Changeset 864

Timestamp:

Mar 19, 2013 9:33:15 AM (10 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:

• GSASIIplot.py (modified) (1 diff)
• GSASIIstruct.py (modified) (1 diff)
• help/Charge Flipping - sucrose.htm (added)
• help/Charge Flipping in GSAS.htm (added)
• help/Fit Peaks.htm (modified) (33 diffs)
• help/Fit Peaks_files/filelist.xml (modified) (2 diffs)
• help/Fit Peaks_files/image002.png (modified) (previous)
• help/Fit Peaks_files/image007.png (modified) (previous)
• help/Fit Peaks_files/image008.png (modified) (previous)
• help/Fit Peaks_files/image009.png (modified) (previous)
• help/Fit Peaks_files/image010.png (modified) (previous)
• help/Fit Peaks_files/image012.png (modified) (previous)
• help/Fit Peaks_files/image013.png (modified) (previous)
• help/Fit Peaks_files/image014.png (modified) (previous)
• help/Fit Peaks_files/image015.png (modified) (previous)
• help/Fit Peaks_files/image016.png (modified) (previous)
• help/Fit Peaks_files/image017.png (modified) (previous)
• help/Fit Peaks_files/image018.png (modified) (previous)
• help/Fit Peaks_files/image019.png (modified) (previous)
• help/Fit Peaks_files/image020.png (modified) (previous)
• help/Fit Peaks_files/image021.png (modified) (previous)
• help/Fit Peaks_files/image022.png (modified) (previous)
• help/Fit Peaks_files/image023.png (modified) (previous)

trunk/GSASIIplot.py

@@ -1504 +1504 @@
                         sum = np.sum(np.multiply(Shkl,Strm))
                         sum = np.where(sum > 0.01,sum,0.01)
-                        sum = np.sqrt(sum)*math.pi/0.018      #centidegrees to radians!
+                        sum = np.sqrt(sum)*math.pi/1.8      #centidegrees to radians!
                         return sum*xyz
                         

trunk/GSASIIstruct.py

@@ -2265 +2265 @@
                     except ValueError:
                         pass
-    print np.sum(pDerv),pDerv.shape
     return pDerv
 

trunk/help/Fit Peaks.htm

@@ -23 +23 @@
   <o:Author>Von Dreele</o:Author>
   <o:LastAuthor>Von Dreele</o:LastAuthor>
-  <o:Revision>22</o:Revision>
-  <o:TotalTime>429</o:TotalTime>
+  <o:Revision>29</o:Revision>
+  <o:TotalTime>717</o:TotalTime>
   <o:Created>2012-05-05T16:28:00Z</o:Created>
-  <o:LastSaved>2012-10-16T19:18:00Z</o:LastSaved>
-  <o:Pages>2</o:Pages>
-  <o:Words>1952</o:Words>
-  <o:Characters>11133</o:Characters>
+  <o:LastSaved>2013-03-18T17:01:00Z</o:LastSaved>
+  <o:Pages>11</o:Pages>
+  <o:Words>2632</o:Words>
+  <o:Characters>15009</o:Characters>
   <o:Company>Argonne National Laboratory</o:Company>
-  <o:Lines>92</o:Lines>
-  <o:Paragraphs>26</o:Paragraphs>
-  <o:CharactersWithSpaces>13059</o:CharactersWithSpaces>
+  <o:Lines>125</o:Lines>
+  <o:Paragraphs>35</o:Paragraphs>
+  <o:CharactersWithSpaces>17606</o:CharactersWithSpaces>
   <o:Version>14.00</o:Version>
  </o:DocumentProperties>
@@ -40 +40 @@
  </o:OfficeDocumentSettings>
 </xml><![endif]-->
-<link rel=dataStoreItem href="Fit%20Peaks_files/item0030.xml"
-target="Fit%20Peaks_files/props031.xml">
+<link rel=dataStoreItem href="Fit%20Peaks_files/item0035.xml"
+target="Fit%20Peaks_files/props036.xml">
 <link rel=themeData href="Fit%20Peaks_files/themedata.thmx">
 <link rel=colorSchemeMapping href="Fit%20Peaks_files/colorschememapping.xml">
@@ -356 +356 @@
         mso-generic-font-family:swiss;
         mso-font-pitch:variable;
-        mso-font-signature:-520092929 1073786111 9 0 415 0;}
+        mso-font-signature:-536870145 1073786111 1 0 415 0;}
 @font-face
         {font-family:Tahoma;
@@ -1113 +1113 @@
         mso-ascii-theme-font:minor-latin;
         mso-hansi-font-family:Calibri;
-        mso-hansi-theme-font:minor-latin;
-        mso-bidi-font-family:"Times New Roman";
-        mso-bidi-theme-font:minor-bidi;}
+        mso-hansi-theme-font:minor-latin;}
 </style>
 <![endif]--><!--[if gte mso 9]><xml>
- <o:shapedefaults v:ext="edit" spidmax="1027"/>
+ <o:shapedefaults v:ext="edit" spidmax="1026"/>
 </xml><![endif]--><!--[if gte mso 9]><xml>
  <o:shapelayout v:ext="edit">
@@ -1145 +1143 @@
 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Use
 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
-minor-latin'>Import/Powder Data/from GSAS file</span></b> menu item to read the
-data file into the current GSAS-II project. This read option is set to read any
-of the powder data formats (except neutron TOF time map files) defined for GSAS
-(angles in <span class=SpellE>centidegrees</span>). Other submenu items will
-read the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
-style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>cif</span></b></span>
-format or the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
-style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>xye</span></b></span>
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>Import/Powder Data/from GSAS file</span></b>
+menu item to read the data file into the current GSAS-II project. This read
+option is set to read any of the powder data formats (except neutron TOF time
+map files) defined for GSAS (angles in <span class=SpellE>centidegrees</span>).
+Other submenu items will read the <span class=SpellE><b style='mso-bidi-font-weight:
+normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
+minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
+mso-bidi-theme-font:minor-latin'>cif</span></b></span> format or the <span
+class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
+"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
+minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>xye</span></b></span>
 format (angles in degrees) used by <span class=SpellE>Topas</span>, etc.<span
 style='mso-spacerun:yes'>  </span>Change the file directory to <b
 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
-minor-latin'>Exercises/LaB6</span></b><span style='font-family:"Calibri","sans-serif";
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>Exercises/LaB6</span></b><span
+style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
+mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
 minor-latin'> to find the file; you may need to change the file type to <b
 style='mso-bidi-font-weight:normal'>All files (*.*)</b> to find the desired
@@ -1170 +1170 @@
 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
-minor-latin'>11bmb_3844.fxye</span></b><span style='font-family:"Calibri","sans-serif";
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>11bmb_3844.fxye</span></b><span
+style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
+mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
 minor-latin'> data</span> file in the first dialog and press <b
 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
-minor-latin'>Open</span></b>. There will be a Dialog box asking <span
-class=GramE><b style='mso-bidi-font-weight:normal'><span style='font-family:
-"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
-minor-latin;mso-bidi-theme-font:minor-latin'>Is</span></b></span><b
-style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>Open</span></b>. There will be a
+Dialog box asking <span class=GramE><b style='mso-bidi-font-weight:normal'><span
+style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
+mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
+minor-latin'>Is</span></b></span><b style='mso-bidi-font-weight:normal'><span
+style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
+mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
 minor-latin'> this the file you want?</span></b> Press <span class=GramE><b
 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
-minor-latin'>Yes</span></b></span> button to proceed.</p>
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>Yes</span></b></span> button to
+proceed.</p>
 
 <p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
@@ -1191 +1194 @@
 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>The
 file <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
-minor-latin'>11bmb_3844.prm</span></b> instrument parameter file is
-automatically selected; it was produced by 11BM-B instrument processing
-software when the corresponding <span class=SpellE><b style='mso-bidi-font-weight:
-normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
-minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>fxye</span></b></span>
-file was created from the 12 detector raw data. If absent or the name doesn’t
-match the data file name, a file dialog will appear for you to select the
-correct instrument parameter file.</p>
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>11bmb_3844.prm</span></b> instrument
+parameter file is automatically selected; it was produced by 11BM-B instrument
+processing software when the corresponding <span class=SpellE><b
+style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>fxye</span></b></span> file was
+created from the 12 detector raw data. If absent or the name doesn’t match the
+data file name, a file dialog will appear for you to select the correct
+instrument parameter file.</p>
 
 <p class=MsoNormal>At this point the <b style='mso-bidi-font-weight:normal'><span
 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II data
-tree</span></b> window will have several entries </p>
+mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
+minor-latin'>GSAS-II data tree</span></b> window will have several entries </p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
@@ -1226 +1230 @@
  <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
  <o:lock v:ext="edit" aspectratio="t"/>
-</v:shapetype><v:shape id="Picture_x0020_1" o:spid="_x0000_i1046" type="#_x0000_t75"
+</v:shapetype><v:shape id="Picture_x0020_1" o:spid="_x0000_i1052" type="#_x0000_t75"
  style='width:225pt;height:187.5pt;visibility:visible;mso-wrap-style:square'>
  <v:imagedata src="Fit%20Peaks_files/image001.png" o:title=""/>
@@ -1236 +1240 @@
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
- id="Picture_x0020_2" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:525pt;
+ id="Picture_x0020_2" o:spid="_x0000_i1051" type="#_x0000_t75" style='width:525pt;
  height:450pt;visibility:visible;mso-wrap-style:square'>
  <v:imagedata src="Fit%20Peaks_files/image002.png" o:title=""/>
@@ -1247 +1251 @@
 more data than we need, so it is helpful to cut down the range. Click on the <b
 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
-minor-latin'>Limits</span></b> item in the <b style='mso-bidi-font-weight:normal'><span
-style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II data
-tree</span></b>. The small window is repainted. Use the <b style='mso-bidi-font-weight:
-normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
-minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>changed</span></b>
-row of entry boxes to set <span class=SpellE><b style='mso-bidi-font-weight:
-normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
-minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Tmin</span></b></span>
-and <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
-style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Tmax</span></b></span>
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>Limits</span></b> item in the <b
+style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>GSAS-II data tree</span></b>. The
+small window is repainted. Use the <b style='mso-bidi-font-weight:normal'><span
+style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
+mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
+minor-latin'>changed</span></b> row of entry boxes to set <span class=SpellE><b
+style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>Tmin</span></b></span> and <span
+class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
+"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
+minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>Tmax</span></b></span>
 to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
-minor-latin'>4</span></b> and <b style='mso-bidi-font-weight:normal'><span
-style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>27.5</span></b>.
-Notice on the plot that the limit lines have moved to these positions; the
-green lower limit is just below the 1<sup>st</sup> peak and the red upper limit
-is in a wide gap between peaks. You may also drag the limit lines to the
-desired location or place them by a left mouse click on a data point for the
-lower limit or a right click on a data point for the upper limit.</p>
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>4</span></b> and <b style='mso-bidi-font-weight:
+normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
+minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
+mso-bidi-theme-font:minor-latin'>27.5</span></b>. Notice on the plot that the
+limit lines have moved to these positions; the green lower limit is just below
+the 1<sup>st</sup> peak and the red upper limit is in a wide gap between peaks.
+You may also drag the limit lines to the desired location or place them by a
+left mouse click on a data point for the lower limit or a right click on a data
+point for the upper limit.</p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
- id="Picture_x0020_3" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:225pt;
+ id="Picture_x0020_3" o:spid="_x0000_i1050" type="#_x0000_t75" style='width:225pt;
  height:120pt;visibility:visible;mso-wrap-style:square'>
  <v:imagedata src="Fit%20Peaks_files/image003.png" o:title=""/>
@@ -1285 +1292 @@
 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Click
 on the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
-minor-latin'>Peak List</span></b> item in the <b style='mso-bidi-font-weight:
-normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
-minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II
-data tree</span></b>. This creates an empty window of peak positions (the <b
-style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
-minor-latin'>Limits</span></b> window is erased). At this point it is wise <span
-class=GramE>to<span style='mso-spacerun:yes'>  </span>zoom</span> in on the
-data that will be used for indexing. </p>
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>Peak List</span></b> item in the <b
+style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>GSAS-II data tree</span></b>. This
+creates an empty window of peak positions (the <b style='mso-bidi-font-weight:
+normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
+minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
+mso-bidi-theme-font:minor-latin'>Limits</span></b> window is erased). At this
+point it is wise <span class=GramE>to<span style='mso-spacerun:yes'> 
+</span>zoom</span> in on the data that will be used for indexing. </p>
 
 <p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
@@ -1301 +1309 @@
 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Click
 on the Zoom button, <span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
- id="Picture_x0020_4" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:21.75pt;
+ id="Picture_x0020_4" o:spid="_x0000_i1049" type="#_x0000_t75" style='width:21.75pt;
  height:18.75pt;visibility:visible;mso-wrap-style:square'>
  <v:imagedata src="Fit%20Peaks_files/image004.jpg" o:title="" croptop="1f"
@@ -1317 +1325 @@
 style='mso-bidi-font-weight:normal'>Important</b>: Click on the Zoom <span
 style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_5"
- o:spid="_x0000_i1042" type="#_x0000_t75" style='width:23.25pt;height:20.25pt;
+ o:spid="_x0000_i1048" type="#_x0000_t75" style='width:23.25pt;height:20.25pt;
  visibility:visible;mso-wrap-style:square'>
  <v:imagedata src="Fit%20Peaks_files/image004.jpg" o:title="" croptop="1f"
@@ -1328 +1336 @@
 auto;text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
-style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Using
-the left mouse button, click on a data point near the top of each peak to be
-added to the peak list. It is usually best to start at the upper end of the
-pattern as the next peak to pick isn’t obscured by the tool tip. As this is
-done, a vertical blue line is drawn in the plot window<span
-style='mso-spacerun:yes'>  </span>for each peak selected</p>
+style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Under
+<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Peak Fitting</span></b>
+in the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Peak List</span></b>
+window select <b style='mso-bidi-font-weight:normal'><span style='font-family:
+"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
+minor-latin'>Auto search</span></b>. The plot window will immediately show that
+all peaks were picked with a blue vertical line on each one</p>
 
 <p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
-auto'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_6"
- o:spid="_x0000_i1041" type="#_x0000_t75" style='width:525pt;height:450pt;
+auto'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_27"
+ o:spid="_x0000_i1047" type="#_x0000_t75" style='width:525pt;height:450pt;
  visibility:visible;mso-wrap-style:square'>
  <v:imagedata src="Fit%20Peaks_files/image007.png" o:title=""/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
-src="Fit%20Peaks_files/image007.png" v:shapes="Picture_x0020_6"><![endif]></span></p>
+src="Fit%20Peaks_files/image007.png" v:shapes="Picture_x0020_27"><![endif]></span></p>
 
 <p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
-auto'><span class=GramE>and</span> peaks are added to the <b style='mso-bidi-font-weight:
-normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
-minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak
-List</span></b> window in order of increasing 2<span style='font-family:Symbol'>Q</span>.</p>
+auto'><span class=GramE>and</span> peaks are shown in the <b style='mso-bidi-font-weight:
+normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
+minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
+mso-bidi-theme-font:minor-latin'>Peak List</span></b> window in order of
+increasing 2<span style='font-family:Symbol'>Q</span>.</p>
 
 <p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
 auto'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_7"
- o:spid="_x0000_i1040" type="#_x0000_t75" style='width:401.25pt;height:262.5pt;
+ o:spid="_x0000_i1046" type="#_x0000_t75" style='width:401.25pt;height:262.5pt;
  visibility:visible;mso-wrap-style:square'>
  <v:imagedata src="Fit%20Peaks_files/image008.png" o:title=""/>
@@ -1357 +1369 @@
 src="Fit%20Peaks_files/image008.png" v:shapes="Picture_x0020_7"><![endif]></span></p>
 
-<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
-auto'>Note that if peaks are not being added, you probably have not exited zoom
-mode.</p>
-
-<p class=MsoListParagraphCxSpLast style='margin-left:39.0pt;mso-add-space:auto'>Add
-approximately 20-25 peaks total to the peak list (there will be 20 in this
-example). Be sure to add the lowest angle peaks that are visible in the plot.
-You may drag a peak position as needed; be sure the zoom/shift buttons are off.
-A position may be deleted with a right click with the mouse on the blue line.</p>
+<p class=MsoListParagraphCxSpLast style='margin-left:39.0pt;mso-add-space:auto'>There
+will be 23 peaks in this example. You should examine both the list and the plot
+to be sure the auto search did not pick a peak twice (there may be three of
+these!) or skip a peak or shoulder. You can add a peak to the list by pressing
+the left mouse button with the pointer on a data point at the peak top or
+shoulder. You may drag a peak position as needed; be sure the zoom/shift
+buttons are off. A position may be deleted with a right click with the mouse on
+the blue line. You can also delete a peak by selecting the row in the <span
+class=GramE>table,</span> it will be highlighted in blue. Then press the Delete
+key; it will be removed from the table and the plot. The list will always show
+the peaks sorted by position. When done you should have 20 unique peak
+positions.</p>
 
 <h2>Step 4: Refine Peak Positions</h2>
 
 <p class=MsoNormal>This refinement proceeds stepwise; first doing the default
-refinement and then adding <span class=GramE>a parameters</span> to complete
-the fitting,</p>
+refinement and then adding parameters to complete the fitting,</p>
 
 <p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
@@ -1379 +1393 @@
 flags turned on by default. Use the menu item <b style='mso-bidi-font-weight:
 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
-minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak
-Fitting/LSQ <span class=SpellE>PeakFit</span> </span></b>on the<b
-style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
-minor-latin'> Peak List </span></b>window. Do <b style='mso-bidi-font-weight:
-normal'>NOT</b> use the <b style='mso-bidi-font-weight:normal'><span
-style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Calculate/Refine</span></b>
-menu item in the <b style='mso-bidi-font-weight:normal'><span style='font-family:
+minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
+mso-bidi-theme-font:minor-latin'>Peak Fitting/LSQ <span class=SpellE>PeakFit</span>
+</span></b>on the<b style='mso-bidi-font-weight:normal'><span style='font-family:
 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
-minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II data tree</span></b>
-window; that it to be used for Rietveld/Pawley refinements. You will be asked
-to save the current project before the fit will proceed; change directory if
-desired and provide a suitable name (we assume <b style='mso-bidi-font-weight:
-normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
-minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>LaB6</span></b>).
-A window will show the progress of the refinement and will close when the
-least-squares fit <span class=GramE>is</span> complete (usually very fast). The
-plot is updated with the fit, the peak list window is updated with the new peak
-values and a summary of the refinement is shown on the console window as well.</p>
+minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'> Peak
+List </span></b>window. Do <b style='mso-bidi-font-weight:normal'>NOT</b> use
+the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>Calculate/Refine</span></b> menu item
+in the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>GSAS-II data tree</span></b> window;
+that it to be used for Rietveld/Pawley refinements. You will be asked to save
+the current project before the fit will proceed; change directory if desired
+and provide a suitable name (we assume <b style='mso-bidi-font-weight:normal'><span
+style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
+mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
+minor-latin'>LaB6</span></b>). A window will show the progress of the
+refinement and will close when the least-squares fit <span class=GramE>is</span>
+complete (usually very fast). The plot is updated with the fit, the peak list
+window is updated with the new peak values and a summary of the refinement is
+shown on the console window as well.</p>
 
 <p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
- id="Picture_x0020_8" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:525pt;
- height:450pt;visibility:visible;mso-wrap-style:square'>
+ id="_x0000_i1045" type="#_x0000_t75" style='width:525pt;height:450pt;
+ visibility:visible;mso-wrap-style:square'>
  <v:imagedata src="Fit%20Peaks_files/image009.png" o:title=""/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
-src="Fit%20Peaks_files/image009.png" v:shapes="Picture_x0020_8"><![endif]></span></p>
+src="Fit%20Peaks_files/image009.png" v:shapes="_x0000_i1045"><![endif]></span></p>
 
 <p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
- id="Picture_x0020_9" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:401.25pt;
+ id="Picture_x0020_24" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:401.25pt;
  height:262.5pt;visibility:visible;mso-wrap-style:square'>
  <v:imagedata src="Fit%20Peaks_files/image010.png" o:title=""/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=535 height=350
-src="Fit%20Peaks_files/image010.png" v:shapes="Picture_x0020_9"><![endif]></span></p>
+src="Fit%20Peaks_files/image010.png" v:shapes="Picture_x0020_24"><![endif]></span></p>
 
 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
@@ -1435 +1451 @@
 check-boxes. The entire column of checkboxes is highlighted in blue. Press the <b
 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
-minor-latin'>y</span></b> key to turn on all refinement flags (<b
-style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>y</span></b> key to turn on all
+refinement flags (<b style='mso-bidi-font-weight:normal'><span
+style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
+mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
 minor-latin'>n</span></b> would turn them off).</p>
 
 <p class=MsoNormal style='margin-left:.5in'>Next, repeat the refinement using
 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
-minor-latin'>Peak Fitting/LSQ <span class=SpellE>PeakFit</span></span></b> menu
-item in the <b style='mso-bidi-font-weight:normal'><span style='font-family:
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>Peak Fitting/LSQ <span class=SpellE>PeakFit</span></span></b>
+menu item in the <b style='mso-bidi-font-weight:normal'><span style='font-family:
 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
-minor-latin;mso-bidi-theme-font:minor-latin'>Peak List</span></b> window.</p>
-
-<p class=MsoNormal style='margin-left:.5in'><span
-style='mso-spacerun:yes'> </span>Now, select peak widths for refinement. <span
-style='mso-fareast-font-family:"Times New Roman"'>This can be performed in 2
-different ways. &nbsp;Method&nbsp;1:&nbsp;refine sigma (Gaussian width) and/or
-gamma (Lorentzian width) for individual peaks. &nbsp;To do this, click the
-refinement flags for sigma and/or gamma in the Peak List window.
+minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>Peak
+List</span></b> window.</p>
+
+<p class=MsoNormal style='margin-left:.5in'>Now, select peak widths for
+refinement. <span style='mso-fareast-font-family:"Times New Roman"'>This can be
+performed in 2 different ways. &nbsp;Method&nbsp;1:&nbsp;refine sigma (Gaussian
+width) and/or gamma (Lorentzian width) for individual peaks. &nbsp;To do this,
+click the refinement flags for sigma and/or gamma in the Peak List window.
 &nbsp;&nbsp;Method&nbsp;2: preferably,&nbsp;the LS&nbsp;refinement of&nbsp;peak
 widths can be&nbsp;constrained to&nbsp;follow an instrumental broadening
@@ -1465 +1482 @@
 to an instrumental broadening equation, first<b> s</b></span>elect the <b
 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
-minor-latin'>Instrumental Parameters</span></b> item in the data tree. <span
-class=GramE>This opens a window for peak profile terms<b> </b><span
-style='mso-bidi-font-weight:bold'>and also create</span></span><span
-style='mso-bidi-font-weight:bold'> a new plot window&nbsp;showing the
-instrument profile resolution curve.</span></p>
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>Instrumental Parameters</span></b>
+item in the data tree. This opens a window for peak profile terms<b> </b><span
+style='mso-bidi-font-weight:bold'>and also creates a new plot
+window&nbsp;showing the instrument profile resolution curve.</span></p>
 
 <p class=MsoNormal style='margin-left:.5in'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
- id="Picture_x0020_10" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:422.25pt;
+ id="Picture_x0020_10" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:422.25pt;
  height:154.5pt;visibility:visible;mso-wrap-style:square'>
  <v:imagedata src="Fit%20Peaks_files/image011.png" o:title=""/>
@@ -1484 +1500 @@
 values for the peaks in Peak List. Select the refine flag checkbox for Gaussian
 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
-minor-latin'>U</span></b>, <b style='mso-bidi-font-weight:normal'><span
-style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>V</span></b>,
-<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
-minor-latin'>W</span></b>, and Lorentzian <b style='mso-bidi-font-weight:normal'><span
-style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>X</span></b>,
-<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
-minor-latin'>Y</span></b>. </p>
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>U</span></b>, <b style='mso-bidi-font-weight:
+normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
+minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
+mso-bidi-theme-font:minor-latin'>V</span></b>, <b style='mso-bidi-font-weight:
+normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
+minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
+mso-bidi-theme-font:minor-latin'>W</span></b>, and Lorentzian <b
+style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>X</span></b>, <b style='mso-bidi-font-weight:
+normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
+minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
+mso-bidi-theme-font:minor-latin'>Y</span></b>. </p>
 
 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
@@ -1502 +1520 @@
 repeat the refinement. First click on the <b style='mso-bidi-font-weight:normal'><span
 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak List</span></b>
-item in the data tree and then refine using the <b style='mso-bidi-font-weight:
-normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
-minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak
-Fitting/LSQ <span class=SpellE>PeakFit</span></span></b> menu item. At this
-point a good fit should be seen by zooming in on individual peaks. (For example
-see </p>
+mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
+minor-latin'>Peak List</span></b> item in the data tree and then refine using
+the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>Peak Fitting/LSQ <span class=SpellE>PeakFit</span></span></b>
+menu item. At this point a good fit should be seen by zooming in on individual
+peaks. For example see </p>
 
 <p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
- id="Picture_x0020_11" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:525pt;
+ id="Picture_x0020_11" o:spid="_x0000_i1042" type="#_x0000_t75" style='width:525pt;
  height:450pt;visibility:visible;mso-wrap-style:square'>
  <v:imagedata src="Fit%20Peaks_files/image012.png" o:title=""/>
@@ -1517 +1535 @@
 src="Fit%20Peaks_files/image012.png" v:shapes="Picture_x0020_11"><![endif]></span></p>
 
-<p class=MsoListParagraphCxSpLast>The <span class=SpellE>Rwp</span> is ~6% as
-shown on the console window. Again the <b style='mso-bidi-font-weight:normal'><span
-style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak List</span></b>
-entries are all updated with new values and those in <b style='mso-bidi-font-weight:
-normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
-minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Instrument
-Parameters</span></b> are also updated.</p>
+<p class=MsoListParagraphCxSpLast>Notice that the peak position is slightly to
+the right of the peak top. This is a consequence of the peak asymmetry arising
+from axial divergence in the diffractometer. The <span class=SpellE>Rwp</span>
+is ~6% as shown on the console window. Again the <b style='mso-bidi-font-weight:
+normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
+minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
+mso-bidi-theme-font:minor-latin'>Peak List</span></b> entries are all updated
+with new values and those in <b style='mso-bidi-font-weight:normal'><span
+style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
+mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
+minor-latin'>Instrument Parameters</span></b> are also updated.</p>
 
 <h2><span class=GramE>Step 5.</span> Prepare Indexing Peak List</h2>
@@ -1531 +1552 @@
 class=SpellE>autoindexing</span>. It is found in the <b style='mso-bidi-font-weight:
 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
-minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Index
-Peak List</span></b> item in the data tree. In the initially empty window
-created by this action, use menu item <b style='mso-bidi-font-weight:normal'><span
-style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Index Peaks
-Operations/Load</span></b> to copy the fitted peaks from the <b
-style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
+minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
+mso-bidi-theme-font:minor-latin'>Index Peak List</span></b> item in the data
+tree. In the initially empty window created by this action, use menu item <b
+style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>Index Peaks Operations/Load</span></b>
+to copy the fitted peaks from the <b style='mso-bidi-font-weight:normal'><span
+style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
+mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
 minor-latin'>Peak List</span></b>.</p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
- id="Picture_x0020_12" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:367.5pt;
+ id="Picture_x0020_26" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:367.5pt;
  height:225pt;visibility:visible;mso-wrap-style:square'>
  <v:imagedata src="Fit%20Peaks_files/image013.png" o:title=""/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=490 height=300
-src="Fit%20Peaks_files/image013.png" v:shapes="Picture_x0020_12"><![endif]></span></p>
+src="Fit%20Peaks_files/image013.png" v:shapes="Picture_x0020_26"><![endif]></span></p>
 
 <p class=MsoNormal>Note that by default all peaks are selected to be used. You
@@ -1556 +1578 @@
 <p class=MsoNormal>Select the <b style='mso-bidi-font-weight:normal'><span
 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Unit Cells
-List</span></b> data item. This brings up a window for indexing and cell refinement
-options</p>
+mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
+minor-latin'>Unit Cells List</span></b> data item. This brings up a window for
+indexing and cell refinement options</p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
- id="Picture_x0020_13" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:527.25pt;
+ id="Picture_x0020_13" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:527.25pt;
  height:204pt;visibility:visible;mso-wrap-style:square'>
  <v:imagedata src="Fit%20Peaks_files/image014.png" o:title=""/>
@@ -1569 +1591 @@
 <p class=MsoNormal>For the most rapid search (since we know the right answer),
 select <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
-minor-latin'>Cubic-P</span></b> and launch the search using menu item <b
-style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
-minor-latin'>Cell Index/Index Cell</span></b>. The search then runs and the console
-shows a running list of possible cells as they are found; the sorted by M20
-list of possible matching cells is shown in the <b style='mso-bidi-font-weight:
-normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
-minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Unit
-Cells List</span></b> window</p>
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>Cubic-P</span></b> and launch the
+search using menu item <b style='mso-bidi-font-weight:normal'><span
+style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
+mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
+minor-latin'>Cell Index/Index Cell</span></b>. The search then runs and the
+console shows a running list of possible cells as they are found; the sorted by
+M20 list of possible matching cells is shown in the <b style='mso-bidi-font-weight:
+normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
+minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
+mso-bidi-theme-font:minor-latin'>Unit Cells List</span></b> window</p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
- id="Picture_x0020_14" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:527.25pt;
+ id="Picture_x0020_28" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:527.25pt;
  height:376.5pt;visibility:visible;mso-wrap-style:square'>
  <v:imagedata src="Fit%20Peaks_files/image015.png" o:title=""/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=703 height=502
-src="Fit%20Peaks_files/image015.png" v:shapes="Picture_x0020_14"><![endif]></span></p>
+src="Fit%20Peaks_files/image015.png" v:shapes="Picture_x0020_28"><![endif]></span></p>
 
 <h2><span class=GramE>Step 7.</span> Review Cell Choices</h2>
@@ -1591 +1614 @@
 <p class=MsoNormal>Review the list of cells associated with the <b
 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
-minor-latin'>Unit Cells List</span></b> data item. Note that as one selects a
-unit cell, the generated reflections for that cell are shown in the plot with
-dashed red lines. Sliding the cursor over these lines shows a small popup
-window with the indexed <span class=SpellE>hkl</span> for them. Note how the
-first cell in the list (M20~3000) with a=5.87864 Å generates very many lines
-with no corresponding peaks (NB: this solution might not always show up!)</p>
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>Unit Cells List</span></b> data item.
+Note that as one selects a unit cell, the generated reflections for that cell
+are shown in the plot with dashed red lines. Sliding the cursor over these
+lines shows a small popup window with the indexed <span class=SpellE>hkl</span>
+for them. Note how the first cell in the list (M20~2970) with a=5.87864 Å
+generates very many lines with no corresponding peaks (NB: this solution might
+not always show up!)</p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
- id="Picture_x0020_15" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:525pt;
+ id="Picture_x0020_38" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:525pt;
  height:450pt;visibility:visible;mso-wrap-style:square'>
  <v:imagedata src="Fit%20Peaks_files/image016.png" o:title=""/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
-src="Fit%20Peaks_files/image016.png" v:shapes="Picture_x0020_15"><![endif]></span><span
+src="Fit%20Peaks_files/image016.png" v:shapes="Picture_x0020_38"><![endif]></span><span
 style='mso-spacerun:yes'> </span></p>
 
@@ -1611 +1635 @@
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
- id="Picture_x0020_16" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:525pt;
+ id="Picture_x0020_39" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:525pt;
  height:450pt;visibility:visible;mso-wrap-style:square'>
  <v:imagedata src="Fit%20Peaks_files/image017.png" o:title=""/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
-src="Fit%20Peaks_files/image017.png" v:shapes="Picture_x0020_16"><![endif]></span></p>
+src="Fit%20Peaks_files/image017.png" v:shapes="Picture_x0020_39"><![endif]></span></p>
 
 <h2><span class=GramE>Step 8.</span> Select/Refine Cell</h2>
 
-<p class=MsoNormal>Select the cell with M20 ~ 2900 with a = 4.1568 Å. This
+<p class=MsoNormal>Select the cell with M20 ~ 2970 with a = 4.15683 Å. This
 indexes all peaks with almost a perfect fit to the peak positions (compare
 dashed red lines to solid blue ones). Import the cell information using the <b
 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
-minor-latin'>Cell Index/Copy Cell</span></b> menu option. Then optimize the
-cell by refining the lattice parameters and the two-theta zero: click on the
-refine checkbox next to the <b style='mso-bidi-font-weight:normal'><span
-style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Zero offset</span></b>
-value and then the <b style='mso-bidi-font-weight:normal'><span
-style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Cell
-Index/Refine Cell</span></b> menu option. <span class=GramE>The a</span> cell
-parameter value shifts from 4.15679 to 4.15684 when zero is refined. Press the <b
-style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
-minor-latin'>Show refined <span class=SpellE>hkl</span> positions + Zero offset</span></b>
-button to update the plot including the refined <b style='mso-bidi-font-weight:
-normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
-minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Zero
-offset</span></b> (in this case hardly anything happens!) </p>
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>Cell Index/Copy Cell</span></b> menu
+option. Then optimize the cell by refining the lattice parameters and the
+two-theta zero: click on the refine checkbox next to the <b style='mso-bidi-font-weight:
+normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
+minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
+mso-bidi-theme-font:minor-latin'>Zero offset</span></b> value and then the <b
+style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>Cell Index/Refine Cell</span></b> menu
+option. The M20 improves to ~3600 and <span class=GramE>the a</span> cell
+parameter value shifts from 4.15683 to 4.15691 when zero is refined. (NB: The
+certificate value for NIST SRM 660a is 4.15692 Å). Press the <b
+style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>Show refined <span class=SpellE>hkl</span>
+positions + Zero offset</span></b> button to update the plot including the
+refined <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>Zero offset</span></b> (in this case
+hardly anything happens!) </p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
- id="Picture_x0020_17" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:527.25pt;
- height:334.5pt;visibility:visible;mso-wrap-style:square'>
+ id="_x0000_i1036" type="#_x0000_t75" style='width:527.25pt;height:334.5pt;
+ visibility:visible;mso-wrap-style:square'>
  <v:imagedata src="Fit%20Peaks_files/image018.png" o:title=""/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=703 height=446
-src="Fit%20Peaks_files/image018.png" v:shapes="Picture_x0020_17"><![endif]></span></p>
+src="Fit%20Peaks_files/image018.png" v:shapes="_x0000_i1036"><![endif]></span></p>
 
 <p class=MsoNormal>Notice that a new entry heads the list in the <b
 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
-minor-latin'>Indexing Result</span></b> section of the <b style='mso-bidi-font-weight:
-normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
-minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Cell
-Index/Refine</span></b> window with an improved M20(=3614.66) and a new value
-for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
-minor-latin'>Zero offset</span></b> is shown.</p>
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>Indexing Result</span></b> section of
+the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>Cell Index/Refine</span></b> window
+with an improved M20(=3607.97) and a new value for <b style='mso-bidi-font-weight:
+normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
+minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
+mso-bidi-theme-font:minor-latin'>Zero offset</span></b> is shown.</p>
 
 <p class=MsoNormal>(Optional) Finally, use of the <b style='mso-bidi-font-weight:
 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
-minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Cell
-Index/New phase</span></b> menu option allows one to create a phase with these
-lattice parameters in the data tree under <b style='mso-bidi-font-weight:normal'><span
-style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Phases</span></b>.<span
+minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
+mso-bidi-theme-font:minor-latin'>Cell Index/New phase</span></b> menu option
+allows one to create a phase with these lattice parameters in the data tree
+under <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>Phases</span></b>.<span
 style='mso-spacerun:yes'>  </span>A name for the new phase is requested. This
 creates the tree item <b style='mso-bidi-font-weight:normal'><span
 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Phases</span></b>
-(if it wasn’t already present). This new phase can be used in future analysis
-(e.g. Rietveld or Pawley refinement).</p>
-
-<p class=MsoNormal>To continue with the second part of this exercise, <span
-class=GramE>do the menu item</span> <b style='mso-bidi-font-weight:normal'><span
-style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>File/Close
+mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
+minor-latin'>Phases</span></b> (if it wasn’t already present). This new phase
+can be used in future analysis (e.g. Rietveld or Pawley refinement).</p>
+
+<p class=MsoNormal>To continue with the second part of this exercise, select
+the menu item <b style='mso-bidi-font-weight:normal'><span style='font-family:
+"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
+minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>File/Close
 project</span></b> in the <b style='mso-bidi-font-weight:normal'><span
 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II data
-tree </span></b>window. You will be asked if you want it saved; if <span
-class=GramE><b style='mso-bidi-font-weight:normal'><span style='font-family:
-"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
-minor-latin;mso-bidi-theme-font:minor-latin'>Yes</span></b></span> then all the
-peak fitting/indexing &amp; cell refinement results will be saved to the <b
-style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
-minor-latin'>LaB6.gpx</span></b> file. If <b style='mso-bidi-font-weight:normal'><span
-style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>No</span></b>
-then the file will remain as it was when created at Step 4 above.</p>
+mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
+minor-latin'>GSAS-II data tree </span></b>window. You will be asked if you want
+it saved; if <span class=GramE><b style='mso-bidi-font-weight:normal'><span
+style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
+mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
+minor-latin'>Yes</span></b></span> then all the peak fitting/indexing &amp;
+cell refinement results will be saved to the <b style='mso-bidi-font-weight:
+normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
+minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
+mso-bidi-theme-font:minor-latin'>LaB6.gpx</span></b> file. If <b
+style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>No</span></b> then the file will
+remain as it was when created at Step 4 above.</p>
 
 <h1><a name="kryptonite_peak_fit">2<sup>nd</sup> Fit Peaks/</a><span
@@ -1700 +1731 @@
 new mineral <a href="http://en.wikipedia.org/wiki/Jadarite"><span class=SpellE>jadarite</span></a>
 (aka “<a href="http://en.wikipedia.org/wiki/Kryptonite">kryptonite</a>”). The
-data was also collected on 11BM-B at APS. The unit cell is monoclinic so is a
-more substantial test of the indexing capability of GSAS-II.</p>
+data was also collected on 11BM-B at APS. The unit cell is monoclinic so is a more
+substantial test of the indexing capability of GSAS-II.</p>
 
 <h2><span class=GramE>Step 1.</span> Read in the data. </h2>
@@ -1707 +1738 @@
 <p class=MsoNormal>The file is <b style='mso-bidi-font-weight:normal'><span
 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>\Exercises\<span
-class=SpellE>krptonite</span>\11bmb_6231.fxye</span></b>; it has a
+mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
+minor-latin'>\Exercises\kryptonite\11bmb_6231.fxye</span></b>; it has a
 corresponding <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>prm</span></b></span>
-file. Load them in &amp; the plot is</p>
+mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
+minor-latin'>prm</span></b></span> file. Load them in &amp; the plot is</p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
- id="Picture_x0020_18" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:525pt;
- height:450pt;visibility:visible;mso-wrap-style:square'>
+ id="_x0000_i1035" type="#_x0000_t75" style='width:525pt;height:450pt;
+ visibility:visible;mso-wrap-style:square'>
  <v:imagedata src="Fit%20Peaks_files/image019.png" o:title=""/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
-src="Fit%20Peaks_files/image019.png" v:shapes="Picture_x0020_18"><![endif]></span></p>
+src="Fit%20Peaks_files/image019.png" v:shapes="_x0000_i1035"><![endif]></span></p>
 
 <p class=MsoNormal>I’ve zoomed in &amp; shifted the plot some to highlight the
@@ -1728 +1759 @@
 <p class=MsoNormal>Set the limits as <b style='mso-bidi-font-weight:normal'><span
 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>3</span></b>
-and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
-minor-latin'>10</span></b>.</p>
+mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
+minor-latin'>3</span></b> and <b style='mso-bidi-font-weight:normal'><span
+style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
+mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
+minor-latin'>9</span></b>.</p>
 
 <h2>Step 3 Pick peaks</h2>
 
 <p class=MsoNormal>Pick all peaks you can see between the limits (including the
-small ones). Note some peaks have shoulders most notably at 5.07, 6.04,
-7.81deg. I found 28 peaks (there were a few very weak ones I skipped – they
-might be from a second phase? We’ll see later).</p>
-
-<p class=MsoNormal><!--[if gte vml 1]><v:shape id="Picture_x0020_19" o:spid="_x0000_s1026"
- type="#_x0000_t75" style='position:absolute;margin-left:0;margin-top:0;
- width:525pt;height:450pt;z-index:251658240;visibility:visible;
- mso-wrap-style:square;mso-width-percent:0;mso-height-percent:0;
- mso-wrap-distance-left:9pt;mso-wrap-distance-top:0;mso-wrap-distance-right:9pt;
- mso-wrap-distance-bottom:0;mso-position-horizontal:left;
- mso-position-horizontal-relative:text;mso-position-vertical:top;
- mso-position-vertical-relative:text;mso-width-percent:0;mso-height-percent:0;
- mso-width-relative:page;mso-height-relative:page'>
+small ones); use <b style='mso-bidi-font-weight:normal'><span style='font-family:
+"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
+minor-latin'>Auto search</span></b> to start and then fill in by hand. Note
+some peaks have shoulders most notably at 5.07, 6.04, 7.81deg. I found 28 peaks
+(there was one very weak shoulder at ~7.3 deg. I skipped – it might be from a
+second phase? We’ll see later).</p>
+
+<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
+ id="Picture_x0020_33" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:525pt;
+ height:450pt;visibility:visible;mso-wrap-style:square'>
  <v:imagedata src="Fit%20Peaks_files/image020.png" o:title=""/>
- <w:wrap type="square"/>
-</v:shape><![endif]--><![if !vml]><img width=700 height=600
-src="Fit%20Peaks_files/image020.png" align=left hspace=12 v:shapes="Picture_x0020_19"><![endif]><br
+</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
+src="Fit%20Peaks_files/image020.png" v:shapes="Picture_x0020_33"><![endif]></span><br
 clear=all style='mso-special-character:line-break'>
 </p>
@@ -1758 +1786 @@
 <h2><span class=GramE>Step 4.</span> Refine peaks</h2>
 
-<p class=MsoNormal>Following the steps above, refine the peaks and the profile
-shape parameters in <b style='mso-bidi-font-weight:normal'><span
-style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Instrument
-Parameters</span></b>. You will be asked for a project file name at the first
-refinement (I used ‘<span class=SpellE><b style='mso-bidi-font-weight:normal'><span
-style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>jadarite</span></b></span><b
-style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
-minor-latin'>’</span></b>). In the end my refinement converged at <span
-class=SpellE>Rwp</span>=13.18% and some peaks do show some discrepancy as the
-sample is more complex than the simple <b style='mso-bidi-font-weight:normal'><span
-style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>U</span></b>,
-<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
-minor-latin'>V</span></b>, <b style='mso-bidi-font-weight:normal'><span
-style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>W</span></b>,
-<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
-minor-latin'>X</span></b>, <b style='mso-bidi-font-weight:normal'><span
-style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Y</span></b>
-model can accommodate. However, this is good enough to proceed.</p>
+<p class=MsoNormal>Following the steps used in the LaB<sub>6</sub> example
+above, refine the peaks and the profile shape parameters in <b
+style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>Instrument Parameters</span></b>. You
+will be asked for a project file name at the first refinement (I used ‘<span
+class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
+"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
+minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>jadarite</span></b></span><b
+style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>’</span></b>). In the end my
+refinement converged at <span class=SpellE>Rwp</span>=11.41% and some peaks do
+show some discrepancy as the sample is more complex than the simple <b
+style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>U</span></b>, <b style='mso-bidi-font-weight:
+normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
+minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
+mso-bidi-theme-font:minor-latin'>V</span></b>, <b style='mso-bidi-font-weight:
+normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
+minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
+mso-bidi-theme-font:minor-latin'>W</span></b>, <b style='mso-bidi-font-weight:
+normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
+minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
+mso-bidi-theme-font:minor-latin'>X</span></b>, <b style='mso-bidi-font-weight:
+normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
+minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
+mso-bidi-theme-font:minor-latin'>Y</span></b> model can accommodate. Make sure no
+peaks drift away during refinement (one weak one at ~6.67 is particularly
+troublesome). However, this is good enough to proceed.</p>
 
 <h2><span class=GramE>Step 5.</span> Prepare Indexing Peak List</h2>
@@ -1789 +1822 @@
 <p class=MsoNormal>As before do <b style='mso-bidi-font-weight:normal'><span
 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Operations/Load/Reload</span></b>
-in the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
-minor-latin'>Index Peak List</span></b> window.</p>
+mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
+minor-latin'>Operations/Load/Reload</span></b> in the <b style='mso-bidi-font-weight:
+normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
+minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
+mso-bidi-theme-font:minor-latin'>Index Peak List</span></b> window.</p>
 
 <h2><span class=GramE>Step 6.</span> Index the cell</h2>
@@ -1803 +1837 @@
 <p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span
 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Monoclinic-P</span></b>
-and do <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
-minor-latin'>Cell Index/Refine/Index cell</span></b> in the <b
-style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
-minor-latin'>Unit Cells List</span></b> window. Progress will be much slower
-and suitable results will be slow in coming so be patient. Watch the console
-window; the right answer will have an obviously large M20 (~630) and a volume
-of ~594Å<sup>3</sup> (10<sup>th</sup> column of console display). Once this is
-seen (it may take more than one try to get this) you can stop the indexing
-search by pressing <b style='mso-bidi-font-weight:normal'><span
-style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Cancel</span></b>
-on the progress bar window. Notice the ‘<b style='mso-bidi-font-weight:normal'>keep’</b>
-column; this allows you to keep some solutions from one indexing run to the
-next. It may take more than one press to fully stop it. My result was </p>
+mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
+minor-latin'>Monoclinic-P</span></b> and do <b style='mso-bidi-font-weight:
+normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
+minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
+mso-bidi-theme-font:minor-latin'>Cell Index/Refine/Index cell</span></b> in the
+<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>Unit Cells List</span></b> window.
+Progress will be much slower and suitable results will be slow in coming so be
+patient. Watch the console window; the right answer will have an obviously
+large M20 (~372) and a volume of ~594Å<sup>3</sup> (10<sup>th</sup> column of
+console display). Once this is seen (it may take more than one try to get this)
+you can stop the indexing search by pressing <b style='mso-bidi-font-weight:
+normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
+minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
+mso-bidi-theme-font:minor-latin'>Cancel</span></b> on the progress bar window.
+Notice the ‘<b style='mso-bidi-font-weight:normal'>keep’</b> column; this
+allows you to keep some solutions from one indexing run to the next. It may
+take more than one press to fully stop it. My result was </p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
- id="Picture_x0020_24" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:527.25pt;
- height:376.5pt;visibility:visible;mso-wrap-style:square'>
+ id="Picture_x0020_21" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:525pt;
+ height:450pt;visibility:visible;mso-wrap-style:square'>
  <v:imagedata src="Fit%20Peaks_files/image021.png" o:title=""/>
+</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
+src="Fit%20Peaks_files/image021.png" v:shapes="Picture_x0020_21"><![endif]><!--[if gte vml 1]><v:shape
+ id="_x0000_i1032" type="#_x0000_t75" style='width:527.25pt;height:376.5pt;
+ visibility:visible;mso-wrap-style:square'>
+ <v:imagedata src="Fit%20Peaks_files/image022.png" o:title=""/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=703 height=502
-src="Fit%20Peaks_files/image021.png" v:shapes="Picture_x0020_24"><![endif]></span></p>
-
-<p class=MsoNormal>Notice two equally good M20 results with different volumes;
-other solutions may be obtained as you keep trying the indexing. Be sure to use
-keep to keep good ones as you try new indexing runs. The best solution is the
-one with the smaller volume. The plot shows every peak indexed including a
-couple of weak peaks not selected for the peak fitting.</p>
+src="Fit%20Peaks_files/image022.png" v:shapes="_x0000_i1032"><![endif]></span></p>
+
+<p class=MsoNormal>Notice other equally good M20 results with different
+volumes; other solutions may be obtained as you keep trying the indexing. Be
+sure to use <b style='mso-bidi-font-weight:normal'><span style='font-family:
+"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
+minor-latin'>Keep</span></b> to keep good ones as you try new indexing runs.
+The best solution is the one with the smaller volume. The plot shows every peak
+indexed including a weak peak not selected for the peak fitting, although the
+weak peak at 2<span style='font-family:Symbol;mso-char-type:symbol;mso-symbol-font-family:
+Symbol'><span style='mso-char-type:symbol;mso-symbol-font-family:Symbol'>Q</span></span>~7.3
+has a shoulder that wasn’t indexed. I presume that is a contaminant. Copy the
+best cell and try to refine it along with the <b style='mso-bidi-font-weight:
+normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
+minor-latin;mso-hansi-theme-font:minor-latin'>Zero offset</span></b>. I
+obtained an improved M20 ~444 and slightly different lattice parameters. Try
+different space groups, pressing the <b style='mso-bidi-font-weight:normal'><span
+style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
+mso-hansi-theme-font:minor-latin'>Show <span class=SpellE>hkl</span> positions</span></b>
+each time to see which lines vanish. By sliding the cursor over the index lines
+without any visible peak you can see that the missing ones are 010, 100, 001,
+110, 030, 111, 20-1, 10-2, 041, 050, 21-2 &amp; 23-1. Many of these are
+accidental but the 0k0; k&#8800;2n and h0l; h+l&#8800;2n ones characterize the
+space group P2<sub>1</sub>/n. Armed with this information you can <b
+style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>Make new phase</span></b> for the
+indexed cell (I called it ‘<b style='mso-bidi-font-weight:normal'><span
+style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
+mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
+minor-latin'>kryptonite’</span></b>) and select <b style='mso-bidi-font-weight:
+normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
+minor-latin;mso-hansi-theme-font:minor-latin'>Phases/kryptonite</span></b> from
+the GSAS-II data tree.</p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
- id="Picture_x0020_21" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:525pt;
- height:450pt;visibility:visible;mso-wrap-style:square'>
- <v:imagedata src="Fit%20Peaks_files/image022.png" o:title=""/>
-</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
-src="Fit%20Peaks_files/image022.png" v:shapes="Picture_x0020_21"><![endif]></span></p>
-
-<p class=MsoNormal>Although the weak peak at 2<span style='font-family:Symbol;
-mso-char-type:symbol;mso-symbol-font-family:Symbol'><span style='mso-char-type:
-symbol;mso-symbol-font-family:Symbol'>Q</span></span>~7.3 has a shoulder that
-wasn’t indexed. I presume that is a contaminant. By sliding the cursor over the
-index lines without any visible peak you can see that the missing ones are
-(010, 100, 001, 110, 030, 111, 20-1, 10-2, 041, 050, 21-2, 23-1, 22-2, 141,
-201,102, 15-1, 112, &amp; 24-1). Many of these are accidental but the 0k0; k&#8800;2n
-and h0l; h+l&#8800;2n ones characterize the space group P2<sub>1</sub>/n. Armed
-with this information you can <b style='mso-bidi-font-weight:normal'><span
-style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Make new
-phase</span></b> for the indexed cell (I called it ‘<b style='mso-bidi-font-weight:
-normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
-minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>kryptonite’</span></b>)
-and set the space group in the <b style='mso-bidi-font-weight:normal'><span
-style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Phase Data
-for kryptonite</span></b> window.</p>
+ id="Picture_x0020_35" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:545.25pt;
+ height:303.75pt;visibility:visible;mso-wrap-style:square'>
+ <v:imagedata src="Fit%20Peaks_files/image023.png" o:title=""/>
+</v:shape><![endif]--><![if !vml]><img border=0 width=727 height=405
+src="Fit%20Peaks_files/image023.png" v:shapes="Picture_x0020_35"><![endif]></span><span
+style='mso-spacerun:yes'> </span></p>
+
+<p class=MsoNormal>Notice that the lattice parameters and space group have been
+set for you. If you set the space group here a dialog box will appear.</p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
- id="Picture_x0020_22" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:597.75pt;
- height:214.5pt;visibility:visible;mso-wrap-style:square'>
- <v:imagedata src="Fit%20Peaks_files/image023.png" o:title=""/>
-</v:shape><![endif]--><![if !vml]><img border=0 width=797 height=286
-src="Fit%20Peaks_files/image023.png" v:shapes="Picture_x0020_22"><![endif]></span></p>
-
-<p class=MsoNormal>Setting the space group will show a window with some
-information. Press <b style='mso-bidi-font-weight:normal'><span
-style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>OK</span></b>
-to close it.</p>
-
-<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
- id="Picture_x0020_23" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:333.75pt;
+ id="Picture_x0020_23" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:333.75pt;
  height:209.25pt;visibility:visible;mso-wrap-style:square'>
  <v:imagedata src="Fit%20Peaks_files/image024.png" o:title=""/>
@@ -1882 +1922 @@
 <p class=MsoNormal>This concludes this exercise; <span class=GramE><b
 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
-minor-latin'>Save</span></b></span> the project file as it is needed for the <b
-style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>Save</span></b></span> the project
+file as it is needed for the <b style='mso-bidi-font-weight:normal'><span
+style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
+mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
 minor-latin'><a href="Charge%20Flipping%20in%20GSAS.htm">Charge Flipping</a></span></b>
 exercise. The features of the <b style='mso-bidi-font-weight:normal'><span
 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Phase Data</span></b>
-window will be presented in other exercises.</p>
+mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
+minor-latin'>Phase Data</span></b> window will be presented in other exercises.</p>
+
+<h1><a name="sucrose_peak_fit"></a>3<sup>rd</sup> Fit Peaks/<span class=SpellE>Autoindexing</span>
+in GSAS-II </h1>
+
+<p class=MsoNormal>In this exercise we will fit peaks and index them for sucrose
+in preparation for a charge flipping exercise. The data was also collected on
+11BM-B at APS. The unit cell is monoclinic so is a more substantial test of the
+indexing capability of GSAS-II.</p>
+
+<h2><span class=GramE>Step 1.</span> Read in the data. </h2>
+
+<p class=MsoNormal>The file is <b style='mso-bidi-font-weight:normal'><span
+style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
+mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
+minor-latin'>\Exercises\sucrose\11bmb_8716.fxye</span></b>; it has a
+corresponding <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
+style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
+mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
+minor-latin'>prm</span></b></span> file and is for Domino® sugar ground under
+acetone. <span class=GramE>The other <span class=SpellE><b style='mso-bidi-font-weight:
+normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
+minor-latin;mso-hansi-theme-font:minor-latin'>fxye</span></b></span> file in
+this directory <b style='mso-bidi-font-weight:normal'><span style='font-family:
+"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
+minor-latin'>11bmb_8714.fxye</span></b> is for Domino® 10X powdered sugar used
+“as is” out of the box.</span> Load the <b style='mso-bidi-font-weight:normal'><span
+style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
+mso-hansi-theme-font:minor-latin'>8716</span></b> file in &amp; the plot is</p>
+
+<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
+ id="Picture_x0020_29" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:525pt;
+ height:450pt;visibility:visible;mso-wrap-style:square'>
+ <v:imagedata src="Fit%20Peaks_files/image025.png" o:title=""/>
+</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
+src="Fit%20Peaks_files/image025.png" v:shapes="Picture_x0020_29"><![endif]></span></p>
+
+<p class=MsoNormal>I’ve zoomed in &amp; shifted the plot some to highlight the
+lower part of the pattern.</p>
+
+<h2>Step 2 Set limits</h2>
+
+<p class=MsoNormal>Set the limits as <b style='mso-bidi-font-weight:normal'><span
+style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
+mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
+minor-latin'>2</span></b> and <b style='mso-bidi-font-weight:normal'><span
+style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
+mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
+minor-latin'>8</span></b>.</p>
+
+<h2>Step 3 Pick peaks</h2>
+
+<p class=MsoNormal>Pick all peaks you can see between the limits (including the
+small ones); use <b style='mso-bidi-font-weight:normal'><span style='font-family:
+"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
+minor-latin'>Auto search</span></b> to start and then fill in by hand. Note the
+shoulder at ~6.3 <span class=SpellE>deg</span> that should be added to the
+list. I skipped a couple of very weak peaks; the total list has 28 peaks.</p>
+
+<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
+ id="Picture_x0020_30" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:525pt;
+ height:450pt;visibility:visible;mso-wrap-style:square'>
+ <v:imagedata src="Fit%20Peaks_files/image026.png" o:title=""/>
+</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
+src="Fit%20Peaks_files/image026.png" v:shapes="Picture_x0020_30"><![endif]></span><br
+clear=all style='mso-special-character:line-break'>
+</p>
+
+<h2><span class=GramE>Step 4.</span> Refine peaks</h2>
+
+<p class=MsoNormal>Following the steps used in the LaB<sub>6</sub> and
+kryptonite examples above, refine the peaks and the profile shape parameters in
+<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>Instrument Parameters</span></b>. You
+will be asked for a project file name at the first refinement (I used ‘<b
+style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>sucrose’</span></b>). In the end my
+refinement converged at <span class=SpellE>Rwp</span>=7.15% and some peaks do
+show some discrepancy as the sample is more complex than the simple <b
+style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>U</span></b>, <b style='mso-bidi-font-weight:
+normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
+minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
+mso-bidi-theme-font:minor-latin'>V</span></b>, <b style='mso-bidi-font-weight:
+normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
+minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
+mso-bidi-theme-font:minor-latin'>W</span></b>, <b style='mso-bidi-font-weight:
+normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
+minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
+mso-bidi-theme-font:minor-latin'>X</span></b>, <b style='mso-bidi-font-weight:
+normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
+minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
+mso-bidi-theme-font:minor-latin'>Y</span></b> model can accommodate. Make sure
+no peaks drift away during refinement. However, this is good enough to proceed.</p>
+
+<h2><span class=GramE>Step 5.</span> Prepare Indexing Peak List</h2>
+
+<p class=MsoNormal>As before do <b style='mso-bidi-font-weight:normal'><span
+style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
+mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
+minor-latin'>Operations/Load/Reload</span></b> in the <b style='mso-bidi-font-weight:
+normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
+minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
+mso-bidi-theme-font:minor-latin'>Index Peak List</span></b> window.</p>
+
+<h2><span class=GramE>Step 6.</span> Index the cell</h2>
+
+<p class=MsoNormal>Let’s assume that we know the cell in primitive monoclinic.
+In a real world case we wouldn’t know this and we would have to try each <span
+class=SpellE>Bravais</span> lattice. These can be done as a group, but it takes
+time to go through all the bad cases.</p>
+
+<p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span
+style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
+mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
+minor-latin'>Monoclinic-P</span></b> and do <b style='mso-bidi-font-weight:
+normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
+minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
+mso-bidi-theme-font:minor-latin'>Cell Index/Refine/Index cell</span></b> in the
+<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>Unit Cells List</span></b> window. Progress
+will be much slower than for LaB<sub>6</sub> but oddly much faster than for
+kryptonite and suitable results may appear almost immediately. Watch the
+console window; the right answer will have an obviously large M20 (~900) and a
+volume of ~704Å<sup>3</sup> (10<sup>th</sup> column of console display). Once
+this is seen (it may take more than one try to get this) you can stop the
+indexing search by pressing <b style='mso-bidi-font-weight:normal'><span
+style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
+mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
+minor-latin'>Cancel</span></b> on the progress bar window. Notice the ‘<b
+style='mso-bidi-font-weight:normal'>keep’</b> column; this allows you to keep
+some solutions from one indexing run to the next. It may take more than one
+press to fully stop it. My result was </p>
+
+<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
+ id="Picture_x0020_31" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:525pt;
+ height:450pt;visibility:visible;mso-wrap-style:square'>
+ <v:imagedata src="Fit%20Peaks_files/image027.png" o:title=""/>
+</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
+src="Fit%20Peaks_files/image027.png" v:shapes="Picture_x0020_31"><![endif]><!--[if gte vml 1]><v:shape
+ id="Picture_x0020_32" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:527.25pt;
+ height:376.5pt;visibility:visible;mso-wrap-style:square'>
+ <v:imagedata src="Fit%20Peaks_files/image028.png" o:title=""/>
+</v:shape><![endif]--><![if !vml]><img border=0 width=703 height=502
+src="Fit%20Peaks_files/image028.png" v:shapes="Picture_x0020_32"><![endif]></span></p>
+
+<p class=MsoNormal>Notice there may be other equally good M20 results with
+different volumes; still other solutions may be obtained as you keep trying the
+indexing. Be sure to use <b style='mso-bidi-font-weight:normal'><span
+style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
+mso-hansi-theme-font:minor-latin'>Keep</span></b> to keep good ones as you try
+new indexing runs. The best solution is the one with the smaller volume and &#946;
+&gt; 90 deg. The plot shows every peak indexed including the weak peaks not
+selected for the peak fitting. Copy the best cell and try to refine it along
+with the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Zero offset</span></b>.
+I obtained an improved M20 ~1257 and slightly different lattice parameters. Try
+different space groups, pressing the <b style='mso-bidi-font-weight:normal'><span
+style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
+mso-hansi-theme-font:minor-latin'>Show <span class=SpellE>hkl</span> positions</span></b>
+each time to see which lines vanish. The correct space group is P2<sub>1</sub>.
+Armed with this information you can <b style='mso-bidi-font-weight:normal'><span
+style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
+mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
+minor-latin'>Make new phase</span></b> for the indexed cell (I called it ‘<b
+style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>sucrose</span></b>) and select <b
+style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b>
+from the GSAS-II data tree.</p>
+
+<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
+ id="Picture_x0020_34" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:545.25pt;
+ height:303.75pt;visibility:visible;mso-wrap-style:square'>
+ <v:imagedata src="Fit%20Peaks_files/image029.png" o:title=""/>
+</v:shape><![endif]--><![if !vml]><img border=0 width=727 height=405
+src="Fit%20Peaks_files/image029.png" v:shapes="Picture_x0020_34"><![endif]></span><span
+style='mso-spacerun:yes'> </span></p>
+
+<p class=MsoNormal>Notice that the lattice parameters and space group have been
+set for you. This concludes this exercise; <b style='mso-bidi-font-weight:normal'><span
+style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
+mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
+minor-latin'>Save</span></b> the project file as it is needed for the sucrose <b
+style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'><a href="Charge%20Flipping%20-%20sucrose.htm">Charge
+Flipping</a></span></b> exercise. The features of the <b style='mso-bidi-font-weight:
+normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
+minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
+mso-bidi-theme-font:minor-latin'>Phase Data</span></b> window will be presented
+in other exercises.</p>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
 
 </div>

trunk/help/Fit Peaks_files/filelist.xml

@@ -1 +1 @@
 <xml xmlns:o="urn:schemas-microsoft-com:office:office">
  <o:MainFile HRef="../Fit%20Peaks.htm"/>
- <o:File HRef="item0030.xml"/>
- <o:File HRef="props031.xml"/>
+ <o:File HRef="item0035.xml"/>
+ <o:File HRef="props036.xml"/>
  <o:File HRef="themedata.thmx"/>
  <o:File HRef="colorschememapping.xml"/>
@@ -29 +29 @@
  <o:File HRef="image023.png"/>
  <o:File HRef="image024.png"/>
+ <o:File HRef="image025.png"/>
+ <o:File HRef="image026.png"/>
+ <o:File HRef="image027.png"/>
+ <o:File HRef="image028.png"/>
+ <o:File HRef="image029.png"/>
  <o:File HRef="filelist.xml"/>
 </xml>