Changeset 895


Ignore:
Timestamp:
Apr 30, 2013 3:32:36 PM (9 years ago)
Author:
vondreele
Message:

update tutorials

Location:
trunk/help
Files:
42 edited

Legend:

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

    r676 r895  
    2525  <o:Author>Von Dreele</o:Author>
    2626  <o:LastAuthor>Von Dreele</o:LastAuthor>
    27   <o:Revision>13</o:Revision>
    28   <o:TotalTime>124</o:TotalTime>
     27  <o:Revision>14</o:Revision>
     28  <o:TotalTime>137</o:TotalTime>
    2929  <o:Created>2012-05-04T19:00:00Z</o:Created>
    30   <o:LastSaved>2012-07-03T19:08:00Z</o:LastSaved>
     30  <o:LastSaved>2013-04-30T17:13:00Z</o:LastSaved>
    3131  <o:Pages>4</o:Pages>
    32   <o:Words>706</o:Words>
    33   <o:Characters>4028</o:Characters>
     32  <o:Words>695</o:Words>
     33  <o:Characters>3966</o:Characters>
    3434  <o:Company>Argonne National Laboratory</o:Company>
    3535  <o:Lines>33</o:Lines>
    3636  <o:Paragraphs>9</o:Paragraphs>
    37   <o:CharactersWithSpaces>4725</o:CharactersWithSpaces>
     37  <o:CharactersWithSpaces>4652</o:CharactersWithSpaces>
    3838  <o:Version>14.00</o:Version>
    3939 </o:DocumentProperties>
     
    4848<!--[if gte mso 9]><xml>
    4949 <w:WordDocument>
     50  <w:Zoom>156</w:Zoom>
    5051  <w:SpellingState>Clean</w:SpellingState>
    5152  <w:GrammarState>Clean</w:GrammarState>
     
    359360        mso-generic-font-family:swiss;
    360361        mso-font-pitch:variable;
    361         mso-font-signature:-520092929 1073786111 9 0 415 0;}
     362        mso-font-signature:-536870145 1073786111 1 0 415 0;}
    362363@font-face
    363364        {font-family:Tahoma;
     
    798799        mso-ascii-theme-font:minor-latin;
    799800        mso-hansi-font-family:Calibri;
    800         mso-hansi-theme-font:minor-latin;
    801         mso-bidi-font-family:"Times New Roman";
    802         mso-bidi-theme-font:minor-bidi;}
     801        mso-hansi-theme-font:minor-latin;}
    803802</style>
    804803<![endif]--><!--[if gte mso 9]><xml>
     
    823822in bold face below as <b style='mso-bidi-font-weight:normal'><span
    824823style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    825 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Help/About
    826 GSAS-II</span></b>, which lists first the name of the menu (here <b
    827 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    828 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    829 minor-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";
    831 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    832 minor-latin'>About GSAS-II</span></b>).</p>
     824mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     825minor-latin'>Help/About GSAS-II</span></b>, which lists first the name of the
     826menu (here <b style='mso-bidi-font-weight:normal'><span style='font-family:
     827"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     828minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>Help</span></b>)
     829and second the name of the entry in the menu (here <b style='mso-bidi-font-weight:
     830normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     831minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     832mso-bidi-theme-font:minor-latin'>About GSAS-II</span></b>).</p>
    833833
    834834<p class=MsoNormal>If you have not done so already, <u><span style='color:#0070C0'><a
     
    847847depend on your OS. Change the search directory to <b style='mso-bidi-font-weight:
    848848normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    849 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>/Exercises/images</span></b>
    850 and then select the file </p>
     849minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     850mso-bidi-theme-font:minor-latin'>/Exercises/images</span></b> and then select
     851the file </p>
    851852
    852853<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span
    853854style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    854 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>La_hex_+45deg-00015.tif</span></b>
    855 and press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    856 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    857 minor-latin'>Open</span></b>.<span style='mso-no-proof:yes'> <o:p></o:p></span></p>
     855mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     856minor-latin'>La_hex_+45deg-00015.tif</span></b> and press <b style='mso-bidi-font-weight:
     857normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     858minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     859mso-bidi-theme-font:minor-latin'>Open</span></b>.<span style='mso-no-proof:
     860yes'> <o:p></o:p></span></p>
    858861
    859862<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
     
    877880 <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
    878881 <o:lock v:ext="edit" aspectratio="t"/>
    879 </v:shapetype><v:shape id="Picture_x0020_6" o:spid="_x0000_i1032" type="#_x0000_t75"
    880  style='width:225pt;height:203.25pt;visibility:visible;mso-wrap-style:square'>
     882</v:shapetype><v:shape id="_x0000_i1032" type="#_x0000_t75" style='width:300pt;
     883 height:187.5pt;visibility:visible;mso-wrap-style:square'>
    881884 <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image001.png"
    882885  o:title=""/>
    883 </v:shape><![endif]--><![if !vml]><img border=0 width=300 height=271
     886</v:shape><![endif]--><![if !vml]><img border=0 width=400 height=250
    884887src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image001.png"
    885 v:shapes="Picture_x0020_6"><![endif]></span></p>
     888v:shapes="_x0000_i1032"><![endif]></span></p>
    886889
    887890<p class=MsoNormal>At this point the data tree window will have several
    888891entries; the highlighted one specifies the contents of the data window as <b
    889892style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    890 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    891 minor-latin'>Image Controls</span><o:p></o:p></b></p>
     893mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     894Calibri;mso-bidi-theme-font:minor-latin'>Image Controls</span><o:p></o:p></b></p>
    892895
    893896<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    894  id="_x0000_i1031" type="#_x0000_t75" style='width:472.5pt;height:310.5pt;
    895  visibility:visible;mso-wrap-style:square'>
     897 id="Picture_x0020_10" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:472.5pt;
     898 height:342pt;visibility:visible;mso-wrap-style:square'>
    896899 <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image002.png"
    897900  o:title=""/>
    898 </v:shape><![endif]--><![if !vml]><img border=0 width=630 height=414
     901</v:shape><![endif]--><![if !vml]><img border=0 width=630 height=456
    899902src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image002.png"
    900 v:shapes="_x0000_i1031"><![endif]></span></p>
     903v:shapes="Picture_x0020_10"><![endif]></span></p>
    901904
    902905<p class=MsoNormal><span style='mso-spacerun:yes'> </span>The plot window shows
    903906the image; notice the elliptical shape of the powder diffraction rings. The
    904907blue <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    905 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    906 minor-latin;color:#4F81BD;mso-themecolor:accent1'>X</span></b> marks the
    907 default beam location (image center); your calibration will correctly place it.
    908 Also notice that the values shown in the plot window status bar (at bottom of
    909 plot window) change as you move the cursor over the plot; these values are at
    910 present in error as they are computed from the default calibration values. They
    911 will be correct after you finish the calibration.</p>
     908mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     909Calibri;mso-bidi-theme-font:minor-latin;color:#4F81BD;mso-themecolor:accent1'>X</span></b>
     910marks the default beam location (image center); your calibration will correctly
     911place it. Also notice that the values shown in the plot window status bar (at
     912bottom of plot window) change as you move the cursor over the plot; these
     913values are at present in error as they are computed from the default
     914calibration values. They will be correct after you finish the calibration.</p>
    912915
    913916<p class=MsoNormal><span style='mso-spacerun:yes'> </span><span
    914 style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_4"
     917style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_11"
    915918 o:spid="_x0000_i1030" type="#_x0000_t75" style='width:525pt;height:450pt;
    916919 visibility:visible;mso-wrap-style:square'>
     
    919922</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
    920923src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image003.png"
    921 v:shapes="Picture_x0020_4"><![endif]></span></p>
     924v:shapes="Picture_x0020_11"><![endif]></span></p>
    922925
    923926<h1><span style='mso-spacerun:yes'> </span>Step 2: Edit image parameters</h1>
     
    927930needs to be added manually. In this case set the <b style='mso-bidi-font-weight:
    928931normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    929 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>wavelength</span></b>
    930 to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    931 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    932 minor-latin'>0.10798</span></b>. It is also helpful to change the display of
    933 the image so that it is easier to see the diffraction rings. Lowering the
    934 maximum intensity to 10,000 to 20,000 counts will help (note that this can be
    935 done by moving the <span class=GramE>slider,</span> or by typing a value in the
    936 box and then clicking on another control or pressing the <b style='mso-bidi-font-weight:
     932minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     933mso-bidi-theme-font:minor-latin'>wavelength</span></b> to <b style='mso-bidi-font-weight:
    937934normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    938 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Enter</span></b>
    939 or <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    940 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    941 minor-latin'>Tab</span></b> key). You may also wish to select another color
    942 scheme using the <b style='mso-bidi-font-weight:normal'><span style='font-family:
    943 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    944 minor-latin;mso-bidi-theme-font:minor-latin'>Color bar</span></b> selector. </p>
     935minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     936mso-bidi-theme-font:minor-latin'>0.10798</span></b>. It is also helpful to
     937change the display of the image so that it is easier to see the diffraction
     938rings. Lowering the maximum intensity to 10,000 to 20,000 counts will help
     939(note that this can be done by moving the <span class=GramE>slider,</span> or
     940by typing a value in the box and then clicking on another control or pressing
     941the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     942mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     943Calibri;mso-bidi-theme-font:minor-latin'>Enter</span></b> or <b
     944style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     945mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     946Calibri;mso-bidi-theme-font:minor-latin'>Tab</span></b> key). You may also wish
     947to select another color scheme using the <b style='mso-bidi-font-weight:normal'><span
     948style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     949mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     950minor-latin'>Color bar</span></b> selector. </p>
    945951
    946952<h1><span style='mso-spacerun:yes'> </span>Step 3: Calibrate</h1>
     
    951957used as a sample in the box labeled <span class=SpellE><b style='mso-bidi-font-weight:
    952958normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    953 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Calibrant</span></b></span>;
    954 select <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    955 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    956 minor-latin'>LaB6 SRM660a</span></b></p>
     959minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     960mso-bidi-theme-font:minor-latin'>Calibrant</span></b></span>; select <b
     961style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     962mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     963Calibri;mso-bidi-theme-font:minor-latin'>LaB6 SRM660a</span></b></p>
    957964
    958965<h3><span style='mso-spacerun:yes'> </span>Second: </h3>
     
    960967<p class=MsoNormal><span style='mso-spacerun:yes'>   </span>Use the <b
    961968style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    962 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    963 minor-latin'>Operations/Calibrate</span></b> menu item (note this menu is on
    964 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    965 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     969mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     970Calibri;mso-bidi-theme-font:minor-latin'>Operations/Calibrate</span></b> menu
     971item (note this menu is on the <b style='mso-bidi-font-weight:normal'><span
     972style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     973mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    966974minor-latin'>Image Controls</span></b> window or for the Mac, the <span
    967975class=GramE><b style='mso-bidi-font-weight:normal'><span style='font-family:
    968976"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    969 minor-latin;mso-bidi-theme-font:minor-latin'>Image<span
     977minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>Image<span
    970978style='mso-spacerun:yes'>  </span>Controls</span></b></span> window must be
    971979active to place this into the system menu bar). At this point the status line
    972980on the bottom of the <b style='mso-bidi-font-weight:normal'><span
    973981style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    974 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Image
    975 Controls</span></b> window changes with a prompt to select points for
    976 calibration.</p>
     982mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     983minor-latin'>Image Controls</span></b> window changes with a prompt to select
     984points for calibration.</p>
    977985
    978986<h3>Third: </h3>
     
    982990is defined, a red &quot;<b style='mso-bidi-font-weight:normal'><span
    983991style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    984 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin;color:red'>+</span></b>&quot;
    985 is added to the plot. You need not hit the ring exactly as the code will search
    986 for the locally highest point. </p>
     992mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     993minor-latin;color:red'>+</span></b>&quot; is added to the plot. You need not
     994hit the ring exactly as the code will search for the locally highest point. </p>
    987995
    988996<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    10121020located and an ellipse is optimized for each ring. The indexed rings are first
    10131021shown in red as the calibration proceeds and center of each ellipse is noted
    1014 with a blue &quot;<span style='color:#4F81BD;mso-themecolor:accent1'>+</span>&quot;.
    1015 When all rings have been fitted, the entire ensemble of rings is refitted to
    1016 the detector parameters and the rings are then shown in blue. The beam position
    1017 (blue “<span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1018 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin;
    1019 color:#4F81BD;mso-themecolor:accent1'>X</span>”) is now correctly positioned.</p>
     1022with a blue &quot;<b style='mso-bidi-font-weight:normal'><span
     1023style='color:#4F81BD;mso-themecolor:accent1'>+</span></b>&quot;. When all rings
     1024have been fitted, the entire ensemble of rings is refitted to the detector
     1025parameters and the rings are then shown in blue. The beam position (blue “<span
     1026style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1027mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1028minor-latin;color:#4F81BD;mso-themecolor:accent1'>X</span>”) is now correctly
     1029positioned.</p>
    10201030
    10211031<p class=MsoNormal><span style='mso-spacerun:yes'> </span><span
     
    10321042<p class=MsoNormal>The derived calibration results are shown in the <b
    10331043style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1034 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1035 minor-latin'>Image Controls</span></b> window.</p>
     1044mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1045Calibri;mso-bidi-theme-font:minor-latin'>Image Controls</span></b> window.</p>
    10361046
    10371047<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1038  id="Picture_x0020_10" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:472.5pt;
    1039  height:310.5pt;visibility:visible;mso-wrap-style:square'>
     1048 id="Picture_x0020_13" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:472.5pt;
     1049 height:342pt;visibility:visible;mso-wrap-style:square'>
    10401050 <v:imagedata src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image006.png"
    10411051  o:title=""/>
    1042 </v:shape><![endif]--><![if !vml]><img border=0 width=630 height=414
     1052</v:shape><![endif]--><![if !vml]><img border=0 width=630 height=456
    10431053src="Calibration%20of%20an%20area%20detector%20in%20GSAS_files/image006.png"
    1044 v:shapes="Picture_x0020_10"><![endif]></span><span
     1054v:shapes="Picture_x0020_13"><![endif]></span><span
    10451055style='mso-spacerun:yes'> </span></p>
    10461056
    10471057<p class=MsoNormal><span class=GramE>and</span> the console window shows
    1048 details of the fit; a trial refinement for the wavelength is also given for you
    1049 to consider.</p>
     1058details of the fit.</p>
    10501059
    10511060<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    10611070points selected by the program, click on the <b style='mso-bidi-font-weight:
    10621071normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1063 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>show
    1064 ring picks?</span></b> <span class=GramE>check</span> box </p>
     1072minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1073mso-bidi-theme-font:minor-latin'>show ring picks?</span></b> <span class=GramE>check</span>
     1074box </p>
    10651075
    10661076<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    10791089This can be repaired by changing the pixel search range to 10 and using the <b
    10801090style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1081 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1082 minor-latin'>Operations/Recalibrate</span></b> menu item.</p>
     1091mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1092Calibri;mso-bidi-theme-font:minor-latin'>Operations/Recalibrate</span></b> menu
     1093item.</p>
    10831094
    10841095<p class=MsoNormal>Assuming that these calibration results will be applied to
    10851096other images in the same GSAS-II project, click on <b style='mso-bidi-font-weight:
    10861097normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1087 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Use
    1088 as default for all images</span></b>. You may also save a copy of the
    1089 calibration values to a file <span style='font-family:"Calibri","sans-serif";
    1090 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1098minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1099mso-bidi-theme-font:minor-latin'>Use as default for all images</span></b>. You
     1100may also save a copy of the calibration values to a file <span
     1101style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1102mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    10911103minor-latin'>(<span class=SpellE><i style='mso-bidi-font-style:normal'>name</i><b
    10921104style='mso-bidi-font-weight:normal'>.imctrl</b></span></span>) with the <b
    10931105style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1094 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1095 minor-latin'>Operations/Save Controls</span></b> menu item. To save the
    1096 project, including the now-derived calibration information, use the <b
     1106mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1107Calibri;mso-bidi-theme-font:minor-latin'>Operations/Save Controls</span></b>
     1108menu item. To save the project, including the now-derived calibration information,
     1109use the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1110mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1111Calibri;mso-bidi-theme-font:minor-latin'>File/Save</span> </b><b
    10971112style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1098 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1099 minor-latin'>File/Save</span> </b><b style='mso-bidi-font-weight:normal'><span
     1113mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1114Calibri;mso-bidi-theme-font:minor-latin'>Project</span></b><span
    11001115style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1101 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Project</span></b><span
    1102 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1103 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'> </span>menu
    1104 item associated with the data tree window; as this project has not been saved
    1105 before the file save dialog will need a file name. Don’t enter the extension;
    1106 it will be set to “<b style='mso-bidi-font-weight:normal'><span
    1107 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1108 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>.<span
    1109 class=SpellE>gpx</span></span></b>”.</p>
     1116mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1117minor-latin'> </span>menu item associated with the data tree window; as this
     1118project has not been saved before the file save dialog will need a file name.
     1119Don’t enter the extension; it will be set to “<b style='mso-bidi-font-weight:
     1120normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1121minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1122mso-bidi-theme-font:minor-latin'>.<span class=SpellE>gpx</span></span></b>”.</p>
    11101123
    11111124<h2>Next step: <span class=MsoHyperlink><span style='color:#0070C0'><a
  • trunk/help/Fit Peaks.htm

    r864 r895  
    2323  <o:Author>Von Dreele</o:Author>
    2424  <o:LastAuthor>Von Dreele</o:LastAuthor>
    25   <o:Revision>29</o:Revision>
    26   <o:TotalTime>717</o:TotalTime>
     25  <o:Revision>30</o:Revision>
     26  <o:TotalTime>770</o:TotalTime>
    2727  <o:Created>2012-05-05T16:28:00Z</o:Created>
    28   <o:LastSaved>2013-03-18T17:01:00Z</o:LastSaved>
     28  <o:LastSaved>2013-04-30T18:16:00Z</o:LastSaved>
    2929  <o:Pages>11</o:Pages>
    30   <o:Words>2632</o:Words>
    31   <o:Characters>15009</o:Characters>
     30  <o:Words>2633</o:Words>
     31  <o:Characters>15011</o:Characters>
    3232  <o:Company>Argonne National Laboratory</o:Company>
    3333  <o:Lines>125</o:Lines>
    3434  <o:Paragraphs>35</o:Paragraphs>
    35   <o:CharactersWithSpaces>17606</o:CharactersWithSpaces>
     35  <o:CharactersWithSpaces>17609</o:CharactersWithSpaces>
    3636  <o:Version>14.00</o:Version>
    3737 </o:DocumentProperties>
     
    4040 </o:OfficeDocumentSettings>
    4141</xml><![endif]-->
    42 <link rel=dataStoreItem href="Fit%20Peaks_files/item0035.xml"
    43 target="Fit%20Peaks_files/props036.xml">
    4442<link rel=themeData href="Fit%20Peaks_files/themedata.thmx">
    4543<link rel=colorSchemeMapping href="Fit%20Peaks_files/colorschememapping.xml">
     
    11451143mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    11461144Calibri;mso-bidi-theme-font:minor-latin'>Import/Powder Data/from GSAS file</span></b>
    1147 menu item to read the data file into the current GSAS-II project. This read
    1148 option is set to read any of the powder data formats (except neutron TOF time
    1149 map files) defined for GSAS (angles in <span class=SpellE>centidegrees</span>).
    1150 Other submenu items will read the <span class=SpellE><b style='mso-bidi-font-weight:
    1151 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1152 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
    1153 mso-bidi-theme-font:minor-latin'>cif</span></b></span> format or the <span
    1154 class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
    1155 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1156 minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>xye</span></b></span>
    1157 format (angles in degrees) used by <span class=SpellE>Topas</span>, etc.<span
     1145menu item to read the data file into the current GSAS-II project. This read option
     1146is set to read any of the powder data formats defined for GSAS (angles in <span
     1147class=SpellE>centidegrees</span>, TOF in µsec). Other submenu items will read
     1148the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
     1149style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1150mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1151minor-latin'>cif</span></b></span> format or the <span class=SpellE><b
     1152style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1153mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1154Calibri;mso-bidi-theme-font:minor-latin'>xye</span></b></span> format (angles
     1155in degrees) used by <span class=SpellE>Topas</span>, etc.<span
    11581156style='mso-spacerun:yes'>  </span>Change the file directory to <b
    11591157style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     
    12301228 <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
    12311229 <o:lock v:ext="edit" aspectratio="t"/>
    1232 </v:shapetype><v:shape id="Picture_x0020_1" o:spid="_x0000_i1052" type="#_x0000_t75"
    1233  style='width:225pt;height:187.5pt;visibility:visible;mso-wrap-style:square'>
     1230</v:shapetype><v:shape id="Picture_x0020_29" o:spid="_x0000_i1052" type="#_x0000_t75"
     1231 style='width:300pt;height:187.5pt;visibility:visible;mso-wrap-style:square'>
    12341232 <v:imagedata src="Fit%20Peaks_files/image001.png" o:title=""/>
    1235 </v:shape><![endif]--><![if !vml]><img border=0 width=300 height=250
    1236 src="Fit%20Peaks_files/image001.png" v:shapes="Picture_x0020_1"><![endif]></span></p>
     1233</v:shape><![endif]--><![if !vml]><img border=0 width=400 height=250
     1234src="Fit%20Peaks_files/image001.png" v:shapes="Picture_x0020_29"><![endif]></span></p>
    12371235
    12381236<p class=MsoNormal><span class=GramE>and</span> the plot window will show the
     
    13011299minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
    13021300mso-bidi-theme-font:minor-latin'>Limits</span></b> window is erased). At this
    1303 point it is wise <span class=GramE>to<span style='mso-spacerun:yes'> 
    1304 </span>zoom</span> in on the data that will be used for indexing. </p>
     1301point it is wise to zoom in on the data that will be used for indexing. </p>
    13051302
    13061303<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
     
    13621359
    13631360<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
    1364 auto'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_7"
     1361auto'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_30"
    13651362 o:spid="_x0000_i1046" type="#_x0000_t75" style='width:401.25pt;height:262.5pt;
    13661363 visibility:visible;mso-wrap-style:square'>
    13671364 <v:imagedata src="Fit%20Peaks_files/image008.png" o:title=""/>
    13681365</v:shape><![endif]--><![if !vml]><img border=0 width=535 height=350
    1369 src="Fit%20Peaks_files/image008.png" v:shapes="Picture_x0020_7"><![endif]></span></p>
     1366src="Fit%20Peaks_files/image008.png" v:shapes="Picture_x0020_30"><![endif]></span></p>
    13701367
    13711368<p class=MsoListParagraphCxSpLast style='margin-left:39.0pt;mso-add-space:auto'>There
    1372 will be 23 peaks in this example. You should examine both the list and the plot
    1373 to be sure the auto search did not pick a peak twice (there may be three of
    1374 these!) or skip a peak or shoulder. You can add a peak to the list by pressing
    1375 the left mouse button with the pointer on a data point at the peak top or
    1376 shoulder. You may drag a peak position as needed; be sure the zoom/shift
    1377 buttons are off. A position may be deleted with a right click with the mouse on
    1378 the blue line. You can also delete a peak by selecting the row in the <span
    1379 class=GramE>table,</span> it will be highlighted in blue. Then press the Delete
    1380 key; it will be removed from the table and the plot. The list will always show
    1381 the peaks sorted by position. When done you should have 20 unique peak
    1382 positions.</p>
     1369will be 22-23 peaks in this example. You should examine both the list and the
     1370plot to be sure the auto search did not pick a peak twice (there may be three
     1371of these!) or skip a peak or shoulder. You can add a peak to the list by
     1372pressing the left mouse button with the pointer on a data point at the peak top
     1373or shoulder; be sure the zoom/shift buttons are off. You may drag a peak
     1374position as needed. A position may be deleted with a right click with the mouse
     1375on the blue line. You can also delete a peak by selecting the row in the table;
     1376it will be highlighted in blue. Then press the <b style='mso-bidi-font-weight:
     1377normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1378minor-latin;mso-hansi-theme-font:minor-latin'>Delete</span></b> key; it will be
     1379removed from the table and the plot. The list will always show the peaks sorted
     1380by position. When done you should have 20 unique peak positions.</p>
    13831381
    13841382<h2>Step 4: Refine Peak Positions</h2>
     
    14171415
    14181416<p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1419  id="_x0000_i1045" type="#_x0000_t75" style='width:525pt;height:450pt;
    1420  visibility:visible;mso-wrap-style:square'>
     1417 id="Picture_x0020_8" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:525pt;
     1418 height:450pt;visibility:visible;mso-wrap-style:square'>
    14211419 <v:imagedata src="Fit%20Peaks_files/image009.png" o:title=""/>
    14221420</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
    1423 src="Fit%20Peaks_files/image009.png" v:shapes="_x0000_i1045"><![endif]></span></p>
     1421src="Fit%20Peaks_files/image009.png" v:shapes="Picture_x0020_8"><![endif]></span></p>
    14241422
    14251423<p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    14481446style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
    14491447style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    1450 class=GramE>single-click</span> on the refine label above the peak position
    1451 check-boxes. The entire column of checkboxes is highlighted in blue. Press the <b
    1452 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1448class=GramE>single-click</span> on the <b style='mso-bidi-font-weight:normal'><span
     1449style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1450mso-hansi-theme-font:minor-latin'>refine</span></b> label above the peak
     1451position check-boxes. The entire column of checkboxes is highlighted in blue.
     1452Press the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    14531453mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    14541454Calibri;mso-bidi-theme-font:minor-latin'>y</span></b> key to turn on all
     
    15571557style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    15581558mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    1559 Calibri;mso-bidi-theme-font:minor-latin'>Index Peaks Operations/Load</span></b>
     1559Calibri;mso-bidi-theme-font:minor-latin'>Index Peaks Operations/Load/Reload</span></b>
    15601560to copy the fitted peaks from the <b style='mso-bidi-font-weight:normal'><span
    15611561style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     
    15961596style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    15971597mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    1598 minor-latin'>Cell Index/Index Cell</span></b>. The search then runs and the
    1599 console shows a running list of possible cells as they are found; the sorted by
    1600 M20 list of possible matching cells is shown in the <b style='mso-bidi-font-weight:
    1601 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1602 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
    1603 mso-bidi-theme-font:minor-latin'>Unit Cells List</span></b> window</p>
     1598minor-latin'>Cell Index/Refine/Index Cell</span></b>. The search then runs and
     1599the console shows a running list of possible cells as they are found; the
     1600sorted by M20 list of possible matching cells is shown in the <b
     1601style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1602mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1603Calibri;mso-bidi-theme-font:minor-latin'>Unit Cells List</span></b> window</p>
    16041604
    16051605<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    16481648style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    16491649mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    1650 Calibri;mso-bidi-theme-font:minor-latin'>Cell Index/Copy Cell</span></b> menu
    1651 option. Then optimize the cell by refining the lattice parameters and the
     1650Calibri;mso-bidi-theme-font:minor-latin'>Cell Index/Refine/Copy Cell</span></b>
     1651menu option. Then optimize the cell by refining the lattice parameters and the
    16521652two-theta zero: click on the refine checkbox next to the <b style='mso-bidi-font-weight:
    16531653normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     
    16561656style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    16571657mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    1658 Calibri;mso-bidi-theme-font:minor-latin'>Cell Index/Refine Cell</span></b> menu
    1659 option. The M20 improves to ~3600 and <span class=GramE>the a</span> cell
     1658Calibri;mso-bidi-theme-font:minor-latin'>Cell Index/Refine/Refine Cell</span></b>
     1659menu option. The M20 improves to ~3600 and <span class=GramE>the a</span> cell
    16601660parameter value shifts from 4.15683 to 4.15691 when zero is refined. (NB: The
    16611661certificate value for NIST SRM 660a is 4.15692 Å). Press the <b
    16621662style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    16631663mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    1664 Calibri;mso-bidi-theme-font:minor-latin'>Show refined <span class=SpellE>hkl</span>
    1665 positions + Zero offset</span></b> button to update the plot including the
    1666 refined <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1664Calibri;mso-bidi-theme-font:minor-latin'>Show <span class=SpellE>hkl</span>
     1665positions </span></b>button to update the plot including the refined <b
     1666style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    16671667mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    16681668Calibri;mso-bidi-theme-font:minor-latin'>Zero offset</span></b> (in this case
     
    16701670
    16711671<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1672  id="_x0000_i1036" type="#_x0000_t75" style='width:527.25pt;height:334.5pt;
    1673  visibility:visible;mso-wrap-style:square'>
     1672 id="Picture_x0020_17" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:527.25pt;
     1673 height:334.5pt;visibility:visible;mso-wrap-style:square'>
    16741674 <v:imagedata src="Fit%20Peaks_files/image018.png" o:title=""/>
    16751675</v:shape><![endif]--><![if !vml]><img border=0 width=703 height=446
    1676 src="Fit%20Peaks_files/image018.png" v:shapes="_x0000_i1036"><![endif]></span></p>
     1676src="Fit%20Peaks_files/image018.png" v:shapes="Picture_x0020_17"><![endif]></span></p>
    16771677
    16781678<p class=MsoNormal>Notice that a new entry heads the list in the <b
     
    16821682the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    16831683mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    1684 Calibri;mso-bidi-theme-font:minor-latin'>Cell Index/Refine</span></b> window
    1685 with an improved M20(=3607.97) and a new value for <b style='mso-bidi-font-weight:
     1684Calibri;mso-bidi-theme-font:minor-latin'>Cell Index/Refine/Refine</span></b>
     1685window with an improved M20(=3607.97) and a new value for <b style='mso-bidi-font-weight:
    16861686normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    16871687minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     
    16911691normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    16921692minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
    1693 mso-bidi-theme-font:minor-latin'>Cell Index/New phase</span></b> menu option
    1694 allows one to create a phase with these lattice parameters in the data tree
    1695 under <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1696 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    1697 Calibri;mso-bidi-theme-font:minor-latin'>Phases</span></b>.<span
     1693mso-bidi-theme-font:minor-latin'>Cell Index/Refine/New phase</span></b> menu
     1694option allows one to create a phase with these lattice parameters in the data
     1695tree under <b style='mso-bidi-font-weight:normal'><span style='font-family:
     1696"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1697minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>Phases</span></b>.<span
    16981698style='mso-spacerun:yes'>  </span>A name for the new phase is requested. This
    16991699creates the tree item <b style='mso-bidi-font-weight:normal'><span
     
    17311731new mineral <a href="http://en.wikipedia.org/wiki/Jadarite"><span class=SpellE>jadarite</span></a>
    17321732(aka “<a href="http://en.wikipedia.org/wiki/Kryptonite">kryptonite</a>”). The
    1733 data was also collected on 11BM-B at APS. The unit cell is monoclinic so is a more
    1734 substantial test of the indexing capability of GSAS-II.</p>
     1733data was also collected on 11BM-B at APS. The unit cell is monoclinic so it is
     1734a more substantial test of the indexing capability of GSAS-II.</p>
    17351735
    17361736<h2><span class=GramE>Step 1.</span> Read in the data. </h2>
     
    17461746
    17471747<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1748  id="_x0000_i1035" type="#_x0000_t75" style='width:525pt;height:450pt;
    1749  visibility:visible;mso-wrap-style:square'>
     1748 id="Picture_x0020_18" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:525pt;
     1749 height:450pt;visibility:visible;mso-wrap-style:square'>
    17501750 <v:imagedata src="Fit%20Peaks_files/image019.png" o:title=""/>
    17511751</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
    1752 src="Fit%20Peaks_files/image019.png" v:shapes="_x0000_i1035"><![endif]></span></p>
     1752src="Fit%20Peaks_files/image019.png" v:shapes="Picture_x0020_18"><![endif]></span></p>
    17531753
    17541754<p class=MsoNormal>I’ve zoomed in &amp; shifted the plot some to highlight the
     
    17761776
    17771777<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1778  id="Picture_x0020_33" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:525pt;
    1779  height:450pt;visibility:visible;mso-wrap-style:square'>
     1778 id="_x0000_i1034" type="#_x0000_t75" style='width:525pt;height:450pt;
     1779 visibility:visible;mso-wrap-style:square'>
    17801780 <v:imagedata src="Fit%20Peaks_files/image020.png" o:title=""/>
    17811781</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
    1782 src="Fit%20Peaks_files/image020.png" v:shapes="Picture_x0020_33"><![endif]></span><br
     1782src="Fit%20Peaks_files/image020.png" v:shapes="_x0000_i1034"><![endif]></span><br
    17831783clear=all style='mso-special-character:line-break'>
    17841784</p>
     
    18141814normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    18151815minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
    1816 mso-bidi-theme-font:minor-latin'>Y</span></b> model can accommodate. Make sure no
    1817 peaks drift away during refinement (one weak one at ~6.67 is particularly
     1816mso-bidi-theme-font:minor-latin'>Y</span></b> model can accommodate. Make sure
     1817no peaks drift away during refinement (one weak one at ~6.67 is particularly
    18181818troublesome). However, this is good enough to proceed.</p>
    18191819
     
    18531853minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
    18541854mso-bidi-theme-font:minor-latin'>Cancel</span></b> on the progress bar window.
    1855 Notice the ‘<b style='mso-bidi-font-weight:normal'>keep’</b> column; this
    1856 allows you to keep some solutions from one indexing run to the next. It may
    1857 take more than one press to fully stop it. My result was </p>
     1855Notice the ‘<b style='mso-bidi-font-weight:normal'><span style='font-family:
     1856"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1857minor-latin'>keep</span></b>’ column; this allows you to keep some solutions
     1858from one indexing run to the next. It may take more than one press to fully
     1859stop it. My result was </p>
    18581860
    18591861<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1860  id="Picture_x0020_21" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:525pt;
    1861  height:450pt;visibility:visible;mso-wrap-style:square'>
     1862 id="_x0000_i1033" type="#_x0000_t75" style='width:525pt;height:450pt;
     1863 visibility:visible;mso-wrap-style:square'>
    18621864 <v:imagedata src="Fit%20Peaks_files/image021.png" o:title=""/>
    18631865</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
    1864 src="Fit%20Peaks_files/image021.png" v:shapes="Picture_x0020_21"><![endif]><!--[if gte vml 1]><v:shape
    1865  id="_x0000_i1032" type="#_x0000_t75" style='width:527.25pt;height:376.5pt;
    1866  visibility:visible;mso-wrap-style:square'>
     1866src="Fit%20Peaks_files/image021.png" v:shapes="_x0000_i1033"><![endif]><!--[if gte vml 1]><v:shape
     1867 id="Picture_x0020_21" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:527.25pt;
     1868 height:376.5pt;visibility:visible;mso-wrap-style:square'>
    18671869 <v:imagedata src="Fit%20Peaks_files/image022.png" o:title=""/>
    18681870</v:shape><![endif]--><![if !vml]><img border=0 width=703 height=502
    1869 src="Fit%20Peaks_files/image022.png" v:shapes="_x0000_i1032"><![endif]></span></p>
     1871src="Fit%20Peaks_files/image022.png" v:shapes="Picture_x0020_21"><![endif]></span></p>
    18701872
    18711873<p class=MsoNormal>Notice other equally good M20 results with different
     
    19031905
    19041906<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1905  id="Picture_x0020_35" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:545.25pt;
    1906  height:303.75pt;visibility:visible;mso-wrap-style:square'>
     1907 id="_x0000_i1031" type="#_x0000_t75" style='width:545.25pt;height:303.75pt;
     1908 visibility:visible;mso-wrap-style:square'>
    19071909 <v:imagedata src="Fit%20Peaks_files/image023.png" o:title=""/>
    19081910</v:shape><![endif]--><![if !vml]><img border=0 width=727 height=405
    1909 src="Fit%20Peaks_files/image023.png" v:shapes="Picture_x0020_35"><![endif]></span><span
     1911src="Fit%20Peaks_files/image023.png" v:shapes="_x0000_i1031"><![endif]></span><span
    19101912style='mso-spacerun:yes'> </span></p>
    19111913
     
    19361938in GSAS-II </h1>
    19371939
    1938 <p class=MsoNormal>In this exercise we will fit peaks and index them for sucrose
    1939 in preparation for a charge flipping exercise. The data was also collected on
    1940 11BM-B at APS. The unit cell is monoclinic so is a more substantial test of the
    1941 indexing capability of GSAS-II.</p>
     1940<p class=MsoNormal>In this exercise we will fit peaks and index them for
     1941sucrose in preparation for a charge flipping exercise. The data was also
     1942collected on 11BM-B at APS. The unit cell is monoclinic so is a more
     1943substantial test of the indexing capability of GSAS-II.</p>
    19421944
    19431945<h2><span class=GramE>Step 1.</span> Read in the data. </h2>
     
    19621964
    19631965<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1964  id="Picture_x0020_29" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:525pt;
     1966 id="Picture_x0020_31" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:525pt;
    19651967 height:450pt;visibility:visible;mso-wrap-style:square'>
    19661968 <v:imagedata src="Fit%20Peaks_files/image025.png" o:title=""/>
    19671969</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
    1968 src="Fit%20Peaks_files/image025.png" v:shapes="Picture_x0020_29"><![endif]></span></p>
     1970src="Fit%20Peaks_files/image025.png" v:shapes="Picture_x0020_31"><![endif]></span></p>
    19691971
    19701972<p class=MsoNormal>I’ve zoomed in &amp; shifted the plot some to highlight the
     
    19911993
    19921994<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1993  id="Picture_x0020_30" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:525pt;
     1995 id="Picture_x0020_32" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:525pt;
    19941996 height:450pt;visibility:visible;mso-wrap-style:square'>
    19951997 <v:imagedata src="Fit%20Peaks_files/image026.png" o:title=""/>
    19961998</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
    1997 src="Fit%20Peaks_files/image026.png" v:shapes="Picture_x0020_30"><![endif]></span><br
     1999src="Fit%20Peaks_files/image026.png" v:shapes="Picture_x0020_32"><![endif]></span><br
    19982000clear=all style='mso-special-character:line-break'>
    19992001</p>
     
    20552057<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    20562058mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    2057 Calibri;mso-bidi-theme-font:minor-latin'>Unit Cells List</span></b> window. Progress
    2058 will be much slower than for LaB<sub>6</sub> but oddly much faster than for
    2059 kryptonite and suitable results may appear almost immediately. Watch the
    2060 console window; the right answer will have an obviously large M20 (~900) and a
    2061 volume of ~704Å<sup>3</sup> (10<sup>th</sup> column of console display). Once
    2062 this is seen (it may take more than one try to get this) you can stop the
     2059Calibri;mso-bidi-theme-font:minor-latin'>Unit Cells List</span></b> window.
     2060Progress will be much slower than for LaB<sub>6</sub> but oddly much faster
     2061than for kryptonite and suitable results may appear almost immediately. Watch
     2062the console window; the right answer will have an obviously large M20 (~900)
     2063and a volume of ~704Å<sup>3</sup> (10<sup>th</sup> column of console display).
     2064Once this is seen (it may take more than one try to get this) you can stop the
    20632065indexing search by pressing <b style='mso-bidi-font-weight:normal'><span
    20642066style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     
    20702072
    20712073<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2072  id="Picture_x0020_31" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:525pt;
     2074 id="Picture_x0020_33" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:527.25pt;
     2075 height:376.5pt;visibility:visible;mso-wrap-style:square'>
     2076 <v:imagedata src="Fit%20Peaks_files/image027.png" o:title=""/>
     2077</v:shape><![endif]--><![if !vml]><img border=0 width=703 height=502
     2078src="Fit%20Peaks_files/image027.png" v:shapes="Picture_x0020_33"><![endif]><!--[if gte vml 1]><v:shape
     2079 id="Picture_x0020_34" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:525pt;
    20732080 height:450pt;visibility:visible;mso-wrap-style:square'>
    2074  <v:imagedata src="Fit%20Peaks_files/image027.png" o:title=""/>
     2081 <v:imagedata src="Fit%20Peaks_files/image028.png" o:title=""/>
    20752082</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
    2076 src="Fit%20Peaks_files/image027.png" v:shapes="Picture_x0020_31"><![endif]><!--[if gte vml 1]><v:shape
    2077  id="Picture_x0020_32" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:527.25pt;
    2078  height:376.5pt;visibility:visible;mso-wrap-style:square'>
    2079  <v:imagedata src="Fit%20Peaks_files/image028.png" o:title=""/>
    2080 </v:shape><![endif]--><![if !vml]><img border=0 width=703 height=502
    2081 src="Fit%20Peaks_files/image028.png" v:shapes="Picture_x0020_32"><![endif]></span></p>
     2083src="Fit%20Peaks_files/image028.png" v:shapes="Picture_x0020_34"><![endif]></span></p>
    20822084
    20832085<p class=MsoNormal>Notice there may be other equally good M20 results with
     
    20862088style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    20872089mso-hansi-theme-font:minor-latin'>Keep</span></b> to keep good ones as you try
    2088 new indexing runs. The best solution is the one with the smaller volume and &#946;
    2089 &gt; 90 deg. The plot shows every peak indexed including the weak peaks not
    2090 selected for the peak fitting. Copy the best cell and try to refine it along
    2091 with the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    2092 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Zero offset</span></b>.
    2093 I obtained an improved M20 ~1257 and slightly different lattice parameters. Try
    2094 different space groups, pressing the <b style='mso-bidi-font-weight:normal'><span
    2095 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    2096 mso-hansi-theme-font:minor-latin'>Show <span class=SpellE>hkl</span> positions</span></b>
    2097 each time to see which lines vanish. The correct space group is P2<sub>1</sub>.
    2098 Armed with this information you can <b style='mso-bidi-font-weight:normal'><span
    2099 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    2100 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    2101 minor-latin'>Make new phase</span></b> for the indexed cell (I called it ‘<b
    2102 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    2103 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    2104 Calibri;mso-bidi-theme-font:minor-latin'>sucrose</span></b>) and select <b
    2105 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    2106 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b>
    2107 from the GSAS-II data tree.</p>
     2090new indexing runs. The best solution is the one with the smaller volume and
     2091&#946; &gt; 90 deg. The plot shows every peak indexed including the weak peaks
     2092not selected for the peak fitting. Copy the best cell and try to refine it
     2093along with the <b style='mso-bidi-font-weight:normal'><span style='font-family:
     2094"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     2095minor-latin'>Zero offset</span></b>. I obtained an improved M20 ~1257 and
     2096slightly different lattice parameters. Try different space groups, pressing the
     2097<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2098mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Show <span
     2099class=SpellE>hkl</span> positions</span></b> each time to see which lines
     2100vanish. The correct space group is P2<sub>1</sub>. Armed with this information
     2101you can <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2102mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     2103Calibri;mso-bidi-theme-font:minor-latin'>Make new phase</span></b> for the
     2104indexed cell (I called it ‘<b style='mso-bidi-font-weight:normal'><span
     2105style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2106mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     2107minor-latin'>sucrose</span></b>) and select <b style='mso-bidi-font-weight:
     2108normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     2109minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b> from
     2110the GSAS-II data tree.</p>
    21082111
    21092112<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2110  id="Picture_x0020_34" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:545.25pt;
     2113 id="Picture_x0020_35" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:545.25pt;
    21112114 height:303.75pt;visibility:visible;mso-wrap-style:square'>
    21122115 <v:imagedata src="Fit%20Peaks_files/image029.png" o:title=""/>
    21132116</v:shape><![endif]--><![if !vml]><img border=0 width=727 height=405
    2114 src="Fit%20Peaks_files/image029.png" v:shapes="Picture_x0020_34"><![endif]></span><span
     2117src="Fit%20Peaks_files/image029.png" v:shapes="Picture_x0020_35"><![endif]></span><span
    21152118style='mso-spacerun:yes'> </span></p>
    21162119
     
    21222125style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    21232126mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    2124 Calibri;mso-bidi-theme-font:minor-latin'><a href="Charge%20Flipping%20-%20sucrose.htm">Charge
    2125 Flipping</a></span></b> exercise. The features of the <b style='mso-bidi-font-weight:
    2126 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    2127 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
    2128 mso-bidi-theme-font:minor-latin'>Phase Data</span></b> window will be presented
    2129 in other exercises.</p>
     2127Calibri;mso-bidi-theme-font:minor-latin'><a
     2128href="Charge%20Flipping%20-%20sucrose.htm">Charge Flipping</a></span></b>
     2129exercise. The features of the <b style='mso-bidi-font-weight:normal'><span
     2130style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2131mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     2132minor-latin'>Phase Data</span></b> window will be presented in other exercises.</p>
    21302133
    21312134<p class=MsoNormal><o:p>&nbsp;</o:p></p>
  • trunk/help/Fit Peaks_files/filelist.xml

    r864 r895  
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    4  <o:File HRef="props036.xml"/>
    53 <o:File HRef="themedata.thmx"/>
    64 <o:File HRef="colorschememapping.xml"/>
  • trunk/help/Integration of area detector data in GSAS.htm

    r676 r895  
    2525  <o:Author>Von Dreele</o:Author>
    2626  <o:LastAuthor>Von Dreele</o:LastAuthor>
    27   <o:Revision>11</o:Revision>
    28   <o:TotalTime>109</o:TotalTime>
     27  <o:Revision>12</o:Revision>
     28  <o:TotalTime>118</o:TotalTime>
    2929  <o:Created>2012-05-04T20:46:00Z</o:Created>
    30   <o:LastSaved>2012-07-03T19:15:00Z</o:LastSaved>
     30  <o:LastSaved>2013-04-30T17:23:00Z</o:LastSaved>
    3131  <o:Pages>3</o:Pages>
    32   <o:Words>800</o:Words>
    33   <o:Characters>4563</o:Characters>
     32  <o:Words>808</o:Words>
     33  <o:Characters>4610</o:Characters>
    3434  <o:Company>Argonne National Laboratory</o:Company>
    3535  <o:Lines>38</o:Lines>
    3636  <o:Paragraphs>10</o:Paragraphs>
    37   <o:CharactersWithSpaces>5353</o:CharactersWithSpaces>
     37  <o:CharactersWithSpaces>5408</o:CharactersWithSpaces>
    3838  <o:Version>14.00</o:Version>
    3939 </o:DocumentProperties>
     
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    977976intentionally tilted at 45 degrees, are used. Note that menu entries are listed
    978977in <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    979 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    980 minor-latin'>bold face</span></b> below as <b style='mso-bidi-font-weight:normal'><span
    981 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    982 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Help/About
    983 GSAS-II</span></b>, which lists first the name of the menu (here <b
     978mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     979Calibri;mso-bidi-theme-font:minor-latin'>bold face</span></b> below as <b
    984980style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    985 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     981mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     982Calibri;mso-bidi-theme-font:minor-latin'>Help/About GSAS-II</span></b>, which
     983lists first the name of the menu (here <b style='mso-bidi-font-weight:normal'><span
     984style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     985mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    986986minor-latin'>Help</span></b>) and second the name of the entry in the menu
    987987(here <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    988 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    989 minor-latin'>About GSAS-II</span></b>).</p>
     988mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     989Calibri;mso-bidi-theme-font:minor-latin'>About GSAS-II</span></b>).</p>
    990990
    991991<h2>Prerequisite:<span style='mso-spacerun:yes'>  </span><a
     
    10021002longer needed. The <b style='mso-bidi-font-weight:normal'><span
    10031003style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1004 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Image
    1005 Controls/Clear Calibration</span></b> menu entry removes these from the plot,
    1006 but<u> does not clear the calibration results</u>. Use of this menu item is not
    1007 required, but does speed future display of results. </p>
     1004mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1005minor-latin'>Image Controls/Clear Calibration</span></b> menu entry removes
     1006these from the plot, but<u> does not clear the calibration results</u>. Use of
     1007this menu item is not required, but does speed future display of results. </p>
    10081008
    10091009<h2>Step 2: Integration Settings</h2>
     
    10111011<p class=MsoNormal>In the simplest case, all that is needed is to click on the <b
    10121012style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1013 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1014 minor-latin'>Do full integration?</span></b> <span class=GramE>check</span> box
    1015 and adjust the inner and outer 2-theta values with the <b style='mso-bidi-font-weight:
    1016 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1017 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Inner
    1018 2-theta</span></b> and<b style='mso-bidi-font-weight:normal'> </b><b
    1019 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1020 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1021 minor-latin'>Outer 2-theta</span></b> controls. Change the limits to <b
    1022 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1023 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1024 minor-latin'>1</span></b> and <b style='mso-bidi-font-weight:normal'><span
    1025 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1026 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>7</span></b>
    1027 for this data. Note that changes are displayed when numbers are placed in the
    1028 boxes only after pressing return or tab key or by clicking on some other item
    1029 in the window.</p>
    1030 
    1031 <p class=MsoNormal>It is helpful to see the two-theta limits on the plot
    1032 visually, while adjusting the two-theta range. This is done by clicking on the <b
    1033 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1034 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1013mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1014Calibri;mso-bidi-theme-font:minor-latin'>Do full integration?</span></b> <span
     1015class=GramE>check</span> box and adjust the inner and outer 2-theta values with
     1016the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1017mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1018Calibri;mso-bidi-theme-font:minor-latin'>Inner 2-theta</span></b> and<b
     1019style='mso-bidi-font-weight:normal'> </b><b style='mso-bidi-font-weight:normal'><span
     1020style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1021mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1022minor-latin'>Outer 2-theta</span></b> controls. It is helpful to see the
     1023two-theta limits on the plot visually, while adjusting the two-theta range.
     1024This is done by clicking on the <b style='mso-bidi-font-weight:normal'><span
     1025style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1026mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    10351027minor-latin'>Show integration limits?</span></b> <span class=GramE>check</span>
    10361028box. Note that inner limit is shown as a green ellipse at 2deg and the outer is
    10371029shown as a red ellipse at 5deg by default. These limits may also be dragged to
    1038 the desired values; a small popup window shows the value. </p>
     1030the desired values; a small popup window shows the value. <o:p></o:p></p>
     1031
     1032<p class=MsoNormal>Change the limits to <b style='mso-bidi-font-weight:normal'><span
     1033style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1034mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1035minor-latin'>1</span></b> and <b style='mso-bidi-font-weight:normal'><span
     1036style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1037mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1038minor-latin'>7</span></b> for this data. Note that changes are displayed when
     1039numbers are placed in the boxes only after pressing return or tab key or by
     1040clicking on some other item in the window.</p>
    10391041
    10401042<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
     
    10591061 <o:lock v:ext="edit" aspectratio="t"/>
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    1061  style='width:472.5pt;height:310.5pt;visibility:visible;mso-wrap-style:square'>
     1063 style='width:472.5pt;height:342pt;visibility:visible;mso-wrap-style:square'>
    10621064 <v:imagedata src="Integration%20of%20area%20detector%20data%20in%20GSAS_files/image001.png"
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     1066</v:shape><![endif]--><![if !vml]><img border=0 width=630 height=456
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    10701072<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span
    10711073style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1072 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Azimuth
    1073 offset</span></b>: The image vertical axis (from the beam center, going down)
    1074 is labeled with the azimuth value placed in the <b style='mso-bidi-font-weight:
     1074mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1075minor-latin'>Azimuth offset</span></b>: The image vertical axis (from the beam
     1076center, going down) is labeled with the azimuth value placed in the <b
     1077style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1078mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1079Calibri;mso-bidi-theme-font:minor-latin'>Azimuth offset</span></b> box. This is
     1080usually zero unless the image plate has been rotated about its normal axis.</p>
     1081
     1082<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span
     1083style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1084mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1085minor-latin'>Start/End azimuth</span></b>: The integration is started at the
     1086Start azimuth angle in the left box, and when the <b style='mso-bidi-font-weight:
    10751087normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1076 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Azimuth
    1077 offset</span></b> box. This is usually zero unless the image plate has been
    1078 rotated about its normal axis.</p>
     1088minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1089mso-bidi-theme-font:minor-latin'>Do full integration?</span></b> <span
     1090class=GramE>checkbox</span> is not checked, the integration will be run only to
     1091the maximum value specified. When the range is less than 360 degrees, the
     1092integration range will be shown (if selected) with the high and low limits
     1093plotted and only segments of the max and min ellipses drawn. These limits may
     1094also be dragged on the plot to desired locations.</p>
    10791095
    10801096<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span
    10811097style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1082 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Start/End
    1083 azimuth</span></b>: The integration is started at the Start azimuth angle in
    1084 the left box, and when the <b style='mso-bidi-font-weight:normal'><span
    1085 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1086 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Do full
    1087 integration?</span></b> <span class=GramE>checkbox</span> is not checked, the
    1088 integration will be run only to the maximum value specified. When the range is
    1089 less than 360 degrees, the integration range will be shown (if selected) with
    1090 the high and low limits plotted and only segments of the max and min ellipses
    1091 drawn. These limits may also be dragged on the plot to desired locations.</p>
     1098mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1099minor-latin'>Number of 2-theta bins</span></b>: The resulting 1-D powder
     1100pattern after integration will consist of this many points. This number should
     1101be on the order of the number of pixels in one direction (since resolution
     1102cannot be much better than this) or less, if instrumental resolution and sample
     1103broadening does not require that many points. Some trial and error may be
     1104needed, but there should more than 6 points across each peak
     1105full-width-at-half-maximum (FWHM) in the final pattern to be useful for further
     1106analysis. In this case <b style='mso-bidi-font-weight:normal'><span
     1107style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1108mso-hansi-theme-font:minor-latin'>5000</span></b> is a better choice than the
     1109default.</p>
    10921110
    10931111<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span
    10941112style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1095 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Number of
    1096 2-theta bins</span></b>: The resulting 1-D powder pattern after integration
    1097 will consist of this many points. This number should be on the order of the
    1098 number of pixels in one direction (since resolution cannot be much better than
    1099 this) or less, if instrumental resolution and sample broadening does not
    1100 require that many points. Some trial and error may be needed, but there should
    1101 more than 6 points across each peak full-width-at-half-maximum (FWHM) in the
    1102 final pattern to be useful for further analysis.</p>
     1113mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1114minor-latin'>Number of azimuth bins</span></b>: In cases where the diffraction
     1115experiment shows changes as a function of azimuthal angle, the integration can
     1116be performed as a function of angle. This number specifies the number of bins
     1117to use by azimuthal angle. The process of breaking up the integration in this
     1118way is sometimes called &quot;caking&quot; since the integration region grows
     1119with distance from the beam-center, with a shape like a slice of cake or pie.
     1120When more than one azimuthal bin is used, the regions are shown in the plot
     1121with dashed lines, when the Show integration limits?&quot; check box is
     1122checked. </p>
    11031123
    11041124<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span
    11051125style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1106 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Number of
    1107 azimuth bins</span></b>: In cases where the diffraction experiment shows
    1108 changes as a function of azimuthal angle, the integration can be performed as a
    1109 function of angle. This number specifies the number of bins to use by azimuthal
    1110 angle. The process of breaking up the integration in this way is sometimes
    1111 called &quot;caking&quot; since the integration region grows with distance from
    1112 the beam-center, with a shape like a slice of cake or pie. When more than one
    1113 azimuthal bin is used, the regions are shown in the plot with dashed lines,
    1114 when the Show integration limits?&quot; check box is checked. </p>
     1126mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1127minor-latin'>Appl. det. absorption</span></b> and <b style='mso-bidi-font-weight:
     1128normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1129minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1130mso-bidi-theme-font:minor-latin'>value</span></b>: The scattered ray beams are
     1131partially absorbed by the detector depending on the scattering angle. This
     1132reduces the intensity of higher angle data more than low angle data. The value
     1133is dependent on the wavelength and the materials used for the front surface of
     1134the detector, so some experimentation with a standard is needed to establish an
     1135appropriate value.</p>
    11151136
    11161137<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span
    11171138style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1118 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Appl. det.
    1119 absorption</span></b> and <b style='mso-bidi-font-weight:normal'><span
    1120 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1121 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>value</span></b>:
    1122 The scattered ray beams are partially absorbed by the detector depending on the
    1123 scattering angle. This reduces the intensity of higher angle data more than low
    1124 angle data. The value is dependent on the wavelength and the materials used for
    1125 the front surface of the detector, so some experimentation with a standard is
    1126 needed to establish an appropriate value.</p>
    1127 
    1128 <p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span
    1129 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1130 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Background
    1131 Image</span> </b>and<b style='mso-bidi-font-weight:normal'> </b><b
     1139mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1140minor-latin'>Background Image</span> </b>and<b style='mso-bidi-font-weight:
     1141normal'> </b><b style='mso-bidi-font-weight:normal'><span style='font-family:
     1142"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1143minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>Multiplier</span></b>:
     1144You can designate a previously read in image as background which will then be
     1145used to modify each data image as they are integrated. Note that the <b
    11321146style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1133 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1134 minor-latin'>Multiplier</span></b>: You can designate a previously read in
    1135 image as background which will then be used to modify each data image as they
    1136 are integrated. Note that the <b style='mso-bidi-font-weight:normal'><span
    1137 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1138 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Multiplier</span></b>
    1139 must be negative for it to be subtracted. Note that all images used in this way
    1140 must be exactly the same format (number of pixels &amp; pixel size).</p>
     1147mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1148Calibri;mso-bidi-theme-font:minor-latin'>Multiplier</span></b> must be negative
     1149for it to be subtracted. Note that all images used in this way must be exactly
     1150the same format (number of pixels &amp; pixel size).</p>
    11411151
    11421152<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
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     1153 id="Picture_x0020_7" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:525pt;
     1154 height:450pt;visibility:visible;mso-wrap-style:square'>
    11451155 <v:imagedata src="Integration%20of%20area%20detector%20data%20in%20GSAS_files/image002.png"
    11461156  o:title=""/>
    1147 </v:shape><![endif]--><![if !vml]><img border=0 width=624 height=535
    1148 src="Integration%20of%20area%20detector%20data%20in%20GSAS_files/image003.png"
    1149 v:shapes="Picture_x0020_1"><![endif]></span></p>
     1157</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
     1158src="Integration%20of%20area%20detector%20data%20in%20GSAS_files/image002.png"
     1159v:shapes="Picture_x0020_7"><![endif]></span></p>
    11501160
    11511161<h2>Step 3: Perform integration </h2>
     
    11531163<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Use the <b
    11541164style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1155 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1156 minor-latin'>Image Operations/Integrate</span></b> image data menu item to
    1157 start the integration. This will take at least a few seconds. If multiple
    1158 images have been read in, the <b style='mso-bidi-font-weight:normal'><span
    1159 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1160 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Integrate All</span></b>
    1161 menu item can be used. This is most useful when the <b style='mso-bidi-font-weight:
     1165mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1166Calibri;mso-bidi-theme-font:minor-latin'>Image Operations/Integrate</span></b>
     1167image data menu item to start the integration. This will take at least a few
     1168seconds. If multiple images have been read in, the <b style='mso-bidi-font-weight:
    11621169normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1163 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Use
    1164 as Default</span></b> option is in use for one image.</p>
     1170minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1171mso-bidi-theme-font:minor-latin'>Integrate All</span></b> menu item can be
     1172used. This is most useful when the <b style='mso-bidi-font-weight:normal'><span
     1173style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1174mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1175minor-latin'>Use as Default</span></b> option is in use for one image.</p>
    11651176
    11661177<p class=MsoNormal><span style='mso-spacerun:yes'> </span>At this point the
     
    11691180
    11701181<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1171  id="Picture_x0020_3" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:225pt;
    1172  height:203.25pt;visibility:visible;mso-wrap-style:square'>
     1182 id="Picture_x0020_8" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:300pt;
     1183 height:187.5pt;visibility:visible;mso-wrap-style:square'>
     1184 <v:imagedata src="Integration%20of%20area%20detector%20data%20in%20GSAS_files/image003.png"
     1185  o:title=""/>
     1186</v:shape><![endif]--><![if !vml]><img border=0 width=400 height=250
     1187src="Integration%20of%20area%20detector%20data%20in%20GSAS_files/image003.png"
     1188v:shapes="Picture_x0020_8"><![endif]></span><span
     1189style='mso-spacerun:yes'> </span></p>
     1190
     1191<p class=MsoNormal>Two plots are added to the plot window: One (with tab <b
     1192style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1193mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1194Calibri;mso-bidi-theme-font:minor-latin'>2D Integration</span></b>) shows the
     1195diffraction intensity as a function of both 2-theta and (when there is more
     1196than one azimuthal integration region) azimuthal angle.</p>
     1197
     1198<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1199 id="Picture_x0020_9" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:525pt;
     1200 height:450pt;visibility:visible;mso-wrap-style:square'>
    11731201 <v:imagedata src="Integration%20of%20area%20detector%20data%20in%20GSAS_files/image004.png"
    11741202  o:title=""/>
    1175 </v:shape><![endif]--><![if !vml]><img border=0 width=300 height=271
     1203</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
    11761204src="Integration%20of%20area%20detector%20data%20in%20GSAS_files/image004.png"
    1177 v:shapes="Picture_x0020_3"><![endif]></span><span
     1205v:shapes="Picture_x0020_9"><![endif]></span><span
    11781206style='mso-spacerun:yes'> </span></p>
    11791207
    1180 <p class=MsoNormal>Two plots are added to the plot window: One (with tab <b
    1181 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1182 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1183 minor-latin'>2D Integration</span></b>) shows the diffraction intensity as a function
    1184 of both 2-theta and (when there is more than one azimuthal integration region)
    1185 azimuthal angle.</p>
     1208<p class=MsoNormal><span class=GramE>and</span> a conventional 1-D powder
     1209pattern(s) for each &quot;slice&quot;</p>
    11861210
    11871211<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1188  id="Picture_x0020_4" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:525pt;
     1212 id="Picture_x0020_10" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:525pt;
    11891213 height:450pt;visibility:visible;mso-wrap-style:square'>
    11901214 <v:imagedata src="Integration%20of%20area%20detector%20data%20in%20GSAS_files/image005.png"
     
    11921216</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
    11931217src="Integration%20of%20area%20detector%20data%20in%20GSAS_files/image005.png"
    1194 v:shapes="Picture_x0020_4"><![endif]></span><span
    1195 style='mso-spacerun:yes'> </span></p>
    1196 
    1197 <p class=MsoNormal><span class=GramE>and</span> a conventional 1-D powder
    1198 pattern(s) for each &quot;slice&quot;</p>
    1199 
    1200 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1201  id="Picture_x0020_5" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:525pt;
    1202  height:450pt;visibility:visible;mso-wrap-style:square'>
    1203  <v:imagedata src="Integration%20of%20area%20detector%20data%20in%20GSAS_files/image006.png"
    1204   o:title=""/>
    1205 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
    1206 src="Integration%20of%20area%20detector%20data%20in%20GSAS_files/image006.png"
    1207 v:shapes="Picture_x0020_5"><![endif]></span></p>
     1218v:shapes="Picture_x0020_10"><![endif]></span></p>
    12081219
    12091220<p class=MsoNormal>Again you could save the project with <b style='mso-bidi-font-weight:
    12101221normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1211 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>File/Save
    1212 project</span></b> on the main <b style='mso-bidi-font-weight:normal'><span
    1213 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1214 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II data
    1215 tree</span></b> menu although it is not needed for any further tutorials.</p>
     1222minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1223mso-bidi-theme-font:minor-latin'>File/Save project</span></b> on the main <b
     1224style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1225mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1226Calibri;mso-bidi-theme-font:minor-latin'>GSAS-II data tree</span></b> menu
     1227although it is not needed for any further tutorials.</p>
    12161228
    12171229<h2>Next demo: <a href="Fit%20Peaks.htm"><span style='color:windowtext;
  • trunk/help/Integration of area detector data in GSAS_files/filelist.xml

    r676 r895  
    88 <o:File HRef="image004.png"/>
    99 <o:File HRef="image005.png"/>
    10  <o:File HRef="image006.png"/>
    1110 <o:File HRef="filelist.xml"/>
    1211</xml>
  • trunk/help/Laboratory X.htm

    r720 r895  
    2323  <o:Author>Von Dreele</o:Author>
    2424  <o:LastAuthor>Von Dreele</o:LastAuthor>
    25   <o:Revision>18</o:Revision>
    26   <o:TotalTime>1510</o:TotalTime>
     25  <o:Revision>19</o:Revision>
     26  <o:TotalTime>1591</o:TotalTime>
    2727  <o:Created>2012-05-08T16:04:00Z</o:Created>
    28   <o:LastSaved>2012-08-16T19:34:00Z</o:LastSaved>
     28  <o:LastSaved>2013-04-30T20:30:00Z</o:LastSaved>
    2929  <o:Pages>9</o:Pages>
    30   <o:Words>3133</o:Words>
    31   <o:Characters>17863</o:Characters>
     30  <o:Words>3099</o:Words>
     31  <o:Characters>17666</o:Characters>
    3232  <o:Company>Argonne National Laboratory</o:Company>
    33   <o:Lines>148</o:Lines>
     33  <o:Lines>147</o:Lines>
    3434  <o:Paragraphs>41</o:Paragraphs>
    35   <o:CharactersWithSpaces>20955</o:CharactersWithSpaces>
     35  <o:CharactersWithSpaces>20724</o:CharactersWithSpaces>
    3636  <o:Version>14.00</o:Version>
    3737 </o:DocumentProperties>
     
    349349        mso-generic-font-family:swiss;
    350350        mso-font-pitch:variable;
    351         mso-font-signature:-520092929 1073786111 9 0 415 0;}
     351        mso-font-signature:-536870145 1073786111 1 0 415 0;}
    352352@font-face
    353353        {font-family:Tahoma;
     
    937937        mso-ascii-theme-font:minor-latin;
    938938        mso-hansi-font-family:Calibri;
    939         mso-hansi-theme-font:minor-latin;
    940         mso-bidi-font-family:"Times New Roman";
    941         mso-bidi-theme-font:minor-bidi;}
     939        mso-hansi-theme-font:minor-latin;}
    942940table.MsoTableGrid
    943941        {mso-style-name:"Table Grid";
     
    959957        mso-ascii-theme-font:minor-latin;
    960958        mso-hansi-font-family:Calibri;
    961         mso-hansi-theme-font:minor-latin;
    962         mso-bidi-font-family:"Times New Roman";
    963         mso-bidi-theme-font:minor-bidi;}
     959        mso-hansi-theme-font:minor-latin;}
    964960</style>
    965961<![endif]--><!--[if gte mso 9]><xml>
     
    980976<p class=MsoNormal>In this tutorial you will refine the structure of <span
    981977class=SpellE>fluoroapatite</span>, <span class=GramE>Ca<sub>5</sub>F(</span>PO<sub>4</sub>)<sub>3</sub>,
    982 using constant wavelength laboratory X-ray powder diffraction data. At the
    983 completion of the refinement you will then prepare a drawing of the <span
    984 class=SpellE>fluoroapatite</span> structure. The structure is hexagonal with
    985 four different kinds of atoms spread over seven different sites. The data was
    986 taken on a conventional Bragg-Brentano powder diffractometer using <span
    987 class=SpellE>CuK</span><sub><span style='font-family:Symbol'>a</span></sub>
    988 radiation.</p>
     978using constant wavelength laboratory X-ray powder diffraction data. At the completion
     979of the refinement you will then prepare a drawing of the <span class=SpellE>fluoroapatite</span>
     980structure. The structure is hexagonal with four different kinds of atoms spread
     981over seven different sites. The data was taken on a conventional Bragg-Brentano
     982powder diffractometer using <span class=SpellE>CuK</span><sub><span
     983style='font-family:Symbol'>a</span></sub> radiation.</p>
    989984
    990985<p class=MsoNormal>If you have not done so already, <a
     
    1002997style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Use
    1003998the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1004 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1005 minor-latin'>Import/Import Powder Data/from GSAS file</span></b> menu item to
    1006 read the data file into GSAS-II. This read option is set to read any of the
    1007 powder data formats (except neutron TOF time map files) defined for GSAS
    1008 (angles in <span class=SpellE>centidegrees</span>). The <span class=SpellE><b
    1009 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1010 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     999mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1000Calibri;mso-bidi-theme-font:minor-latin'>Import/Import Powder Data/from GSAS
     1001file</span></b> menu item to read the data file into GSAS-II. This read option
     1002is set to read any of the powder data formats (except neutron TOF time map
     1003files) defined for GSAS (angles in <span class=SpellE>centidegrees</span>). The
     1004<span class=SpellE><b style='mso-bidi-font-weight:normal'><span
     1005style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1006mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    10111007minor-latin'>xye</span></b></span> format (angles in degrees) used by <span
    10121008class=SpellE>Topas</span>, etc. can also be read via the <b style='mso-bidi-font-weight:
    10131009normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1014 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Import/Import
    1015 Powder Data</span></b> menus.<span style='mso-spacerun:yes'>  </span>Change the
    1016 file directory to <b style='mso-bidi-font-weight:normal'><span
    1017 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1018 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Exercises/<span
    1019 class=SpellE>fluroapatite</span></span></b><span style='font-family:"Calibri","sans-serif";
    1020 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1010minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1011mso-bidi-theme-font:minor-latin'>Import/Import Powder Data</span></b>
     1012menus.<span style='mso-spacerun:yes'>  </span>Change the file directory to <b
     1013style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1014mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1015Calibri;mso-bidi-theme-font:minor-latin'>Exercises/<span class=SpellE>fluroapatite</span></span></b><span
     1016style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1017mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    10211018minor-latin'> to find the file; you will need to change the file type to <b
    1022 style='mso-bidi-font-weight:normal'>All files (*.*)</b> to find the desired
     1019style='mso-bidi-font-weight:normal'>any file (*.*)</b> to find the desired
    10231020file.</span></p>
    10241021
     
    10271024style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
    10281025the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1029 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1030 minor-latin'>FAP.XRA</span></b><span style='font-family:"Calibri","sans-serif";
    1031 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1026mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1027Calibri;mso-bidi-theme-font:minor-latin'>FAP.XRA</span></b><span
     1028style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1029mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    10321030minor-latin'> data</span> file in the first dialog and press <b
    10331031style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1034 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1035 minor-latin'>Open</span></b>. There will be a Dialog box asking <span
    1036 class=GramE><b style='mso-bidi-font-weight:normal'><span style='font-family:
    1037 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1038 minor-latin;mso-bidi-theme-font:minor-latin'>Is</span></b></span><b
    1039 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1040 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1032mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1033Calibri;mso-bidi-theme-font:minor-latin'>Open</span></b>. There will be a
     1034Dialog box asking <span class=GramE><b style='mso-bidi-font-weight:normal'><span
     1035style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1036mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1037minor-latin'>Is</span></b></span><b style='mso-bidi-font-weight:normal'><span
     1038style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1039mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    10411040minor-latin'> this the file you want?</span></b> Press <span class=GramE><b
    10421041style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1043 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1044 minor-latin'>Yes</span></b></span> button to proceed.</p>
     1042mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1043Calibri;mso-bidi-theme-font:minor-latin'>Yes</span></b></span> button to
     1044proceed.</p>
    10451045
    10461046<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l2 level1 lfo2'><![if !supportLists]><span
     
    10481048style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
    10491049the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1050 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1051 minor-latin'>INST_XRY.PRM</span></b> instrument parameter file in the second
    1052 dialog and press <b style='mso-bidi-font-weight:normal'><span style='font-family:
    1053 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1054 minor-latin;mso-bidi-theme-font:minor-latin'>Open</span></b>.</p>
     1050mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1051Calibri;mso-bidi-theme-font:minor-latin'>INST_XRY.PRM</span></b> instrument
     1052parameter file in the second dialog and press <b style='mso-bidi-font-weight:
     1053normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1054minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1055mso-bidi-theme-font:minor-latin'>Open</span></b>.</p>
    10551056
    10561057<p class=MsoNormal>At this point the <b style='mso-bidi-font-weight:normal'><span
    10571058style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1058 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II data
    1059 tree</span></b> window will have several entries and the plot window will show
    1060 the powder pattern</p>
     1059mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1060minor-latin'>GSAS-II data tree</span></b> window will have several entries and
     1061the plot window will show the powder pattern</p>
    10611062
    10621063<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
     
    10801081 <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
    10811082 <o:lock v:ext="edit" aspectratio="t"/>
    1082 </v:shapetype><v:shape id="Picture_x0020_2" o:spid="_x0000_i1044" type="#_x0000_t75"
     1083</v:shapetype><v:shape id="Picture_x0020_6" o:spid="_x0000_i1044" type="#_x0000_t75"
    10831084 style='width:525pt;height:450pt;visibility:visible;mso-wrap-style:square'>
    10841085 <v:imagedata src="Laboratory%20X_files/image001.png" o:title=""/>
    10851086</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
    1086 src="Laboratory%20X_files/image001.png" v:shapes="Picture_x0020_2"><![endif]></span></p>
     1087src="Laboratory%20X_files/image001.png" v:shapes="Picture_x0020_6"><![endif]></span></p>
    10871088
    10881089<h2>Step 2: Create the phase</h2>
     
    13351336information from the file FAP.EXP use the <b style='mso-bidi-font-weight:normal'><span
    13361337style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1337 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Import/Import
    1338 Phase menu</span></b> <span class=SpellE>menu</span> to see a <span
    1339 class=SpellE>pulldown</span> menu. Select <b style='mso-bidi-font-weight:normal'><span
    1340 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1341 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>from GSAS .EXP
    1342 file. </span></b>The file selection dialog will still be set to the directory
    1343 the data was found; click on <b style='mso-bidi-font-weight:normal'><span
    1344 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1345 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>FAP.EXP</span></b>
    1346 and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1347 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1348 minor-latin'>Open</span></b> to open it. A small dialog box with a phase name
    1349 of ‘<span class=SpellE><b style='mso-bidi-font-weight:normal'><span
    1350 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1351 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>fap</span></b></span>’
    1352 will appear. We didn’t change it so press <b style='mso-bidi-font-weight:normal'><span
    1353 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1354 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>OK</span></b>
    1355 to accept it. </p>
     1338mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1339minor-latin'>Import/Import Phase menu</span></b> <span class=SpellE>menu</span>
     1340to see a <span class=SpellE>pulldown</span> menu. Select <b style='mso-bidi-font-weight:
     1341normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1342minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1343mso-bidi-theme-font:minor-latin'>from GSAS .EXP file. </span></b>The file
     1344selection dialog will still be set to the directory the data was found; click
     1345on <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1346mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1347Calibri;mso-bidi-theme-font:minor-latin'>FAP.EXP</span></b> and <b
     1348style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1349mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1350Calibri;mso-bidi-theme-font:minor-latin'>Open</span></b> to open it. A small
     1351dialog box with a phase name of ‘<span class=SpellE><b style='mso-bidi-font-weight:
     1352normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1353minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1354mso-bidi-theme-font:minor-latin'>fap</span></b></span>’ will appear. We didn’t
     1355change it so press <b style='mso-bidi-font-weight:normal'><span
     1356style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1357mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1358minor-latin'>OK</span></b> to accept it. </p>
    13561359
    13571360<h2>Step 3 Add the powder data to the phase</h2>
     
    13591362<p class=MsoNormal>The <b style='mso-bidi-font-weight:normal'><span
    13601363style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1361 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II data
    1362 tree</span></b> should now have a <b style='mso-bidi-font-weight:normal'><span
    1363 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1364 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Phase</span></b>
    1365 entry of <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
    1366 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1367 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>fap</span></b></span>.
     1364mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1365minor-latin'>GSAS-II data tree</span></b> should now have a <b
     1366style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1367mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1368Calibri;mso-bidi-theme-font:minor-latin'>Phase</span></b> entry of <span
     1369class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
     1370"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1371minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>fap</span></b></span>.
    13681372Select it.to view the <span class=SpellE>fap</span> phase information</p>
    13691373
    13701374<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1371  id="Picture_x0020_4" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:425.25pt;
    1372  height:365.25pt;visibility:visible;mso-wrap-style:square'>
     1375 id="_x0000_i1043" type="#_x0000_t75" style='width:545.25pt;height:454.5pt;
     1376 visibility:visible;mso-wrap-style:square'>
    13731377 <v:imagedata src="Laboratory%20X_files/image002.png" o:title=""/>
    1374 </v:shape><![endif]--><![if !vml]><img border=0 width=567 height=487
    1375 src="Laboratory%20X_files/image002.png" v:shapes="Picture_x0020_4"><![endif]></span></p>
    1376 
    1377 <p class=MsoNormal>You can see that the number of each kind of atom gives 2 formula
    1378 units per cell. To add the powder data to this phase click on the Data tab and
    1379 then select <b style='mso-bidi-font-weight:normal'><span style='font-family:
    1380 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1381 minor-latin;mso-bidi-theme-font:minor-latin'>Edit/Add powder histograms</span></b>
    1382 from the menu. A <b style='mso-bidi-font-weight:normal'><span style='font-family:
    1383 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1384 minor-latin;mso-bidi-theme-font:minor-latin'>Use data</span></b> window will
    1385 appear with only one choice <b style='mso-bidi-font-weight:normal'><span
    1386 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1387 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>PWDR FAP.XRA:
    1388 BANK 1</span></b>. Select it and press <b style='mso-bidi-font-weight:normal'><span
    1389 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1390 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>OK</span></b>.
    1391 The <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1392 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1393 minor-latin'>Data</span></b> tab will change; press the <b style='mso-bidi-font-weight:
    1394 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1395 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Show
    1396 PWDR FAP.XRA: BANK 1</span></b> check box; the window will change again</p>
     1378</v:shape><![endif]--><![if !vml]><img border=0 width=727 height=606
     1379src="Laboratory%20X_files/image002.png" v:shapes="_x0000_i1043"><![endif]></span></p>
     1380
     1381<p class=MsoNormal>You can see that the number of each kind of atom gives 2
     1382formula units per cell. To add the powder data to this phase click on the Data
     1383tab and then select <b style='mso-bidi-font-weight:normal'><span
     1384style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1385mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1386minor-latin'>Edit/Add powder histograms</span></b> from the menu. A <b
     1387style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1388mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1389Calibri;mso-bidi-theme-font:minor-latin'>Use data</span></b> window will appear
     1390with only one choice <b style='mso-bidi-font-weight:normal'><span
     1391style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1392mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1393minor-latin'>PWDR FAP.XRA: BANK 1</span></b>. Select it and press <b
     1394style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1395mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1396Calibri;mso-bidi-theme-font:minor-latin'>OK</span></b>. The <b
     1397style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1398mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1399Calibri;mso-bidi-theme-font:minor-latin'>Data</span></b> tab will change; press
     1400the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1401mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1402Calibri;mso-bidi-theme-font:minor-latin'>Show PWDR FAP.XRA: BANK 1</span></b>
     1403check box; the window will change again</p>
    13971404
    13981405<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1399  id="Picture_x0020_13" o:spid="_x0000_i1042" type="#_x0000_t75" style='width:342.75pt;
    1400  height:274.5pt;visibility:visible;mso-wrap-style:square'>
     1406 id="_x0000_i1042" type="#_x0000_t75" style='width:480pt;height:315pt;
     1407 visibility:visible;mso-wrap-style:square'>
    14011408 <v:imagedata src="Laboratory%20X_files/image003.png" o:title=""/>
    1402 </v:shape><![endif]--><![if !vml]><img border=0 width=457 height=366
    1403 src="Laboratory%20X_files/image003.png" v:shapes="Picture_x0020_13"><![endif]></span></p>
    1404 
    1405 <p class=MsoNormal>We will return to this window later when we consider the
    1406 effect of crystallite size and mustrain broadening.</p>
     1409</v:shape><![endif]--><![if !vml]><img border=0 width=640 height=420
     1410src="Laboratory%20X_files/image003.png" v:shapes="_x0000_i1042"><![endif]></span></p>
     1411
     1412<p class=MsoNormal>We will return to this window later when we consider the effect
     1413of crystallite size and mustrain broadening.</p>
    14071414
    14081415<h2>Step 4: Adjust background parameterization</h2>
     
    14131420this very well so find the <b style='mso-bidi-font-weight:normal'><span
    14141421style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1415 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Background</span></b>
    1416 item under <b style='mso-bidi-font-weight:normal'><span style='font-family:
    1417 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1418 minor-latin;mso-bidi-theme-font:minor-latin'>PWDR FAP.XRA: BANK1</span></b> in
    1419 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1420 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1421 minor-latin'>GSAS-II data tree</span></b> and press it. The <b
    1422 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1423 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1424 minor-latin'>Background</span></b> window will appear</p>
     1422mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1423minor-latin'>Background</span></b> item under <b style='mso-bidi-font-weight:
     1424normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1425minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1426mso-bidi-theme-font:minor-latin'>PWDR FAP.XRA: BANK1</span></b> in the <b
     1427style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1428mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1429Calibri;mso-bidi-theme-font:minor-latin'>GSAS-II data tree</span></b> and press
     1430it. The <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1431mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1432Calibri;mso-bidi-theme-font:minor-latin'>Background</span></b> window will
     1433appear</p>
    14251434
    14261435<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    14331442<p class=MsoNormal>Change the background function to <b style='mso-bidi-font-weight:
    14341443normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1435 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>log
    1436 interpolate</span></b> and the number of coefficients. <span class=GramE>to</span>
    1437 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1438 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1439 minor-latin'>9. </span></b>This will background points at the two limits and at
    1440 equal spaces in the <span class=GramE>log(</span>2<span style='font-family:
    1441 Symbol'>Q</span>) in between so there are more where the background is changing
    1442 most rapidly. A linear interpolation is then used to compute the background for
    1443 all points in the pattern during the Rietveld refinement.</p>
     1444minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1445mso-bidi-theme-font:minor-latin'>log interpolate</span></b> and the number of
     1446coefficients to <b style='mso-bidi-font-weight:normal'><span style='font-family:
     1447"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1448minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>9. </span></b>This
     1449will put background points at the two limits and at equal spaces in <span
     1450class=GramE>log(</span>2<span style='font-family:Symbol'>Q</span>) in between
     1451so there are more where the background is changing most rapidly. A linear
     1452interpolation is then used to compute the background for all points in the
     1453pattern during the Rietveld refinement.</p>
    14441454
    14451455<h2>Step 5 1<sup>st</sup> Rietveld refinement</h2>
     
    14481458refinement; the histogram scale (found in <b style='mso-bidi-font-weight:normal'><span
    14491459style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1450 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Sample
    1451 Parameters</span></b>) and background will be refined. Press <b
    1452 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1453 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1454 minor-latin'>Calculate/Refine</span></b> in the <b style='mso-bidi-font-weight:
    1455 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1456 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II
    1457 data tree</span></b> menu. You will be asked for a project file <span
    1458 class=GramE>name,</span> we used ‘<span class=SpellE>f<b style='mso-bidi-font-weight:
    1459 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1460 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>ap</span></b></span>’
     1460mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1461minor-latin'>Sample Parameters</span></b>) and background will be refined.
     1462Press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1463mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1464Calibri;mso-bidi-theme-font:minor-latin'>Calculate/Refine</span></b> in the <b
     1465style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1466mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1467Calibri;mso-bidi-theme-font:minor-latin'>GSAS-II data tree</span></b> menu. You
     1468will be asked for a project file <span class=GramE>name,</span> we used ‘<span
     1469class=SpellE>f<b style='mso-bidi-font-weight:normal'><span style='font-family:
     1470"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1471minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>ap</span></b></span>’
    14611472and made the file <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
    14621473style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1463 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>fap.gpx</span></b></span>.
    1464 The <span class=GramE>refinement proceeds and when complete</span> (<span
    1465 class=SpellE>Rwp</span> ~42.8%) a small dialog box will appear asking <b
    1466 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1467 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1474mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1475minor-latin'>fap.gpx</span></b></span>. The <span class=GramE>refinement
     1476proceeds and when complete</span> (<span class=SpellE>Rwp</span> ~42.8%) a
     1477small dialog box will appear asking <b style='mso-bidi-font-weight:normal'><span
     1478style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1479mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    14681480minor-latin'>Load new result?</span></b> Press <b style='mso-bidi-font-weight:
    14691481normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1470 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>OK</span></b>;
    1471 the windows will be updated and a new plot is displayed.</p>
     1482minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1483mso-bidi-theme-font:minor-latin'>OK</span></b>; the windows will be updated and
     1484a new plot is displayed.</p>
    14721485
    14731486<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1474  id="Picture_x0020_14" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:525pt;
    1475  height:450pt;visibility:visible;mso-wrap-style:square'>
     1487 id="_x0000_i1040" type="#_x0000_t75" style='width:525pt;height:450pt;
     1488 visibility:visible;mso-wrap-style:square'>
    14761489 <v:imagedata src="Laboratory%20X_files/image005.png" o:title=""/>
    14771490</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
    1478 src="Laboratory%20X_files/image005.png" v:shapes="Picture_x0020_14"><![endif]></span></p>
     1491src="Laboratory%20X_files/image005.png" v:shapes="_x0000_i1040"><![endif]></span></p>
    14791492
    14801493<p class=MsoNormal><span class=GramE>Expanding the plot shows that much of the
     
    14851498errors in laboratory data, not the zero point. The lattice parameter flag is on
    14861499the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1487 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1488 minor-latin'>General</span></b> tab for the <b style='mso-bidi-font-weight:
     1500mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1501Calibri;mso-bidi-theme-font:minor-latin'>General</span></b> tab for 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-font-family:
     1504Calibri;mso-bidi-theme-font:minor-latin'>Phase</span></b> <span class=SpellE><b
     1505style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1506mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1507Calibri;mso-bidi-theme-font:minor-latin'>fap</span></b></span> and the sample
     1508displacement is found on the <b style='mso-bidi-font-weight:normal'><span
     1509style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1510mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1511minor-latin'>Sample Parameters</span></b> item under <b style='mso-bidi-font-weight:
    14891512normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1490 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Phase</span></b>
    1491 <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
    1492 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1493 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>fap</span></b></span>
    1494 and the sample displacement is found on the <b style='mso-bidi-font-weight:
    1495 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1496 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Sample
    1497 Parameters</span></b> item under <b style='mso-bidi-font-weight:normal'><span
    1498 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1499 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>PWDR FAP.XRA:
    1500 BANK1 </span></b>in the <b style='mso-bidi-font-weight:normal'><span
    1501 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1502 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II data
    1503 tree</span></b>. Go to both places and set those flags.</p>
     1513minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1514mso-bidi-theme-font:minor-latin'>PWDR FAP.XRA: BANK1 </span></b>in the <b
     1515style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1516mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1517Calibri;mso-bidi-theme-font:minor-latin'>GSAS-II data tree</span></b>. Go to
     1518both places and set those flags.</p>
    15041519
    15051520<h2>Step 6 2<sup>nd</sup> Rietveld refinement</h2>
     
    15071522<p class=MsoNormal>Now do the Rietveld refinement by <b style='mso-bidi-font-weight:
    15081523normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1509 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Calculate/Refine</span></b>
    1510 menu on <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1511 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1512 minor-latin'>GSAS-II data tree</span></b> window. The plot will <span
    1513 class=GramE>be</span><w:Sdt ShowingPlcHdr="t" Temporary="t" ID="568603642">[Type
    1514  a quote from the document or the summary of an interesting point. You can
    1515  position the text box anywhere in the document. Use the Drawing Tools tab to
    1516  change the formatting of the pull quote text box.]</w:Sdt></p>
     1524minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1525mso-bidi-theme-font:minor-latin'>Calculate/Refine</span></b> menu on <b
     1526style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1527mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1528Calibri;mso-bidi-theme-font:minor-latin'>GSAS-II data tree</span></b> window.
     1529The plot will be</p>
    15171530
    15181531<p class=MsoNormal><!--[if gte vml 1]><v:shapetype id="_x0000_t202"
     
    15921605</table>
    15931606
    1594 </span><![endif]><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1595  id="Picture_x0020_18" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:525pt;
     1607</span><![endif]><span style='font-size:10.0pt;font-family:"Calibri","sans-serif";
     1608mso-ascii-theme-font:minor-latin;mso-fareast-font-family:Calibri;mso-fareast-theme-font:
     1609minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:"Times New Roman";
     1610mso-bidi-theme-font:minor-bidi;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1611 id="Picture_x0020_25" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:525pt;
    15961612 height:450pt;visibility:visible;mso-wrap-style:square'>
    15971613 <v:imagedata src="Laboratory%20X_files/image008.png" o:title=""/>
    15981614</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
    1599 src="Laboratory%20X_files/image008.png" v:shapes="Picture_x0020_18"><![endif]></span></p>
     1615src="Laboratory%20X_files/image008.png" v:shapes="Picture_x0020_25"><![endif]></span></p>
    16001616
    16011617<p class=MsoNormal><span class=GramE>noticeably</span> improved (<span
     
    16081624<p class=MsoNormal>Select the <b style='mso-bidi-font-weight:normal'><span
    16091625style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1610 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Phases/<span
    1611 class=SpellE>fap</span></span></b> item in the <b style='mso-bidi-font-weight:
    1612 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1613 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II
    1614 data tree</span></b> and then select the <b style='mso-bidi-font-weight:normal'><span
    1615 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1616 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Data</span></b>
    1617 tab, change the size value to 1.0 and set the refine flags for both size and <span
    1618 class=SpellE>mustrain</span>. The window should look like</p>
     1626mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1627minor-latin'>Phases/<span class=SpellE>fap</span></span></b> item in the <b
     1628style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1629mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1630Calibri;mso-bidi-theme-font:minor-latin'>GSAS-II data tree</span></b> and then
     1631select the <b style='mso-bidi-font-weight:normal'><span style='font-family:
     1632"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1633minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>Data</span></b>
     1634tab and set the refine flags for both size and <span class=SpellE>mustrain</span>.
     1635The window should look like</p>
    16191636
    16201637<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    16271644<p class=MsoNormal>Now do the refinement; press the <b style='mso-bidi-font-weight:
    16281645normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1629 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Calculate/Refine</span></b>
    1630 menu item on the <b style='mso-bidi-font-weight:normal'><span style='font-family:
    1631 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1632 minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II data tree</span></b>
    1633 window. Do not be alarmed about how the <span class=SpellE>Rwp</span> jumps
    1634 around on the progress bar; that is a consequence of how the <span
    1635 class=SpellE>Levenberg</span>-Marquardt algorithm does a least squares
    1636 minimization. The result in the end is noticeably better than before (<span
    1637 class=SpellE>Rwp</span>=11.4%)</p>
     1646minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1647mso-bidi-theme-font:minor-latin'>Calculate/Refine</span></b> menu item on the <b
     1648style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1649mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1650Calibri;mso-bidi-theme-font:minor-latin'>GSAS-II data tree</span></b> window.
     1651Do not be alarmed about how the <span class=SpellE>Rwp</span> jumps around on
     1652the progress bar; that is a consequence of how the <span class=SpellE>Levenberg</span>-Marquardt
     1653algorithm does a least squares minimization. The result in the end is
     1654noticeably better than before (<span class=SpellE>Rwp</span>=11.4%)</p>
    16381655
    16391656<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1640  id="Picture_x0020_21" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:525pt;
     1657 id="Picture_x0020_26" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:525pt;
    16411658 height:450pt;visibility:visible;mso-wrap-style:square'>
    16421659 <v:imagedata src="Laboratory%20X_files/image010.png" o:title=""/>
    16431660</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
    1644 src="Laboratory%20X_files/image010.png" v:shapes="Picture_x0020_21"><![endif]></span></p>
     1661src="Laboratory%20X_files/image010.png" v:shapes="Picture_x0020_26"><![endif]></span></p>
    16451662
    16461663<h2><span class=GramE>Step 8.</span> 4<sup>th</sup> Rietveld refinement</h2>
     
    16481665<p class=MsoNormal>Now we can refine atom parameters. Select <b
    16491666style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1650 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1651 minor-latin'>Phases/<span class=SpellE>fap</span> </span></b>and the <b
    1652 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1653 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1654 minor-latin'>Atoms</span></b> tab; the <b style='mso-bidi-font-weight:normal'><span
    1655 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1656 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Phase data
    1657 for <span class=SpellE>fap</span></span></b> window will display</p>
     1667mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1668Calibri;mso-bidi-theme-font:minor-latin'>Phases/<span class=SpellE>fap</span> </span></b>and
     1669the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1670mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1671Calibri;mso-bidi-theme-font:minor-latin'>Atoms</span></b> tab; the <b
     1672style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1673mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1674Calibri;mso-bidi-theme-font:minor-latin'>Phase data for <span class=SpellE>fap</span></span></b>
     1675window will display</p>
    16581676
    16591677<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    16661684<p class=MsoNormal>Double click the <b style='mso-bidi-font-weight:normal'><span
    16671685style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1668 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>refine</span></b>
    1669 column header; a new window will show <b style='mso-bidi-font-weight:normal'><span
    1670 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1671 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Refinement
    1672 controls</span></b></p>
     1686mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1687minor-latin'>refine</span></b> column header; a new window will show <b
     1688style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1689mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1690Calibri;mso-bidi-theme-font:minor-latin'>Refinement controls</span></b></p>
    16731691
    16741692<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    16811699<p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span
    16821700style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1683 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>X -
    1684 coordinates</span></b> and <b style='mso-bidi-font-weight:normal'><span
    1685 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1686 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>U - thermal
    1687 parameters</span></b> and press <b style='mso-bidi-font-weight:normal'><span
    1688 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1689 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>OK</span></b>.
    1690 The <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1691 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1692 minor-latin'>Atoms</span></b> tab will show new <b style='mso-bidi-font-weight:
     1701mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1702minor-latin'>X - coordinates</span></b> and <b style='mso-bidi-font-weight:
    16931703normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1694 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>refine</span></b>
    1695 flags</p>
     1704minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1705mso-bidi-theme-font:minor-latin'>U - thermal parameters</span></b> and press <b
     1706style='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-font-family:
     1708Calibri;mso-bidi-theme-font:minor-latin'>OK</span></b>. The <b
     1709style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1710mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1711Calibri;mso-bidi-theme-font:minor-latin'>Atoms</span></b> tab will show new <b
     1712style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1713mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1714Calibri;mso-bidi-theme-font:minor-latin'>refine</span></b> flags</p>
    16961715
    16971716<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    17041723<p class=MsoNormal>Now run the refinement; press the <b style='mso-bidi-font-weight:
    17051724normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1706 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Calculate/Refine</span></b>
    1707 menu item on the <b style='mso-bidi-font-weight:normal'><span style='font-family:
    1708 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1709 minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II data tree</span></b>
    1710 window. The result is a bit better (<span class=SpellE>Rwp</span>=10.20%) and
    1711 the plot is pretty much the same as before</p>
     1725minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1726mso-bidi-theme-font:minor-latin'>Calculate/Refine</span></b> menu item on the <b
     1727style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1728mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1729Calibri;mso-bidi-theme-font:minor-latin'>GSAS-II data tree</span></b> window.
     1730The result is a bit better (<span class=SpellE>Rwp</span>=10.20%) and the plot
     1731is pretty much the same as before</p>
    17121732
    17131733<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1714  id="Picture_x0020_25" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:525pt;
    1715  height:450pt;visibility:visible;mso-wrap-style:square'>
     1734 id="_x0000_i1033" type="#_x0000_t75" style='width:525pt;height:450pt;
     1735 visibility:visible;mso-wrap-style:square'>
    17161736 <v:imagedata src="Laboratory%20X_files/image014.png" o:title=""/>
    17171737</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
    1718 src="Laboratory%20X_files/image014.png" v:shapes="Picture_x0020_25"><![endif]></span></p>
     1738src="Laboratory%20X_files/image014.png" v:shapes="_x0000_i1033"><![endif]></span></p>
    17191739
    17201740<p class=MsoNormal><span class=GramE>and</span> the atom parameters are</p>
    17211741
    17221742<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1723  id="Picture_x0020_26" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:525pt;
     1743 id="Picture_x0020_28" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:525pt;
    17241744 height:225pt;visibility:visible;mso-wrap-style:square'>
    17251745 <v:imagedata src="Laboratory%20X_files/image015.png" o:title=""/>
    17261746</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=300
    1727 src="Laboratory%20X_files/image015.png" v:shapes="Picture_x0020_26"><![endif]></span></p>
     1747src="Laboratory%20X_files/image015.png" v:shapes="Picture_x0020_28"><![endif]></span></p>
    17281748
    17291749<p class=MsoNormal>The refinement is now essentially complete. The file <span
     
    19121932Begin by finding <b style='mso-bidi-font-weight:normal'><span style='font-family:
    19131933"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1914 minor-latin;mso-bidi-theme-font:minor-latin'>Phases/<span class=SpellE>fap</span></span></b>
    1915 in <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1916 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1934minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>Phases/<span
     1935class=SpellE>fap</span></span></b> in <b style='mso-bidi-font-weight:normal'><span
     1936style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1937mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    19171938minor-latin'>GSAS-II data tree</span></b> and selecting the <b
    19181939style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1919 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1920 minor-latin'>Drawing Options</span></b> tab. The <b style='mso-bidi-font-weight:
    1921 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1922 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Phase
    1923 data for <span class=SpellE>fap</span></span></b> window shows <b
    1924 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1925 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1926 minor-latin'>Drawing controls</span></b></p>
     1940mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1941Calibri;mso-bidi-theme-font:minor-latin'>Drawing Options</span></b> tab. The <b
     1942style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1943mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1944Calibri;mso-bidi-theme-font:minor-latin'>Phase data for <span class=SpellE>fap</span></span></b>
     1945window shows <b style='mso-bidi-font-weight:normal'><span style='font-family:
     1946"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1947minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>Drawing
     1948controls</span></b></p>
    19271949
    19281950<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    19351957<p class=MsoNormal>The plot will show a new tab marked <span class=SpellE><b
    19361958style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1937 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1938 minor-latin'>fap</span></b></span> showing some balls in various colors.</p>
     1959mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1960Calibri;mso-bidi-theme-font:minor-latin'>fap</span></b></span> showing some
     1961balls in various colors.</p>
    19391962
    19401963<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    19471970<p class=MsoNormal>Notice the slider controls in <b style='mso-bidi-font-weight:
    19481971normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1949 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Drawing
    1950 controls; </span></b>you can change them to change the how the structure is
    1951 displayed. Set the <b style='mso-bidi-font-weight:normal'><span
    1952 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1953 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Show unit
    1954 cell?</span></b> <span class=GramE>check</span> box (the drawing will show the
    1955 unit cell edges) and then press the <b style='mso-bidi-font-weight:normal'><span
    1956 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1957 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Draw atoms</span></b>
    1958 tab; this will show the list of atoms that are drawn in the picture.</p>
     1972minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1973mso-bidi-theme-font:minor-latin'>Drawing controls; </span></b>you can change
     1974them to change the how the structure is displayed. Set the <b style='mso-bidi-font-weight:
     1975normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1976minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1977mso-bidi-theme-font:minor-latin'>Show unit cell?</span></b> <span class=GramE>check</span>
     1978box if needed (the drawing will show the unit cell edges) and then press the <b
     1979style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1980mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1981Calibri;mso-bidi-theme-font:minor-latin'>Draw atoms</span></b> tab; this will
     1982show the list of atoms that are drawn in the picture.</p>
    19591983
    19601984<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1961  id="Picture_x0020_30" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:450pt;
     1985 id="Picture_x0020_29" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:450pt;
    19621986 height:225pt;visibility:visible;mso-wrap-style:square'>
    19631987 <v:imagedata src="Laboratory%20X_files/image019.png" o:title=""/>
    19641988</v:shape><![endif]--><![if !vml]><img border=0 width=600 height=300
    1965 src="Laboratory%20X_files/image019.png" v:shapes="Picture_x0020_30"><![endif]></span></p>
     1989src="Laboratory%20X_files/image019.png" v:shapes="Picture_x0020_29"><![endif]></span></p>
    19661990
    19671991<p class=MsoNormal>This is a copy of what is in the <b style='mso-bidi-font-weight:
    19681992normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1969 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Atoms</span></b>
    1970 table; there are columns that allow you to change how the atoms are displayed,
    1971 their labels and their color all controlled on an atom-by-atom basis. Now if
    1972 the contents of the <b style='mso-bidi-font-weight:normal'><span
    1973 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1974 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Atoms</span></b>
    1975 table change (e.g. by refinement) then you must manually update the <b
    1976 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1977 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1978 minor-latin'>Draw Atoms</span></b> table by erasing all the <b
    1979 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1980 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1981 minor-latin'>Draw Atoms</span></b>. They are then automatically refreshed from
    1982 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1983 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1993minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1994mso-bidi-theme-font:minor-latin'>Atoms</span></b> table; there are columns that
     1995allow you to change how the atoms are displayed, their labels and their color
     1996all controlled on an atom-by-atom basis. Now if the contents of the <b
     1997style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1998mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1999Calibri;mso-bidi-theme-font:minor-latin'>Atoms</span></b> table change (e.g. by
     2000refinement) then you must manually update the <b style='mso-bidi-font-weight:
     2001normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     2002minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     2003mso-bidi-theme-font:minor-latin'>Draw Atoms</span></b> table by erasing all the
     2004<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2005mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     2006Calibri;mso-bidi-theme-font:minor-latin'>Draw Atoms</span></b>. They are then
     2007automatically refreshed from the <b style='mso-bidi-font-weight:normal'><span
     2008style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2009mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    19842010minor-latin'>Atoms</span></b> table with the new values. Do this by selecting
    19852011all the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1986 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1987 minor-latin'>Draw Atoms</span></b>; double click the blank in the upper left
    1988 corner of the table. All atoms will be highlighted in dark gray. Then press <b
    1989 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1990 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     2012mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     2013Calibri;mso-bidi-theme-font:minor-latin'>Draw Atoms</span></b>; double click
     2014the blank in the upper left corner of the table. All atoms will be highlighted
     2015in dark gray. Then press <b style='mso-bidi-font-weight:normal'><span
     2016style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2017mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    19912018minor-latin'>Edit/Delete atoms</span></b> in the <b style='mso-bidi-font-weight:
    19922019normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1993 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Draw
    1994 Atoms</span></b> menu. All the atoms will vanish and then reappear with updated
    1995 values. Now we can draw the structure assured that we are using the final
    1996 result from the refinement. </p>
     2020minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     2021mso-bidi-theme-font:minor-latin'>Draw Atoms</span></b> menu. All the atoms will
     2022vanish and then reappear with updated values. Now we can draw the structure
     2023assured that we are using the final result from the refinement. </p>
    19972024
    19982025<p class=MsoNormal>To build the structure model we want to show with PO<sub>4</sub>
     
    20052032all the atoms in the <b style='mso-bidi-font-weight:normal'><span
    20062033style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    2007 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Draw Atoms</span></b>
    2008 tab by double clicking in upper left corner box of the table. All atoms in the
    2009 table are then displayed in dark gray and they all are green on the drawing
    2010 indicating their selection.</p>
     2034mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     2035minor-latin'>Draw Atoms</span></b> tab by double clicking in upper left corner
     2036box of the table. All atoms in the table are then displayed in dark gray and
     2037they all are green on the drawing indicating their selection.</p>
    20112038
    20122039<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l0 level1 lfo4'><![if !supportLists]><span
     
    20142041style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
    20152042<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    2016 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    2017 minor-latin'>Edit/Fill unit cell</span></b> from the <b style='mso-bidi-font-weight:
    2018 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    2019 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Draw
    2020 Atoms</span></b> menu. The drawing will show the unit cell filled with atoms in
    2021 positions equivalent to the original set and the <b style='mso-bidi-font-weight:
    2022 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    2023 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Draw
    2024 Atoms</span></b> table will have all of them listed. The <span class=SpellE><b
    2025 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    2026 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    2027 minor-latin'>Sym</span></b></span><b style='mso-bidi-font-weight:normal'><span
    2028 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    2029 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'> Op</span></b>
    2030 column in the table shows the symmetry operator number and unit cell
    2031 translation used to generate that position.</p>
     2043mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     2044Calibri;mso-bidi-theme-font:minor-latin'>Edit/Fill unit cell</span></b> from
     2045the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2046mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     2047Calibri;mso-bidi-theme-font:minor-latin'>Draw Atoms</span></b> menu. The
     2048drawing will show the unit cell filled with atoms in positions equivalent to
     2049the original set and the <b style='mso-bidi-font-weight:normal'><span
     2050style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2051mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     2052minor-latin'>Draw Atoms</span></b> table will have all of them listed. The <span
     2053class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
     2054"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     2055minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>Sym</span></b></span><b
     2056style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2057mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     2058Calibri;mso-bidi-theme-font:minor-latin'> Op</span></b> column in the table
     2059shows the symmetry operator number and unit cell translation used to generate
     2060that position.</p>
    20322061
    20332062<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l0 level1 lfo4'><![if !supportLists]><span
     
    20362065click on the column label <b style='mso-bidi-font-weight:normal'><span
    20372066style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    2038 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Type</span></b>.
    2039 A small dialog window will appear with a list of element types in this
    2040 structure. Select <b style='mso-bidi-font-weight:normal'><span
    2041 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    2042 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>P</span></b>
    2043 by checking the box and then press <b style='mso-bidi-font-weight:normal'><span
    2044 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    2045 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>OK</span></b>.
    2046 All the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    2047 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    2048 minor-latin'>P</span></b> atoms will be bright green and they will be
    2049 highlighted in dark gray in the table</p>
     2067mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     2068minor-latin'>Type</span></b>. A small dialog window will appear with a list of
     2069element types in this structure. Select <b style='mso-bidi-font-weight:normal'><span
     2070style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2071mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     2072minor-latin'>P</span></b> by checking the box and then press <b
     2073style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2074mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     2075Calibri;mso-bidi-theme-font:minor-latin'>OK</span></b>. All the <b
     2076style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2077mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     2078Calibri;mso-bidi-theme-font:minor-latin'>P</span></b> atoms will be bright
     2079green and they will be highlighted in dark gray in the table</p>
    20502080
    20512081<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l0 level1 lfo4'><![if !supportLists]><span
     
    20532083style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
    20542084<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    2055 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    2056 minor-latin'>Edit/Fill CN-sphere</span></b> in the <b style='mso-bidi-font-weight:
    2057 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    2058 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Draw
    2059 Atoms</span></b> menu. Each <b style='mso-bidi-font-weight:normal'><span
    2060 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    2061 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>P</span></b>
    2062 atom will now have its full complement of 4 O atoms.</p>
     2085mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     2086Calibri;mso-bidi-theme-font:minor-latin'>Edit/Fill CN-sphere</span></b> in the <b
     2087style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2088mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     2089Calibri;mso-bidi-theme-font:minor-latin'>Draw Atoms</span></b> menu. Each <b
     2090style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2091mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     2092Calibri;mso-bidi-theme-font:minor-latin'>P</span></b> atom will now have its
     2093full complement of 4 O atoms.</p>
    20632094
    20642095<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l0 level1 lfo4'><![if !supportLists]><span
     
    20672098step 3 to select all the <b style='mso-bidi-font-weight:normal'><span
    20682099style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    2069 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>P</span></b>
    2070 atoms again.</p>
     2100mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     2101minor-latin'>P</span></b> atoms again.</p>
    20712102
    20722103<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l0 level1 lfo4'><![if !supportLists]><span
     
    20742105style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
    20752106<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    2076 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    2077 minor-latin'>Edit/Atom style</span></b> from the <b style='mso-bidi-font-weight:
    2078 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    2079 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Draw
    2080 Atoms</span></b> menu. A small dialog bow will appear with a list of possible
    2081 atom drawing styles. Notice the first one is blank; that will cause the atom to
    2082 not be drawn. Select <b style='mso-bidi-font-weight:normal'><span
    2083 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    2084 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>polyhedral</span></b>
    2085 and press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    2086 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    2087 minor-latin'>OK</span></b>. Each <b style='mso-bidi-font-weight:normal'><span
    2088 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    2089 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>P</span></b>
    2090 atom will be drawn as a brass colored polyhedron (with too many faces to be a
    2091 tetrahedron because a nearby <span class=SpellE>Ca</span> atom was included –
    2092 this will be fixed in a moment).</p>
     2107mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     2108Calibri;mso-bidi-theme-font:minor-latin'>Edit/Atom style</span></b> from the <b
     2109style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2110mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     2111Calibri;mso-bidi-theme-font:minor-latin'>Draw Atoms</span></b> menu. A small
     2112dialog bow will appear with a list of possible atom drawing styles. Notice the
     2113first one is blank; that will cause the atom to not be drawn. Select <b
     2114style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2115mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     2116Calibri;mso-bidi-theme-font:minor-latin'>polyhedral</span></b> and press <b
     2117style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2118mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     2119Calibri;mso-bidi-theme-font:minor-latin'>OK</span></b>. Each <b
     2120style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2121mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     2122Calibri;mso-bidi-theme-font:minor-latin'>P</span></b> atom will be drawn as a
     2123brass colored polyhedron (with too many faces to be a tetrahedron because a
     2124nearby <span class=SpellE>Ca</span> atom was included – this will be fixed in a
     2125moment).</p>
    20932126
    20942127<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l0 level1 lfo4'><![if !supportLists]><span
     
    20972130<span class=GramE>do step</span> 3 yet again but this time select the <b
    20982131style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    2099 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    2100 minor-latin'>O</span></b> atoms.</p>
     2132mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     2133Calibri;mso-bidi-theme-font:minor-latin'>O</span></b> atoms.</p>
    21012134
    21022135<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l0 level1 lfo4'><![if !supportLists]><span
     
    21042137style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
    21052138<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    2106 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    2107 minor-latin'>Edit/Atom style</span></b> and pick the blank entry and press <b
    2108 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    2109 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     2139mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     2140Calibri;mso-bidi-theme-font:minor-latin'>Edit/Atom style</span></b> and pick
     2141the blank entry and press <b style='mso-bidi-font-weight:normal'><span
     2142style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2143mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    21102144minor-latin'>OK</span></b>; the O atoms will vanish leaving some odd <span
    21112145class=SpellE>polyhedra</span> and the <span class=SpellE>Ca</span> and F atoms.</p>
     
    21152149style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
    21162150the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    2117 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    2118 minor-latin'>Drawing Options</span></b> tab and change the <b style='mso-bidi-font-weight:
    2119 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    2120 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Bond
     2151mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     2152Calibri;mso-bidi-theme-font:minor-latin'>Drawing Options</span></b> tab and
     2153change the <b style='mso-bidi-font-weight:normal'><span style='font-family:
     2154"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     2155minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>Bond
    21212156search factor</span></b> to <b style='mso-bidi-font-weight:normal'><span
    21222157style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    2123 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>0.80</span></b>
    2124 and press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    2125 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     2158mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     2159minor-latin'>0.80</span></b> and press <b style='mso-bidi-font-weight:normal'><span
     2160style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2161mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    21262162minor-latin'>Enter</span></b>; the odd <span class=SpellE>polyhedra</span> will
    21272163immediately change to tetrahedra.</p>
     
    21322168can adjust the <b style='mso-bidi-font-weight:normal'><span style='font-family:
    21332169"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    2134 minor-latin;mso-bidi-theme-font:minor-latin'>van der Waals scale</span></b> to
    2135 make all the balls any size you desire.</p>
     2170minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>van
     2171der Waals scale</span></b> to make all the balls any size you desire.</p>
    21362172
    21372173<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l0 level1 lfo4'><![if !supportLists]><span
     
    21412177very similar green, you can change this. Select the <b style='mso-bidi-font-weight:
    21422178normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    2143 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Draw
    2144 Atoms</span></b> tab, then do step 3 selecting the <span class=SpellE><b
    2145 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    2146 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     2179minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     2180mso-bidi-theme-font:minor-latin'>Draw Atoms</span></b> tab, then do step 3
     2181selecting the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
     2182style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2183mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    21472184minor-latin'>Ca</span></b></span> atoms.</p>
    21482185
     
    21512188style='font:7.0pt "Times New Roman"'>&nbsp; </span></span></span><![endif]>Select
    21522189<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    2153 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    2154 minor-latin'>Edit/Atom color</span></b> in the <b style='mso-bidi-font-weight:
    2155 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    2156 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Draw
    2157 Atoms</span></b> menu. A color selection dialog box will appear (NB: this
    2158 dialog is operating system dependent – we will assume you are using a Windows7
    2159 machine). The dialog box looks like (I pressed <b style='mso-bidi-font-weight:
    2160 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    2161 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Define
     2190mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     2191Calibri;mso-bidi-theme-font:minor-latin'>Edit/Atom color</span></b> in the <b
     2192style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2193mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     2194Calibri;mso-bidi-theme-font:minor-latin'>Draw Atoms</span></b> menu. A color
     2195selection dialog box will appear (NB: this dialog is operating system dependent
     2196– we will assume you are using a Windows7 machine). The dialog box looks like
     2197(I pressed <b style='mso-bidi-font-weight:normal'><span style='font-family:
     2198"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     2199minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>Define
    21622200Custom Colors</span></b>)</p>
    21632201
     
    21722210to either a) choose your color by finding it in <b style='mso-bidi-font-weight:
    21732211normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    2174 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Basic
    2175 colors</span></b> and then press <b style='mso-bidi-font-weight:normal'><span
    2176 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    2177 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>OK</span></b>
    2178 or b) press <b style='mso-bidi-font-weight:normal'><span style='font-family:
    2179 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    2180 minor-latin;mso-bidi-theme-font:minor-latin'>Define Custom Colors</span></b>, move
     2212minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     2213mso-bidi-theme-font:minor-latin'>Basic colors</span></b> and then press <b
     2214style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2215mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     2216Calibri;mso-bidi-theme-font:minor-latin'>OK</span></b> or b) press <b
     2217style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2218mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     2219Calibri;mso-bidi-theme-font:minor-latin'>Define Custom Colors</span></b>, move
    21812220the cross around on the spectrum display, set the vertical slider for the
    21822221luminosity (<span class=SpellE><b style='mso-bidi-font-weight:normal'><span
    21832222style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    2184 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>ColorSolid</span></b></span>
    2185 will show the result), and then press <b style='mso-bidi-font-weight:normal'><span
    2186 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    2187 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>OK</span></b>.
    2188 The drawing will now show that color for the atoms and the color will appear in
    2189 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    2190 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    2191 minor-latin'>Draw Atoms</span></b> table. If you don’t like your colors select <b
    2192 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    2193 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     2223mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     2224minor-latin'>ColorSolid</span></b></span> will show the result), and then press
     2225<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2226mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     2227Calibri;mso-bidi-theme-font:minor-latin'>OK</span></b>. The drawing will now
     2228show that color for the atoms and the color will appear in the <b
     2229style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2230mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     2231Calibri;mso-bidi-theme-font:minor-latin'>Draw Atoms</span></b> table. If you
     2232don’t like your colors select <b style='mso-bidi-font-weight:normal'><span
     2233style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2234mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    21942235minor-latin'>Edit/Reset atom colors</span></b> to put them back to their
    21952236default colors. In my drawing I’ve made the <span class=SpellE>Ca</span> atoms
     
    22142255start select the <b style='mso-bidi-font-weight:normal'><span style='font-family:
    22152256"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    2216 minor-latin;mso-bidi-theme-font:minor-latin'>Atoms</span></b> tab in <b
    2217 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    2218 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    2219 minor-latin'>Phases/<span class=SpellE>fap</span></span></b>.</p>
     2257minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>Atoms</span></b>
     2258tab in <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2259mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     2260Calibri;mso-bidi-theme-font:minor-latin'>Phases/<span class=SpellE>fap</span></span></b>.</p>
    22202261
    22212262<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l1 level1 lfo6'><![if !supportLists]><span
     
    22252266class=GramE>an</span> “<b style='mso-bidi-font-weight:normal'><span
    22262267style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    2227 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>0</span></b>”).
    2228 Add to the selection the other <span class=SpellE>Ca</span> atom and the P atom
    2229 in the same way with the Ctrl key down; all will be highlighted in dark gray.</p>
     2268mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     2269minor-latin'>0</span></b>”). Add to the selection the other <span class=SpellE>Ca</span>
     2270atom and the P atom in the same way with the Ctrl key down; all will be
     2271highlighted in dark gray.</p>
    22302272
    22312273<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l1 level1 lfo6'><![if !supportLists]><span
     
    22332275style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
    22342276<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    2235 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    2236 minor-latin'>Compute/Distances Angles</span></b> from the <b style='mso-bidi-font-weight:
    2237 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    2238 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Atoms</span></b>
    2239 menu. A small dialog box will appear</p>
     2277mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     2278Calibri;mso-bidi-theme-font:minor-latin'>Compute/Distances Angles</span></b>
     2279from the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2280mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     2281Calibri;mso-bidi-theme-font:minor-latin'>Atoms</span></b> menu. A small dialog
     2282box will appear</p>
    22402283
    22412284<p class=MsoNormal style='margin-left:.25in'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    22512294tetrahedra the <b style='mso-bidi-font-weight:normal'><span style='font-family:
    22522295"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    2253 minor-latin;mso-bidi-theme-font:minor-latin'>Bond</span></b> and <b
    2254 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    2255 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    2256 minor-latin'>Angle search factors</span></b> may be too large for this case.
    2257 Change both to <b style='mso-bidi-font-weight:normal'><span style='font-family:
    2258 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    2259 minor-latin;mso-bidi-theme-font:minor-latin'>0.8</span></b> and press <b
    2260 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    2261 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     2296minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>Bond</span></b>
     2297and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2298mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     2299Calibri;mso-bidi-theme-font:minor-latin'>Angle search factors</span></b> may be
     2300too large for this case. Change both to <b style='mso-bidi-font-weight:normal'><span
     2301style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2302mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     2303minor-latin'>0.8</span></b> and press <b style='mso-bidi-font-weight:normal'><span
     2304style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2305mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    22622306minor-latin'>OK</span></b>. GSAS-II will then display on the console formatted
    22632307tables of individual atom distances and angles with <span class=SpellE>esds</span>
     
    24442488radii to fix this. Setting the <b style='mso-bidi-font-weight:normal'><span
    24452489style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    2446 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Bond</span></b>
    2447 and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    2448 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     2490mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     2491minor-latin'>Bond</span></b> and <b style='mso-bidi-font-weight:normal'><span
     2492style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2493mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    24492494minor-latin'>Angle</span></b> <span class=SpellE>Ca</span> radii to 2.1 and
    245024951.9, respectively, gave</p>
  • trunk/help/Neutron CW Powder Data.htm

    r710 r895  
    2323  <o:Author>Von Dreele</o:Author>
    2424  <o:LastAuthor>Von Dreele</o:LastAuthor>
    25   <o:Revision>12</o:Revision>
    26   <o:TotalTime>670</o:TotalTime>
     25  <o:Revision>13</o:Revision>
     26  <o:TotalTime>694</o:TotalTime>
    2727  <o:Created>2012-05-06T20:38:00Z</o:Created>
    28   <o:LastSaved>2012-08-15T15:04:00Z</o:LastSaved>
     28  <o:LastSaved>2013-04-30T19:06:00Z</o:LastSaved>
    2929  <o:Pages>8</o:Pages>
    30   <o:Words>1783</o:Words>
    31   <o:Characters>10169</o:Characters>
     30  <o:Words>1782</o:Words>
     31  <o:Characters>10161</o:Characters>
    3232  <o:Company>Argonne National Laboratory</o:Company>
    3333  <o:Lines>84</o:Lines>
    3434  <o:Paragraphs>23</o:Paragraphs>
    35   <o:CharactersWithSpaces>11929</o:CharactersWithSpaces>
     35  <o:CharactersWithSpaces>11920</o:CharactersWithSpaces>
    3636  <o:Version>14.00</o:Version>
    3737 </o:DocumentProperties>
     
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    940940        mso-ascii-theme-font:minor-latin;
    941941        mso-hansi-font-family:Calibri;
    942         mso-hansi-theme-font:minor-latin;
    943         mso-bidi-font-family:"Times New Roman";
    944         mso-bidi-theme-font:minor-bidi;}
     942        mso-hansi-theme-font:minor-latin;}
    945943table.MsoTableGrid
    946944        {mso-style-name:"Table Grid";
     
    962960        mso-ascii-theme-font:minor-latin;
    963961        mso-hansi-font-family:Calibri;
    964         mso-hansi-theme-font:minor-latin;
    965         mso-bidi-font-family:"Times New Roman";
    966         mso-bidi-theme-font:minor-bidi;}
     962        mso-hansi-theme-font:minor-latin;}
    967963</style>
    968964<![endif]--><!--[if gte mso 9]><xml>
    969  <o:shapedefaults v:ext="edit" spidmax="1027"/>
     965 <o:shapedefaults v:ext="edit" spidmax="1026"/>
    970966</xml><![endif]--><!--[if gte mso 9]><xml>
    971967 <o:shapelayout v:ext="edit">
     
    982978style='mso-bookmark:_Toc504374004'> Garnet</span></h1>
    983979
    984 <p class=MsoNormal>In this training exercise you will refine the structure of
    985 yttrium iron/aluminum garnet using constant wavelength neutron data. The
    986 structure is cubic with four different atomic sites two of which are occupied
    987 by both iron and aluminum. The data was taken on the D1a powder diffractometer
    988 at the ILL, Grenoble, France using 1.909Å wavelength neutrons.</p>
     980<p class=MsoNormal>In this tutorial you will refine the structure of yttrium
     981iron/aluminum garnet using constant wavelength neutron data. The structure is
     982cubic with four different atomic sites two of which are occupied by both iron
     983and aluminum. The data was taken on the D1a powder diffractometer at the ILL,
     984Grenoble, France using 1.909Å wavelength neutrons.</p>
    989985
    990986<p class=MsoNormal>If you have not done so already, <a
     
    997993style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Use
    998994the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    999 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1000 minor-latin'>Import/Powder Data/from GSAS file</span></b> menu item to read the
    1001 data file into GSAS-II. This read option is set to read any of the powder data formats
    1002 (except neutron TOF time map files) defined for GSAS (angles in <span
    1003 class=SpellE>centidegrees</span>). Other submenu items will read the <span
    1004 class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
    1005 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1006 minor-latin;mso-bidi-theme-font:minor-latin'>cif</span></b></span> format or
    1007 the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
    1008 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1009 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>xye</span></b></span>
    1010 format (angles in degrees) used by <span class=SpellE>Topas</span>, etc.<span
     995mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     996Calibri;mso-bidi-theme-font:minor-latin'>Import/Powder Data/from GSAS file</span></b>
     997menu item to read the data file into GSAS-II. This read option is set to read
     998any of the powder data formats (except neutron TOF time map files) defined for
     999GSAS (angles in <span class=SpellE>centidegrees</span>). Other submenu items
     1000will read the <span class=SpellE><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-font-family:Calibri;mso-bidi-theme-font:
     1003minor-latin'>cif</span></b></span> format or the <span class=SpellE><b
     1004style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1005mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1006Calibri;mso-bidi-theme-font:minor-latin'>xye</span></b></span> format (angles
     1007in degrees) used by <span class=SpellE>Topas</span>, etc.<span
    10111008style='mso-spacerun:yes'>  </span>Change the file directory to <b
    10121009style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1013 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1014 minor-latin'>Exercises/garnet</span></b><span style='font-family:"Calibri","sans-serif";
    1015 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1010mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1011Calibri;mso-bidi-theme-font:minor-latin'>Exercises/garnet</span></b><span
     1012style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1013mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    10161014minor-latin'> to find the file; you will need to change the file type to <b
    10171015style='mso-bidi-font-weight:normal'>All files (*.*)</b> to find the desired
     
    10231021the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
    10241022style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1025 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>garnet.raw</span></b></span><span
    1026 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1027 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'> data</span>
    1028 file in the first dialog and press <b style='mso-bidi-font-weight:normal'><span
    1029 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1030 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Open</span></b>.
    1031 There will be a Dialog box asking <span class=GramE><b style='mso-bidi-font-weight:
    1032 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1033 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Is</span></b></span><b
    1034 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1035 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1023mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1024minor-latin'>garnet.raw</span></b></span><span style='font-family:"Calibri","sans-serif";
     1025mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1026Calibri;mso-bidi-theme-font:minor-latin'> data</span> file in the first dialog
     1027and press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1028mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1029Calibri;mso-bidi-theme-font:minor-latin'>Open</span></b>. There will be a
     1030Dialog box asking <span class=GramE><b style='mso-bidi-font-weight:normal'><span
     1031style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1032mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1033minor-latin'>Is</span></b></span><b style='mso-bidi-font-weight:normal'><span
     1034style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1035mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    10361036minor-latin'> this the file you want?</span></b> Press <span class=GramE><b
    10371037style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1038 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1039 minor-latin'>Yes</span></b></span> button to proceed.</p>
     1038mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1039Calibri;mso-bidi-theme-font:minor-latin'>Yes</span></b></span> button to
     1040proceed.</p>
    10401041
    10411042<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l1 level1 lfo2'><![if !supportLists]><span
     
    10431044style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
    10441045the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1045 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1046 minor-latin'>inst_d1a.prm</span></b> instrument parameter file in the second
    1047 dialog and press <b style='mso-bidi-font-weight:normal'><span style='font-family:
    1048 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1049 minor-latin;mso-bidi-theme-font:minor-latin'>Open</span></b>.</p>
     1046mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1047Calibri;mso-bidi-theme-font:minor-latin'>inst_d1a.prm</span></b> instrument
     1048parameter file in the second dialog and press <b style='mso-bidi-font-weight:
     1049normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1050minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1051mso-bidi-theme-font:minor-latin'>Open</span></b>.</p>
    10501052
    10511053<p class=MsoNormal>At this point the <b style='mso-bidi-font-weight:normal'><span
    10521054style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1053 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II data
    1054 tree</span></b> window will have several entries and the plot window will show
    1055 the powder pattern</p>
     1055mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1056minor-latin'>GSAS-II data tree</span></b> window will have several entries and
     1057the plot window will show the powder pattern</p>
    10561058
    10571059<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
     
    10751077 <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
    10761078 <o:lock v:ext="edit" aspectratio="t"/>
    1077 </v:shapetype><v:shape id="Picture_x0020_1" o:spid="_x0000_i1044" type="#_x0000_t75"
    1078  style='width:525pt;height:450pt;visibility:visible;mso-wrap-style:square'>
     1079</v:shapetype><v:shape id="_x0000_i1045" type="#_x0000_t75" style='width:525pt;
     1080 height:450pt;visibility:visible;mso-wrap-style:square'>
    10791081 <v:imagedata src="Neutron%20CW%20Powder%20Data_files/image001.png" o:title=""/>
    10801082</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
    1081 src="Neutron%20CW%20Powder%20Data_files/image001.png" v:shapes="Picture_x0020_1"><![endif]></span></p>
     1083src="Neutron%20CW%20Powder%20Data_files/image001.png" v:shapes="_x0000_i1045"><![endif]></span></p>
    10821084
    10831085<h2>Step 2: Create the phase</h2>
     
    10871089style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Use
    10881090the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1089 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1090 minor-latin'>Data/Add phase</span></b> menu item to begin creation of the new
    1091 phase for this garnet; enter a phase name in the dialog box, we assume ‘<b
    1092 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1093 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1091mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1092Calibri;mso-bidi-theme-font:minor-latin'>Data/Add phase</span></b> menu item to
     1093begin creation of the new phase for this garnet; enter a phase name in the
     1094dialog box, we assume ‘<b style='mso-bidi-font-weight:normal'><span
     1095style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1096mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    10941097minor-latin'>garnet</span></b>’.</p>
    10951098
     
    10991102the bottom of the <b style='mso-bidi-font-weight:normal'><span
    11001103style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1101 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II tree</span></b>
    1102 find <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1103 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1104mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1105minor-latin'>GSAS-II tree</span></b> find <b style='mso-bidi-font-weight:normal'><span
     1106style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1107mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    11041108minor-latin'>Phases</span></b> &amp; click the ’<b style='mso-bidi-font-weight:
    11051109normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1106 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>+</span></b>’
    1107 box to expand it. Then click on <b style='mso-bidi-font-weight:normal'><span
    1108 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1109 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>garnet</span></b>
    1110 to select it; the <b style='mso-bidi-font-weight:normal'><span
    1111 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1112 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Phase data
    1113 for garnet</span></b> window will appear and the <b style='mso-bidi-font-weight:
    1114 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1115 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>General</span></b>
    1116 tab is visible.<span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_2"
    1117  o:spid="_x0000_i1043" type="#_x0000_t75" style='width:660pt;height:234pt;
     1110minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1111mso-bidi-theme-font:minor-latin'>+</span></b>’ box to expand it. Then click on <b
     1112style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1113mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1114Calibri;mso-bidi-theme-font:minor-latin'>garnet</span></b> to select it; the <b
     1115style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1116mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1117Calibri;mso-bidi-theme-font:minor-latin'>Phase data for garnet</span></b>
     1118window will appear and the <span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1119 id="_x0000_i1044" type="#_x0000_t75" style='width:622.5pt;height:323.25pt;
    11181120 visibility:visible;mso-wrap-style:square'>
    11191121 <v:imagedata src="Neutron%20CW%20Powder%20Data_files/image002.png" o:title=""/>
    1120 </v:shape><![endif]--><![if !vml]><img border=0 width=880 height=312
    1121 src="Neutron%20CW%20Powder%20Data_files/image002.png" v:shapes="Picture_x0020_2"><![endif]></span></p>
     1122</v:shape><![endif]--><![if !vml]><img border=0 width=830 height=431
     1123src="Neutron%20CW%20Powder%20Data_files/image002.png" v:shapes="_x0000_i1044"><![endif]></span><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-font-family:
     1126Calibri;mso-bidi-theme-font:minor-latin'>General</span></b> tab is visible.</p>
    11221127
    11231128<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l0 level1 lfo4'><![if !supportLists]><span
     
    11251130style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>The
    11261131<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1127 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1128 minor-latin'>Phase type</span></b> is correctly set to “<b style='mso-bidi-font-weight:
     1132mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1133Calibri;mso-bidi-theme-font:minor-latin'>Phase type</span></b> is correctly set
     1134to “<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1135mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1136Calibri;mso-bidi-theme-font:minor-latin'>nuclear</span></b>”; other options
     1137will become valid in the future. Enter the space group ‘<b style='mso-bidi-font-weight:
    11291138normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1130 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>nuclear</span></b>”;
    1131 other options will become valid in the future. Enter the space group ‘<b
    1132 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1133 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1134 minor-latin'>I a 3 d</span></b>’ (spaces between axial fields are required in
    1135 GSAS-II) and press <b style='mso-bidi-font-weight:normal'><span
    1136 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1137 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Enter</span></b>,
    1138 the space group information window will appear</p>
     1139minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1140mso-bidi-theme-font:minor-latin'>I a 3 d</span></b>’ (spaces between axial
     1141fields are required in GSAS-II) and press <b style='mso-bidi-font-weight:normal'><span
     1142style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1143mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1144minor-latin'>Enter</span></b>, the space group information window will appear</p>
    11391145
    11401146<p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1141  id="Picture_x0020_3" o:spid="_x0000_i1042" type="#_x0000_t75" style='width:333.75pt;
     1147 id="Picture_x0020_3" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:333.75pt;
    11421148 height:355.5pt;visibility:visible;mso-wrap-style:square'>
    11431149 <v:imagedata src="Neutron%20CW%20Powder%20Data_files/image003.png" o:title=""/>
     
    11471153<p class=MsoListParagraphCxSpMiddle>Press <b style='mso-bidi-font-weight:normal'><span
    11481154style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1149 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>OK</span></b>
    1150 to exit. The <b style='mso-bidi-font-weight:normal'><span style='font-family:
    1151 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1152 minor-latin;mso-bidi-theme-font:minor-latin'>General</span></b> tab display
    1153 will change (principally changes in lattice parameter display).</p>
     1155mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1156minor-latin'>OK</span></b> to exit. The <b style='mso-bidi-font-weight:normal'><span
     1157style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1158mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1159minor-latin'>General</span></b> tab display will change (principally changes in
     1160lattice parameter display).</p>
    11541161
    11551162<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l0 level1 lfo4'><![if !supportLists]><span
     
    11581165the lattice parameter for garnet (a=<b style='mso-bidi-font-weight:normal'><span
    11591166style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1160 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>12.19</span></b>)
    1161 in the appropriate field and press <b style='mso-bidi-font-weight:normal'><span
    1162 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1163 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Enter</span></b>.
    1164 The display will change again to show the cell volume.</p>
     1167mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1168minor-latin'>12.19</span></b>) in the appropriate field and press <b
     1169style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1170mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1171Calibri;mso-bidi-theme-font:minor-latin'>Enter</span></b>. The display will
     1172change again to show the cell volume.</p>
    11651173
    11661174<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l0 level1 lfo4'><![if !supportLists]><span
     
    11681176style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Click
    11691177on the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1170 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1171 minor-latin'>Data</span></b> tab in the <b style='mso-bidi-font-weight:normal'><span
    1172 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1173 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Phase data
    1174 for garnet </span></b>window and select <b style='mso-bidi-font-weight:normal'><span
    1175 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1176 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Edit/Add
     1178mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1179Calibri;mso-bidi-theme-font:minor-latin'>Data</span></b> tab in the <b
     1180style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1181mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1182Calibri;mso-bidi-theme-font:minor-latin'>Phase data for garnet </span></b>window
     1183and select <b style='mso-bidi-font-weight:normal'><span style='font-family:
     1184"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1185minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>Edit/Add
    11771186powder histograms</span></b> in the menu for this window. A <b
    11781187style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1179 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1180 minor-latin'>Use data</span></b> window will appear with only one choice <b
    1181 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1182 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1188mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1189Calibri;mso-bidi-theme-font:minor-latin'>Use data</span></b> window will appear
     1190with only one choice <b style='mso-bidi-font-weight:normal'><span
     1191style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1192mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    11831193minor-latin'>PWDR <span class=SpellE>garnet.raw</span>: BANK 1</span></b>.
    11841194Select it and press <b style='mso-bidi-font-weight:normal'><span
    11851195style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1186 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>OK</span></b>.
    1187 The <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1188 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1196mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1197minor-latin'>OK</span></b>. The <b style='mso-bidi-font-weight:normal'><span
     1198style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1199mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    11891200minor-latin'>Data</span></b> tab will change; press the <b style='mso-bidi-font-weight:
    11901201normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1191 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Show
    1192 PWDR <span class=SpellE>garnet.raw</span>: BANK 1</span></b> check box; the
    1193 window will change again</p>
     1202minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1203mso-bidi-theme-font:minor-latin'>Show PWDR <span class=SpellE>garnet.raw</span>:
     1204BANK 1</span></b> check box; the window will change again</p>
    11941205
    11951206<p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1196  id="_x0000_i1041" type="#_x0000_t75" style='width:350.25pt;height:342pt;
    1197  visibility:visible;mso-wrap-style:square'>
     1207 id="Picture_x0020_24" o:spid="_x0000_i1042" type="#_x0000_t75" style='width:480pt;
     1208 height:370.5pt;visibility:visible;mso-wrap-style:square'>
    11981209 <v:imagedata src="Neutron%20CW%20Powder%20Data_files/image004.png" o:title=""/>
    1199 </v:shape><![endif]--><![if !vml]><img border=0 width=467 height=456
    1200 src="Neutron%20CW%20Powder%20Data_files/image004.png" v:shapes="_x0000_i1041"><![endif]></span></p>
     1210</v:shape><![endif]--><![if !vml]><img border=0 width=640 height=494
     1211src="Neutron%20CW%20Powder%20Data_files/image004.png" v:shapes="Picture_x0020_24"><![endif]></span></p>
    12011212
    12021213<p class=MsoListParagraphCxSpLast>I’ve pulled down the bottom of the window to
     
    12111222<p class=MsoNormal>Click on the <b style='mso-bidi-font-weight:normal'><span
    12121223style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1213 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Atoms</span></b>
    1214 tab; this is where you will insert the atoms for the garnet structure. The 6
    1215 sets of atom coordinates are:</p>
     1224mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1225minor-latin'>Atoms</span></b> tab; this is where you will insert the atoms for
     1226the garnet structure. The 6 sets of atom coordinates are:</p>
    12161227
    12171228<table class=MsoTableGrid border=1 cellspacing=0 cellpadding=0
     
    14211432<p class=MsoNormal>To begin use the <b style='mso-bidi-font-weight:normal'><span
    14221433style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1423 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Edit/Append
    1424 atom</span></b> in the menu on the <b style='mso-bidi-font-weight:normal'><span
    1425 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1426 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Atoms</span></b>
    1427 tab 6 times to create the default set of atom places in the table; the table
    1428 will look like</p>
     1434mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1435minor-latin'>Edit/Append atom</span></b> in the menu on the <b
     1436style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1437mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1438Calibri;mso-bidi-theme-font:minor-latin'>Atoms</span></b> tab 6 times to create
     1439the default set of atom places in the table; the table will look like</p>
    14291440
    14301441<p class=MsoNormal style='text-indent:.5in'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1431  id="Picture_x0020_6" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:525pt;
     1442 id="Picture_x0020_6" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:525pt;
    14321443 height:195pt;visibility:visible;mso-wrap-style:square'>
    14331444 <v:imagedata src="Neutron%20CW%20Powder%20Data_files/image005.png" o:title=""/>
     
    14371448<p class=MsoNormal>Then for each atom to be inserted, double click on the “<b
    14381449style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1439 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1440 minor-latin'>H</span></b>” in the <b style='mso-bidi-font-weight:normal'><span
    1441 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1442 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Type</span></b>
    1443 column; a Periodic Table will appear</p>
     1450mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1451Calibri;mso-bidi-theme-font:minor-latin'>H</span></b>” in the <b
     1452style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1453mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1454Calibri;mso-bidi-theme-font:minor-latin'>Type</span></b> column; a Periodic
     1455Table will appear</p>
    14441456
    14451457<p class=MsoNormal style='text-indent:.5in'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1446  id="Picture_x0020_7" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:582pt;
     1458 id="Picture_x0020_7" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:582pt;
    14471459 height:208.5pt;visibility:visible;mso-wrap-style:square'>
    14481460 <v:imagedata src="Neutron%20CW%20Powder%20Data_files/image006.png" o:title=""/>
     
    14531465possible valences (usually choose the “zero” one). Select “<b style='mso-bidi-font-weight:
    14541466normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1455 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Y</span></b>”,
    1456 the Table will vanish and the <b style='mso-bidi-font-weight:normal'><span
    1457 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1458 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Name</span></b>
    1459 and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1460 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1461 minor-latin'>Type</span></b> for that atom will change. Then enter the values
    1462 for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1463 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1467minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1468mso-bidi-theme-font:minor-latin'>Y</span></b>”, the Table will vanish and the <b
     1469style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1470mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1471Calibri;mso-bidi-theme-font:minor-latin'>Name</span></b> and <b
     1472style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1473mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1474Calibri;mso-bidi-theme-font:minor-latin'>Type</span></b> for that atom will
     1475change. Then enter the values for <b style='mso-bidi-font-weight:normal'><span
     1476style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1477mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    14641478minor-latin'>x</span></b>, <b style='mso-bidi-font-weight:normal'><span
    14651479style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1466 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>y</span></b>
    1467 and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1468 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1480mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1481minor-latin'>y</span></b> and <b style='mso-bidi-font-weight:normal'><span
     1482style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1483mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    14691484minor-latin'>z</span></b>; you can use Tab to move to the next one. You may use
    14701485fractions for the atom coordinates (e.g. 1/4, 3/8). Do this for each atom in
    14711486the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1472 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1473 minor-latin'>Atoms</span></b> table. You can leave both <span class=SpellE><b
    1474 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1475 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1487mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1488Calibri;mso-bidi-theme-font:minor-latin'>Atoms</span></b> table. You can leave
     1489both <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
     1490style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1491mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    14761492minor-latin'>frac</span></b></span> and <span class=SpellE><b style='mso-bidi-font-weight:
    14771493normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1478 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Uiso</span></b></span>
    1479 at the default values. Your result should look like</p>
    1480 
    1481 <p class=MsoNormal><!--[if gte vml 1]><v:shape id="Picture_x0020_9" o:spid="_x0000_s1026"
    1482  type="#_x0000_t75" style='position:absolute;margin-left:0;margin-top:0;
    1483  width:525.05pt;height:225.05pt;z-index:251658240;visibility:visible;
    1484  mso-wrap-style:square;mso-width-percent:0;mso-height-percent:0;
    1485  mso-wrap-distance-left:9pt;mso-wrap-distance-top:0;mso-wrap-distance-right:9pt;
    1486  mso-wrap-distance-bottom:0;mso-position-horizontal:left;
    1487  mso-position-horizontal-relative:text;mso-position-vertical:top;
    1488  mso-position-vertical-relative:text;mso-width-percent:0;mso-height-percent:0;
    1489  mso-width-relative:page;mso-height-relative:page'>
     1494minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1495mso-bidi-theme-font:minor-latin'>Uiso</span></b></span> at the default values.
     1496Your result should look like</p>
     1497
     1498<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1499 id="Picture_x0020_26" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:525pt;
     1500 height:225pt;visibility:visible;mso-wrap-style:square'>
    14901501 <v:imagedata src="Neutron%20CW%20Powder%20Data_files/image007.png" o:title=""/>
    1491  <w:wrap type="square"/>
    1492 </v:shape><![endif]--><![if !vml]><img width=700 height=300
    1493 src="Neutron%20CW%20Powder%20Data_files/image007.png" align=left hspace=12
    1494 v:shapes="Picture_x0020_9"><![endif]><br clear=all>
     1502</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=300
     1503src="Neutron%20CW%20Powder%20Data_files/image007.png" v:shapes="Picture_x0020_26"><![endif]></span><br
     1504clear=all>
    14951505You can now do your first Rietveld refinement on this problem. To do this, do <b
    14961506style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1497 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1498 minor-latin'>Calculate/Refine</span></b> in the <b style='mso-bidi-font-weight:
    1499 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1500 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II
    1501 data tree</span></b> menu; a file dialog will ask you for a name for this
    1502 project; you can change the directory if you wish. We assume the name “<b
    1503 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1504 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1507mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1508Calibri;mso-bidi-theme-font:minor-latin'>Calculate/Refine</span></b> in the <b
     1509style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1510mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1511Calibri;mso-bidi-theme-font:minor-latin'>GSAS-II data tree</span></b> menu; a
     1512file dialog will ask you for a name for this project; you can change the
     1513directory if you wish. We assume the name “<b style='mso-bidi-font-weight:normal'><span
     1514style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1515mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    15051516minor-latin'>YAG</span></b>”; the current project will be saved as <span
    15061517class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
    15071518"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1508 minor-latin;mso-bidi-theme-font:minor-latin'>YAG.gpx</span></b></span> and the
    1509 first backup file (<b style='mso-bidi-font-weight:normal'><span
    1510 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1511 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>YAG.bak0.gpx</span></b>)
    1512 will also be created and then the Rietveld refinement will be performed. By
    1513 default, only the histogram scale factor (found under <b style='mso-bidi-font-weight:
     1519minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>YAG.gpx</span></b></span>
     1520and the first backup file (<b style='mso-bidi-font-weight:normal'><span
     1521style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1522mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1523minor-latin'>YAG.bak0.gpx</span></b>) will also be created and then the
     1524Rietveld refinement will be performed. By default, only the histogram scale
     1525factor (found under <b style='mso-bidi-font-weight:normal'><span
     1526style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1527mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1528minor-latin'>Sample Parameters</span></b> for <b style='mso-bidi-font-weight:
    15141529normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1515 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Sample
    1516 Parameters</span></b> for <b style='mso-bidi-font-weight:normal'><span
    1517 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1518 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>PWDR <span
    1519 class=SpellE>garnet.raw</span>: BANK1</span></b> in the <b style='mso-bidi-font-weight:
    1520 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1521 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II
    1522 data tree</span></b>) and 3 background coefficients are refined. The resulting
    1523 powder pattern</p>
     1530minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1531mso-bidi-theme-font:minor-latin'>PWDR <span class=SpellE>garnet.raw</span>:
     1532BANK1</span></b> in the <b style='mso-bidi-font-weight:normal'><span
     1533style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1534mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1535minor-latin'>GSAS-II data tree</span></b>) and 3 background coefficients are
     1536refined. The resulting powder pattern</p>
    15241537
    15251538<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1526  id="Picture_x0020_10" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:525pt;
     1539 id="Picture_x0020_27" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:525pt;
    15271540 height:450pt;visibility:visible;mso-wrap-style:square'>
    15281541 <v:imagedata src="Neutron%20CW%20Powder%20Data_files/image008.png" o:title=""/>
    15291542</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
    1530 src="Neutron%20CW%20Powder%20Data_files/image008.png" v:shapes="Picture_x0020_10"><![endif]></span></p>
     1543src="Neutron%20CW%20Powder%20Data_files/image008.png" v:shapes="Picture_x0020_27"><![endif]></span></p>
    15311544
    15321545<p class=MsoNormal><span class=GramE>shows</span> a pretty poor fit (<span
     
    15341547class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
    15351548"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1536 minor-latin;mso-bidi-theme-font:minor-latin'>YAG.lst</span></b></span> file.
    1537 What appears to be in error includes some structural features (I’d first
     1549minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>YAG.lst</span></b></span>
     1550file. What appears to be in error includes some structural features (I’d first
    15381551suspect site fractions for the Fe/Al sites) and something about the peak
    15391552positions (lattice parameter &amp; zero point). We can introduce all these
     
    15441557style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Go
    15451558to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1546 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1547 minor-latin'>PWDR garnet.raw:BaNK1/Instrument Parameters</span></b> and check
    1548 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1549 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1559mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1560Calibri;mso-bidi-theme-font:minor-latin'>PWDR garnet.raw:BaNK1/Instrument
     1561Parameters</span></b> and check the <b style='mso-bidi-font-weight:normal'><span
     1562style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1563mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    15501564minor-latin'>Refine?</span></b> <span class=GramE>for</span> <b
    15511565style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1552 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1553 minor-latin'>Zero.</span></b></p>
     1566mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1567Calibri;mso-bidi-theme-font:minor-latin'>Zero.</span></b></p>
    15541568
    15551569<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
     
    15571571style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Go
    15581572to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1559 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1560 minor-latin'>Phases/garnet</span></b> and check <b style='mso-bidi-font-weight:
    1561 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1562 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Refine
    1563 unit cell</span></b> in the <b style='mso-bidi-font-weight:normal'><span
    1564 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1565 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>General</span></b>
    1566 tab.</p>
     1573mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1574Calibri;mso-bidi-theme-font:minor-latin'>Phases/garnet</span></b> and check <b
     1575style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1576mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1577Calibri;mso-bidi-theme-font:minor-latin'>Refine unit cell</span></b> in the <b
     1578style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1579mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1580Calibri;mso-bidi-theme-font:minor-latin'>General</span></b> tab.</p>
    15671581
    15681582<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
     
    15701584style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Next
    15711585go to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1572 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1573 minor-latin'>Constraints</span></b> in the main “<b style='mso-bidi-font-weight:
     1586mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1587Calibri;mso-bidi-theme-font:minor-latin'>Constraints</span></b> in the main “<b
     1588style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1589mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1590Calibri;mso-bidi-theme-font:minor-latin'>Loaded Data</span></b>” list in the <b
     1591style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1592mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1593Calibri;mso-bidi-theme-font:minor-latin'>GSAS-II data tree</span></b>. You will
     1594see an empty window with 3 tabs; <span class=GramE><b style='mso-bidi-font-weight:
    15741595normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1575 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Loaded
    1576 Data</span></b>” list in the <b style='mso-bidi-font-weight:normal'><span
    1577 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1578 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II data
    1579 tree</span></b>. You will see an empty window with 3 tabs; <span class=GramE><b
    1580 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1581 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1582 minor-latin'>Phase constraints</span></b> is</span> the one you want. Select <b
    1583 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1584 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1585 minor-latin'>Edit/Add equivalence</span></b> from the menu. You will see the
    1586 following new window</p>
     1596minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1597mso-bidi-theme-font:minor-latin'>Phase constraints</span></b> is</span> the one
     1598you want. Select <b style='mso-bidi-font-weight:normal'><span style='font-family:
     1599"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1600minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>Edit/Add
     1601equivalence</span></b> from the menu. You will see the following new window</p>
    15871602
    15881603<p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    15951610<p class=MsoListParagraphCxSpMiddle><span class=GramE>select</span> <b
    15961611style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1597 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1598 minor-latin'>0::AUiso:1 for Fe(2)</span></b> and press <b style='mso-bidi-font-weight:
    1599 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1600 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>OK</span></b>;
    1601 a new window will appear</p>
     1612mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1613Calibri;mso-bidi-theme-font:minor-latin'>0::AUiso:1 for Fe(2)</span></b> and
     1614press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1615mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1616Calibri;mso-bidi-theme-font:minor-latin'>OK</span></b>; a new window will
     1617appear</p>
    16021618
    16031619<p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1604  id="Picture_x0020_12" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:259.5pt;
     1620 id="Picture_x0020_28" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:259.5pt;
    16051621 height:271.5pt;visibility:visible;mso-wrap-style:square'>
    16061622 <v:imagedata src="Neutron%20CW%20Powder%20Data_files/image010.png" o:title=""/>
    16071623</v:shape><![endif]--><![if !vml]><img border=0 width=346 height=362
    1608 src="Neutron%20CW%20Powder%20Data_files/image010.png" v:shapes="Picture_x0020_12"><![endif]></span></p>
     1624src="Neutron%20CW%20Powder%20Data_files/image010.png" v:shapes="Picture_x0020_28"><![endif]></span></p>
    16091625
    16101626<p class=MsoListParagraphCxSpMiddle><span class=GramE>select</span> <b
    16111627style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1612 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1613 minor-latin'>0::AUiso:2 for Al(3)</span></b> and press <b style='mso-bidi-font-weight:
    1614 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1615 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>OK</span></b>.
    1616 That will form the first equivalence you need between the Fe and Al atoms that
    1617 occupy the atom site at 0<span class=GramE>,0,0</span> in the cell. This shows
    1618 up in the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1619 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1620 minor-latin'>Constraints</span></b> window.</p>
     1628mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1629Calibri;mso-bidi-theme-font:minor-latin'>0::AUiso:2 for Al(3)</span></b> and
     1630press <b style='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-font-family:
     1632Calibri;mso-bidi-theme-font:minor-latin'>OK</span></b>. That will form the
     1633first equivalence you need between the Fe and Al atoms that occupy the atom
     1634site at 0<span class=GramE>,0,0</span> in the cell. This shows up in the <b
     1635style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1636mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1637Calibri;mso-bidi-theme-font:minor-latin'>Constraints</span></b> window.</p>
    16211638
    16221639<p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    16291646<p class=MsoListParagraphCxSpMiddle>Now do the same for the atoms <b
    16301647style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1631 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1632 minor-latin'>0::AUiso:3 for Al(4)</span></b> and <b style='mso-bidi-font-weight:
    1633 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1634 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>0::AUiso:4
    1635 for Fe(5)</span></b> to make that pair of atoms have the same <span
    1636 class=SpellE>Uiso</span>.</p>
     1648mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1649Calibri;mso-bidi-theme-font:minor-latin'>0::AUiso:3 for Al(4)</span></b> and <b
     1650style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1651mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1652Calibri;mso-bidi-theme-font:minor-latin'>0::AUiso:4 for Fe(5)</span></b> to
     1653make that pair of atoms have the same <span class=SpellE>Uiso</span>.</p>
    16371654
    16381655<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
     
    16401657style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Next
    16411658select <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1642 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1643 minor-latin'>Edit/Add constraint</span></b> from the <b style='mso-bidi-font-weight:
    1644 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1645 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Phase
    1646 Constraints</span></b> tab. A now familiar window will appear; select <b
    1647 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1648 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1659mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1660Calibri;mso-bidi-theme-font:minor-latin'>Edit/Add constraint</span></b> from
     1661the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1662mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1663Calibri;mso-bidi-theme-font:minor-latin'>Phase Constraints</span></b> tab. A
     1664now familiar window will appear; select <b style='mso-bidi-font-weight:normal'><span
     1665style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1666mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    16491667minor-latin'>0:<span class=GramE>:Afrac:1</span> for Fe(2)</span></b> and press
    16501668OK. Again you will see the same second window; select <b style='mso-bidi-font-weight:
    16511669normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1652 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>0:<span
    1653 class=GramE>:Afrac:2</span> for Al(3)</span></b> and press <b style='mso-bidi-font-weight:
     1670minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1671mso-bidi-theme-font:minor-latin'>0:<span class=GramE>:Afrac:2</span> for Al(3)</span></b>
     1672and press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1673mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1674Calibri;mso-bidi-theme-font:minor-latin'>OK</span></b>. Do the same thing for <b
     1675style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1676mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1677Calibri;mso-bidi-theme-font:minor-latin'>0::Afrac:3 for Al(4)</span></b> – you
     1678may have to scroll down the list to see this – and <b style='mso-bidi-font-weight:
    16541679normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1655 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>OK</span></b>.
    1656 Do the same thing for <b style='mso-bidi-font-weight:normal'><span
    1657 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1658 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>0::Afrac:3
    1659 for Al(4)</span></b> – you may have to scroll down the list to see this – and <b
    1660 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1661 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1662 minor-latin'>0::Afrac:4 for Fe(5)</span></b>. When done the <b
    1663 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1664 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1665 minor-latin'>Constraints</span></b> window should look like</p>
     1680minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1681mso-bidi-theme-font:minor-latin'>0::Afrac:4 for Fe(5)</span></b>. When done the
     1682<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1683mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1684Calibri;mso-bidi-theme-font:minor-latin'>Constraints</span></b> window should
     1685look like</p>
    16661686
    16671687<p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    16731693
    16741694<p class=MsoListParagraphCxSpMiddle>This process set the
    1675 equivalences/constraints for the two Fe/Al sites in the garnet so that
    1676 refinement of <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
    1677 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1678 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>frac</span></b></span>
     1695equivalences/constraints for the two Fe/Al sites in the garnet so that refinement
     1696of <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
     1697style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1698mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1699minor-latin'>frac</span></b></span> and <span class=SpellE><b style='mso-bidi-font-weight:
     1700normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1701minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1702mso-bidi-theme-font:minor-latin'>Uiso</span></b></span> will succeed. GSAS-II
     1703constraints will correct the site fractions and <span class=SpellE>Uiso</span>
     1704values so that they conform to the constraints as written. You need not be
     1705concerned about their starting values beforehand. Also note the way each
     1706parameter was named; the general form is <b style='mso-bidi-font-weight:normal'><span
     1707style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1708mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1709minor-latin'>p<span class=GramE>:h:name:num</span></span></b> where <b
     1710style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1711mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1712Calibri;mso-bidi-theme-font:minor-latin'>p</span></b> is a phase number, <b
     1713style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1714mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1715Calibri;mso-bidi-theme-font:minor-latin'>h</span></b> is a histogram number, <b
     1716style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1717mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1718Calibri;mso-bidi-theme-font:minor-latin'>name</span></b> is the parameter name
    16791719and <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
    16801720style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1681 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Uiso</span></b></span>
    1682 will succeed. GSAS-II constraints will correct the site fractions and <span
    1683 class=SpellE>Uiso</span> values so that they conform to the constraints as
    1684 written. You need not be concerned about their starting values beforehand. Also
    1685 note the way each parameter was named; the general form is <b style='mso-bidi-font-weight:
    1686 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1687 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>p<span
    1688 class=GramE>:h:name:num</span></span></b> where <b style='mso-bidi-font-weight:
    1689 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1690 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>p</span></b>
    1691 is a phase number, <b style='mso-bidi-font-weight:normal'><span
    1692 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1693 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>h</span></b>
    1694 is a histogram number, <b style='mso-bidi-font-weight:normal'><span
    1695 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1696 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>name</span></b>
    1697 is the parameter name and <span class=SpellE><b style='mso-bidi-font-weight:
    1698 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1699 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>num</span></b></span>
    1700 is an optional number (e.g. an atom number).</p>
     1721mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1722minor-latin'>num</span></b></span> is an optional number (e.g. an atom number).</p>
    17011723
    17021724<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
     
    17041726style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Go
    17051727to the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1706 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1707 minor-latin'>Phases/garnet</span></b> item in the <b style='mso-bidi-font-weight:
    1708 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1709 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II
    1710 data tree</span></b> and select the <b style='mso-bidi-font-weight:normal'><span
    1711 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1712 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Atoms</span></b>
     1728mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1729Calibri;mso-bidi-theme-font:minor-latin'>Phases/garnet</span></b> item in the <b
     1730style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1731mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1732Calibri;mso-bidi-theme-font:minor-latin'>GSAS-II data tree</span></b> and
     1733select the <b style='mso-bidi-font-weight:normal'><span style='font-family:
     1734"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1735minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>Atoms</span></b>
    17131736tab. Note the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
    17141737style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1715 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>frac</span></b></span>
    1716 values are unchanged from what you originally entered. Don’t <span class=GramE>worry,</span>
    1717 they will be corrected in the next refinement. We now have to set the
    1718 refinement of <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
    1719 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1720 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>frac</span></b></span>
     1738mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1739minor-latin'>frac</span></b></span> values are unchanged from what you
     1740originally entered. Don’t <span class=GramE>worry,</span> they will be
     1741corrected in the next refinement. We now have to set the refinement of <span
     1742class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
     1743"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1744minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>frac</span></b></span>
    17211745for the Fe/Al sites. There are many ways to do <span class=GramE>this,</span>
    17221746we will show you one method now. Select row <b style='mso-bidi-font-weight:
    17231747normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1724 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>1</span></b>
    1725 for <span class=GramE>Fe(</span>2) and then holding the Ctrl key down select
    1726 rows <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1727 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1728 minor-latin'>2-4</span></b>; they will appear all gray. Next select <b
    1729 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1730 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1731 minor-latin'>Edit/Set atom refinement flags</span></b> from the <b
    1732 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1733 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1748minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1749mso-bidi-theme-font:minor-latin'>1</span></b> for <span class=GramE>Fe(</span>2)
     1750and then holding the Ctrl key down select rows <b style='mso-bidi-font-weight:
     1751normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1752minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1753mso-bidi-theme-font:minor-latin'>2-4</span></b>; they will appear all gray.
     1754Next select <b style='mso-bidi-font-weight:normal'><span style='font-family:
     1755"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1756minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>Edit/Set
     1757atom refinement flags</span></b> from the <b style='mso-bidi-font-weight:normal'><span
     1758style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1759mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    17341760minor-latin'>Atoms</span></b> menu; a new window will appear</p>
    17351761
     
    17441770<p class=MsoListParagraphCxSpMiddle>For now select <b style='mso-bidi-font-weight:
    17451771normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1746 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>F
    1747 – site fraction</span></b>. You could select all <span class=GramE>three,</span>
    1748 GSAS-II would refine <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
    1749 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1750 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>frac</span></b></span>
    1751 &amp; <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
    1752 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1753 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Uiso</span></b></span>
     1772minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1773mso-bidi-theme-font:minor-latin'>F – site fraction</span></b>. You could select
     1774all <span class=GramE>three,</span> GSAS-II would refine <span class=SpellE><b
     1775style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1776mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1777Calibri;mso-bidi-theme-font:minor-latin'>frac</span></b></span> &amp; <span
     1778class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
     1779"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1780minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>Uiso</span></b></span>
    17541781but not the coordinates as they are fixed as special positions in this case.
    17551782The <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1756 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1757 minor-latin'>Atom</span></b> window will have an <b style='mso-bidi-font-weight:
    1758 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1759 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>F</span></b>
    1760 in the refine column each of these atoms.</p>
     1783mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1784Calibri;mso-bidi-theme-font:minor-latin'>Atom</span></b> window will have an <b
     1785style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1786mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1787Calibri;mso-bidi-theme-font:minor-latin'>F</span></b> in the refine column each
     1788of these atoms.</p>
    17611789
    17621790<p class=MsoListParagraphCxSpLast><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    17701798<p class=MsoNormal>You are now ready for your second Rietveld refinement;
    17711799select <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1772 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1773 minor-latin'>Calculate/Refine</span></b> from the GSAS-II data tree window.
    1774 There is now a much better fit with <span class=SpellE>Rwp</span> ~12% and a
    1775 powder pattern that looks like</p>
     1800mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1801Calibri;mso-bidi-theme-font:minor-latin'>Calculate/Refine</span></b> from the
     1802GSAS-II data tree window. There is now a much better fit with <span
     1803class=SpellE>Rwp</span> ~12% and a powder pattern that looks like</p>
    17761804
    17771805<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1778  id="Picture_x0020_17" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:525pt;
     1806 id="Picture_x0020_29" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:525pt;
    17791807 height:450pt;visibility:visible;mso-wrap-style:square'>
    17801808 <v:imagedata src="Neutron%20CW%20Powder%20Data_files/image015.png" o:title=""/>
    17811809</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
    1782 src="Neutron%20CW%20Powder%20Data_files/image015.png" v:shapes="Picture_x0020_17"><![endif]></span></p>
     1810src="Neutron%20CW%20Powder%20Data_files/image015.png" v:shapes="Picture_x0020_29"><![endif]></span></p>
    17831811
    17841812<p class=MsoNormal>There appears to be some differences in peak intensities and
     
    17871815class=GramE>O(</span>xyz) parameters. Go to <b style='mso-bidi-font-weight:
    17881816normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1789 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Phases/garnet</span></b>
    1790 and select the <b style='mso-bidi-font-weight:normal'><span style='font-family:
    1791 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1792 minor-latin;mso-bidi-theme-font:minor-latin'>Atoms</span></b> tab.</p>
     1817minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1818mso-bidi-theme-font:minor-latin'>Phases/garnet</span></b> and select the <b
     1819style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1820mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1821Calibri;mso-bidi-theme-font:minor-latin'>Atoms</span></b> tab.</p>
    17931822
    17941823<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    18011830<p class=MsoNormal>Notice that the <span class=SpellE><b style='mso-bidi-font-weight:
    18021831normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1803 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>frac</span></b></span>
    1804 values for the Fe/Al atoms now conform to the constraints. For each atom in
    1805 turn, double click on the refine box. A pull down list will appear, select <b
    1806 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1807 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1808 minor-latin'>U</span></b> for the Y atom, <b style='mso-bidi-font-weight:normal'><span
    1809 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1810 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>FU</span></b>
    1811 for Fe/Al atoms and <b style='mso-bidi-font-weight:normal'><span
    1812 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1813 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>XU</span></b>
    1814 for the O atom. Your list should look like</p>
     1832minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1833mso-bidi-theme-font:minor-latin'>frac</span></b></span> values for the Fe/Al
     1834atoms now conform to the constraints. For each atom in turn, double click on
     1835the refine box. A pull down list will appear, select <b style='mso-bidi-font-weight:
     1836normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1837minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1838mso-bidi-theme-font:minor-latin'>U</span></b> for the Y atom, <b
     1839style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1840mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1841Calibri;mso-bidi-theme-font:minor-latin'>FU</span></b> for Fe/Al atoms and <b
     1842style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1843mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1844Calibri;mso-bidi-theme-font:minor-latin'>XU</span></b> for the O atom. Your
     1845list should look like</p>
    18151846
    18161847<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    18241855third Rietveld refinement; select <b style='mso-bidi-font-weight:normal'><span
    18251856style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1826 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Calculate/Refine</span></b>.
    1827 The resulting fit is</p>
     1857mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1858minor-latin'>Calculate/Refine</span></b>. The resulting fit is</p>
    18281859
    18291860<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1830  id="Picture_x0020_20" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:525pt;
     1861 id="Picture_x0020_30" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:525pt;
    18311862 height:450pt;visibility:visible;mso-wrap-style:square'>
    18321863 <v:imagedata src="Neutron%20CW%20Powder%20Data_files/image018.png" o:title=""/>
    18331864</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
    1834 src="Neutron%20CW%20Powder%20Data_files/image018.png" v:shapes="Picture_x0020_20"><![endif]></span></p>
     1865src="Neutron%20CW%20Powder%20Data_files/image018.png" v:shapes="Picture_x0020_30"><![endif]></span></p>
    18351866
    18361867<p class=MsoNormal><span class=GramE>with</span> <span class=SpellE>Rwp</span>
     
    18411872found in the <b style='mso-bidi-font-weight:normal'><span style='font-family:
    18421873"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1843 minor-latin;mso-bidi-theme-font:minor-latin'>PWDR <span class=SpellE>garnet.raw</span>:
    1844 BANK1/Instrument Parameters</span></b> window. Go there and select their
    1845 Refine? <span class=GramE>flags</span>. Next go to Sample Parameters.</p>
     1874minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>PWDR <span
     1875class=SpellE>garnet.raw</span>: BANK1/Instrument Parameters</span></b> window.
     1876Go there and select their <b style='mso-bidi-font-weight:normal'><span
     1877style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1878mso-hansi-theme-font:minor-latin'>Refine?</span></b> <span class=GramE>flags</span>.
     1879Next go to <b style='mso-bidi-font-weight:normal'><span style='font-family:
     1880"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1881minor-latin'>Sample Parameters</span></b>.</p>
    18461882
    18471883<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    18551891refined. Now you will want to refine both <b style='mso-bidi-font-weight:normal'><span
    18561892style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1857 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Sample X
    1858 displacement</span></b> and <b style='mso-bidi-font-weight:normal'><span
    1859 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1860 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Sample Y
    1861 displacement</span></b>. The values will be in <span style='font-family:Symbol'>m</span>m
    1862 if the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1863 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1864 minor-latin'>Goniometer radius</span></b> is correct; enter 650 for that value.
    1865 Now you can do another Rietveld refinement; the fit</p>
     1893mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1894minor-latin'>Sample X displacement</span></b> and <b style='mso-bidi-font-weight:
     1895normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1896minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1897mso-bidi-theme-font:minor-latin'>Sample Y displacement</span></b>. The values
     1898will be in <span style='font-family:Symbol'>m</span>m if the <b
     1899style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1900mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1901Calibri;mso-bidi-theme-font:minor-latin'>Goniometer radius</span></b> is
     1902correct; enter 650 for that value. Now you can do another Rietveld refinement;
     1903the fit</p>
    18661904
    18671905<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    18751913class=SpellE>Rwp</span> = 4.87%. You can look at the <span class=SpellE><b
    18761914style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1877 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1878 minor-latin'>YAG.lst</span></b></span> output file for all the parameters and
    1879 their respective <span class=SpellE>esds</span>. I’ve pasted some of my results
    1880 in below for you to compare.</p>
     1915mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1916Calibri;mso-bidi-theme-font:minor-latin'>YAG.lst</span></b></span> output file
     1917for all the parameters and their respective <span class=SpellE>esds</span>.
     1918I’ve pasted some of my results in below for you to compare.</p>
    18811919
    18821920<p class=MsoNormal><span style='font-family:"Courier New"'>Number of function
     
    19011939
    19021940<p class=MsoNormal><span style='font-family:"Courier New"'>Atoms:<span
    1903 style='mso-spacerun:yes'>                                               </span><o:p></o:p></span></p>
     1941style='mso-spacerun:yes'>                                         </span><span
     1942style='mso-spacerun:yes'>      </span><o:p></o:p></span></p>
    19041943
    19051944<p class=MsoNormal><span style='font-family:"Courier New"'><span
     
    19201959<p class=MsoNormal><span style='font-family:"Courier New"'><span
    19211960style='mso-spacerun:yes'> </span><span class=GramE>values</span>:<span
    1922 style='mso-spacerun:yes'>   </span>0.12500 <span
    1923 style='mso-spacerun:yes'>  </span>0.00000<span style='mso-spacerun:yes'>  
    1924 </span>0.25000<span style='mso-spacerun:yes'>   </span>1.000 0.00453<o:p></o:p></span></p>
     1961style='mso-spacerun:yes'>   </span>0.12500<span style='mso-spacerun:yes'>  
     1962</span>0.00000<span style='mso-spacerun:yes'>   </span>0.25000<span
     1963style='mso-spacerun:yes'>   </span>1.000 0.00453<o:p></o:p></span></p>
    19251964
    19261965<p class=MsoNormal><span style='font-family:"Courier New"'><span
    19271966style='mso-spacerun:yes'> </span><span class=GramE>sig</span><span
    19281967style='mso-spacerun:yes'>   </span>:<span
    1929 style='mso-spacerun:yes'>                                       </span>0.00033<o:p></o:p></span></p>
     1968style='mso-spacerun:yes'>                     </span><span
     1969style='mso-spacerun:yes'>                  </span>0.00033<o:p></o:p></span></p>
    19301970
    19311971<p class=MsoNormal><span style='font-family:"Courier New"'><span
     
    19521992<p class=MsoNormal><span style='font-family:"Courier New"'><span
    19531993style='mso-spacerun:yes'> </span><span class=GramE>values</span>:<span
    1954 style='mso-spacerun:yes'>   </span>0.00000<span style='mso-spacerun:yes'>  
     1994style='mso-spacerun:yes'>  </span><span
     1995style='mso-spacerun:yes'> </span>0.00000<span style='mso-spacerun:yes'>  
    19551996</span>0.00000<span style='mso-spacerun:yes'>   </span>0.00000<span
    19561997style='mso-spacerun:yes'>   </span>0.425 0.00347<o:p></o:p></span></p>
     
    19912032style='mso-spacerun:yes'> </span><span class=GramE>sig</span><span
    19922033style='mso-spacerun:yes'>   </span>:<span
    1993 style='mso-spacerun:yes'>                            </span><span
    1994 style='mso-spacerun:yes'>     </span>0.007 0.00069<o:p></o:p></span></p>
     2034style='mso-spacerun:yes'>                                 </span>0.007 0.00069<o:p></o:p></span></p>
    19952035
    19962036<p class=MsoNormal><span style='font-family:"Courier New"'><span
     
    20172057<p class=MsoNormal><span style='font-family:"Courier New"'>Sample
    20182058Parameters:<span
    2019 style='mso-spacerun:yes'>                                                     
    2020 </span><span style='mso-spacerun:yes'>        </span><o:p></o:p></span></p>
     2059style='mso-spacerun:yes'>                                                             
     2060</span><o:p></o:p></span></p>
    20212061
    20222062<p class=MsoNormal><span style='font-family:"Courier New"'><span
     
    20442084
    20452085<p class=MsoNormal><span style='font-family:"Courier New"'><span
    2046 style='mso-spacerun:yes'> </span><span
    2047 style='mso-spacerun:yes'>                                                                               
     2086style='mso-spacerun:yes'>                                                                                
    20482087</span><o:p></o:p></span></p>
    20492088
     
    20642103<p class=MsoNormal><span style='font-family:"Courier New"'><span
    20652104style='mso-spacerun:yes'> </span><span class=GramE>value :</span><span
    2066 style='mso-spacerun:yes'>   </span><span
    2067 style='mso-spacerun:yes'> </span>1.909000<span style='mso-spacerun:yes'>  
     2105style='mso-spacerun:yes'>    </span>1.909000<span style='mso-spacerun:yes'>  
    20682106</span>-0.084918<span style='mso-spacerun:yes'>    </span>0.000000<span
    20692107style='mso-spacerun:yes'>  </span>266.108676 -655.916341<span
     
    20802118<p class=MsoNormal>A useful display to examine is given by selecting <b
    20812119style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    2082 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    2083 minor-latin'>Covariance</span></b> in the GSAS-II data tree</p>
     2120mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     2121Calibri;mso-bidi-theme-font:minor-latin'>Covariance</span></b> in the GSAS-II
     2122data tree</p>
    20842123
    20852124<p class=MsoNormal><span style='font-family:"Courier New";mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    20912130style='font-family:"Courier New"'><o:p></o:p></span></p>
    20922131
    2093 <p class=MsoNormal>This is a graphical rendering of the variance covariance
     2132<p class=MsoNormal>This is a graphical rendering of the variance-covariance
    20942133matrix from the last refinement. This matrix is symmetric about the diagonal;
    20952134moving your cursor about it will display parameter names, values and <span
     
    20992138class=SpellE>covariances</span> naturally occur for profile coefficients and
    21002139for background parameters. You can change the color scheme, the default is <span
    2101 class=SpellE>RdYlGn</span>. If during the course of one of your refinements you
    2102 see white bands in this display: that is the signature of some singularities in
    2103 your refinement. The offending parameter(s) should not be refined
    2104 independently; perhaps a constraint/equivalence is needed.</p>
     2140class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
     2141"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     2142minor-latin'>RdYlGn</span></b></span>. If during the course of one of your
     2143refinements you see white bands in this display: that is the signature of some
     2144singularities in your refinement. The offending parameter(s) should not be
     2145refined independently; perhaps a constraint/equivalence is needed.</p>
    21052146
    21062147</div>
  • trunk/help/Starting GSAS.htm

    r639 r895  
    2323  <o:Author>Von Dreele</o:Author>
    2424  <o:LastAuthor>Von Dreele</o:LastAuthor>
    25   <o:Revision>3</o:Revision>
    26   <o:TotalTime>27</o:TotalTime>
     25  <o:Revision>4</o:Revision>
     26  <o:TotalTime>29</o:TotalTime>
    2727  <o:Created>2012-05-05T14:50:00Z</o:Created>
    28   <o:LastSaved>2012-05-07T20:05:00Z</o:LastSaved>
     28  <o:LastSaved>2013-04-30T19:10:00Z</o:LastSaved>
    2929  <o:Pages>1</o:Pages>
    3030  <o:Words>295</o:Words>
    31   <o:Characters>1685</o:Characters>
     31  <o:Characters>1684</o:Characters>
    3232  <o:Lines>14</o:Lines>
    3333  <o:Paragraphs>3</o:Paragraphs>
    34   <o:CharactersWithSpaces>1977</o:CharactersWithSpaces>
     34  <o:CharactersWithSpaces>1976</o:CharactersWithSpaces>
    3535  <o:Version>14.00</o:Version>
    3636 </o:DocumentProperties>
     
    4242<!--[if gte mso 9]><xml>
    4343 <w:WordDocument>
     44  <w:Zoom>FullPage</w:Zoom>
    4445  <w:SpellingState>Clean</w:SpellingState>
    4546  <w:GrammarState>Clean</w:GrammarState>
     
    348349        mso-generic-font-family:swiss;
    349350        mso-font-pitch:variable;
    350         mso-font-signature:-520092929 1073786111 9 0 415 0;}
     351        mso-font-signature:-536870145 1073786111 1 0 415 0;}
    351352@font-face
    352353        {font-family:Tahoma;
     
    832833        mso-ascii-theme-font:minor-latin;
    833834        mso-hansi-font-family:Calibri;
    834         mso-hansi-theme-font:minor-latin;
    835         mso-bidi-font-family:"Times New Roman";
    836         mso-bidi-theme-font:minor-bidi;}
     835        mso-hansi-theme-font:minor-latin;}
    837836</style>
    838837<![endif]--><!--[if gte mso 9]><xml>
     
    861860<p class=MsoNormal><span class=GramE><b style='mso-bidi-font-weight:normal'><span
    862861style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    863 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>python</span></b></span><b
    864 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    865 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     862mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     863minor-latin'>python</span></b></span><b style='mso-bidi-font-weight:normal'><span
     864style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     865mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    866866minor-latin'> GSASII.py<o:p></o:p></span></b></p>
    867867
    868868<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span
    869869style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    870 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'><o:p>&nbsp;</o:p></span></b></p>
     870mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     871minor-latin'><o:p>&nbsp;</o:p></span></b></p>
    871872
    872873<p class=MsoNormal>This will work if the default python is as described in the
     
    885886in the upper right, is labeled <span class=GSAS-IItextChar><span
    886887style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     888mso-hansi-theme-font:minor-latin'>GSASII data tree</span></span>, the second,
     889immediately under the first is labeled <b style='mso-bidi-font-weight:normal'><span
     890style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    887891mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    888 minor-latin'>GSASII data tree</span></span>, the second, immediately under the
    889 first is labeled <b style='mso-bidi-font-weight:normal'><span style='font-family:
    890 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    891 minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II data display</span></b>
    892 and the third on the left is labeled <b style='mso-bidi-font-weight:normal'><span
    893 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    894 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II Plots</span></b>.
    895 These windows may be moved anywhere on the screen. On Linux and Windows a menu
    896 bar 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
    898 appear in the system menu bar location (usually at the screen top) depending on
    899 which GSAS-II window has the focus. On my Windows machine the screen looked
    900 like</p>
     892minor-latin'>GSAS-II data display</span></b> and the third on the left is
     893labeled <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     894mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     895Calibri;mso-bidi-theme-font:minor-latin'>GSAS-II Plots</span></b>. These
     896windows may be moved anywhere on the screen. On Linux and Windows a menu bar
     897appears at the top of the data tree and data display windows; on a Mac these
     898menus will appear in the system menu bar location (usually at the screen top)
     899depending on which GSAS-II window has the focus. On my Windows machine the
     900screen looked like</p>
    901901
    902902<p class=MsoNormal><o:p>&nbsp;</o:p></p>
  • trunk/help/Starting GSAS_files/filelist.xml

    r600 r895  
    55 <o:File HRef="themedata.thmx"/>
    66 <o:File HRef="colorschememapping.xml"/>
    7  <o:File HRef="image001.png"/>
     7 <o:File HRef="image001.jpg"/>
    88 <o:File HRef="image002.jpg"/>
    99 <o:File HRef="image003.png"/>
  • trunk/help/Starting GSAS_files/props011.xml

    r601 r895  
    11<?xml version="1.0" encoding="UTF-8" standalone="no"?>
    2 <ds:datastoreItem ds:itemID="{A2F73058-FD0F-469A-8BEE-B03300174261}" 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>
     2<ds:datastoreItem ds:itemID="{A0DA2E80-1BB9-4F0C-9FC6-CC6D743B1943}" 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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