Changeset 588

Timestamp:

May 6, 2012 3:14:22 PM (11 years ago)

Author:

vondreele

Message:

 

Location:

trunk/help

Files:

• Calibration of an area detector in GSAS.htm (modified) (13 diffs)
• Calibration of an area detector in GSAS_files/filelist.xml (modified) (2 diffs)
• Calibration of an area detector in GSAS_files/image001.png (modified) (previous)
• Calibration of an area detector in GSAS_files/image006.png (modified) (previous)
• Calibration of an area detector in GSAS_files/image007.png (modified) (previous)
• Calibration of an area detector in GSAS_files/image008.png (modified) (previous)
• Calibration of an area detector in GSAS_files/image009.png (modified) (previous)
• Calibration of an area detector in GSAS_files/image010.png (modified) (previous)
• Fit Peaks.htm (modified) (18 diffs)
• Fit Peaks_files/filelist.xml (modified) (1 diff)
• Fit Peaks_files/themedata.thmx (modified) (previous)
• Integration of area detector data in GSAS.htm (modified) (30 diffs)
• Integration of area detector data in GSAS_files/filelist.xml (modified) (1 diff)
• Integration of area detector data in GSAS_files/themedata.thmx (modified) (previous)
• Starting GSAS.htm (modified) (25 diffs)
• Starting GSAS_files/filelist.xml (modified) (1 diff)
• Starting GSAS_files/image002.jpg (modified) (previous)
• Starting GSAS_files/themedata.thmx (modified) (previous)
• gsasII.html (modified) (62 diffs)
• gsasII.html - Shortcut.lnk (deleted)
• gsasII_files/filelist.xml (modified) (1 diff)
• gsasII_files/props011.xml (modified) (1 diff)
• gsasII_files/themedata.thmx (modified) (previous)

trunk/help/Calibration of an area detector in GSAS.htm

@@ -25 +25 @@
   <o:Author>Von Dreele</o:Author>
   <o:LastAuthor>Von Dreele</o:LastAuthor>
-  <o:Revision>4</o:Revision>
-  <o:TotalTime>86</o:TotalTime>
+  <o:Revision>11</o:Revision>
+  <o:TotalTime>120</o:TotalTime>
   <o:Created>2012-05-04T19:00:00Z</o:Created>
-  <o:LastSaved>2012-05-04T21:08:00Z</o:LastSaved>
+  <o:LastSaved>2012-05-05T17:10:00Z</o:LastSaved>
   <o:Pages>4</o:Pages>
-  <o:Words>910</o:Words>
-  <o:Characters>5188</o:Characters>
+  <o:Words>709</o:Words>
+  <o:Characters>4045</o:Characters>
   <o:Company>Argonne National Laboratory</o:Company>
-  <o:Lines>43</o:Lines>
-  <o:Paragraphs>12</o:Paragraphs>
-  <o:CharactersWithSpaces>6086</o:CharactersWithSpaces>
+  <o:Lines>33</o:Lines>
+  <o:Paragraphs>9</o:Paragraphs>
+  <o:CharactersWithSpaces>4745</o:CharactersWithSpaces>
   <o:Version>14.00</o:Version>
  </o:DocumentProperties>
@@ -72 +72 @@
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 intentionally tilted at 45 degrees, are used. Note that menu entries are listed
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-    <p class=MsoNormal>========================================================================<br>
-    <span style='mso-spacerun:yes'>               </span>General Structure
-    Analysis System-II<br>
-    <span style='mso-spacerun:yes'>             </span>by Robert B. Von <span
-    class=SpellE>Dreele</span> and Brian H. Toby<br>
-    <span style='mso-spacerun:yes'>      </span><span
-    style='mso-spacerun:yes'>         </span>Argonne National Laboratory(C),
-    2010<br>
-    <span style='mso-spacerun:yes'> </span>This product includes software
-    developed by the <span class=SpellE>UChicago</span> Argonne, LLC,<br>
-    <span style='mso-spacerun:yes'>            </span>as Operator of Argonne
-    National Laboratory.<br>
-    ========================================================================<br>
-    d:\pyGSAS&gt;python d:\pyGSAS\\GSASII.py<br>
-    Available python module versions for GSASII<span class=GramE>:</span><br>
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-    <span class=SpellE>wxpython</span>:<span style='mso-spacerun:yes'>   
-    </span>2.8.10.1<br>
-    <span class=SpellE>matplotlib</span>:<span style='mso-spacerun:yes'> 
-    </span>1.0.1<br>
-    <span class=SpellE>numpy</span>:<span style='mso-spacerun:yes'>      
-    </span>1.5.1<br>
-    <span class=SpellE>scipy</span>:<span style='mso-spacerun:yes'>      
-    </span>0.9.0rc2<br>
-    OpenGL:<span style='mso-spacerun:yes'>      </span>3.0.1<br>
-    Max threads<span style='mso-spacerun:yes'>  </span>2<br>
-    This is GSAS-II version:<span style='mso-spacerun:yes'>      </span>0.1.5<o:p></o:p></p>
-    </div>
-    <![if !mso]></td>
-   </tr>
-  </table>
-  <![endif]></v:textbox>
- <w:wrap type="none"/>
- <w:anchorlock/>
-</v:shape><![endif]--><![if !vml]><img width=601 height=396
-src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image001.png"
-alt="Text Box: ========================================================================&#13;&#10;               General Structure Analysis System-II&#13;&#10;             by Robert B. Von Dreele and Brian H. Toby&#13;&#10;               Argonne National Laboratory(C), 2010&#13;&#10; This product includes software developed by the UChicago Argonne, LLC,&#13;&#10;            as Operator of Argonne National Laboratory.&#13;&#10;========================================================================&#13;&#10;d:\pyGSAS&gt;python d:\pyGSAS\\GSASII.py&#13;&#10;Available python module versions for GSASII:&#13;&#10;python:      2.7.1&#13;&#10;wxpython:    2.8.10.1&#13;&#10;matplotlib:  1.0.1&#13;&#10;numpy:       1.5.1&#13;&#10;scipy:       0.9.0rc2&#13;&#10;OpenGL:      3.0.1&#13;&#10;Max threads  2&#13;&#10;This is GSAS-II version:      0.1.5&#13;&#10;"
-v:shapes="Text_x0020_Box_x0020_2"><![endif]><!--[if gte vml 1]><v:shapetype
+in bold face below 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'>Help/About
+GSAS-II</span></b>, which lists first the name of the menu (here <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'>Help</span></b>) and second the name of the entry in the menu
+(here <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'>About GSAS-II</span></b>).</p>
+
+<p class=MsoNormal><span style='font-size:11.0pt'><o:p>&nbsp;</o:p></span></p>
+
+<p class=MsoNormal>If you have not done so already, <u><span style='color:#0070C0'><a
+href="Starting%20GSAS.htm">start GSAS-II</a></span></u>.<o:p></o:p></p>
+
+<h1>Step 1: read in the data file</h1>
+
+<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Use the <b
+style='mso-bidi-font-weight:normal'>Data/Read image data</b> menu item to read
+the data file into the current GSAS-II project. </p>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
+
+<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
  id="_x0000_t75" coordsize="21600,21600" o:spt="75" o:preferrelative="t"
  path="m@4@5l@4@11@9@11@9@5xe" filled="f" stroked="f">
@@ -935 +865 @@
  <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
  <o:lock v:ext="edit" aspectratio="t"/>
-</v:shapetype><![endif]--><!--[if mso & !supportInlineShapes & supportFields]><v:shape
- id="_x0000_i1034" type="#_x0000_t75" style='width:443.25pt;height:289.2pt'>
- <v:imagedata croptop="-65520f" cropbottom="65520f"/>
-</v:shape><span style='mso-element:field-end'></span><![endif]--></p>
-
-<p class=MsoNormal>The GSAS-II program has now been started and an empty
-project file is created. The project file contains all data and results related
-to the project you are working on. (Exception: image files are not stored in
-the project; to save space only the file name is saved.) <o:p></o:p></p>
-
-<p class=MsoNormal><span style='mso-spacerun:yes'> </span>You should see three
-windows, two of which are empty. One, in the upper right, is labeled GSASII
-data tree, the second, immediately under the first is labeled GSAS-II data
-display and the third on the left is labeled GSAS-II Plots. These windows may
-be moved anywhere on the screen. On Linux and Windows a menu bar appears at the
-top <span class=GramE>of <span style='mso-spacerun:yes'> </span>the</span> data
-tree and data display windows; on a Mac these menus will appear in the system
-menu bar location (usually at the screen top) depending on which GSAS-II window
-has the focus. <o:p></o:p></p>
-
-<h1>Step 3: read in the data file<o:p></o:p></h1>
-
-<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Use the <b
-style='mso-bidi-font-weight:normal'>Data/Read image data</b> menu item to read
-the data file into the current GSAS-II project. <o:p></o:p></p>
-
-<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
- id="Picture_x0020_1" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:225pt;
- height:204.75pt;visibility:visible;mso-wrap-style:square'>
- <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image002.png"
+</v:shapetype><v:shape id="Picture_x0020_1" o:spid="_x0000_i1033" type="#_x0000_t75"
+ style='width:225pt;height:204.75pt;visibility:visible;mso-wrap-style:square'>
+ <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image001.png"
   o:title="" croptop="9965f" cropbottom="37297f" cropleft="53272f" cropright="5473f"/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=300 height=273
-src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image003.jpg"
+src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image002.jpg"
 v:shapes="Picture_x0020_1"><![endif]></span><span
 style='mso-spacerun:yes'> </span></p>
 
 <p class=MsoNormal>A file selection dialog will be shown; its appearance will
-depend on your OS. Change the search directory if necessary and then select the
-file </p>
-
-<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><i style='mso-bidi-font-style:
-normal'>La_hex_+45deg-<span class=GramE>00015.tif<span style='font-weight:normal;
-font-style:normal'> <span style='mso-spacerun:yes'> </span>and</span></span></i></b>
-press Open.<span style='mso-no-proof:yes'> </span></p>
+depend on your OS. Change the search 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/images</span></b>
+and then select the file </p>
+
+<p class=MsoNormal><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'>La_hex_+45deg-00015.tif</span></b>
+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>.<span style='mso-no-proof:yes'> <o:p></o:p></span></p>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
  id="Picture_x0020_6" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:225pt;
  height:203.25pt;visibility:visible;mso-wrap-style:square'>
- <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image006.png"
+ <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image003.png"
   o:title=""/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=300 height=271
-src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image006.png"
+src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image003.png"
 v:shapes="Picture_x0020_6"><![endif]></span></p>
 
-<p class=MsoNormal>At this point the data tree window will have several entries;
-the highlighted one specifies the contents of the data window as <b
-style='mso-bidi-font-weight:normal'>Image Controls</b><o:p></o:p></p>
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
+
+<p class=MsoNormal>At this point the data tree window will have several
+entries; the highlighted one specifies the contents of the data window 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'>Image Controls</span><o:p></o:p></b></p>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
  id="Picture_x0020_5" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:510.75pt;
  height:303pt;visibility:visible;mso-wrap-style:square'>
- <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image007.png"
+ <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image004.png"
   o:title=""/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=681 height=404
-src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image007.png"
+src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image004.png"
 v:shapes="Picture_x0020_5"><![endif]></span></p>
 
-<p class=MsoNormal><span style='mso-spacerun:yes'> </span><span class=GramE>the</span>
-plot window shows the image; notice the elliptical shape of the powder
-diffraction rings. The x marks the default beam location (image center); your
-calibration will correctly place it.<o:p></o:p></p>
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
+
+<p class=MsoNormal><span style='mso-spacerun:yes'> </span>The plot window shows
+the image; notice the elliptical shape of the powder diffraction rings. The
+blue <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;color:#4F81BD;mso-themecolor:accent1'>X</span></b> marks the
+default beam location (image center); your calibration will correctly place it.
+Also notice that the values shown in the plot window status bar (at bottom of
+plot window) change as you move the cursor over the plot; these values are at
+present in error as they are computed from the default calibration values. They
+will be correct after you finish the calibration.</p>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
 
 <p class=MsoNormal><span style='mso-spacerun:yes'> </span><span
@@ -1011 +936 @@
  o:spid="_x0000_i1030" type="#_x0000_t75" style='width:525pt;height:450pt;
  visibility:visible;mso-wrap-style:square'>
- <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image008.png"
+ <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image005.png"
   o:title=""/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
-src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image008.png"
-v:shapes="Picture_x0020_4"><![endif]></span><o:p></o:p></p>
-
-<h1><span style='mso-spacerun:yes'> </span>Step 4: Edit image parameters<o:p></o:p></h1>
+src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image005.png"
+v:shapes="Picture_x0020_4"><![endif]></span></p>
+
+<h1><span style='mso-spacerun:yes'> </span>Step 2: Edit image parameters</h1>
 
 <p class=MsoNormal><span style='mso-spacerun:yes'> </span>Note that, alas, very
 few image formats contain all of the important metadata about the image, so it
 needs to be added manually. In this case set the <b style='mso-bidi-font-weight:
-normal'>wavelength</b> to <b style='mso-bidi-font-weight:normal'>0.10798</b>.
-It is also helpful to change the display of the image so that it is easier to
-see the diffraction rings. Lowering the maximum intensity to 10,000 to 20,000
-counts will help (note that this can be done by moving the <span class=GramE>slider,</span>
-or by typing a value in the box and then clicking on another control or the
-typing the Enter/return key). You may also wish to select another color scheme
-using the Color bar selector. <o:p></o:p></p>
-
-<h1><span style='mso-spacerun:yes'> </span>Step 5: Calibrate<o:p></o:p></h1>
-
-<h3><span style='mso-spacerun:yes'> </span>First: <o:p></o:p></h3>
+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'>wavelength</span></b>
+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'>0.10798</span></b>. It is also helpful to change the display of
+the image so that it is easier to see the diffraction rings. Lowering the
+maximum intensity to 10,000 to 20,000 counts will help (note that this can be
+done by moving the <span class=GramE>slider,</span> or by typing a value in the
+box and then clicking on another control or 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;mso-bidi-theme-font:minor-latin'>Enter</span></b>
+or <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'>Tab</span></b> key). You may also wish to select another color
+scheme 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'>Color bar</span></b> selector. </p>
+
+<h1><span style='mso-spacerun:yes'> </span>Step 3: Calibrate</h1>
+
+<h3><span style='mso-spacerun:yes'> </span>First: </h3>
 
 <p class=MsoNormal><span style='mso-spacerun:yes'>   </span>Set the material
 used as a sample in the box labeled <span class=SpellE><b style='mso-bidi-font-weight:
-normal'>Calibrant</b></span>; select <b style='mso-bidi-font-weight:normal'>LaB6
-SRM660a</b><o:p></o:p></p>
-
-<h3><span style='mso-spacerun:yes'> </span>Second: <o:p></o:p></h3>
+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'>Calibrant</span></b></span>;
+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'>LaB6 SRM660a</span></b></p>
+
+<h3><span style='mso-spacerun:yes'> </span>Second: </h3>
 
 <p class=MsoNormal><span style='mso-spacerun:yes'>   </span>Use the <b
-style='mso-bidi-font-weight:normal'>Operations/Calibrate</b> menu item (note
-this menu is on the <b style='mso-bidi-font-weight:normal'>Image Controls</b>
-window or for the Mac, the <span class=GramE><b style='mso-bidi-font-weight:
-normal'>Image<span style='mso-spacerun:yes'>  </span>Controls</b></span> window
-must be active to place this into the system menu bar). At this point the
-status line on the bottom of the <b style='mso-bidi-font-weight:normal'>Image
-Controls</b> window changes with a prompt to select points for calibration.<o:p></o:p></p>
-
-<h3>Third: <o:p></o:p></h3>
+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/Calibrate</span></b> menu item (note this menu is 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'>Image Controls</span></b> window or for the Mac, the <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'>Image<span
+style='mso-spacerun:yes'>  </span>Controls</span></b></span> window must be
+active to place this into the system menu bar). At this point the status line
+on the bottom 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'>Image
+Controls</span></b> window changes with a prompt to select points for
+calibration.</p>
+
+<h3>Third: </h3>
 
 <p class=MsoNormal><span style='mso-spacerun:yes'>  </span>Use the left mouse
 button to click on at least five locations on the innermost ring. As each point
-is defined, a red &quot;+&quot; is added to the plot. You need not hit the ring
-exactly as the code will search for the locally highest point. <o:p></o:p></p>
+is defined, a red &quot;<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;color:red'>+</span></b>&quot;
+is added to the plot. You need not hit the ring exactly as the code will search
+for the locally highest point. </p>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
  id="Picture_x0020_8" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:525pt;
  height:450pt;visibility:visible;mso-wrap-style:square'>
- <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image009.png"
+ <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image006.png"
   o:title=""/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
-src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image009.png"
-v:shapes="Picture_x0020_8"><![endif]></span><o:p></o:p></p>
+src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image006.png"
+v:shapes="Picture_x0020_8"><![endif]></span></p>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
 
 <p class=MsoNormal><span style='mso-spacerun:yes'>  </span>To remove a point
@@ -1070 +1024 @@
 you have a single-button mouse, hold the Command (<span style='font-family:
 "Cambria Math","serif";mso-bidi-font-family:"Cambria Math"'>&#8984;</span>) key
-down and click]. <o:p></o:p></p>
-
-<h3><span style='mso-spacerun:yes'> </span>Fourth:<o:p></o:p></h3>
+down and click]. </p>
+
+<h3><span style='mso-spacerun:yes'> </span>Fourth:</h3>
 
 <p class=MsoNormal><span style='mso-spacerun:yes'>  </span>When done, press the
@@ -1078 +1032 @@
 if you have a single-button mouse, hold the Command (<span style='font-family:
 "Cambria Math","serif";mso-bidi-font-family:"Cambria Math"'>&#8984;</span>) key
-down and click].<o:p></o:p></p>
+down and click].</p>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
 
 <p class=MsoNormal><span style='mso-spacerun:yes'> </span>The calibration is
 then performed. First the rings are located and an ellipse is optimized for
 each ring. The indexed rings are first shown in red as the calibration proceeds
-and center of each ellipse is noted with a blue &quot;+&quot;. When all rings
-have been fitted, the entire ensemble of rings is refitted to the detector
-parameters and the rings are then shown in blue.<o:p></o:p></p>
+and center of each ellipse is noted with a blue &quot;<span style='color:#4F81BD;
+mso-themecolor:accent1'>+</span>&quot;. When all rings have been fitted, the
+entire ensemble of rings is refitted to the detector parameters and the rings
+are then shown in blue. The beam position (blue “<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;color:#4F81BD;mso-themecolor:accent1'>X</span>”) is now correctly
+positioned.</p>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
 
 <p class=MsoNormal><span style='mso-spacerun:yes'> </span><span
@@ -1091 +1053 @@
  o:spid="_x0000_i1028" type="#_x0000_t75" style='width:525pt;height:450pt;
  visibility:visible;mso-wrap-style:square'>
+ <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image007.png"
+  o:title=""/>
+</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
+src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image007.png"
+v:shapes="Picture_x0020_9"><![endif]></span><span
+style='mso-spacerun:yes'> </span></p>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
+
+<p class=MsoNormal>The derived calibration results 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-theme-font:
+minor-latin'>Image Controls</span></b> window.</p>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
+
+<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
+ id="Picture_x0020_12" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:510.75pt;
+ height:303pt;visibility:visible;mso-wrap-style:square'>
+ <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image008.png"
+  o:title=""/>
+</v:shape><![endif]--><![if !vml]><img border=0 width=681 height=404
+src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image008.png"
+v:shapes="Picture_x0020_12"><![endif]></span><span
+style='mso-spacerun:yes'> </span></p>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
+
+<p class=MsoNormal><span class=GramE>and</span> the console window shows
+details of the fit; a trial refinement for the wavelength is also given for you
+to consider.</p>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
+
+<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
+ id="Picture_x0020_14" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:396.75pt;
+ height:134.25pt;visibility:visible;mso-wrap-style:square'>
+ <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image009.png"
+  o:title=""/>
+</v:shape><![endif]--><![if !vml]><img border=0 width=529 height=179
+src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image009.png"
+v:shapes="Picture_x0020_14"><![endif]></span></p>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
+
+<p class=MsoNormal><span style='mso-spacerun:yes'> </span>To see the actual
+points selected by the program, 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'>show
+ring picks?</span></b> <span class=GramE>check</span> box </p>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
+
+<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
+ id="Picture_x0020_15" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:525pt;
+ height:450pt;visibility:visible;mso-wrap-style:square'>
  <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image010.png"
   o:title=""/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
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-v:shapes="Picture_x0020_9"><![endif]></span><span
-style='mso-spacerun:yes'> </span></p>
-
-<p class=MsoNormal>The derived calibration results are shown in the Image
-Controls window.<o:p></o:p></p>
-
-<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
- id="Picture_x0020_12" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:510.75pt;
- height:303pt;visibility:visible;mso-wrap-style:square'>
- <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image011.png"
-  o:title=""/>
-</v:shape><![endif]--><![if !vml]><img border=0 width=681 height=404
-src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image011.png"
-v:shapes="Picture_x0020_12"><![endif]></span><span
-style='mso-spacerun:yes'> </span></p>
-
-<p class=MsoNormal><span class=GramE>and</span> the console window shows
-details of the fit; a trial refinement for the wavelength is also given for you
-to consider.</p>
-
-<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
- id="Picture_x0020_14" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:396.75pt;
- height:134.25pt;visibility:visible;mso-wrap-style:square'>
- <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image012.png"
-  o:title=""/>
-</v:shape><![endif]--><![if !vml]><img border=0 width=529 height=179
-src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image012.png"
-v:shapes="Picture_x0020_14"><![endif]></span><o:p></o:p></p>
-
-<p class=MsoNormal><span style='mso-spacerun:yes'> </span>To see the actual
-points selected by the program, click on the &quot;show ring picks?&quot; check
-button <o:p></o:p></p>
-
-<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
- id="Picture_x0020_15" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:525pt;
- height:450pt;visibility:visible;mso-wrap-style:square'>
- <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image013.png"
-  o:title=""/>
-</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
-src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image013.png"
 v:shapes="Picture_x0020_15"><![endif]></span><span
-style='mso-spacerun:yes'> </span></p>
-
-<p class=MsoNormal>When this is done, it sometimes occurs that the points selected
-for the outermost ring are scattered between that and the next ring. This can
-be repaired by changing the pixel search range to 10 and using the <b
-style='mso-bidi-font-weight:normal'>Operations/Recalibrate</b> menu item.<o:p></o:p></p>
+style='mso-spacerun:yes'> </span><span style='color:#1F497D;mso-themecolor:
+text2'><o:p></o:p></span></p>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
+
+<p class=MsoNormal>When this is done, it sometimes occurs that the points
+selected for the outermost rings are scattered between that and the next ring.
+This can be repaired by changing the pixel search range to 10 and 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'>Operations/Recalibrate</span></b> menu item.</p>
 
 <p class=MsoNormal>Assuming that these calibration results will be applied to
 other images in the same GSAS-II project, click on <b style='mso-bidi-font-weight:
-normal'>Use as default for all images</b>. You may also save a copy of the
-calibration values to a file (<span class=SpellE><i style='mso-bidi-font-style:
-normal'>name</i><b style='mso-bidi-font-weight:normal'>.imctrl</b></span>) with
-the <b style='mso-bidi-font-weight:normal'>Operations/Save Controls</b> menu
-item. To save the project, including the now-derived calibration information,
-use the <b style='mso-bidi-font-weight:normal'>File/Save Project</b> menu item
-associated with the data tree window; as this project has not been saved before
-the file save dialog will need a file name. Don’t enter the extension; it will
-be set to “.<span class=SpellE>gpx</span>”.<o:p></o:p></p>
-
-<h2>Next step: <a href="Integration%20of%20area%20detector%20data%20in%20GSAS.htm">Integrate
-the Data</a></h2>
+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'>Use
+as default for all images</span></b>. You may also save a copy of the
+calibration values to a file <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 class=SpellE><i style='mso-bidi-font-style:normal'>name</i><b
+style='mso-bidi-font-weight:normal'>.imctrl</b></span></span>) 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'>Operations/Save Controls</span></b> menu item. To save the
+project, including the now-derived calibration information, 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'>File/Save</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'>Project</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:minor-latin'> </span>menu
+item associated with the data tree window; as this project has not been saved
+before the file save dialog will need a file name. Don’t enter the extension;
+it will be set 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'>.<span
+class=SpellE>gpx</span></span></b>”.</p>
+
+<h2>Next step: <span class=MsoHyperlink><span style='color:#0070C0'><a
+href="Integration%20of%20area%20detector%20data%20in%20GSAS.htm"><u>Integrate
+the Data</u></a></span></span></h2>
 
 </div>

trunk/help/Calibration of an area detector in GSAS_files/filelist.xml

@@ -4 +4 @@
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  <o:File HRef="image001.png"/>
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+ <o:File HRef="image002.jpg"/>
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@@ -11 +13 @@
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 </xml>

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   <o:Author>Von Dreele</o:Author>
   <o:LastAuthor>Von Dreele</o:LastAuthor>
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         {mso-style-name:"Title Char";
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-        {mso-style-name:"Heading 1 Char";
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+        mso-bidi-font-family:Tahoma;}
 span.SpellE
         {mso-style-name:"";
         mso-spl-e:yes;}
+span.GramE
+        {mso-style-name:"";
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         {mso-style-type:export-only;
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         mso-ansi-font-size:10.0pt;
         mso-bidi-font-size:10.0pt;
+        font-family:"Calibri","sans-serif";
         mso-ascii-font-family:Calibri;
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         {page:WordSection1;}
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@@ -677 +1115 @@
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 <![endif]--><!--[if gte mso 9]><xml>
- <o:shapedefaults v:ext="edit" spidmax="2050"/>
+ <o:shapedefaults v:ext="edit" spidmax="1026"/>
 </xml><![endif]--><!--[if gte mso 9]><xml>
  <o:shapelayout v:ext="edit">
@@ -684 +1122 @@
 </head>
 
-<body lang=EN-US style='tab-interval:.5in'>
+<body lang=EN-US link=blue vlink=purple style='tab-interval:.5in'>
 
 <div class=WordSection1>
 
-<h1><span style='mso-spacerun:yes'> </span>Fit Peaks/<span class=SpellE>Autoindexing</span>
-in GSAS-II </h1>
-
-<p class=MsoNormal>In this exercise you will use the GSAS-II program to search
-for a unit cell that matches a set of diffraction peaks -- a process known as
-auto-indexing. First peaks must be located and optimized and then indexing can be
-done.</p>
-
-<h2>Step 1: read in data</h2>
-
-<p class=MsoNormal>Download the sample data file and matching instrument
-parameter file from these links:</p>
-
-<p class=MsoNormal><span style='mso-spacerun:yes'>   
-</span>https://subversion.xor.aps.anl.gov/trac/pyGSAS/browser/Examples/powder%20data/11bmb_3844.fxye?format=raw</p>
-
-<p class=MsoNormal><span style='mso-spacerun:yes'>   
-</span>https://subversion.xor.aps.anl.gov/trac/pyGSAS/browser/Examples/powder%20data/11bmb_3844.prm?format=raw</p>
-
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>
-
-<p class=MsoNormal><span style='mso-spacerun:yes'>    </span>(One can also use
-this links<span style='mso-spacerun:yes'>    </span></p>
-
-<p class=MsoNormal><span style='mso-spacerun:yes'>   
-</span>https://subversion.xor.aps.anl.gov/pyGSAS/Examples/powder%20data/11bmb_3844.fxye
-and </p>
-
-<p class=MsoNormal><span style='mso-spacerun:yes'>   
-</span>https://subversion.xor.aps.anl.gov/pyGSAS/Examples/powder%20data/11bmb_3844.prm</p>
-
-<p class=MsoNormal><span style='mso-spacerun:yes'>    </span>to obtain the
-file, but this is more complex).</p>
-
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>
-
-<h2>Step 2: Start GSAS-II </h2>
-
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>
-
-<p class=MsoNormal><span style='mso-spacerun:yes'> </span>This is done in
-different ways, depending on your OS and how GSAS-II is installed.</p>
-
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>
-
-<p class=MsoNormal>=== Step 3: read in the data file ===</p>
-
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>
-
-<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Use the '''Data/Read
-powder data''' menu item to read the data file into the current GSAS-II
-project. </p>
+<h1>Fit Peaks/<span class=SpellE>Autoindexing</span> in GSAS-II </h1>
+
+<p class=MsoNormal>In this exercise you will use GSAS-II to search for a unit
+cell that matches a set of diffraction peaks -- a process known as
+auto-indexing. First peaks must be located and optimized and then indexing can
+be done.</p>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
+
+<p class=MsoNormal>If you have not done so already, <a
+href="Starting%20GSAS.htm">start GSAS-II</a>.</p>
+
+<h2>Step 1: read in the data file</h2>
+
+<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
+style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
+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'>Data/Read powder data</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>). It will also 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'>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:
+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
+file.</span></p>
+
+<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
+style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
+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:
+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:
+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>
+
+<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
+style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
+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.prm</span></b> instrument parameter file in the second
+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>. The 11BM-B
+instrument processing software automatically produced this file 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.</p>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></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>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
+
+<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
+ id="_x0000_t75" coordsize="21600,21600" o:spt="75" o:preferrelative="t"
+ path="m@4@5l@4@11@9@11@9@5xe" filled="f" stroked="f">
+ <v:stroke joinstyle="miter"/>
+ <v:formulas>
+  <v:f eqn="if lineDrawn pixelLineWidth 0"/>
+  <v:f eqn="sum @0 1 0"/>
+  <v:f eqn="sum 0 0 @1"/>
+  <v:f eqn="prod @2 1 2"/>
+  <v:f eqn="prod @3 21600 pixelWidth"/>
+  <v:f eqn="prod @3 21600 pixelHeight"/>
+  <v:f eqn="sum @0 0 1"/>
+  <v:f eqn="prod @6 1 2"/>
+  <v:f eqn="prod @7 21600 pixelWidth"/>
+  <v:f eqn="sum @8 21600 0"/>
+  <v:f eqn="prod @7 21600 pixelHeight"/>
+  <v:f eqn="sum @10 21600 0"/>
+ </v:formulas>
+ <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_i1047" 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=""/>
+</v:shape><![endif]--><![if !vml]><img border=0 width=300 height=250
+src="Fit%20Peaks_files/image001.png" v:shapes="Picture_x0020_1"><![endif]></span></p>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
+
+<p class=MsoNormal><span class=GramE>and</span> the plot window will show the
+powder pattern</p>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
+
+<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
+ id="Picture_x0020_2" o:spid="_x0000_i1046" type="#_x0000_t75" style='width:525pt;
+ height:450pt;visibility:visible;mso-wrap-style:square'>
+ <v:imagedata src="Fit%20Peaks_files/image002.png" o:title=""/>
+</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
+src="Fit%20Peaks_files/image002.png" v:shapes="Picture_x0020_2"><![endif]></span></p>
+
+<h2>Step 2: Select Limits </h2>
+
+<p class=MsoNormal><span style='mso-spacerun:yes'> </span>This pattern has much
+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>
+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>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
+
+<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
+ id="Picture_x0020_4" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:225pt;
+ height:120pt;visibility:visible;mso-wrap-style:square'>
+ <v:imagedata src="Fit%20Peaks_files/image003.png" o:title=""/>
+</v:shape><![endif]--><![if !vml]><img border=0 width=300 height=160
+src="Fit%20Peaks_files/image003.png" v:shapes="Picture_x0020_4"><![endif]></span></p>
+
+<h2>Step 3: Determine Peak Positions</h2>
+
+<p class=MsoListParagraph style='margin-left:39.0pt;mso-add-space: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'>1.<span
+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 to </p>
+
+<p class=MsoNormal><span style='mso-spacerun:yes'> </span><span class=GramE>zoom</span>
+in on the data that will be used for indexing. </p>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
+
+<p class=MsoListParagraph style='margin-left:39.0pt;mso-add-space: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'>2.<span
+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_5" o:spid="_x0000_i1044" 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"
+  cropbottom="-1f" cropleft="35827f" cropright="19224f"/>
+</v:shape><![endif]--><![if !vml]><img border=0 width=29 height=25
+src="Fit%20Peaks_files/image005.jpg" v:shapes="Picture_x0020_5"><![endif]></span>,
+then press the left mouse in one corner of the region to be used; holding the
+mouse button down, drag over the region to the opposite corner; a box will be
+drawn over the region to be zoomed. </p>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
+
+<p class=MsoListParagraph style='margin-left:39.0pt;mso-add-space: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'>3.<span
+style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
+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_6"
+ o:spid="_x0000_i1043" 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"
+  cropbottom="-1f" cropleft="35827f" cropright="19224f"/>
+</v:shape><![endif]--><![if !vml]><img border=0 width=31 height=27
+src="Fit%20Peaks_files/image006.jpg" v:shapes="Picture_x0020_6"><![endif]></span><span
+style='mso-spacerun:yes'> </span>button again to turn off the zoom mode. </p>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
+
+<p class=MsoListParagraphCxSpFirst style='margin-left:39.0pt;mso-add-space:
+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>
+
+<p class=MsoListParagraphCxSpMiddle><o:p>&nbsp;</o:p></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="_x0000_i1042"
+ 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="_x0000_i1042"><![endif]></span></p>
+
+<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
+auto'><o:p>&nbsp;</o:p></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>
+
+<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
+auto'><o:p>&nbsp;</o:p></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_i1041" 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=""/>
+</v:shape><![endif]--><![if !vml]><img border=0 width=535 height=350
+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'><o:p>&nbsp;</o:p></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=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
+auto'><o:p>&nbsp;</o:p></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>
+
+<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>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
+
+<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
+style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
+style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Refine
+the peak intensities and the background. These parameters have their refinement
+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:
+"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>
+
+<p class=MsoListParagraphCxSpMiddle><o:p>&nbsp;</o:p></p>
+
+<p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
+ id="Picture_x0020_8" o:spid="_x0000_i1040" 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>
+
+<p class=MsoListParagraphCxSpMiddle><o:p>&nbsp;</o:p></p>
+
+<p class=MsoListParagraphCxSpLast><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
+ id="Picture_x0020_9" o:spid="_x0000_i1039" 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>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
+
+<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
+style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
+style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Now
+add refinement of the peak positions. This can be done by clicking on all the refinement
+flags for the individual peaks or it is possible to set them all at the same
+time using this recipe: </p>
+
+<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
+auto;text-indent:-.25in;mso-list:l2 level2 lfo6'><![if !supportLists]><span
+style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
+style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
+class=GramE>single-click</span> on any value in the table to select it, for
+example the first peak position. A black box appears around the value. If the
+field if opened for editing (the box turns to blue), select a different item in
+the table.</p>
+
+<p class=MsoListParagraphCxSpLast style='margin-left:1.0in;mso-add-space:auto;
+text-indent:-.25in;mso-list:l2 level2 lfo6'><![if !supportLists]><span
+style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
+style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
+class=GramE>double-click</span> on the refine label above the peak position
+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:
+minor-latin'>n</span></b> would turn them off).</p>
 
 <p class=MsoNormal><span style='mso-spacerun:yes'> </span></p>
 
-<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Select the
-{{{11bmb_3844.fxye}}} data file in the first dialog and press Open.</p>
-
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>
-
-<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Select the
-{{{11bmb_3844.prm}}} instrument parameter file in the second dialog and press
-Open.</p>
-
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>
-
-<p class=MsoNormal><span style='mso-spacerun:yes'>    </span>At this point the
-data tree window will have several entries </p>
-
-<p class=MsoNormal><span style='mso-spacerun:yes'>   
-</span>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d3w2.png
-view]);</p>
-
-<p class=MsoNormal><span style='mso-spacerun:yes'>    </span>and the plot
-window will show the powder pattern</p>
-
-<p class=MsoNormal><span style='mso-spacerun:yes'>   
-</span>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d3w1.png
-view]).</p>
-
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>
-
-<p class=MsoNormal>=== Step 4: Select Data Range ===</p>
-
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>
-
-<p class=MsoNormal><span style='mso-spacerun:yes'> </span>This pattern has much
-more data than we need, so it is helpful to cut down the range. Click on the Limits
-item in the data tree. A new window is created. Use the &quot;changed&quot; row
-of entry boxes to set <span class=SpellE>Tmin</span> and <span class=SpellE>Tmax</span>
-to 4 and 30. You may also drag the limits 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-spacerun:yes'> </span>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d3w3.png
-view]). </p>
-
-<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Note the green and
-red vertical lines in the plot window move. </p>
-
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>
-
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>
-
-<p class=MsoNormal>=== Step 5: Determine Peak Positions ===</p>
-
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>
-
-<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Click on the Peak
-List item in the data tree. This creates an empty window of peak positions. At
-this point it is wise to </p>
-
-<p class=MsoNormal><span style='mso-spacerun:yes'> </span>zoom in on the data
-that will be used for indexing. This can be done by clicking on this button:</p>
-
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>
-
-<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Click on the
-magnification button: [[Image(d3z1.png)]], then press the left mouse in one
-corner of the region to be used; holding the mouse button down, drag over the
-region to the opposite corner. </p>
-
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>
-
-<p class=MsoNormal><span style='mso-spacerun:yes'> </span>'''Important:'''
-Click on the magnification [[Image(d3z1.png)]] button again to turn off the
-zoom mode. </p>
-
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>
-
-<p class=MsoNormal><span style='mso-spacerun:yes'>  </span>Using the left mouse
-button click on a data point near the top of each peak to be added to the peak
-list. As this is done, a line is </p>
-
-<p class=MsoNormal><span style='mso-spacerun:yes'>  </span>drawn in the plot
-window</p>
-
-<p class=MsoNormal><span style='mso-spacerun:yes'> 
-</span>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d3w4.png
-view]) and</p>
-
-<p class=MsoNormal><span style='mso-spacerun:yes'>  </span>peaks are added to
-the Peak List window</p>
-
-<p class=MsoNormal><span style='mso-spacerun:yes'> 
-</span>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d3w5.png
-view]). Note that if peaks are </p>
-
-<p class=MsoNormal><span style='mso-spacerun:yes'>  </span>not being added, you
-probably have not exited zoom mode.</p>
-
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>
-
-<p class=MsoNormal><span style='mso-spacerun:yes'>  </span>Once peaks in that
-region have been added, move to a new region of the pattern. This can be done
-by clicking on the shift button: [[Image(d3z2.png)]]. Dragging with the left
-mouse will shift the data to follow the mouse. Clicking with the right button (on
-the Mac, control + mouse) and moving up increases the vertical scale and to the
-right increases the horizontal scale.<span style='mso-spacerun:yes'> 
-</span>'''Important:''' Click on the shift [[Image(d3z2.png)]] button again to
-turn off this mode. </p>
-
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>
-
-<p class=MsoNormal><span style='mso-spacerun:yes'>  </span>Again, using the
-left mouse button, click on the tops of more peaks to be added to the peak
-list. Note that if peaks are </p>
-
-<p class=MsoNormal><span style='mso-spacerun:yes'>  </span>not being added, you
-probably have not exited shift mode.</p>
-
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>
-
-<p class=MsoNormal><span style='mso-spacerun:yes'>  </span>Add approximately 24
-peaks total to the peak list. 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=MsoNormal><o:p>&nbsp;</o:p></p>
-
-<p class=MsoNormal>=== Step 6: Refine Peak Positions ===</p>
-
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>
-
-<p class=MsoNormal>First, refine the peak intensities and the background. These
-parameters have their refinement flag turned on by default. Use the menu item
-'''Peak Fitting/LSQ !<span class=SpellE>PeakFit</span>'''. A window will show
-the progress of the refinement and will close when the least squares is
-complete. A summary of the refinement is shown on the console window as well.</p>
-
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>
-
-<p class=MsoNormal>Second, add refinement of the peak positions. This can be
-done by clicking on all the refinement flags for the individual peaks or it is
-possible to set them all at the same time using this recipe: </p>
-
-<p class=MsoNormal><span style='mso-spacerun:yes'> </span>* single-click on any
-value in the table to select it, for example the first peak position. A black
-box appears around the value. If the field if opened for editing (the box turns
-to blue), select a different item in the table.</p>
-
-<p class=MsoNormal><span style='mso-spacerun:yes'> </span>* double-click on the
-refine label above the peak position check-boxes. The entire column of
-checkboxes is highlighted in blue. Press the y key to turn on all refinement
-flags (n would turn them off).</p>
+<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
+style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
+style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>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:"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><span style='mso-spacerun:yes'> </span></p>
 
-<p class=MsoNormal>Third, repeat the refinement using the '''Peak Fitting/LSQ !<span
-class=SpellE>PeakFit</span>''' menu item.</p>
-
-<p class=MsoNormal><span style='mso-spacerun:yes'> </span></p>
-
-<p class=MsoNormal>Fourth, select peak widths for refinement. This can be done
-by refining sigma (Gaussian width) and/or gamma (Lorentzian width) for
-individual peaks, but here we constrain the peaks to follow an instrumental
-broadening equation. Select the Instrumental Parameters item in the data tree. </p>
-
-<p class=MsoNormal>This opens a window for peak profile terms</p>
-
-<p class=MsoNormal>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d3w6.png
-view]). </p>
-
-<p class=MsoNormal>Select the refine flag checkbox for Gaussian U, V, W,
-Lorentzian X, Y and the asymmetry parameter SH/L. </p>
-
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>
-
-<p class=MsoNormal>Fifth, repeat the refinement. First click on the Peak List
-item in the data tree and then refine using the '''Peak Fitting/LSQ !<span
-class=SpellE>PeakFit</span>''' menu item. At this point a good fit should be
-seen by zooming in on individual peaks. (For example see </p>
-
-<p class=MsoNormal>[https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d3w7.png
-this]). The <span class=SpellE>Rwp</span> is ~6% as shown on the console
-window.</p>
-
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>
-
-<p class=MsoNormal>=== Prepare Indexing Peak List ===</p>
-
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>
+<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![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]>Now,
+select peak widths for refinement. This can be done by refining sigma (Gaussian
+width) and/or gamma (Lorentzian width) for individual peaks, but here we can
+constrain the peaks to follow an instrumental broadening equation. 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'>Instrumental Parameters</span></b> item in the data tree. This
+opens a window for peak profile terms<br>
+<br>
+<span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_10"
+ o:spid="_x0000_i1038" 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=""/>
+</v:shape><![endif]--><![if !vml]><img border=0 width=563 height=206
+src="Fit%20Peaks_files/image011.png" v:shapes="Picture_x0020_10"><![endif]></span></p>
+
+<p class=MsoListParagraphCxSpMiddle><o:p>&nbsp;</o:p></p>
+
+<p class=MsoListParagraphCxSpLast>The plot window shows the resolution curves
+corresponding to the values of the Gaussian U, V, W, Lorentzian X &amp; Y
+coefficients; ‘+’ marks show the individual values based on the sig &amp; gam
+values for the peaks in Peak List. Select the refine flag checkbox for Gaussian
+U, V, W, and Lorentzian X, Y. </p>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
+
+<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
+style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>5.<span
+style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Then,
+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>
+
+<p class=MsoListParagraphCxSpMiddle><o:p>&nbsp;</o:p></p>
+
+<p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
+ id="Picture_x0020_11" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:525pt;
+ height:450pt;visibility:visible;mso-wrap-style:square'>
+ <v:imagedata src="Fit%20Peaks_files/image012.png" o:title=""/>
+</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
+src="Fit%20Peaks_files/image012.png" v:shapes="Picture_x0020_11"><![endif]></span></p>
+
+<p class=MsoListParagraphCxSpMiddle><o:p>&nbsp;</o:p></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>
+
+<h2><span class=GramE>Step 5.</span> Prepare Indexing Peak List</h2>
 
 <p class=MsoNormal>A separate list of peaks is kept for use in <span
-class=SpellE>autoindexing</span>. This list is manipulated by clicking on the
-Index Peak List item in the data tree. In the initially empty window created by
-this action, use menu item '''Index Peaks Operations/Load''' to copy over the
-fitted peaks from the Peak List tree entry</p>
-
-<p class=MsoNormal>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d4w1.png
-view]). </p>
-
-<p class=MsoNormal>Note that by default all peaks are selected to be used. </p>
-
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>
-
-<p class=MsoNormal>=== Run <span class=SpellE>Autoindexing</span> ===</p>
-
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>
-
-<p class=MsoNormal>Select the Unit Cells List data item. This brings up a
-window for indexing and cell refinement options</p>
-
-<p class=MsoNormal>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d4w2.png
-view]). For the most rapid search (since we know the right answer), select
-Cubic-P and launch the search using menu item '''Cell Index/Index Cell'''. The
-search then runs and he 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
-window</p>
-
-<p class=MsoNormal>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d4w3.png
-view]). </p>
-
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>
-
-<p class=MsoNormal>=== Review Cell Choices === </p>
-
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>
-
-<p class=MsoNormal>Review the list of cells associated with the Unit Cells List
-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 8.312 A cell generates very many lines with no
-corresponding peaks </p>
-
-<p class=MsoNormal>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d4w4.png
-view])</p>
-
-<p class=MsoNormal>while the 2.939 A cell generates not enough lines to match
-all the peaks</p>
-
-<p class=MsoNormal>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d4w5.png
-view]). </p>
-
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>
-
-<p class=MsoNormal>=== Select/Refine Cell === </p>
-
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>
-
-<p class=MsoNormal>Select the top option, a 4.1568 A cell with M20 figure of
-merit of 2700. This indexes all peaks, though peak positions are not exactly
-perfect if one zooms in enough. Import the cell information using the '''Cell
-Index/Copy Cell''' menu option. Then optimize the cell by refining the lattice
-parameters and the two-theta zero: click on the refine checkbox next to the
-Zero offset value and then the '''Cell Index/Refine Cell''' menu option. The a
-cell parameter value shifts from 4.15679 to 4.15684 when zero is refined. </p>
-
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>
-
-<p class=MsoNormal>(Optional) Finally, use of the '''Cell Index/New phase'''
-menu option allows one to assign a phase with these lattice parameters to the
-data set (histogram). A name for the new phase is then requested. This adds a
-Phases entry to the data tree, as well as an entry for the new phase. This new
-phase can be used in future code.</p>
+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'>Peak List</span></b>.</p>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
+
+<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
+ id="Picture_x0020_12" o:spid="_x0000_i1036" 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>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
+
+<p class=MsoNormal>Note that by default all peaks are selected to be used. You
+may choose to not use a fitted peak (e.g. if suspected as from a contaminant).</p>
+
+<h2><span class=GramE>Step 6.</span> Run <span class=SpellE>Autoindexing</span></h2>
+
+<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>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
+
+<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
+ id="Picture_x0020_13" o:spid="_x0000_i1035" 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=""/>
+</v:shape><![endif]--><![if !vml]><img border=0 width=703 height=272
+src="Fit%20Peaks_files/image014.png" v:shapes="Picture_x0020_13"><![endif]></span></p>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
+
+<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>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
+
+<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
+ id="Picture_x0020_14" o:spid="_x0000_i1034" 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>
+
+<h2><span class=GramE>Step 7.</span> Review Cell Choices</h2>
+
+<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=2961.34) with a=5.87864 Å generates very many lines
+with no corresponding peaks</p>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
+
+<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
+ id="Picture_x0020_15" o:spid="_x0000_i1033" 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
+style='mso-spacerun:yes'> </span></p>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
+
+<p class=MsoNormal><span class=GramE>while</span> the (M20=609.02) cell with
+a=2.93932 Å generates not enough lines to match all the peaks</p>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
+
+<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
+ id="Picture_x0020_16" o:spid="_x0000_i1032" 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>
+
+<h2><span class=GramE>Step 8.</span> Select/Refine Cell</h2>
+
+<p class=MsoNormal>Select the cell with M20 = 2961.34 with a = 4.1568 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>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
+
+<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
+ id="Picture_x0020_17" o:spid="_x0000_i1031" 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>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></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>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></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
+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><o:p>&nbsp;</o:p></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
+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>
+
+<h1>2<sup>nd</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 the
+new mineral <span class=SpellE>jadarite</span> (aka “kryptonite”). 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-theme-font:minor-latin'>\Exercises\<span
+class=SpellE>krptonite</span>\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>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
+
+<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
+ id="Picture_x0020_18" o:spid="_x0000_i1030" 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>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></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 3 and 10.</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><o:p>&nbsp;</o:p></p>
+
+<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
+ id="Picture_x0020_19" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:525pt;
+ height:450pt;visibility:visible;mso-wrap-style:square'>
+ <v:imagedata src="Fit%20Peaks_files/image020.png" o:title=""/>
+</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
+src="Fit%20Peaks_files/image020.png" v:shapes="Picture_x0020_19"><![endif]></span></p>
+
+<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 Instrument parameters. You will be asked for a project file
+name at the first refinement (I used ‘<span class=SpellE>jadarite</span>’). 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 U, V, W, X, Y model can accommodate. 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-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>
+
+<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-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. It may take more than one press to fully stop it.
+My result was </p>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
+
+<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
+ id="Picture_x0020_20" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:527.25pt;
+ height:376.5pt;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=703 height=502
+src="Fit%20Peaks_files/image021.png" v:shapes="Picture_x0020_20"><![endif]></span></p>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
+
+<p class=MsoNormal>Notice an equally good M20 result with twice the volume. The
+plot shows every peak indexed including a couple of weak peaks not selected for
+the peak fitting.</p>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></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><o:p>&nbsp;</o:p></p>
+
+<p class=MsoNormal>Although the weak peak at 2<span style='font-family:Symbol'>Q</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 ‘kryptonite’) and set
+the space group in the Phase Data for kryptonite window.</p>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></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><o:p>&nbsp;</o:p></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><o:p>&nbsp;</o:p></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;
+ height:209.25pt;visibility:visible;mso-wrap-style:square'>
+ <v:imagedata src="Fit%20Peaks_files/image024.png" o:title=""/>
+</v:shape><![endif]--><![if !vml]><img border=0 width=445 height=279
+src="Fit%20Peaks_files/image024.png" v:shapes="Picture_x0020_23"><![endif]></span></p>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
+
+<p class=MsoNormal>This concludes this exercise. The features of the Phase Data
+window will be presented in other exercises.</p>
 
 </div>

trunk/help/Fit Peaks_files/filelist.xml

@@ -3 +3 @@
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trunk/help/Integration of area detector data in GSAS.htm

@@ -8 +8 @@
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   <o:Author>Von Dreele</o:Author>
   <o:LastAuthor>Von Dreele</o:LastAuthor>
-  <o:Revision>7</o:Revision>
-  <o:TotalTime>91</o:TotalTime>
+  <o:Revision>9</o:Revision>
+  <o:TotalTime>102</o:TotalTime>
   <o:Created>2012-05-04T20:46:00Z</o:Created>
-  <o:LastSaved>2012-05-05T14:48:00Z</o:LastSaved>
+  <o:LastSaved>2012-05-05T16:23:00Z</o:LastSaved>
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   <o:Company>Argonne National Laboratory</o:Company>
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 detector at APS 11-ID-C with a wavelength 0.10798 A, where the detector was
 intentionally tilted at 45 degrees, are used. Note that menu entries are listed
-in <b style='mso-bidi-font-weight:normal'>bold face</b> below as <b
-style='mso-bidi-font-weight:normal'>Help/About GSAS-II</b>, which lists first
-the name of the menu (here <b style='mso-bidi-font-weight:normal'>Help</b>) and
-second the name of the entry in the menu (here <b style='mso-bidi-font-weight:
-normal'>About GSAS-II</b>).</p>
+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'>bold face</span></b> below 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'>Help/About
+GSAS-II</span></b>, which lists first the name of the menu (here <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'>Help</span></b>) and second the name of the entry in the menu
+(here <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'>About GSAS-II</span></b>).</p>
 
 <h2>Prerequisite:<span style='mso-spacerun:yes'>  </span><a
@@ -971 +991 @@
 
 <p class=MsoNormal>This assumes that an image data set has been read in and
-calibration results have been derived, see the<span style='mso-spacerun:yes'> 
-</span><a href="Calibration%20of%20an%20area%20detector%20in%20GSAS.htm">Calibration
-Demo</a></p>
+calibration results have been derived, see the <a
+href="Calibration%20of%20an%20area%20detector%20in%20GSAS.htm">Calibration Demo</a></p>
 
 <h2>Step 1: Clear calibration plot</h2>
@@ -979 +998 @@
 <p class=MsoNormal>Assuming the previous step was calibration, the image plot
 will show the located rings and possibly all the picked points. These are no
-longer needed. The <b style='mso-bidi-font-weight:normal'>Image Controls/Clear
-Calibration</b> menu entry removes these from the plot, but<u> does not clear
-the calibration results</u>. Use of this menu item is not required, but does
-speed future display of results. </p>
+longer needed. 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'>Image
+Controls/Clear Calibration</span></b> menu entry removes these from the plot,
+but<u> does not clear the calibration results</u>. Use of this menu item is not
+required, but does speed future display of results. </p>
 
 <h2>Step 2: Integration Settings</h2>
 
 <p class=MsoNormal>In the simplest case, all that is needed is to click on the <b
-style='mso-bidi-font-weight:normal'>Do full integration?</b> check box and
-adjust the inner and outer 2-theta values with the <b style='mso-bidi-font-weight:
-normal'>Inner 2-theta</b> and<b style='mso-bidi-font-weight:normal'> Outer
-2-theta</b> controls. Change the limits to 1 and 7 for this data. Note that
-changes are displayed when numbers are placed in the boxes only after pressing
-return or by clicking on some other item in the window or by pressing the tab key.
-</p>
+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'>Do full integration?</span></b> <span class=GramE>check</span> box
+and adjust the inner and outer 2-theta values 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'>Inner
+2-theta</span></b> and<b style='mso-bidi-font-weight:normal'> </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'>Outer 2-theta</span></b> controls. Change the limits 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'>1</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'>7</span></b>
+for this data. Note that changes are displayed when numbers are placed in the
+boxes only after pressing return or tab key or by clicking on some other item
+in the window.</p>
+
+<p class=MsoNormal><span style='mso-spacerun:yes'> </span></p>
 
 <p class=MsoNormal>It is helpful to see the two-theta limits on the plot
 visually, while adjusting the two-theta range. This is done by clicking on the <b
-style='mso-bidi-font-weight:normal'>Show integration limits?</b> check box.
-Note that inner limit is shown as a green ellipse at 2deg and the outer is
+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 integration limits?</span></b> <span class=GramE>check</span>
+box. Note that inner limit is shown as a green ellipse at 2deg and the outer is
 shown as a red ellipse at 5deg by default. These limits may also be dragged to
 the desired values; a small popup window shows the value. </p>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
@@ -1027 +1065 @@
   o:title=""/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=624 height=370
-src="Integration%20of%20area%20detector%20data%20in%20GSAS_files/image008.png"
+src="Integration%20of%20area%20detector%20data%20in%20GSAS_files/image002.png"
 v:shapes="Picture_x0020_2"><![endif]></span></p>
 
 <h3>Other useful controls:</h3>
 
-<p class=MsoNormal><b style='mso-bidi-font-weight:normal'>Azimuth offset</b>:
-The image vertical axis (from the beam center, going down) is labeled with the
-azimuth value placed in the <b style='mso-bidi-font-weight:normal'>Azimuth
-offset</b> box. This is usually zero.</p>
-
-<p class=MsoNormal><b style='mso-bidi-font-weight:normal'>Start/End azimuth</b>:
-The integration is started at the Start azimuth angle in the left box, and when
-the <b style='mso-bidi-font-weight:normal'>Do full integration?</b> checkbox is
-not checked, the integration will be run only to the maximum value specified.
-When the range is less than 360 degrees, the integration range will be shown
-(if selected) with the high and low limits plotted and only segments of the max
-and min ellipses drawn. These limits may also be dragged on the plot to desired
-locations.</p>
-
-<p class=MsoNormal><b style='mso-bidi-font-weight:normal'>Number of 2-theta
-bins</b>: The resulting 1-D powder pattern after integration will consist of
-this many points. This number should be on the order of the number of pixels in
-one direction (since resolution cannot be much better than this) or less, if
-instrumental resolution does not require that many points.</p>
-
-<p class=MsoNormal>Some trial and error may be needed, but there should more
-than 6 points across each peak full-width-at-half-maximum (FWHM) in the final
-pattern to be useful for further analysis.</p>
-
-<p class=MsoNormal><b style='mso-bidi-font-weight:normal'>Number of azimuth
-bins</b>: In cases where the diffraction experiment shows changes as a function
-of azimuthal angle, the integration can be performed as a function of angle.
-This number specifies the number of bins to use by azimuthal angle. The process
-of breaking up the integration in this way is sometimes called
-&quot;caking&quot; since the integration region grows with distance from the
-beam-center, with a shape like a slice of cake or pie. When more than one
+<p class=MsoNormal><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'>Azimuth
+offset</span></b>: The image vertical axis (from the beam center, going down)
+is labeled with the azimuth value placed 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'>Azimuth
+offset</span></b> box. This is usually zero unless the image plate has been
+rotated about its normal axis.</p>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
+
+<p class=MsoNormal><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'>Start/End
+azimuth</span></b>: The integration is started at the Start azimuth angle in
+the left box, and when 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'>Do full
+integration?</span></b> <span class=GramE>checkbox</span> is not checked, the
+integration will be run only to the maximum value specified. When the range is
+less than 360 degrees, the integration range will be shown (if selected) with
+the high and low limits plotted and only segments of the max and min ellipses
+drawn. These limits may also be dragged on the plot to desired locations.</p>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
+
+<p class=MsoNormal><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'>Number of
+2-theta bins</span></b>: The resulting 1-D powder pattern after integration
+will consist of this many points. This number should be on the order of the
+number of pixels in one direction (since resolution cannot be much better than
+this) or less, if instrumental resolution and sample broadening does not
+require that many points. Some trial and error may be needed, but there should
+more than 6 points across each peak full-width-at-half-maximum (FWHM) in the
+final pattern to be useful for further analysis.</p>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
+
+<p class=MsoNormal><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'>Number of
+azimuth bins</span></b>: In cases where the diffraction experiment shows
+changes as a function of azimuthal angle, the integration can be performed as a
+function of angle. This number specifies the number of bins to use by azimuthal
+angle. The process of breaking up the integration in this way is sometimes
+called &quot;caking&quot; since the integration region grows with distance from
+the beam-center, with a shape like a slice of cake or pie. When more than one
 azimuthal bin is used, the regions are shown in the plot with dashed lines,
 when the Show integration limits?&quot; check box is checked. </p>
 
-<p class=MsoNormal><b style='mso-bidi-font-weight:normal'>Background Image </b>and<b
-style='mso-bidi-font-weight:normal'> Multiplier</b>: You can designate a
-previously read in image as <b style='mso-bidi-font-weight:normal'>Background</b>
-which will then be used to modify each data image as they are integrated. Note
-that the <b style='mso-bidi-font-weight:normal'>Multiplier</b> must be negative
-for it to be subtracted. Note that all images used in this way must be exactly
-the same format (number of pixels &amp; pixel size).</p>
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
+
+<p class=MsoNormal><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'>Background
+Image</span> </b>and<b style='mso-bidi-font-weight:normal'> </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'>Multiplier</span></b>: You can designate a previously read in
+image as background which will then be used to modify each data image as they
+are integrated. Note that 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'>Multiplier</span></b>
+must be negative for it to be subtracted. Note that all images used in this way
+must be exactly the same format (number of pixels &amp; pixel size).</p>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
@@ -1080 +1146 @@
   o:title=""/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=624 height=535
-src="Integration%20of%20area%20detector%20data%20in%20GSAS_files/image009.png"
+src="Integration%20of%20area%20detector%20data%20in%20GSAS_files/image004.png"
 v:shapes="Picture_x0020_1"><![endif]></span></p>
 
@@ -1086 +1152 @@
 
 <p class=MsoNormal><span style='mso-spacerun:yes'> </span>Use the <b
-style='mso-bidi-font-weight:normal'>Image Operations/Integrate</b> image data
-menu item to start the integration. This will take at least a few seconds. If
-multiple images have been read in, the <b style='mso-bidi-font-weight:normal'>Integrate
-All</b> menu item can be used. This is most useful when the <b
-style='mso-bidi-font-weight:normal'>Use as Default</b> option is in use for one
-image.</p>
+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'>Image Operations/Integrate</span></b> image data menu item to
+start the integration. This will take at least a few seconds. If multiple
+images have been read 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'>Integrate All</span></b>
+menu item can be used. This is most useful when 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'>Use
+as Default</span></b> option is in use for one image.</p>
 
 <p class=MsoNormal><span style='mso-spacerun:yes'> </span>At this point the
 data tree window will have new entries as each azimuthal &quot;slice&quot;
 added to the data tree as a powder pattern</p>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
@@ -1107 +1180 @@
 style='mso-spacerun:yes'> </span></p>
 
-<p class=MsoNormal>two plots are added to the plot window: One (with tab 2D
-Integration) shows the diffraction intensity as a function of both 2-theta and
-(when there is more than one azimuthal integration region) azimuthal angle</p>
+<p class=MsoNormal>Two plots are added to the plot window: One (with tab <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'>2D Integration</span></b>) shows the diffraction intensity as a function
+of both 2-theta and (when there is more than one azimuthal integration region)
+azimuthal angle.</p>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
@@ -1119 +1197 @@
 src="Integration%20of%20area%20detector%20data%20in%20GSAS_files/image006.png"
 v:shapes="Picture_x0020_4"><![endif]></span><span
-style='mso-spacerun:yes'> </span>c</p>
-
-<p class=MsoNormal>and a conventional 1-D powder pattern(s) for each
-&quot;slice&quot;</p>
+style='mso-spacerun:yes'> </span></p>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
+
+<p class=MsoNormal><span class=GramE>and</span> a conventional 1-D powder
+pattern(s) for each &quot;slice&quot;</p>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
@@ -1133 +1215 @@
 v:shapes="Picture_x0020_5"><![endif]></span></p>
 
-<p class=MsoNormal>Again you should save the project with <b style='mso-bidi-font-weight:
-normal'>File/Save project</b> on the main GSAS-II data tree menu.</p>
-
-<h2>Next demo: <a href="Fit%20Peaks.htm">Fit Peaks and <span class=SpellE>Autoindexing</span></a></h2>
-
 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
 
+<p class=MsoNormal>Again you could save the project with <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/Save
+project</span></b> on the main <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> menu although it is not needed for any further tutorials.</p>
+
+<h2>Next demo: <a href="Fit%20Peaks.htm"><span style='color:windowtext;
+text-decoration:none;text-underline:none'>Fit Peaks and <span class=SpellE>Autoindexing</span></span></a></h2>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
+
 </div>
 

trunk/help/Integration of area detector data in GSAS_files/filelist.xml

@@ -4 +4 @@
  <o:File HRef="colorschememapping.xml"/>
  <o:File HRef="image001.png"/>
- <o:File HRef="image008.png"/>
+ <o:File HRef="image002.png"/>
  <o:File HRef="image003.png"/>
- <o:File HRef="image009.png"/>
+ <o:File HRef="image004.png"/>
  <o:File HRef="image005.png"/>
  <o:File HRef="image006.png"/>

trunk/help/Starting GSAS.htm

@@ -8 +8 @@
 <meta http-equiv=Content-Type content="text/html; charset=windows-1252">
 <meta name=ProgId content=Word.Document>
-<meta name=Generator content="Microsoft Word 12">
-<meta name=Originator content="Microsoft Word 12">
+<meta name=Generator content="Microsoft Word 14">
+<meta name=Originator content="Microsoft Word 14">
 <link rel=File-List href="Starting%20GSAS_files/filelist.xml">
 <link rel=Edit-Time-Data href="Starting%20GSAS_files/editdata.mso">
@@ -23 +23 @@
   <o:Author>Von Dreele</o:Author>
   <o:LastAuthor>Von Dreele</o:LastAuthor>
-  <o:Revision>1</o:Revision>
-  <o:TotalTime>19</o:TotalTime>
+  <o:Revision>2</o:Revision>
+  <o:TotalTime>25</o:TotalTime>
   <o:Created>2012-05-05T14:50:00Z</o:Created>
-  <o:LastSaved>2012-05-05T15:21:00Z</o:LastSaved>
-  <o:Pages>2</o:Pages>
-  <o:Words>248</o:Words>
-  <o:Characters>1418</o:Characters>
-  <o:Lines>11</o:Lines>
+  <o:LastSaved>2012-05-05T15:36:00Z</o:LastSaved>
+  <o:Pages>1</o:Pages>
+  <o:Words>295</o:Words>
+  <o:Characters>1685</o:Characters>
+  <o:Lines>14</o:Lines>
   <o:Paragraphs>3</o:Paragraphs>
-  <o:CharactersWithSpaces>1663</o:CharactersWithSpaces>
-  <o:Version>12.00</o:Version>
+  <o:CharactersWithSpaces>1977</o:CharactersWithSpaces>
+  <o:Version>14.00</o:Version>
  </o:DocumentProperties>
 </xml><![endif]-->
-<link rel=dataStoreItem href="Starting%20GSAS_files/item0001.xml"
-target="Starting%20GSAS_files/props0002.xml">
+<link rel=dataStoreItem href="Starting%20GSAS_files/item0008.xml"
+target="Starting%20GSAS_files/props009.xml">
 <link rel=themeData href="Starting%20GSAS_files/themedata.thmx">
 <link rel=colorSchemeMapping href="Starting%20GSAS_files/colorschememapping.xml">
@@ -43 +43 @@
  <w:WordDocument>
   <w:SpellingState>Clean</w:SpellingState>
+  <w:GrammarState>Clean</w:GrammarState>
   <w:TrackMoves>false</w:TrackMoves>
   <w:TrackFormatting/>
@@ -342 +343 @@
  /* Font Definitions */
  @font-face
-        {font-family:"Cambria Math";
-        panose-1:2 4 5 3 5 4 6 3 2 4;
-        mso-font-charset:0;
-        mso-generic-font-family:roman;
-        mso-font-pitch:variable;
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-@font-face
         {font-family:Calibri;
         panose-1:2 15 5 2 2 2 4 3 2 4;
@@ -391 +385 @@
         font-weight:bold;}
 h2
-        {mso-style-priority:9;
-        mso-style-unhide:no;
+        {mso-style-noshow:yes;
+        mso-style-priority:9;
         mso-style-qformat:yes;
         mso-style-link:"Heading 2 Char";
@@ -407 +401 @@
         font-weight:bold;}
 h3
-        {mso-style-priority:9;
-        mso-style-unhide:no;
+        {mso-style-noshow:yes;
+        mso-style-priority:9;
         mso-style-qformat:yes;
         mso-style-link:"Heading 3 Char";
@@ -530 +524 @@
         color:gray;}
 p.MsoNoSpacing, li.MsoNoSpacing, div.MsoNoSpacing
-        {mso-style-priority:1;
+        {mso-style-noshow:yes;
+        mso-style-priority:1;
         mso-style-unhide:no;
         mso-style-qformat:yes;
@@ -542 +537 @@
         mso-fareast-theme-font:minor-fareast;}
 p.MsoListParagraph, li.MsoListParagraph, div.MsoListParagraph
-        {mso-style-priority:34;
+        {mso-style-noshow:yes;
+        mso-style-priority:34;
         mso-style-unhide:no;
         mso-style-qformat:yes;
@@ -557 +553 @@
         mso-fareast-theme-font:minor-fareast;}
 p.MsoListParagraphCxSpFirst, li.MsoListParagraphCxSpFirst, div.MsoListParagraphCxSpFirst
-        {mso-style-priority:34;
+        {mso-style-noshow:yes;
+        mso-style-priority:34;
         mso-style-unhide:no;
         mso-style-qformat:yes;
@@ -573 +570 @@
         mso-fareast-theme-font:minor-fareast;}
 p.MsoListParagraphCxSpMiddle, li.MsoListParagraphCxSpMiddle, div.MsoListParagraphCxSpMiddle
-        {mso-style-priority:34;
+        {mso-style-noshow:yes;
+        mso-style-priority:34;
         mso-style-unhide:no;
         mso-style-qformat:yes;
@@ -589 +587 @@
         mso-fareast-theme-font:minor-fareast;}
 p.MsoListParagraphCxSpLast, li.MsoListParagraphCxSpLast, div.MsoListParagraphCxSpLast
-        {mso-style-priority:34;
+        {mso-style-noshow:yes;
+        mso-style-priority:34;
         mso-style-unhide:no;
         mso-style-qformat:yes;
@@ -615 +614 @@
         text-decoration:underline;
         text-underline:single;}
-span.BalloonTextChar
-        {mso-style-name:"Balloon Text Char";
-        mso-style-noshow:yes;
-        mso-style-priority:99;
-        mso-style-unhide:no;
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-        mso-bidi-font-size:8.0pt;
-        font-family:"Tahoma","sans-serif";
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-        mso-fareast-theme-font:minor-fareast;
-        mso-hansi-font-family:Tahoma;
-        mso-bidi-font-family:Tahoma;}
-span.DocumentMapChar
-        {mso-style-name:"Document Map Char";
-        mso-style-noshow:yes;
-        mso-style-priority:99;
-        mso-style-unhide:no;
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-        mso-bidi-font-size:8.0pt;
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-        mso-ascii-font-family:Tahoma;
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-        mso-fareast-theme-font:minor-fareast;
-        mso-hansi-font-family:Tahoma;
-        mso-bidi-font-family:Tahoma;}
 span.Heading1Char
         {mso-style-name:"Heading 1 Char";
@@ -663 +632 @@
 span.Heading2Char
         {mso-style-name:"Heading 2 Char";
+        mso-style-noshow:yes;
         mso-style-priority:9;
         mso-style-unhide:no;
@@ -678 +648 @@
 span.Heading3Char
         {mso-style-name:"Heading 3 Char";
+        mso-style-noshow:yes;
         mso-style-priority:9;
         mso-style-unhide:no;
@@ -744 +715 @@
         mso-hansi-font-family:"Courier New";
         mso-bidi-font-family:"Courier New";}
+span.DocumentMapChar
+        {mso-style-name:"Document Map Char";
+        mso-style-noshow:yes;
+        mso-style-priority:99;
+        mso-style-unhide:no;
+        mso-style-locked:yes;
+        mso-style-link:"Document Map";
+        mso-ansi-font-size:8.0pt;
+        mso-bidi-font-size:8.0pt;
+        font-family:"Tahoma","sans-serif";
+        mso-ascii-font-family:Tahoma;
+        mso-fareast-font-family:"Times New Roman";
+        mso-fareast-theme-font:minor-fareast;
+        mso-hansi-font-family:Tahoma;
+        mso-bidi-font-family:Tahoma;}
+span.BalloonTextChar
+        {mso-style-name:"Balloon Text Char";
+        mso-style-noshow:yes;
+        mso-style-priority:99;
+        mso-style-unhide:no;
+        mso-style-locked:yes;
+        mso-style-link:"Balloon Text";
+        mso-ansi-font-size:8.0pt;
+        mso-bidi-font-size:8.0pt;
+        font-family:"Tahoma","sans-serif";
+        mso-ascii-font-family:Tahoma;
+        mso-fareast-font-family:"Times New Roman";
+        mso-fareast-theme-font:minor-fareast;
+        mso-hansi-font-family:Tahoma;
+        mso-bidi-font-family:Tahoma;}
+span.GSAS-IItextChar
+        {mso-style-name:"GSAS-II text Char";
+        mso-style-unhide:no;
+        mso-style-locked:yes;
+        mso-style-link:"GSAS-II text";
+        mso-ansi-font-size:12.0pt;
+        mso-bidi-font-size:12.0pt;
+        font-family:"Times New Roman","serif";
+        mso-ascii-font-family:"Times New Roman";
+        mso-fareast-font-family:"Times New Roman";
+        mso-fareast-theme-font:minor-fareast;
+        mso-hansi-font-family:"Times New Roman";
+        mso-bidi-font-family:Calibri;
+        mso-bidi-theme-font:minor-latin;
+        font-weight:bold;
+        mso-bidi-font-weight:normal;}
 p.GSAS-IItext, li.GSAS-IItext, div.GSAS-IItext
         {mso-style-name:"GSAS-II text";
+        mso-style-noshow:yes;
+        mso-style-priority:99;
         mso-style-unhide:no;
         mso-style-link:"GSAS-II text Char";
@@ -763 +782 @@
         font-weight:bold;
         mso-bidi-font-weight:normal;}
-span.GSAS-IItextChar
-        {mso-style-name:"GSAS-II text Char";
-        mso-style-unhide:no;
-        mso-style-locked:yes;
-        mso-style-link:"GSAS-II text";
-        mso-ansi-font-size:12.0pt;
-        mso-bidi-font-size:12.0pt;
-        font-family:"Times New Roman","serif";
-        mso-fareast-font-family:"Times New Roman";
-        mso-fareast-theme-font:minor-fareast;
-        mso-bidi-font-family:Calibri;
-        mso-bidi-theme-font:minor-latin;
-        font-weight:bold;
-        mso-bidi-font-weight:normal;}
+span.SpellE
+        {mso-style-name:"";
+        mso-spl-e:yes;}
+span.GramE
+        {mso-style-name:"";
+        mso-gram-e:yes;}
 .MsoChpDefault
         {mso-style-type:export-only;
         mso-default-props:yes;
+        font-size:10.0pt;
+        mso-ansi-font-size:10.0pt;
+        mso-bidi-font-size:10.0pt;
+        font-family:"Calibri","sans-serif";
         mso-ascii-font-family:Calibri;
         mso-ascii-theme-font:minor-latin;
@@ -788 +803 @@
         mso-bidi-font-family:"Times New Roman";
         mso-bidi-theme-font:minor-bidi;}
-.MsoPapDefault
-        {mso-style-type:export-only;
-        margin-bottom:10.0pt;
-        line-height:115%;}
 @page WordSection1
         {size:8.5in 11.0in;
@@ -811 +822 @@
         mso-style-noshow:yes;
         mso-style-priority:99;
-        mso-style-qformat:yes;
         mso-style-parent:"";
         mso-padding-alt:0in 5.4pt 0in 5.4pt;
-        mso-para-margin-top:0in;
-        mso-para-margin-right:0in;
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-        mso-para-margin-left:0in;
-        line-height:115%;
-        mso-pagination:widow-orphan;
-        font-size:11.0pt;
+        mso-para-margin:0in;
+        mso-para-margin-bottom:.0001pt;
+        mso-pagination:widow-orphan;
+        font-size:10.0pt;
         font-family:"Calibri","sans-serif";
         mso-ascii-font-family:Calibri;
@@ -830 +837 @@
 </style>
 <![endif]--><!--[if gte mso 9]><xml>
- <o:shapedefaults v:ext="edit" spidmax="2050"/>
+ <o:shapedefaults v:ext="edit" spidmax="1026"/>
 </xml><![endif]--><!--[if gte mso 9]><xml>
  <o:shapelayout v:ext="edit">
@@ -847 +854 @@
 
 <p class=MsoNormal>One common way is start a console window, set the current
-directory to the location of GSAS-II <span style='mso-spacerun:yes'> </span>and
-then enter:</p>
+directory to the location of GSAS-<span class=GramE>II<span
+style='mso-spacerun:yes'>  </span>and</span> then enter:</p>
 
 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
 
-<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span
+<p class=MsoNormal><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'>python
-GSASII.py<o:p></o:p></span></b></p>
+mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>python</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'> GSASII.py<o:p></o:p></span></b></p>
 
 <p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span
@@ -869 +878 @@
 <p class=MsoNormal>On Windows, there is a GSASII.bat file in the main GSASII
 directory you can use as a shortcut. Put a shortcut to it someplace convenient
-(maybe your Desktop?) </p>
+(maybe <span class=GramE>your</span> Desktop?) </p>
 
 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
@@ -877 +886 @@
 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'>GSASII data tree</span></span>, the second, immediately under the first
-is labeled <b style='mso-bidi-font-weight:normal'><span style='font-family:
+minor-latin'>GSASII data tree</span></span>, the second, immediately under the
+first is labeled <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 display</span></b>
@@ -885 +894 @@
 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II Plots</span></b>.
 These windows may be moved anywhere on the screen. On Linux and Windows a menu
-bar appears at the top of<span style='mso-spacerun:yes'>  </span>the data tree
-and data display windows; on a Mac these menus will appear in the system menu
-bar location (usually at the screen top) depending on which GSAS-II window has
-the focus. On my Windows machine the screen looked like</p>
+bar appears at the top <span class=GramE>of<span style='mso-spacerun:yes'> 
+</span>the</span> data tree and data display windows; on a Mac these menus will
+appear in the system menu bar location (usually at the screen top) depending on
+which GSAS-II window has the focus. On my Windows machine the screen looked
+like</p>
 
 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
@@ -912 +922 @@
  <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
  <o:lock v:ext="edit" aspectratio="t"/>
-</v:shapetype><v:shape id="Picture_x0020_3" o:spid="_x0000_i1025" type="#_x0000_t75"
+</v:shapetype><v:shape id="Picture_x0020_3" o:spid="_x0000_i1026" type="#_x0000_t75"
  style='width:468pt;height:263.25pt;visibility:visible;mso-wrap-style:square'>
  <v:imagedata src="Starting%20GSAS_files/image001.png" o:title=""/>
@@ -925 +935 @@
 file name is saved.) The console window displays a banner and some information
 about the version of python and the packages used by GSAS-II. This console
-window (here in the lower left) will display important information as data processing
-by GSAS-II proceeds. You may wish to cut-and-paste parts of this window to
-another place if desired.</p>
+window (here in the lower left) will display important information as data
+processing by GSAS-II proceeds. You may wish to cut-and-paste parts of this
+window to another place if desired.</p>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
+
+<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
+ id="Picture_x0020_2" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:465.75pt;
+ height:215.25pt;visibility:visible;mso-wrap-style:square'>
+ <v:imagedata src="Starting%20GSAS_files/image003.png" o:title=""/>
+</v:shape><![endif]--><![if !vml]><img width=621 height=287
+src="Starting%20GSAS_files/image004.gif" v:shapes="Picture_x0020_2"><![endif]></span></p>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
+
+<p class=MsoNormal>We suggest that you change the properties of this window to
+(in Windows: Properties/Layout) to have 9999 for the height and 150 for the
+width and to allow “<span class=SpellE>QuickEdit</span> Mode” (if available)
+for easy cut/paste operation. You can perhaps also change the font, font size,
+font color and background color if desired.</p>
 
 </div>

trunk/help/Starting GSAS_files/filelist.xml

@@ -1 +1 @@
 <xml xmlns:o="urn:schemas-microsoft-com:office:office">
  <o:MainFile HRef="../Starting%20GSAS.htm"/>
- <o:File HRef="item0001.xml"/>
- <o:File HRef="props0002.xml"/>
+ <o:File HRef="item0008.xml"/>
+ <o:File HRef="props009.xml"/>
  <o:File HRef="themedata.thmx"/>
  <o:File HRef="colorschememapping.xml"/>
  <o:File HRef="image001.png"/>
  <o:File HRef="image002.jpg"/>
+ <o:File HRef="image003.png"/>
+ <o:File HRef="image004.gif"/>
  <o:File HRef="filelist.xml"/>
 </xml>

trunk/help/gsasII.html

@@ -8 +8 @@
 <meta http-equiv=Content-Type content="text/html; charset=us-ascii">
 <meta name=ProgId content=Word.Document>
-<meta name=Generator content="Microsoft Word 12">
-<meta name=Originator content="Microsoft Word 12">
+<meta name=Generator content="Microsoft Word 14">
+<meta name=Originator content="Microsoft Word 14">
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 <link rel=Edit-Time-Data href="gsasII_files/editdata.mso">
@@ -25 +25 @@
   <o:Author>Von Dreele</o:Author>
   <o:LastAuthor>Von Dreele</o:LastAuthor>
-  <o:Revision>81</o:Revision>
+  <o:Revision>82</o:Revision>
   <o:TotalTime>2819</o:TotalTime>
   <o:Created>2011-11-28T16:49:00Z</o:Created>
-  <o:LastSaved>2012-05-05T14:55:00Z</o:LastSaved>
+  <o:LastSaved>2012-05-05T15:39:00Z</o:LastSaved>
   <o:Pages>8</o:Pages>
-  <o:Words>7190</o:Words>
-  <o:Characters>40988</o:Characters>
+  <o:Words>7195</o:Words>
+  <o:Characters>41018</o:Characters>
   <o:Company>Argonne National Laboratory</o:Company>
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   <o:Paragraphs>96</o:Paragraphs>
-  <o:CharactersWithSpaces>48082</o:CharactersWithSpaces>
-  <o:Version>12.00</o:Version>
+  <o:CharactersWithSpaces>48117</o:CharactersWithSpaces>
+  <o:Version>14.00</o:Version>
  </o:DocumentProperties>
 </xml><![endif]-->
 <link rel=dataStoreItem href="gsasII_files/item0010.xml"
-target="gsasII_files/props0011.xml">
+target="gsasII_files/props011.xml">
 <link rel=themeData href="gsasII_files/themedata.thmx">
 <link rel=colorSchemeMapping href="gsasII_files/colorschememapping.xml">
@@ -47 +47 @@
   <w:Zoom>FullPage</w:Zoom>
   <w:SpellingState>Clean</w:SpellingState>
+  <w:GrammarState>Clean</w:GrammarState>
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   <w:TrackFormatting/>
@@ -473 +474 @@
         font-weight:bold;}
 p.MsoTitle, li.MsoTitle, div.MsoTitle
-        {mso-style-priority:10;
+        {mso-style-noshow:yes;
+        mso-style-priority:10;
         mso-style-unhide:no;
         mso-style-qformat:yes;
@@ -505 +507 @@
         mso-font-kerning:14.0pt;}
 p.MsoTitleCxSpFirst, li.MsoTitleCxSpFirst, div.MsoTitleCxSpFirst
-        {mso-style-priority:10;
+        {mso-style-noshow:yes;
+        mso-style-priority:10;
         mso-style-unhide:no;
         mso-style-qformat:yes;
@@ -536 +539 @@
         mso-font-kerning:14.0pt;}
 p.MsoTitleCxSpMiddle, li.MsoTitleCxSpMiddle, div.MsoTitleCxSpMiddle
-        {mso-style-priority:10;
+        {mso-style-noshow:yes;
+        mso-style-priority:10;
         mso-style-unhide:no;
         mso-style-qformat:yes;
@@ -567 +571 @@
         mso-font-kerning:14.0pt;}
 p.MsoTitleCxSpLast, li.MsoTitleCxSpLast, div.MsoTitleCxSpLast
-        {mso-style-priority:10;
+        {mso-style-noshow:yes;
+        mso-style-priority:10;
         mso-style-unhide:no;
         mso-style-qformat:yes;
@@ -600 +605 @@
         mso-font-kerning:14.0pt;}
 a:link, span.MsoHyperlink
-        {mso-style-noshow:yes;
-        mso-style-priority:99;
+        {mso-style-priority:99;
         color:blue;
         text-decoration:underline;
@@ -869 +873 @@
         mso-hansi-font-family:"Courier New";
         mso-bidi-font-family:"Courier New";}
+span.TitleChar
+        {mso-style-name:"Title Char";
+        mso-style-priority:10;
+        mso-style-unhide:no;
+        mso-style-locked:yes;
+        mso-style-link:Title;
+        mso-ansi-font-size:26.0pt;
+        mso-bidi-font-size:26.0pt;
+        font-family:"Cambria","serif";
+        mso-ascii-font-family:Cambria;
+        mso-ascii-theme-font:major-latin;
+        mso-fareast-font-family:"Times New Roman";
+        mso-fareast-theme-font:major-fareast;
+        mso-hansi-font-family:Cambria;
+        mso-hansi-theme-font:major-latin;
+        mso-bidi-font-family:"Times New Roman";
+        mso-bidi-theme-font:major-bidi;
+        color:#17365D;
+        mso-themecolor:text2;
+        mso-themeshade:191;
+        letter-spacing:.25pt;
+        mso-font-kerning:14.0pt;}
 span.DocumentMapChar
         {mso-style-name:"Document Map Char";
@@ -899 +925 @@
         mso-hansi-font-family:Tahoma;
         mso-bidi-font-family:Tahoma;}
-span.TitleChar
-        {mso-style-name:"Title Char";
-        mso-style-priority:10;
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-        mso-style-link:Title;
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-        mso-fareast-font-family:"Times New Roman";
-        mso-fareast-theme-font:major-fareast;
-        mso-hansi-font-family:Cambria;
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-        mso-font-kerning:14.0pt;}
 span.SpellE
         {mso-style-name:"";
         mso-spl-e:yes;}
+span.GramE
+        {mso-style-name:"";
+        mso-gram-e:yes;}
 .MsoChpDefault
         {mso-style-type:export-only;
@@ -1913 +1920 @@
         mso-style-noshow:yes;
         mso-style-priority:99;
-        mso-style-qformat:yes;
         mso-style-parent:"";
         mso-padding-alt:0in 5.4pt 0in 5.4pt;
@@ -1925 +1931 @@
 <link href=gsasIIfav.png rel="SHORTCUT ICON">
 <!--[if gte mso 9]><xml>
- <o:shapedefaults v:ext="edit" spidmax="3074"/>
+ <o:shapedefaults v:ext="edit" spidmax="1027"/>
 </xml><![endif]--><!--[if gte mso 9]><xml>
  <o:shapelayout v:ext="edit">
@@ -1956 +1962 @@
  <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
  <o:lock v:ext="edit" aspectratio="t"/>
-</v:shapetype><v:shape id="Picture_x0020_2" o:spid="_x0000_s1028" type="#_x0000_t75"
- alt="Description: Description: GSAS-II logo" style='position:absolute;
- margin-left:56pt;margin-top:0;width:96pt;height:96pt;z-index:1;visibility:visible;
- mso-wrap-style:square;mso-wrap-distance-left:0;mso-wrap-distance-top:0;
+</v:shapetype><v:shape id="Picture_x0020_2" o:spid="_x0000_s1026" type="#_x0000_t75"
+ alt="Description: Description: Description: GSAS-II logo" style='position:absolute;
+ margin-left:44.8pt;margin-top:0;width:96pt;height:96pt;z-index:251657728;
+ visibility:visible;mso-wrap-style:square;mso-width-percent:0;
+ mso-height-percent:0;mso-wrap-distance-left:0;mso-wrap-distance-top:0;
  mso-wrap-distance-right:0;mso-wrap-distance-bottom:0;
  mso-position-horizontal:right;mso-position-horizontal-relative:text;
- mso-position-vertical:absolute;mso-position-vertical-relative:line'
- o:allowoverlap="f">
+ mso-position-vertical:absolute;mso-position-vertical-relative:line;
+ mso-width-percent:0;mso-height-percent:0;mso-width-relative:page;
+ mso-height-relative:page' o:allowoverlap="f">
  <v:imagedata src="gsas2logo.png"/>
  <w:wrap type="square" anchory="line"/>
 </v:shape><![endif]--><![if !vml]><img width=128 height=128 src=gsas2logo.png
-align=right alt="Description: Description: GSAS-II logo" v:shapes="Picture_x0020_2"><![endif]><span
+align=right alt="Description: Description: Description: GSAS-II logo" v:shapes="Picture_x0020_2"><![endif]><span
 style='mso-fareast-font-family:"Times New Roman"'>Help for GSAS-II<o:p></o:p></span></h1>
 
@@ -1984 +1992 @@
 <h2><strong>GSAS-II tutorials:<o:p></o:p></strong></h2>
 
-<p class=MsoNormal><strong>Starting GSAS-II<o:p></o:p></strong></p>
+<p class=MsoNormal><strong><a href="Starting%20GSAS.htm"><span
+style='font-weight:normal'>Starting GSAS-II</span></a><o:p></o:p></strong></p>
 
 <p class=MsoNormal><strong><a
@@ -1997 +2006 @@
 normal'>Powder pattern peak picking, fitting and indexing</span></a><o:p></o:p></strong></p>
 
-<p class=MsoNormal><strong>Lab X-ray powder pattern <span class=SpellE>Rietveld</span>
-refinement (future)<o:p></o:p></strong></p>
-
-<p class=MsoNormal><strong>CW Neutron powder pattern <span class=SpellE>Rietveld</span>
-refinement (future)<o:p></o:p></strong></p>
-
-<p class=MsoNormal><strong>Synchrotron X-ray powder pattern <span class=SpellE>Rietveld</span>
-refinement (future)<o:p></o:p></strong></p>
-
-<p class=MsoNormal><strong>Crystal structure drawing (balls &amp; sticks, etc.)
+<p class=MsoNormal><strong>Lab X-ray powder pattern Rietveld refinement
 (future)<o:p></o:p></strong></p>
+
+<p class=MsoNormal><strong>CW Neutron powder pattern Rietveld refinement
+(future)<o:p></o:p></strong></p>
+
+<p class=MsoNormal><strong>Synchrotron X-ray powder pattern Rietveld refinement
+(future)<o:p></o:p></strong></p>
+
+<p class=MsoNormal><span class=GramE><strong>Crystal structure drawing (balls
+&amp; sticks, etc.)</strong></span><strong> (<span class=GramE>future</span>)<o:p></o:p></strong></p>
 
 <p class=MsoNormal><strong>Crystal structure drawing (<span class=SpellE>polyhedra</span>)
 (future)<o:p></o:p></strong></p>
 
-<p class=MsoNormal><strong>Distance/Angle/Torsion calculations(future)<o:p></o:p></strong></p>
-
-<p class=MsoNormal><strong>Charge flipping structure solution(future)<o:p></o:p></strong></p>
-
-<p class=MsoNormal><strong>etc., etc.<o:p></o:p></strong></p>
+<p class=MsoNormal><strong>Distance/Angle/Torsion <span class=GramE>calculations(</span>future)<o:p></o:p></strong></p>
+
+<p class=MsoNormal><strong>Charge flipping structure <span class=GramE>solution(</span>future)<o:p></o:p></strong></p>
+
+<p class=MsoNormal><span class=GramE><strong>etc., etc.</strong></span><strong><o:p></o:p></strong></p>
 
 <div class=MsoNormal align=center style='text-align:center'><span
@@ -2062 +2071 @@
 style='mso-bidi-font-weight:normal'>Open project&#8230;</b> - Open a previously
 saved GSAS-II project file (name.gpx). If you currently have a project file
-open, you are asked if it is OK to over write it; Cancel will cancel the
-process. <b style='mso-bidi-font-weight:normal'>NB</b>: you may open a backup <span
+open, you are asked if it is OK to over write it; Cancel will cancel the process.
+<b style='mso-bidi-font-weight:normal'>NB</b>: you may open a backup <span
 class=SpellE>gpx</span> file (e.g. name.bak3.gpx) to recover a previous version
 of your project. Remember to <b style='mso-bidi-font-weight:normal'>Save As</b>&#8230;
@@ -2086 +2095 @@
 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Save
 As&#8230;</span></b><span style='mso-fareast-font-family:"Times New Roman"'> -
-Save the current project to a new file. A file dialog will be shown to enter the
-name (and change directory if desired). If the file exists, you will be asked
-if it OK to overwrite.</span></p>
+Save the current project to a new file. A file dialog will be shown to enter
+the name (and change directory if desired). If the file exists, you will be
+asked if it OK to overwrite.</span></p>
 
 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
@@ -2118 +2127 @@
 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
-style='mso-bidi-font-weight:normal'>Read powder data&#8230;</b> - Read in powder
-diffraction patterns (multiple patterns can be selected). GSAS-II can read most
-of the old GSAS powder format files with the position in <span class=SpellE>centidegrees</span>
-2-theta. It can also read &#8220;<span class=SpellE>xye</span>&#8221; format
-files used by <span class=SpellE>topas</span> where the position is in degrees
-2-theta. As each file is read, an old GSAS style &#8220;instrument parameter
-file&#8221; is searched for; if not found a <span class=SpellE>CuK</span><span
-style='font-family:Symbol'>a</span> laboratory data set is assumed. </p>
+style='mso-bidi-font-weight:normal'>Read powder data&#8230;</b> - Read in
+powder diffraction patterns (multiple patterns can be selected). GSAS-II can
+read most of the old GSAS powder format files with the position in <span
+class=SpellE>centidegrees</span> 2-theta. It can also read &#8220;<span
+class=SpellE>xye</span>&#8221; format files used by <span class=SpellE>topas</span>
+where the position is in degrees 2-theta. As each file is read, an old GSAS
+style &#8220;instrument parameter file&#8221; is searched for; if not found a <span
+class=SpellE>CuK</span><span style='font-family:Symbol'>a</span> laboratory
+data set is assumed. </p>
 
 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
@@ -2228 +2238 @@
 The total number of refined parameters is also shown at the top of the list.
 The value of each parameter is also given. The parameter names are of the form
-&#8216;p:h:name:id&#8217; where &#8216;p&#8217; is the phase index,
-&#8216;h&#8217; is the histogram index and &#8216;id&#8217; is the item index
-(if needed). Indexes all begin with &#8216;0&#8217; (zero). Note that for atom
-positions the value is not a <span class=SpellE>refinable</span> parameter, but
-the shift in the value is. Position names are, e.g. &#8216;0::Ax:0&#8217; for
-the x-position of the <span class=SpellE>zeroth</span> atom in the <span
-class=SpellE>zeroth</span> phase while shift names have a &#8216;d&#8217; in
-then, e.g. &#8216;0::dAx:0&#8217;. </p>
+&#8216;p<span class=GramE>:h:name:id&#8217;</span> where &#8216;p&#8217; is the
+phase index, &#8216;h&#8217; is the histogram index and &#8216;id&#8217; is the
+item index (if needed). Indexes all begin with &#8216;0&#8217; (zero). Note
+that for atom positions the value is not a <span class=SpellE>refinable</span>
+parameter, but the shift in the value is. Position names are, e.g. &#8216;0:<span
+class=GramE>:Ax:0&#8217;</span> for the x-position of the <span class=SpellE>zeroth</span>
+atom in the <span class=SpellE>zeroth</span> phase while shift names have a
+&#8216;d&#8217; in then, e.g. &#8216;0::dAx:0&#8217;. </p>
 
 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
@@ -2413 +2423 @@
 
 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Two
-of the main refinement tools are the <span class=SpellE>fortran</span> MINPACK <span
-class=SpellE>lmdif</span> and <span class=SpellE>lmder</span> algorithms
-wrapped in python as provided in the <span class=SpellE>Scipy</span> package
-and a third one is a python version utilizing only the <span class=SpellE>numpy</span>
-package. The purpose is to </span>minimize the sum of the squares of M<span
-style='mso-fareast-font-family:"Times New Roman"'> nonlinear functions in N
-variables by a modification of the <span class=SpellE>Levenberg</span>-Marquardt
+of the main refinement tools are the <span class=SpellE><span class=GramE>fortran</span></span>
+MINPACK <span class=SpellE>lmdif</span> and <span class=SpellE>lmder</span>
+algorithms wrapped in python as provided in the <span class=SpellE>Scipy</span>
+package and a third one is a python version utilizing only the <span
+class=SpellE>numpy</span> package. The purpose is to </span>minimize the sum of
+the squares of M<span style='mso-fareast-font-family:"Times New Roman"'>
+nonlinear functions in N variables by a modification of the <span class=SpellE>Levenberg</span>-Marquardt
 algorithm. The <span class=SpellE>lmdif</span> and <span class=SpellE>lmder</span>
 routines were written by </span>Burton S. <span class=SpellE>Garbow</span>,
-Kenneth E. <span class=SpellE>Hillstrom</span>, Jorge J. More (Argonne National
-Laboratory, 1980). The python/numpy version was developed by us based on the
-material in Numerical Recipes (Press, Flannery, <span class=SpellE>Teulosky</span>
+Kenneth E. <span class=SpellE>Hillstrom</span>, <span class=GramE>Jorge</span>
+J. <span class=GramE>More (Argonne National Laboratory, 1980).</span> The
+python/numpy version was developed by us based on the material in Numerical
+Recipes (Press, Flannery, <span class=SpellE><span class=GramE>Teulosky</span></span>
 &amp; <span class=SpellE>Vetterling</span>) for the <span class=SpellE>Levenberg</span>-Marquardt
 algorithm.<span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
@@ -2459 +2470 @@
 the first cycle of refinement. This value is modified by the least squares
 routine. The allowed range is 10<sup>-5</sup> to 100. Smaller values may be
-needed if your initial refinement trials immediately diverge, however make sure
-your starting parameter values are &#8216;reasonable&#8217;. The selected
-default (=1.0) normally gives good performance.<o:p></o:p></span></p>
+needed if your initial <span class=GramE>refinement</span> trials immediately
+diverge, however make sure your starting parameter values are
+&#8216;reasonable&#8217;. The selected default (=1.0) normally gives good
+performance.<o:p></o:p></span></p>
 
 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l15 level1 lfo2'><![if !supportLists]><span
@@ -2501 +2513 @@
 "Times New Roman"'>m</span><span style='mso-fareast-font-family:"Times New Roman"'>strain
 and crystallite size parameters). &#8216;Histogram constraints&#8217; are those
-that depend only on the data set (e.g. profile coefficients U,V,W,X and Y).<o:p></o:p></span></p>
+that depend only on the data set (e.g. profile coefficients U<span class=GramE>,V,W,X</span>
+and Y).<o:p></o:p></span></p>
 
 <h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
@@ -2521 +2534 @@
 auto;text-indent:-.25in;mso-list:l17 level2 lfo3'><![if !supportLists]><span
 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
-style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
-style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Add
-Hold</span></b><span style='mso-fareast-font-family:"Times New Roman"'> &#8211;
-select a parameter that you wish to remain fixed although other parameters of
-the same type may be selected as a group for refinement. For example, if the
-space group for a phase has a polar axis (e.g. the b-axis in P2<sub>1</sub>),
-then one atom y-parameter is arbitrary and should be selected for a Hold to
-keep the structure from drifting up or down the y-axis during refinement. If
-selected, a dialog box will appear showing the list of available parameters;
-select one and then OK to implement it, Cancel will cancel the operation. The
-held parameter will be shown in the constraint window with the keyword
-&#8216;FIXED&#8217;. A Delete button can be used to remove it.<o:p></o:p></span></p>
+style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
+class=GramE><b style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:
+"Times New Roman"'>Add</span></b></span><b style='mso-bidi-font-weight:normal'><span
+style='mso-fareast-font-family:"Times New Roman"'> Hold</span></b><span
+style='mso-fareast-font-family:"Times New Roman"'> &#8211; select a parameter
+that you wish to remain fixed although other parameters of the same type may be
+selected as a group for refinement. For example, if the space group for a phase
+has a polar axis (e.g. the b-axis in P2<sub>1</sub>), then one atom y-parameter
+is arbitrary and should be selected for a Hold to keep the structure from
+drifting up or down the y-axis during refinement. If selected, a dialog box
+will appear showing the list of available parameters; select one and then OK to
+implement it, Cancel will cancel the operation. The held parameter will be
+shown in the constraint window with the keyword &#8216;FIXED&#8217;. A Delete
+button can be used to remove it.<o:p></o:p></span></p>
 
 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
@@ -2543 +2558 @@
 with a non-unitary multiplier for some). Examples are a list of atoms with the
 same thermal motion <span class=SpellE>Uiso</span>, sets of profile
-coefficients U,V,W across multiple data sets. If selected, a dialog box will
-appear with a list of the available parameters. Select one and press OK; a
-second dialog box will appear with only those parameters that can be made
-equivalent to the first one. Choose those and press OK. Cancel in either dialog
-will cancel the operation. The equivalenced parameters will show as an equation
-of the form M<sub>1</sub>*P<sub>1</sub>+M<sub>2</sub>*P<sub>2</sub>=0; usually
-M1=1.0 and M2=-1.0, but can be changed via the &#8216;Edit&#8217; button. The
-keyword &#8216;EQUIV&#8217; marks it as an equivalence. A Delete button can be
-used to remove it.<o:p></o:p></span></p>
+coefficients U<span class=GramE>,V,W</span> across multiple data sets. If
+selected, a dialog box will appear with a list of the available parameters.
+Select one and press OK; a second dialog box will appear with only those
+parameters that can be made equivalent to the first one. Choose those and press
+OK. Cancel in either dialog will cancel the operation. The equivalenced
+parameters will show as an equation of the form M<sub>1</sub>*P<sub>1</sub>+M<sub>2</sub>*P<sub>2</sub>=0;
+usually M1=1.0 and M2=-1.0, but can be changed via the &#8216;Edit&#8217;
+button. The keyword &#8216;EQUIV&#8217; marks it as <span class=GramE>an
+equivalence</span>. A Delete button can be used to remove it.<o:p></o:p></span></p>
 
 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
@@ -2567 +2582 @@
 the operation. The equivalenced parameters will show as an equation of the form
 M<sub>1</sub>*P<sub>1</sub>+M<sub>2</sub>*P<sub>2</sub>+&#8230;=C; the
-multipliers M1, M2, &#8230; and C can be changed via the &#8216;Edit&#8217;
-button. The keyword &#8216;CONSTR&#8217; marks it as a constraint. A Delete
-button can be used to remove it.<o:p></o:p></span></p>
+multipliers M1, <span class=GramE>M2, &#8230;</span> and C can be changed via
+the &#8216;Edit&#8217; button. The keyword &#8216;CONSTR&#8217; marks it as a
+constraint. A Delete button can be used to remove it.<o:p></o:p></span></p>
 
 <p class=MsoListParagraphCxSpLast style='margin-left:1.0in;mso-add-space:auto;
@@ -2599 +2614 @@
 <p class=MsoNormal>In this window is tabulated the results of your sequential
 refinement. The columns are the parameter names; the naming convention is
-&#8216;p:h:name:n&#8217; where p is the phase number, h is the histogram
-number, name is the parameter name, and num (if needed) is the item number
-(e.g. atom number). The rows are the data sets used in the sequential
-refinement.</p>
+&#8216;p<span class=GramE>:h:name:n&#8217;</span> where p is the phase number,
+h is the histogram number, name is the parameter name, and num (if needed) is
+the item number (e.g. atom number). The rows are the data sets used in the
+sequential refinement.</p>
 
 <h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
@@ -2706 +2721 @@
 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Copy</span></b><span
-style='mso-fareast-font-family:"Times New Roman"'> &#8211; this copies the limits
-shown to other selected powder patterns. If used, a dialog box (Copy
+style='mso-fareast-font-family:"Times New Roman"'> &#8211; this copies the
+limits shown to other selected powder patterns. If used, a dialog box (Copy
 Parameters) will appear showing the list of available powder patterns, you can
 copy the limits parameters to any or all of them; select &#8216;All&#8217; to
@@ -2722 +2737 @@
 for the background:<o:p></o:p></span></p>
 
-<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>1). A
-continuous empirical function (&#8216;<span class=SpellE>chebyschev</span>&#8217;,
-&#8216;cosine&#8217;, &#8216;<span class=SpellE>lin</span> interpolate&#8217;,
-&#8216;inv interpolate&#8217; &amp; &#8216;log interpolate&#8217;). The latter
-three select fixed points with spacing that is either equal, inversely equal or
-equal on a log scale of the x-coordinate. The set of magnitudes at each point
-then comprise the background variables. All are refined when refine is
-selected.<o:p></o:p></span></p>
+<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>1).
+A continuous empirical function (&#8216;<span class=SpellE>chebyschev</span>&#8217;,
+&#8216;cosine&#8217;, &#8216;<span class=SpellE><span class=GramE>lin</span></span>
+interpolate&#8217;, &#8216;inv interpolate&#8217; &amp; &#8216;log
+interpolate&#8217;). The latter three select fixed points with spacing that is <span
+class=GramE>either equal</span>, inversely equal or equal on a log scale of the
+x-coordinate. The set of magnitudes at each point then comprise the background
+variables. All are refined when refine is selected.<o:p></o:p></span></p>
 
 <p class=MsoNormal style='tab-stops:0in'><span style='mso-fareast-font-family:
@@ -2774 +2789 @@
 1'>&nbsp;&nbsp;&nbsp;&nbsp; </span><o:p></o:p></span></p>
 
-<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>where
-A,R &amp; U are the possible variables and can be individually selected as
-desired; Q = 2</span><span style='font-family:Symbol;mso-fareast-font-family:
-"Times New Roman"'>p</span><span style='mso-fareast-font-family:"Times New Roman"'>/d.<o:p></o:p></span></p>
+<p class=MsoNormal><span class=GramE><span style='mso-fareast-font-family:"Times New Roman"'>where</span></span><span
+style='mso-fareast-font-family:"Times New Roman"'> A,R &amp; U are the possible
+variables and can be individually selected as desired; Q = 2</span><span
+style='font-family:Symbol;mso-fareast-font-family:"Times New Roman"'>p</span><span
+style='mso-fareast-font-family:"Times New Roman"'>/d.<o:p></o:p></span></p>
 
 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>3).
 A set of individual Bragg peaks using the pseudo-Voigt profile function as
-their shapes. Their parameters are &#8216;pos&#8217;, &#8217;<span
-class=SpellE>int</span>&#8217;, &#8216;sig&#8217; &amp; &#8216;<span
-class=SpellE>gam</span>&#8217;; each can be selected for refinement. The
-default values for sig &amp; gam (=0.10) are for very sharp peaks, you may
-adjust them accordingly to the kind of peak you are trying to fit before trying
-to refine them.<o:p></o:p></span></p>
+their shapes. Their parameters are &#8216;<span class=SpellE>pos</span>&#8217;,
+&#8217;<span class=SpellE>int</span>&#8217;, &#8216;sig&#8217; &amp;
+&#8216;gam&#8217;; each can be selected for refinement. The default values for
+sig &amp; gam (=0.10) are for very sharp peaks, you may adjust them accordingly
+to the kind of peak you are trying to fit before trying to refine them.<o:p></o:p></span></p>
 
 <h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
@@ -2814 +2829 @@
 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Copy
 flags </span></b><span style='mso-fareast-font-family:"Times New Roman"'>&#8211;
-this copies only the refinement flags shown to other selected powder patterns.
-If used, a dialog box (Copy Refinement Flags) will appear showing the list of
-available powder patterns, you can copy the refinement flags to any or all of
-them; select &#8216;All&#8217; to copy them to all patterns. Then select
-&#8216;OK&#8217; to do the copy; &#8216;Cancel&#8217; to cancel the operation.<o:p></o:p></span></p>
+<span class=GramE>this copies</span> only the refinement flags shown to other
+selected powder patterns. If used, a dialog box (Copy Refinement Flags) will
+appear showing the list of available powder patterns, you can copy the
+refinement flags to any or all of them; select &#8216;All&#8217; to copy them
+to all patterns. Then select &#8216;OK&#8217; to do the copy;
+&#8216;Cancel&#8217; to cancel the operation.<o:p></o:p></span></p>
 
 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l19 level1 lfo7'><![if !supportLists]><span
@@ -2979 +2995 @@
 profile coefficients. <b style='mso-bidi-font-weight:normal'>NB</b>: In certain
 circumstances some choices are ignored e.g. Zero is not refined during peak
-fitting. Also some choices may lead to unstable refinement, e.g. Lam refinement
-and lattice parameter refinement. Examine the &#8216;</span><a
-href="#Covariance"><span style='mso-fareast-font-family:"Times New Roman"'>Covariance&#8217;</span></a><span
+fitting. Also some choices may lead to unstable refinement, e.g. <span
+class=GramE>Lam</span> refinement and lattice parameter refinement. Examine the
+&#8216;</span><a href="#Covariance"><span style='mso-fareast-font-family:"Times New Roman"'>Covariance&#8217;</span></a><span
 style='mso-fareast-font-family:"Times New Roman"'> display for highly
 correlated parameters.<o:p></o:p></span></p>
@@ -2993 +3009 @@
 fixed. All values can be changed in this window.<o:p></o:p></span></p>
 
-<h5><a name="Powder_Peaks"></a><a name="Peak_List"><span style='mso-bookmark:
-Powder_Peaks'><span style='mso-fareast-font-family:"Times New Roman"'>What can
-I do here?</span></span></a><span style='mso-bookmark:Peak_List'><span
-style='mso-bookmark:Powder_Peaks'><span style='mso-fareast-font-family:"Times New Roman";
+<h5><a name="Peak_List"></a><a name="Powder_Peaks"><span style='mso-bookmark:
+Peak_List'><span style='mso-fareast-font-family:"Times New Roman"'>What can I
+do here?</span></span></a><span style='mso-bookmark:Powder_Peaks'><span
+style='mso-bookmark:Peak_List'><span style='mso-fareast-font-family:"Times New Roman";
 color:windowtext;font-weight:normal;mso-bidi-font-weight:bold'><o:p></o:p></span></span></span></h5>
 
 <h5 style='margin-left:.5in;text-indent:-.25in;mso-list:l6 level1 lfo11'><span
-style='mso-bookmark:Peak_List'><span style='mso-bookmark:Powder_Peaks'><![if !supportLists]><span
+style='mso-bookmark:Powder_Peaks'><span style='mso-bookmark:Peak_List'><![if !supportLists]><span
 style='mso-fareast-font-family:"Times New Roman";color:windowtext;font-weight:
 normal;mso-bidi-font-weight:bold'><span style='mso-list:Ignore'>1.<span
@@ -3006 +3022 @@
 style='mso-fareast-font-family:"Times New Roman";color:windowtext;font-weight:
 normal;mso-bidi-font-weight:bold'>Menu &#8216;</span></span></span><span
-style='mso-bookmark:Peak_List'><span style='mso-bookmark:Powder_Peaks'><span
+style='mso-bookmark:Powder_Peaks'><span style='mso-bookmark:Peak_List'><span
 style='mso-fareast-font-family:"Times New Roman";color:windowtext'>File&#8217;</span></span></span><span
-style='mso-bookmark:Peak_List'><span style='mso-bookmark:Powder_Peaks'><span
+style='mso-bookmark:Powder_Peaks'><span style='mso-bookmark:Peak_List'><span
 style='mso-fareast-font-family:"Times New Roman";color:windowtext;font-weight:
 normal;mso-bidi-font-weight:bold'> &#8211; <o:p></o:p></span></span></span></h5>
@@ -3014 +3030 @@
 <p class=MsoListParagraphCxSpFirst style='margin-left:1.0in;mso-add-space:auto;
 text-indent:-.25in;mso-list:l6 level2 lfo11;tab-stops:list 1.0in'><span
-style='mso-bookmark:Peak_List'><span style='mso-bookmark:Powder_Peaks'><![if !supportLists]><span
+style='mso-bookmark:Powder_Peaks'><span style='mso-bookmark:Peak_List'><![if !supportLists]><span
 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Copy</span></b></span></span><span
-style='mso-bookmark:Peak_List'><span style='mso-bookmark:Powder_Peaks'><span
+style='mso-bookmark:Powder_Peaks'><span style='mso-bookmark:Peak_List'><span
 style='mso-fareast-font-family:"Times New Roman"'> &#8211; this copies the
 sample parameters shown to other selected powder patterns. If used, a dialog
@@ -3028 +3044 @@
 <p class=MsoListParagraphCxSpLast style='margin-left:1.0in;mso-add-space:auto;
 text-indent:-.25in;mso-list:l6 level2 lfo11;tab-stops:list 1.0in'><span
-style='mso-bookmark:Peak_List'><span style='mso-bookmark:Powder_Peaks'><![if !supportLists]><span
+style='mso-bookmark:Powder_Peaks'><span style='mso-bookmark:Peak_List'><![if !supportLists]><span
 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Copy
-flags</span></b></span></span><span style='mso-bookmark:Peak_List'><span
-style='mso-bookmark:Powder_Peaks'><span style='mso-fareast-font-family:"Times New Roman"'>
+flags</span></b></span></span><span style='mso-bookmark:Powder_Peaks'><span
+style='mso-bookmark:Peak_List'><span style='mso-fareast-font-family:"Times New Roman"'>
 - &#8211; this copies the sample parameter refinement flags shown to other
 selected powder patterns. If used, a dialog box (Copy refinement flags) will
@@ -3041 +3057 @@
 &#8216;Cancel&#8217; to cancel the operation. <o:p></o:p></span></span></span></p>
 
-<h4><span style='mso-bookmark:Peak_List'><span style='mso-bookmark:Powder_Peaks'><span
+<h4><span style='mso-bookmark:Powder_Peaks'><span style='mso-bookmark:Peak_List'><span
 style='mso-fareast-font-family:"Times New Roman"'>Peak List</span></span></span><span
 style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h4>
@@ -3127 +3143 @@
 style='mso-fareast-font-family:"Times New Roman";color:windowtext;font-weight:
 normal;mso-bidi-font-weight:bold'>&#8211; this resets the values of sigma and
-gamma to those computed from the instrument parameters U, V, W, X &amp; Y.<o:p></o:p></span></span></h5>
+gamma to those computed from the instrument parameters U, V, W, <span
+class=GramE>X</span> &amp; Y.<o:p></o:p></span></span></h5>
 
 <h5 style='margin-left:1.0in;text-indent:-.25in;mso-list:l9 level2 lfo12;
@@ -3257 +3274 @@
 <p class=MsoNormal>This window </p>
 
-<h4><a name="I_Q"></a><span style='mso-fareast-font-family:"Times New Roman"'>I(Q),
+<h4><a name="I_Q"></a><span class=GramE><span style='mso-fareast-font-family:
+"Times New Roman"'>I(</span></span><span style='mso-fareast-font-family:"Times New Roman"'>Q),
 <a name="S_Q"></a>S(Q), <a name="F_Q"></a>F(Q) &amp; <a name="G_R"></a>G(R)<o:p></o:p></span></h4>
 
@@ -3359 +3377 @@
 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Space
 group</span></b><span style='mso-fareast-font-family:"Times New Roman"'>
-&#8211; this should be set when the phase is initialized; it can be changed later.
-Be careful about the impact on Atom site symmetry and multiplicity if you do.
-GSAS-II will recognize any legal space group symbol using the short Hermann-<span
-class=SpellE>Mauguin</span> forms; put a space between the axial fields (e.g.
-&#8216;F d 3 m&#8217; not &#8216;Fd3m&#8217;). For space groups with a choice
-of origin (e.g. F d 3 m), GSAS-II always uses the 2<sup>nd</sup> setting where
-the center of inversion is located at the origin. The choice of space group
-will set the available unit cell parameters.<u><o:p></o:p></u></span></p>
+&#8211; this should be set when the phase is initialized; it can be changed
+later. Be careful about the impact on Atom site symmetry and multiplicity if
+you do. GSAS-II will recognize any legal space group symbol using the short
+Hermann-<span class=SpellE>Mauguin</span> forms; put a space between the axial
+fields (e.g. &#8216;F d 3 m&#8217; not &#8216;Fd3m&#8217;). For space groups
+with a choice of origin (e.g. F d 3 m), GSAS-II always uses the 2<sup>nd</sup>
+setting where the center of inversion is located at the origin. The choice of
+space group will set the available unit cell parameters.<u><o:p></o:p></u></span></p>
 
 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
@@ -3476 +3494 @@
 auto;text-indent:-.25in;mso-list:l0 level2 lfo14'><![if !supportLists]><span
 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>e.<span
-style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
-style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>a,
-b, c, alpha, beta, gamma</span></b><span style='mso-fareast-font-family:"Times New Roman"'>
-&#8211; lattice parameters; only those permitted by the space group are shown.
-The volume is computed from the values entered.<u><o:p></o:p></u></span></p>
+style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
+class=GramE><b style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:
+"Times New Roman"'>a</span></b></span><b style='mso-bidi-font-weight:normal'><span
+style='mso-fareast-font-family:"Times New Roman"'>, b, c, alpha, beta, gamma</span></b><span
+style='mso-fareast-font-family:"Times New Roman"'> &#8211; lattice parameters;
+only those permitted by the space group are shown. The volume is computed from
+the values entered.<u><o:p></o:p></u></span></p>
 
 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l0 level1 lfo14'><![if !supportLists]><span
@@ -3551 +3571 @@
 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Atom
 Selection from plot: select an atom by a left click of the mouse while holding
-down the Shift key and pointed at the center of the displayed atom, it will
-turn green if successful and the corresponding entry in the table will be
+down the Shift key and pointed at the center of the displayed atom, it will turn
+green if successful and the corresponding entry in the table will be
 highlighted (in grey); any previous selections will be cleared. To add to .your
 selection use the right mouse button (Shift down); if a previously selection is
@@ -3572 +3592 @@
 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Double
 left click a Style, Label or Color column: a dialog box is shown that allows
-you to select a rendering option for all the atoms. For Color a color choice dialog
-is displayed that covers the entire color spectrum. Choose a color by any of
-the means available, press the &#8220;Add to Custom Colors&#8221;, select that
-color in the Custom colors display and then press OK. <b style='mso-bidi-font-weight:
-normal'>NB</b>: selecting Color will make all atoms have the same color and for
-Style &#8220;blank&#8221; means the atoms aren&#8217;t rendered and thus the
-plot will not show any atoms or bonds!</p>
+you to select a rendering option for all the atoms. For Color a color choice
+dialog is displayed that covers the entire color spectrum. Choose a color by
+any of the means available, press the &#8220;Add to Custom Colors&#8221;,
+select that color in the Custom colors display and then press OK. <b
+style='mso-bidi-font-weight:normal'>NB</b>: selecting Color will make all atoms
+have the same color and for Style &#8220;blank&#8221; means the atoms
+aren&#8217;t rendered and thus the plot will not show any atoms or bonds!</p>
 
 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l10 level1 lfo15'><![if !supportLists]><span
@@ -3667 +3687 @@
 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>j.<span
 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Delete
-atoms</b> &#8211; clear the entire draw atom table; it is then refilled from
-the Atoms table. You should do this operation after any changes in the Atoms
-table, e.g. by a structure refinement.</p>
+</span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Delete atoms</b>
+&#8211; clear the entire draw atom table; it is then refilled from the Atoms
+table. You should do this operation after any changes in the Atoms table, e.g.
+by a structure refinement.</p>
 
 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l10 level1 lfo15'><![if !supportLists]><span
@@ -3685 +3705 @@
 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
 style='mso-bidi-font-weight:normal'>Dist. Ang.</b> <b style='mso-bidi-font-weight:
-normal'>Tors. </b>&#8211; when 2-4 atoms are selected, a distance, angle or
-torsion angle will be found for them. The angles are computed for the atoms in
-their selection order. The torsion angle is a right hand angle about the A2-A3
-vector for the sequence of atoms A1-A2-A3-A4. An estimated standard deviation
-is given for the calculated value if a current variance-covariance matrix is
-available. The result is shown on the console window; it may be cut &amp;
-pasted to another application (e.g. Microsoft Word).</p>
+normal'>Tors. </b>&#8211; <span class=GramE>when</span> 2-4 atoms are selected,
+a distance, angle or torsion angle will be found for them. The angles are
+computed for the atoms in their selection order. The torsion angle is a right
+hand angle about the A2-A3 vector for the sequence of atoms A1-A2-A3-A4. An
+estimated standard deviation is given for the calculated value if a current
+variance-covariance matrix is available. The result is shown on the console
+window; it may be cut &amp; pasted to another application (e.g. Microsoft
+Word).</p>
 
 <p class=MsoListParagraphCxSpLast style='margin-left:1.0in;mso-add-space:auto;
@@ -3735 +3756 @@
 set as &#8216;Pawley <span class=SpellE>dmin</span>&#8217; in the General tab
 for this phase. By default the refine flags are not set and the <span
-class=SpellE>Fsq</span>(<span class=SpellE>hkl</span>) = 100.0.</p>
+class=SpellE><span class=GramE>Fsq</span></span><span class=GramE>(</span><span
+class=SpellE>hkl</span>) = 100.0.</p>
 
 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
@@ -3742 +3764 @@
 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
 style='mso-bidi-font-weight:normal'>Pawley estimate</b> &#8211; this attempts
-an estimate of <span class=SpellE>Fsq</span>(<span class=SpellE>hkl</span>)
-from the peak heights of the reflection as seen in the 1<sup>st</sup> powder
-pattern of those selected in the <a href="#Data">Data</a> tab.</p>
+an estimate of <span class=SpellE><span class=GramE>Fsq</span></span><span
+class=GramE>(</span><span class=SpellE>hkl</span>) from the peak heights of the
+reflection as seen in the 1<sup>st</sup> powder pattern of those selected in
+the <a href="#Data">Data</a> tab.</p>
 
 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
@@ -3766 +3789 @@
 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>You
-can change the individual <span class=SpellE>Fsq</span>(<span class=SpellE>hkl</span>)
-values by selecting it, typing in the new value and then pressing enter or
-selecting somewhere else in the table.</p>
+can change the individual <span class=SpellE><span class=GramE>Fsq</span></span><span
+class=GramE>(</span><span class=SpellE>hkl</span>) values by selecting it,
+typing in the new value and then pressing enter or selecting somewhere else in
+the table.</p>
 
 <p class=MsoListParagraphCxSpLast><o:p>&nbsp;</o:p></p>
@@ -3776 +3800 @@
 <span style='mso-bookmark:Map_peaks'></span>
 
-<p class=MsoNormal>This gives the list (magnitude, x y &amp; z) of all peaks found
-within the unit cell from the last Fourier map search sorted in order of
-decreasing peak magnitude. The crystal structure plot shows each peak position
-as a white 3-D cross.</p>
+<p class=MsoNormal>This gives the list (magnitude, x y &amp; z) of all peaks
+found within the unit cell from the last Fourier map search sorted in order of decreasing
+peak magnitude. The crystal structure plot shows each peak position as a white
+3-D cross.</p>
 
 <h5>What can I do here?</h5>
@@ -3843 +3867 @@
 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
 mso-no-proof:yes'><img border=0 width=225 height=31 id="_x0000_i1032"
-src=graphbar.jpg alt="Description: Description: D:\pyGSAS\help\graphbar.jpg"></span><span
+src=graphbar.jpg
+alt="Description: Description: Description: D:\pyGSAS\help\graphbar.jpg"></span><span
 style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
 
@@ -3894 +3919 @@
 
 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>The
-powder patterns that are part of your project are shown on this page. They can be
-displayed as a stack of powder patterns, just a single pattern or as a contour
-image of the peak intensities. What can be done here will depend on which is
-displayed and on which item in the GSAS-II data tree you have selected.<o:p></o:p></span></p>
+powder patterns that are part of your project are shown on this page. They can
+be displayed as a stack of powder patterns, just a single pattern or as a
+contour image of the peak intensities. What can be done here will depend on
+which is displayed and on which item in the GSAS-II data tree you have
+selected.<o:p></o:p></span></p>
 
 <h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
@@ -3922 +3948 @@
 auto;text-indent:-.25in;mso-list:l4 level2 lfo22;tab-stops:list 1.0in'><![if !supportLists]><span
 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
-style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
-style='mso-bidi-font-weight:normal'>l: offset left</b> &#8211; for a waterfall
+style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
+class=GramE><b style='mso-bidi-font-weight:normal'>l</b></span><b
+style='mso-bidi-font-weight:normal'>: offset left</b> &#8211; for a waterfall
 plot of multiple powder profiles, increase the offset to the left. Does not
 apply if only one pattern.</p>
@@ -3930 +3957 @@
 auto;text-indent:-.25in;mso-list:l4 level2 lfo22;tab-stops:list 1.0in'><![if !supportLists]><span
 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
-style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
-style='mso-bidi-font-weight:normal'>r: offset right</b> - for a waterfall plot
+style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
+class=GramE><b style='mso-bidi-font-weight:normal'>r</b></span><b
+style='mso-bidi-font-weight:normal'>: offset right</b> - for a waterfall plot
 of multiple powder profiles, increase the offset to the left. Does not apply if
 only one pattern.</p>
@@ -3938 +3966 @@
 auto;text-indent:-.25in;mso-list:l4 level2 lfo22;tab-stops:list 1.0in'><![if !supportLists]><span
 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span
-style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
-style='mso-bidi-font-weight:normal'>d: offset down</b> - for a waterfall plot
-of multiple powder profiles, increase the offset down. Does not apply if only
-one pattern.</p>
+style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
+class=GramE><b style='mso-bidi-font-weight:normal'>d</b></span><b
+style='mso-bidi-font-weight:normal'>: offset down</b> - for a waterfall plot of
+multiple powder profiles, increase the offset down. Does not apply if only one
+pattern.</p>
 
 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
 auto;text-indent:-.25in;mso-list:l4 level2 lfo22;tab-stops:list 1.0in'><![if !supportLists]><span
 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>d.<span
-style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
-style='mso-bidi-font-weight:normal'>u: offset up</b> - for a waterfall plot of multiple
-powder profiles, increase the offset up. Does not apply if only one pattern.</p>
+style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
+class=GramE><b style='mso-bidi-font-weight:normal'>u</b></span><b
+style='mso-bidi-font-weight:normal'>: offset up</b> - for a waterfall plot of
+multiple powder profiles, increase the offset up. Does not apply if only one
+pattern.</p>
 
 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
 auto;text-indent:-.25in;mso-list:l4 level2 lfo22;tab-stops:list 1.0in'><![if !supportLists]><span
 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>e.<span
-style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
-style='mso-bidi-font-weight:normal'>o: reset offset</b> - for a waterfall plot
+style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
+class=GramE><b style='mso-bidi-font-weight:normal'>o</b></span><b
+style='mso-bidi-font-weight:normal'>: reset offset</b> - for a waterfall plot
 of multiple powder profiles, reset to no offset. Does not apply if only one
 pattern.</p>
@@ -3961 +3993 @@
 auto;text-indent:-.25in;mso-list:l4 level2 lfo22;tab-stops:list 1.0in'><![if !supportLists]><span
 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>f.<span
-style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
-style='mso-bidi-font-weight:normal'>n: log(I) on/off</b> &#8211; changes the
+style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
+class=GramE><b style='mso-bidi-font-weight:normal'>n</b></span><b
+style='mso-bidi-font-weight:normal'>: log(I) on/off</b> &#8211; changes the
 y-axis to be the log10 of the intensity; difference curve is not shown for
 log(I) on.</p>
@@ -3969 +4002 @@
 auto;text-indent:-.25in;mso-list:l4 level2 lfo22;tab-stops:list 1.0in'><![if !supportLists]><span
 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>g.<span
-style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
-style='mso-bidi-font-weight:normal'>c: contour on/off</b> &#8211; if multiple
-powder profiles, then a contour plot is shown of the observed intensities. All
-data sets must be the same length as the first one to be included in the contour
+style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
+class=GramE><b style='mso-bidi-font-weight:normal'>c</b></span><b
+style='mso-bidi-font-weight:normal'>: contour on/off</b> &#8211; if multiple powder
+profiles, then a contour plot is shown of the observed intensities. All data
+sets must be the same length as the first one to be included in the contour
 plot.</p>
 
@@ -3988 +4022 @@
 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>i.<span
 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>s: toggle
-single plot</b> &#8211; for multiple powder profiles, this will show only the
-one selected from the data tree. The offset options are not active.</p>
+</span></span></span><![endif]><span class=GramE><b style='mso-bidi-font-weight:
+normal'>s</b></span><b style='mso-bidi-font-weight:normal'>: toggle single plot</b>
+&#8211; for multiple powder profiles, this will show only the one selected from
+the data tree. The offset options are not active.</p>
 
 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
@@ -3996 +4031 @@
 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>j.<span
 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>w: toggle
-divide by sig</b> &#8211; for the pattern selected from the data tree, this
-will divide the observed, calculated and difference curves by the <span
-class=SpellE>esd</span> for the data points. Other data sets are not shown.</p>
+</span></span></span><![endif]><span class=GramE><b style='mso-bidi-font-weight:
+normal'>w</b></span><b style='mso-bidi-font-weight:normal'>: toggle divide by
+sig</b> &#8211; for the pattern selected from the data tree, this will divide
+the observed, calculated and difference curves by the <span class=SpellE>esd</span>
+for the data points. Other data sets are not shown.</p>
 
 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
@@ -4017 +4053 @@
 auto;text-indent:-.25in;mso-list:l4 level2 lfo22;tab-stops:list 1.0in'><![if !supportLists]><span
 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
-style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
-style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>d:
-lower contour max</span></b><span style='mso-fareast-font-family:"Times New Roman"'>
-&#8211; this lowers the level chosen for the highest contour color.<o:p></o:p></span></p>
+style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
+class=GramE><b style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:
+"Times New Roman"'>d</span></b></span><b style='mso-bidi-font-weight:normal'><span
+style='mso-fareast-font-family:"Times New Roman"'>: lower contour max</span></b><span
+style='mso-fareast-font-family:"Times New Roman"'> &#8211; this lowers the
+level chosen for the highest contour color.<o:p></o:p></span></p>
 
 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
@@ -4033 +4071 @@
 auto;text-indent:-.25in;mso-list:l4 level2 lfo22;tab-stops:list 1.0in'><![if !supportLists]><span
 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span
-style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
-style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>i:
-interpolation method</span></b><span style='mso-fareast-font-family:"Times New Roman"'>
-&#8211; this changes the method used to represent the contours. If selected a
-dialog box appears with all the possible choices. Default is
-&#8216;nearest&#8217;; the other useful choice is &#8216;bilinear&#8217;, this
-will smooth out the contours. <o:p></o:p></span></p>
+style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
+class=GramE><b style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:
+"Times New Roman"'>i</span></b></span><b style='mso-bidi-font-weight:normal'><span
+style='mso-fareast-font-family:"Times New Roman"'>: interpolation method</span></b><span
+style='mso-fareast-font-family:"Times New Roman"'> &#8211; this changes the
+method used to represent the contours. If selected a dialog box appears with
+all the possible choices. Default is &#8216;nearest&#8217;; the other useful
+choice is &#8216;bilinear&#8217;, this will smooth out the contours. <o:p></o:p></span></p>
 
 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
 auto;text-indent:-.25in;mso-list:l4 level2 lfo22;tab-stops:list 1.0in'><![if !supportLists]><span
 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>d.<span
-style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
-style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>s:
-color scheme</span></b><span style='mso-fareast-font-family:"Times New Roman"'>
-&#8211; this changes the color scheme for the contouring. Default is
-&#8216;Paired&#8217;, black/ white options are &#8216;Greys&#8217; and
-&#8216;binary&#8217; (for black on white) or &#8216;gray&#8217; (for white on
-black). Others can be very colorful (but not useful)!<o:p></o:p></span></p>
+style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
+class=GramE><b style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:
+"Times New Roman"'>s</span></b></span><b style='mso-bidi-font-weight:normal'><span
+style='mso-fareast-font-family:"Times New Roman"'>: color scheme</span></b><span
+style='mso-fareast-font-family:"Times New Roman"'> &#8211; this changes the
+color scheme for the contouring. Default is <span class=GramE>&#8216;Paired&#8217;,</span>
+black/ white options are &#8216;Greys&#8217; and &#8216;binary&#8217; (for
+black on white) or &#8216;gray&#8217; (for white on black). Others can be very
+colorful (but not useful)!<o:p></o:p></span></p>
 
 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
 auto;text-indent:-.25in;mso-list:l4 level2 lfo22;tab-stops:list 1.0in'><![if !supportLists]><span
 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>e.<span
-style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
-style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>c:
-contour off/on</span></b><span style='mso-fareast-font-family:"Times New Roman"'>
-&#8211; this turns off contouring and returns to a waterfall plot with any
-offsets applied.<o:p></o:p></span></p>
+style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
+class=GramE><b style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:
+"Times New Roman"'>c</span></b></span><b style='mso-bidi-font-weight:normal'><span
+style='mso-fareast-font-family:"Times New Roman"'>: contour off/on</span></b><span
+style='mso-fareast-font-family:"Times New Roman"'> &#8211; this turns off
+contouring and returns to a waterfall plot with any offsets applied.<o:p></o:p></span></p>
 
 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l4 level1 lfo22'><![if !supportLists]><span
@@ -4104 +4146 @@
 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Move
 the mouse cursor across the plot. If on a diagonal cell, the parameter name,
-value and <span class=SpellE>esd</span> is shown both as a tool tip and in the right
-hand portion of the status bar. If the cursor is off the diagonal, the two
-parameter names and their covariance are shown in the tool tip and the status
-bar.</p>
+value and <span class=SpellE>esd</span> is shown both as a tool tip and in the
+right hand portion of the status bar. If the cursor is off the diagonal, the
+two parameter names and their covariance are shown in the tool tip and the
+status bar.</p>
 
 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l7 level1 lfo23'><![if !supportLists]><span
@@ -4117 +4159 @@
 <p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l7 level1 lfo23'><![if !supportLists]><span
 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
-style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Type
-&#8216;s&#8217; &#8211; A color scheme selection dialog is shown. Select a
-color scheme and press OK, the new color scheme will be plotted. The default is
-&#8216;<span class=SpellE>RdYlGn</span>&#8217;.</p>
+style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
+class=GramE>Type &#8216;s&#8217;</span> &#8211; A color scheme selection dialog
+is shown. Select a color scheme and press <span class=GramE>OK,</span> the new
+color scheme will be plotted. The default is &#8216;<span class=SpellE>RdYlGn</span>&#8217;.</p>
 
 <h4><a name="Structure_Factors"><span style='mso-fareast-font-family:"Times New Roman"'>Structure
@@ -4154 +4196 @@
 style='font-family:Symbol;mso-fareast-font-family:"Times New Roman"'>D</span><span
 style='mso-fareast-font-family:"Times New Roman"'>q/q) <span class=SpellE>vs</span>
-q(=2</span><span style='font-family:Symbol;mso-fareast-font-family:"Times New Roman"'>p</span><span
-style='mso-fareast-font-family:"Times New Roman"'>/d) from the Gaussian and
-Lorentzian parts of the profile function. The computed curves are based on the
-values of U, V, W, X and Y shown in the Instrument Parameters window in
-parentheses. These are the values for the instrument contribution that were set
-when the powder pattern was first read in to GSAS-II. If individual peak fitting
-has been performed, the values of &#8216;sig&#8217; &amp; &#8216;gam&#8217; for
-the peaks are plotted as &#8216;+&#8217;; these are computed from the fitted
-values of U, V, W, X and Y as well as any sig or gam individually refined.<o:p></o:p></span></p>
+<span class=GramE>q(</span>=2</span><span style='font-family:Symbol;mso-fareast-font-family:
+"Times New Roman"'>p</span><span style='mso-fareast-font-family:"Times New Roman"'>/d)
+from the Gaussian and Lorentzian parts of the profile function. The computed
+curves are based on the values of U, V, W, X and Y shown in the Instrument
+Parameters window in parentheses. These are the values for the instrument
+contribution that were set when the powder pattern was first read in to
+GSAS-II. If individual peak fitting has been performed, the values of
+&#8216;sig&#8217; &amp; &#8216;gam&#8217; for the peaks are plotted as
+&#8216;+&#8217;; these are computed from the fitted values of U, V, W, X and Y
+as well as any sig or gam individually refined.<o:p></o:p></span></p>
 
 <h4><span style='mso-fareast-font-family:"Times New Roman"'>Texture </span></h4>

trunk/help/gsasII_files/filelist.xml

@@ -2 +2 @@
  <o:MainFile HRef="../gsasII.html"/>
  <o:File HRef="item0010.xml"/>
- <o:File HRef="props0011.xml"/>
+ <o:File HRef="props011.xml"/>
  <o:File HRef="themedata.thmx"/>
  <o:File HRef="colorschememapping.xml"/>

trunk/help/gsasII_files/props011.xml

@@ -1 +1 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
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+<ds:datastoreItem ds:itemID="{C08B664B-EBAE-424A-8DB5-BCA8A35A496B}" xmlns:ds="http://schemas.openxmlformats.org/officeDocument/2006/customXml"><ds:schemaRefs><ds:schemaRef ds:uri="http://schemas.openxmlformats.org/officeDocument/2006/bibliography"/></ds:schemaRefs></ds:datastoreItem>