE>Step 5.</span> Prepare Indexing Peak List</h2>
     
    17891822<p class=MsoNormal>As before do <b style='mso-bidi-font-weight:normal'><span
    17901823style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1791 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Operations/Load/Reload</span></b>
    1792 in the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1793 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1794 minor-latin'>Index Peak List</span></b> window.</p>
     1824mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1825minor-latin'>Operations/Load/Reload</span></b> in the <b style='mso-bidi-font-weight:
     1826normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1827minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1828mso-bidi-theme-font:minor-latin'>Index Peak List</span></b> window.</p>
    17951829
    17961830<h2><span class=GramE>Step 6.</span> Index the cell</h2>
     
    18031837<p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span
    18041838style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1805 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Monoclinic-P</span></b>
    1806 and do <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1807 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1808 minor-latin'>Cell Index/Refine/Index cell</span></b> in the <b
    1809 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1810 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1811 minor-latin'>Unit Cells List</span></b> window. Progress will be much slower
    1812 and suitable results will be slow in coming so be patient. Watch the console
    1813 window; the right answer will have an obviously large M20 (~630) and a volume
    1814 of ~594Å<sup>3</sup> (10<sup>th</sup> column of console display). Once this is
    1815 seen (it may take more than one try to get this) you can stop the indexing
    1816 search by pressing <b style='mso-bidi-font-weight:normal'><span
    1817 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1818 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Cancel</span></b>
    1819 on the progress bar window. Notice the ‘<b style='mso-bidi-font-weight:normal'>keep’</b>
    1820 column; this allows you to keep some solutions from one indexing run to the
    1821 next. It may take more than one press to fully stop it. My result was </p>
     1839mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1840minor-latin'>Monoclinic-P</span></b> and do <b style='mso-bidi-font-weight:
     1841normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1842minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1843mso-bidi-theme-font:minor-latin'>Cell Index/Refine/Index cell</span></b> in the
     1844<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1845mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1846Calibri;mso-bidi-theme-font:minor-latin'>Unit Cells List</span></b> window.
     1847Progress will be much slower and suitable results will be slow in coming so be
     1848patient. Watch the console window; the right answer will have an obviously
     1849large M20 (~372) and a volume of ~594Å<sup>3</sup> (10<sup>th</sup> column of
     1850console display). Once this is seen (it may take more than one try to get this)
     1851you can stop the indexing search by pressing <b style='mso-bidi-font-weight:
     1852normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1853minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1854mso-bidi-theme-font:minor-latin'>Cancel</span></b> on the progress bar window.
     1855Notice the ‘<b style='mso-bidi-font-weight:normal'>keep’</b> column; this
     1856allows you to keep some solutions from one indexing run to the next. It may
     1857take more than one press to fully stop it. My result was </p>
    18221858
    18231859<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1824  id="Picture_x0020_24" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:527.25pt;
    1825  height:376.5pt;visibility:visible;mso-wrap-style:square'>
     1860 id="Picture_x0020_21" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:525pt;
     1861 height:450pt;visibility:visible;mso-wrap-style:square'>
    18261862 <v:imagedata src="Fit%20Peaks_files/image021.png" o:title=""/>
     1863</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
     1864src="Fit%20Peaks_files/image021.png" v:shapes="Picture_x0020_21"><![endif]><!--[if gte vml 1]><v:shape
     1865 id="_x0000_i1032" type="#_x0000_t75" style='width:527.25pt;height:376.5pt;
     1866 visibility:visible;mso-wrap-style:square'>
     1867 <v:imagedata src="Fit%20Peaks_files/image022.png" o:title=""/>
    18271868</v:shape><![endif]--><![if !vml]><img border=0 width=703 height=502
    1828 src="Fit%20Peaks_files/image021.png" v:shapes="Picture_x0020_24"><![endif]></span></p>
    1829 
    1830 <p class=MsoNormal>Notice two equally good M20 results with different volumes;
    1831 other solutions may be obtained as you keep trying the indexing. Be sure to use
    1832 keep to keep good ones as you try new indexing runs. The best solution is the
    1833 one with the smaller volume. The plot shows every peak indexed including a
    1834 couple of weak peaks not selected for the peak fitting.</p>
     1869src="Fit%20Peaks_files/image022.png" v:shapes="_x0000_i1032"><![endif]></span></p>
     1870
     1871<p class=MsoNormal>Notice other equally good M20 results with different
     1872volumes; other solutions may be obtained as you keep trying the indexing. Be
     1873sure to use <b style='mso-bidi-font-weight:normal'><span style='font-family:
     1874"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1875minor-latin'>Keep</span></b> to keep good ones as you try new indexing runs.
     1876The best solution is the one with the smaller volume. The plot shows every peak
     1877indexed including a weak peak not selected for the peak fitting, although the
     1878weak peak at 2<span style='font-family:Symbol;mso-char-type:symbol;mso-symbol-font-family:
     1879Symbol'><span style='mso-char-type:symbol;mso-symbol-font-family:Symbol'>Q</span></span>~7.3
     1880has a shoulder that wasn’t indexed. I presume that is a contaminant. Copy the
     1881best cell and try to refine it along with the <b style='mso-bidi-font-weight:
     1882normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1883minor-latin;mso-hansi-theme-font:minor-latin'>Zero offset</span></b>. I
     1884obtained an improved M20 ~444 and slightly different lattice parameters. Try
     1885different space groups, pressing the <b style='mso-bidi-font-weight:normal'><span
     1886style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1887mso-hansi-theme-font:minor-latin'>Show <span class=SpellE>hkl</span> positions</span></b>
     1888each time to see which lines vanish. By sliding the cursor over the index lines
     1889without any visible peak you can see that the missing ones are 010, 100, 001,
     1890110, 030, 111, 20-1, 10-2, 041, 050, 21-2 &amp; 23-1. Many of these are
     1891accidental but the 0k0; k&#8800;2n and h0l; h+l&#8800;2n ones characterize the
     1892space group P2<sub>1</sub>/n. Armed with this information you can <b
     1893style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1894mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1895Calibri;mso-bidi-theme-font:minor-latin'>Make new phase</span></b> for the
     1896indexed cell (I called it ‘<b style='mso-bidi-font-weight:normal'><span
     1897style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1898mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1899minor-latin'>kryptonite’</span></b>) and select <b style='mso-bidi-font-weight:
     1900normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1901minor-latin;mso-hansi-theme-font:minor-latin'>Phases/kryptonite</span></b> from
     1902the GSAS-II data tree.</p>
    18351903
    18361904<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1837  id="Picture_x0020_21" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:525pt;
    1838  height:450pt;visibility:visible;mso-wrap-style:square'>
    1839  <v:imagedata src="Fit%20Peaks_files/image022.png" o:title=""/>
    1840 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
    1841 src="Fit%20Peaks_files/image022.png" v:shapes="Picture_x0020_21"><![endif]></span></p>
    1842 
    1843 <p class=MsoNormal>Although the weak peak at 2<span style='font-family:Symbol;
    1844 mso-char-type:symbol;mso-symbol-font-family:Symbol'><span style='mso-char-type:
    1845 symbol;mso-symbol-font-family:Symbol'>Q</span></span>~7.3 has a shoulder that
    1846 wasn’t indexed. I presume that is a contaminant. By sliding the cursor over the
    1847 index lines without any visible peak you can see that the missing ones are
    1848 (010, 100, 001, 110, 030, 111, 20-1, 10-2, 041, 050, 21-2, 23-1, 22-2, 141,
    1849 201,102, 15-1, 112, &amp; 24-1). Many of these are accidental but the 0k0; k&#8800;2n
    1850 and h0l; h+l&#8800;2n ones characterize the space group P2<sub>1</sub>/n. Armed
    1851 with this information you can <b style='mso-bidi-font-weight:normal'><span
    1852 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1853 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Make new
    1854 phase</span></b> for the indexed cell (I called it ‘<b style='mso-bidi-font-weight:
    1855 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1856 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>kryptonite’</span></b>)
    1857 and set the space group in the <b style='mso-bidi-font-weight:normal'><span
    1858 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1859 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Phase Data
    1860 for kryptonite</span></b> window.</p>
     1905 id="Picture_x0020_35" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:545.25pt;
     1906 height:303.75pt;visibility:visible;mso-wrap-style:square'>
     1907 <v:imagedata src="Fit%20Peaks_files/image023.png" o:title=""/>
     1908</v:shape><![endif]--><![if !vml]><img border=0 width=727 height=405
     1909src="Fit%20Peaks_files/image023.png" v:shapes="Picture_x0020_35"><![endif]></span><span
     1910style='mso-spacerun:yes'> </span></p>
     1911
     1912<p class=MsoNormal>Notice that the lattice parameters and space group have been
     1913set for you. If you set the space group here a dialog box will appear.</p>
    18611914
    18621915<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1863  id="Picture_x0020_22" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:597.75pt;
    1864  height:214.5pt;visibility:visible;mso-wrap-style:square'>
    1865  <v:imagedata src="Fit%20Peaks_files/image023.png" o:title=""/>
    1866 </v:shape><![endif]--><![if !vml]><img border=0 width=797 height=286
    1867 src="Fit%20Peaks_files/image023.png" v:shapes="Picture_x0020_22"><![endif]></span></p>
    1868 
    1869 <p class=MsoNormal>Setting the space group will show a window with some
    1870 information. Press <b style='mso-bidi-font-weight:normal'><span
    1871 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1872 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>OK</span></b>
    1873 to close it.</p>
    1874 
    1875 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1876  id="Picture_x0020_23" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:333.75pt;
     1916 id="Picture_x0020_23" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:333.75pt;
    18771917 height:209.25pt;visibility:visible;mso-wrap-style:square'>
    18781918 <v:imagedata src="Fit%20Peaks_files/image024.png" o:title=""/>
     
    18821922<p class=MsoNormal>This concludes this exercise; <span class=GramE><b
    18831923style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1884 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1885 minor-latin'>Save</span></b></span> the project file as it is needed for the <b
    1886 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1887 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1924mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1925Calibri;mso-bidi-theme-font:minor-latin'>Save</span></b></span> the project
     1926file as it is needed for the <b style='mso-bidi-font-weight:normal'><span
     1927style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1928mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    18881929minor-latin'><a href="Charge%20Flipping%20in%20GSAS.htm">Charge Flipping</a></span></b>
    18891930exercise. The features of the <b style='mso-bidi-font-weight:normal'><span
    18901931style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1891 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Phase Data</span></b>
    1892 window will be presented in other exercises.</p>
     1932mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1933minor-latin'>Phase Data</span></b> window will be presented in other exercises.</p>
     1934
     1935<h1><a name="sucrose_peak_fit"></a>3<sup>rd</sup> Fit Peaks/<span class=SpellE>Autoindexing</span>
     1936in GSAS-II </h1>
     1937
     1938<p class=MsoNormal>In this exercise we will fit peaks and index them for sucrose
     1939in preparation for a charge flipping exercise. The data was also collected on
     194011BM-B at APS. The unit cell is monoclinic so is a more substantial test of the
     1941indexing capability of GSAS-II.</p>
     1942
     1943<h2><span class=GramE>Step 1.</span> Read in the data. </h2>
     1944
     1945<p class=MsoNormal>The file is <b style='mso-bidi-font-weight:normal'><span
     1946style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1947mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1948minor-latin'>\Exercises\sucrose\11bmb_8716.fxye</span></b>; it has a
     1949corresponding <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
     1950style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1951mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1952minor-latin'>prm</span></b></span> file and is for Domino® sugar ground under
     1953acetone. <span class=GramE>The other <span class=SpellE><b style='mso-bidi-font-weight:
     1954normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1955minor-latin;mso-hansi-theme-font:minor-latin'>fxye</span></b></span> file in
     1956this directory <b style='mso-bidi-font-weight:normal'><span style='font-family:
     1957"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1958minor-latin'>11bmb_8714.fxye</span></b> is for Domino® 10X powdered sugar used
     1959“as is” out of the box.</span> Load the <b style='mso-bidi-font-weight:normal'><span
     1960style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1961mso-hansi-theme-font:minor-latin'>8716</span></b> file in &amp; the plot is</p>
     1962
     1963<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1964 id="Picture_x0020_29" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:525pt;
     1965 height:450pt;visibility:visible;mso-wrap-style:square'>
     1966 <v:imagedata src="Fit%20Peaks_files/image025.png" o:title=""/>
     1967</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
     1968src="Fit%20Peaks_files/image025.png" v:shapes="Picture_x0020_29"><![endif]></span></p>
     1969
     1970<p class=MsoNormal>I’ve zoomed in &amp; shifted the plot some to highlight the
     1971lower part of the pattern.</p>
     1972
     1973<h2>Step 2 Set limits</h2>
     1974
     1975<p class=MsoNormal>Set the limits as <b style='mso-bidi-font-weight:normal'><span
     1976style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1977mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1978minor-latin'>2</span></b> and <b style='mso-bidi-font-weight:normal'><span
     1979style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1980mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1981minor-latin'>8</span></b>.</p>
     1982
     1983<h2>Step 3 Pick peaks</h2>
     1984
     1985<p class=MsoNormal>Pick all peaks you can see between the limits (including the
     1986small ones); use <b style='mso-bidi-font-weight:normal'><span style='font-family:
     1987"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1988minor-latin'>Auto search</span></b> to start and then fill in by hand. Note the
     1989shoulder at ~6.3 <span class=SpellE>deg</span> that should be added to the
     1990list. I skipped a couple of very weak peaks; the total list has 28 peaks.</p>
     1991
     1992<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1993 id="Picture_x0020_30" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:525pt;
     1994 height:450pt;visibility:visible;mso-wrap-style:square'>
     1995 <v:imagedata src="Fit%20Peaks_files/image026.png" o:title=""/>
     1996</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
     1997src="Fit%20Peaks_files/image026.png" v:shapes="Picture_x0020_30"><![endif]></span><br
     1998clear=all style='mso-special-character:line-break'>
     1999</p>
     2000
     2001<h2><span class=GramE>Step 4.</span> Refine peaks</h2>
     2002
     2003<p class=MsoNormal>Following the steps used in the LaB<sub>6</sub> and
     2004kryptonite examples above, refine the peaks and the profile shape parameters in
     2005<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2006mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     2007Calibri;mso-bidi-theme-font:minor-latin'>Instrument Parameters</span></b>. You
     2008will be asked for a project file name at the first refinement (I used ‘<b
     2009style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2010mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     2011Calibri;mso-bidi-theme-font:minor-latin'>sucrose’</span></b>). In the end my
     2012refinement converged at <span class=SpellE>Rwp</span>=7.15% and some peaks do
     2013show some discrepancy as the sample is more complex than the simple <b
     2014style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2015mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     2016Calibri;mso-bidi-theme-font:minor-latin'>U</span></b>, <b style='mso-bidi-font-weight:
     2017normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     2018minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     2019mso-bidi-theme-font:minor-latin'>V</span></b>, <b style='mso-bidi-font-weight:
     2020normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     2021minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     2022mso-bidi-theme-font:minor-latin'>W</span></b>, <b style='mso-bidi-font-weight:
     2023normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     2024minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     2025mso-bidi-theme-font:minor-latin'>X</span></b>, <b style='mso-bidi-font-weight:
     2026normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     2027minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     2028mso-bidi-theme-font:minor-latin'>Y</span></b> model can accommodate. Make sure
     2029no peaks drift away during refinement. However, this is good enough to proceed.</p>
     2030
     2031<h2><span class=GramE>Step 5.</span> Prepare Indexing Peak List</h2>
     2032
     2033<p class=MsoNormal>As before do <b style='mso-bidi-font-weight:normal'><span
     2034style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2035mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     2036minor-latin'>Operations/Load/Reload</span></b> in the <b style='mso-bidi-font-weight:
     2037normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     2038minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     2039mso-bidi-theme-font:minor-latin'>Index Peak List</span></b> window.</p>
     2040
     2041<h2><span class=GramE>Step 6.</span> Index the cell</h2>
     2042
     2043<p class=MsoNormal>Let’s assume that we know the cell in primitive monoclinic.
     2044In a real world case we wouldn’t know this and we would have to try each <span
     2045class=SpellE>Bravais</span> lattice. These can be done as a group, but it takes
     2046time to go through all the bad cases.</p>
     2047
     2048<p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span
     2049style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2050mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     2051minor-latin'>Monoclinic-P</span></b> and do <b style='mso-bidi-font-weight:
     2052normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     2053minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     2054mso-bidi-theme-font:minor-latin'>Cell Index/Refine/Index cell</span></b> in the
     2055<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2056mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     2057Calibri;mso-bidi-theme-font:minor-latin'>Unit Cells List</span></b> window. Progress
     2058will be much slower than for LaB<sub>6</sub> but oddly much faster than for
     2059kryptonite and suitable results may appear almost immediately. Watch the
     2060console window; the right answer will have an obviously large M20 (~900) and a
     2061volume of ~704Å<sup>3</sup> (10<sup>th</sup> column of console display). Once
     2062this is seen (it may take more than one try to get this) you can stop the
     2063indexing search by pressing <b style='mso-bidi-font-weight:normal'><span
     2064style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2065mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     2066minor-latin'>Cancel</span></b> on the progress bar window. Notice the ‘<b
     2067style='mso-bidi-font-weight:normal'>keep’</b> column; this allows you to keep
     2068some solutions from one indexing run to the next. It may take more than one
     2069press to fully stop it. My result was </p>
     2070
     2071<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     2072 id="Picture_x0020_31" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:525pt;
     2073 height:450pt;visibility:visible;mso-wrap-style:square'>
     2074 <v:imagedata src="Fit%20Peaks_files/image027.png" o:title=""/>
     2075</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
     2076src="Fit%20Peaks_files/image027.png" v:shapes="Picture_x0020_31"><![endif]><!--[if gte vml 1]><v:shape
     2077 id="Picture_x0020_32" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:527.25pt;
     2078 height:376.5pt;visibility:visible;mso-wrap-style:square'>
     2079 <v:imagedata src="Fit%20Peaks_files/image028.png" o:title=""/>
     2080</v:shape><![endif]--><![if !vml]><img border=0 width=703 height=502
     2081src="Fit%20Peaks_files/image028.png" v:shapes="Picture_x0020_32"><![endif]></span></p>
     2082
     2083<p class=MsoNormal>Notice there may be other equally good M20 results with
     2084different volumes; still other solutions may be obtained as you keep trying the
     2085indexing. Be sure to use <b style='mso-bidi-font-weight:normal'><span
     2086style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2087mso-hansi-theme-font:minor-latin'>Keep</span></b> to keep good ones as you try
     2088new indexing runs. The best solution is the one with the smaller volume and &#946;
     2089&gt; 90 deg. The plot shows every peak indexed including the weak peaks not
     2090selected for the peak fitting. Copy the best cell and try to refine it along
     2091with the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2092mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Zero offset</span></b>.
     2093I obtained an improved M20 ~1257 and slightly different lattice parameters. Try
     2094different space groups, pressing the <b style='mso-bidi-font-weight:normal'><span
     2095style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2096mso-hansi-theme-font:minor-latin'>Show <span class=SpellE>hkl</span> positions</span></b>
     2097each time to see which lines vanish. The correct space group is P2<sub>1</sub>.
     2098Armed with this information you can <b style='mso-bidi-font-weight:normal'><span
     2099style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2100mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     2101minor-latin'>Make new phase</span></b> for the indexed cell (I called it ‘<b
     2102style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2103mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     2104Calibri;mso-bidi-theme-font:minor-latin'>sucrose</span></b>) and select <b
     2105style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2106mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b>
     2107from the GSAS-II data tree.</p>
     2108
     2109<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     2110 id="Picture_x0020_34" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:545.25pt;
     2111 height:303.75pt;visibility:visible;mso-wrap-style:square'>
     2112 <v:imagedata src="Fit%20Peaks_files/image029.png" o:title=""/>
     2113</v:shape><![endif]--><![if !vml]><img border=0 width=727 height=405
     2114src="Fit%20Peaks_files/image029.png" v:shapes="Picture_x0020_34"><![endif]></span><span
     2115style='mso-spacerun:yes'> </span></p>
     2116
     2117<p class=MsoNormal>Notice that the lattice parameters and space group have been
     2118set for you. This concludes this exercise; <b style='mso-bidi-font-weight:normal'><span
     2119style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2120mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     2121minor-latin'>Save</span></b> the project file as it is needed for the sucrose <b
     2122style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2123mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     2124Calibri;mso-bidi-theme-font:minor-latin'><a href="Charge%20Flipping%20-%20sucrose.htm">Charge
     2125Flipping</a></span></b> exercise. The features of the <b style='mso-bidi-font-weight:
     2126normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     2127minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     2128mso-bidi-theme-font:minor-latin'>Phase Data</span></b> window will be presented
     2129in other exercises.</p>
     2130
     2131<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    18932132
    18942133</div>
  • trunk/help/Fit Peaks_files/filelist.xml

    r782 r864  
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