Changeset 588


Ignore:
Timestamp:
May 6, 2012 3:14:22 PM (9 years ago)
Author:
vondreele
Message:
 
Location:
trunk/help
Files:
1 deleted
22 edited

Legend:

Unmodified
Added
Removed
  • trunk/help/Calibration of an area detector in GSAS.htm

    r585 r588  
    2525  <o:Author>Von Dreele</o:Author>
    2626  <o:LastAuthor>Von Dreele</o:LastAuthor>
    27   <o:Revision>4</o:Revision>
    28   <o:TotalTime>86</o:TotalTime>
     27  <o:Revision>11</o:Revision>
     28  <o:TotalTime>120</o:TotalTime>
    2929  <o:Created>2012-05-04T19:00:00Z</o:Created>
    30   <o:LastSaved>2012-05-04T21:08:00Z</o:LastSaved>
     30  <o:LastSaved>2012-05-05T17:10:00Z</o:LastSaved>
    3131  <o:Pages>4</o:Pages>
    32   <o:Words>910</o:Words>
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     32  <o:Words>709</o:Words>
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    3434  <o:Company>Argonne National Laboratory</o:Company>
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    3838  <o:Version>14.00</o:Version>
    3939 </o:DocumentProperties>
     
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    425 h2
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    451 h3
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    725 span.GramE
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    743771@page WordSection1
    744772        {size:8.5in 11.0in;
     
    762790        mso-style-parent:"";
    763791        mso-padding-alt:0in 5.4pt 0in 5.4pt;
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    771796        font-family:"Calibri","sans-serif";
    772797        mso-ascii-font-family:Calibri;
     
    778803</style>
    779804<![endif]--><!--[if gte mso 9]><xml>
    780  <o:shapedefaults v:ext="edit" spidmax="1027"/>
     805 <o:shapedefaults v:ext="edit" spidmax="1026"/>
    781806</xml><![endif]--><!--[if gte mso 9]><xml>
    782807 <o:shapelayout v:ext="edit">
     
    785810</head>
    786811
    787 <body lang=EN-US link=blue vlink=purple style='tab-interval:.5in'>
     812<body lang=EN-US link="#000000" vlink=purple style='tab-interval:.5in'>
    788813
    789814<div class=WordSection1>
    790815
    791 <div style='mso-element:para-border-div;border:none;border-bottom:solid #4F81BD 1.0pt;
    792 mso-border-bottom-themecolor:accent1;padding:0in 0in 4.0pt 0in'>
    793 
    794 <p class=MsoTitle><span class=Heading1Char><span style='font-size:14.0pt'>Calibration
     816<p class=MsoNormal><span class=Heading1Char><span style='font-size:24.0pt'>Calibration
    795817of an area detector in GSAS-II</span></span><b><span style='font-size:14.0pt;
    796818color:#365F91;mso-themecolor:accent1;mso-themeshade:191'><o:p></o:p></span></b></p>
    797819
    798 </div>
    799 
    800 <p class=MsoNormal>In this demo, data collected with a Perkin-Elmer area
     820<p class=MsoNormal>In this tutorial, data collected with a Perkin-Elmer area
    801821detector at APS 11-ID-C with a wavelength 0.10798 A, where the detector was
    802822intentionally tilted at 45 degrees, are used. Note that menu entries are listed
    803 in bold face below as <b style='mso-bidi-font-weight:normal'>Help/About GSAS-II</b>,
    804 which lists first the name of the menu (here <b style='mso-bidi-font-weight:
    805 normal'>Help</b>) and second the name of the entry in the menu (here <b
    806 style='mso-bidi-font-weight:normal'>About GSAS-II</b>).<o:p></o:p></p>
    807 
    808 <h2><span style='mso-spacerun:yes'> </span>Step 1: Download the data file <o:p></o:p></h2>
    809 
    810 <p class=MsoNormal>Download the sample data file from one of these links:</p>
    811 
    812 <p class=MsoNormal><a
    813 href="https://subversion.xor.aps.anl.gov/trac/pyGSAS/browser/Examples/images/tilt-11ID/La_hex_%2B45deg-00015.tif?format=raw">https://subversion.xor.aps.anl.gov/trac/pyGSAS/browser/Examples/images/tilt-11ID/La_hex_%2B45deg-00015.tif?format=raw</a><o:p></o:p></p>
    814 
    815 <p class=MsoNormal><span style='mso-spacerun:yes'>    </span><span class=GramE>or</span>
    816 </p>
    817 
    818 <p class=MsoNormal><a
    819 href="https://subversion.xor.aps.anl.gov/pyGSAS/Examples/images/tilt-11ID/La_hex_+45deg-00015.tif">https://subversion.xor.aps.anl.gov/pyGSAS/Examples/images/tilt-11ID/La_hex_+45deg-00015.tif</a><o:p></o:p></p>
    820 
    821 <h2>Step 2: Start GSAS-II </h2>
    822 
    823 <p class=MsoNormal>This is done in different ways, depending on your OS and how
    824 GSAS-II is installed. A console window is opened (if necessary) and displays a banner
    825 and some information about the version of python and the packages used by
    826 GSAS-II. This console window will display important information as data
    827 processing by GSAS-II proceeds. You may wish to cut-and-paste parts of this
    828 window to another place if desired.<o:p></o:p></p>
    829 
    830 <p class=MsoNormal style='line-height:normal'><span
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    873 " strokecolor="#eeece1 [3214]" strokeweight="4.5pt">
    874  <v:textbox style='mso-fit-shape-to-text:t'>
    875   <![if !mso]>
    876   <table cellpadding=0 cellspacing=0 width="100%">
    877    <tr>
    878     <td><![endif]>
    879     <div>
    880     <p class=MsoNormal>========================================================================<br>
    881     <span style='mso-spacerun:yes'>               </span>General Structure
    882     Analysis System-II<br>
    883     <span style='mso-spacerun:yes'>             </span>by Robert B. Von <span
    884     class=SpellE>Dreele</span> and Brian H. Toby<br>
    885     <span style='mso-spacerun:yes'>      </span><span
    886     style='mso-spacerun:yes'>         </span>Argonne National Laboratory(C),
    887     2010<br>
    888     <span style='mso-spacerun:yes'> </span>This product includes software
    889     developed by the <span class=SpellE>UChicago</span> Argonne, LLC,<br>
    890     <span style='mso-spacerun:yes'>            </span>as Operator of Argonne
    891     National Laboratory.<br>
    892     ========================================================================<br>
    893     d:\pyGSAS&gt;python d:\pyGSAS\\GSASII.py<br>
    894     Available python module versions for GSASII<span class=GramE>:</span><br>
    895     python:<span style='mso-spacerun:yes'>      </span>2.7.1<br>
    896     <span class=SpellE>wxpython</span>:<span style='mso-spacerun:yes'>   
    897     </span>2.8.10.1<br>
    898     <span class=SpellE>matplotlib</span>:<span style='mso-spacerun:yes'> 
    899     </span>1.0.1<br>
    900     <span class=SpellE>numpy</span>:<span style='mso-spacerun:yes'>      
    901     </span>1.5.1<br>
    902     <span class=SpellE>scipy</span>:<span style='mso-spacerun:yes'>      
    903     </span>0.9.0rc2<br>
    904     OpenGL:<span style='mso-spacerun:yes'>      </span>3.0.1<br>
    905     Max threads<span style='mso-spacerun:yes'>  </span>2<br>
    906     This is GSAS-II version:<span style='mso-spacerun:yes'>      </span>0.1.5<o:p></o:p></p>
    907     </div>
    908     <![if !mso]></td>
    909    </tr>
    910   </table>
    911   <![endif]></v:textbox>
    912  <w:wrap type="none"/>
    913  <w:anchorlock/>
    914 </v:shape><![endif]--><![if !vml]><img width=601 height=396
    915 src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image001.png"
    916 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;"
    917 v:shapes="Text_x0020_Box_x0020_2"><![endif]><!--[if gte vml 1]><v:shapetype
     823in bold face below as <b style='mso-bidi-font-weight:normal'><span
     824style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     825mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Help/About
     826GSAS-II</span></b>, which lists first the name of the menu (here <b
     827style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     828mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     829minor-latin'>Help</span></b>) and second the name of the entry in the menu
     830(here <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     831mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     832minor-latin'>About GSAS-II</span></b>).</p>
     833
     834<p class=MsoNormal><span style='font-size:11.0pt'><o:p>&nbsp;</o:p></span></p>
     835
     836<p class=MsoNormal>If you have not done so already, <u><span style='color:#0070C0'><a
     837href="Starting%20GSAS.htm">start GSAS-II</a></span></u>.<o:p></o:p></p>
     838
     839<h1>Step 1: read in the data file</h1>
     840
     841<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Use the <b
     842style='mso-bidi-font-weight:normal'>Data/Read image data</b> menu item to read
     843the data file into the current GSAS-II project. </p>
     844
     845<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     846
     847<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
    918848 id="_x0000_t75" coordsize="21600,21600" o:spt="75" o:preferrelative="t"
    919849 path="m@4@5l@4@11@9@11@9@5xe" filled="f" stroked="f">
     
    935865 <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
    936866 <o:lock v:ext="edit" aspectratio="t"/>
    937 </v:shapetype><![endif]--><!--[if mso & !supportInlineShapes & supportFields]><v:shape
    938  id="_x0000_i1034" type="#_x0000_t75" style='width:443.25pt;height:289.2pt'>
    939  <v:imagedata croptop="-65520f" cropbottom="65520f"/>
    940 </v:shape><span style='mso-element:field-end'></span><![endif]--></p>
    941 
    942 <p class=MsoNormal>The GSAS-II program has now been started and an empty
    943 project file is created. The project file contains all data and results related
    944 to the project you are working on. (Exception: image files are not stored in
    945 the project; to save space only the file name is saved.) <o:p></o:p></p>
    946 
    947 <p class=MsoNormal><span style='mso-spacerun:yes'> </span>You should see three
    948 windows, two of which are empty. One, in the upper right, is labeled GSASII
    949 data tree, the second, immediately under the first is labeled GSAS-II data
    950 display and the third on the left is labeled GSAS-II Plots. These windows may
    951 be moved anywhere on the screen. On Linux and Windows a menu bar appears at the
    952 top <span class=GramE>of <span style='mso-spacerun:yes'> </span>the</span> data
    953 tree and data display windows; on a Mac these menus will appear in the system
    954 menu bar location (usually at the screen top) depending on which GSAS-II window
    955 has the focus. <o:p></o:p></p>
    956 
    957 <h1>Step 3: read in the data file<o:p></o:p></h1>
    958 
    959 <p class=MsoNormal><span style='mso-spacerun:yes'> </span>Use the <b
    960 style='mso-bidi-font-weight:normal'>Data/Read image data</b> menu item to read
    961 the data file into the current GSAS-II project. <o:p></o:p></p>
    962 
    963 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    964  id="Picture_x0020_1" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:225pt;
    965  height:204.75pt;visibility:visible;mso-wrap-style:square'>
    966  <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image002.png"
     867</v:shapetype><v:shape id="Picture_x0020_1" o:spid="_x0000_i1033" type="#_x0000_t75"
     868 style='width:225pt;height:204.75pt;visibility:visible;mso-wrap-style:square'>
     869 <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image001.png"
    967870  o:title="" croptop="9965f" cropbottom="37297f" cropleft="53272f" cropright="5473f"/>
    968871</v:shape><![endif]--><![if !vml]><img border=0 width=300 height=273
    969 src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image003.jpg"
     872src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image002.jpg"
    970873v:shapes="Picture_x0020_1"><![endif]></span><span
    971874style='mso-spacerun:yes'> </span></p>
    972875
    973876<p class=MsoNormal>A file selection dialog will be shown; its appearance will
    974 depend on your OS. Change the search directory if necessary and then select the
    975 file </p>
    976 
    977 <p class=MsoNormal><b style='mso-bidi-font-weight:normal'><i style='mso-bidi-font-style:
    978 normal'>La_hex_+45deg-<span class=GramE>00015.tif<span style='font-weight:normal;
    979 font-style:normal'> <span style='mso-spacerun:yes'> </span>and</span></span></i></b>
    980 press Open.<span style='mso-no-proof:yes'> </span></p>
     877depend on your OS. Change the search directory to <b style='mso-bidi-font-weight:
     878normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     879minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>/Exercises/images</span></b>
     880and then select the file </p>
     881
     882<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span
     883style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     884mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>La_hex_+45deg-00015.tif</span></b>
     885and press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     886mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     887minor-latin'>Open</span></b>.<span style='mso-no-proof:yes'> <o:p></o:p></span></p>
     888
     889<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    981890
    982891<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    983892 id="Picture_x0020_6" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:225pt;
    984893 height:203.25pt;visibility:visible;mso-wrap-style:square'>
    985  <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image006.png"
     894 <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image003.png"
    986895  o:title=""/>
    987896</v:shape><![endif]--><![if !vml]><img border=0 width=300 height=271
    988 src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image006.png"
     897src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image003.png"
    989898v:shapes="Picture_x0020_6"><![endif]></span></p>
    990899
    991 <p class=MsoNormal>At this point the data tree window will have several entries;
    992 the highlighted one specifies the contents of the data window as <b
    993 style='mso-bidi-font-weight:normal'>Image Controls</b><o:p></o:p></p>
     900<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     901
     902<p class=MsoNormal>At this point the data tree window will have several
     903entries; the highlighted one specifies the contents of the data window as <b
     904style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     905mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     906minor-latin'>Image Controls</span><o:p></o:p></b></p>
     907
     908<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    994909
    995910<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    996911 id="Picture_x0020_5" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:510.75pt;
    997912 height:303pt;visibility:visible;mso-wrap-style:square'>
    998  <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image007.png"
     913 <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image004.png"
    999914  o:title=""/>
    1000915</v:shape><![endif]--><![if !vml]><img border=0 width=681 height=404
    1001 src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image007.png"
     916src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image004.png"
    1002917v:shapes="Picture_x0020_5"><![endif]></span></p>
    1003918
    1004 <p class=MsoNormal><span style='mso-spacerun:yes'> </span><span class=GramE>the</span>
    1005 plot window shows the image; notice the elliptical shape of the powder
    1006 diffraction rings. The x marks the default beam location (image center); your
    1007 calibration will correctly place it.<o:p></o:p></p>
     919<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     920
     921<p class=MsoNormal><span style='mso-spacerun:yes'> </span>The plot window shows
     922the image; notice the elliptical shape of the powder diffraction rings. The
     923blue <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     924mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     925minor-latin;color:#4F81BD;mso-themecolor:accent1'>X</span></b> marks the
     926default beam location (image center); your calibration will correctly place it.
     927Also notice that the values shown in the plot window status bar (at bottom of
     928plot window) change as you move the cursor over the plot; these values are at
     929present in error as they are computed from the default calibration values. They
     930will be correct after you finish the calibration.</p>
     931
     932<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    1008933
    1009934<p class=MsoNormal><span style='mso-spacerun:yes'> </span><span
     
    1011936 o:spid="_x0000_i1030" type="#_x0000_t75" style='width:525pt;height:450pt;
    1012937 visibility:visible;mso-wrap-style:square'>
    1013  <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image008.png"
     938 <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image005.png"
    1014939  o:title=""/>
    1015940</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
    1016 src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image008.png"
    1017 v:shapes="Picture_x0020_4"><![endif]></span><o:p></o:p></p>
    1018 
    1019 <h1><span style='mso-spacerun:yes'> </span>Step 4: Edit image parameters<o:p></o:p></h1>
     941src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image005.png"
     942v:shapes="Picture_x0020_4"><![endif]></span></p>
     943
     944<h1><span style='mso-spacerun:yes'> </span>Step 2: Edit image parameters</h1>
    1020945
    1021946<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Note that, alas, very
    1022947few image formats contain all of the important metadata about the image, so it
    1023948needs to be added manually. In this case set the <b style='mso-bidi-font-weight:
    1024 normal'>wavelength</b> to <b style='mso-bidi-font-weight:normal'>0.10798</b>.
    1025 It is also helpful to change the display of the image so that it is easier to
    1026 see the diffraction rings. Lowering the maximum intensity to 10,000 to 20,000
    1027 counts will help (note that this can be done by moving the <span class=GramE>slider,</span>
    1028 or by typing a value in the box and then clicking on another control or the
    1029 typing the Enter/return key). You may also wish to select another color scheme
    1030 using the Color bar selector. <o:p></o:p></p>
    1031 
    1032 <h1><span style='mso-spacerun:yes'> </span>Step 5: Calibrate<o:p></o:p></h1>
    1033 
    1034 <h3><span style='mso-spacerun:yes'> </span>First: <o:p></o:p></h3>
     949normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     950minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>wavelength</span></b>
     951to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     952mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     953minor-latin'>0.10798</span></b>. It is also helpful to change the display of
     954the image so that it is easier to see the diffraction rings. Lowering the
     955maximum intensity to 10,000 to 20,000 counts will help (note that this can be
     956done by moving the <span class=GramE>slider,</span> or by typing a value in the
     957box and then clicking on another control or pressing the <b style='mso-bidi-font-weight:
     958normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     959minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Enter</span></b>
     960or <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     961mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     962minor-latin'>Tab</span></b> key). You may also wish to select another color
     963scheme using the <b style='mso-bidi-font-weight:normal'><span style='font-family:
     964"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     965minor-latin;mso-bidi-theme-font:minor-latin'>Color bar</span></b> selector. </p>
     966
     967<h1><span style='mso-spacerun:yes'> </span>Step 3: Calibrate</h1>
     968
     969<h3><span style='mso-spacerun:yes'> </span>First: </h3>
    1035970
    1036971<p class=MsoNormal><span style='mso-spacerun:yes'>   </span>Set the material
    1037972used as a sample in the box labeled <span class=SpellE><b style='mso-bidi-font-weight:
    1038 normal'>Calibrant</b></span>; select <b style='mso-bidi-font-weight:normal'>LaB6
    1039 SRM660a</b><o:p></o:p></p>
    1040 
    1041 <h3><span style='mso-spacerun:yes'> </span>Second: <o:p></o:p></h3>
     973normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     974minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Calibrant</span></b></span>;
     975select <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     976mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     977minor-latin'>LaB6 SRM660a</span></b></p>
     978
     979<h3><span style='mso-spacerun:yes'> </span>Second: </h3>
    1042980
    1043981<p class=MsoNormal><span style='mso-spacerun:yes'>   </span>Use the <b
    1044 style='mso-bidi-font-weight:normal'>Operations/Calibrate</b> menu item (note
    1045 this menu is on the <b style='mso-bidi-font-weight:normal'>Image Controls</b>
    1046 window or for the Mac, the <span class=GramE><b style='mso-bidi-font-weight:
    1047 normal'>Image<span style='mso-spacerun:yes'>  </span>Controls</b></span> window
    1048 must be active to place this into the system menu bar). At this point the
    1049 status line on the bottom of the <b style='mso-bidi-font-weight:normal'>Image
    1050 Controls</b> window changes with a prompt to select points for calibration.<o:p></o:p></p>
    1051 
    1052 <h3>Third: <o:p></o:p></h3>
     982style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     983mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     984minor-latin'>Operations/Calibrate</span></b> menu item (note this menu is on
     985the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     986mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     987minor-latin'>Image Controls</span></b> window or for the Mac, the <span
     988class=GramE><b style='mso-bidi-font-weight:normal'><span style='font-family:
     989"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     990minor-latin;mso-bidi-theme-font:minor-latin'>Image<span
     991style='mso-spacerun:yes'>  </span>Controls</span></b></span> window must be
     992active to place this into the system menu bar). At this point the status line
     993on the bottom of the <b style='mso-bidi-font-weight:normal'><span
     994style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     995mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Image
     996Controls</span></b> window changes with a prompt to select points for
     997calibration.</p>
     998
     999<h3>Third: </h3>
    10531000
    10541001<p class=MsoNormal><span style='mso-spacerun:yes'>  </span>Use the left mouse
    10551002button to click on at least five locations on the innermost ring. As each point
    1056 is defined, a red &quot;+&quot; is added to the plot. You need not hit the ring
    1057 exactly as the code will search for the locally highest point. <o:p></o:p></p>
     1003is defined, a red &quot;<b style='mso-bidi-font-weight:normal'><span
     1004style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1005mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin;color:red'>+</span></b>&quot;
     1006is added to the plot. You need not hit the ring exactly as the code will search
     1007for the locally highest point. </p>
     1008
     1009<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    10581010
    10591011<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    10601012 id="Picture_x0020_8" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:525pt;
    10611013 height:450pt;visibility:visible;mso-wrap-style:square'>
    1062  <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image009.png"
     1014 <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image006.png"
    10631015  o:title=""/>
    10641016</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
    1065 src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image009.png"
    1066 v:shapes="Picture_x0020_8"><![endif]></span><o:p></o:p></p>
     1017src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image006.png"
     1018v:shapes="Picture_x0020_8"><![endif]></span></p>
     1019
     1020<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    10671021
    10681022<p class=MsoNormal><span style='mso-spacerun:yes'>  </span>To remove a point
     
    10701024you have a single-button mouse, hold the Command (<span style='font-family:
    10711025"Cambria Math","serif";mso-bidi-font-family:"Cambria Math"'>&#8984;</span>) key
    1072 down and click]. <o:p></o:p></p>
    1073 
    1074 <h3><span style='mso-spacerun:yes'> </span>Fourth:<o:p></o:p></h3>
     1026down and click]. </p>
     1027
     1028<h3><span style='mso-spacerun:yes'> </span>Fourth:</h3>
    10751029
    10761030<p class=MsoNormal><span style='mso-spacerun:yes'>  </span>When done, press the
     
    10781032if you have a single-button mouse, hold the Command (<span style='font-family:
    10791033"Cambria Math","serif";mso-bidi-font-family:"Cambria Math"'>&#8984;</span>) key
    1080 down and click].<o:p></o:p></p>
     1034down and click].</p>
     1035
     1036<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    10811037
    10821038<p class=MsoNormal><span style='mso-spacerun:yes'> </span>The calibration is
    10831039then performed. First the rings are located and an ellipse is optimized for
    10841040each ring. The indexed rings are first shown in red as the calibration proceeds
    1085 and center of each ellipse is noted with a blue &quot;+&quot;. When all rings
    1086 have been fitted, the entire ensemble of rings is refitted to the detector
    1087 parameters and the rings are then shown in blue.<o:p></o:p></p>
     1041and center of each ellipse is noted with a blue &quot;<span style='color:#4F81BD;
     1042mso-themecolor:accent1'>+</span>&quot;. When all rings have been fitted, the
     1043entire ensemble of rings is refitted to the detector parameters and the rings
     1044are then shown in blue. The beam position (blue “<span style='font-family:"Calibri","sans-serif";
     1045mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1046minor-latin;color:#4F81BD;mso-themecolor:accent1'>X</span>”) is now correctly
     1047positioned.</p>
     1048
     1049<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    10881050
    10891051<p class=MsoNormal><span style='mso-spacerun:yes'> </span><span
     
    10911053 o:spid="_x0000_i1028" type="#_x0000_t75" style='width:525pt;height:450pt;
    10921054 visibility:visible;mso-wrap-style:square'>
     1055 <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image007.png"
     1056  o:title=""/>
     1057</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
     1058src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image007.png"
     1059v:shapes="Picture_x0020_9"><![endif]></span><span
     1060style='mso-spacerun:yes'> </span></p>
     1061
     1062<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1063
     1064<p class=MsoNormal>The derived calibration results are shown in the <b
     1065style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1066mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1067minor-latin'>Image Controls</span></b> window.</p>
     1068
     1069<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1070
     1071<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1072 id="Picture_x0020_12" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:510.75pt;
     1073 height:303pt;visibility:visible;mso-wrap-style:square'>
     1074 <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image008.png"
     1075  o:title=""/>
     1076</v:shape><![endif]--><![if !vml]><img border=0 width=681 height=404
     1077src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image008.png"
     1078v:shapes="Picture_x0020_12"><![endif]></span><span
     1079style='mso-spacerun:yes'> </span></p>
     1080
     1081<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1082
     1083<p class=MsoNormal><span class=GramE>and</span> the console window shows
     1084details of the fit; a trial refinement for the wavelength is also given for you
     1085to consider.</p>
     1086
     1087<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1088
     1089<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1090 id="Picture_x0020_14" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:396.75pt;
     1091 height:134.25pt;visibility:visible;mso-wrap-style:square'>
     1092 <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image009.png"
     1093  o:title=""/>
     1094</v:shape><![endif]--><![if !vml]><img border=0 width=529 height=179
     1095src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image009.png"
     1096v:shapes="Picture_x0020_14"><![endif]></span></p>
     1097
     1098<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1099
     1100<p class=MsoNormal><span style='mso-spacerun:yes'> </span>To see the actual
     1101points selected by the program, click on the <b style='mso-bidi-font-weight:
     1102normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1103minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>show
     1104ring picks?</span></b> <span class=GramE>check</span> box </p>
     1105
     1106<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1107
     1108<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1109 id="Picture_x0020_15" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:525pt;
     1110 height:450pt;visibility:visible;mso-wrap-style:square'>
    10931111 <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image010.png"
    10941112  o:title=""/>
    10951113</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
    10961114src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image010.png"
    1097 v:shapes="Picture_x0020_9"><![endif]></span><span
    1098 style='mso-spacerun:yes'> </span></p>
    1099 
    1100 <p class=MsoNormal>The derived calibration results are shown in the Image
    1101 Controls window.<o:p></o:p></p>
    1102 
    1103 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1104  id="Picture_x0020_12" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:510.75pt;
    1105  height:303pt;visibility:visible;mso-wrap-style:square'>
    1106  <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image011.png"
    1107   o:title=""/>
    1108 </v:shape><![endif]--><![if !vml]><img border=0 width=681 height=404
    1109 src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image011.png"
    1110 v:shapes="Picture_x0020_12"><![endif]></span><span
    1111 style='mso-spacerun:yes'> </span></p>
    1112 
    1113 <p class=MsoNormal><span class=GramE>and</span> the console window shows
    1114 details of the fit; a trial refinement for the wavelength is also given for you
    1115 to consider.</p>
    1116 
    1117 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1118  id="Picture_x0020_14" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:396.75pt;
    1119  height:134.25pt;visibility:visible;mso-wrap-style:square'>
    1120  <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image012.png"
    1121   o:title=""/>
    1122 </v:shape><![endif]--><![if !vml]><img border=0 width=529 height=179
    1123 src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image012.png"
    1124 v:shapes="Picture_x0020_14"><![endif]></span><o:p></o:p></p>
    1125 
    1126 <p class=MsoNormal><span style='mso-spacerun:yes'> </span>To see the actual
    1127 points selected by the program, click on the &quot;show ring picks?&quot; check
    1128 button <o:p></o:p></p>
    1129 
    1130 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1131  id="Picture_x0020_15" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:525pt;
    1132  height:450pt;visibility:visible;mso-wrap-style:square'>
    1133  <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image013.png"
    1134   o:title=""/>
    1135 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
    1136 src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image013.png"
    11371115v:shapes="Picture_x0020_15"><![endif]></span><span
    1138 style='mso-spacerun:yes'> </span></p>
    1139 
    1140 <p class=MsoNormal>When this is done, it sometimes occurs that the points selected
    1141 for the outermost ring are scattered between that and the next ring. This can
    1142 be repaired by changing the pixel search range to 10 and using the <b
    1143 style='mso-bidi-font-weight:normal'>Operations/Recalibrate</b> menu item.<o:p></o:p></p>
     1116style='mso-spacerun:yes'> </span><span style='color:#1F497D;mso-themecolor:
     1117text2'><o:p></o:p></span></p>
     1118
     1119<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1120
     1121<p class=MsoNormal>When this is done, it sometimes occurs that the points
     1122selected for the outermost rings are scattered between that and the next ring.
     1123This can be repaired by changing the pixel search range to 10 and using the <b
     1124style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1125mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1126minor-latin'>Operations/Recalibrate</span></b> menu item.</p>
    11441127
    11451128<p class=MsoNormal>Assuming that these calibration results will be applied to
    11461129other images in the same GSAS-II project, click on <b style='mso-bidi-font-weight:
    1147 normal'>Use as default for all images</b>. You may also save a copy of the
    1148 calibration values to a file (<span class=SpellE><i style='mso-bidi-font-style:
    1149 normal'>name</i><b style='mso-bidi-font-weight:normal'>.imctrl</b></span>) with
    1150 the <b style='mso-bidi-font-weight:normal'>Operations/Save Controls</b> menu
    1151 item. To save the project, including the now-derived calibration information,
    1152 use the <b style='mso-bidi-font-weight:normal'>File/Save Project</b> menu item
    1153 associated with the data tree window; as this project has not been saved before
    1154 the file save dialog will need a file name. Don’t enter the extension; it will
    1155 be set to “.<span class=SpellE>gpx</span>”.<o:p></o:p></p>
    1156 
    1157 <h2>Next step: <a href="Integration%20of%20area%20detector%20data%20in%20GSAS.htm">Integrate
    1158 the Data</a></h2>
     1130normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1131minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Use
     1132as default for all images</span></b>. You may also save a copy of the
     1133calibration values to a file <span style='font-family:"Calibri","sans-serif";
     1134mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1135minor-latin'>(<span class=SpellE><i style='mso-bidi-font-style:normal'>name</i><b
     1136style='mso-bidi-font-weight:normal'>.imctrl</b></span></span>) with the <b
     1137style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1138mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1139minor-latin'>Operations/Save Controls</span></b> menu item. To save the
     1140project, including the now-derived calibration information, use the <b
     1141style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1142mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
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     1144style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1145mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Project</span></b><span
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     1147mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'> </span>menu
     1148item associated with the data tree window; as this project has not been saved
     1149before the file save dialog will need a file name. Don’t enter the extension;
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     1154
     1155<h2>Next step: <span class=MsoHyperlink><span style='color:#0070C0'><a
     1156href="Integration%20of%20area%20detector%20data%20in%20GSAS.htm"><u>Integrate
     1157the Data</u></a></span></span></h2>
    11591158
    11601159</div>
  • trunk/help/Calibration of an area detector in GSAS_files/filelist.xml

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     732        margin-bottom:0in;
     733        margin-left:.5in;
     734        margin-bottom:.0001pt;
     735        mso-add-space:auto;
     736        mso-pagination:widow-orphan;
     737        font-size:12.0pt;
     738        font-family:"Times New Roman","serif";
     739        mso-fareast-font-family:"Times New Roman";
     740        mso-fareast-theme-font:minor-fareast;}
     741span.MsoIntenseReference
     742        {mso-style-priority:32;
     743        mso-style-unhide:no;
     744        mso-style-qformat:yes;
     745        font-variant:small-caps;
     746        color:#C0504D;
     747        mso-themecolor:accent2;
     748        letter-spacing:.25pt;
     749        font-weight:bold;
     750        text-decoration:underline;
     751        text-underline:single;}
     752span.Heading1Char
     753        {mso-style-name:"Heading 1 Char";
     754        mso-style-priority:9;
     755        mso-style-unhide:no;
     756        mso-style-locked:yes;
     757        mso-style-link:"Heading 1";
     758        mso-ansi-font-size:24.0pt;
     759        mso-bidi-font-size:24.0pt;
     760        font-family:"Times New Roman","serif";
     761        mso-ascii-font-family:"Times New Roman";
     762        mso-fareast-font-family:"Times New Roman";
     763        mso-fareast-theme-font:minor-fareast;
     764        mso-hansi-font-family:"Times New Roman";
     765        mso-bidi-font-family:"Times New Roman";
     766        mso-font-kerning:18.0pt;
     767        font-weight:bold;}
     768span.Heading2Char
     769        {mso-style-name:"Heading 2 Char";
     770        mso-style-noshow:yes;
     771        mso-style-priority:9;
     772        mso-style-unhide:no;
     773        mso-style-locked:yes;
     774        mso-style-link:"Heading 2";
     775        mso-ansi-font-size:18.0pt;
     776        mso-bidi-font-size:18.0pt;
     777        font-family:"Times New Roman","serif";
     778        mso-ascii-font-family:"Times New Roman";
     779        mso-fareast-font-family:"Times New Roman";
     780        mso-fareast-theme-font:minor-fareast;
     781        mso-hansi-font-family:"Times New Roman";
     782        mso-bidi-font-family:"Times New Roman";
     783        font-weight:bold;}
     784span.Heading3Char
     785        {mso-style-name:"Heading 3 Char";
     786        mso-style-noshow:yes;
     787        mso-style-priority:9;
     788        mso-style-unhide:no;
     789        mso-style-locked:yes;
     790        mso-style-link:"Heading 3";
     791        mso-ansi-font-size:13.5pt;
     792        mso-bidi-font-size:13.5pt;
     793        font-family:"Times New Roman","serif";
     794        mso-ascii-font-family:"Times New Roman";
     795        mso-fareast-font-family:"Times New Roman";
     796        mso-fareast-theme-font:minor-fareast;
     797        mso-hansi-font-family:"Times New Roman";
     798        mso-bidi-font-family:"Times New Roman";
     799        font-weight:bold;}
     800span.Heading4Char
     801        {mso-style-name:"Heading 4 Char";
     802        mso-style-noshow:yes;
     803        mso-style-priority:9;
     804        mso-style-unhide:no;
     805        mso-style-locked:yes;
     806        mso-style-link:"Heading 4";
     807        mso-ansi-font-size:13.0pt;
     808        mso-bidi-font-size:13.0pt;
     809        font-family:"Cambria","serif";
     810        mso-ascii-font-family:Cambria;
     811        mso-ascii-theme-font:major-latin;
     812        mso-fareast-font-family:"Times New Roman";
     813        mso-fareast-theme-font:major-fareast;
     814        mso-hansi-font-family:Cambria;
     815        mso-hansi-theme-font:major-latin;
     816        mso-bidi-font-family:"Times New Roman";
     817        mso-bidi-theme-font:major-bidi;
     818        color:#4F81BD;
     819        mso-themecolor:accent1;
     820        font-weight:bold;
     821        font-style:italic;}
     822span.Heading5Char
     823        {mso-style-name:"Heading 5 Char";
     824        mso-style-noshow:yes;
     825        mso-style-priority:9;
     826        mso-style-unhide:no;
     827        mso-style-locked:yes;
     828        mso-style-link:"Heading 5";
     829        mso-ansi-font-size:12.0pt;
     830        mso-bidi-font-size:12.0pt;
     831        font-family:"Times New Roman","serif";
     832        mso-ascii-font-family:"Times New Roman";
     833        mso-fareast-font-family:"Times New Roman";
     834        mso-fareast-theme-font:minor-fareast;
     835        mso-hansi-font-family:"Times New Roman";
     836        mso-bidi-font-family:"Times New Roman";
     837        color:#4F4FFF;
     838        font-weight:bold;}
     839span.HTMLPreformattedChar
     840        {mso-style-name:"HTML Preformatted Char";
     841        mso-style-noshow:yes;
     842        mso-style-priority:99;
     843        mso-style-unhide:no;
     844        mso-style-locked:yes;
     845        mso-style-link:"HTML Preformatted";
     846        font-family:"Courier New";
     847        mso-ascii-font-family:"Courier New";
     848        mso-fareast-font-family:"Times New Roman";
     849        mso-hansi-font-family:"Courier New";
     850        mso-bidi-font-family:"Courier New";}
    564851span.TitleChar
    565852        {mso-style-name:"Title Char";
     
    584871        letter-spacing:.25pt;
    585872        mso-font-kerning:14.0pt;}
    586 span.Heading1Char
    587         {mso-style-name:"Heading 1 Char";
    588         mso-style-priority:9;
     873span.DocumentMapChar
     874        {mso-style-name:"Document Map Char";
     875        mso-style-noshow:yes;
     876        mso-style-priority:99;
    589877        mso-style-unhide:no;
    590878        mso-style-locked:yes;
    591         mso-style-link:"Heading 1";
    592         mso-ansi-font-size:14.0pt;
    593         mso-bidi-font-size:14.0pt;
    594         font-family:"Cambria","serif";
    595         mso-ascii-font-family:Cambria;
    596         mso-ascii-theme-font:major-latin;
    597         mso-fareast-font-family:"Times New Roman";
    598         mso-fareast-theme-font:major-fareast;
    599         mso-hansi-font-family:Cambria;
    600         mso-hansi-theme-font:major-latin;
    601         mso-bidi-font-family:"Times New Roman";
    602         mso-bidi-theme-font:major-bidi;
    603         color:#365F91;
    604         mso-themecolor:accent1;
    605         mso-themeshade:191;
    606         font-weight:bold;}
    607 span.Heading2Char
    608         {mso-style-name:"Heading 2 Char";
    609         mso-style-priority:9;
     879        mso-style-link:"Document Map";
     880        mso-ansi-font-size:8.0pt;
     881        mso-bidi-font-size:8.0pt;
     882        font-family:"Tahoma","sans-serif";
     883        mso-ascii-font-family:Tahoma;
     884        mso-fareast-font-family:"Times New Roman";
     885        mso-fareast-theme-font:minor-fareast;
     886        mso-hansi-font-family:Tahoma;
     887        mso-bidi-font-family:Tahoma;}
     888span.BalloonTextChar
     889        {mso-style-name:"Balloon Text Char";
     890        mso-style-noshow:yes;
     891        mso-style-priority:99;
    610892        mso-style-unhide:no;
    611893        mso-style-locked:yes;
    612         mso-style-link:"Heading 2";
    613         mso-ansi-font-size:13.0pt;
    614         mso-bidi-font-size:13.0pt;
    615         font-family:"Cambria","serif";
    616         mso-ascii-font-family:Cambria;
    617         mso-ascii-theme-font:major-latin;
    618         mso-fareast-font-family:"Times New Roman";
    619         mso-fareast-theme-font:major-fareast;
    620         mso-hansi-font-family:Cambria;
    621         mso-hansi-theme-font:major-latin;
    622         mso-bidi-font-family:"Times New Roman";
    623         mso-bidi-theme-font:major-bidi;
    624         color:#4F81BD;
    625         mso-themecolor:accent1;
    626         font-weight:bold;}
     894        mso-style-link:"Balloon Text";
     895        mso-ansi-font-size:8.0pt;
     896        mso-bidi-font-size:8.0pt;
     897        font-family:"Tahoma","sans-serif";
     898        mso-ascii-font-family:Tahoma;
     899        mso-fareast-font-family:"Times New Roman";
     900        mso-fareast-theme-font:minor-fareast;
     901        mso-hansi-font-family:Tahoma;
     902        mso-bidi-font-family:Tahoma;}
    627903span.SpellE
    628904        {mso-style-name:"";
    629905        mso-spl-e:yes;}
     906span.GramE
     907        {mso-style-name:"";
     908        mso-gram-e:yes;}
    630909.MsoChpDefault
    631910        {mso-style-type:export-only;
     
    634913        mso-ansi-font-size:10.0pt;
    635914        mso-bidi-font-size:10.0pt;
     915        font-family:"Calibri","sans-serif";
    636916        mso-ascii-font-family:Calibri;
    637917        mso-ascii-theme-font:minor-latin;
     
    650930div.WordSection1
    651931        {page:WordSection1;}
     932 /* List Definitions */
     933 @list l0
     934        {mso-list-id:608973138;
     935        mso-list-type:hybrid;
     936        mso-list-template-ids:-1449999034 67698703 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
     937@list l0:level1
     938        {mso-level-tab-stop:none;
     939        mso-level-number-position:left;
     940        text-indent:-.25in;}
     941@list l0:level2
     942        {mso-level-number-format:alpha-lower;
     943        mso-level-tab-stop:none;
     944        mso-level-number-position:left;
     945        text-indent:-.25in;}
     946@list l0:level3
     947        {mso-level-number-format:roman-lower;
     948        mso-level-tab-stop:none;
     949        mso-level-number-position:right;
     950        text-indent:-9.0pt;}
     951@list l0:level4
     952        {mso-level-tab-stop:none;
     953        mso-level-number-position:left;
     954        text-indent:-.25in;}
     955@list l0:level5
     956        {mso-level-number-format:alpha-lower;
     957        mso-level-tab-stop:none;
     958        mso-level-number-position:left;
     959        text-indent:-.25in;}
     960@list l0:level6
     961        {mso-level-number-format:roman-lower;
     962        mso-level-tab-stop:none;
     963        mso-level-number-position:right;
     964        text-indent:-9.0pt;}
     965@list l0:level7
     966        {mso-level-tab-stop:none;
     967        mso-level-number-position:left;
     968        text-indent:-.25in;}
     969@list l0:level8
     970        {mso-level-number-format:alpha-lower;
     971        mso-level-tab-stop:none;
     972        mso-level-number-position:left;
     973        text-indent:-.25in;}
     974@list l0:level9
     975        {mso-level-number-format:roman-lower;
     976        mso-level-tab-stop:none;
     977        mso-level-number-position:right;
     978        text-indent:-9.0pt;}
     979@list l1
     980        {mso-list-id:894583186;
     981        mso-list-type:hybrid;
     982        mso-list-template-ids:1821937756 67698703 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
     983@list l1:level1
     984        {mso-level-tab-stop:none;
     985        mso-level-number-position:left;
     986        margin-left:39.0pt;
     987        text-indent:-.25in;}
     988@list l1:level2
     989        {mso-level-number-format:alpha-lower;
     990        mso-level-tab-stop:none;
     991        mso-level-number-position:left;
     992        margin-left:75.0pt;
     993        text-indent:-.25in;}
     994@list l1:level3
     995        {mso-level-number-format:roman-lower;
     996        mso-level-tab-stop:none;
     997        mso-level-number-position:right;
     998        margin-left:111.0pt;
     999        text-indent:-9.0pt;}
     1000@list l1:level4
     1001        {mso-level-tab-stop:none;
     1002        mso-level-number-position:left;
     1003        margin-left:147.0pt;
     1004        text-indent:-.25in;}
     1005@list l1:level5
     1006        {mso-level-number-format:alpha-lower;
     1007        mso-level-tab-stop:none;
     1008        mso-level-number-position:left;
     1009        margin-left:183.0pt;
     1010        text-indent:-.25in;}
     1011@list l1:level6
     1012        {mso-level-number-format:roman-lower;
     1013        mso-level-tab-stop:none;
     1014        mso-level-number-position:right;
     1015        margin-left:219.0pt;
     1016        text-indent:-9.0pt;}
     1017@list l1:level7
     1018        {mso-level-tab-stop:none;
     1019        mso-level-number-position:left;
     1020        margin-left:255.0pt;
     1021        text-indent:-.25in;}
     1022@list l1:level8
     1023        {mso-level-number-format:alpha-lower;
     1024        mso-level-tab-stop:none;
     1025        mso-level-number-position:left;
     1026        margin-left:291.0pt;
     1027        text-indent:-.25in;}
     1028@list l1:level9
     1029        {mso-level-number-format:roman-lower;
     1030        mso-level-tab-stop:none;
     1031        mso-level-number-position:right;
     1032        margin-left:327.0pt;
     1033        text-indent:-9.0pt;}
     1034@list l2
     1035        {mso-list-id:983856491;
     1036        mso-list-type:hybrid;
     1037        mso-list-template-ids:-44896332 67698703 67698713 461011134 67698703 67698713 67698715 67698703 67698713 67698715;}
     1038@list l2:level1
     1039        {mso-level-tab-stop:none;
     1040        mso-level-number-position:left;
     1041        text-indent:-.25in;}
     1042@list l2:level2
     1043        {mso-level-number-format:alpha-lower;
     1044        mso-level-tab-stop:none;
     1045        mso-level-number-position:left;
     1046        text-indent:-.25in;}
     1047@list l2:level3
     1048        {mso-level-start-at:0;
     1049        mso-level-number-format:bullet;
     1050        mso-level-text:\F0B7;
     1051        mso-level-tab-stop:none;
     1052        mso-level-number-position:left;
     1053        margin-left:117.0pt;
     1054        text-indent:-.25in;
     1055        font-family:Symbol;
     1056        mso-fareast-font-family:"Times New Roman";
     1057        mso-fareast-theme-font:minor-fareast;
     1058        mso-bidi-font-family:"Times New Roman";}
     1059@list l2:level4
     1060        {mso-level-tab-stop:none;
     1061        mso-level-number-position:left;
     1062        text-indent:-.25in;}
     1063@list l2:level5
     1064        {mso-level-number-format:alpha-lower;
     1065        mso-level-tab-stop:none;
     1066        mso-level-number-position:left;
     1067        text-indent:-.25in;}
     1068@list l2:level6
     1069        {mso-level-number-format:roman-lower;
     1070        mso-level-tab-stop:none;
     1071        mso-level-number-position:right;
     1072        text-indent:-9.0pt;}
     1073@list l2:level7
     1074        {mso-level-tab-stop:none;
     1075        mso-level-number-position:left;
     1076        text-indent:-.25in;}
     1077@list l2:level8
     1078        {mso-level-number-format:alpha-lower;
     1079        mso-level-tab-stop:none;
     1080        mso-level-number-position:left;
     1081        text-indent:-.25in;}
     1082@list l2:level9
     1083        {mso-level-number-format:roman-lower;
     1084        mso-level-tab-stop:none;
     1085        mso-level-number-position:right;
     1086        text-indent:-9.0pt;}
     1087ol
     1088        {margin-bottom:0in;}
     1089ul
     1090        {margin-bottom:0in;}
    6521091-->
    6531092</style>
     
    6611100        mso-style-noshow:yes;
    6621101        mso-style-priority:99;
    663         mso-style-qformat:yes;
    6641102        mso-style-parent:"";
    6651103        mso-padding-alt:0in 5.4pt 0in 5.4pt;
     
    6771115</style>
    6781116<![endif]--><!--[if gte mso 9]><xml>
    679  <o:shapedefaults v:ext="edit" spidmax="2050"/>
     1117 <o:shapedefaults v:ext="edit" spidmax="1026"/>
    6801118</xml><![endif]--><!--[if gte mso 9]><xml>
    6811119 <o:shapelayout v:ext="edit">
     
    6841122</head>
    6851123
    686 <body lang=EN-US style='tab-interval:.5in'>
     1124<body lang=EN-US link=blue vlink=purple style='tab-interval:.5in'>
    6871125
    6881126<div class=WordSection1>
    6891127
    690 <h1><span style='mso-spacerun:yes'> </span>Fit Peaks/<span class=SpellE>Autoindexing</span>
    691 in GSAS-II </h1>
    692 
    693 <p class=MsoNormal>In this exercise you will use the GSAS-II program to search
    694 for a unit cell that matches a set of diffraction peaks -- a process known as
    695 auto-indexing. First peaks must be located and optimized and then indexing can be
    696 done.</p>
    697 
    698 <h2>Step 1: read in data</h2>
    699 
    700 <p class=MsoNormal>Download the sample data file and matching instrument
    701 parameter file from these links:</p>
    702 
    703 <p class=MsoNormal><span style='mso-spacerun:yes'>   
    704 </span>https://subversion.xor.aps.anl.gov/trac/pyGSAS/browser/Examples/powder%20data/11bmb_3844.fxye?format=raw</p>
    705 
    706 <p class=MsoNormal><span style='mso-spacerun:yes'>   
    707 </span>https://subversion.xor.aps.anl.gov/trac/pyGSAS/browser/Examples/powder%20data/11bmb_3844.prm?format=raw</p>
    708 
    709 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    710 
    711 <p class=MsoNormal><span style='mso-spacerun:yes'>    </span>(One can also use
    712 this links<span style='mso-spacerun:yes'>    </span></p>
    713 
    714 <p class=MsoNormal><span style='mso-spacerun:yes'>   
    715 </span>https://subversion.xor.aps.anl.gov/pyGSAS/Examples/powder%20data/11bmb_3844.fxye
    716 and </p>
    717 
    718 <p class=MsoNormal><span style='mso-spacerun:yes'>   
    719 </span>https://subversion.xor.aps.anl.gov/pyGSAS/Examples/powder%20data/11bmb_3844.prm</p>
    720 
    721 <p class=MsoNormal><span style='mso-spacerun:yes'>    </span>to obtain the
    722 file, but this is more complex).</p>
    723 
    724 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    725 
    726 <h2>Step 2: Start GSAS-II </h2>
    727 
    728 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    729 
    730 <p class=MsoNormal><span style='mso-spacerun:yes'> </span>This is done in
    731 different ways, depending on your OS and how GSAS-II is installed.</p>
    732 
    733 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    734 
    735 <p class=MsoNormal>=== Step 3: read in the data file ===</p>
    736 
    737 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    738 
    739 <p class=MsoNormal><span style='mso-spacerun:yes'> </span>Use the '''Data/Read
    740 powder data''' menu item to read the data file into the current GSAS-II
    741 project. </p>
     1128<h1>Fit Peaks/<span class=SpellE>Autoindexing</span> in GSAS-II </h1>
     1129
     1130<p class=MsoNormal>In this exercise you will use GSAS-II to search for a unit
     1131cell that matches a set of diffraction peaks -- a process known as
     1132auto-indexing. First peaks must be located and optimized and then indexing can
     1133be done.</p>
     1134
     1135<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1136
     1137<p class=MsoNormal>If you have not done so already, <a
     1138href="Starting%20GSAS.htm">start GSAS-II</a>.</p>
     1139
     1140<h2>Step 1: read in the data file</h2>
     1141
     1142<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
     1143style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
     1144style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Use
     1145the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1146mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1147minor-latin'>Data/Read powder data</span></b> menu item to read the data file
     1148into the current GSAS-II project. This read option is set to read any of the
     1149powder data formats (except neutron TOF time map files) defined for GSAS
     1150(angles in <span class=SpellE>centidegrees</span>). It will also read the <span
     1151class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
     1152"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1153minor-latin;mso-bidi-theme-font:minor-latin'>xye</span></b></span> format
     1154(angles in degrees) used by <span class=SpellE>Topas</span>, etc.<span
     1155style='mso-spacerun:yes'>  </span>Change the file directory to <b
     1156style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1157mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1158minor-latin'>Exercises/LaB6</span></b><span style='font-family:"Calibri","sans-serif";
     1159mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1160minor-latin'> to find the file; you may need to change the file type to <b
     1161style='mso-bidi-font-weight:normal'>All files (*.*)</b> to find the desired
     1162file.</span></p>
     1163
     1164<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
     1165style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
     1166style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
     1167the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1168mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1169minor-latin'>11bmb_3844.fxye</span></b><span style='font-family:"Calibri","sans-serif";
     1170mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1171minor-latin'> data</span> file in the first dialog and press <b
     1172style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1173mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1174minor-latin'>Open</span></b>. There will be a Dialog box asking <span
     1175class=GramE><b style='mso-bidi-font-weight:normal'><span style='font-family:
     1176"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1177minor-latin;mso-bidi-theme-font:minor-latin'>Is</span></b></span><b
     1178style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1179mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1180minor-latin'> this the file you want?</span></b> Press <span class=GramE><b
     1181style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1182mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1183minor-latin'>Yes</span></b></span> button to proceed.</p>
     1184
     1185<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
     1186style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
     1187style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
     1188the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1189mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1190minor-latin'>11bmb_3844.prm</span></b> instrument parameter file in the second
     1191dialog and press <b style='mso-bidi-font-weight:normal'><span style='font-family:
     1192"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1193minor-latin;mso-bidi-theme-font:minor-latin'>Open</span></b>. The 11BM-B
     1194instrument processing software automatically produced this file when the
     1195corresponding <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
     1196style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1197mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>fxye</span></b></span>
     1198file was created from the 12 detector raw data.</p>
     1199
     1200<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1201
     1202<p class=MsoNormal>At this point the <b style='mso-bidi-font-weight:normal'><span
     1203style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1204mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II data
     1205tree</span></b> window will have several entries </p>
     1206
     1207<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1208
     1209<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
     1210 id="_x0000_t75" coordsize="21600,21600" o:spt="75" o:preferrelative="t"
     1211 path="m@4@5l@4@11@9@11@9@5xe" filled="f" stroked="f">
     1212 <v:stroke joinstyle="miter"/>
     1213 <v:formulas>
     1214  <v:f eqn="if lineDrawn pixelLineWidth 0"/>
     1215  <v:f eqn="sum @0 1 0"/>
     1216  <v:f eqn="sum 0 0 @1"/>
     1217  <v:f eqn="prod @2 1 2"/>
     1218  <v:f eqn="prod @3 21600 pixelWidth"/>
     1219  <v:f eqn="prod @3 21600 pixelHeight"/>
     1220  <v:f eqn="sum @0 0 1"/>
     1221  <v:f eqn="prod @6 1 2"/>
     1222  <v:f eqn="prod @7 21600 pixelWidth"/>
     1223  <v:f eqn="sum @8 21600 0"/>
     1224  <v:f eqn="prod @7 21600 pixelHeight"/>
     1225  <v:f eqn="sum @10 21600 0"/>
     1226 </v:formulas>
     1227 <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
     1228 <o:lock v:ext="edit" aspectratio="t"/>
     1229</v:shapetype><v:shape id="Picture_x0020_1" o:spid="_x0000_i1047" type="#_x0000_t75"
     1230 style='width:225pt;height:187.5pt;visibility:visible;mso-wrap-style:square'>
     1231 <v:imagedata src="Fit%20Peaks_files/image001.png" o:title=""/>
     1232</v:shape><![endif]--><![if !vml]><img border=0 width=300 height=250
     1233src="Fit%20Peaks_files/image001.png" v:shapes="Picture_x0020_1"><![endif]></span></p>
     1234
     1235<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1236
     1237<p class=MsoNormal><span class=GramE>and</span> the plot window will show the
     1238powder pattern</p>
     1239
     1240<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1241
     1242<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1243 id="Picture_x0020_2" o:spid="_x0000_i1046" type="#_x0000_t75" style='width:525pt;
     1244 height:450pt;visibility:visible;mso-wrap-style:square'>
     1245 <v:imagedata src="Fit%20Peaks_files/image002.png" o:title=""/>
     1246</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
     1247src="Fit%20Peaks_files/image002.png" v:shapes="Picture_x0020_2"><![endif]></span></p>
     1248
     1249<h2>Step 2: Select Limits </h2>
     1250
     1251<p class=MsoNormal><span style='mso-spacerun:yes'> </span>This pattern has much
     1252more data than we need, so it is helpful to cut down the range. Click on the <b
     1253style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1254mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1255minor-latin'>Limits</span></b> item in the <b style='mso-bidi-font-weight:normal'><span
     1256style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1257mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II data
     1258tree</span></b>. The small window is repainted. Use the <b style='mso-bidi-font-weight:
     1259normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1260minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>changed</span></b>
     1261row of entry boxes to set <span class=SpellE><b style='mso-bidi-font-weight:
     1262normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1263minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Tmin</span></b></span>
     1264and <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
     1265style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1266mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Tmax</span></b></span>
     1267to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1268mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1269minor-latin'>4</span></b> and <b style='mso-bidi-font-weight:normal'><span
     1270style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1271mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>27.5</span></b>.
     1272Notice on the plot that the limit lines have moved to these positions; the
     1273green lower limit is just below the 1<sup>st</sup> peak and the red upper limit
     1274is in a wide gap between peaks. You may also drag the limit lines to the
     1275desired location or place them by a left mouse click on a data point for the
     1276lower limit or a right click on a data point for the upper limit.</p>
     1277
     1278<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1279
     1280<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1281 id="Picture_x0020_4" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:225pt;
     1282 height:120pt;visibility:visible;mso-wrap-style:square'>
     1283 <v:imagedata src="Fit%20Peaks_files/image003.png" o:title=""/>
     1284</v:shape><![endif]--><![if !vml]><img border=0 width=300 height=160
     1285src="Fit%20Peaks_files/image003.png" v:shapes="Picture_x0020_4"><![endif]></span></p>
     1286
     1287<h2>Step 3: Determine Peak Positions</h2>
     1288
     1289<p class=MsoListParagraph style='margin-left:39.0pt;mso-add-space:auto;
     1290text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
     1291style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
     1292style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Click
     1293on the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1294mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1295minor-latin'>Peak List</span></b> item in the <b style='mso-bidi-font-weight:
     1296normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1297minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II
     1298data tree</span></b>. This creates an empty window of peak positions (the <b
     1299style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1300mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1301minor-latin'>Limits</span></b> window is erased). At this point it is wise to </p>
     1302
     1303<p class=MsoNormal><span style='mso-spacerun:yes'> </span><span class=GramE>zoom</span>
     1304in on the data that will be used for indexing. </p>
     1305
     1306<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1307
     1308<p class=MsoListParagraph style='margin-left:39.0pt;mso-add-space:auto;
     1309text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
     1310style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
     1311style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Click
     1312on the Zoom button, <span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1313 id="Picture_x0020_5" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:21.75pt;
     1314 height:18.75pt;visibility:visible;mso-wrap-style:square'>
     1315 <v:imagedata src="Fit%20Peaks_files/image004.jpg" o:title="" croptop="1f"
     1316  cropbottom="-1f" cropleft="35827f" cropright="19224f"/>
     1317</v:shape><![endif]--><![if !vml]><img border=0 width=29 height=25
     1318src="Fit%20Peaks_files/image005.jpg" v:shapes="Picture_x0020_5"><![endif]></span>,
     1319then press the left mouse in one corner of the region to be used; holding the
     1320mouse button down, drag over the region to the opposite corner; a box will be
     1321drawn over the region to be zoomed. </p>
     1322
     1323<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1324
     1325<p class=MsoListParagraph style='margin-left:39.0pt;mso-add-space:auto;
     1326text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
     1327style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
     1328style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     1329style='mso-bidi-font-weight:normal'>Important</b>: Click on the Zoom <span
     1330style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_6"
     1331 o:spid="_x0000_i1043" type="#_x0000_t75" style='width:23.25pt;height:20.25pt;
     1332 visibility:visible;mso-wrap-style:square'>
     1333 <v:imagedata src="Fit%20Peaks_files/image004.jpg" o:title="" croptop="1f"
     1334  cropbottom="-1f" cropleft="35827f" cropright="19224f"/>
     1335</v:shape><![endif]--><![if !vml]><img border=0 width=31 height=27
     1336src="Fit%20Peaks_files/image006.jpg" v:shapes="Picture_x0020_6"><![endif]></span><span
     1337style='mso-spacerun:yes'> </span>button again to turn off the zoom mode. </p>
     1338
     1339<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1340
     1341<p class=MsoListParagraphCxSpFirst style='margin-left:39.0pt;mso-add-space:
     1342auto;text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
     1343style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
     1344style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Using
     1345the left mouse button, click on a data point near the top of each peak to be added
     1346to the peak list. It is usually best to start at the upper end of the pattern
     1347as the next peak to pick isn’t obscured by the tool tip. As this is done, a
     1348vertical blue line is drawn in the plot window<span style='mso-spacerun:yes'> 
     1349</span>for each peak selected</p>
     1350
     1351<p class=MsoListParagraphCxSpMiddle><o:p>&nbsp;</o:p></p>
     1352
     1353<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
     1354auto'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="_x0000_i1042"
     1355 type="#_x0000_t75" style='width:525pt;height:450pt;visibility:visible;
     1356 mso-wrap-style:square'>
     1357 <v:imagedata src="Fit%20Peaks_files/image007.png" o:title=""/>
     1358</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
     1359src="Fit%20Peaks_files/image007.png" v:shapes="_x0000_i1042"><![endif]></span></p>
     1360
     1361<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
     1362auto'><o:p>&nbsp;</o:p></p>
     1363
     1364<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
     1365auto'><span class=GramE>and</span> peaks are added to the <b style='mso-bidi-font-weight:
     1366normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1367minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak
     1368List</span></b> window in order of increasing 2<span style='font-family:Symbol'>Q</span>.</p>
     1369
     1370<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
     1371auto'><o:p>&nbsp;</o:p></p>
     1372
     1373<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
     1374auto'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_7"
     1375 o:spid="_x0000_i1041" type="#_x0000_t75" style='width:401.25pt;height:262.5pt;
     1376 visibility:visible;mso-wrap-style:square'>
     1377 <v:imagedata src="Fit%20Peaks_files/image008.png" o:title=""/>
     1378</v:shape><![endif]--><![if !vml]><img border=0 width=535 height=350
     1379src="Fit%20Peaks_files/image008.png" v:shapes="Picture_x0020_7"><![endif]></span></p>
     1380
     1381<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
     1382auto'><o:p>&nbsp;</o:p></p>
     1383
     1384<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
     1385auto'>Note that if peaks are not being added, you probably have not exited zoom
     1386mode.</p>
     1387
     1388<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
     1389auto'><o:p>&nbsp;</o:p></p>
     1390
     1391<p class=MsoListParagraphCxSpLast style='margin-left:39.0pt;mso-add-space:auto'>Add
     1392approximately 20-25 peaks total to the peak list (there will be 20 in this
     1393example). Be sure to add the lowest angle peaks that are visible in the plot.
     1394You may drag a peak position as needed; be sure the zoom/shift buttons are off.
     1395A position may be deleted with a right click with the mouse on the blue line.</p>
     1396
     1397<h2>Step 4: Refine Peak Positions</h2>
     1398
     1399<p class=MsoNormal>This refinement proceeds stepwise; first doing the default
     1400refinement and then adding <span class=GramE>a parameters</span> to complete
     1401the fitting,</p>
     1402
     1403<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1404
     1405<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
     1406style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
     1407style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Refine
     1408the peak intensities and the background. These parameters have their refinement
     1409flags turned on by default. Use the menu item <b style='mso-bidi-font-weight:
     1410normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1411minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak
     1412Fitting/LSQ <span class=SpellE>PeakFit</span> </span></b>on the<b
     1413style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1414mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1415minor-latin'> Peak List </span></b>window. Do <b style='mso-bidi-font-weight:
     1416normal'>NOT</b> use the <b style='mso-bidi-font-weight:normal'><span
     1417style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1418mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Calculate/Refine</span></b>
     1419menu item in the <b style='mso-bidi-font-weight:normal'><span style='font-family:
     1420"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1421minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II data tree</span></b>
     1422window; that it to be used for Rietveld/Pawley refinements. You will be asked
     1423to save the current project before the fit will proceed; change directory if
     1424desired and provide a suitable name (we assume <b style='mso-bidi-font-weight:
     1425normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1426minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>LaB6</span></b>).
     1427A window will show the progress of the refinement and will close when the
     1428least-squares fit <span class=GramE>is</span> complete (usually very fast). The
     1429plot is updated with the fit, the peak list window is updated with the new peak
     1430values and a summary of the refinement is shown on the console window as well.</p>
     1431
     1432<p class=MsoListParagraphCxSpMiddle><o:p>&nbsp;</o:p></p>
     1433
     1434<p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1435 id="Picture_x0020_8" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:525pt;
     1436 height:450pt;visibility:visible;mso-wrap-style:square'>
     1437 <v:imagedata src="Fit%20Peaks_files/image009.png" o:title=""/>
     1438</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
     1439src="Fit%20Peaks_files/image009.png" v:shapes="Picture_x0020_8"><![endif]></span></p>
     1440
     1441<p class=MsoListParagraphCxSpMiddle><o:p>&nbsp;</o:p></p>
     1442
     1443<p class=MsoListParagraphCxSpLast><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1444 id="Picture_x0020_9" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:401.25pt;
     1445 height:262.5pt;visibility:visible;mso-wrap-style:square'>
     1446 <v:imagedata src="Fit%20Peaks_files/image010.png" o:title=""/>
     1447</v:shape><![endif]--><![if !vml]><img border=0 width=535 height=350
     1448src="Fit%20Peaks_files/image010.png" v:shapes="Picture_x0020_9"><![endif]></span></p>
     1449
     1450<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1451
     1452<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
     1453style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
     1454style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Now
     1455add refinement of the peak positions. This can be done by clicking on all the refinement
     1456flags for the individual peaks or it is possible to set them all at the same
     1457time using this recipe: </p>
     1458
     1459<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     1460auto;text-indent:-.25in;mso-list:l2 level2 lfo6'><![if !supportLists]><span
     1461style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
     1462style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     1463class=GramE>single-click</span> on any value in the table to select it, for
     1464example the first peak position. A black box appears around the value. If the
     1465field if opened for editing (the box turns to blue), select a different item in
     1466the table.</p>
     1467
     1468<p class=MsoListParagraphCxSpLast style='margin-left:1.0in;mso-add-space:auto;
     1469text-indent:-.25in;mso-list:l2 level2 lfo6'><![if !supportLists]><span
     1470style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
     1471style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     1472class=GramE>double-click</span> on the refine label above the peak position
     1473check-boxes. The entire column of checkboxes is highlighted in blue. Press the <b
     1474style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1475mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1476minor-latin'>y</span></b> key to turn on all refinement flags (<b
     1477style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1478mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1479minor-latin'>n</span></b> would turn them off).</p>
    7421480
    7431481<p class=MsoNormal><span style='mso-spacerun:yes'> </span></p>
    7441482
    745 <p class=MsoNormal><span style='mso-spacerun:yes'> </span>Select the
    746 {{{11bmb_3844.fxye}}} data file in the first dialog and press Open.</p>
    747 
    748 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    749 
    750 <p class=MsoNormal><span style='mso-spacerun:yes'> </span>Select the
    751 {{{11bmb_3844.prm}}} instrument parameter file in the second dialog and press
    752 Open.</p>
    753 
    754 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    755 
    756 <p class=MsoNormal><span style='mso-spacerun:yes'>    </span>At this point the
    757 data tree window will have several entries </p>
    758 
    759 <p class=MsoNormal><span style='mso-spacerun:yes'>   
    760 </span>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d3w2.png
    761 view]);</p>
    762 
    763 <p class=MsoNormal><span style='mso-spacerun:yes'>    </span>and the plot
    764 window will show the powder pattern</p>
    765 
    766 <p class=MsoNormal><span style='mso-spacerun:yes'>   
    767 </span>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d3w1.png
    768 view]).</p>
    769 
    770 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    771 
    772 <p class=MsoNormal>=== Step 4: Select Data Range ===</p>
    773 
    774 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    775 
    776 <p class=MsoNormal><span style='mso-spacerun:yes'> </span>This pattern has much
    777 more data than we need, so it is helpful to cut down the range. Click on the Limits
    778 item in the data tree. A new window is created. Use the &quot;changed&quot; row
    779 of entry boxes to set <span class=SpellE>Tmin</span> and <span class=SpellE>Tmax</span>
    780 to 4 and 30. You may also drag the limits lines to the desired location or
    781 place them by a left mouse click on a data point for the lower limit or a right
    782 click on a data point for the upper limit.</p>
    783 
    784 <p class=MsoNormal><span
    785 style='mso-spacerun:yes'> </span>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d3w3.png
    786 view]). </p>
    787 
    788 <p class=MsoNormal><span style='mso-spacerun:yes'> </span>Note the green and
    789 red vertical lines in the plot window move. </p>
    790 
    791 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    792 
    793 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    794 
    795 <p class=MsoNormal>=== Step 5: Determine Peak Positions ===</p>
    796 
    797 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    798 
    799 <p class=MsoNormal><span style='mso-spacerun:yes'> </span>Click on the Peak
    800 List item in the data tree. This creates an empty window of peak positions. At
    801 this point it is wise to </p>
    802 
    803 <p class=MsoNormal><span style='mso-spacerun:yes'> </span>zoom in on the data
    804 that will be used for indexing. This can be done by clicking on this button:</p>
    805 
    806 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    807 
    808 <p class=MsoNormal><span style='mso-spacerun:yes'> </span>Click on the
    809 magnification button: [[Image(d3z1.png)]], then press the left mouse in one
    810 corner of the region to be used; holding the mouse button down, drag over the
    811 region to the opposite corner. </p>
    812 
    813 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    814 
    815 <p class=MsoNormal><span style='mso-spacerun:yes'> </span>'''Important:'''
    816 Click on the magnification [[Image(d3z1.png)]] button again to turn off the
    817 zoom mode. </p>
    818 
    819 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    820 
    821 <p class=MsoNormal><span style='mso-spacerun:yes'>  </span>Using the left mouse
    822 button click on a data point near the top of each peak to be added to the peak
    823 list. As this is done, a line is </p>
    824 
    825 <p class=MsoNormal><span style='mso-spacerun:yes'>  </span>drawn in the plot
    826 window</p>
    827 
    828 <p class=MsoNormal><span style='mso-spacerun:yes'> 
    829 </span>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d3w4.png
    830 view]) and</p>
    831 
    832 <p class=MsoNormal><span style='mso-spacerun:yes'>  </span>peaks are added to
    833 the Peak List window</p>
    834 
    835 <p class=MsoNormal><span style='mso-spacerun:yes'> 
    836 </span>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d3w5.png
    837 view]). Note that if peaks are </p>
    838 
    839 <p class=MsoNormal><span style='mso-spacerun:yes'>  </span>not being added, you
    840 probably have not exited zoom mode.</p>
    841 
    842 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    843 
    844 <p class=MsoNormal><span style='mso-spacerun:yes'>  </span>Once peaks in that
    845 region have been added, move to a new region of the pattern. This can be done
    846 by clicking on the shift button: [[Image(d3z2.png)]]. Dragging with the left
    847 mouse will shift the data to follow the mouse. Clicking with the right button (on
    848 the Mac, control + mouse) and moving up increases the vertical scale and to the
    849 right increases the horizontal scale.<span style='mso-spacerun:yes'> 
    850 </span>'''Important:''' Click on the shift [[Image(d3z2.png)]] button again to
    851 turn off this mode. </p>
    852 
    853 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    854 
    855 <p class=MsoNormal><span style='mso-spacerun:yes'>  </span>Again, using the
    856 left mouse button, click on the tops of more peaks to be added to the peak
    857 list. Note that if peaks are </p>
    858 
    859 <p class=MsoNormal><span style='mso-spacerun:yes'>  </span>not being added, you
    860 probably have not exited shift mode.</p>
    861 
    862 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    863 
    864 <p class=MsoNormal><span style='mso-spacerun:yes'>  </span>Add approximately 24
    865 peaks total to the peak list. Be sure to add the lowest angle peaks that are
    866 visible in the plot. You may drag a peak position as needed; be sure the
    867 zoom/shift buttons are off. A position may be deleted with a right click with
    868 the mouse on the blue line.</p>
    869 
    870 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    871 
    872 <p class=MsoNormal>=== Step 6: Refine Peak Positions ===</p>
    873 
    874 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    875 
    876 <p class=MsoNormal>First, refine the peak intensities and the background. These
    877 parameters have their refinement flag turned on by default. Use the menu item
    878 '''Peak Fitting/LSQ !<span class=SpellE>PeakFit</span>'''. A window will show
    879 the progress of the refinement and will close when the least squares is
    880 complete. A summary of the refinement is shown on the console window as well.</p>
    881 
    882 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    883 
    884 <p class=MsoNormal>Second, add refinement of the peak positions. This can be
    885 done by clicking on all the refinement flags for the individual peaks or it is
    886 possible to set them all at the same time using this recipe: </p>
    887 
    888 <p class=MsoNormal><span style='mso-spacerun:yes'> </span>* single-click on any
    889 value in the table to select it, for example the first peak position. A black
    890 box appears around the value. If the field if opened for editing (the box turns
    891 to blue), select a different item in the table.</p>
    892 
    893 <p class=MsoNormal><span style='mso-spacerun:yes'> </span>* double-click on the
    894 refine label above the peak position check-boxes. The entire column of
    895 checkboxes is highlighted in blue. Press the y key to turn on all refinement
    896 flags (n would turn them off).</p>
     1483<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
     1484style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
     1485style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Next,
     1486repeat the refinement using the <b style='mso-bidi-font-weight:normal'><span
     1487style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1488mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak
     1489Fitting/LSQ <span class=SpellE>PeakFit</span></span></b> menu item in the <b
     1490style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1491mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1492minor-latin'>Peak List</span></b> window.</p>
    8971493
    8981494<p class=MsoNormal><span style='mso-spacerun:yes'> </span></p>
    8991495
    900 <p class=MsoNormal>Third, repeat the refinement using the '''Peak Fitting/LSQ !<span
    901 class=SpellE>PeakFit</span>''' menu item.</p>
    902 
    903 <p class=MsoNormal><span style='mso-spacerun:yes'> </span></p>
    904 
    905 <p class=MsoNormal>Fourth, select peak widths for refinement. This can be done
    906 by refining sigma (Gaussian width) and/or gamma (Lorentzian width) for
    907 individual peaks, but here we constrain the peaks to follow an instrumental
    908 broadening equation. Select the Instrumental Parameters item in the data tree. </p>
    909 
    910 <p class=MsoNormal>This opens a window for peak profile terms</p>
    911 
    912 <p class=MsoNormal>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d3w6.png
    913 view]). </p>
    914 
    915 <p class=MsoNormal>Select the refine flag checkbox for Gaussian U, V, W,
    916 Lorentzian X, Y and the asymmetry parameter SH/L. </p>
    917 
    918 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    919 
    920 <p class=MsoNormal>Fifth, repeat the refinement. First click on the Peak List
    921 item in the data tree and then refine using the '''Peak Fitting/LSQ !<span
    922 class=SpellE>PeakFit</span>''' menu item. At this point a good fit should be
    923 seen by zooming in on individual peaks. (For example see </p>
    924 
    925 <p class=MsoNormal>[https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d3w7.png
    926 this]). The <span class=SpellE>Rwp</span> is ~6% as shown on the console
    927 window.</p>
    928 
    929 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    930 
    931 <p class=MsoNormal>=== Prepare Indexing Peak List ===</p>
    932 
    933 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1496<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
     1497style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
     1498style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Now,
     1499select peak widths for refinement. This can be done by refining sigma (Gaussian
     1500width) and/or gamma (Lorentzian width) for individual peaks, but here we can
     1501constrain the peaks to follow an instrumental broadening equation. Select the <b
     1502style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1503mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1504minor-latin'>Instrumental Parameters</span></b> item in the data tree. This
     1505opens a window for peak profile terms<br>
     1506<br>
     1507<span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_10"
     1508 o:spid="_x0000_i1038" type="#_x0000_t75" style='width:422.25pt;height:154.5pt;
     1509 visibility:visible;mso-wrap-style:square'>
     1510 <v:imagedata src="Fit%20Peaks_files/image011.png" o:title=""/>
     1511</v:shape><![endif]--><![if !vml]><img border=0 width=563 height=206
     1512src="Fit%20Peaks_files/image011.png" v:shapes="Picture_x0020_10"><![endif]></span></p>
     1513
     1514<p class=MsoListParagraphCxSpMiddle><o:p>&nbsp;</o:p></p>
     1515
     1516<p class=MsoListParagraphCxSpLast>The plot window shows the resolution curves
     1517corresponding to the values of the Gaussian U, V, W, Lorentzian X &amp; Y
     1518coefficients; ‘+’ marks show the individual values based on the sig &amp; gam
     1519values for the peaks in Peak List. Select the refine flag checkbox for Gaussian
     1520U, V, W, and Lorentzian X, Y. </p>
     1521
     1522<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1523
     1524<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
     1525style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>5.<span
     1526style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Then,
     1527repeat the refinement. First click on the <b style='mso-bidi-font-weight:normal'><span
     1528style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1529mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak List</span></b>
     1530item in the data tree and then refine using the <b style='mso-bidi-font-weight:
     1531normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1532minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak
     1533Fitting/LSQ <span class=SpellE>PeakFit</span></span></b> menu item. At this
     1534point a good fit should be seen by zooming in on individual peaks. (For example
     1535see </p>
     1536
     1537<p class=MsoListParagraphCxSpMiddle><o:p>&nbsp;</o:p></p>
     1538
     1539<p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1540 id="Picture_x0020_11" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:525pt;
     1541 height:450pt;visibility:visible;mso-wrap-style:square'>
     1542 <v:imagedata src="Fit%20Peaks_files/image012.png" o:title=""/>
     1543</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
     1544src="Fit%20Peaks_files/image012.png" v:shapes="Picture_x0020_11"><![endif]></span></p>
     1545
     1546<p class=MsoListParagraphCxSpMiddle><o:p>&nbsp;</o:p></p>
     1547
     1548<p class=MsoListParagraphCxSpLast>The <span class=SpellE>Rwp</span> is ~6% as
     1549shown on the console window. Again the <b style='mso-bidi-font-weight:normal'><span
     1550style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1551mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak List</span></b>
     1552entries are all updated with new values and those in <b style='mso-bidi-font-weight:
     1553normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1554minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Instrument
     1555Parameters</span></b> are also updated.</p>
     1556
     1557<h2><span class=GramE>Step 5.</span> Prepare Indexing Peak List</h2>
    9341558
    9351559<p class=MsoNormal>A separate list of peaks is kept for use in <span
    936 class=SpellE>autoindexing</span>. This list is manipulated by clicking on the
    937 Index Peak List item in the data tree. In the initially empty window created by
    938 this action, use menu item '''Index Peaks Operations/Load''' to copy over the
    939 fitted peaks from the Peak List tree entry</p>
    940 
    941 <p class=MsoNormal>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d4w1.png
    942 view]). </p>
    943 
    944 <p class=MsoNormal>Note that by default all peaks are selected to be used. </p>
    945 
    946 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    947 
    948 <p class=MsoNormal>=== Run <span class=SpellE>Autoindexing</span> ===</p>
    949 
    950 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    951 
    952 <p class=MsoNormal>Select the Unit Cells List data item. This brings up a
    953 window for indexing and cell refinement options</p>
    954 
    955 <p class=MsoNormal>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d4w2.png
    956 view]). For the most rapid search (since we know the right answer), select
    957 Cubic-P and launch the search using menu item '''Cell Index/Index Cell'''. The
    958 search then runs and he console shows a running list of possible cells as they
    959 are found; the sorted by M20 list of possible matching cells is shown in the
    960 window</p>
    961 
    962 <p class=MsoNormal>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d4w3.png
    963 view]). </p>
    964 
    965 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    966 
    967 <p class=MsoNormal>=== Review Cell Choices === </p>
    968 
    969 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    970 
    971 <p class=MsoNormal>Review the list of cells associated with the Unit Cells List
    972 data item. Note that as one selects a unit cell, the generated reflections for that
    973 cell are shown in the plot with dashed red lines. Sliding the cursor over these
    974 lines shows a small popup window with the indexed <span class=SpellE>hkl</span>
    975 for them. Note how the 8.312 A cell generates very many lines with no
    976 corresponding peaks </p>
    977 
    978 <p class=MsoNormal>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d4w4.png
    979 view])</p>
    980 
    981 <p class=MsoNormal>while the 2.939 A cell generates not enough lines to match
    982 all the peaks</p>
    983 
    984 <p class=MsoNormal>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d4w5.png
    985 view]). </p>
    986 
    987 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    988 
    989 <p class=MsoNormal>=== Select/Refine Cell === </p>
    990 
    991 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    992 
    993 <p class=MsoNormal>Select the top option, a 4.1568 A cell with M20 figure of
    994 merit of 2700. This indexes all peaks, though peak positions are not exactly
    995 perfect if one zooms in enough. Import the cell information using the '''Cell
    996 Index/Copy Cell''' menu option. Then optimize the cell by refining the lattice
    997 parameters and the two-theta zero: click on the refine checkbox next to the
    998 Zero offset value and then the '''Cell Index/Refine Cell''' menu option. The a
    999 cell parameter value shifts from 4.15679 to 4.15684 when zero is refined. </p>
    1000 
    1001 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    1002 
    1003 <p class=MsoNormal>(Optional) Finally, use of the '''Cell Index/New phase'''
    1004 menu option allows one to assign a phase with these lattice parameters to the
    1005 data set (histogram). A name for the new phase is then requested. This adds a
    1006 Phases entry to the data tree, as well as an entry for the new phase. This new
    1007 phase can be used in future code.</p>
     1560class=SpellE>autoindexing</span>. It is found in the <b style='mso-bidi-font-weight:
     1561normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1562minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Index
     1563Peak List</span></b> item in the data tree. In the initially empty window
     1564created by this action, use menu item <b style='mso-bidi-font-weight:normal'><span
     1565style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1566mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Index Peaks
     1567Operations/Load</span></b> to copy the fitted peaks from the <b
     1568style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1569mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1570minor-latin'>Peak List</span></b>.</p>
     1571
     1572<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1573
     1574<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1575 id="Picture_x0020_12" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:367.5pt;
     1576 height:225pt;visibility:visible;mso-wrap-style:square'>
     1577 <v:imagedata src="Fit%20Peaks_files/image013.png" o:title=""/>
     1578</v:shape><![endif]--><![if !vml]><img border=0 width=490 height=300
     1579src="Fit%20Peaks_files/image013.png" v:shapes="Picture_x0020_12"><![endif]></span></p>
     1580
     1581<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1582
     1583<p class=MsoNormal>Note that by default all peaks are selected to be used. You
     1584may choose to not use a fitted peak (e.g. if suspected as from a contaminant).</p>
     1585
     1586<h2><span class=GramE>Step 6.</span> Run <span class=SpellE>Autoindexing</span></h2>
     1587
     1588<p class=MsoNormal>Select the <b style='mso-bidi-font-weight:normal'><span
     1589style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1590mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Unit Cells
     1591List</span></b> data item. This brings up a window for indexing and cell
     1592refinement options</p>
     1593
     1594<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1595
     1596<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1597 id="Picture_x0020_13" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:527.25pt;
     1598 height:204pt;visibility:visible;mso-wrap-style:square'>
     1599 <v:imagedata src="Fit%20Peaks_files/image014.png" o:title=""/>
     1600</v:shape><![endif]--><![if !vml]><img border=0 width=703 height=272
     1601src="Fit%20Peaks_files/image014.png" v:shapes="Picture_x0020_13"><![endif]></span></p>
     1602
     1603<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1604
     1605<p class=MsoNormal>For the most rapid search (since we know the right answer),
     1606select <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1607mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1608minor-latin'>Cubic-P</span></b> and launch the search using menu item <b
     1609style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1610mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1611minor-latin'>Cell Index/Index Cell</span></b>. The search then runs and the
     1612console shows a running list of possible cells as they are found; the sorted by
     1613M20 list of possible matching cells is shown in the <b style='mso-bidi-font-weight:
     1614normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1615minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Unit
     1616Cells List</span></b> window</p>
     1617
     1618<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1619
     1620<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1621 id="Picture_x0020_14" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:527.25pt;
     1622 height:376.5pt;visibility:visible;mso-wrap-style:square'>
     1623 <v:imagedata src="Fit%20Peaks_files/image015.png" o:title=""/>
     1624</v:shape><![endif]--><![if !vml]><img border=0 width=703 height=502
     1625src="Fit%20Peaks_files/image015.png" v:shapes="Picture_x0020_14"><![endif]></span></p>
     1626
     1627<h2><span class=GramE>Step 7.</span> Review Cell Choices</h2>
     1628
     1629<p class=MsoNormal>Review the list of cells associated with the <b
     1630style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1631mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1632minor-latin'>Unit Cells List</span></b> data item. Note that as one selects a
     1633unit cell, the generated reflections for that cell are shown in the plot with
     1634dashed red lines. Sliding the cursor over these lines shows a small popup
     1635window with the indexed <span class=SpellE>hkl</span> for them. Note how the
     1636first cell in the list (M20=2961.34) with a=5.87864 Å generates very many lines
     1637with no corresponding peaks</p>
     1638
     1639<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1640
     1641<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1642 id="Picture_x0020_15" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:525pt;
     1643 height:450pt;visibility:visible;mso-wrap-style:square'>
     1644 <v:imagedata src="Fit%20Peaks_files/image016.png" o:title=""/>
     1645</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
     1646src="Fit%20Peaks_files/image016.png" v:shapes="Picture_x0020_15"><![endif]></span><span
     1647style='mso-spacerun:yes'> </span></p>
     1648
     1649<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1650
     1651<p class=MsoNormal><span class=GramE>while</span> the (M20=609.02) cell with
     1652a=2.93932 Å generates not enough lines to match all the peaks</p>
     1653
     1654<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1655
     1656<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1657 id="Picture_x0020_16" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:525pt;
     1658 height:450pt;visibility:visible;mso-wrap-style:square'>
     1659 <v:imagedata src="Fit%20Peaks_files/image017.png" o:title=""/>
     1660</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
     1661src="Fit%20Peaks_files/image017.png" v:shapes="Picture_x0020_16"><![endif]></span></p>
     1662
     1663<h2><span class=GramE>Step 8.</span> Select/Refine Cell</h2>
     1664
     1665<p class=MsoNormal>Select the cell with M20 = 2961.34 with a = 4.1568 Å. This
     1666indexes all peaks with almost a perfect fit to the peak positions (compare
     1667dashed red lines to solid blue ones). Import the cell information using the <b
     1668style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1669mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1670minor-latin'>Cell Index/Copy Cell</span></b> menu option. Then optimize the
     1671cell by refining the lattice parameters and the two-theta zero: click on the
     1672refine checkbox next to the <b style='mso-bidi-font-weight:normal'><span
     1673style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1674mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Zero offset</span></b>
     1675value and then the <b style='mso-bidi-font-weight:normal'><span
     1676style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1677mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Cell
     1678Index/Refine Cell</span></b> menu option. <span class=GramE>The a</span> cell
     1679parameter value shifts from 4.15679 to 4.15684 when zero is refined. Press the <b
     1680style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1681mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1682minor-latin'>Show refined <span class=SpellE>hkl</span> positions + Zero offset</span></b>
     1683button to update the plot including the refined <b style='mso-bidi-font-weight:
     1684normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1685minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Zero
     1686offset</span></b> (in this case hardly anything happens!) </p>
     1687
     1688<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1689
     1690<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1691 id="Picture_x0020_17" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:527.25pt;
     1692 height:334.5pt;visibility:visible;mso-wrap-style:square'>
     1693 <v:imagedata src="Fit%20Peaks_files/image018.png" o:title=""/>
     1694</v:shape><![endif]--><![if !vml]><img border=0 width=703 height=446
     1695src="Fit%20Peaks_files/image018.png" v:shapes="Picture_x0020_17"><![endif]></span></p>
     1696
     1697<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1698
     1699<p class=MsoNormal>Notice that a new entry heads the list in the <b
     1700style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1701mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1702minor-latin'>Indexing Result</span></b> section of the <b style='mso-bidi-font-weight:
     1703normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1704minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Cell
     1705Index/Refine</span></b> window with an improved M20(=3614.66) and a new value
     1706for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1707mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1708minor-latin'>Zero offset</span></b> is shown.</p>
     1709
     1710<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1711
     1712<p class=MsoNormal>(Optional) Finally, use of the <b style='mso-bidi-font-weight:
     1713normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1714minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Cell
     1715Index/New phase</span></b> menu option allows one to create a phase with these
     1716lattice parameters in the data tree under <b style='mso-bidi-font-weight:normal'><span
     1717style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1718mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Phases</span></b>.<span
     1719style='mso-spacerun:yes'>  </span>A name for the new phase is requested. This
     1720creates the tree item <b style='mso-bidi-font-weight:normal'><span
     1721style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1722mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Phases</span></b>
     1723(if it wasn’t already present). This new phase can be used in future analysis
     1724(e.g. Rietveld or Pawley refinement).</p>
     1725
     1726<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1727
     1728<p class=MsoNormal>To continue with the second part of this exercise, <span
     1729class=GramE>do the menu item</span> <b style='mso-bidi-font-weight:normal'><span
     1730style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1731mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>File/Close
     1732project</span></b> in the <b style='mso-bidi-font-weight:normal'><span
     1733style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1734mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II data
     1735tree </span></b>window. You will be asked if you want it saved; if <span
     1736class=GramE><b style='mso-bidi-font-weight:normal'><span style='font-family:
     1737"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1738minor-latin;mso-bidi-theme-font:minor-latin'>Yes</span></b></span> then all the
     1739peak fitting/indexing &amp; cell refinement results will be saved to the <b
     1740style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1741mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1742minor-latin'>LaB6.gpx</span></b> file. If <b style='mso-bidi-font-weight:normal'><span
     1743style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1744mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>No</span></b>
     1745then the file will remain as it was when created at Step 4 above.</p>
     1746
     1747<h1>2<sup>nd</sup> Fit Peaks/<span class=SpellE>Autoindexing</span> in GSAS-II </h1>
     1748
     1749<p class=MsoNormal>In this exercise we will fit peaks and index them for the
     1750new mineral <span class=SpellE>jadarite</span> (aka “kryptonite”). The data was
     1751also collected on 11BM-B at APS. The unit cell is monoclinic so is a more
     1752substantial test of the indexing capability of GSAS-II.</p>
     1753
     1754<h2><span class=GramE>Step 1.</span> Read in the data. </h2>
     1755
     1756<p class=MsoNormal>The file is <b style='mso-bidi-font-weight:normal'><span
     1757style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1758mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>\Exercises\<span
     1759class=SpellE>krptonite</span>\11bmb_6231.fxye</span></b>; it has a
     1760corresponding <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
     1761style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1762mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>prm</span></b></span>
     1763file. Load them in &amp; the plot is</p>
     1764
     1765<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1766
     1767<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1768 id="Picture_x0020_18" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:525pt;
     1769 height:450pt;visibility:visible;mso-wrap-style:square'>
     1770 <v:imagedata src="Fit%20Peaks_files/image019.png" o:title=""/>
     1771</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
     1772src="Fit%20Peaks_files/image019.png" v:shapes="Picture_x0020_18"><![endif]></span></p>
     1773
     1774<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1775
     1776<p class=MsoNormal>I’ve zoomed in &amp; shifted the plot some to highlight the
     1777lower part of the pattern.</p>
     1778
     1779<h2>Step 2 Set limits</h2>
     1780
     1781<p class=MsoNormal>Set the limits as 3 and 10.</p>
     1782
     1783<h2>Step 3 Pick peaks</h2>
     1784
     1785<p class=MsoNormal>Pick all peaks you can see between the limits (including the
     1786small ones). Note some peaks have shoulders most notably at 5.07, 6.04,
     17877.81deg. I found 28 peaks (there were a few very weak ones I skipped – they
     1788might be from a second phase? We’ll see later).</p>
     1789
     1790<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1791
     1792<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1793 id="Picture_x0020_19" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:525pt;
     1794 height:450pt;visibility:visible;mso-wrap-style:square'>
     1795 <v:imagedata src="Fit%20Peaks_files/image020.png" o:title=""/>
     1796</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
     1797src="Fit%20Peaks_files/image020.png" v:shapes="Picture_x0020_19"><![endif]></span></p>
     1798
     1799<h2><span class=GramE>Step 4.</span> Refine peaks</h2>
     1800
     1801<p class=MsoNormal>Following the steps above, refine the peaks and the profile
     1802shape parameters in Instrument parameters. You will be asked for a project file
     1803name at the first refinement (I used ‘<span class=SpellE>jadarite</span>’). In
     1804the end my refinement converged at <span class=SpellE>Rwp</span>=13.18% and
     1805some peaks do show some discrepancy as the sample is more complex than the
     1806simple U, V, W, X, Y model can accommodate. However, this is good enough to
     1807proceed.</p>
     1808
     1809<h2><span class=GramE>Step 5.</span> Prepare Indexing Peak List</h2>
     1810
     1811<p class=MsoNormal>As before do <b style='mso-bidi-font-weight:normal'><span
     1812style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1813mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Operations/Load/Reload</span></b>
     1814in the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1815mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1816minor-latin'>Index Peak List</span></b> window.</p>
     1817
     1818<h2><span class=GramE>Step 6.</span> Index the cell</h2>
     1819
     1820<p class=MsoNormal>Let’s assume that we know the cell in primitive monoclinic.
     1821In a real world case we wouldn’t know this and we would have to try each <span
     1822class=SpellE>Bravais</span> lattice. These can be done as a group, but it takes
     1823time to go through all the bad cases.</p>
     1824
     1825<p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span
     1826style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1827mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Monoclinic-P</span></b>
     1828and do <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1829mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1830minor-latin'>Cell Index/Refine/Index cell</span></b> in the <b
     1831style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1832mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1833minor-latin'>Unit Cells List</span></b> window. Progress will be much slower
     1834and suitable results will be slow in coming so be patient. Watch the console
     1835window; the right answer will have an obviously large M20 (~630) and a volume
     1836of ~594Å<sup>3</sup> (10<sup>th</sup> column of console display). Once this is
     1837seen (it may take more than one try to get this) you can stop the indexing
     1838search by pressing <b style='mso-bidi-font-weight:normal'><span
     1839style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1840mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Cancel</span></b>
     1841on the progress bar window. It may take more than one press to fully stop it.
     1842My result was </p>
     1843
     1844<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1845
     1846<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1847 id="Picture_x0020_20" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:527.25pt;
     1848 height:376.5pt;visibility:visible;mso-wrap-style:square'>
     1849 <v:imagedata src="Fit%20Peaks_files/image021.png" o:title=""/>
     1850</v:shape><![endif]--><![if !vml]><img border=0 width=703 height=502
     1851src="Fit%20Peaks_files/image021.png" v:shapes="Picture_x0020_20"><![endif]></span></p>
     1852
     1853<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1854
     1855<p class=MsoNormal>Notice an equally good M20 result with twice the volume. The
     1856plot shows every peak indexed including a couple of weak peaks not selected for
     1857the peak fitting.</p>
     1858
     1859<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1860
     1861<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1862 id="Picture_x0020_21" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:525pt;
     1863 height:450pt;visibility:visible;mso-wrap-style:square'>
     1864 <v:imagedata src="Fit%20Peaks_files/image022.png" o:title=""/>
     1865</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
     1866src="Fit%20Peaks_files/image022.png" v:shapes="Picture_x0020_21"><![endif]></span></p>
     1867
     1868<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1869
     1870<p class=MsoNormal>Although the weak peak at 2<span style='font-family:Symbol'>Q</span>~7.3
     1871has a shoulder that wasn’t indexed. I presume that is a contaminant. By sliding
     1872the cursor over the index lines without any visible peak you can see that the
     1873missing ones are (010, 100, 001, 110, 030, 111, 20-1, 10-2, 041, 050, 21-2,
     187423-1, 22-2, 141, 201,102, 15-1, 112, &amp; 24-1). Many of these are accidental
     1875but the 0k0; k&#8800;2n and h0l; h+l&#8800;2n ones characterize the space group
     1876P2<sub>1</sub>/n. Armed with this information you can <b style='mso-bidi-font-weight:
     1877normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1878minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Make
     1879new phase</span></b> for the indexed cell (I called it ‘kryptonite’) and set
     1880the space group in the Phase Data for kryptonite window.</p>
     1881
     1882<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1883
     1884<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1885 id="Picture_x0020_22" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:597.75pt;
     1886 height:214.5pt;visibility:visible;mso-wrap-style:square'>
     1887 <v:imagedata src="Fit%20Peaks_files/image023.png" o:title=""/>
     1888</v:shape><![endif]--><![if !vml]><img border=0 width=797 height=286
     1889src="Fit%20Peaks_files/image023.png" v:shapes="Picture_x0020_22"><![endif]></span></p>
     1890
     1891<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1892
     1893<p class=MsoNormal>Setting the space group will show a window with some
     1894information. Press <b style='mso-bidi-font-weight:normal'><span
     1895style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1896mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>OK</span></b>
     1897to close it.</p>
     1898
     1899<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1900
     1901<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1902 id="Picture_x0020_23" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:333.75pt;
     1903 height:209.25pt;visibility:visible;mso-wrap-style:square'>
     1904 <v:imagedata src="Fit%20Peaks_files/image024.png" o:title=""/>
     1905</v:shape><![endif]--><![if !vml]><img border=0 width=445 height=279
     1906src="Fit%20Peaks_files/image024.png" v:shapes="Picture_x0020_23"><![endif]></span></p>
     1907
     1908<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1909
     1910<p class=MsoNormal>This concludes this exercise. The features of the Phase Data
     1911window will be presented in other exercises.</p>
    10081912
    10091913</div>
  • trunk/help/Fit Peaks_files/filelist.xml

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     888        mso-hansi-font-family:Tahoma;
     889        mso-bidi-font-family:Tahoma;}
     890span.BalloonTextChar
     891        {mso-style-name:"Balloon Text Char";
     892        mso-style-noshow:yes;
     893        mso-style-priority:99;
     894        mso-style-unhide:no;
     895        mso-style-locked:yes;
     896        mso-style-link:"Balloon Text";
     897        mso-ansi-font-size:8.0pt;
     898        mso-bidi-font-size:8.0pt;
     899        font-family:"Tahoma","sans-serif";
     900        mso-ascii-font-family:Tahoma;
     901        mso-fareast-font-family:"Times New Roman";
     902        mso-fareast-theme-font:minor-fareast;
     903        mso-hansi-font-family:Tahoma;
     904        mso-bidi-font-family:Tahoma;}
    895905span.SpellE
    896906        {mso-style-name:"";
    897907        mso-spl-e:yes;}
     908span.GramE
     909        {mso-style-name:"";
     910        mso-gram-e:yes;}
    898911.MsoChpDefault
    899912        {mso-style-type:export-only;
     
    902915        mso-ansi-font-size:10.0pt;
    903916        mso-bidi-font-size:10.0pt;
     917        font-family:"Calibri","sans-serif";
    904918        mso-ascii-font-family:Calibri;
    905919        mso-ascii-theme-font:minor-latin;
     
    929943        mso-style-noshow:yes;
    930944        mso-style-priority:99;
    931         mso-style-qformat:yes;
    932945        mso-style-parent:"";
    933946        mso-padding-alt:0in 5.4pt 0in 5.4pt;
     
    945958</style>
    946959<![endif]--><!--[if gte mso 9]><xml>
    947  <o:shapedefaults v:ext="edit" spidmax="3074"/>
     960 <o:shapedefaults v:ext="edit" spidmax="1026"/>
    948961</xml><![endif]--><!--[if gte mso 9]><xml>
    949962 <o:shapelayout v:ext="edit">
     
    961974detector at APS 11-ID-C with a wavelength 0.10798 A, where the detector was
    962975intentionally tilted at 45 degrees, are used. Note that menu entries are listed
    963 in <b style='mso-bidi-font-weight:normal'>bold face</b> below as <b
    964 style='mso-bidi-font-weight:normal'>Help/About GSAS-II</b>, which lists first
    965 the name of the menu (here <b style='mso-bidi-font-weight:normal'>Help</b>) and
    966 second the name of the entry in the menu (here <b style='mso-bidi-font-weight:
    967 normal'>About GSAS-II</b>).</p>
     976in <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     977mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     978minor-latin'>bold face</span></b> below as <b style='mso-bidi-font-weight:normal'><span
     979style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     980mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Help/About
     981GSAS-II</span></b>, which lists first the name of the menu (here <b
     982style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     983mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     984minor-latin'>Help</span></b>) and second the name of the entry in the menu
     985(here <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     986mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     987minor-latin'>About GSAS-II</span></b>).</p>
    968988
    969989<h2>Prerequisite:<span style='mso-spacerun:yes'>  </span><a
     
    971991
    972992<p class=MsoNormal>This assumes that an image data set has been read in and
    973 calibration results have been derived, see the<span style='mso-spacerun:yes'> 
    974 </span><a href="Calibration%20of%20an%20area%20detector%20in%20GSAS.htm">Calibration
    975 Demo</a></p>
     993calibration results have been derived, see the <a
     994href="Calibration%20of%20an%20area%20detector%20in%20GSAS.htm">Calibration Demo</a></p>
    976995
    977996<h2>Step 1: Clear calibration plot</h2>
     
    979998<p class=MsoNormal>Assuming the previous step was calibration, the image plot
    980999will show the located rings and possibly all the picked points. These are no
    981 longer needed. The <b style='mso-bidi-font-weight:normal'>Image Controls/Clear
    982 Calibration</b> menu entry removes these from the plot, but<u> does not clear
    983 the calibration results</u>. Use of this menu item is not required, but does
    984 speed future display of results. </p>
     1000longer needed. The <b style='mso-bidi-font-weight:normal'><span
     1001style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1002mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Image
     1003Controls/Clear Calibration</span></b> menu entry removes these from the plot,
     1004but<u> does not clear the calibration results</u>. Use of this menu item is not
     1005required, but does speed future display of results. </p>
    9851006
    9861007<h2>Step 2: Integration Settings</h2>
    9871008
    9881009<p class=MsoNormal>In the simplest case, all that is needed is to click on the <b
    989 style='mso-bidi-font-weight:normal'>Do full integration?</b> check box and
    990 adjust the inner and outer 2-theta values with the <b style='mso-bidi-font-weight:
    991 normal'>Inner 2-theta</b> and<b style='mso-bidi-font-weight:normal'> Outer
    992 2-theta</b> controls. Change the limits to 1 and 7 for this data. Note that
    993 changes are displayed when numbers are placed in the boxes only after pressing
    994 return or by clicking on some other item in the window or by pressing the tab key.
    995 </p>
     1010style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1011mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1012minor-latin'>Do full integration?</span></b> <span class=GramE>check</span> box
     1013and adjust the inner and outer 2-theta values with the <b style='mso-bidi-font-weight:
     1014normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1015minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Inner
     10162-theta</span></b> and<b style='mso-bidi-font-weight:normal'> </b><b
     1017style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1018mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1019minor-latin'>Outer 2-theta</span></b> controls. Change the limits to <b
     1020style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1021mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1022minor-latin'>1</span></b> and <b style='mso-bidi-font-weight:normal'><span
     1023style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1024mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>7</span></b>
     1025for this data. Note that changes are displayed when numbers are placed in the
     1026boxes only after pressing return or tab key or by clicking on some other item
     1027in the window.</p>
     1028
     1029<p class=MsoNormal><span style='mso-spacerun:yes'> </span></p>
    9961030
    9971031<p class=MsoNormal>It is helpful to see the two-theta limits on the plot
    9981032visually, while adjusting the two-theta range. This is done by clicking on the <b
    999 style='mso-bidi-font-weight:normal'>Show integration limits?</b> check box.
    1000 Note that inner limit is shown as a green ellipse at 2deg and the outer is
     1033style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1034mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1035minor-latin'>Show integration limits?</span></b> <span class=GramE>check</span>
     1036box. Note that inner limit is shown as a green ellipse at 2deg and the outer is
    10011037shown as a red ellipse at 5deg by default. These limits may also be dragged to
    10021038the desired values; a small popup window shows the value. </p>
     1039
     1040<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    10031041
    10041042<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
     
    10271065  o:title=""/>
    10281066</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=370
    1029 src="Integration%20of%20area%20detector%20data%20in%20GSAS_files/image008.png"
     1067src="Integration%20of%20area%20detector%20data%20in%20GSAS_files/image002.png"
    10301068v:shapes="Picture_x0020_2"><![endif]></span></p>
    10311069
    10321070<h3>Other useful controls:</h3>
    10331071
    1034 <p class=MsoNormal><b style='mso-bidi-font-weight:normal'>Azimuth offset</b>:
    1035 The image vertical axis (from the beam center, going down) is labeled with the
    1036 azimuth value placed in the <b style='mso-bidi-font-weight:normal'>Azimuth
    1037 offset</b> box. This is usually zero.</p>
    1038 
    1039 <p class=MsoNormal><b style='mso-bidi-font-weight:normal'>Start/End azimuth</b>:
    1040 The integration is started at the Start azimuth angle in the left box, and when
    1041 the <b style='mso-bidi-font-weight:normal'>Do full integration?</b> checkbox is
    1042 not checked, the integration will be run only to the maximum value specified.
    1043 When the range is less than 360 degrees, the integration range will be shown
    1044 (if selected) with the high and low limits plotted and only segments of the max
    1045 and min ellipses drawn. These limits may also be dragged on the plot to desired
    1046 locations.</p>
    1047 
    1048 <p class=MsoNormal><b style='mso-bidi-font-weight:normal'>Number of 2-theta
    1049 bins</b>: The resulting 1-D powder pattern after integration will consist of
    1050 this many points. This number should be on the order of the number of pixels in
    1051 one direction (since resolution cannot be much better than this) or less, if
    1052 instrumental resolution does not require that many points.</p>
    1053 
    1054 <p class=MsoNormal>Some trial and error may be needed, but there should more
    1055 than 6 points across each peak full-width-at-half-maximum (FWHM) in the final
    1056 pattern to be useful for further analysis.</p>
    1057 
    1058 <p class=MsoNormal><b style='mso-bidi-font-weight:normal'>Number of azimuth
    1059 bins</b>: In cases where the diffraction experiment shows changes as a function
    1060 of azimuthal angle, the integration can be performed as a function of angle.
    1061 This number specifies the number of bins to use by azimuthal angle. The process
    1062 of breaking up the integration in this way is sometimes called
    1063 &quot;caking&quot; since the integration region grows with distance from the
    1064 beam-center, with a shape like a slice of cake or pie. When more than one
     1072<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span
     1073style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1074mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Azimuth
     1075offset</span></b>: The image vertical axis (from the beam center, going down)
     1076is labeled with the azimuth value placed in the <b style='mso-bidi-font-weight:
     1077normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1078minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Azimuth
     1079offset</span></b> box. This is usually zero unless the image plate has been
     1080rotated about its normal axis.</p>
     1081
     1082<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1083
     1084<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span
     1085style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1086mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Start/End
     1087azimuth</span></b>: The integration is started at the Start azimuth angle in
     1088the left box, and when the <b style='mso-bidi-font-weight:normal'><span
     1089style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1090mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Do full
     1091integration?</span></b> <span class=GramE>checkbox</span> is not checked, the
     1092integration will be run only to the maximum value specified. When the range is
     1093less than 360 degrees, the integration range will be shown (if selected) with
     1094the high and low limits plotted and only segments of the max and min ellipses
     1095drawn. These limits may also be dragged on the plot to desired locations.</p>
     1096
     1097<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1098
     1099<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span
     1100style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1101mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Number of
     11022-theta bins</span></b>: The resulting 1-D powder pattern after integration
     1103will consist of this many points. This number should be on the order of the
     1104number of pixels in one direction (since resolution cannot be much better than
     1105this) or less, if instrumental resolution and sample broadening does not
     1106require that many points. Some trial and error may be needed, but there should
     1107more than 6 points across each peak full-width-at-half-maximum (FWHM) in the
     1108final pattern to be useful for further analysis.</p>
     1109
     1110<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1111
     1112<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span
     1113style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1114mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Number of
     1115azimuth bins</span></b>: In cases where the diffraction experiment shows
     1116changes as a function of azimuthal angle, the integration can be performed as a
     1117function of angle. This number specifies the number of bins to use by azimuthal
     1118angle. The process of breaking up the integration in this way is sometimes
     1119called &quot;caking&quot; since the integration region grows with distance from
     1120the beam-center, with a shape like a slice of cake or pie. When more than one
    10651121azimuthal bin is used, the regions are shown in the plot with dashed lines,
    10661122when the Show integration limits?&quot; check box is checked. </p>
    10671123
    1068 <p class=MsoNormal><b style='mso-bidi-font-weight:normal'>Background Image </b>and<b
    1069 style='mso-bidi-font-weight:normal'> Multiplier</b>: You can designate a
    1070 previously read in image as <b style='mso-bidi-font-weight:normal'>Background</b>
    1071 which will then be used to modify each data image as they are integrated. Note
    1072 that the <b style='mso-bidi-font-weight:normal'>Multiplier</b> must be negative
    1073 for it to be subtracted. Note that all images used in this way must be exactly
    1074 the same format (number of pixels &amp; pixel size).</p>
     1124<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1125
     1126<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span
     1127style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1128mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Background
     1129Image</span> </b>and<b style='mso-bidi-font-weight:normal'> </b><b
     1130style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1131mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1132minor-latin'>Multiplier</span></b>: You can designate a previously read in
     1133image as background which will then be used to modify each data image as they
     1134are integrated. Note that the <b style='mso-bidi-font-weight:normal'><span
     1135style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1136mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Multiplier</span></b>
     1137must be negative for it to be subtracted. Note that all images used in this way
     1138must be exactly the same format (number of pixels &amp; pixel size).</p>
     1139
     1140<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    10751141
    10761142<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    10801146  o:title=""/>
    10811147</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=535
    1082 src="Integration%20of%20area%20detector%20data%20in%20GSAS_files/image009.png"
     1148src="Integration%20of%20area%20detector%20data%20in%20GSAS_files/image004.png"
    10831149v:shapes="Picture_x0020_1"><![endif]></span></p>
    10841150
     
    10861152
    10871153<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Use the <b
    1088 style='mso-bidi-font-weight:normal'>Image Operations/Integrate</b> image data
    1089 menu item to start the integration. This will take at least a few seconds. If
    1090 multiple images have been read in, the <b style='mso-bidi-font-weight:normal'>Integrate
    1091 All</b> menu item can be used. This is most useful when the <b
    1092 style='mso-bidi-font-weight:normal'>Use as Default</b> option is in use for one
    1093 image.</p>
     1154style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1155mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1156minor-latin'>Image Operations/Integrate</span></b> image data menu item to
     1157start the integration. This will take at least a few seconds. If multiple
     1158images have been read in, the <b style='mso-bidi-font-weight:normal'><span
     1159style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1160mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Integrate All</span></b>
     1161menu item can be used. This is most useful when the <b style='mso-bidi-font-weight:
     1162normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1163minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Use
     1164as Default</span></b> option is in use for one image.</p>
    10941165
    10951166<p class=MsoNormal><span style='mso-spacerun:yes'> </span>At this point the
    10961167data tree window will have new entries as each azimuthal &quot;slice&quot;
    10971168added to the data tree as a powder pattern</p>
     1169
     1170<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    10981171
    10991172<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    11071180style='mso-spacerun:yes'> </span></p>
    11081181
    1109 <p class=MsoNormal>two plots are added to the plot window: One (with tab 2D
    1110 Integration) shows the diffraction intensity as a function of both 2-theta and
    1111 (when there is more than one azimuthal integration region) azimuthal angle</p>
     1182<p class=MsoNormal>Two plots are added to the plot window: One (with tab <b
     1183style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1184mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1185minor-latin'>2D Integration</span></b>) shows the diffraction intensity as a function
     1186of both 2-theta and (when there is more than one azimuthal integration region)
     1187azimuthal angle.</p>
     1188
     1189<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    11121190
    11131191<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    11191197src="Integration%20of%20area%20detector%20data%20in%20GSAS_files/image006.png"
    11201198v:shapes="Picture_x0020_4"><![endif]></span><span
    1121 style='mso-spacerun:yes'> </span>c</p>
    1122 
    1123 <p class=MsoNormal>and a conventional 1-D powder pattern(s) for each
    1124 &quot;slice&quot;</p>
     1199style='mso-spacerun:yes'> </span></p>
     1200
     1201<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1202
     1203<p class=MsoNormal><span class=GramE>and</span> a conventional 1-D powder
     1204pattern(s) for each &quot;slice&quot;</p>
     1205
     1206<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    11251207
    11261208<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    11331215v:shapes="Picture_x0020_5"><![endif]></span></p>
    11341216
    1135 <p class=MsoNormal>Again you should save the project with <b style='mso-bidi-font-weight:
    1136 normal'>File/Save project</b> on the main GSAS-II data tree menu.</p>
    1137 
    1138 <h2>Next demo: <a href="Fit%20Peaks.htm">Fit Peaks and <span class=SpellE>Autoindexing</span></a></h2>
    1139 
    11401217<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    11411218
     1219<p class=MsoNormal>Again you could save the project with <b style='mso-bidi-font-weight:
     1220normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1221minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>File/Save
     1222project</span></b> on the main <b style='mso-bidi-font-weight:normal'><span
     1223style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1224mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II data
     1225tree</span></b> menu although it is not needed for any further tutorials.</p>
     1226
     1227<h2>Next demo: <a href="Fit%20Peaks.htm"><span style='color:windowtext;
     1228text-decoration:none;text-underline:none'>Fit Peaks and <span class=SpellE>Autoindexing</span></span></a></h2>
     1229
     1230<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1231
    11421232</div>
    11431233
  • trunk/help/Integration of area detector data in GSAS_files/filelist.xml

    r586 r588  
    44 <o:File HRef="colorschememapping.xml"/>
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     8 <o:File HRef="image004.png"/>
    99 <o:File HRef="image005.png"/>
    1010 <o:File HRef="image006.png"/>
  • trunk/help/Starting GSAS.htm

    r586 r588  
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    2323  <o:Author>Von Dreele</o:Author>
    2424  <o:LastAuthor>Von Dreele</o:LastAuthor>
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    2727  <o:Created>2012-05-05T14:50:00Z</o:Created>
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     718        {mso-style-name:"Document Map Char";
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     728        mso-fareast-font-family:"Times New Roman";
     729        mso-fareast-theme-font:minor-fareast;
     730        mso-hansi-font-family:Tahoma;
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     733        {mso-style-name:"Balloon Text Char";
     734        mso-style-noshow:yes;
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     739        mso-ansi-font-size:8.0pt;
     740        mso-bidi-font-size:8.0pt;
     741        font-family:"Tahoma","sans-serif";
     742        mso-ascii-font-family:Tahoma;
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     744        mso-fareast-theme-font:minor-fareast;
     745        mso-hansi-font-family:Tahoma;
     746        mso-bidi-font-family:Tahoma;}
     747span.GSAS-IItextChar
     748        {mso-style-name:"GSAS-II text Char";
     749        mso-style-unhide:no;
     750        mso-style-locked:yes;
     751        mso-style-link:"GSAS-II text";
     752        mso-ansi-font-size:12.0pt;
     753        mso-bidi-font-size:12.0pt;
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     757        mso-fareast-theme-font:minor-fareast;
     758        mso-hansi-font-family:"Times New Roman";
     759        mso-bidi-font-family:Calibri;
     760        mso-bidi-theme-font:minor-latin;
     761        font-weight:bold;
     762        mso-bidi-font-weight:normal;}
    746763p.GSAS-IItext, li.GSAS-IItext, div.GSAS-IItext
    747764        {mso-style-name:"GSAS-II text";
     765        mso-style-noshow:yes;
     766        mso-style-priority:99;
    748767        mso-style-unhide:no;
    749768        mso-style-link:"GSAS-II text Char";
     
    763782        font-weight:bold;
    764783        mso-bidi-font-weight:normal;}
    765 span.GSAS-IItextChar
    766         {mso-style-name:"GSAS-II text Char";
    767         mso-style-unhide:no;
    768         mso-style-locked:yes;
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    771         mso-bidi-font-size:12.0pt;
    772         font-family:"Times New Roman","serif";
    773         mso-fareast-font-family:"Times New Roman";
    774         mso-fareast-theme-font:minor-fareast;
    775         mso-bidi-font-family:Calibri;
    776         mso-bidi-theme-font:minor-latin;
    777         font-weight:bold;
    778         mso-bidi-font-weight:normal;}
     784span.SpellE
     785        {mso-style-name:"";
     786        mso-spl-e:yes;}
     787span.GramE
     788        {mso-style-name:"";
     789        mso-gram-e:yes;}
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     796        font-family:"Calibri","sans-serif";
    782797        mso-ascii-font-family:Calibri;
    783798        mso-ascii-theme-font:minor-latin;
     
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    789804        mso-bidi-theme-font:minor-bidi;}
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    794805@page WordSection1
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    811822        mso-style-noshow:yes;
    812823        mso-style-priority:99;
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    819         mso-para-margin-left:0in;
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     828        mso-pagination:widow-orphan;
     829        font-size:10.0pt;
    823830        font-family:"Calibri","sans-serif";
    824831        mso-ascii-font-family:Calibri;
     
    830837</style>
    831838<![endif]--><!--[if gte mso 9]><xml>
    832  <o:shapedefaults v:ext="edit" spidmax="2050"/>
     839 <o:shapedefaults v:ext="edit" spidmax="1026"/>
    833840</xml><![endif]--><!--[if gte mso 9]><xml>
    834841 <o:shapelayout v:ext="edit">
     
    847854
    848855<p class=MsoNormal>One common way is start a console window, set the current
    849 directory to the location of GSAS-II <span style='mso-spacerun:yes'> </span>and
    850 then enter:</p>
     856directory to the location of GSAS-<span class=GramE>II<span
     857style='mso-spacerun:yes'>  </span>and</span> then enter:</p>
    851858
    852859<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    853860
    854 <p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span
     861<p class=MsoNormal><span class=GramE><b style='mso-bidi-font-weight:normal'><span
    855862style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    856 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>python
    857 GSASII.py<o:p></o:p></span></b></p>
     863mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>python</span></b></span><b
     864style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     865mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     866minor-latin'> GSASII.py<o:p></o:p></span></b></p>
    858867
    859868<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span
     
    869878<p class=MsoNormal>On Windows, there is a GSASII.bat file in the main GSASII
    870879directory you can use as a shortcut. Put a shortcut to it someplace convenient
    871 (maybe your Desktop?) </p>
     880(maybe <span class=GramE>your</span> Desktop?) </p>
    872881
    873882<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    877886style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    878887mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    879 minor-latin'>GSASII data tree</span></span>, the second, immediately under the first
    880 is labeled <b style='mso-bidi-font-weight:normal'><span style='font-family:
     888minor-latin'>GSASII data tree</span></span>, the second, immediately under the
     889first is labeled <b style='mso-bidi-font-weight:normal'><span style='font-family:
    881890"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    882891minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II data display</span></b>
     
    885894mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II Plots</span></b>.
    886895These windows may be moved anywhere on the screen. On Linux and Windows a menu
    887 bar appears at the top of<span style='mso-spacerun:yes'>  </span>the data tree
    888 and data display windows; on a Mac these menus will appear in the system menu
    889 bar location (usually at the screen top) depending on which GSAS-II window has
    890 the focus. On my Windows machine the screen looked like</p>
     896bar appears at the top <span class=GramE>of<span style='mso-spacerun:yes'> 
     897</span>the</span> data tree and data display windows; on a Mac these menus will
     898appear in the system menu bar location (usually at the screen top) depending on
     899which GSAS-II window has the focus. On my Windows machine the screen looked
     900like</p>
    891901
    892902<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    912922 <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
    913923 <o:lock v:ext="edit" aspectratio="t"/>
    914 </v:shapetype><v:shape id="Picture_x0020_3" o:spid="_x0000_i1025" type="#_x0000_t75"
     924</v:shapetype><v:shape id="Picture_x0020_3" o:spid="_x0000_i1026" type="#_x0000_t75"
    915925 style='width:468pt;height:263.25pt;visibility:visible;mso-wrap-style:square'>
    916926 <v:imagedata src="Starting%20GSAS_files/image001.png" o:title=""/>
     
    925935file name is saved.) The console window displays a banner and some information
    926936about the version of python and the packages used by GSAS-II. This console
    927 window (here in the lower left) will display important information as data processing
    928 by GSAS-II proceeds. You may wish to cut-and-paste parts of this window to
    929 another place if desired.</p>
     937window (here in the lower left) will display important information as data
     938processing by GSAS-II proceeds. You may wish to cut-and-paste parts of this
     939window to another place if desired.</p>
     940
     941<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     942
     943<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     944 id="Picture_x0020_2" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:465.75pt;
     945 height:215.25pt;visibility:visible;mso-wrap-style:square'>
     946 <v:imagedata src="Starting%20GSAS_files/image003.png" o:title=""/>
     947</v:shape><![endif]--><![if !vml]><img width=621 height=287
     948src="Starting%20GSAS_files/image004.gif" v:shapes="Picture_x0020_2"><![endif]></span></p>
     949
     950<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     951
     952<p class=MsoNormal>We suggest that you change the properties of this window to
     953(in Windows: Properties/Layout) to have 9999 for the height and 150 for the
     954width and to allow “<span class=SpellE>QuickEdit</span> Mode” (if available)
     955for easy cut/paste operation. You can perhaps also change the font, font size,
     956font color and background color if desired.</p>
    930957
    931958</div>
  • trunk/help/Starting GSAS_files/filelist.xml

    r586 r588  
    11<xml xmlns:o="urn:schemas-microsoft-com:office:office">
    22 <o:MainFile HRef="../Starting%20GSAS.htm"/>
    3  <o:File HRef="item0001.xml"/>
    4  <o:File HRef="props0002.xml"/>
     3 <o:File HRef="item0008.xml"/>
     4 <o:File HRef="props009.xml"/>
    55 <o:File HRef="themedata.thmx"/>
    66 <o:File HRef="colorschememapping.xml"/>
    77 <o:File HRef="image001.png"/>
    88 <o:File HRef="image002.jpg"/>
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    2525  <o:Author>Von Dreele</o:Author>
    2626  <o:LastAuthor>Von Dreele</o:LastAuthor>
    27   <o:Revision>81</o:Revision>
     27  <o:Revision>82</o:Revision>
    2828  <o:TotalTime>2819</o:TotalTime>
    2929  <o:Created>2011-11-28T16:49:00Z</o:Created>
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    1969 align=right alt="Description: Description: GSAS-II logo" v:shapes="Picture_x0020_2"><![endif]><span
     1977align=right alt="Description: Description: Description: GSAS-II logo" v:shapes="Picture_x0020_2"><![endif]><span
    19701978style='mso-fareast-font-family:"Times New Roman"'>Help for GSAS-II<o:p></o:p></span></h1>
    19711979
     
    19841992<h2><strong>GSAS-II tutorials:<o:p></o:p></strong></h2>
    19851993
    1986 <p class=MsoNormal><strong>Starting GSAS-II<o:p></o:p></strong></p>
     1994<p class=MsoNormal><strong><a href="Starting%20GSAS.htm"><span
     1995style='font-weight:normal'>Starting GSAS-II</span></a><o:p></o:p></strong></p>
    19871996
    19881997<p class=MsoNormal><strong><a
     
    19972006normal'>Powder pattern peak picking, fitting and indexing</span></a><o:p></o:p></strong></p>
    19982007
    1999 <p class=MsoNormal><strong>Lab X-ray powder pattern <span class=SpellE>Rietveld</span>
    2000 refinement (future)<o:p></o:p></strong></p>
    2001 
    2002 <p class=MsoNormal><strong>CW Neutron powder pattern <span class=SpellE>Rietveld</span>
    2003 refinement (future)<o:p></o:p></strong></p>
    2004 
    2005 <p class=MsoNormal><strong>Synchrotron X-ray powder pattern <span class=SpellE>Rietveld</span>
    2006 refinement (future)<o:p></o:p></strong></p>
    2007 
    2008 <p class=MsoNormal><strong>Crystal structure drawing (balls &amp; sticks, etc.)
     2008<p class=MsoNormal><strong>Lab X-ray powder pattern Rietveld refinement
    20092009(future)<o:p></o:p></strong></p>
     2010
     2011<p class=MsoNormal><strong>CW Neutron powder pattern Rietveld refinement
     2012(future)<o:p></o:p></strong></p>
     2013
     2014<p class=MsoNormal><strong>Synchrotron X-ray powder pattern Rietveld refinement
     2015(future)<o:p></o:p></strong></p>
     2016
     2017<p class=MsoNormal><span class=GramE><strong>Crystal structure drawing (balls
     2018&amp; sticks, etc.)</strong></span><strong> (<span class=GramE>future</span>)<o:p></o:p></strong></p>
    20102019
    20112020<p class=MsoNormal><strong>Crystal structure drawing (<span class=SpellE>polyhedra</span>)
    20122021(future)<o:p></o:p></strong></p>
    20132022
    2014 <p class=MsoNormal><strong>Distance/Angle/Torsion calculations(future)<o:p></o:p></strong></p>
    2015 
    2016 <p class=MsoNormal><strong>Charge flipping structure solution(future)<o:p></o:p></strong></p>
    2017 
    2018 <p class=MsoNormal><strong>etc., etc.<o:p></o:p></strong></p>
     2023<p class=MsoNormal><strong>Distance/Angle/Torsion <span class=GramE>calculations(</span>future)<o:p></o:p></strong></p>
     2024
     2025<p class=MsoNormal><strong>Charge flipping structure <span class=GramE>solution(</span>future)<o:p></o:p></strong></p>
     2026
     2027<p class=MsoNormal><span class=GramE><strong>etc., etc.</strong></span><strong><o:p></o:p></strong></p>
    20192028
    20202029<div class=MsoNormal align=center style='text-align:center'><span
     
    20622071style='mso-bidi-font-weight:normal'>Open project&#8230;</b> - Open a previously
    20632072saved GSAS-II project file (name.gpx). If you currently have a project file
    2064 open, you are asked if it is OK to over write it; Cancel will cancel the
    2065 process. <b style='mso-bidi-font-weight:normal'>NB</b>: you may open a backup <span
     2073open, you are asked if it is OK to over write it; Cancel will cancel the process.
     2074<b style='mso-bidi-font-weight:normal'>NB</b>: you may open a backup <span
    20662075class=SpellE>gpx</span> file (e.g. name.bak3.gpx) to recover a previous version
    20672076of your project. Remember to <b style='mso-bidi-font-weight:normal'>Save As</b>&#8230;
     
    20862095style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Save
    20872096As&#8230;</span></b><span style='mso-fareast-font-family:"Times New Roman"'> -
    2088 Save the current project to a new file. A file dialog will be shown to enter the
    2089 name (and change directory if desired). If the file exists, you will be asked
    2090 if it OK to overwrite.</span></p>
     2097Save the current project to a new file. A file dialog will be shown to enter
     2098the name (and change directory if desired). If the file exists, you will be
     2099asked if it OK to overwrite.</span></p>
    20912100
    20922101<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    21182127style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
    21192128style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    2120 style='mso-bidi-font-weight:normal'>Read powder data&#8230;</b> - Read in powder
    2121 diffraction patterns (multiple patterns can be selected). GSAS-II can read most
    2122 of the old GSAS powder format files with the position in <span class=SpellE>centidegrees</span>
    2123 2-theta. It can also read &#8220;<span class=SpellE>xye</span>&#8221; format
    2124 files used by <span class=SpellE>topas</span> where the position is in degrees
    2125 2-theta. As each file is read, an old GSAS style &#8220;instrument parameter
    2126 file&#8221; is searched for; if not found a <span class=SpellE>CuK</span><span
    2127 style='font-family:Symbol'>a</span> laboratory data set is assumed. </p>
     2129style='mso-bidi-font-weight:normal'>Read powder data&#8230;</b> - Read in
     2130powder diffraction patterns (multiple patterns can be selected). GSAS-II can
     2131read most of the old GSAS powder format files with the position in <span
     2132class=SpellE>centidegrees</span> 2-theta. It can also read &#8220;<span
     2133class=SpellE>xye</span>&#8221; format files used by <span class=SpellE>topas</span>
     2134where the position is in degrees 2-theta. As each file is read, an old GSAS
     2135style &#8220;instrument parameter file&#8221; is searched for; if not found a <span
     2136class=SpellE>CuK</span><span style='font-family:Symbol'>a</span> laboratory
     2137data set is assumed. </p>
    21282138
    21292139<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    22282238The total number of refined parameters is also shown at the top of the list.
    22292239The value of each parameter is also given. The parameter names are of the form
    2230 &#8216;p:h:name:id&#8217; where &#8216;p&#8217; is the phase index,
    2231 &#8216;h&#8217; is the histogram index and &#8216;id&#8217; is the item index
    2232 (if needed). Indexes all begin with &#8216;0&#8217; (zero). Note that for atom
    2233 positions the value is not a <span class=SpellE>refinable</span> parameter, but
    2234 the shift in the value is. Position names are, e.g. &#8216;0::Ax:0&#8217; for
    2235 the x-position of the <span class=SpellE>zeroth</span> atom in the <span
    2236 class=SpellE>zeroth</span> phase while shift names have a &#8216;d&#8217; in
    2237 then, e.g. &#8216;0::dAx:0&#8217;. </p>
     2240&#8216;p<span class=GramE>:h:name:id&#8217;</span> where &#8216;p&#8217; is the
     2241phase index, &#8216;h&#8217; is the histogram index and &#8216;id&#8217; is the
     2242item index (if needed). Indexes all begin with &#8216;0&#8217; (zero). Note
     2243that for atom positions the value is not a <span class=SpellE>refinable</span>
     2244parameter, but the shift in the value is. Position names are, e.g. &#8216;0:<span
     2245class=GramE>:Ax:0&#8217;</span> for the x-position of the <span class=SpellE>zeroth</span>
     2246atom in the <span class=SpellE>zeroth</span> phase while shift names have a
     2247&#8216;d&#8217; in then, e.g. &#8216;0::dAx:0&#8217;. </p>
    22382248
    22392249<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    24132423
    24142424<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Two
    2415 of the main refinement tools are the <span class=SpellE>fortran</span> MINPACK <span
    2416 class=SpellE>lmdif</span> and <span class=SpellE>lmder</span> algorithms
    2417 wrapped in python as provided in the <span class=SpellE>Scipy</span> package
    2418 and a third one is a python version utilizing only the <span class=SpellE>numpy</span>
    2419 package. The purpose is to </span>minimize the sum of the squares of M<span
    2420 style='mso-fareast-font-family:"Times New Roman"'> nonlinear functions in N
    2421 variables by a modification of the <span class=SpellE>Levenberg</span>-Marquardt
     2425of the main refinement tools are the <span class=SpellE><span class=GramE>fortran</span></span>
     2426MINPACK <span class=SpellE>lmdif</span> and <span class=SpellE>lmder</span>
     2427algorithms wrapped in python as provided in the <span class=SpellE>Scipy</span>
     2428package and a third one is a python version utilizing only the <span
     2429class=SpellE>numpy</span> package. The purpose is to </span>minimize the sum of
     2430the squares of M<span style='mso-fareast-font-family:"Times New Roman"'>
     2431nonlinear functions in N variables by a modification of the <span class=SpellE>Levenberg</span>-Marquardt
    24222432algorithm. The <span class=SpellE>lmdif</span> and <span class=SpellE>lmder</span>
    24232433routines were written by </span>Burton S. <span class=SpellE>Garbow</span>,
    2424 Kenneth E. <span class=SpellE>Hillstrom</span>, Jorge J. More (Argonne National
    2425 Laboratory, 1980). The python/numpy version was developed by us based on the
    2426 material in Numerical Recipes (Press, Flannery, <span class=SpellE>Teulosky</span>
     2434Kenneth E. <span class=SpellE>Hillstrom</span>, <span class=GramE>Jorge</span>
     2435J. <span class=GramE>More (Argonne National Laboratory, 1980).</span> The
     2436python/numpy version was developed by us based on the material in Numerical
     2437Recipes (Press, Flannery, <span class=SpellE><span class=GramE>Teulosky</span></span>
    24272438&amp; <span class=SpellE>Vetterling</span>) for the <span class=SpellE>Levenberg</span>-Marquardt
    24282439algorithm.<span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
     
    24592470the first cycle of refinement. This value is modified by the least squares
    24602471routine. The allowed range is 10<sup>-5</sup> to 100. Smaller values may be
    2461 needed if your initial refinement trials immediately diverge, however make sure
    2462 your starting parameter values are &#8216;reasonable&#8217;. The selected
    2463 default (=1.0) normally gives good performance.<o:p></o:p></span></p>
     2472needed if your initial <span class=GramE>refinement</span> trials immediately
     2473diverge, however make sure your starting parameter values are
     2474&#8216;reasonable&#8217;. The selected default (=1.0) normally gives good
     2475performance.<o:p></o:p></span></p>
    24642476
    24652477<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l15 level1 lfo2'><![if !supportLists]><span
     
    25012513"Times New Roman"'>m</span><span style='mso-fareast-font-family:"Times New Roman"'>strain
    25022514and crystallite size parameters). &#8216;Histogram constraints&#8217; are those
    2503 that depend only on the data set (e.g. profile coefficients U,V,W,X and Y).<o:p></o:p></span></p>
     2515that depend only on the data set (e.g. profile coefficients U<span class=GramE>,V,W,X</span>
     2516and Y).<o:p></o:p></span></p>
    25042517
    25052518<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
     
    25212534auto;text-indent:-.25in;mso-list:l17 level2 lfo3'><![if !supportLists]><span
    25222535style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
    2523 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    2524 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Add
    2525 Hold</span></b><span style='mso-fareast-font-family:"Times New Roman"'> &#8211;
    2526 select a parameter that you wish to remain fixed although other parameters of
    2527 the same type may be selected as a group for refinement. For example, if the
    2528 space group for a phase has a polar axis (e.g. the b-axis in P2<sub>1</sub>),
    2529 then one atom y-parameter is arbitrary and should be selected for a Hold to
    2530 keep the structure from drifting up or down the y-axis during refinement. If
    2531 selected, a dialog box will appear showing the list of available parameters;
    2532 select one and then OK to implement it, Cancel will cancel the operation. The
    2533 held parameter will be shown in the constraint window with the keyword
    2534 &#8216;FIXED&#8217;. A Delete button can be used to remove it.<o:p></o:p></span></p>
     2536style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     2537class=GramE><b style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:
     2538"Times New Roman"'>Add</span></b></span><b style='mso-bidi-font-weight:normal'><span
     2539style='mso-fareast-font-family:"Times New Roman"'> Hold</span></b><span
     2540style='mso-fareast-font-family:"Times New Roman"'> &#8211; select a parameter
     2541that you wish to remain fixed although other parameters of the same type may be
     2542selected as a group for refinement. For example, if the space group for a phase
     2543has a polar axis (e.g. the b-axis in P2<sub>1</sub>), then one atom y-parameter
     2544is arbitrary and should be selected for a Hold to keep the structure from
     2545drifting up or down the y-axis during refinement. If selected, a dialog box
     2546will appear showing the list of available parameters; select one and then OK to
     2547implement it, Cancel will cancel the operation. The held parameter will be
     2548shown in the constraint window with the keyword &#8216;FIXED&#8217;. A Delete
     2549button can be used to remove it.<o:p></o:p></span></p>
    25352550
    25362551<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    25432558with a non-unitary multiplier for some). Examples are a list of atoms with the
    25442559same thermal motion <span class=SpellE>Uiso</span>, sets of profile
    2545 coefficients U,V,W across multiple data sets. If selected, a dialog box will
    2546 appear with a list of the available parameters. Select one and press OK; a
    2547 second dialog box will appear with only those parameters that can be made
    2548 equivalent to the first one. Choose those and press OK. Cancel in either dialog
    2549 will cancel the operation. The equivalenced parameters will show as an equation
    2550 of the form M<sub>1</sub>*P<sub>1</sub>+M<sub>2</sub>*P<sub>2</sub>=0; usually
    2551 M1=1.0 and M2=-1.0, but can be changed via the &#8216;Edit&#8217; button. The
    2552 keyword &#8216;EQUIV&#8217; marks it as an equivalence. A Delete button can be
    2553 used to remove it.<o:p></o:p></span></p>
     2560coefficients U<span class=GramE>,V,W</span> across multiple data sets. If
     2561selected, a dialog box will appear with a list of the available parameters.
     2562Select one and press OK; a second dialog box will appear with only those
     2563parameters that can be made equivalent to the first one. Choose those and press
     2564OK. Cancel in either dialog will cancel the operation. The equivalenced
     2565parameters 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;
     2566usually M1=1.0 and M2=-1.0, but can be changed via the &#8216;Edit&#8217;
     2567button. The keyword &#8216;EQUIV&#8217; marks it as <span class=GramE>an
     2568equivalence</span>. A Delete button can be used to remove it.<o:p></o:p></span></p>
    25542569
    25552570<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    25672582the operation. The equivalenced parameters will show as an equation of the form
    25682583M<sub>1</sub>*P<sub>1</sub>+M<sub>2</sub>*P<sub>2</sub>+&#8230;=C; the
    2569 multipliers M1, M2, &#8230; and C can be changed via the &#8216;Edit&#8217;
    2570 button. The keyword &#8216;CONSTR&#8217; marks it as a constraint. A Delete
    2571 button can be used to remove it.<o:p></o:p></span></p>
     2584multipliers M1, <span class=GramE>M2, &#8230;</span> and C can be changed via
     2585the &#8216;Edit&#8217; button. The keyword &#8216;CONSTR&#8217; marks it as a
     2586constraint. A Delete button can be used to remove it.<o:p></o:p></span></p>
    25722587
    25732588<p class=MsoListParagraphCxSpLast style='margin-left:1.0in;mso-add-space:auto;
     
    25992614<p class=MsoNormal>In this window is tabulated the results of your sequential
    26002615refinement. The columns are the parameter names; the naming convention is
    2601 &#8216;p:h:name:n&#8217; where p is the phase number, h is the histogram
    2602 number, name is the parameter name, and num (if needed) is the item number
    2603 (e.g. atom number). The rows are the data sets used in the sequential
    2604 refinement.</p>
     2616&#8216;p<span class=GramE>:h:name:n&#8217;</span> where p is the phase number,
     2617h is the histogram number, name is the parameter name, and num (if needed) is
     2618the item number (e.g. atom number). The rows are the data sets used in the
     2619sequential refinement.</p>
    26052620
    26062621<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
     
    27062721style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    27072722style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Copy</span></b><span
    2708 style='mso-fareast-font-family:"Times New Roman"'> &#8211; this copies the limits
    2709 shown to other selected powder patterns. If used, a dialog box (Copy
     2723style='mso-fareast-font-family:"Times New Roman"'> &#8211; this copies the
     2724limits shown to other selected powder patterns. If used, a dialog box (Copy
    27102725Parameters) will appear showing the list of available powder patterns, you can
    27112726copy the limits parameters to any or all of them; select &#8216;All&#8217; to
     
    27222737for the background:<o:p></o:p></span></p>
    27232738
    2724 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>1). A
    2725 continuous empirical function (&#8216;<span class=SpellE>chebyschev</span>&#8217;,
    2726 &#8216;cosine&#8217;, &#8216;<span class=SpellE>lin</span> interpolate&#8217;,
    2727 &#8216;inv interpolate&#8217; &amp; &#8216;log interpolate&#8217;). The latter
    2728 three select fixed points with spacing that is either equal, inversely equal or
    2729 equal on a log scale of the x-coordinate. The set of magnitudes at each point
    2730 then comprise the background variables. All are refined when refine is
    2731 selected.<o:p></o:p></span></p>
     2739<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>1).
     2740A continuous empirical function (&#8216;<span class=SpellE>chebyschev</span>&#8217;,
     2741&#8216;cosine&#8217;, &#8216;<span class=SpellE><span class=GramE>lin</span></span>
     2742interpolate&#8217;, &#8216;inv interpolate&#8217; &amp; &#8216;log
     2743interpolate&#8217;). The latter three select fixed points with spacing that is <span
     2744class=GramE>either equal</span>, inversely equal or equal on a log scale of the
     2745x-coordinate. The set of magnitudes at each point then comprise the background
     2746variables. All are refined when refine is selected.<o:p></o:p></span></p>
    27322747
    27332748<p class=MsoNormal style='tab-stops:0in'><span style='mso-fareast-font-family:
     
    277427891'>&nbsp;&nbsp;&nbsp;&nbsp; </span><o:p></o:p></span></p>
    27752790
    2776 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>where
    2777 A,R &amp; U are the possible variables and can be individually selected as
    2778 desired; Q = 2</span><span style='font-family:Symbol;mso-fareast-font-family:
    2779 "Times New Roman"'>p</span><span style='mso-fareast-font-family:"Times New Roman"'>/d.<o:p></o:p></span></p>
     2791<p class=MsoNormal><span class=GramE><span style='mso-fareast-font-family:"Times New Roman"'>where</span></span><span
     2792style='mso-fareast-font-family:"Times New Roman"'> A,R &amp; U are the possible
     2793variables and can be individually selected as desired; Q = 2</span><span
     2794style='font-family:Symbol;mso-fareast-font-family:"Times New Roman"'>p</span><span
     2795style='mso-fareast-font-family:"Times New Roman"'>/d.<o:p></o:p></span></p>
    27802796
    27812797<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>3).
    27822798A set of individual Bragg peaks using the pseudo-Voigt profile function as
    2783 their shapes. Their parameters are &#8216;pos&#8217;, &#8217;<span
    2784 class=SpellE>int</span>&#8217;, &#8216;sig&#8217; &amp; &#8216;<span
    2785 class=SpellE>gam</span>&#8217;; each can be selected for refinement. The
    2786 default values for sig &amp; gam (=0.10) are for very sharp peaks, you may
    2787 adjust them accordingly to the kind of peak you are trying to fit before trying
    2788 to refine them.<o:p></o:p></span></p>
     2799their shapes. Their parameters are &#8216;<span class=SpellE>pos</span>&#8217;,
     2800&#8217;<span class=SpellE>int</span>&#8217;, &#8216;sig&#8217; &amp;
     2801&#8216;gam&#8217;; each can be selected for refinement. The default values for
     2802sig &amp; gam (=0.10) are for very sharp peaks, you may adjust them accordingly
     2803to the kind of peak you are trying to fit before trying to refine them.<o:p></o:p></span></p>
    27892804
    27902805<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
     
    28142829style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Copy
    28152830flags </span></b><span style='mso-fareast-font-family:"Times New Roman"'>&#8211;
    2816 this copies only the refinement flags shown to other selected powder patterns.
    2817 If used, a dialog box (Copy Refinement Flags) will appear showing the list of
    2818 available powder patterns, you can copy the refinement flags to any or all of
    2819 them; select &#8216;All&#8217; to copy them to all patterns. Then select
    2820 &#8216;OK&#8217; to do the copy; &#8216;Cancel&#8217; to cancel the operation.<o:p></o:p></span></p>
     2831<span class=GramE>this copies</span> only the refinement flags shown to other
     2832selected powder patterns. If used, a dialog box (Copy Refinement Flags) will
     2833appear showing the list of available powder patterns, you can copy the
     2834refinement flags to any or all of them; select &#8216;All&#8217; to copy them
     2835to all patterns. Then select &#8216;OK&#8217; to do the copy;
     2836&#8216;Cancel&#8217; to cancel the operation.<o:p></o:p></span></p>
    28212837
    28222838<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l19 level1 lfo7'><![if !supportLists]><span
     
    29792995profile coefficients. <b style='mso-bidi-font-weight:normal'>NB</b>: In certain
    29802996circumstances some choices are ignored e.g. Zero is not refined during peak
    2981 fitting. Also some choices may lead to unstable refinement, e.g. Lam refinement
    2982 and lattice parameter refinement. Examine the &#8216;</span><a
    2983 href="#Covariance"><span style='mso-fareast-font-family:"Times New Roman"'>Covariance&#8217;</span></a><span
     2997fitting. Also some choices may lead to unstable refinement, e.g. <span
     2998class=GramE>Lam</span> refinement and lattice parameter refinement. Examine the
     2999&#8216;</span><a href="#Covariance"><span style='mso-fareast-font-family:"Times New Roman"'>Covariance&#8217;</span></a><span
    29843000style='mso-fareast-font-family:"Times New Roman"'> display for highly
    29853001correlated parameters.<o:p></o:p></span></p>
     
    29933009fixed. All values can be changed in this window.<o:p></o:p></span></p>
    29943010
    2995 <h5><a name="Powder_Peaks"></a><a name="Peak_List"><span style='mso-bookmark:
    2996 Powder_Peaks'><span style='mso-fareast-font-family:"Times New Roman"'>What can
    2997 I do here?</span></span></a><span style='mso-bookmark:Peak_List'><span
    2998 style='mso-bookmark:Powder_Peaks'><span style='mso-fareast-font-family:"Times New Roman";
     3011<h5><a name="Peak_List"></a><a name="Powder_Peaks"><span style='mso-bookmark:
     3012Peak_List'><span style='mso-fareast-font-family:"Times New Roman"'>What can I
     3013do here?</span></span></a><span style='mso-bookmark:Powder_Peaks'><span
     3014style='mso-bookmark:Peak_List'><span style='mso-fareast-font-family:"Times New Roman";
    29993015color:windowtext;font-weight:normal;mso-bidi-font-weight:bold'><o:p></o:p></span></span></span></h5>
    30003016
    30013017<h5 style='margin-left:.5in;text-indent:-.25in;mso-list:l6 level1 lfo11'><span
    3002 style='mso-bookmark:Peak_List'><span style='mso-bookmark:Powder_Peaks'><![if !supportLists]><span
     3018style='mso-bookmark:Powder_Peaks'><span style='mso-bookmark:Peak_List'><![if !supportLists]><span
    30033019style='mso-fareast-font-family:"Times New Roman";color:windowtext;font-weight:
    30043020normal;mso-bidi-font-weight:bold'><span style='mso-list:Ignore'>1.<span
     
    30063022style='mso-fareast-font-family:"Times New Roman";color:windowtext;font-weight:
    30073023normal;mso-bidi-font-weight:bold'>Menu &#8216;</span></span></span><span
    3008 style='mso-bookmark:Peak_List'><span style='mso-bookmark:Powder_Peaks'><span
     3024style='mso-bookmark:Powder_Peaks'><span style='mso-bookmark:Peak_List'><span
    30093025style='mso-fareast-font-family:"Times New Roman";color:windowtext'>File&#8217;</span></span></span><span
    3010 style='mso-bookmark:Peak_List'><span style='mso-bookmark:Powder_Peaks'><span
     3026style='mso-bookmark:Powder_Peaks'><span style='mso-bookmark:Peak_List'><span
    30113027style='mso-fareast-font-family:"Times New Roman";color:windowtext;font-weight:
    30123028normal;mso-bidi-font-weight:bold'> &#8211; <o:p></o:p></span></span></span></h5>
     
    30143030<p class=MsoListParagraphCxSpFirst style='margin-left:1.0in;mso-add-space:auto;
    30153031text-indent:-.25in;mso-list:l6 level2 lfo11;tab-stops:list 1.0in'><span
    3016 style='mso-bookmark:Peak_List'><span style='mso-bookmark:Powder_Peaks'><![if !supportLists]><span
     3032style='mso-bookmark:Powder_Peaks'><span style='mso-bookmark:Peak_List'><![if !supportLists]><span
    30173033style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
    30183034style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    30193035style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Copy</span></b></span></span><span
    3020 style='mso-bookmark:Peak_List'><span style='mso-bookmark:Powder_Peaks'><span
     3036style='mso-bookmark:Powder_Peaks'><span style='mso-bookmark:Peak_List'><span
    30213037style='mso-fareast-font-family:"Times New Roman"'> &#8211; this copies the
    30223038sample parameters shown to other selected powder patterns. If used, a dialog
     
    30283044<p class=MsoListParagraphCxSpLast style='margin-left:1.0in;mso-add-space:auto;
    30293045text-indent:-.25in;mso-list:l6 level2 lfo11;tab-stops:list 1.0in'><span
    3030 style='mso-bookmark:Peak_List'><span style='mso-bookmark:Powder_Peaks'><![if !supportLists]><span
     3046style='mso-bookmark:Powder_Peaks'><span style='mso-bookmark:Peak_List'><![if !supportLists]><span
    30313047style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
    30323048style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    30333049style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Copy
    3034 flags</span></b></span></span><span style='mso-bookmark:Peak_List'><span
    3035 style='mso-bookmark:Powder_Peaks'><span style='mso-fareast-font-family:"Times New Roman"'>
     3050flags</span></b></span></span><span style='mso-bookmark:Powder_Peaks'><span
     3051style='mso-bookmark:Peak_List'><span style='mso-fareast-font-family:"Times New Roman"'>
    30363052- &#8211; this copies the sample parameter refinement flags shown to other
    30373053selected powder patterns. If used, a dialog box (Copy refinement flags) will
     
    30413057&#8216;Cancel&#8217; to cancel the operation. <o:p></o:p></span></span></span></p>
    30423058
    3043 <h4><span style='mso-bookmark:Peak_List'><span style='mso-bookmark:Powder_Peaks'><span
     3059<h4><span style='mso-bookmark:Powder_Peaks'><span style='mso-bookmark:Peak_List'><span
    30443060style='mso-fareast-font-family:"Times New Roman"'>Peak List</span></span></span><span
    30453061style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h4>
     
    31273143style='mso-fareast-font-family:"Times New Roman";color:windowtext;font-weight:
    31283144normal;mso-bidi-font-weight:bold'>&#8211; this resets the values of sigma and
    3129 gamma to those computed from the instrument parameters U, V, W, X &amp; Y.<o:p></o:p></span></span></h5>
     3145gamma to those computed from the instrument parameters U, V, W, <span
     3146class=GramE>X</span> &amp; Y.<o:p></o:p></span></span></h5>
    31303147
    31313148<h5 style='margin-left:1.0in;text-indent:-.25in;mso-list:l9 level2 lfo12;
     
    32573274<p class=MsoNormal>This window </p>
    32583275
    3259 <h4><a name="I_Q"></a><span style='mso-fareast-font-family:"Times New Roman"'>I(Q),
     3276<h4><a name="I_Q"></a><span class=GramE><span style='mso-fareast-font-family:
     3277"Times New Roman"'>I(</span></span><span style='mso-fareast-font-family:"Times New Roman"'>Q),
    32603278<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>
    32613279
     
    33593377style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Space
    33603378group</span></b><span style='mso-fareast-font-family:"Times New Roman"'>
    3361 &#8211; this should be set when the phase is initialized; it can be changed later.
    3362 Be careful about the impact on Atom site symmetry and multiplicity if you do.
    3363 GSAS-II will recognize any legal space group symbol using the short Hermann-<span
    3364 class=SpellE>Mauguin</span> forms; put a space between the axial fields (e.g.
    3365 &#8216;F d 3 m&#8217; not &#8216;Fd3m&#8217;). For space groups with a choice
    3366 of origin (e.g. F d 3 m), GSAS-II always uses the 2<sup>nd</sup> setting where
    3367 the center of inversion is located at the origin. The choice of space group
    3368 will set the available unit cell parameters.<u><o:p></o:p></u></span></p>
     3379&#8211; this should be set when the phase is initialized; it can be changed
     3380later. Be careful about the impact on Atom site symmetry and multiplicity if
     3381you do. GSAS-II will recognize any legal space group symbol using the short
     3382Hermann-<span class=SpellE>Mauguin</span> forms; put a space between the axial
     3383fields (e.g. &#8216;F d 3 m&#8217; not &#8216;Fd3m&#8217;). For space groups
     3384with a choice of origin (e.g. F d 3 m), GSAS-II always uses the 2<sup>nd</sup>
     3385setting where the center of inversion is located at the origin. The choice of
     3386space group will set the available unit cell parameters.<u><o:p></o:p></u></span></p>
    33693387
    33703388<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    34763494auto;text-indent:-.25in;mso-list:l0 level2 lfo14'><![if !supportLists]><span
    34773495style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>e.<span
    3478 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    3479 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>a,
    3480 b, c, alpha, beta, gamma</span></b><span style='mso-fareast-font-family:"Times New Roman"'>
    3481 &#8211; lattice parameters; only those permitted by the space group are shown.
    3482 The volume is computed from the values entered.<u><o:p></o:p></u></span></p>
     3496style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     3497class=GramE><b style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:
     3498"Times New Roman"'>a</span></b></span><b style='mso-bidi-font-weight:normal'><span
     3499style='mso-fareast-font-family:"Times New Roman"'>, b, c, alpha, beta, gamma</span></b><span
     3500style='mso-fareast-font-family:"Times New Roman"'> &#8211; lattice parameters;
     3501only those permitted by the space group are shown. The volume is computed from
     3502the values entered.<u><o:p></o:p></u></span></p>
    34833503
    34843504<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l0 level1 lfo14'><![if !supportLists]><span
     
    35513571style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Atom
    35523572Selection from plot: select an atom by a left click of the mouse while holding
    3553 down the Shift key and pointed at the center of the displayed atom, it will
    3554 turn green if successful and the corresponding entry in the table will be
     3573down the Shift key and pointed at the center of the displayed atom, it will turn
     3574green if successful and the corresponding entry in the table will be
    35553575highlighted (in grey); any previous selections will be cleared. To add to .your
    35563576selection use the right mouse button (Shift down); if a previously selection is
     
    35723592style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Double
    35733593left click a Style, Label or Color column: a dialog box is shown that allows
    3574 you to select a rendering option for all the atoms. For Color a color choice dialog
    3575 is displayed that covers the entire color spectrum. Choose a color by any of
    3576 the means available, press the &#8220;Add to Custom Colors&#8221;, select that
    3577 color in the Custom colors display and then press OK. <b style='mso-bidi-font-weight:
    3578 normal'>NB</b>: selecting Color will make all atoms have the same color and for
    3579 Style &#8220;blank&#8221; means the atoms aren&#8217;t rendered and thus the
    3580 plot will not show any atoms or bonds!</p>
     3594you to select a rendering option for all the atoms. For Color a color choice
     3595dialog is displayed that covers the entire color spectrum. Choose a color by
     3596any of the means available, press the &#8220;Add to Custom Colors&#8221;,
     3597select that color in the Custom colors display and then press OK. <b
     3598style='mso-bidi-font-weight:normal'>NB</b>: selecting Color will make all atoms
     3599have the same color and for Style &#8220;blank&#8221; means the atoms
     3600aren&#8217;t rendered and thus the plot will not show any atoms or bonds!</p>
    35813601
    35823602<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l10 level1 lfo15'><![if !supportLists]><span
     
    36673687style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>j.<span
    36683688style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    3669 </span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Delete
    3670 atoms</b> &#8211; clear the entire draw atom table; it is then refilled from
    3671 the Atoms table. You should do this operation after any changes in the Atoms
    3672 table, e.g. by a structure refinement.</p>
     3689</span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Delete atoms</b>
     3690&#8211; clear the entire draw atom table; it is then refilled from the Atoms
     3691table. You should do this operation after any changes in the Atoms table, e.g.
     3692by a structure refinement.</p>
    36733693
    36743694<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l10 level1 lfo15'><![if !supportLists]><span
     
    36853705style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    36863706style='mso-bidi-font-weight:normal'>Dist. Ang.</b> <b style='mso-bidi-font-weight:
    3687 normal'>Tors. </b>&#8211; when 2-4 atoms are selected, a distance, angle or
    3688 torsion angle will be found for them. The angles are computed for the atoms in
    3689 their selection order. The torsion angle is a right hand angle about the A2-A3
    3690 vector for the sequence of atoms A1-A2-A3-A4. An estimated standard deviation
    3691 is given for the calculated value if a current variance-covariance matrix is
    3692 available. The result is shown on the console window; it may be cut &amp;
    3693 pasted to another application (e.g. Microsoft Word).</p>
     3707normal'>Tors. </b>&#8211; <span class=GramE>when</span> 2-4 atoms are selected,
     3708a distance, angle or torsion angle will be found for them. The angles are
     3709computed for the atoms in their selection order. The torsion angle is a right
     3710hand angle about the A2-A3 vector for the sequence of atoms A1-A2-A3-A4. An
     3711estimated standard deviation is given for the calculated value if a current
     3712variance-covariance matrix is available. The result is shown on the console
     3713window; it may be cut &amp; pasted to another application (e.g. Microsoft
     3714Word).</p>
    36943715
    36953716<p class=MsoListParagraphCxSpLast style='margin-left:1.0in;mso-add-space:auto;
     
    37353756set as &#8216;Pawley <span class=SpellE>dmin</span>&#8217; in the General tab
    37363757for this phase. By default the refine flags are not set and the <span
    3737 class=SpellE>Fsq</span>(<span class=SpellE>hkl</span>) = 100.0.</p>
     3758class=SpellE><span class=GramE>Fsq</span></span><span class=GramE>(</span><span
     3759class=SpellE>hkl</span>) = 100.0.</p>
    37383760
    37393761<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    37423764style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    37433765style='mso-bidi-font-weight:normal'>Pawley estimate</b> &#8211; this attempts
    3744 an estimate of <span class=SpellE>Fsq</span>(<span class=SpellE>hkl</span>)
    3745 from the peak heights of the reflection as seen in the 1<sup>st</sup> powder
    3746 pattern of those selected in the <a href="#Data">Data</a> tab.</p>
     3766an estimate of <span class=SpellE><span class=GramE>Fsq</span></span><span
     3767class=GramE>(</span><span class=SpellE>hkl</span>) from the peak heights of the
     3768reflection as seen in the 1<sup>st</sup> powder pattern of those selected in
     3769the <a href="#Data">Data</a> tab.</p>
    37473770
    37483771<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    37663789style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
    37673790style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>You
    3768 can change the individual <span class=SpellE>Fsq</span>(<span class=SpellE>hkl</span>)
    3769 values by selecting it, typing in the new value and then pressing enter or
    3770 selecting somewhere else in the table.</p>
     3791can change the individual <span class=SpellE><span class=GramE>Fsq</span></span><span
     3792class=GramE>(</span><span class=SpellE>hkl</span>) values by selecting it,
     3793typing in the new value and then pressing enter or selecting somewhere else in
     3794the table.</p>
    37713795
    37723796<p class=MsoListParagraphCxSpLast><o:p>&nbsp;</o:p></p>
     
    37763800<span style='mso-bookmark:Map_peaks'></span>
    37773801
    3778 <p class=MsoNormal>This gives the list (magnitude, x y &amp; z) of all peaks found
    3779 within the unit cell from the last Fourier map search sorted in order of
    3780 decreasing peak magnitude. The crystal structure plot shows each peak position
    3781 as a white 3-D cross.</p>
     3802<p class=MsoNormal>This gives the list (magnitude, x y &amp; z) of all peaks
     3803found within the unit cell from the last Fourier map search sorted in order of decreasing
     3804peak magnitude. The crystal structure plot shows each peak position as a white
     38053-D cross.</p>
    37823806
    37833807<h5>What can I do here?</h5>
     
    38433867<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
    38443868mso-no-proof:yes'><img border=0 width=225 height=31 id="_x0000_i1032"
    3845 src=graphbar.jpg alt="Description: Description: D:\pyGSAS\help\graphbar.jpg"></span><span
     3869src=graphbar.jpg
     3870alt="Description: Description: Description: D:\pyGSAS\help\graphbar.jpg"></span><span
    38463871style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
    38473872
     
    38943919
    38953920<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>The
    3896 powder patterns that are part of your project are shown on this page. They can be
    3897 displayed as a stack of powder patterns, just a single pattern or as a contour
    3898 image of the peak intensities. What can be done here will depend on which is
    3899 displayed and on which item in the GSAS-II data tree you have selected.<o:p></o:p></span></p>
     3921powder patterns that are part of your project are shown on this page. They can
     3922be displayed as a stack of powder patterns, just a single pattern or as a
     3923contour image of the peak intensities. What can be done here will depend on
     3924which is displayed and on which item in the GSAS-II data tree you have
     3925selected.<o:p></o:p></span></p>
    39003926
    39013927<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
     
    39223948auto;text-indent:-.25in;mso-list:l4 level2 lfo22;tab-stops:list 1.0in'><![if !supportLists]><span
    39233949style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
    3924 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    3925 style='mso-bidi-font-weight:normal'>l: offset left</b> &#8211; for a waterfall
     3950style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     3951class=GramE><b style='mso-bidi-font-weight:normal'>l</b></span><b
     3952style='mso-bidi-font-weight:normal'>: offset left</b> &#8211; for a waterfall
    39263953plot of multiple powder profiles, increase the offset to the left. Does not
    39273954apply if only one pattern.</p>
     
    39303957auto;text-indent:-.25in;mso-list:l4 level2 lfo22;tab-stops:list 1.0in'><![if !supportLists]><span
    39313958style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
    3932 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    3933 style='mso-bidi-font-weight:normal'>r: offset right</b> - for a waterfall plot
     3959style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     3960class=GramE><b style='mso-bidi-font-weight:normal'>r</b></span><b
     3961style='mso-bidi-font-weight:normal'>: offset right</b> - for a waterfall plot
    39343962of multiple powder profiles, increase the offset to the left. Does not apply if
    39353963only one pattern.</p>
     
    39383966auto;text-indent:-.25in;mso-list:l4 level2 lfo22;tab-stops:list 1.0in'><![if !supportLists]><span
    39393967style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span
    3940 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    3941 style='mso-bidi-font-weight:normal'>d: offset down</b> - for a waterfall plot
    3942 of multiple powder profiles, increase the offset down. Does not apply if only
    3943 one pattern.</p>
     3968style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     3969class=GramE><b style='mso-bidi-font-weight:normal'>d</b></span><b
     3970style='mso-bidi-font-weight:normal'>: offset down</b> - for a waterfall plot of
     3971multiple powder profiles, increase the offset down. Does not apply if only one
     3972pattern.</p>
    39443973
    39453974<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    39463975auto;text-indent:-.25in;mso-list:l4 level2 lfo22;tab-stops:list 1.0in'><![if !supportLists]><span
    39473976style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>d.<span
    3948 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    3949 style='mso-bidi-font-weight:normal'>u: offset up</b> - for a waterfall plot of multiple
    3950 powder profiles, increase the offset up. Does not apply if only one pattern.</p>
     3977style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     3978class=GramE><b style='mso-bidi-font-weight:normal'>u</b></span><b
     3979style='mso-bidi-font-weight:normal'>: offset up</b> - for a waterfall plot of
     3980multiple powder profiles, increase the offset up. Does not apply if only one
     3981pattern.</p>
    39513982
    39523983<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    39533984auto;text-indent:-.25in;mso-list:l4 level2 lfo22;tab-stops:list 1.0in'><![if !supportLists]><span
    39543985style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>e.<span
    3955 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    3956 style='mso-bidi-font-weight:normal'>o: reset offset</b> - for a waterfall plot
     3986style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     3987class=GramE><b style='mso-bidi-font-weight:normal'>o</b></span><b
     3988style='mso-bidi-font-weight:normal'>: reset offset</b> - for a waterfall plot
    39573989of multiple powder profiles, reset to no offset. Does not apply if only one
    39583990pattern.</p>
     
    39613993auto;text-indent:-.25in;mso-list:l4 level2 lfo22;tab-stops:list 1.0in'><![if !supportLists]><span
    39623994style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>f.<span
    3963 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    3964 style='mso-bidi-font-weight:normal'>n: log(I) on/off</b> &#8211; changes the
     3995style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     3996class=GramE><b style='mso-bidi-font-weight:normal'>n</b></span><b
     3997style='mso-bidi-font-weight:normal'>: log(I) on/off</b> &#8211; changes the
    39653998y-axis to be the log10 of the intensity; difference curve is not shown for
    39663999log(I) on.</p>
     
    39694002auto;text-indent:-.25in;mso-list:l4 level2 lfo22;tab-stops:list 1.0in'><![if !supportLists]><span
    39704003style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>g.<span
    3971 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    3972 style='mso-bidi-font-weight:normal'>c: contour on/off</b> &#8211; if multiple
    3973 powder profiles, then a contour plot is shown of the observed intensities. All
    3974 data sets must be the same length as the first one to be included in the contour
     4004style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     4005class=GramE><b style='mso-bidi-font-weight:normal'>c</b></span><b
     4006style='mso-bidi-font-weight:normal'>: contour on/off</b> &#8211; if multiple powder
     4007profiles, then a contour plot is shown of the observed intensities. All data
     4008sets must be the same length as the first one to be included in the contour
    39754009plot.</p>
    39764010
     
    39884022style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>i.<span
    39894023style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    3990 </span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>s: toggle
    3991 single plot</b> &#8211; for multiple powder profiles, this will show only the
    3992 one selected from the data tree. The offset options are not active.</p>
     4024</span></span></span><![endif]><span class=GramE><b style='mso-bidi-font-weight:
     4025normal'>s</b></span><b style='mso-bidi-font-weight:normal'>: toggle single plot</b>
     4026&#8211; for multiple powder profiles, this will show only the one selected from
     4027the data tree. The offset options are not active.</p>
    39934028
    39944029<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    39964031style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>j.<span
    39974032style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    3998 </span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>w: toggle
    3999 divide by sig</b> &#8211; for the pattern selected from the data tree, this
    4000 will divide the observed, calculated and difference curves by the <span
    4001 class=SpellE>esd</span> for the data points. Other data sets are not shown.</p>
     4033</span></span></span><![endif]><span class=GramE><b style='mso-bidi-font-weight:
     4034normal'>w</b></span><b style='mso-bidi-font-weight:normal'>: toggle divide by
     4035sig</b> &#8211; for the pattern selected from the data tree, this will divide
     4036the observed, calculated and difference curves by the <span class=SpellE>esd</span>
     4037for the data points. Other data sets are not shown.</p>
    40024038
    40034039<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    40174053auto;text-indent:-.25in;mso-list:l4 level2 lfo22;tab-stops:list 1.0in'><![if !supportLists]><span
    40184054style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
    4019 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    4020 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>d:
    4021 lower contour max</span></b><span style='mso-fareast-font-family:"Times New Roman"'>
    4022 &#8211; this lowers the level chosen for the highest contour color.<o:p></o:p></span></p>
     4055style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     4056class=GramE><b style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:
     4057"Times New Roman"'>d</span></b></span><b style='mso-bidi-font-weight:normal'><span
     4058style='mso-fareast-font-family:"Times New Roman"'>: lower contour max</span></b><span
     4059style='mso-fareast-font-family:"Times New Roman"'> &#8211; this lowers the
     4060level chosen for the highest contour color.<o:p></o:p></span></p>
    40234061
    40244062<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    40334071auto;text-indent:-.25in;mso-list:l4 level2 lfo22;tab-stops:list 1.0in'><![if !supportLists]><span
    40344072style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span
    4035 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    4036 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>i:
    4037 interpolation method</span></b><span style='mso-fareast-font-family:"Times New Roman"'>
    4038 &#8211; this changes the method used to represent the contours. If selected a
    4039 dialog box appears with all the possible choices. Default is
    4040 &#8216;nearest&#8217;; the other useful choice is &#8216;bilinear&#8217;, this
    4041 will smooth out the contours. <o:p></o:p></span></p>
     4073style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     4074class=GramE><b style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:
     4075"Times New Roman"'>i</span></b></span><b style='mso-bidi-font-weight:normal'><span
     4076style='mso-fareast-font-family:"Times New Roman"'>: interpolation method</span></b><span
     4077style='mso-fareast-font-family:"Times New Roman"'> &#8211; this changes the
     4078method used to represent the contours. If selected a dialog box appears with
     4079all the possible choices. Default is &#8216;nearest&#8217;; the other useful
     4080choice is &#8216;bilinear&#8217;, this will smooth out the contours. <o:p></o:p></span></p>
    40424081
    40434082<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    40444083auto;text-indent:-.25in;mso-list:l4 level2 lfo22;tab-stops:list 1.0in'><![if !supportLists]><span
    40454084style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>d.<span
    4046 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    4047 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>s:
    4048 color scheme</span></b><span style='mso-fareast-font-family:"Times New Roman"'>
    4049 &#8211; this changes the color scheme for the contouring. Default is
    4050 &#8216;Paired&#8217;, black/ white options are &#8216;Greys&#8217; and
    4051 &#8216;binary&#8217; (for black on white) or &#8216;gray&#8217; (for white on
    4052 black). Others can be very colorful (but not useful)!<o:p></o:p></span></p>
     4085style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     4086class=GramE><b style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:
     4087"Times New Roman"'>s</span></b></span><b style='mso-bidi-font-weight:normal'><span
     4088style='mso-fareast-font-family:"Times New Roman"'>: color scheme</span></b><span
     4089style='mso-fareast-font-family:"Times New Roman"'> &#8211; this changes the
     4090color scheme for the contouring. Default is <span class=GramE>&#8216;Paired&#8217;,</span>
     4091black/ white options are &#8216;Greys&#8217; and &#8216;binary&#8217; (for
     4092black on white) or &#8216;gray&#8217; (for white on black). Others can be very
     4093colorful (but not useful)!<o:p></o:p></span></p>
    40534094
    40544095<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    40554096auto;text-indent:-.25in;mso-list:l4 level2 lfo22;tab-stops:list 1.0in'><![if !supportLists]><span
    40564097style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>e.<span
    4057 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    4058 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>c:
    4059 contour off/on</span></b><span style='mso-fareast-font-family:"Times New Roman"'>
    4060 &#8211; this turns off contouring and returns to a waterfall plot with any
    4061 offsets applied.<o:p></o:p></span></p>
     4098style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     4099class=GramE><b style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:
     4100"Times New Roman"'>c</span></b></span><b style='mso-bidi-font-weight:normal'><span
     4101style='mso-fareast-font-family:"Times New Roman"'>: contour off/on</span></b><span
     4102style='mso-fareast-font-family:"Times New Roman"'> &#8211; this turns off
     4103contouring and returns to a waterfall plot with any offsets applied.<o:p></o:p></span></p>
    40624104
    40634105<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l4 level1 lfo22'><![if !supportLists]><span
     
    41044146style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Move
    41054147the mouse cursor across the plot. If on a diagonal cell, the parameter name,
    4106 value and <span class=SpellE>esd</span> is shown both as a tool tip and in the right
    4107 hand portion of the status bar. If the cursor is off the diagonal, the two
    4108 parameter names and their covariance are shown in the tool tip and the status
    4109 bar.</p>
     4148value and <span class=SpellE>esd</span> is shown both as a tool tip and in the
     4149right hand portion of the status bar. If the cursor is off the diagonal, the
     4150two parameter names and their covariance are shown in the tool tip and the
     4151status bar.</p>
    41104152
    41114153<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l7 level1 lfo23'><![if !supportLists]><span
     
    41174159<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l7 level1 lfo23'><![if !supportLists]><span
    41184160style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
    4119 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Type
    4120 &#8216;s&#8217; &#8211; A color scheme selection dialog is shown. Select a
    4121 color scheme and press OK, the new color scheme will be plotted. The default is
    4122 &#8216;<span class=SpellE>RdYlGn</span>&#8217;.</p>
     4161style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     4162class=GramE>Type &#8216;s&#8217;</span> &#8211; A color scheme selection dialog
     4163is shown. Select a color scheme and press <span class=GramE>OK,</span> the new
     4164color scheme will be plotted. The default is &#8216;<span class=SpellE>RdYlGn</span>&#8217;.</p>
    41234165
    41244166<h4><a name="Structure_Factors"><span style='mso-fareast-font-family:"Times New Roman"'>Structure
     
    41544196style='font-family:Symbol;mso-fareast-font-family:"Times New Roman"'>D</span><span
    41554197style='mso-fareast-font-family:"Times New Roman"'>q/q) <span class=SpellE>vs</span>
    4156 q(=2</span><span style='font-family:Symbol;mso-fareast-font-family:"Times New Roman"'>p</span><span
    4157 style='mso-fareast-font-family:"Times New Roman"'>/d) from the Gaussian and
    4158 Lorentzian parts of the profile function. The computed curves are based on the
    4159 values of U, V, W, X and Y shown in the Instrument Parameters window in
    4160 parentheses. These are the values for the instrument contribution that were set
    4161 when the powder pattern was first read in to GSAS-II. If individual peak fitting
    4162 has been performed, the values of &#8216;sig&#8217; &amp; &#8216;gam&#8217; for
    4163 the peaks are plotted as &#8216;+&#8217;; these are computed from the fitted
    4164 values of U, V, W, X and Y as well as any sig or gam individually refined.<o:p></o:p></span></p>
     4198<span class=GramE>q(</span>=2</span><span style='font-family:Symbol;mso-fareast-font-family:
     4199"Times New Roman"'>p</span><span style='mso-fareast-font-family:"Times New Roman"'>/d)
     4200from the Gaussian and Lorentzian parts of the profile function. The computed
     4201curves are based on the values of U, V, W, X and Y shown in the Instrument
     4202Parameters window in parentheses. These are the values for the instrument
     4203contribution that were set when the powder pattern was first read in to
     4204GSAS-II. If individual peak fitting has been performed, the values of
     4205&#8216;sig&#8217; &amp; &#8216;gam&#8217; for the peaks are plotted as
     4206&#8216;+&#8217;; these are computed from the fitted values of U, V, W, X and Y
     4207as well as any sig or gam individually refined.<o:p></o:p></span></p>
    41654208
    41664209<h4><span style='mso-fareast-font-family:"Times New Roman"'>Texture </span></h4>
  • trunk/help/gsasII_files/filelist.xml

    r586 r588  
    22 <o:MainFile HRef="../gsasII.html"/>
    33 <o:File HRef="item0010.xml"/>
    4  <o:File HRef="props0011.xml"/>
     4 <o:File HRef="props011.xml"/>
    55 <o:File HRef="themedata.thmx"/>
    66 <o:File HRef="colorschememapping.xml"/>
  • trunk/help/gsasII_files/props011.xml

    r585 r588  
    11<?xml version="1.0" encoding="UTF-8" standalone="no"?>
    2 <ds:datastoreItem ds:itemID="{D62DA604-1FFD-4090-94B3-48BD01137B9A}" 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>
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