Changeset 5333


Ignore:
Timestamp:
Sep 14, 2022 11:12:00 AM (9 months ago)
Author:
vondreele
Message:

finish Cluster Analysis help pages.

Location:
trunk/help
Files:
19 edited

Legend:

Unmodified
Added
Removed

  • trunk/help/gsasII.html

    r5332 r5333  
    2424 <o:DocumentProperties>
    2525  <o:Author>Von Dreele</o:Author>
    26   <o:LastAuthor>Von Dreele, Robert B.</o:LastAuthor>
    27   <o:Revision>222</o:Revision>
    28   <o:TotalTime>7991</o:TotalTime>
     26  <o:LastAuthor>Robert Von Dreele</o:LastAuthor>
     27  <o:Revision>227</o:Revision>
     28  <o:TotalTime>8347</o:TotalTime>
    2929  <o:Created>2011-11-28T16:49:00Z</o:Created>
    30   <o:LastSaved>2022-09-09T19:03:00Z</o:LastSaved>
    31   <o:Pages>43</o:Pages>
    32   <o:Words>17907</o:Words>
    33   <o:Characters>102071</o:Characters>
     30  <o:LastSaved>2022-09-14T16:10:00Z</o:LastSaved>
     31  <o:Pages>1</o:Pages>
     32  <o:Words>18329</o:Words>
     33  <o:Characters>104478</o:Characters>
    3434  <o:Company>Argonne National Laboratory</o:Company>
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    36   <o:Paragraphs>239</o:Paragraphs>
    37   <o:CharactersWithSpaces>119739</o:CharactersWithSpaces>
     35  <o:Lines>870</o:Lines>
     36  <o:Paragraphs>245</o:Paragraphs>
     37  <o:CharactersWithSpaces>122562</o:CharactersWithSpaces>
    3838  <o:Version>16.00</o:Version>
    3939 </o:DocumentProperties>
    … …  
    4242 </o:OfficeDocumentSettings>
    4343</xml><![endif]-->
    44 <link rel=dataStoreItem href="gsasII_files/item0054.xml"
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    5351  <w:TrackFormatting/>
    … …  
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    … …  
    50905091<link href=gsasIIfav.png rel="SHORTCUT ICON">
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    50945095 <o:shapelayout v:ext="edit">
    … …  
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    … …  
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    53325372style='mso-spacerun:yes'> </span>- Shifts the plot to the left, relative to the
    53335373axes </p>
    … …  
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     5468 <o:lock v:ext="edit" aspectratio="t"/>
     5469 <w:wrap type="none"/>
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    53575476
    … …  
    53595478style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
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     5486 mso-top-percent:-10001;mso-position-horizontal:absolute;
     5487 mso-position-horizontal-relative:char;mso-position-vertical:absolute;
     5488 mso-position-vertical-relative:line;mso-left-percent:-10001;mso-top-percent:-10001;
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     5518 <o:lock v:ext="edit" aspectratio="t"/>
     5519 <w:wrap type="none"/>
     5520 <w:anchorlock/>
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    53675525style='mso-spacerun:yes'> </span>- Shifts the plot down, relative to the axes </p>
    53685526
    … …  
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     5531style='mso-element:field-begin;mso-field-lock:yes'></span><span
     5532style='mso-spacerun:yes'> </span>SHAPE <span
     5533style='mso-spacerun:yes'> </span>\* MERGEFORMAT <span style='mso-element:field-separator'></span><![endif]--><!--[if gte vml 1]><v:rect
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     5535 visibility:visible;mso-wrap-style:square;mso-left-percent:-10001;
     5536 mso-top-percent:-10001;mso-position-horizontal:absolute;
     5537 mso-position-horizontal-relative:char;mso-position-vertical:absolute;
     5538 mso-position-vertical-relative:line;mso-left-percent:-10001;mso-top-percent:-10001;
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     5568 <o:lock v:ext="edit" aspectratio="t"/>
     5569 <w:wrap type="none"/>
     5570 <w:anchorlock/>
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    53785575style='mso-spacerun:yes'> </span>- Zooms in on the plot (magnifies) along the
    53795576horizontal (x) direction to show more details. </p>
    … …  
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     5582style='mso-element:field-begin;mso-field-lock:yes'></span><span
     5583style='mso-spacerun:yes'> </span>SHAPE <span
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     5586 visibility:visible;mso-wrap-style:square;mso-left-percent:-10001;
     5587 mso-top-percent:-10001;mso-position-horizontal:absolute;
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     5619 <o:lock v:ext="edit" aspectratio="t"/>
     5620 <w:wrap type="none"/>
     5621 <w:anchorlock/>
     5622</v:rect><![endif]--><!--[if mso & !supportInlineShapes & supportFields]><v:shape
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     5624 <v:imagedata croptop="-65520f" cropbottom="65520f"/>
     5625</v:shape><span style='mso-element:field-end'></span><![endif]--><span
    53905626style='mso-spacerun:yes'> </span>- Zooms out on the plot (demagnifies) along
    53915627the horizontal (x) direction. </p>
    … …  
    53945630style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    53955631Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5396 </span></span></span><![endif]><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
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    5399  <v:imagedata src="gsasII_files/image015.png" o:title=""/>
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    5401 src="gsasII_files/image026.png" v:shapes="Picture_x0020_12"><![endif]></span><span
     5632</span></span></span><![endif]><!--[if mso & !supportInlineShapes & supportFields]><span
     5633style='mso-element:field-begin;mso-field-lock:yes'></span><span
     5634style='mso-spacerun:yes'> </span>SHAPE <span
     5635style='mso-spacerun:yes'> </span>\* MERGEFORMAT <span style='mso-element:field-separator'></span><![endif]--><!--[if gte vml 1]><v:rect
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     5637 visibility:visible;mso-wrap-style:square;mso-left-percent:-10001;
     5638 mso-top-percent:-10001;mso-position-horizontal:absolute;
     5639 mso-position-horizontal-relative:char;mso-position-vertical:absolute;
     5640 mso-position-vertical-relative:line;mso-left-percent:-10001;mso-top-percent:-10001;
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     5667AAAAAAAAAAAAAAAALgIAAGRycy9lMm9Eb2MueG1sUEsBAi0AFAAGAAgAAAAhAIFvbsbZAAAAAwEA
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     5670 <o:lock v:ext="edit" aspectratio="t"/>
     5671 <w:wrap type="none"/>
     5672 <w:anchorlock/>
     5673</v:rect><![endif]--><!--[if mso & !supportInlineShapes & supportFields]><v:shape
     5674 id="_x0000_i1053" type="#_x0000_t75" style='width:12.75pt;height:12.75pt'>
     5675 <v:imagedata croptop="-65520f" cropbottom="65520f"/>
     5676</v:shape><span style='mso-element:field-end'></span><![endif]--><span
    54025677style='mso-spacerun:yes'> </span>- Zooms in on the plot (magnifies) along the
    54035678vertical (y) direction to show more details. </p>
    … …  
    54065681style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    54075682Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5408 </span></span></span><![endif]><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
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    5411  <v:imagedata src="gsasII_files/image017.png" o:title=""/>
    5412 </v:shape><![endif]--><![if !vml]><img border=0 width=17 height=17
    5413 src="gsasII_files/image027.png" v:shapes="Picture_x0020_13"><![endif]></span><span
     5683</span></span></span><![endif]><!--[if mso & !supportInlineShapes & supportFields]><span
     5684style='mso-element:field-begin;mso-field-lock:yes'></span><span
     5685style='mso-spacerun:yes'> </span>SHAPE <span
     5686style='mso-spacerun:yes'> </span>\* MERGEFORMAT <span style='mso-element:field-separator'></span><![endif]--><!--[if gte vml 1]><v:rect
     5687 id="Picture_x0020_13" o:spid="_x0000_s1026" style='width:12.75pt;height:12.75pt;
     5688 visibility:visible;mso-wrap-style:square;mso-left-percent:-10001;
     5689 mso-top-percent:-10001;mso-position-horizontal:absolute;
     5690 mso-position-horizontal-relative:char;mso-position-vertical:absolute;
     5691 mso-position-vertical-relative:line;mso-left-percent:-10001;mso-top-percent:-10001;
     5692 v-text-anchor:top' o:gfxdata="UEsDBBQABgAIAAAAIQC2gziS/gAAAOEBAAATAAAAW0NvbnRlbnRfVHlwZXNdLnhtbJSRQU7DMBBF
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     5721 <o:lock v:ext="edit" aspectratio="t"/>
     5722 <w:wrap type="none"/>
     5723 <w:anchorlock/>
     5724</v:rect><![endif]--><!--[if mso & !supportInlineShapes & supportFields]><v:shape
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     5726 <v:imagedata croptop="-65520f" cropbottom="65520f"/>
     5727</v:shape><span style='mso-element:field-end'></span><![endif]--><span
    54145728style='mso-spacerun:yes'> </span>- Zooms out on the plot (demagnifies) along
    54155729the vertical (y) direction. </p>
    … …  
    542457383-dimensional structure drawings there will be below the toolbar may be a
    54255739status bar that on the left may show either an instruction for a keyed input or
    5426 a pull down selection of keyed input; on the right may be displayed position
    5427 dependent information that is updated as the mouse is moved over the plot
    5428 region.<span style='mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:
    5429 minor-fareast'><o:p></o:p></span></p>
     5740a <span class=GramE>pull down</span> selection of keyed input; on the right may
     5741be displayed position dependent information that is updated as the mouse is
     5742moved over the plot region.<span style='mso-fareast-font-family:"Times New Roman";
     5743mso-fareast-theme-font:minor-fareast'><o:p></o:p></span></p>
    54305744
    54315745<p class=MsoListParagraphCxSpLast><span style='mso-fareast-font-family:"Times New Roman";
    … …  
    54645778<p class=MsoListParagraphCxSpMiddle>Note that as files are saved during a
    54655779structure refinement, copies of the previous version are saved as backup files,
    5466 named as {project}.bak{<i>i</i>}.gpx, where <i>i</i> starts as 0 and is increased
    5467 after each save operation. NB: you may open a backup .gpx file (e.g.
    5468 name.bak3.gpx) to return to a previous version of your project, but if you do
    5469 so, it is best to immediately use the <b'>Save As... menu command (you may wish
    5470 to use name.gpx to overwrite the current version or select a new name.) If you
    5471 forget specify a project name, then name.bak3 will be considered the project
    5472 name and backups will then be named name.bak3.bak0.gpx, etc.</p>
     5780named as {project}.bak{<i>i</i>}.gpx, where <i>i</i> starts as 0 and is
     5781increased after each save operation. NB: you may open a backup .gpx file (<span
     5782class=GramE>e.g.</span> name.bak3.gpx) to return to a previous version of your
     5783project, but if you do so, it is best to immediately use the <b'>Save As...
     5784menu command (you may wish to use name.gpx to overwrite the current version or
     5785select a new name.) If you forget <span class=GramE>specify</span> a project
     5786name, then name.bak3 will be considered the project name and backups will then
     5787be named name.bak3.bak0.gpx, etc.</p>
    54735788
    54745789<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l37 level1 lfo3'><![if !supportLists]><span
    54755790style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    54765791Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5477 </span></span></span><![endif]><b>Save project<span style='mso-spacerun:yes'> 
    5478 </span>- </b>Save the current project. If this is a new project that has not
    5479 yet been saved, you will be prompted for a new name in a file dialog (you may
    5480 optionally change the directory in that dialog). If the file exists, you will
    5481 be asked if it is OK to overwrite it. Once a file name has been used to read or
    5482 save a project, the name is shown after ‘Loaded Data:’ in the first item in the
    5483 data tree. </p>
     5792</span></span></span><![endif]><b>Save <span class=GramE>project<span
     5793style='mso-spacerun:yes'>  </span>-</span> </b>Save the current project. If
     5794this is a new project that has not yet been saved, you will be prompted for a
     5795new name in a file dialog (you may optionally change the directory in that
     5796dialog). If the file exists, you will be asked if it is OK to overwrite it.
     5797Once a file name has been used to read or save a project, the name is shown
     5798after ‘Loaded Data:’ in the first item in the data tree. </p>
    54845799
    54855800<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l37 level1 lfo3'><![if !supportLists]><span
    … …  
    54965811style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    54975812Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5498 </span></span></span><![endif]><b>New Project<span style='mso-spacerun:yes'> 
    5499 </span>- </b>Discards any changes made to the current project since the last
    5500 save and creates a new empty project. </p>
     5813</span></span></span><![endif]><b>New <span class=GramE>Project<span
     5814style='mso-spacerun:yes'>  </span>-</span> </b>Discards any changes made to the
     5815current project since the last save and creates a new empty project. </p>
    55015816
    55025817<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l37 level1 lfo3'><![if !supportLists]><span
    55035818style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    55045819Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5505 </span></span></span><![endif]><b>Preferences<span style='mso-spacerun:yes'> 
    5506 </span>- </b>Provides access to GSAS-II configuration settings, as described in
    5507 the <a href="#Preferences">Configuration Variables</a> section. </p>
     5820</span></span></span><![endif]><span class=GramE><b>Preferences<span
     5821style='mso-spacerun:yes'>  </span>-</b></span><b> </b>Provides access to
     5822GSAS-II configuration settings, as described in the <a href="#Preferences">Configuration
     5823Variables</a> section. </p>
    55085824
    55095825<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l37 level1 lfo3'><![if !supportLists]><span
    … …  
    55225838style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    55235839Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5524 </span></span></span><![endif]><b>wx.inspection tool - </b>Debugging tool.</p>
     5840</span></span></span><![endif]><span class=GramE><b>wx.inspection</b></span><b>
     5841tool - </b>Debugging tool.</p>
    55255842
    55265843<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l37 level1 lfo3'><![if !supportLists]><span
    55275844style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    55285845Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5529 </span></span></span><![endif]><b>Quit<span style='mso-spacerun:yes'>  </span>-
    5530 </b>Exit the GSAS-II program. You will be asked if the project should be saved
    5531 or not (Cancel aborts the quit). You can also exit GSAS-II by pressing the red
    5532 X in the upper right (Windows) or left (Mac). Pressing the red X on the console
    5533 will kill the GSAS-II run without any save.</p>
     5846</span></span></span><![endif]><span class=GramE><b>Quit<span
     5847style='mso-spacerun:yes'>  </span>-</b></span><b> </b>Exit the GSAS-II program.
     5848You will be asked if the project should be saved or not (Cancel aborts the
     5849quit). You can also exit GSAS-II by pressing the red X in the upper right
     5850(Windows) or left (Mac). Pressing the red X on the console will kill the
     5851GSAS-II run without any save.</p>
    55345852
    55355853<p class=MsoListParagraphCxSpMiddle style='margin-left:.25in;mso-add-space:
    … …  
    55835901
    55845902<p class=MsoListParagraphCxSpMiddle>Note that nonstandard space group symbols
    5585 are permitted; space group names must have spaces between the axial fields
    5586 (e.g. use ‘P n a 21’ not ‘Pna21’). </p>
     5903are permitted; space group names must have spaces between the axial fields (<span
     5904class=GramE>e.g.</span> use ‘P n a 21’ not ‘Pna21’). </p>
    55875905
    55885906<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l38 level1 lfo4'><![if !supportLists]><span
    … …  
    55975915Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    55985916</span></span></span><![endif]><b>Rename tree entry - </b>Rename a histogram
    5599 entry. This should only be done before the histogram is used in any phases:
    5600 e.g. only rename data immediately after reading. </p>
     5917entry. This should only be done before the histogram is used in any phases: <span
     5918class=GramE>e.g.</span> only rename data immediately after reading. </p>
    56015919
    56025920<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l38 level1 lfo4'><![if !supportLists]><span
    … …  
    56045922Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    56055923</span></span></span><![endif]><b>Delete data entries - </b>This will remove a
    5606 data (e.g. PWDR) item from the data tree. A dialog box with a list of choices
    5607 for histograms is presented; it has filter capability to ease this process. Be
    5608 sure to remove histograms from all phases before deleting them from the tree. </p>
     5924data (<span class=GramE>e.g.</span> PWDR) item from the data tree. A dialog box
     5925with a list of choices for histograms is presented; it has filter capability to
     5926ease this process. Be sure to remove histograms from all phases before deleting
     5927them from the tree. </p>
    56095928
    56105929<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l38 level1 lfo4'><![if !supportLists]><span
    … …  
    56635982
    56645983<p class=MsoListParagraphCxSpMiddle>Note that for atom positions, the
    5665 coordinate values (named as ‘p::A<i>w</i>:n’, where p is the phase number, n is
    5666 the atom number and <i>w</i> is x, y or z) is not a refinable parameter, but
    5667 the shift in the value is. The refined parameters are ‘p::A<i>w</i>:n’. The
    5668 reason this is done is that by treating an atom position as x+dx,y+dy,z+dz
    5669 where the “d” values indicate shifts from the starting position and the shifts
    5670 are refined rather than the x,y, or z values is that this simplifies symmetry
     5984coordinate values (named as ‘<span class=GramE>p::</span>A<i>w</i>:n’, where p
     5985is the phase number, n is the atom number and <i>w</i> is x, y or z) is not a
     5986refinable parameter, but the shift in the value is. The refined parameters are
     5987‘<span class=GramE>p::</span>A<i>w</i>:n’. The reason this is done is that by
     5988treating an atom position as x+<span class=GramE>dx,y</span>+dy,z+dz where the
     5989“d” values indicate shifts from the starting position and the shifts are
     5990refined rather than the x,y, or z values is that this simplifies symmetry
    56715991constraints. As an example, suppose we have an atom on a symmetry constrained
    5672 site, x,1/2-x,z. The process needed to define this constraint, so that if x
    5673 moves positively y has to move negatively by the same amount would be messy.
    5674 With refinement of shifts, all we need to do is constrain dy (‘0::dAy:n’) to be
    5675 equal to -dx (-1*‘0::dAx:n’). </p>
     5992site, x,1/2-<span class=GramE>x,z.</span> The process needed to define this
     5993constraint, so that if x moves positively y <span class=GramE>has to</span> move
     5994negatively by the same amount would be messy. With refinement of shifts, all we
     5995need to do is constrain dy (‘<span class=GramE>0::</span>dAy:n’) to be equal to
     5996-dx (-1*‘0::dAx:n’). </p>
    56765997
    56775998<p class=MsoListParagraphCxSpMiddle>Press the window exit button to exit this
    … …  
    56846005</span></span></span><![endif]><b>Refine/Sequential refine - </b>This performs
    56856006the refinement (Pawley/Rietveld or single crystal) according to the controls
    5686 set in the <b><a href="#Controls">Controls</a></b> data tree item. This menu item
    5687 name will reflect the choice of doing a sequential refinement selected in the <b><a
    5688 href="#Controls">Controls</a></b> data tree item.</p>
     6007set in the <b><a href="#Controls">Controls</a></b> data tree item. This menu
     6008item name will reflect the choice of doing a sequential refinement selected in
     6009the <b><a href="#Controls">Controls</a></b> data tree item.</p>
    56896010
    56906011<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l2 level1 lfo5'><![if !supportLists]><span
    … …  
    56946015refinement where the contributions from each phase (phase partial intensities)
    56956016are written for each histogram and each phase in that histogram into a single
    5696 file named <tt><i><span style='font-size:10.0pt'>project</span></i></tt><tt><span
    5697 style='font-size:10.0pt'>.partials</span></tt> where <tt><i><span
     6017file named <span class=GramE><tt><i><span style='font-size:10.0pt'>project</span></i></tt><tt><span
     6018style='font-size:10.0pt'>.partials</span></tt></span> where <tt><i><span
    56986019style='font-size:10.0pt'>project</span></i></tt> is the GSAS-II project (.gpx)
    56996020name. This file is intended for internal use in GSAS-II and will be deleted if
    57006021additional refinements are performed (making the information in them obsolete;
    5701 use this menu command to recreate them if needed.) When the <tt><span
    5702 style='font-size:10.0pt'>.partials</span></tt> file is created, the user can
    5703 optionally choose to export the intensity information in a series of ASCII
     6022use this menu command to recreate them if needed.) When <span class=GramE>the <tt><span
     6023style='font-size:10.0pt'>.partials</span></tt></span> file is created, the user
     6024can optionally choose to export the intensity information in a series of ASCII
    57046025files named <tt><i><span style='font-size:10.0pt'>prefix</span></i></tt><tt><span
    57056026style='font-size:10.0pt'>_part_</span></tt><i>N</i><tt><span style='font-size:
    … …  
    57536074import of data. Each entry when selected with the mouse shows further submenus
    57546075with specific imports that are available. Any of these files can be accessed
    5755 from a zip file. GSAS-II can read many different image file formats including
    5756 MAR345 files, Quantum ADSC files, and tiff files from Perkin-Elmer, Pilatus,
    5757 and GE. Although many of these formats have data fields that should contain
    5758 relevant information for the exposure (e.g. wavelength), these are rarely
    5759 filled in correctly by the data acquisition software. Thus, you should have
    5760 separately noted this information as it will be needed. In some cases, this
    5761 information may be in a separate “metadata” file; GSAS-II will look for this
    5762 and attempt to open it as well as the image file. <br>
     6076from a zip file. GSAS-II can read many different <span class=GramE>image</span>
     6077file formats including MAR345 files, Quantum ADSC files, and tiff files from
     6078Perkin-Elmer, Pilatus, and GE. Although many of these formats have data fields
     6079that should contain relevant information for the exposure (<span class=GramE>e.g.</span>
     6080wavelength), these are rarely filled in correctly by the data acquisition
     6081software. Thus, you should have separately noted this information as it will be
     6082needed. In some cases, this information may be in a separate “metadata” file;
     6083GSAS-II will look for this and attempt to open it as well as the image file. <br>
    57636084NB: gain maps can be imported but they must be 1000*the gain value (typically
    57646085~1) as integers; if used, GSAS-II will rescale the gain map by 1/1000 and apply
    … …  
    57766097style='font-family:"Courier New";mso-fareast-font-family:"Courier New"'><span
    57776098style='mso-list:Ignore'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
    5778 </span></span></span><![endif]><b>GSAS .EXP</b> - This reads one phase from a
    5779 (old) gsas experiment file (name.EXP). The file name is found in a directory
    5780 dialog; you can change directories as needed. Only .EXP (or .exp) file names
    5781 are shown. If the selected file has more than one phase, a dialog is shown with
    5782 the choices; only one can be chosen. If you want more than one, redo this
    5783 command. After selecting a phase, a dialog box is shown with the proposed phase
    5784 name. You can change it if desired. </p>
     6099</span></span></span><![endif]><span class=GramE><b>GSAS .EXP</b></span> - This
     6100reads one phase from a (old) gsas experiment file (name.EXP). The file name is
     6101found in a directory dialog; you can change directories as needed. <span
     6102class=GramE>Only .EXP</span> (or .exp) file names are shown. If the selected
     6103file has more than one phase, a dialog is shown with the <span class=GramE>choices;</span>
     6104only one can be chosen. If you want more than one, redo this command. After
     6105selecting a phase, a dialog box is shown with the proposed phase name. You can
     6106change it if desired. </p>
    57856107
    57866108<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    … …  
    57916113phase information from a Protein Data Base file (name.PDB or name.ENT). The
    57926114file name is found in a directory dialog; you can change directories as needed.
    5793 Only .PDB (or .pdb) or .ENT (or .ent) file names are shown. Be careful that the
    5794 space group symbol on the ‘CRYST1’ record in the PDB file follows the GSAS-II
    5795 conventions (e.g. with spaces between axial fields). A dialog box is shown with
    5796 the proposed phase name. You can change it if desired. </p>
     6115Only .PDB (or .pdb) <span class=GramE>or .ENT</span> (or .ent) file names are
     6116shown. Be careful that the space group symbol on the ‘CRYST1’ record in the PDB
     6117file follows the GSAS-II conventions (<span class=GramE>e.g.</span> with spaces
     6118between axial fields). A dialog box is shown with the proposed phase name. You
     6119can change it if desired. </p>
    57976120
    57986121<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    … …  
    58016124style='mso-list:Ignore'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
    58026125</span></span></span><![endif]><b>CIF file</b> - This reads one phase from a
    5803 Crystallographic Information File ({name}.CIF (or .cif). The file name is found
    5804 in a directory dialog; you can change directories as needed. If the selected
    5805 file has more than one phase, a dialog is shown with the choices; only one can
    5806 be chosen. If you want more than one, redo this command. After selecting a
    5807 phase, a dialog box is shown with the proposed phase name. You can change it if
    5808 desired. </p>
     6126Crystallographic Information File ({name<span class=GramE>}.CIF</span> (or
     6127.cif). The file name is found in a directory dialog; you can change directories
     6128as needed. If the selected file has more than one phase, a dialog is shown with
     6129the <span class=GramE>choices;</span> only one can be chosen. If you want more
     6130than one, redo this command. After selecting a phase, a dialog box is shown
     6131with the proposed phase name. You can change it if desired. </p>
    58096132
    58106133<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    … …  
    58416164data set, such as data type, calibration constants (such as wavelength) and
    58426165default profile parameters are read from a separate file, either a (old) GSAS
    5843 instrument parameter file (usually .prm, .ins or .inst extension) or a new
    5844 GSAS-II .instparm file. <span style='mso-fareast-font-family:"Times New Roman";
    5845 mso-fareast-theme-font:minor-fareast'><o:p></o:p></span></p>
     6166instrument parameter file (<span class=GramE>usually .prm</span>, .ins or .inst
     6167extension) or a new GSAS-II .instparm file. <span style='mso-fareast-font-family:
     6168"Times New Roman";mso-fareast-theme-font:minor-fareast'><o:p></o:p></span></p>
    58466169
    58476170<p class=MsoListParagraphCxSpMiddle>Note that it is possible to apply
    58486171corrections to the 2-theta, intensity or weight values by adding a Python
    5849 command(s) to the instrument (.instprm) parameter with a variable named
    5850 CorrectionCode. See the <tt><span style='font-size:10.0pt'>CorrectionCode.instprm.sample</span></tt>
     6172command(s) to the instrument <span class=GramE>(.instprm</span>) parameter with
     6173a variable named CorrectionCode. See the <tt><span style='font-size:10.0pt'>CorrectionCode.instprm.sample</span></tt>
    58516174file provided in the GSAS-II source directory for an example of how this is
    58526175done. <span style='mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:
    … …  
    58586181style='mso-list:Ignore'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
    58596182</span></span></span><![endif]><b>CIF file</b> - This reads one powder pattern
    5860 (histogram) from a Crystallographic Information File ({name}.CIF). The file
    5861 name is found in a directory dialog; you can change directories as needed. Only
    5862 one .cif can be chosen. If you want more than one, redo this command. </p>
     6183(histogram) from a Crystallographic Information File ({name<span class=GramE>}.CIF</span>).
     6184The file name is found in a directory dialog; you can change directories as
     6185needed. Only <span class=GramE>one .cif</span> can be chosen. If you want more
     6186than one, redo this command. </p>
    58636187
    58646188<p class=MsoListParagraphCxSpMiddle style='margin-left:.75in;mso-add-space:
    … …  
    58786202</span></span></span><![endif]><b>GSAS .fxye files</b> - This reads powder
    58796203patterns (histograms) from the defined GSAS format powder data files. GSAS file
    5880 types STD, ESD, FXY and FXYE are recognized. Neutron TOF data with a ‘TIME-MAP’
    5881 are also recognized. The file names are found in a directory dialog; you can
    5882 change directories as needed. If the selected files have more than one powder
    5883 pattern, a dialog is shown with the choice(s). </p>
     6204<span class=GramE>types</span> STD, ESD, FXY and FXYE are recognized. Neutron
     6205TOF data with a ‘TIME-MAP’ are also recognized. The file names are found in a
     6206directory dialog; you can change directories as needed. If the selected files
     6207have more than one powder pattern, a dialog is shown with the choice(s). </p>
    58846208
    58856209<p class=MsoListParagraphCxSpMiddle style='margin-left:.75in;mso-add-space:
    … …  
    59046228style='font-family:"Courier New";mso-fareast-font-family:"Courier New"'><span
    59056229style='mso-list:Ignore'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
    5906 </span></span></span><![endif]><i>other supported formats</i> – Bruker .RAW;
    5907 FullProf .dat; Panalytical .xrdml; Comma-separated .csv; Rigaku .ras &amp; .txt
    5908 </p>
     6230</span></span></span><![endif]><i>other supported formats</i> – <span
     6231class=GramE>Bruker .RAW</span>; FullProf .dat; Panalytical .xrdml;
     6232Comma-separated .csv; Rigaku .ras &amp; .txt </p>
    59096233
    59106234<p class=MsoNormal style='text-indent:.5in'>Other formats that are supported,
    … …  
    59246248histogram with all zero intensity values in it using a set of instrument
    59256249parameters that are read in from a file or one of the default sets provided
    5926 when Cancel is pressed at the prompt to select a file. The user is able to
    5927 specify the data range and step size. One or more crystalline phases must also
    5928 be provided to perform a crystallographic simulation. When the
    5929 &quot;Refine&quot; menu command is initially used, the intensities are computed
    5930 from these phases and the &quot;observed&quot; intensity values are set from
    5931 these computed values, with superimposed &quot;random&quot; noise added based
    5932 on the calculated values as σ=sqrt(I) (increase the histogram scale factor to
    5933 change this, if desired). Further refinements can then be used to fit to these
    5934 simulated data. To reset the &quot;observed&quot; intensity values back to
    5935 zero, to recompute them, use the &quot;Edit range&quot; button on the
    5936 &quot;PWDR&quot; tree item that is created by this option. </p>
     6250when Cancel is pressed at the prompt to select a file. The user <span
     6251class=GramE>is able to</span> specify the data range and step size. One or more
     6252crystalline phases must also be provided to perform a crystallographic
     6253simulation. When the &quot;Refine&quot; menu command is initially used, the
     6254intensities are computed from these phases and the &quot;observed&quot;
     6255intensity values are set from these computed values, with superimposed
     6256&quot;random&quot; noise added based on the calculated values as σ=sqrt(I)
     6257(increase the histogram scale factor to change this, if desired). Further
     6258refinements can then be used to fit to these simulated data. To reset the
     6259&quot;observed&quot; intensity values back to zero, to recompute them, use the
     6260&quot;Edit range&quot; button on the &quot;PWDR&quot; tree item that is created
     6261by this option. </p>
    59376262
    59386263<p class=MsoListParagraphCxSpMiddle style='margin-left:.75in;mso-add-space:
    … …  
    59446269file extension must determine the importer that will be used and a filter
    59456270pattern is specified to determine which files will be read (e.g. use &quot;<tt><span
    5946 style='font-size:10.0pt'>*June23*.fxye</span></tt>&quot; so that only files
    5947 that contain the string &quot;June23&quot; will be read. </p>
     6271style='font-size:10.0pt'>*June23<span class=GramE>*.fxye</span></span></tt>&quot;
     6272so that only files that contain the string &quot;June23&quot; will be read. </p>
    59486273
    59496274<p class=MsoListParagraphCxSpMiddle style='margin-left:.75in;mso-add-space:
    … …  
    59556280fundamental parameters that describe a constant wavelength (most likely
    59566281Bragg-Brentano) powder diffraction instrument. The user must first specify the
    5957 data range to be used and then a set of FP (fundamental parameter) values. The
    5958 FP values and a source spectrum can be supplied using a nomenclature similar to
    5959 Topas (described further below). They will then be converted to the SI units
    5960 and parameter names used in the NIST FPA code. Alternately a file can be
    5961 supplied with the parameter values used directly in that program. With this
    5962 input, a series of peaks are computed across the specified data range and the <a
     6282data range to be used and then a set of <span class=GramE>FP</span>
     6283(fundamental parameter) values. The FP values and a source spectrum can be
     6284supplied using a nomenclature <span class=GramE>similar to</span> Topas
     6285(described further below). They will then be converted to the SI units and
     6286parameter names used in the NIST FPA code. Alternately a file can be supplied
     6287with the parameter values used directly in that program. With this input, a
     6288series of peaks are computed across the specified data range and the <a
    59636289href="gsasII-pwdr.html#PWDR_Instrument_Parameters">Instrumental Parameters</a>
    59646290that determine the instrumental profile (U, V, W, X, Y and SH/L) are determined
    … …  
    60996425  mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt;
    61006426  mso-border-alt:solid windowtext .5pt;padding:0in 5.4pt 0in 5.4pt'>
    6101   <p class=MsoNormal>Illuminated sample length in axial direction. Typically
    6102   the same as filament_length.</p>
     6427  <p class=MsoNormal>Illuminated sample length in axial direction. <span
     6428  class=GramE>Typically</span> the same as filament_length.</p>
    61036429  </td>
    61046430 </tr>
    … …  
    61196445  mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt;
    61206446  mso-border-alt:solid windowtext .5pt;padding:0in 5.4pt 0in 5.4pt'>
    6121   <p class=MsoNormal>Length of the receiving slit in axial direction. Typically
    6122   the same as filament_length.</p>
     6447  <p class=MsoNormal>Length of the receiving slit in axial direction. <span
     6448  class=GramE>Typically</span> the same as filament_length.</p>
    61236449  </td>
    61246450 </tr>
    … …  
    61336459  mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt;
    61346460  mso-border-alt:solid windowtext .5pt;padding:0in 5.4pt 0in 5.4pt'>
    6135   <p class=MsoNormal>cm<sup>-1</sup></p>
     6461  <p class=MsoNormal><span class=GramE>cm<sup>-1</sup></span></p>
    61366462  </td>
    61376463  <td width=354 valign=top style='width:265.6pt;border-top:none;border-left:
    … …  
    64316757  mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt;
    64326758  mso-border-alt:solid windowtext .5pt;padding:0in 5.4pt 0in 5.4pt'>
    6433   <p class=MsoNormal>Width of transition region from high-intensity, roughly flat
    6434   region of the x-ray tube output to the to the tube tails region as a fraction
    6435   of the IBM bandwidth</p>
     6759  <p class=MsoNormal>Width of transition region from high-intensity, roughly
     6760  flat region of the x-ray tube output to the to the tube tails region as a
     6761  fraction of the IBM bandwidth</p>
    64366762  </td>
    64376763 </tr>
    … …  
    64826808</div>
    64836809
    6484 <p class=MsoNormal style='margin-left:.75in'><span style='color:white;
    6485 mso-color-alt:windowtext'>If you use this, please cite M.H. Mendenhall, K.
    6486 Mullen &amp; J.P. Cline (2015), </span><i>J. Res. of NIST</i>, <b>120</b>,
     6810<p class=MsoNormal style='margin-left:.75in'>If you use this, please cite M.H.
     6811Mendenhall, K. Mullen &amp; J.P. Cline (2015), <i>J. Res. of NIST</i>, <b>120</b>,
    64876812p223. DOI: 10.6028/jres.120.014. If the incident beam monochromator model is
    64886813used, please also cite: M.H. Mendenhall, D. Black &amp; J.P. Cline (2019), <i>J.
    … …  
    64956820style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    64966821Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    6497 </span></span></span><![endif]><b>Structure Factor</b> - Reads single crystal input
    6498 from a variety of file types. Results are placed in the GSAS-II data tree as
    6499 ‘HKLF file name’ </p>
     6822</span></span></span><![endif]><b>Structure Factor</b> - Reads single crystal
     6823input from a variety of file types. Results are placed in the GSAS-II data tree
     6824as ‘HKLF file name’ </p>
    65006825
    65016826<p class=MsoListParagraphCxSpMiddle style='margin-left:.75in;mso-add-space:
    … …  
    65036828style='font-family:"Courier New";mso-fareast-font-family:"Courier New"'><span
    65046829style='mso-list:Ignore'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
    6505 </span></span></span><![endif]><b>F**2 HKL file</b> - This reads squared
    6506 structure factors (as F**2) and sig(F**2) from a SHELX format .hkl file. The
    6507 file names are found in a directory dialog; you can change directories as
    6508 needed. You must know the file contains structure factors (as F**2) as the file
    6509 itself has no internal indication of this. </p>
     6830</span></span></span><![endif]><b>F**2 HKL file</b> - <span class=GramE>This
     6831reads</span> squared structure factors (as F**2) and sig(F**2) from a SHELX
     6832format .hkl file. The file names are found in a directory dialog; you can
     6833change directories as needed. You must know the file contains structure factors
     6834(as F**2) as the file itself has no internal indication of this. </p>
    65106835
    65116836<p class=MsoListParagraphCxSpMiddle style='margin-left:.75in;mso-add-space:
    … …  
    65246849style='mso-list:Ignore'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
    65256850</span></span></span><![endif]><b>CIF file</b> - This reads structure factors
    6526 (as F**2 or F) and sig(F**2 or F) from a .CIF (or .cif) or .FCF (or .fcf)
    6527 format file. The file names are found in a directory dialog; you can change
    6528 directories as needed. The internal structure of this file indicates in which
    6529 form the structure factors are used. </p>
     6851(as F**2 or F) and <span class=GramE>sig(</span>F**2 or F) from a .CIF (or
     6852.cif) or .FCF (or .fcf) format file. The file names are found in a directory
     6853dialog; you can change directories as needed. The internal structure of this
     6854file indicates in which form the structure factors are used. </p>
    65306855
    65316856<p class=MsoListParagraphCxSpLast style='margin-left:.75in;mso-add-space:auto;
    … …  
    65356860</span></span></span><![endif]><b>guess format from file</b> - This attempts to
    65366861read one data set from a file trying the formats as described above. However,
    6537 since it cannot be determined if SHELX format .hkl contains F or F**2 values,
    6538 do not use this command for those files. On occasion, this command may not
    6539 succeed in correctly determining a file format. If it fails, retry by selecting
    6540 the correct format from the list.</p>
     6862since it cannot be determined if SHELX <span class=GramE>format .hkl</span>
     6863contains F or F**2 values, do not use this command for those files. On
     6864occasion, this command may not succeed in correctly determining a file format.
     6865If it fails, retry by selecting the correct format from the list.</p>
    65416866
    65426867<p class=MsoNormal style='margin-left:.25in;text-indent:.25in'>There are
    … …  
    66416966style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    66426967Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    6643 </span></span></span><![endif]><b>Single crystal data as</b> - Single crystal
    6644 reflection lists can be exported as text files or as a simplified CIF file that
    6645 contains only structure factors. </p>
     6968</span></span></span><![endif]><b>Single crystal data as</b> - Single crystal reflection
     6969lists can be exported as text files or as a simplified CIF file that contains
     6970only structure factors. </p>
    66466971
    66476972<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l30 level1 lfo14'><![if !supportLists]><span
    66486973style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    66496974Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    6650 </span></span></span><![endif]><b>Image data</b> - This exports selected images
    6651 as a portable networks graphics format (PNG) file. Alternately, the image
    6652 controls and masks can be written for selected images. If strain analysis has
    6653 been performed on images, the results can also be exported here as a
    6654 spreadsheet (.csv file). </p>
     6975</span></span></span><![endif]><b>Image data</b> - <span class=GramE>This
     6976exports</span> selected images as a portable networks graphics format (PNG)
     6977file. Alternately, the image controls and masks can be written for selected
     6978images. If strain analysis has been performed on images, the results can also
     6979be exported here as a spreadsheet (.csv file). </p>
    66556980
    66566981<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l30 level1 lfo14'><![if !supportLists]><span
    … …  
    66867011</span></span></span><![endif]><b>Export PDF...</b> - This allows computed PDFs
    66877012peak lists from selected histograms to be written as two simple text files,
    6688 {name}.gr and {name}.sq, containing g(r) and s(q), respectively as 2 columns of
    6689 data; a header on each indicated the source file name and the column headings.
    6690 The file name comes from the PDF entry in the GSAS-II data tree. </p>
     7013{name}.gr and {name<span class=GramE>}.sq</span>, containing g(r) and s(q),
     7014respectively as 2 columns of data; a header on each indicated the source file
     7015name and the column headings. The file name comes from the PDF entry in the
     7016GSAS-II data tree. </p>
    66917017
    66927018<div class=MsoNormal align=center style='text-align:center'><span
    … …  
    67147040project.lst file after a refinement completes (it will contain refinement
    67157041results with residuals, new values &amp; esds) and paste it into this Notebook
    6716 window so it becomes a part of your project file. Some GSAS-II operations
    6717 (e.g., structure refinement &amp; fourier map calculation) will add entries to
    6718 the notebook.</p>
     7042window so it becomes a part of your project file. Some GSAS-II operations (e.g.,
     7043structure refinement &amp; fourier map calculation) will add entries to the
     7044notebook.</p>
    67197045
    67207046<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
    … …  
    67657091style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>analytic
    67667092Jacobian: This uses a numpy-provided <i>leastsq</i> minimizer, which not
    6767 applicable for problem with a large number of histograms as it requires much
    6768 more memory than the Hessian routines. This because it creates a Jacobian
    6769 matrix (J) that is shaped N x M (N parameters x M observations) while the
    6770 Hessian method create a Jacobian matrix only for each histogram; the N x N
    6771 Hessian is the made from summing the J x J<sup>T</sup> products across the
    6772 histograms</p>
     7093applicable for problem with <span class=GramE>a large number of</span>
     7094histograms as it requires much more memory than the Hessian routines. This
     7095because it creates a Jacobian matrix (J) that is shaped N x M (N parameters x M
     7096observations) while the Hessian method create a Jacobian matrix only for each
     7097histogram; the N x N Hessian is the made from summing the J x J<sup>T</sup>
     7098products across the histograms</p>
    67737099
    67747100<p class=MsoListParagraphCxSpMiddle style='margin-left:.75in;mso-add-space:
    … …  
    68017127from Numerical Recipes (Press, Flannery, Teulosky &amp; Vetterling) for the
    68027128Levenberg-Marquardt algorithm. The lmdif and lmder routines were written by
    6803 Burton S. Garbow, Kenneth E. Hillstrom, Jorge J. More (Argonne National Laboratory,
    6804 1980). </p>
     7129Burton S. Garbow, Kenneth E. Hillstrom, Jorge J. More (Argonne National
     7130Laboratory, 1980). </p>
    68057131
    68067132<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l18 level1 lfo17'><![if !supportLists]><span
    … …  
    68287154elements of the Hessian. When λ is large, this down-weights the significance of
    68297155the off-diagonal terms in the Hessian. Thus, when λ is large, the refinement is
    6830 effectively one of steepest-descents, where correlation between variables is
    6831 ignored. Note that steepest-descents minimization is typically slow and may not
    6832 always find the local minimum. This is only used when with the &quot;analytical
    6833 Hessian&quot; minimizer is selected. </p>
     7156effectively one of <span class=GramE>steepest-descents</span>, where
     7157correlation between variables is ignored. Note that steepest-descents
     7158minimization is typically slow and may not always find the local minimum. This
     7159is only used when with the &quot;analytical Hessian&quot; minimizer is
     7160selected. </p>
    68347161
    68357162<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l18 level1 lfo17'><![if !supportLists]><span
    … …  
    68727199style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    68737200Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    6874 </span></span></span><![endif]><b>Min extinct.</b> – Reflections with extinction
    6875 corrections larger than this value are ignored.</p>
     7201</span></span></span><![endif]><b>Min extinct.</b> – Reflections with
     7202extinction corrections larger than this value are ignored.</p>
    68767203
    68777204<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l27 level1 lfo19'><![if !supportLists]><span
    … …  
    68797206Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    68807207</span></span></span><![endif]><b>Max delt-F/sig</b> - Removes reflections that
    6881 are very poorly fit. Should be used only with extreme care, since poorly-fit
    6882 reflections could be an indication that the structure is wrong. </p>
     7208are very poorly fit. Should be used only with extreme care, since <span
     7209class=GramE>poorly-fit</span> reflections could be an indication that the
     7210structure is wrong. </p>
    68837211
    68847212<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l27 level1 lfo19'><![if !supportLists]><span
    … …  
    69217249style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    69227250Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    6923 </span></span></span><![endif]><b>Reverse order?</b> - Normally, in a
    6924 sequential refinement histograms are fit in the order they are in the data tree
    6925 (which can be reordered by dragging tree items), but when this option is
    6926 selected, the sequential fit is performed with the last tree entry first. </p>
     7251</span></span></span><![endif]><b>Reverse order?</b> - Normally, in <span
     7252class=GramE>a sequential refinement histograms</span> are fit in the order they
     7253are in the data tree (which can be reordered by dragging tree items), but when
     7254this option is selected, the sequential fit is performed with the last tree
     7255entry first. </p>
    69277256
    69287257<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l8 level1 lfo20'><![if !supportLists]><span
    … …  
    69497278style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    69507279</span></span><![endif]><b><u>Global Settings</u></b><u>:</u> This is a
    6951 location for parameters that apply to an entire project. At present there is only
    6952 one. <span style='mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:
     7280location for parameters that apply to an entire project. At present there is
     7281only one. <span style='mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:
    69537282minor-fareast'><o:p></o:p></span></p>
    69547283
    … …  
    70307359style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    70317360</span></span></span><![endif]>those pertaining to quantities in each phase
    7032 (naming pattern &quot;<tt><i><span style='font-size:10.0pt'>p</span></i></tt><tt><span
    7033 style='font-size:10.0pt'>::<i>name</i></span></tt>&quot;); examples include
    7034 atom coordinates, thermal motion and site fraction parameters; </p>
     7361(naming pattern &quot;<span class=GramE><tt><i><span style='font-size:10.0pt'>p</span></i></tt><tt><span
     7362style='font-size:10.0pt'>::</span></tt></span><tt><i><span style='font-size:
     736310.0pt'>name</span></i></tt>&quot;); examples include atom coordinates, thermal
     7364motion and site fraction parameters; </p>
    70357365
    70367366<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l26 level1 lfo22;
    … …  
    70427372(naming pattern &quot;:<tt><i><span style='font-size:10.0pt'>h</span></i></tt><tt><span
    70437373style='font-size:10.0pt'>:<i>name</i></span></tt>&quot;); such parameters are
    7044 those that depend only on the data set: the scale factor and profile coefficients
    7045 (e.g. U, V, W, X and Y); </p>
     7374those that depend only on the data set: the scale factor and profile
     7375coefficients (<span class=GramE>e.g.</span> U, V, W, X and Y); </p>
    70467376
    70477377<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l26 level1 lfo22;
    … …  
    70657395style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    70667396Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    7067 </span></span></span><![endif]><b>Holds</b> - Use this to prevent a parameter
    7068 from being refined. Most valuable when refinement of a parameter is selected in
    7069 a group for refinement (such as x, y &amp; z for an atom or unit cell
    7070 parameters) and one must be fixed. For example, if the space group for a phase
    7071 has a polar axis (e.g., the <i>b</i>-axis in P2<sub>1</sub>), then the origin
    7072 with respect to <i>b</i> is arbitrary and it is not possible to refine the y
    7073 coordinates for all atoms. Place a Hold on any one atom y coordinate to keep
    7074 the structure from drifting up or down the y-axis during refinement. </p>
     7397</span></span></span><![endif]><b>Holds</b> - Use this to prevent a parameter from
     7398being refined. Most valuable when refinement of a parameter is selected in a
     7399group for refinement (such as x, y &amp; z for an atom or unit cell parameters)
     7400and one must be fixed. For example, if the space group for a phase has a polar
     7401axis (e.g., the <i>b</i>-axis in P2<sub>1</sub>), then the origin with respect
     7402to <i>b</i> is arbitrary and it is not possible to refine the y coordinates for
     7403all atoms. Place a Hold on any one atom y coordinate to keep the structure from
     7404drifting up or down the y-axis during refinement. </p>
    70757405
    70767406<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l43 level1 lfo23'><![if !supportLists]><span
    … …  
    70827412the actual coordinate values) Examples for typical use are sets of atoms that
    70837413should be constrained to have the same displacement parameters (aka thermal
    7084 motion, Uiso, etc.) or sets of profile coefficients U,V,W across multiple data
    7085 sets. Note that the first selected parameter is treated as independent, and the
    7086 remainder are &quot;slaved&quot; to that parameter as &quot;dependent
    7087 parameters.&quot; All parameters in an equivalence must be varied. If any parameter
    7088 is not varied or is given a &quot;hold,&quot; a warning is displayed and none
    7089 of the parameters are refined. </p>
     7414motion, Uiso, etc.) or sets of profile coefficients <span class=GramE>U,V</span>,W
     7415across multiple data sets. Note that the first selected parameter is treated as
     7416independent, and the remainder are &quot;slaved&quot; to that parameter as
     7417&quot;dependent parameters.&quot; All parameters in an equivalence must be
     7418varied. If any parameter is not varied or is given a &quot;hold,&quot; a
     7419warning is displayed and none of the parameters are refined. </p>
    70907420
    70917421<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l43 level1 lfo23'><![if !supportLists]><span
    … …  
    71067436style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    71077437Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    7108 </span></span></span><![endif]><b>New Var assignment</b> - These are similar to
    7109 constraint equations in that they define a set of parameters and multipliers,
    7110 but rather than specifying a value for the expression, a new parameter is
    7111 assigned to that sum and these constraints have a very different function. This
    7112 replaces a degree of freedom from the original variables with a new one that
    7113 modifies the parameters where the shift is applied according to the ratio
    7114 specified in the expression. This can be used to create new parameters that redefine
    7115 the relationships between items such as coordinates or magnetic moments. The
    7116 new parameter may optionally be named by the user. The new var expression
    7117 creates a new global parameter, where that new parameter is independent, while
    7118 all the parameters in the expression are considered as dependent. The setting
    7119 of the refine flags for the dependent parameters is not used. Only if the new
    7120 var parameter is marked as refine then it will be refined. However, if any
    7121 dependent variable is set as &quot;hold,&quot; the new var parameter will not
    7122 be refined. </p>
     7438</span></span></span><![endif]><b>New Var assignment</b> - These are <span
     7439class=GramE>similar to</span> constraint equations in that they define a set of
     7440parameters and multipliers, but rather than specifying a value for the
     7441expression, a new parameter is assigned to that sum and these constraints have
     7442a very different function. This replaces a degree of freedom from the original
     7443variables with a new one that modifies the parameters where the shift is
     7444applied according to the ratio specified in the expression. This can be used to
     7445create new parameters that redefine the relationships between items such as
     7446coordinates or magnetic moments. The new parameter may optionally be named by
     7447the user. The new var expression creates a new global parameter, where that new
     7448parameter is independent, while all the parameters in the expression are
     7449considered as dependent. The setting of the refine flags for the dependent
     7450parameters is not used. Only if the new var parameter is marked as refine then
     7451it will be refined. However, if any dependent variable is set as
     7452&quot;hold,&quot; the new var parameter will not be refined. </p>
    71237453
    71247454<p class=MsoNormal>Note that when new var and constraint equation constraints
    … …  
    71327462<p class=MsoNormal>New Var constraints are generated when <a
    71337463href="https://iso.byu.edu/iso/isodistort.php">ISODISTORT</a> is used to develop
    7134 mode distortions from a comparison of a high symmetry parent structure (e.g.
    7135 cubic perovskite) with a distorted child substructure. They are developed for
    7136 the phase imported from the special cif file produced by ISODISTORT from a mode
    7137 distortion analysis. </p>
     7464mode distortions from a comparison of a high symmetry parent structure (<span
     7465class=GramE>e.g.</span> cubic perovskite) with a distorted child substructure.
     7466They are developed for the phase imported from the special cif file produced by
     7467ISODISTORT from a mode distortion analysis. </p>
    71387468
    71397469<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
    … …  
    71617491parameters will show as an equation of the form M<sub>1</sub>*P<sub>1</sub>+M<sub>2</sub>*P<sub>2</sub>=0;
    71627492usually M1=1.0 and M2=-1.0 but can be changed via the ‘Edit’ button. The
    7163 equation(s) are shown in the window tagged by ‘EQUIV’ to mark it as an equivalence
    7164 assignment. </p>
     7493equation(s) are shown in the window tagged by ‘EQUIV’ to mark it as an
     7494equivalence assignment. </p>
    71657495
    71667496<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l3 level1 lfo24'><![if !supportLists]><span
    … …  
    72027532normal modes from representational analysis from the coordinates. </p>
    72037533
    7204 <p>In addition to menu commands, this window also offer the following actions
    7205 by pressing buttons:<span style='mso-fareast-font-family:"Times New Roman";
     7534<p>In addition to menu commands, this window also offer the following actions by
     7535pressing buttons:<span style='mso-fareast-font-family:"Times New Roman";
    72067536mso-fareast-theme-font:minor-fareast'><o:p></o:p></span></p>
    72077537
    … …  
    72317561mso-bidi-font-family:Symbol'><span style='mso-list:Ignore'>·<span
    72327562style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    7233 </span></span></span><![endif]><b>Show Generated Constraints</b> - After
    7234 constraints have been processed, a series of relationships are developed to
    7235 determine new variables from the current parameters and &quot;inverse&quot;
    7236 equations that determine dependent parameters from the new variables and
    7237 independent parameters. This shows the resulting relationships, as well as any
     7563</span></span></span><![endif]><b>Show Generated Constraints</b> - After constraints
     7564have been processed, a series of relationships are developed to determine new
     7565variables from the current parameters and &quot;inverse&quot; equations that
     7566determine dependent parameters from the new variables and independent
     7567parameters. This shows the resulting relationships, as well as any
    72387568&quot;Hold&quot; variables. </p>
    72397569
    … …  
    72557585a particular constraint number. When sequential refinement is selected (via the
    72567586<a href="#Controls">Controls tree item</a>), it becomes possible to define
    7257 constraints of form &quot;<tt><i><span style='font-size:10.0pt'>p</span></i></tt>:*:<tt><i><span
     7587constraints of form &quot;<span class=GramE><tt><i><span style='font-size:10.0pt'>p</span></i></tt>:*</span>:<tt><i><span
    72587588style='font-size:10.0pt'>name</span></i></tt>&quot; and &quot;:*:<tt><i><span
    72597589style='font-size:10.0pt'>name</span></i></tt>&quot; (where &quot;<tt><i><span
    … …  
    72847614previously specified with a specific histogram number will be ignored and
    72857615constraints with a &quot;*&quot; where for a histogram number will be used.
    7286 Note that constraints on phase parameters (of form &quot;<tt><i><span
    7287 style='font-size:10.0pt'>p</span></i></tt>::<tt><i><span style='font-size:10.0pt'>name</span></i></tt>&quot;
    7288 -- without a histogram number specified) will be used normally. Note that this
    7289 was the normal operating mode for GSAS-II in earlier versions. </p>
     7616Note that constraints on phase parameters (of form &quot;<span class=GramE><tt><i><span
     7617style='font-size:10.0pt'>p</span></i></tt>::</span><tt><i><span
     7618style='font-size:10.0pt'>name</span></i></tt>&quot; -- without a histogram number
     7619specified) will be used normally. Note that this was the normal operating mode
     7620for GSAS-II in earlier versions. </p>
    72907621
    72917622<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l12 level1 lfo26'><![if !supportLists]><span
    … …  
    73207651style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    73217652Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    7322 </span></span></span><![endif]>Select the tab for the restraint type you wish to
    7323 use. Each will have the same possibilities in the ‘<b style='mso-bidi-font-weight:
     7653</span></span></span><![endif]>Select the tab for the restraint type you wish
     7654to use. Each will have the same possibilities in the ‘<b style='mso-bidi-font-weight:
    73247655normal'>Edit’</b> menu.</p>
    73257656
    … …  
    74647795</span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Add rigid
    74657796body</b> – (Vector rigid bodies) this creates a vector description of a rigid
    7466 body. A dialog box asks the number of atoms (&gt;2) and the number of vectors required
    7467 to create the rigid body. An entry will be created showing a magnitude with the
    7468 vector set to be applied for each vector needed to develop the rigid body.<b
    7469 style='mso-bidi-font-weight:normal'><o:p></o:p></b></p>
     7797body. A dialog box asks the number of atoms (&gt;2) and the number of vectors
     7798required to create the rigid body. An entry will be created showing a magnitude
     7799with the vector set to be applied for each vector needed to develop the rigid
     7800body.<b style='mso-bidi-font-weight:normal'><o:p></o:p></b></p>
    74707801
    74717802<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    … …  
    74757806</span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Import
    74767807XYZ</b> – (Residue rigid bodies) this reads a text file containing a set of
    7477 Cartesian coordinates describing a rigid body model. Each line has atom type
    7478 (e.g. C, Na, etc.) and Cartesian X, Y and Z.</p>
     7808Cartesian coordinates describing a rigid body model. Each line has atom type (<span
     7809class=GramE>e.g.</span> C, Na, etc.) and Cartesian X, Y and Z.</p>
    74797810
    74807811<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    … …  
    75177848has been run. (See the <a href="#Controls">Controls tree item</a> to set the
    75187849histograms to be used in a sequential refinement and use the
    7519 Calculate/Sequential refine menu command to run the refinement.) A number of
    7520 other fitting processes within GSAS-II can be done sequentially, each will have
    7521 its own differently named set of sequential results When any one is selected,
    7522 the window tabulates the sequential refinement results. The columns are the
    7523 parameter names; the naming convention is generally ‘p:h:name:n’ where ‘p’ is
    7524 the phase number,’ h’ is the histogram number, ‘name’ is the parameter name,
    7525 and ‘n’ (if needed) is the item number (e.g. atom number). The rows are the
    7526 data sets used in the sequential refinement.</p>
     7850Calculate/Sequential refine menu command to run the refinement.) <span
     7851class=GramE>A number of</span> other fitting processes within GSAS-II can be
     7852done sequentially, each will have its own differently named set of sequential
     7853results When any one is selected, the window tabulates the sequential
     7854refinement results. The columns are the parameter names; the naming convention
     7855is generally ‘p:h:<span class=GramE>name:n</span>’ where ‘p’ is the phase
     7856number,’ h’ is the histogram number, ‘name’ is the parameter name, and ‘n’ (if
     7857needed) is the item number (e.g. atom number). The rows are the data sets used
     7858in the sequential refinement.</p>
    75277859
    75287860<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
    … …  
    75607892style='font-family:"Courier New";mso-fareast-font-family:"Courier New"'><span
    75617893style='mso-list:Ignore'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
    7562 </span></span></span><![endif]><b>Update phase from row</b> – this updates the
    7563 phase parameters from the entries in the selected row. Normally the phase
    7564 parameters at the end of a sequential fit are those obtained from the last
    7565 histogram.</p>
     7894</span></span></span><![endif]><b>Update phase from row</b> – <span
     7895class=GramE>this updates</span> the phase parameters from the entries in the
     7896selected row. Normally the phase parameters at the end of a sequential fit are
     7897those obtained from the last histogram.</p>
    75667898
    75677899<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    … …  
    76267958Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    76277959</span></span></span><![endif]><span style='mso-bidi-font-weight:bold'>Menu</span>
    7628 ‘<b>Pseudo Vars</b>’ –<span style='mso-bidi-font-weight:bold'> this is used to
    7629 create derived results from sequentially refined parameters; new columns are
    7630 the result.</span></p>
     7960‘<b>Pseudo Vars</b>’ –<span style='mso-bidi-font-weight:bold'> this is used to create
     7961derived results from sequentially refined parameters; new columns are the
     7962result.</span></p>
    76317963
    76327964<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    … …  
    77588090mso-bidi-font-family:Symbol'><span style='mso-list:Ignore'>·<span
    77598091style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    7760 </span></span></span><![endif]>Press ‘l’ – this toggles display of connecting
    7761 lines between the data points</p>
     8092</span></span></span><![endif]>Press ‘l’ – toggles display of connecting lines
     8093between the data points</p>
    77628094
    77638095<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l1 level1 lfo30;
    … …  
    77688100</span></span></span><![endif]>Press ‘s’ – this presents a choice of parameters
    77698101from the table columns to be used for the x-axis. Typically, this is used to
    7770 show parameter variation with e.g. temperature.</p>
     8102show parameter variation with <span class=GramE>e.g.</span> temperature.</p>
    77718103
    77728104<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l1 level1 lfo30;
    … …  
    77878119<p class=MsoNormal>Cluster analysis is a suite of data survey techniques where
    77888120data are grouped by some measure of their similarity. Thus, it can be used as a
    7789 preliminary survey of a large number of data sets in e.g. preparation of
    7790 detailed examination of representative members. In the case of powder
    7791 diffraction pattern (PWDR) data or pair distribution (PDF) data, their
     8121preliminary survey of a large number of data sets in <span class=GramE>e.g.</span>
     8122preparation of detailed examination of representative members. In the case of
     8123powder diffraction pattern (PWDR) data or pair distribution (PDF) data, their
    77928124similarity is determined by considering each pattern as a hyper-dimensional
    77938125vector with one dimension for each data point and then computing some measure
    77948126of how parallel pairs of these vectors are. Consequently, it can be used to
    7795 survey PWDR data entries that have identical scan characteristics (e.g.
    7796 instrument type, step size, radiation type, wavelength) or multiple PDF G(R)
    7797 entries created with the same step sizes and using the same radiation from data
    7798 collected with identical instrument configurations. Cluster analysis is
    7799 available in GSAS-II after it is initiated by the main menu command <b><span
    7800 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    7801 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Calculate/Setup
     8127survey PWDR data entries that have identical scan characteristics (<span
     8128class=GramE>e.g.</span> instrument type, step size, radiation type, wavelength)
     8129or multiple PDF G(R) entries created with the same step sizes and using the
     8130same radiation from data collected with identical instrument configurations.
     8131Cluster analysis is available in GSAS-II after it is initiated by the main menu
     8132command <b><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     8133minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Calculate/Setup
    78028134Cluster Analysis. </span></b>The cluster analysis routines used here are from
    78038135the scipy library and (if available) the scikit-learn library.<span
    … …  
    78208152<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
    78218153
     8154<h4>Cluster Analysis with scipy</h4>
     8155
    78228156<p class=MsoNormal>Doing cluster analysis in GSAS-II requires several steps;
    7823 new steps will become visible in the GUI as previous ones are completed. Redoing
    7824 earlier steps may clear subsequent ones. In order of their appearance, the
    7825 following GUI commands are:</p>
     8157new steps will become visible in the GUI as previous ones are completed.
     8158Redoing earlier steps may clear subsequent ones. In order of their appearance,
     8159the following GUI commands are:</p>
    78268160
    78278161<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    … …  
    78318165Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    78328166</span></span></span><![endif]><b>Select datasets</b> – this brings up a
    7833 selection tool for PWDR (&amp; PDF, if present) entries in the GSAS-II data tree.
    7834 Your selection must be either PWDR or PDF data; otherwise there is no check on
    7835 data similarity so be careful with your selections. Multi-bank TOF data should
    7836 not be mixed for cluster analysis nor should laboratory and synchrotron data.
    7837 Cluster analysis on fewer than 5-10 data sets is probably not useful but should
    7838 be used when you have dozens or even hundreds of data sets.</p>
     8167selection tool for PWDR (&amp; PDF, if present) entries in the GSAS-II data
     8168tree. Your selection must be either PWDR or PDF data; otherwise, there is no
     8169check on data similarity so be careful with your selections. Multi-bank TOF
     8170data should not be mixed for cluster analysis nor should laboratory and
     8171synchrotron data. Cluster analysis on fewer than 5-10 data sets is probably not
     8172useful but should be used when you have dozens or even hundreds of data sets.</p>
    78398173
    78408174<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l39 level1 lfo31'><![if !supportLists]><span
    … …  
    79538287mso-ansi-language:EN-US;mso-fareast-language:EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape
    79548288 id="_x0000_i1025" type="#_x0000_t75" style='width:108.75pt;height:44.25pt'>
    7955  <v:imagedata src="gsasII_files/image028.png" o:title="" chromakey="white"/>
     8289 <v:imagedata src="gsasII_files/image003.png" o:title="" chromakey="white"/>
    79568290</v:shape><![endif]--><![if !vml]><img width=145 height=59
    7957 src="gsasII_files/image029.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
     8291src="gsasII_files/image004.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
    79588292style='font-family:"Cambria Math",serif;color:#4A4A4A'><o:p></o:p></span></p>
    79598293
    … …  
    79668300overflow-wrap: normal;max-width:none;max-height: none;min-width: 0px;
    79678301min-height: 0px;float:none;word-spacing:normal' id=MathJax-Element-27-Frame><span
    7968 style='color:#4A4A4A'>canberra</span> – </span></b><span style='color:#4A4A4A'>Computes
     8302style='color:#4A4A4A'>canberra</span></span> – </b><span style='color:#4A4A4A'>Computes
    79698303the Canberra distance between data vectors as:<o:p></o:p></span></p>
    79708304
    … …  
    80348368mso-ansi-language:EN-US;mso-fareast-language:EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape
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     8370 <v:imagedata src="gsasII_files/image005.png" o:title="" chromakey="white"/>
    80378371</v:shape><![endif]--><![if !vml]><img width=163 height=47
    8038 src="gsasII_files/image031.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
     8372src="gsasII_files/image006.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
    80398373style='color:#4A4A4A'><o:p></o:p></span></p>
    80408374
    … …  
    80868420mso-ansi-language:EN-US;mso-fareast-language:EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape
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     8422 <v:imagedata src="gsasII_files/image007.png" o:title="" chromakey="white"/>
    80898423</v:shape><![endif]--><![if !vml]><img width=158 height=19
    8090 src="gsasII_files/image033.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
     8424src="gsasII_files/image008.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
    80918425style='color:#4A4A4A'><o:p></o:p></span></p>
    80928426
    … …  
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     8479 <v:imagedata src="gsasII_files/image009.png" o:title="" chromakey="white"/>
    81468480</v:shape><![endif]--><![if !vml]><img width=150 height=43
    8147 src="gsasII_files/image035.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
     8481src="gsasII_files/image010.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
    81488482style='color:#4A4A4A'><o:p></o:p></span></p>
    81498483
    … …  
    82308564mso-ansi-language:EN-US;mso-fareast-language:EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape
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     8566 <v:imagedata src="gsasII_files/image011.png" o:title="" chromakey="white"/>
    82338567</v:shape><![endif]--><![if !vml]><img width=225 height=45
    8234 src="gsasII_files/image037.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
     8568src="gsasII_files/image012.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
    82358569style='color:#4A4A4A'><br style='mso-special-character:line-break'>
    82368570<![if !supportLineBreakNewLine]><br style='mso-special-character:line-break'>
    … …  
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     8615 <v:imagedata src="gsasII_files/image013.png" o:title="" chromakey="white"/>
    82828616</v:shape><![endif]--><![if !vml]><img width=141 height=37
    8283 src="gsasII_files/image039.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
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    82848618style='color:#4A4A4A'><br style='mso-special-character:line-break'>
    82858619<![if !supportLineBreakNewLine]><br style='mso-special-character:line-break'>
    … …  
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     8681 <v:imagedata src="gsasII_files/image015.png" o:title="" chromakey="white"/>
    83488682</v:shape><![endif]--><![if !vml]><img width=176 height=57
    8349 src="gsasII_files/image041.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
     8683src="gsasII_files/image016.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
    83508684style='color:#4A4A4A'><o:p></o:p></span></p>
    83518685
    … …  
    84208754mso-ansi-language:EN-US;mso-fareast-language:EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape
    84218755 id="_x0000_i1025" type="#_x0000_t75" style='width:129.75pt;height:42.75pt'>
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     8756 <v:imagedata src="gsasII_files/image017.png" o:title="" chromakey="white"/>
    84238757</v:shape><![endif]--><![if !vml]><img width=173 height=57
    8424 src="gsasII_files/image043.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
     8758src="gsasII_files/image018.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
    84258759style='color:#4A4A4A'><o:p></o:p></span></p>
    84268760
    … …  
    84288762auto'><span style='color:#4A4A4A'>where the exponent, p, = 2 by default; this
    84298763is identical to the Euclidian formula. Some choices for p: 1 is the same as
    8430 city block, and 10 (~<span style='mso-spacerun:yes'>  </span>∞) is essentially
    8431 the same as Chebyschev. The others (3 &amp; 4) give distance results that are
    8432 between Euclidian (p=2) and Chebyschev (p=10 ~ ∞).<o:p></o:p></span></p>
     8764city block, and 10 (<span class=GramE>~<span style='mso-spacerun:yes'> 
     8765</span>∞</span>) is essentially the same as Chebyschev. The others (3 &amp; 4)
     8766give distance results that are between Euclidian (p=2) and Chebyschev (p=10 ~
     8767∞).<o:p></o:p></span></p>
    84338768
    84348769<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    … …  
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     8841 <v:imagedata src="gsasII_files/image019.png" o:title="" chromakey="white"/>
    85078842</v:shape><![endif]--><![if !vml]><img width=220 height=57
    8508 src="gsasII_files/image045.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
     8843src="gsasII_files/image020.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
    85098844style='color:#4A4A4A'><o:p></o:p></span></p>
    85108845
    … …  
    85128847auto'><span style='color:#4A4A4A'>where the variance, <i>V</i>[<i>x<sub>i</sub></i>],
    85138848is computed automatically as the variance in the data point values for each
    8514 data position (i.e. 2</span><span style='font-family:Symbol;mso-ascii-font-family:
    8515 "Times New Roman";mso-hansi-font-family:"Times New Roman";color:#4A4A4A;
    8516 mso-char-type:symbol;mso-symbol-font-family:Symbol'><span style='mso-char-type:
    8517 symbol;mso-symbol-font-family:Symbol'>Q</span></span><span style='color:#4A4A4A'>)
    8518 across the entire data array.<o:p></o:p></span></p>
     8849data position (<span class=GramE>i.e.</span> 2</span><span style='font-family:
     8850Symbol;mso-ascii-font-family:"Times New Roman";mso-hansi-font-family:"Times New Roman";
     8851color:#4A4A4A;mso-char-type:symbol;mso-symbol-font-family:Symbol'><span
     8852style='mso-char-type:symbol;mso-symbol-font-family:Symbol'>Q</span></span><span
     8853style='color:#4A4A4A'>) across the entire data array.<o:p></o:p></span></p>
    85198854
    85208855<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    … …  
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    85748909</v:shape><![endif]--><![if !vml]><img width=161 height=43
    8575 src="gsasII_files/image047.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
     8910src="gsasII_files/image022.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
    85768911style='color:#4A4A4A'><o:p></o:p></span></p>
    85778912
    … …  
    85838918tab is a 3D plot of the result of a Principal Component Analysis (PCA) of the
    85848919distance data; it shows the location of each data set in this space. Clusters
    8585 may be evident from this plot; variable temperature scans tend to show a
    8586 complex path of distance points with cluster grouping corresponding to phases.
    8587 The GUI will be extended to show more steps in cluster analysis.<o:p></o:p></span></p>
     8920may be evident from this plot; variable temperature scans tend to show a complex
     8921path of distance points with cluster grouping corresponding to phases. The GUI
     8922will be extended to show more steps in cluster analysis.<o:p></o:p></span></p>
    85888923
    85898924<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l28 level1 lfo32'><![if !supportLists]><span
    … …  
    86138948
    86148949<p class=MsoListParagraphCxSpMiddle style='margin-left:.75in;mso-add-space:
    8615 auto'><i><span style='color:#4A4A4A'>d</span></i><span style='color:#4A4A4A'>(<i>s,t</i>)<i>
    8616 = min</i>(<i>dist</i>(<i>u</i>(<i>s</i>)<i><sub>i</sub>,v</i>(<i>t</i>)<i><sub>j</sub></i>)<i><o:p></o:p></i></span></p>
     8950auto'><i><span style='color:#4A4A4A'>d</span></i><span style='color:#4A4A4A'>(<span
     8951class=GramE><i>s,t</i></span>)<i> = min</i>(<i>dist</i>(<i>u</i>(<i>s</i>)<i><sub>i</sub>,v</i>(<i>t</i>)<i><sub>j</sub></i>)<i><o:p></o:p></i></span></p>
    86178952
    86188953<p class=MsoListParagraphCxSpMiddle style='margin-left:.75in;mso-add-space:
    … …  
    86298964
    86308965<p class=MsoNormal style='margin-left:.75in'><i><span style='color:#4A4A4A'>d</span></i><span
    8631 style='color:#4A4A4A'>(<i>s,t</i>)<i> = max</i>(<i>dist</i>(<i>u</i>(<i>s</i>)<i><sub>i</sub>,v</i>(<i>t</i>)<i><sub>j</sub></i>)<i><o:p></o:p></i></span></p>
     8966style='color:#4A4A4A'>(<span class=GramE><i>s,t</i></span>)<i> = max</i>(<i>dist</i>(<i>u</i>(<i>s</i>)<i><sub>i</sub>,v</i>(<i>t</i>)<i><sub>j</sub></i>)<i><o:p></o:p></i></span></p>
    86328967
    86338968<p class=MsoNormal style='margin-left:.75in'><span style='color:#4A4A4A'><o:p>&nbsp;</o:p></span></p>
    … …  
    87009035mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape id="_x0000_i1025" type="#_x0000_t75"
    87019036 style='width:159pt;height:39pt'>
    8702  <v:imagedata src="gsasII_files/image048.png" o:title="" chromakey="white"/>
     9037 <v:imagedata src="gsasII_files/image023.png" o:title="" chromakey="white"/>
    87039038</v:shape><![endif]--><![if !vml]><img width=212 height=52
    8704 src="gsasII_files/image049.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
     9039src="gsasII_files/image024.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
    87059040style='color:#4A4A4A'><o:p></o:p></span></p>
    87069041
    … …  
    87129047color:#4A4A4A'><span style='mso-list:Ignore'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
    87139048</span></span></span><![endif]><b><span style='color:#4A4A4A'>weighted</span></b><span
    8714 style='color:#4A4A4A'> – computes the linkage when <i>s</i> is formed with
    8715 clusters <i>u</i> &amp; <i>v</i> and <i>t</i> is another cluster as:<o:p></o:p></span></p>
     9049style='color:#4A4A4A'> – computes the linkage when <i>s</i> is formed with clusters
     9050<i>u</i> &amp; <i>v</i> and <i>t</i> is another cluster as:<o:p></o:p></span></p>
    87169051
    87179052<p class=MsoListParagraphCxSpMiddle style='margin-left:.75in;mso-add-space:
    … …  
    87459080"Times New Roman";mso-ansi-language:EN-US;mso-fareast-language:EN-US;
    87469081mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape id="_x0000_i1025" type="#_x0000_t75"
    8747  style='width:180.65pt;height:14.4pt'>
    8748  <v:imagedata src="gsasII_files/image050.png" o:title="" chromakey="white"/>
     9082 style='width:180.75pt;height:14.25pt'>
     9083 <v:imagedata src="gsasII_files/image025.png" o:title="" chromakey="white"/>
    87499084</v:shape><![endif]--><![if !vml]><img width=241 height=19
    8750 src="gsasII_files/image051.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
     9085src="gsasII_files/image026.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
    87519086style='color:#4A4A4A'><o:p></o:p></span></p>
    87529087
    … …  
    87969131mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape id="_x0000_i1025" type="#_x0000_t75"
    87979132 style='width:103.5pt;height:14.25pt'>
    8798  <v:imagedata src="gsasII_files/image052.png" o:title="" chromakey="white"/>
     9133 <v:imagedata src="gsasII_files/image027.png" o:title="" chromakey="white"/>
    87999134</v:shape><![endif]--><![if !vml]><img width=138 height=19
    8800 src="gsasII_files/image053.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
     9135src="gsasII_files/image028.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
    88019136style='color:#4A4A4A'><o:p></o:p></span></p>
    88029137
    … …  
    88459180mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape id="_x0000_i1025" type="#_x0000_t75"
    88469181 style='width:113.25pt;height:14.25pt'>
    8847  <v:imagedata src="gsasII_files/image054.png" o:title="" chromakey="white"/>
     9182 <v:imagedata src="gsasII_files/image029.png" o:title="" chromakey="white"/>
    88489183</v:shape><![endif]--><![if !vml]><img width=151 height=19
    8849 src="gsasII_files/image055.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
     9184src="gsasII_files/image030.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
    88509185style='color:#4A4A4A'><o:p></o:p></span></p>
    88519186
    … …  
    89699304mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape id="_x0000_i1025" type="#_x0000_t75"
    89709305 style='width:350.25pt;height:42.75pt'>
    8971  <v:imagedata src="gsasII_files/image056.png" o:title="" chromakey="white"/>
     9306 <v:imagedata src="gsasII_files/image031.png" o:title="" chromakey="white"/>
    89729307</v:shape><![endif]--><![if !vml]><img width=467 height=57
    8973 src="gsasII_files/image057.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
     9308src="gsasII_files/image032.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
    89749309style='color:#4A4A4A'><o:p></o:p></span></p>
    89759310
    … …  
    89789313<p class=MsoListParagraphCxSpFirst><span style='color:#4A4A4A'>Changing the
    89799314linkage method results in an automatic recalculation of the hierarchical
    8980 clustering; a Compute button is provided for convenience. The result of this calculation
    8981 is shown as a dendrogram in the same plot tab; the 4<sup>th</sup> plot shows
    8982 the percentage contribution of the leading terms in the PCA to the distance
    8983 data. Usually, 2-3 terms are sufficient to describe the distribution.<o:p></o:p></span></p>
     9315clustering; a Compute button is provided for convenience. The result of this
     9316calculation is shown as a dendrogram in the same plot tab; the 4<sup>th</sup>
     9317plot shows the percentage contribution of the leading terms in the PCA to the
     9318distance data. Usually, 2-3 terms are sufficient to describe the distribution.<o:p></o:p></span></p>
    89849319
    89859320<p class=MsoListParagraphCxSpMiddle style='margin-left:.25in;mso-add-space:
    … …  
    89899324</span></span></span><![endif]><b><span style='color:#4A4A4A'>Select number of
    89909325clusters</span></b><span style='color:#4A4A4A'> for K-means clustering (scipy
    8991 algorithm). The algorithm attempts to group the data points (e.g. as in the PCA
    8992 plot) into the requested number of clusters based on Euclidian distances on a “whitened”
    8993 data array (i.e. not the distance matrix). Use the Compute to repeat the
    8994 K-means clustering; the start points are randomly selected and will sometimes
    8995 yield different results. <b>Cluster populations</b> are shown in the GUI, clusters
    8996 are colored to match the data point colors in the PCA plot.<o:p></o:p></span></p>
     9326algorithm). The algorithm attempts to group the data points (e. g. as in the
     9327PCA plot) into the requested number of clusters based on Euclidian distances on
     9328a “whitened” data array (i. e. not the distance matrix). To whiten the data
     9329matrix the suite of values at each position (e. g. at each 2</span><span
     9330style='font-family:Symbol;mso-ascii-font-family:"Times New Roman";mso-hansi-font-family:
     9331"Times New Roman";color:#4A4A4A;mso-char-type:symbol;mso-symbol-font-family:
     9332Symbol'><span style='mso-char-type:symbol;mso-symbol-font-family:Symbol'>Q</span></span><span
     9333style='color:#4A4A4A'>) are divided by its standard deviation; this reduces the
     9334scale of the PWDR &amp; PDF observations to just numbers of standard deviations
     9335from zero. Use the Compute to repeat the K-means clustering; the start points
     9336are randomly selected and will sometimes yield different results. <b>Cluster
     9337populations</b> are shown in the GUI, clusters are colored to match the data
     9338point colors in the PCA plot.<o:p></o:p></span></p>
    89979339
    89989340<p class=MsoListParagraphCxSpMiddle style='margin-left:.75in;mso-add-space:
    … …  
    90089350style='font-family:"Courier New";mso-fareast-font-family:"Courier New";
    90099351color:#4A4A4A'><span style='mso-list:Ignore'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
    9010 </span></span></span><![endif]><b><span style='color:#4A4A4A'>Select cluster member
    9011 </span></b><span style='color:#4A4A4A'>(use mouse RB on item in displayed list)<b>
    9012 </b>– Displays the PWDR (or PDF) data on the Powder Pattern plot tab for the
    9013 selected item.<o:p></o:p></span></p>
     9352</span></span></span><![endif]><b><span style='color:#4A4A4A'>Select cluster
     9353member </span></b><span style='color:#4A4A4A'>(use mouse RB on item in
     9354displayed list)<b> </b>– Displays the PWDR (or PDF) data on the Powder Pattern
     9355plot tab for the selected item.<o:p></o:p></span></p>
    90149356
    90159357<p class=MsoListParagraphCxSpMiddle style='margin-left:.25in;mso-add-space:
    … …  
    90499391Analysis is shown.<o:p></o:p></span></p>
    90509392
     9393<h4>Cluster Analysis with scikit-learn</h4>
     9394
    90519395<p class=MsoNormal><span style='color:#4A4A4A'>The next section of the GUI only
    90529396appears if the scikit-learn package is installed. It has multiple algorithms
    9053 for doing clustering and detecting outliers (i.e. bad data) in the suite of PWDR
    9054 or PDF patterns. Changing the method or number of clusters results in an
    9055 automatic calculation; the <b>Compute</b> button is provided for convenience. There
    9056 is a reminder to properly cite Scikit-learn if you use it.<o:p></o:p></span></p>
     9397for doing clustering and detecting outliers (i. e. bad data) in the suite of
     9398PWDR or PDF patterns. Changing the method or number of clusters results in an
     9399automatic calculation; the <b>Compute</b> button is provided for convenience.
     9400There is a reminder to properly cite Scikit-learn if you use it.<o:p></o:p></span></p>
    90579401
    90589402<p class=MsoListParagraphCxSpFirst style='margin-left:.25in;mso-add-space:auto;
    9059 text-align:justify;text-indent:-.25in;mso-list:l42 level1 lfo60'><![if !supportLists]><span
     9403text-align:justify;text-indent:-.25in;mso-list:l42 level1 lfo33'><![if !supportLists]><span
    90609404style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    90619405Symbol;color:#4A4A4A'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    … …  
    90659409
    90669410<p class=MsoListParagraphCxSpMiddle style='margin-left:.75in;mso-add-space:
    9067 auto;text-align:justify;text-indent:-.25in;mso-list:l42 level2 lfo60'><![if !supportLists]><span
     9411auto;text-align:justify;text-indent:-.25in;mso-list:l42 level2 lfo33'><![if !supportLists]><span
    90689412style='font-family:"Courier New";mso-fareast-font-family:"Courier New";
    90699413color:#4A4A4A'><span style='mso-list:Ignore'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
    … …  
    90719415style='color:#4A4A4A'>(requires number of clusters)<b> – </b>Uses the
    90729416scikit-learn “K-means++” algorithm for clustering; this gives a better starting
    9073 positions and usually succeeds on the 1<sup>st</sup> try. It uses the “whitened”
     9417position and usually succeeds on the 1<sup>st</sup> try. It uses the “whitened”
    90749418data matrix.<o:p></o:p></span></p>
    90759419
    90769420<p class=MsoListParagraphCxSpMiddle style='margin-left:.75in;mso-add-space:
    9077 auto;text-align:justify;text-indent:-.25in;mso-list:l42 level2 lfo60'><![if !supportLists]><span
     9421auto;text-align:justify;text-indent:-.25in;mso-list:l42 level2 lfo33'><![if !supportLists]><span
    90789422style='font-family:"Courier New";mso-fareast-font-family:"Courier New";
    90799423color:#4A4A4A'><span style='mso-list:Ignore'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
    … …  
    90839427
    90849428<p class=MsoListParagraphCxSpMiddle style='margin-left:.75in;mso-add-space:
    9085 auto;text-align:justify;text-indent:-.25in;mso-list:l42 level2 lfo60'><![if !supportLists]><span
     9429auto;text-align:justify;text-indent:-.25in;mso-list:l42 level2 lfo33'><![if !supportLists]><span
    90869430style='font-family:"Courier New";mso-fareast-font-family:"Courier New";
    90879431color:#4A4A4A'><span style='mso-list:Ignore'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
    … …  
    90909434
    90919435<p class=MsoListParagraphCxSpMiddle style='margin-left:.75in;mso-add-space:
    9092 auto;text-align:justify;text-indent:-.25in;mso-list:l42 level2 lfo60'><![if !supportLists]><span
     9436auto;text-align:justify;text-indent:-.25in;mso-list:l42 level2 lfo33'><![if !supportLists]><span
    90939437style='font-family:"Courier New";mso-fareast-font-family:"Courier New";
    90949438color:#4A4A4A'><span style='mso-list:Ignore'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
    … …  
    90989442
    90999443<p class=MsoListParagraphCxSpMiddle style='margin-left:.75in;mso-add-space:
    9100 auto;text-align:justify'><span style='color:#4A4A4A'><o:p>&nbsp;</o:p></span></p>
    9101 
    9102 <p class=MsoListParagraphCxSpMiddle style='margin-left:.75in;mso-add-space:
    9103 auto;text-align:justify;text-indent:-.25in;mso-list:l42 level2 lfo60'><![if !supportLists]><span
     9444auto;text-align:justify;text-indent:-.25in;mso-list:l42 level2 lfo33'><![if !supportLists]><span
    91049445style='font-family:"Courier New";mso-fareast-font-family:"Courier New";
    91059446color:#4A4A4A'><span style='mso-list:Ignore'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
    … …  
    91199460the PCA plot.<o:p></o:p></span></p>
    91209461
    9121 <p class=MsoNormal><span style='color:#4A4A4A'><o:p>&nbsp;</o:p></span></p>
     9462<h4>Outlier Analysis with scikit-learn</h4>
     9463
     9464<p class=MsoListParagraphCxSpFirst style='margin-left:0in;mso-add-space:auto;
     9465text-align:justify'><span style='color:#4A4A4A'>After selection of the PWDR or
     9466PDF data and doing the distance calculation, one can examine the distance data
     9467for possible “bad” data items. These outliers can be detected by a choice of
     9468methods that make different assumptions how the data “should” be clustered; any
     9469data that do not fall within them are flagged as outliers and are colored
     9470different in the resulting 3D PCA plot from all others that would be in
     9471clusters. Although the chosen distance method affects the appearance of the 3D
     9472PCA plot, the three outlier methods all use the original data, thus are independent
     9473of any selected distance method. The GUI is refreshed showing a listing of the
     9474outlier data; selection of any, displays that data item in the powder pattern
     9475plot tab. Any previous cluster identification, e. g. by K-means, is erased. The
     9476outlier detection methods are:<o:p></o:p></span></p>
     9477
     9478<p class=MsoListParagraphCxSpMiddle style='margin-left:.25in;mso-add-space:
     9479auto;text-align:justify;text-indent:-.25in;mso-list:l42 level1 lfo33'><![if !supportLists]><span
     9480style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
     9481Symbol;color:#4A4A4A'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     9482</span></span></span><![endif]><b><span style='color:#4A4A4A'>One-Class SVM</span></b><span
     9483style='color:#4A4A4A'> – Attempts to form boundaries around the clusters;
     9484outliers are items that fall outside the boundaries.<o:p></o:p></span></p>
     9485
     9486<p class=MsoListParagraphCxSpMiddle style='margin-left:.25in;mso-add-space:
     9487auto;text-align:justify;text-indent:-.25in;mso-list:l42 level1 lfo33'><![if !supportLists]><span
     9488style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
     9489Symbol;color:#4A4A4A'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     9490</span></span></span><![endif]><b><span style='color:#4A4A4A'>Isolation Forest</span></b><span
     9491style='color:#4A4A4A'> – Similar to the above but uses a different algorithm.<o:p></o:p></span></p>
     9492
     9493<p class=MsoListParagraphCxSpMiddle style='margin-left:.25in;mso-add-space:
     9494auto;text-align:justify;text-indent:-.25in;mso-list:l42 level1 lfo33'><![if !supportLists]><span
     9495style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
     9496Symbol;color:#4A4A4A'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     9497</span></span></span><![endif]><b><span style='color:#4A4A4A'>Local Outlier
     9498Factor</span></b><span style='color:#4A4A4A'> – Uses the local density of other
     9499points about each point to determine if it is within a high-density area, i. e.
     9500in a cluster, or not.<o:p></o:p></span></p>
     9501
     9502<p class=MsoListParagraphCxSpMiddle style='margin-left:.25in;mso-add-space:
     9503auto;text-align:justify'><span style='color:#4A4A4A'>Further details of these
     9504methods can be found at </span><a
     9505href="https://scikit-learn.org/stable/modules/outlier_detection.html">2.7.
     9506Novelty and Outlier Detection — scikit-learn 1.1.2 documentation</a>. The
     9507current GSAS-II implementation of these methods all use the default settings
     9508for any of their respective parameters.<span style='color:#4A4A4A'><o:p></o:p></span></p>
     9509
     9510<p class=MsoListParagraphCxSpLast style='margin-left:.25in;mso-add-space:auto;
     9511text-align:justify'><span style='color:#4A4A4A'><o:p>&nbsp;</o:p></span></p>
     9512
     9513<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do with
     9514the plots?</span></h5>
     9515
     9516<p class=MsoNormal><span style='color:#4A4A4A'>For each selection of distance
     9517method, <span class=GramE>i.e.</span> “Euclidian”, a plot tab is created with 2
     9518or 4 plots. They are: 1) the distance matrix displayed in the same way the
     9519refinement covariance matrix is displayed (default coloring is “paired” – same
     9520parameter as the powder pattern contour plot); 2) the 3D PCA analysis plot; 3) the
     9521hierarchical dendrogram plot and 4) the PCA percent contribution plot. Each can
     9522be zoomed independent of the others and the 1<sup>st</sup> three can be
     9523selected to show as a single plot in the tab (see <b>Plot selection</b> above).
     9524A LB mouse selection (&amp; hold button down) of a 3D PCA point will show the
     9525data set name in the plot status line. If clusters are determined by e. g.
     9526K-means, the 3D PCA points will be colored by cluster membership.<o:p></o:p></span></p>
    91229527
    91239528<p class=MsoListParagraph style='margin-left:.75in;mso-add-space:auto'><span
    … …  
    91449549</span></div>
    91459550
    9146 <h2><span style='mso-fareast-font-family:"Times New Roman";color:#4A4A4A'>6.
    9147 Histogram data tree items<o:p></o:p></span></h2>
     9551<h2><span style='mso-fareast-font-family:"Times New Roman";color:#4A4A4A'>6. Histogram
     9552data tree items<o:p></o:p></span></h2>
    91489553
    91499554<p class=MsoNormal><span style='color:#4A4A4A'>These are shown in the data tree
    … …  
    91699574
    91709575<p class=MsoNormal><span style='color:#4A4A4A'>You can change the weight
    9171 factor. This is a multiplier on all of the reflection weights in this
    9172 histogram. Rarely needs to be changed.<o:p></o:p></span></p>
     9576factor. This is a multiplier on <span class=GramE>all of</span> the reflection
     9577weights in this histogram. Rarely needs to be changed.<o:p></o:p></span></p>
    91739578
    91749579<p><span style='color:#4A4A4A'>Menu Commands </span><span style='mso-fareast-font-family:
    91759580"Times New Roman";mso-fareast-theme-font:minor-fareast;color:#4A4A4A'><o:p></o:p></span></p>
    91769581
    9177 <p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l34 level1 lfo33'><![if !supportLists]><span
     9582<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l34 level1 lfo34'><![if !supportLists]><span
    91789583style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    91799584Symbol;color:#4A4A4A'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    … …  
    91859590data).<o:p></o:p></span></p>
    91869591
    9187 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l34 level1 lfo33'><![if !supportLists]><span
     9592<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l34 level1 lfo34'><![if !supportLists]><span
    91889593style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    91899594Symbol;color:#4A4A4A'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    … …  
    91939598structure factors.<o:p></o:p></span></p>
    91949599
    9195 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l34 level1 lfo33'><![if !supportLists]><span
     9600<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l34 level1 lfo34'><![if !supportLists]><span
    91969601style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    91979602Symbol;color:#4A4A4A'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    … …  
    92009605reflection for the selected phase<o:p></o:p></span></p>
    92019606
    9202 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l34 level1 lfo33'><![if !supportLists]><span
     9607<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l34 level1 lfo34'><![if !supportLists]><span
    92039608style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    92049609Symbol;color:#4A4A4A'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    92059610</span></span></span><![endif]><b><span style='color:#4A4A4A'>Plot HKLs</span></b><span
    92069611style='color:#4A4A4A'> (the default plot)– shows a HKL layer with rings scaled
    9207 to F or F2 for Fo and Fc. +/- steps through the layers and h,k or l selects the
    9208 orientation – see K box for all the possible commands.<o:p></o:p></span></p>
    9209 
    9210 <p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l34 level1 lfo33'><![if !supportLists]><span
     9612to F or F2 for Fo and Fc. +/- steps through the layers and <span class=GramE>h,k</span>
     9613or l selects the orientation – see K box for all the possible commands.<o:p></o:p></span></p>
     9614
     9615<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l34 level1 lfo34'><![if !supportLists]><span
    92119616style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    92129617Symbol;color:#4A4A4A'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    … …  
    92359640
    92369641<p class=MsoListParagraphCxSpFirst style='margin-left:.75in;mso-add-space:auto;
    9237 text-indent:-.25in;mso-list:l32 level1 lfo34'><![if !supportLists]><span
     9642text-indent:-.25in;mso-list:l32 level1 lfo35'><![if !supportLists]><span
    92389643class=MsoHyperlink><span style='font-family:Symbol;mso-fareast-font-family:
    92399644Symbol;mso-bidi-font-family:Symbol;color:windowtext;text-decoration:none;
    … …  
    92459650
    92469651<p class=MsoListParagraphCxSpMiddle style='margin-left:1.25in;mso-add-space:
    9247 auto;text-indent:-.25in;mso-list:l32 level2 lfo34'><![if !supportLists]><span
     9652auto;text-indent:-.25in;mso-list:l32 level2 lfo35'><![if !supportLists]><span
    92489653style='font-family:"Courier New";mso-fareast-font-family:"Courier New";
    92499654color:#4A4A4A'><span style='mso-list:Ignore'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
    … …  
    92559660
    92569661<p class=MsoListParagraphCxSpMiddle style='margin-left:1.25in;mso-add-space:
    9257 auto;text-indent:-.25in;mso-list:l32 level2 lfo34'><![if !supportLists]><span
     9662auto;text-indent:-.25in;mso-list:l32 level2 lfo35'><![if !supportLists]><span
    92589663style='font-family:"Courier New";mso-fareast-font-family:"Courier New";
    92599664color:#4A4A4A'><span style='mso-list:Ignore'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
    … …  
    92639668
    92649669<p class=MsoListParagraphCxSpMiddle style='margin-left:1.25in;mso-add-space:
    9265 auto;text-indent:-.25in;mso-list:l32 level2 lfo34'><![if !supportLists]><span
     9670auto;text-indent:-.25in;mso-list:l32 level2 lfo35'><![if !supportLists]><span
    92669671style='font-family:"Courier New";mso-fareast-font-family:"Courier New";
    92679672color:#4A4A4A'><span style='mso-list:Ignore'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
    92689673</span></span></span><![endif]><b><span style='color:#4A4A4A'>Plot HKLs</span></b><span
    92699674style='color:#4A4A4A'> (the default plot)– shows a HKL layer with rings scaled
    9270 to F or F2 for Fo and Fc. +/- steps through the layers and h,k or l selects the
    9271 orientation – see K box for all the possible commands.<o:p></o:p></span></p>
     9675to F or F2 for Fo and Fc. +/- steps through the layers and <span class=GramE>h,k</span>
     9676or l selects the orientation – see K box for all the possible commands.<o:p></o:p></span></p>
    92729677
    92739678<p class=MsoListParagraphCxSpMiddle style='margin-left:1.25in;mso-add-space:
    9274 auto;text-indent:-.25in;mso-list:l32 level2 lfo34'><![if !supportLists]><span
     9679auto;text-indent:-.25in;mso-list:l32 level2 lfo35'><![if !supportLists]><span
    92759680style='font-family:"Courier New";mso-fareast-font-family:"Courier New";
    92769681color:#4A4A4A'><span style='mso-list:Ignore'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
    92779682</span></span></span><![endif]><b><span style='color:#4A4A4A'>Plot 3D HKLs</span></b><span
    9278 style='color:#4A4A4A'> – shows a 3D representation of the unique part
    9279 reciprocal space points for this phase. The save as/key item in the plot status
    9280 bar shows the various commands for modifying this plot.<o:p></o:p></span></p>
     9683style='color:#4A4A4A'> – shows a 3D representation of the unique part reciprocal
     9684space points for this phase. The save as/key item in the plot status bar shows
     9685the various commands for modifying this plot.<o:p></o:p></span></p>
    92819686
    92829687<p class=MsoListParagraphCxSpMiddle style='margin-left:1.25in;mso-add-space:
    9283 auto;text-indent:-.25in;mso-list:l32 level2 lfo34'><![if !supportLists]><span
     9688auto;text-indent:-.25in;mso-list:l32 level2 lfo35'><![if !supportLists]><span
    92849689style='font-family:"Courier New";mso-fareast-font-family:"Courier New";
    92859690color:#4A4A4A'><span style='mso-list:Ignore'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
    … …  
    92889693
    92899694<p class=MsoListParagraphCxSpLast style='margin-left:1.25in;mso-add-space:auto;
    9290 text-indent:-.25in;mso-list:l32 level2 lfo34'><![if !supportLists]><span
     9695text-indent:-.25in;mso-list:l32 level2 lfo35'><![if !supportLists]><span
    92919696style='font-family:"Courier New";mso-fareast-font-family:"Courier New";
    92929697color:#4A4A4A'><span style='mso-list:Ignore'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
    92939698</span></span></span><![endif]><b><span style='color:#4A4A4A'>Show/hide extinct
    9294 reflections</span></b><span style='color:#4A4A4A'> – can exclude space group
    9295 extinctions from the list (not valid for PWDR data).</span><span
    9296 style='mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
    9297 color:#4A4A4A'><o:p></o:p></span></p>
     9699reflections</span></b><span style='color:#4A4A4A'> – can exclude space group extinctions
     9700from the list (not valid for PWDR data).</span><span style='mso-fareast-font-family:
     9701"Times New Roman";mso-fareast-theme-font:minor-fareast;color:#4A4A4A'><o:p></o:p></span></p>
    92989702
    92999703<h5><a name=PDF><span style='mso-fareast-font-family:"Times New Roman"'>What is
    … …  
    93189722<p class=MsoNormal><span style='color:#4A4A4A'>A PDF entry is created from a <a
    93199723href="gsasII-pwdr.html#PWDR">powder histogram (PWDR entry)</a> using the <b>Setup
    9320 PDFs</b> entry in the <a href="#Calculate_menu">Calculate menu</a>. The main PDF
    9321 data tree item displays the same window as the PDF Controls, below. A PDF entry
    9322 can also be imported as G(R) from a file. When this item is selected, the <a
    9323 href="#PDF_S_Q">S(Q) function</a> or <a href="#PDF_G_R">G(R) function</a> (if
    9324 imported) is plotted, see below. <o:p></o:p></span></p>
     9724PDFs</b> entry in the <a href="#Calculate_menu">Calculate menu</a>. The main
     9725PDF data tree item displays the same window as the PDF Controls, below. A PDF
     9726entry can also be imported as G(R) from a file. When this item is selected, the
     9727<a href="#PDF_S_Q">S(Q) function</a> or <a href="#PDF_G_R">G(R) function</a>
     9728(if imported) is plotted, see below. <o:p></o:p></span></p>
    93259729
    93269730<h4><a name="PDF_Controls">PDF Controls</a></h4>
    93279731
    9328 <p class=MsoNormal><span style='color:#4A4A4A'>This window provides parameters
    9329 for computing the pair distribution function [PDF, G(r)] from the <a
    9330 href="#PDF_I_Q">I(Q) function</a>. This can only be done when a chemical
    9331 formula and appropriate control values are provided. If so, clicking on this
    9332 menu item causes the <a href="#PDF_I_Q">I(Q)</a>, <a href="#PDF_S_Q">S(Q)</a>, <a
    9333 href="#PDF_F_Q">F(Q)</a> and <a href="#PDF_G_R">G(R) functions</a> to be
    9334 plotted, as described below. <o:p></o:p></span></p>
     9732<p class=MsoNormal><span style='color:#4A4A4A'>This window provides parameters for
     9733computing the pair distribution function [PDF, G(r)] from the <a href="#PDF_I_Q">I(Q)
     9734function</a>. This can only be done when a chemical formula and appropriate
     9735control values are provided. If so, clicking on this menu item causes the <a
     9736href="#PDF_I_Q">I(Q)</a>, <a href="#PDF_S_Q">S(Q)</a>, <a href="#PDF_F_Q">F(Q)</a>
     9737and <a href="#PDF_G_R">G(R) functions</a> to be plotted, as described below. <o:p></o:p></span></p>
    93359738
    93369739<p class=MsoNormal><span style='color:#4A4A4A'>The <b>Optimize PDF</b> button
    … …  
    93489751<p><span style='color:#4A4A4A'>Available menu commands are:<o:p></o:p></span></p>
    93499752
    9350 <p style='margin-left:.5in;text-indent:-.25in;mso-list:l25 level1 lfo35;
     9753<p style='margin-left:.5in;text-indent:-.25in;mso-list:l25 level1 lfo36;
    93519754tab-stops:list .5in'><![if !supportLists]><span style='font-size:10.0pt;
    93529755mso-bidi-font-size:12.0pt;font-family:Symbol;mso-fareast-font-family:Symbol;
    … …  
    93589761empirical formula must still be entered. <o:p></o:p></span></p>
    93599762
    9360 <p style='margin-left:.5in;text-indent:-.25in;mso-list:l25 level1 lfo35;
     9763<p style='margin-left:.5in;text-indent:-.25in;mso-list:l25 level1 lfo36;
    93619764tab-stops:list .5in'><![if !supportLists]><span style='font-size:10.0pt;
    93629765mso-bidi-font-size:12.0pt;font-family:Symbol;mso-fareast-font-family:Symbol;
    … …  
    93649767style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    93659768</span></span></span><![endif]><b><span style='color:#4A4A4A'>Delete element - </span></b><span
    9366 style='color:#4A4A4A'>Removes a previously-entered element from the chemical
    9367 formula. <o:p></o:p></span></p>
    9368 
    9369 <p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l25 level1 lfo35;
     9769style='color:#4A4A4A'>Removes a <span class=GramE>previously-entered</span>
     9770element from the chemical formula. <o:p></o:p></span></p>
     9771
     9772<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l25 level1 lfo36;
    93709773tab-stops:list .5in'><![if !supportLists]><span style='font-size:10.0pt;
    93719774mso-bidi-font-size:12.0pt;font-family:Symbol;mso-fareast-font-family:Symbol;
    … …  
    93769779entries <o:p></o:p></span></p>
    93779780
    9378 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l25 level1 lfo35;
     9781<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l25 level1 lfo36;
    93799782tab-stops:list .5in'><![if !supportLists]><span style='font-size:10.0pt;
    93809783mso-bidi-font-size:12.0pt;font-family:Symbol;mso-fareast-font-family:Symbol;
    … …  
    93859788from a file (see Save controls). <o:p></o:p></span></p>
    93869789
    9387 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l25 level1 lfo35;
     9790<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l25 level1 lfo36;
    93889791tab-stops:list .5in'><![if !supportLists]><span style='font-size:10.0pt;
    93899792mso-bidi-font-size:12.0pt;font-family:Symbol;mso-fareast-font-family:Symbol;
    … …  
    93939796style='color:#4A4A4A'>Saves the current PDF control values into a file. <o:p></o:p></span></p>
    93949797
    9395 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l25 level1 lfo35;
     9798<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l25 level1 lfo36;
    93969799tab-stops:list .5in'><![if !supportLists]><span style='font-size:10.0pt;
    93979800mso-bidi-font-size:12.0pt;font-family:Symbol;mso-fareast-font-family:Symbol;
    … …  
    94039806this menu item. <o:p></o:p></span></p>
    94049807
    9405 <p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l25 level1 lfo35;
     9808<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l25 level1 lfo36;
    94069809tab-stops:list .5in'><![if !supportLists]><span style='font-size:10.0pt;
    94079810mso-bidi-font-size:12.0pt;font-family:Symbol;mso-fareast-font-family:Symbol;
    … …  
    94279830following keyboard shortcuts are available:<o:p></o:p></span></p>
    94289831
    9429 <p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l57 level1 lfo36;
     9832<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l57 level1 lfo37;
    94309833tab-stops:list .5in'><![if !supportLists]><span style='font-size:10.0pt;
    94319834mso-bidi-font-size:12.0pt;font-family:Symbol;mso-fareast-font-family:Symbol;
    … …  
    94379840same length as the first one to be included in the contour plot. <o:p></o:p></span></p>
    94389841
    9439 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l57 level1 lfo36;
     9842<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l57 level1 lfo37;
    94409843tab-stops:list .5in'><![if !supportLists]><span style='font-size:10.0pt;
    94419844mso-bidi-font-size:12.0pt;font-family:Symbol;mso-fareast-font-family:Symbol;
    … …  
    94479850active. Or all selected items will be plotted on a single axis. <o:p></o:p></span></p>
    94489851
    9449 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l57 level1 lfo36;
     9852<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l57 level1 lfo37;
    94509853tab-stops:list .5in'><![if !supportLists]><span style='font-size:10.0pt;
    94519854mso-bidi-font-size:12.0pt;font-family:Symbol;mso-fareast-font-family:Symbol;
    … …  
    94579860all selected items will be plotted on a single axis. <o:p></o:p></span></p>
    94589861
    9459 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l57 level1 lfo36;
     9862<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l57 level1 lfo37;
    94609863tab-stops:list .5in'><![if !supportLists]><span style='font-size:10.0pt;
    94619864mso-bidi-font-size:12.0pt;font-family:Symbol;mso-fareast-font-family:Symbol;
    … …  
    94669869rather than all. <o:p></o:p></span></p>
    94679870
    9468 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l57 level1 lfo36;
     9871<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l57 level1 lfo37;
    94699872tab-stops:list .5in'><![if !supportLists]><span style='font-size:10.0pt;
    94709873mso-bidi-font-size:12.0pt;font-family:Symbol;mso-fareast-font-family:Symbol;
    … …  
    94759878and name for each PDF. <o:p></o:p></span></p>
    94769879
    9477 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l57 level1 lfo36;
     9880<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l57 level1 lfo37;
    94789881tab-stops:list .5in'><![if !supportLists]><span style='font-size:10.0pt;
    94799882mso-bidi-font-size:12.0pt;font-family:Symbol;mso-fareast-font-family:Symbol;
    … …  
    94859888relative to previous plots. <o:p></o:p></span></p>
    94869889
    9487 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l57 level1 lfo36;
     9890<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l57 level1 lfo37;
    94889891tab-stops:list .5in'><![if !supportLists]><span style='font-size:10.0pt;
    94899892mso-bidi-font-size:12.0pt;font-family:Symbol;mso-fareast-font-family:Symbol;
    … …  
    94949897profiles, increase the offset to the right (or decrease the left offset.) <o:p></o:p></span></p>
    94959898
    9496 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l57 level1 lfo36;
     9899<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l57 level1 lfo37;
    94979900tab-stops:list .5in'><![if !supportLists]><span style='font-size:10.0pt;
    94989901mso-bidi-font-size:12.0pt;font-family:Symbol;mso-fareast-font-family:Symbol;
    … …  
    95039906profiles, increase the offset down. <o:p></o:p></span></p>
    95049907
    9505 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l57 level1 lfo36;
     9908<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l57 level1 lfo37;
    95069909tab-stops:list .5in'><![if !supportLists]><span style='font-size:10.0pt;
    95079910mso-bidi-font-size:12.0pt;font-family:Symbol;mso-fareast-font-family:Symbol;
    … …  
    95129915profiles, increase the offset up. <o:p></o:p></span></p>
    95139916
    9514 <p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l57 level1 lfo36;
     9917<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l57 level1 lfo37;
    95159918tab-stops:list .5in'><![if !supportLists]><span style='font-size:10.0pt;
    95169919mso-bidi-font-size:12.0pt;font-family:Symbol;mso-fareast-font-family:Symbol;
    … …  
    959710000<p class=MsoNormal><span style='color:#4A4A4A'><o:p>&nbsp;</o:p></span></p>
    959810001
    9599 <p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l21 level1 lfo37;
     10002<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l21 level1 lfo38;
    960010003tab-stops:list .5in'><![if !supportLists]><span style='font-size:10.0pt;
    960110004mso-bidi-font-size:12.0pt;font-family:Symbol;mso-fareast-font-family:Symbol;
    … …  
    960910012"Times New Roman";color:#4A4A4A;mso-char-type:symbol;mso-symbol-font-family:
    961010013Symbol'><span style='mso-char-type:symbol;mso-symbol-font-family:Symbol'>Q</span></span><span
    9611 style='color:#4A4A4A'> wide ring sampling area with and without an arc mask
    9612 positioned about 90° azimuth (top of image) with selected polarization values.
    9613 The integrations match with the correct polarization. You will be asked for a 2</span><span
     10014style='color:#4A4A4A'> wide ring sampling area with and without an arc mask positioned
     10015about 90° azimuth (top of image) with selected polarization values. The
     10016integrations match with the correct polarization. You will be asked for a 2</span><span
    961410017style='font-family:Symbol;mso-ascii-font-family:"Times New Roman";mso-hansi-font-family:
    961510018"Times New Roman";color:#4A4A4A;mso-char-type:symbol;mso-symbol-font-family:
    … …  
    962610029takes about 5min, so be patient.<o:p></o:p></span></p>
    962710030
    9628 <p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l21 level1 lfo37;
     10031<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l21 level1 lfo38;
    962910032tab-stops:list .5in'><![if !supportLists]><span style='font-size:10.0pt;
    963010033mso-bidi-font-size:12.0pt;font-family:Symbol;mso-fareast-font-family:Symbol;
    … …  
    964010043GSAS-II data tree. You can view it to see what the map looks like (select its
    964110044IMG entry). The gain map file can be imported into other projects using the
    9642 same detector. If selected in Image Controls, the image is immediately
    9643 corrected for the gain map.<o:p></o:p></span></p>
     10045same detector. If selected in Image Controls, the image is immediately corrected
     10046for the gain map.<o:p></o:p></span></p>
    964410047
    964510048<h4><a name="IMG_Comments">Comments</a></h4>
    … …  
    967510078keyboard/mouse shortcuts. There are five types of masks:<o:p></o:p></span></p>
    967610079
    9677 <p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l41 level1 lfo38;
     10080<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l41 level1 lfo39;
    967810081tab-stops:list .5in'><![if !supportLists]><span style='font-family:Symbol;
    967910082mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol;color:#4A4A4A'><span
    … …  
    968310086image coordinates (mm). <o:p></o:p></span></p>
    968410087
    9685 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l41 level1 lfo38;
     10088<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l41 level1 lfo39;
    968610089tab-stops:list .5in'><![if !supportLists]><span style='font-family:Symbol;
    968710090mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol;color:#4A4A4A'><span
    … …  
    969210095specified in degrees 2-theta. <o:p></o:p></span></p>
    969310096
    9694 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l41 level1 lfo38;
     10097<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l41 level1 lfo39;
    969510098tab-stops:list .5in'><![if !supportLists]><span style='font-family:Symbol;
    969610099mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol;color:#4A4A4A'><span
    969710100style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    969810101</span></span></span><![endif]><b><span style='color:#4A4A4A'>Arc masks</span></b><span
    9699 style='color:#4A4A4A'>: occlude a section of a Bragg reflection, similar to a
    9700 ring mask, except that in addition to the location and thickness of the ring,
    9701 the mask has a starting and ending azimuthal angle. <o:p></o:p></span></p>
    9702 
    9703 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l41 level1 lfo38;
     10102style='color:#4A4A4A'>: occlude a section of a Bragg reflection, <span
     10103class=GramE>similar to</span> a ring mask, except that in addition to the
     10104location and thickness of the ring, the mask has a starting and ending
     10105azimuthal angle. <o:p></o:p></span></p>
     10106
     10107<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l41 level1 lfo39;
    970410108tab-stops:list .5in'><![if !supportLists]><span style='font-family:Symbol;
    970510109mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol;color:#4A4A4A'><span
    … …  
    971010114the polygon mask are not used for integration. <o:p></o:p></span></p>
    971110115
    9712 <p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l41 level1 lfo38;
     10116<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l41 level1 lfo39;
    971310117tab-stops:list .5in'><![if !supportLists]><span style='font-family:Symbol;
    971410118mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol;color:#4A4A4A'><span
    … …  
    973110135
    973210136<p><span style='color:#4A4A4A'>The image is shown, as described above. Note
    9733 that The frame mask, if defined, is displayed in green, while the other types
    9734 of masks are shown in red.<o:p></o:p></span></p>
     10137that <span class=GramE>The</span> frame mask, if defined, is displayed in
     10138green, while the other types of masks are shown in red.<o:p></o:p></span></p>
    973510139
    973610140<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do with
    … …  
    974210146
    974310147<p class=MsoListParagraph style='margin-left:.25in;mso-add-space:auto;
    9744 text-indent:-.25in;mso-list:l46 level1 lfo39;tab-stops:list .25in'><![if !supportLists]><span
     10148text-indent:-.25in;mso-list:l46 level1 lfo40;tab-stops:list .25in'><![if !supportLists]><span
    974510149style='color:#4A4A4A'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    974610150</span></span></span><![endif]><b><span style='color:#4A4A4A'>Spot masks</span></b><span
    … …  
    975310157mso-fareast-theme-font:minor-fareast;color:#4A4A4A'><o:p></o:p></span></p>
    975410158
    9755 <p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l35 level1 lfo40;
     10159<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l35 level1 lfo41;
    975610160tab-stops:list .5in'><![if !supportLists]><span style='font-family:Symbol;
    975710161mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol;color:#4A4A4A'><span
    975810162style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    975910163</span></span></span><![endif]><span style='color:#4A4A4A'>Press the 's' key
    9760 and then left-click successively on multiple locations for spot masks. Press
    9761 the 's' key again or <a href="#Mac_rightclick">right-click*</a> to stop adding
    9762 spot masks. <o:p></o:p></span></p>
    9763 
    9764 <p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l35 level1 lfo40;
     10164and then <span class=GramE>left-click</span> successively on multiple locations
     10165for spot masks. Press the 's' key again or <a href="#Mac_rightclick">right-click*</a>
     10166to stop adding spot masks. <o:p></o:p></span></p>
     10167
     10168<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l35 level1 lfo41;
    976510169tab-stops:list .5in'><![if !supportLists]><span style='font-family:Symbol;
    976610170mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol;color:#4A4A4A'><span
    … …  
    977010174this can be used while the plot is in Zoom or Pan mode.) <o:p></o:p></span></p>
    977110175
    9772 <p><span style='color:#4A4A4A'>The default size for newly-created spot masks is
    9773 determined by the </span><tt><span style='font-size:10.0pt;color:#4A4A4A'>Spot_mask_diameter</span></tt><span
    9774 style='color:#4A4A4A'> <a href="#Preferences">configuration variable</a> or 1.0
    9775 mm, if not specified. </span><span style='mso-fareast-font-family:"Times New Roman";
    9776 mso-fareast-theme-font:minor-fareast;color:#4A4A4A'><o:p></o:p></span></p>
     10176<p><span style='color:#4A4A4A'>The default size for <span class=GramE>newly-created</span>
     10177spot masks is determined by the </span><tt><span style='font-size:10.0pt;
     10178color:#4A4A4A'>Spot_mask_diameter</span></tt><span style='color:#4A4A4A'> <a
     10179href="#Preferences">configuration variable</a> or 1.0 mm, if not specified. </span><span
     10180style='mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
     10181color:#4A4A4A'><o:p></o:p></span></p>
    977710182
    977810183<p><b><span style='color:#4A4A4A'>Edit Spot mask location</span></b><span
    9779 style='color:#4A4A4A'> by left-clicking inside or on the edge the of the mask
    9780 and then drag the spot mask to a new location. <o:p></o:p></span></p>
     10184style='color:#4A4A4A'> by <span class=GramE>left-clicking</span> inside or on
     10185the edge the of the mask and then drag the spot mask to a new location. <o:p></o:p></span></p>
    978110186
    978210187<p><b><span style='color:#4A4A4A'>Edit Spot mask radius</span></b><span
    … …  
    978510190
    978610191<p class=MsoListParagraph style='margin-left:.25in;mso-add-space:auto;
    9787 text-indent:-.25in;mso-list:l46 level1 lfo39;tab-stops:list .25in'><![if !supportLists]><span
     10192text-indent:-.25in;mso-list:l46 level1 lfo40;tab-stops:list .25in'><![if !supportLists]><span
    978810193style='color:#4A4A4A'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    978910194</span></span></span><![endif]><b><span style='color:#4A4A4A'>Ring masks</span></b><span
    … …  
    979310198mso-symbol-font-family:Symbol'><span style='mso-char-type:symbol;mso-symbol-font-family:
    979410199Symbol'>Q</span></span><span style='color:#4A4A4A'> as determined by the
    9795 calibration (e.g. a Bragg diffraction ring).<o:p></o:p></span></p>
     10200calibration (<span class=GramE>e.g.</span> a Bragg diffraction ring).<o:p></o:p></span></p>
    979610201
    979710202<p><b><span style='color:#4A4A4A'>Create Ring masks</span></b><span
    … …  
    980210207color:#4A4A4A'><o:p></o:p></span></p>
    980310208
    9804 <p><span style='color:#4A4A4A'>The default thickness for newly-created ring
    9805 masks is determined by the </span><tt><span style='font-size:10.0pt;color:#4A4A4A'>Ring_mask_thickness</span></tt><span
    9806 style='color:#4A4A4A'> <a href="#Preferences">configuration variable</a> or 0.1
    9807 degrees (2theta) if not specified. <o:p></o:p></span></p>
     10209<p><span style='color:#4A4A4A'>The default thickness for <span class=GramE>newly-created</span>
     10210ring masks is determined by the </span><tt><span style='font-size:10.0pt;
     10211color:#4A4A4A'>Ring_mask_thickness</span></tt><span style='color:#4A4A4A'> <a
     10212href="#Preferences">configuration variable</a> or 0.1 degrees (2theta) if not
     10213specified. <o:p></o:p></span></p>
    980810214
    980910215<p><b><span style='color:#4A4A4A'>Edit Ring mask location</span></b><span
    9810 style='color:#4A4A4A'> by left-clicking on either the inner or outer circle and
    9811 drag the circle to the new radius. <o:p></o:p></span></p>
     10216style='color:#4A4A4A'> by <span class=GramE>left-clicking</span> on either the
     10217inner or outer circle and drag the circle to the new radius. <o:p></o:p></span></p>
    981210218
    981310219<p><b><span style='color:#4A4A4A'>Edit Ring mask thickness</span></b><span
    … …  
    981710223
    981810224<p class=MsoListParagraph style='margin-left:.25in;mso-add-space:auto;
    9819 text-indent:-.25in;mso-list:l46 level1 lfo39;tab-stops:list .25in'><![if !supportLists]><span
     10225text-indent:-.25in;mso-list:l46 level1 lfo40;tab-stops:list .25in'><![if !supportLists]><span
    982010226style='color:#4A4A4A'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    982110227</span></span></span><![endif]><b><span style='color:#4A4A4A'>Arc masks</span></b><span
    … …  
    982410230"Times New Roman";color:#4A4A4A;mso-char-type:symbol;mso-symbol-font-family:
    982510231Symbol'><span style='mso-char-type:symbol;mso-symbol-font-family:Symbol'>Q</span></span><span
    9826 style='color:#4A4A4A'>, similar to a ring mask, except that in addition to the
    9827 location and thickness of the ring, the mask has a starting and ending
    9828 azimuthal angle. <o:p></o:p></span></p>
     10232style='color:#4A4A4A'>, <span class=GramE>similar to</span> a ring mask, except
     10233that in addition to the location and thickness of the ring, the mask has a
     10234starting and ending azimuthal angle. <o:p></o:p></span></p>
    982910235
    983010236<p><b><span style='color:#4A4A4A'>Create Arc masks</span></b><span
    … …  
    983510241color:#4A4A4A'><o:p></o:p></span></p>
    983610242
    9837 <p><span style='color:#4A4A4A'>The default size for newly-created ring masks is
    9838 determined by <a href="#Preferences">configuration variables</a><br>
     10243<p><span style='color:#4A4A4A'>The default size for <span class=GramE>newly-created</span>
     10244ring masks is determined by <a href="#Preferences">configuration variables</a><br>
    983910245thickness: </span><tt><span style='font-size:10.0pt;color:#4A4A4A'>Ring_mask_thickness</span></tt><span
    984010246style='color:#4A4A4A'> (0.1 degrees 2theta if not specified) and <br>
    … …  
    984310249
    984410250<p><b><span style='color:#4A4A4A'>Edit Arc mask location</span></b><span
    9845 style='color:#4A4A4A'> by left-clicking on either the inner or outer circle and
    9846 drag the circle to the new radius. Alternately, left-click on the upper or
    9847 lower arc limit (the straight lines) and drag them to rotate the center of the
    9848 arc azimuthal range to a new position. <o:p></o:p></span></p>
     10251style='color:#4A4A4A'> by <span class=GramE>left-clicking</span> on either the
     10252inner or outer circle and drag the circle to the new radius. Alternately, <span
     10253class=GramE>left-click</span> on the upper or lower arc limit (the straight
     10254lines) and drag them to rotate the center of the arc azimuthal range to a new
     10255position. <o:p></o:p></span></p>
    984910256
    985010257<p><b><span style='color:#4A4A4A'>Edit Arc mask thickness or range</span></b><span
    … …  
    985610263
    985710264<p class=MsoListParagraph style='margin-left:.25in;mso-add-space:auto;
    9858 text-indent:-.25in;mso-list:l46 level1 lfo39;tab-stops:list .25in'><![if !supportLists]><span
     10265text-indent:-.25in;mso-list:l46 level1 lfo40;tab-stops:list .25in'><![if !supportLists]><span
    985910266style='color:#4A4A4A'><span style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    986010267</span></span></span><![endif]><b><span style='color:#4A4A4A'>Polygon masks</span></b><span
    … …  
    986410271
    986510272<p><b><span style='color:#4A4A4A'>Create Polygon masks</span></b><span
    9866 style='color:#4A4A4A'> with a menu command and then by left-clicking
     10273style='color:#4A4A4A'> with a menu command and then by <span class=GramE>left-clicking</span>
    986710274successively on the vertices of the polygon shape surrounding pixels to be
    986810275excluded. After the last point is defined, <a href="#Mac_rightclick">right-click*</a>
    … …  
    987310280
    987410281<p><b><span style='color:#4A4A4A'>Edit Polygon mask</span></b><span
    9875 style='color:#4A4A4A'> by left-clicking on any point at a vertex in the polygon
    9876 mask and drag that point to a new position. If the vertex is dragged to the
    9877 same position as any other vertex in the mask the dragged point is deleted. <o:p></o:p></span></p>
     10282style='color:#4A4A4A'> by <span class=GramE>left-clicking</span> on any point
     10283at a vertex in the polygon mask and drag that point to a new position. If the
     10284vertex is dragged to the same position as any other vertex in the mask the
     10285dragged point is deleted. <o:p></o:p></span></p>
    987810286
    987910287<p><b><span style='color:#4A4A4A'>Add a point to Polygon mask</span></b><span
    … …  
    988310291
    988410292<p class=MsoListParagraph style='margin-left:.25in;mso-add-space:auto;
    9885 text-indent:-.25in;mso-list:l46 level1 lfo39;tab-stops:list .25in'><![if !supportLists]><span
     10293text-indent:-.25in;mso-list:l46 level1 lfo40;tab-stops:list .25in'><![if !supportLists]><span
    988610294style='color:#4A4A4A'><span style='mso-list:Ignore'>5.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    988710295</span></span></span><![endif]><b><span style='color:#4A4A4A'>Frame mask</span></b><span
    … …  
    989210300
    989310301<p><b><span style='color:#4A4A4A'>Create a Frame mask</span></b><span
    9894 style='color:#4A4A4A'> with a menu command and then by left-clicking
     10302style='color:#4A4A4A'> with a menu command and then by <span class=GramE>left-clicking</span>
    989510303successively on the vertices of a polygon. After the last point is defined, <a
    989610304href="#Mac_rightclick">right-click*</a> anywhere to close the frame mask. Alternately,
    … …  
    990310311
    990410312<p><b><span style='color:#4A4A4A'>Edit the Frame mask</span></b><span
    9905 style='color:#4A4A4A'> by left-clicking on any point at a vertex in the frame
    9906 mask and drag that point to a new position. If the vertex is dragged to the
    9907 same position as any other vertex in the mask the dragged point is deleted. <o:p></o:p></span></p>
     10313style='color:#4A4A4A'> by <span class=GramE>left-clicking</span> on any point
     10314at a vertex in the frame mask and drag that point to a new position. If the
     10315vertex is dragged to the same position as any other vertex in the mask the
     10316dragged point is deleted. <o:p></o:p></span></p>
    990810317
    990910318<p><b><span style='color:#4A4A4A'>Add a point to the Frame mask</span></b><span
    … …  
    992010329
    992110330<p class=MsoNormal><span style='color:#4A4A4A'>This allows one to evaluate
    9922 strain typically induced by a pure axial load (e.g. no shear) on a
    9923 polycrystalline sample (e.g. a steel bar). This strain will distort the Bragg
    9924 diffraction rings seen by the 2D detector. This follows the method of He &amp;
    9925 Smith (Baoping Bob He &amp; Kingsley Smith, (1997). Adv. in X-Ray Anal. 41,
    9926 501.) to determine the 3 unique terms of the axial strain tensor. One can
    9927 examine the results as a series of diffraction line d-spacings vs azimuth
     10331strain typically induced by a pure axial load (<span class=GramE>e.g.</span> no
     10332shear) on a polycrystalline sample (e.g. a steel bar). This strain will distort
     10333the Bragg diffraction rings seen by the 2D detector. This follows the method of
     10334He &amp; Smith (Baoping Bob He &amp; Kingsley Smith, (1997). Adv. in X-Ray
     10335Anal. 41, 501.) to determine the 3 unique terms of the axial strain tensor. One
     10336can examine the results as a series of diffraction line d-spacings vs azimuth
    992810337angle; if no strain these are straight, otherwise they will show a single
    992910338sinusoidal variation with maxima at the maximum strain direction (90° &amp;
    … …  
    994210351<p class=MsoNormal><span style='color:#4A4A4A'>Menu Operations - <o:p></o:p></span></p>
    994310352
    9944 <p style='margin-left:.5in;text-indent:-.25in;mso-list:l6 level1 lfo41'><![if !supportLists]><span
     10353<p style='margin-left:.5in;text-indent:-.25in;mso-list:l6 level1 lfo42'><![if !supportLists]><span
    994510354style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    994610355Symbol;color:#4A4A4A'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    … …  
    994910358list; this also can be done by picking a ring from the plot.<o:p></o:p></span></p>
    995010359
    9951 <p style='margin-left:.5in;text-indent:-.25in;mso-list:l6 level1 lfo41'><![if !supportLists]><span
     10360<p style='margin-left:.5in;text-indent:-.25in;mso-list:l6 level1 lfo42'><![if !supportLists]><span
    995210361style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    995310362Symbol;color:#4A4A4A'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    … …  
    996010369value for any residual stress/strain.<o:p></o:p></span></p>
    996110370
    9962 <p style='margin-left:.5in;text-indent:-.25in;mso-list:l6 level1 lfo41'><![if !supportLists]><span
     10371<p style='margin-left:.5in;text-indent:-.25in;mso-list:l6 level1 lfo42'><![if !supportLists]><span
    996310372style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    996410373Symbol;color:#4A4A4A'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    … …  
    996710376with azimuth for each ring.<o:p></o:p></span></p>
    996810377
    9969 <p style='margin-left:.5in;text-indent:-.25in;mso-list:l6 level1 lfo41'><![if !supportLists]><span
     10378<p style='margin-left:.5in;text-indent:-.25in;mso-list:l6 level1 lfo42'><![if !supportLists]><span
    997010379style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    997110380Symbol;color:#4A4A4A'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    … …  
    997410383distribution curves as a simple text file<o:p></o:p></span></p>
    997510384
    9976 <p style='margin-left:.5in;text-indent:-.25in;mso-list:l6 level1 lfo41'><![if !supportLists]><span
     10385<p style='margin-left:.5in;text-indent:-.25in;mso-list:l6 level1 lfo42'><![if !supportLists]><span
    997710386style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    997810387Symbol;color:#4A4A4A'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    997910388</span></span></span><![endif]><b><span style='color:#4A4A4A'>Update d-zero</span></b><span
    9980 style='color:#4A4A4A'> – this updates the d-zero values with the d-zero ave
    9981 ones thus removing any effect of residual stress/strain.<o:p></o:p></span></p>
    9982 
    9983 <p style='margin-left:.5in;text-indent:-.25in;mso-list:l6 level1 lfo41'><![if !supportLists]><span
     10389style='color:#4A4A4A'> – <span class=GramE>this updates</span> the d-zero
     10390values with the d-zero ave ones thus removing any effect of residual
     10391stress/strain.<o:p></o:p></span></p>
     10392
     10393<p style='margin-left:.5in;text-indent:-.25in;mso-list:l6 level1 lfo42'><![if !supportLists]><span
    998410394style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    998510395Symbol;color:#4A4A4A'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    … …  
    999010400fit results</b>.<o:p></o:p></span></p>
    999110401
    9992 <p style='margin-left:.5in;text-indent:-.25in;mso-list:l6 level1 lfo41'><![if !supportLists]><span
     10402<p style='margin-left:.5in;text-indent:-.25in;mso-list:l6 level1 lfo42'><![if !supportLists]><span
    999310403style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    999410404Symbol;color:#4A4A4A'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    … …  
    999610406stress/strain</span></b><span style='color:#4A4A4A'> – this copies the
    999710407stress/strain data from the current image to other selected images in
    9998 preparation for doing an <b>All image fit</b>.<o:p></o:p></span></p>
    9999 
    10000 <p style='margin-left:.5in;text-indent:-.25in;mso-list:l6 level1 lfo41'><![if !supportLists]><span
     10408preparation for doing an <span class=GramE><b>All image</b></span><b> fit</b>.<o:p></o:p></span></p>
     10409
     10410<p style='margin-left:.5in;text-indent:-.25in;mso-list:l6 level1 lfo42'><![if !supportLists]><span
    1000110411style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    1000210412Symbol;color:#4A4A4A'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    1000310413</span></span></span><![endif]><b><span style='color:#4A4A4A'>Save
    1000410414stress/strain</span></b><span style='color:#4A4A4A'> – this saves the current
    10005 stress/strain data to a file with .strsta extension.<o:p></o:p></span></p>
    10006 
    10007 <p style='margin-left:.5in;text-indent:-.25in;mso-list:l6 level1 lfo41'><![if !supportLists]><span
     10415stress/strain data to a file <span class=GramE>with .strsta</span> extension.<o:p></o:p></span></p>
     10416
     10417<p style='margin-left:.5in;text-indent:-.25in;mso-list:l6 level1 lfo42'><![if !supportLists]><span
    1000810418style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    1000910419Symbol;color:#4A4A4A'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    1001010420</span></span></span><![endif]><b><span style='color:#4A4A4A'>Load
    1001110421stress/strain</span></b><span style='color:#4A4A4A'> – this loads previously
    10012 saved stress/strain data from a file with .strsta extension.<o:p></o:p></span></p>
    10013 
    10014 <p style='margin-left:.5in;text-indent:-.25in;mso-list:l6 level1 lfo41'><![if !supportLists]><span
     10422saved stress/strain data from a file <span class=GramE>with .strsta</span>
     10423extension.<o:p></o:p></span></p>
     10424
     10425<p style='margin-left:.5in;text-indent:-.25in;mso-list:l6 level1 lfo42'><![if !supportLists]><span
    1001510426style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    1001610427Symbol;color:#4A4A4A'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    … …  
    1004610457
    1004710458<p class=MsoNormal><span style='color:#4A4A4A'>The Ring intensities plot will
    10048 respond to the following key strokes:<o:p></o:p></span></p>
    10049 
    10050 <p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l9 level1 lfo42'><![if !supportLists]><span
     10459respond to the following <span class=GramE>key strokes</span>:<o:p></o:p></span></p>
     10460
     10461<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l9 level1 lfo43'><![if !supportLists]><span
    1005110462style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    1005210463Symbol;color:#4A4A4A'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    … …  
    1005410465this progressively shifts the RMD lines to the left<o:p></o:p></span></p>
    1005510466
    10056 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l9 level1 lfo42'><![if !supportLists]><span
     10467<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l9 level1 lfo43'><![if !supportLists]><span
    1005710468style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    1005810469Symbol;color:#4A4A4A'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    … …  
    1006010471this progressively shifts the RMD lines to the right<o:p></o:p></span></p>
    1006110472
    10062 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l9 level1 lfo42'><![if !supportLists]><span
     10473<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l9 level1 lfo43'><![if !supportLists]><span
    1006310474style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    1006410475Symbol;color:#4A4A4A'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    … …  
    1006610477this progressively shifts the RMD lines up<o:p></o:p></span></p>
    1006710478
    10068 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l9 level1 lfo42'><![if !supportLists]><span
     10479<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l9 level1 lfo43'><![if !supportLists]><span
    1006910480style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    1007010481Symbol;color:#4A4A4A'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    … …  
    1007210483this progressively shifts the RMD lines down<o:p></o:p></span></p>
    1007310484
    10074 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l9 level1 lfo42'><![if !supportLists]><span
     10485<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l9 level1 lfo43'><![if !supportLists]><span
    1007510486style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    1007610487Symbol;color:#4A4A4A'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    … …  
    1007810489this resets the shifts to zero<o:p></o:p></span></p>
    1007910490
    10080 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l9 level1 lfo42'><![if !supportLists]><span
     10491<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l9 level1 lfo43'><![if !supportLists]><span
    1008110492style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    1008210493Symbol;color:#4A4A4A'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    10083 </span></span></span><![endif]><span style='color:#4A4A4A'>Key ‘<b>g</b>’ –
    10084 this toggles display of a grid on the plot<o:p></o:p></span></p>
    10085 
    10086 <p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l9 level1 lfo42'><![if !supportLists]><span
     10494</span></span></span><![endif]><span style='color:#4A4A4A'>Key ‘<b>g</b>’ – <span
     10495class=GramE>this toggles</span> display of a grid on the plot<o:p></o:p></span></p>
     10496
     10497<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l9 level1 lfo43'><![if !supportLists]><span
    1008710498style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    1008810499Symbol;color:#4A4A4A'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    … …  
    1010110512<p class=MsoNormal><span style='color:#4A4A4A'>This window shows whatever
    1010210513comment lines (preceded by “#”) found when the peaks data file was read by
    10103 GSAS-II. If you are lucky, there will be useful information here (e.g. sample
    10104 name, date collected, wavelength used, etc.). If not, this window will be
    10105 blank. The text is read-only.</span><span style='mso-fareast-font-family:"Times New Roman";
    10106 mso-fareast-theme-font:minor-fareast;color:#4A4A4A'><o:p></o:p></span></p>
     10514GSAS-II. If you are lucky, there will be useful information here (<span
     10515class=GramE>e.g.</span> sample name, date collected, wavelength used, etc.). If
     10516not, this window will be blank. The text is read-only.</span><span
     10517style='mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
     10518color:#4A4A4A'><o:p></o:p></span></p>
    1010710519
    1010810520<h4><a name="PKS_Limits">Limits</a></h4>
    … …  
    1012710539<p><span style='color:#4A4A4A'>Menu ‘<b>Edit Limits</b>’ <o:p></o:p></span></p>
    1012810540
    10129 <p class=MsoListParagraph style='text-indent:-.25in;mso-list:l58 level1 lfo43;
     10541<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l58 level1 lfo44;
    1013010542tab-stops:list .5in'><![if !supportLists]><span style='font-family:Symbol;
    1013110543mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol;color:#4A4A4A'><span
    … …  
    1015610568
    1015710569<p class=MsoListParagraphCxSpFirst style='margin-left:.25in;mso-add-space:auto;
    10158 text-indent:-.25in;mso-list:l13 level1 lfo44'><span style='mso-bookmark:PKS_Instrument_Parameters'><![if !supportLists]><span
     10570text-indent:-.25in;mso-list:l13 level1 lfo45'><span style='mso-bookmark:PKS_Instrument_Parameters'><![if !supportLists]><span
    1015910571class=MsoHyperlink><span style='color:windowtext;text-decoration:none;
    1016010572text-underline:none'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    … …  
    1016510577text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p>
    1016610578
    10167 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l0 level1 lfo45'><span
     10579<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l0 level1 lfo46'><span
    1016810580style='mso-bookmark:PKS_Instrument_Parameters'><![if !supportLists]><span
    1016910581class=MsoHyperlink><span style='font-family:Symbol;mso-fareast-font-family:
    … …  
    1017810590text-underline:none'><o:p></o:p></span></span></span></p>
    1017910591
    10180 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l0 level1 lfo45'><span
     10592<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l0 level1 lfo46'><span
    1018110593style='mso-bookmark:PKS_Instrument_Parameters'><![if !supportLists]><span
    1018210594class=MsoHyperlink><span style='font-family:Symbol;mso-fareast-font-family:
    … …  
    1018510597</span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
    1018610598style='color:#4A4A4A'>Load profile… </span></b><span style='color:#4A4A4A'>-
    10187 loads a GSAS-II instrument parameter file (name.instprm), replacing the
    10188 existing instrument parameter values. All refinement flags are unset.</span><span
    10189 class=MsoHyperlink><b style='mso-bidi-font-weight:normal'><span
     10599loads a GSAS-II instrument parameter file (<span class=GramE>name.instprm</span>),
     10600replacing the existing instrument parameter values. All refinement flags are
     10601unset.</span><span class=MsoHyperlink><b style='mso-bidi-font-weight:normal'><span
    1019010602style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></b></span></span></p>
    1019110603
    10192 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l0 level1 lfo45'><span
     10604<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l0 level1 lfo46'><span
    1019310605style='mso-bookmark:PKS_Instrument_Parameters'><![if !supportLists]><span
    1019410606style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    … …  
    1019610608</span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
    1019710609style='color:#4A4A4A'>Save profile… - </span></b><span style='color:#4A4A4A'>saves
    10198 the current instrument parameter values in a simple text file (name.instprm);
    10199 you will be prompted for the file name – do not change the extension. This file
    10200 may be edited but heed the warning to not change the parameter names, the order
    10201 of the parameter records or add new parameter records as this will invalidate
    10202 the file. You may only change the numeric values if necessary. You can change
    10203 or add comment records (begin with ‘#’).</span></span><span style='mso-bookmark:
    10204 PKS_Instrument_Parameters'><span style='mso-fareast-font-family:"Times New Roman";
    10205 mso-fareast-theme-font:minor-fareast;color:#4A4A4A'><o:p></o:p></span></span></p>
    10206 
    10207 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l0 level1 lfo45'><span
     10610the current instrument parameter values in a simple text file (<span
     10611class=GramE>name.instprm</span>); you will be prompted for the file name – do
     10612not change the extension. This file may be edited but heed the warning to not
     10613change the parameter names, the order of the parameter records or add new
     10614parameter records as this will invalidate the file. You may only change the
     10615numeric values if necessary. You can change or add comment records (begin with
     10616‘#’).</span></span><span style='mso-bookmark:PKS_Instrument_Parameters'><span
     10617style='mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
     10618color:#4A4A4A'><o:p></o:p></span></span></p>
     10619
     10620<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l0 level1 lfo46'><span
    1020810621style='mso-bookmark:PKS_Instrument_Parameters'><![if !supportLists]><span
    1020910622style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    … …  
    1021810631
    1021910632<p class=MsoListParagraphCxSpLast style='margin-left:.25in;mso-add-space:auto;
    10220 text-indent:-.25in;mso-list:l36 level1 lfo46'><span style='mso-bookmark:PKS_Instrument_Parameters'><![if !supportLists]><span
     10633text-indent:-.25in;mso-list:l36 level1 lfo47'><span style='mso-bookmark:PKS_Instrument_Parameters'><![if !supportLists]><span
    1022110634class=MsoHyperlink><span style='color:windowtext;text-decoration:none;
    1022210635text-underline:none'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    … …  
    1024610659style='mso-bookmark:PKS_Index_Peak_List'><b>Unit Cells List</b></span><span
    1024710660style='mso-bookmark:PKS_Index_Peak_List'></span></a><span style='mso-bookmark:
    10248 PKS_Index_Peak_List'><span style='color:#4A4A4A'>. .</span><span
     10661PKS_Index_Peak_List'><span class=GramE><span style='color:#4A4A4A'>. .</span></span><span
    1024910662class=MsoHyperlink><span style='color:windowtext;text-decoration:none;
    1025010663text-underline:none'><o:p></o:p></span></span></span></p>
    … …  
    1025510668
    1025610669<p class=MsoListParagraph style='margin-left:.25in;mso-add-space:auto;
    10257 text-indent:-.25in;mso-list:l10 level1 lfo47'><span style='mso-bookmark:PKS_Index_Peak_List'><![if !supportLists]><span
     10670text-indent:-.25in;mso-list:l10 level1 lfo48'><span style='mso-bookmark:PKS_Index_Peak_List'><![if !supportLists]><span
    1025810671style='color:#4A4A4A'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    1025910672</span></span></span><![endif]><span style='color:#4A4A4A'>You may deselect individual
    … …  
    1030610719<o:p></o:p></span></span></p>
    1030710720
    10308 <p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l53 level1 lfo48;
     10721<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l53 level1 lfo49;
    1030910722tab-stops:list .5in'><span style='mso-bookmark:PKS_Unit_Cells_List'><![if !supportLists]><span
    1031010723style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    … …  
    1031510728changed. <o:p></o:p></span></span></p>
    1031610729
    10317 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l53 level1 lfo48;
     10730<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l53 level1 lfo49;
    1031810731tab-stops:list .5in'><span style='mso-bookmark:PKS_Unit_Cells_List'><![if !supportLists]><span
    1031910732style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    … …  
    1032310736changed. <o:p></o:p></span></span></p>
    1032410737
    10325 <p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l53 level1 lfo48;
     10738<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l53 level1 lfo49;
    1032610739tab-stops:list .5in'><span style='mso-bookmark:PKS_Unit_Cells_List'><![if !supportLists]><span
    1032710740style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    … …  
    1038210795<span style='mso-bookmark:Laue_List'></span>
    1038310796
    10384 <p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l15 level1 lfo49;
     10797<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l15 level1 lfo50;
    1038510798tab-stops:list .5in'><span style='mso-bookmark:PKS_Unit_Cells_List'><![if !supportLists]><span
    1038610799style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Symbol;
    … …  
    1039010803&amp; Pm3m <o:p></o:p></span></span></p>
    1039110804
    10392 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l15 level1 lfo49;
     10805<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l15 level1 lfo50;
    1039310806tab-stops:list .5in'><span style='mso-bookmark:PKS_Unit_Cells_List'><![if !supportLists]><span
    1039410807style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Symbol;
    … …  
    1039810811(hexagonal axes) <o:p></o:p></span></span></p>
    1039910812
    10400 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l15 level1 lfo49;
     10813<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l15 level1 lfo50;
    1040110814tab-stops:list .5in'><span style='mso-bookmark:PKS_Unit_Cells_List'><![if !supportLists]><span
    1040210815style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Symbol;
    … …  
    1040510818</span></span></span><![endif]><span style='color:#4A4A4A'>Hexagonal: P6/mmm <o:p></o:p></span></span></p>
    1040610819
    10407 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l15 level1 lfo49;
     10820<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l15 level1 lfo50;
    1040810821tab-stops:list .5in'><span style='mso-bookmark:PKS_Unit_Cells_List'><![if !supportLists]><span
    1040910822style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Symbol;
    … …  
    1041310826P4/mmm <o:p></o:p></span></span></p>
    1041410827
    10415 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l15 level1 lfo49;
     10828<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l15 level1 lfo50;
    1041610829tab-stops:list .5in'><span style='mso-bookmark:PKS_Unit_Cells_List'><![if !supportLists]><span
    1041710830style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Symbol;
    … …  
    1042110834Immm, Ammm, Bmmm, Cmmm, Pmmm <o:p></o:p></span></span></p>
    1042210835
    10423 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l15 level1 lfo49;
     10836<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l15 level1 lfo50;
    1042410837tab-stops:list .5in'><span style='mso-bookmark:PKS_Unit_Cells_List'><![if !supportLists]><span
    1042510838style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Symbol;
    … …  
    1042910842A2/m, C2/m, P2/m (b-unique) <o:p></o:p></span></span></p>
    1043010843
    10431 <p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l15 level1 lfo49;
     10844<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l15 level1 lfo50;
    1043210845tab-stops:list .5in'><span style='mso-bookmark:PKS_Unit_Cells_List'><![if !supportLists]><span
    1043310846style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Symbol;
    … …  
    1044610859<p class=MsoNormal><span style='color:#4A4A4A'>This window shows whatever
    1044710860comment lines found above the QIE table when the small angle data file was read
    10448 by GSAS-II. If you are lucky, there will be useful information here (e.g.
    10449 sample name, date collected, wavelength used, etc.). If not, this window will
    10450 be blank. The text is read-only.</span><span style='mso-fareast-font-family:
    10451 "Times New Roman";mso-fareast-theme-font:minor-fareast;color:#4A4A4A'><o:p></o:p></span></p>
     10861by GSAS-II. If you are lucky, there will be useful information here (<span
     10862class=GramE>e.g.</span> sample name, date collected, wavelength used, etc.). If
     10863not, this window will be blank. The text is read-only.</span><span
     10864style='mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
     10865color:#4A4A4A'><o:p></o:p></span></p>
    1045210866
    1045310867<h4><a name="SASD_Limits">Limits</a></h4>
    … …  
    1047510889Limits</b>’ <o:p></o:p></span></span></p>
    1047610890
    10477 <p class=MsoListParagraph style='text-indent:-.25in;mso-list:l14 level1 lfo50;
     10891<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l14 level1 lfo51;
    1047810892tab-stops:list .5in'><span style='mso-bookmark:SASD_Limits'><![if !supportLists]><span
    1047910893style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    … …  
    1050610920style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></p>
    1050710921
    10508 <p class=MsoListParagraph style='text-indent:-.25in;mso-list:l14 level1 lfo50;
     10922<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l14 level1 lfo51;
    1050910923tab-stops:list .5in'><![if !supportLists]><span style='font-family:Symbol;
    1051010924mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol;color:#4A4A4A;
    … …  
    1053910953
    1054010954<p class=MsoListParagraphCxSpFirst style='margin-left:.25in;mso-add-space:auto;
    10541 text-indent:-.25in;mso-list:l40 level1 lfo51;tab-stops:list .25in'><span
     10955text-indent:-.25in;mso-list:l40 level1 lfo52;tab-stops:list .25in'><span
    1054210956style='mso-bookmark:SASD_Substances'><![if !supportLists]><span
    1054310957style='color:#4A4A4A'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    … …  
    1054510959substance</b>’ –<o:p></o:p></span></span></p>
    1054610960
    10547 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l5 level1 lfo52;
     10961<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l5 level1 lfo53;
    1054810962tab-stops:list .5in'><span style='mso-bookmark:SASD_Substances'><![if !supportLists]><span
    1054910963style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    … …  
    1055510969in Substances.py. Place your UserSubstances.py in the GSAS-II directory.<o:p></o:p></span></span></p>
    1055610970
    10557 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l5 level1 lfo52;
     10971<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l5 level1 lfo53;
    1055810972tab-stops:list .5in'><span style='mso-bookmark:SASD_Substances'><![if !supportLists]><span
    1055910973style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    … …  
    1056310977substances.<o:p></o:p></span></span></p>
    1056410978
    10565 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l5 level1 lfo52;
     10979<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l5 level1 lfo53;
    1056610980tab-stops:list .5in'><span style='mso-bookmark:SASD_Substances'><![if !supportLists]><span
    1056710981style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    … …  
    1057210986volume/density; GSAS-II will compute the scattering contrast data for it.<o:p></o:p></span></span></p>
    1057310987
    10574 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l5 level1 lfo52;
     10988<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l5 level1 lfo53;
    1057510989tab-stops:list .5in'><span style='mso-bookmark:SASD_Substances'><![if !supportLists]><span
    1057610990style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    … …  
    1058010994other small angle data histograms.<o:p></o:p></span></span></p>
    1058110995
    10582 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l5 level1 lfo52;
     10996<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l5 level1 lfo53;
    1058310997tab-stops:list .5in'><span style='mso-bookmark:SASD_Substances'><![if !supportLists]><span
    1058410998style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    … …  
    1058811002or unit scatterer.<o:p></o:p></span></span></p>
    1058911003
    10590 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l5 level1 lfo52;
     11004<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l5 level1 lfo53;
    1059111005tab-stops:list .5in'><span style='mso-bookmark:SASD_Substances'><![if !supportLists]><span
    1059211006style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    … …  
    1059611010substance.<o:p></o:p></span></span></p>
    1059711011
    10598 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l5 level1 lfo52;
     11012<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l5 level1 lfo53;
    1059911013tab-stops:list .5in'><span style='mso-bookmark:SASD_Substances'><![if !supportLists]><span
    1060011014style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    … …  
    1060411018
    1060511019<p class=MsoListParagraphCxSpLast style='margin-left:.25in;mso-add-space:auto;
    10606 text-indent:-.25in;mso-list:l40 level1 lfo51;tab-stops:list .25in'><span
     11020text-indent:-.25in;mso-list:l40 level1 lfo52;tab-stops:list .25in'><span
    1060711021style='mso-bookmark:SASD_Substances'><![if !supportLists]><span
    1060811022style='color:#4A4A4A'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    … …  
    1063511049
    1063611050<p><span style='mso-bookmark:SASD_Models'><b><span style='color:#4A4A4A'>Command</span></b><span
    10637 style='color:#4A4A4A'> Menu<span style='mso-spacerun:yes'>  </span>- In this
    10638 window you can change parameters associated with a histogram. This histogram
    10639 scale factor is ignored for SASD. Remaining parameters are of use for
    10640 parametric studies and may be changed with the menu commands described here. <o:p></o:p></span></span></p>
    10641 
    10642 <p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l50 level1 lfo53;
     11051style='color:#4A4A4A'> <span class=GramE>Menu<span style='mso-spacerun:yes'> 
     11052</span>-</span> In this window you can change parameters associated with a
     11053histogram. This histogram scale factor is ignored for SASD. Remaining
     11054parameters are of use for parametric studies and may be changed with the menu
     11055commands described here. <o:p></o:p></span></span></p>
     11056
     11057<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l50 level1 lfo54;
    1064311058tab-stops:list .5in'><span style='mso-bookmark:SASD_Models'><![if !supportLists]><span
    1064411059style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    … …  
    1064911064SASD scans<o:p></o:p></span></span></p>
    1065011065
    10651 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l50 level1 lfo53;
     11066<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l50 level1 lfo54;
    1065211067tab-stops:list .5in'><span style='mso-bookmark:SASD_Models'><![if !supportLists]><span
    1065311068style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    1065411069Symbol;color:#4A4A4A'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    1065511070</span></span></span><![endif]><b><span style='color:#4A4A4A'>Load - </span></b><span
    10656 style='color:#4A4A4A'>This loads sample parameters from a previously saved
    10657 .samprm file. <o:p></o:p></span></span></p>
    10658 
    10659 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l50 level1 lfo53;
     11071style='color:#4A4A4A'>This loads sample parameters from a previously <span
     11072class=GramE>saved .samprm</span> file. <o:p></o:p></span></span></p>
     11073
     11074<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l50 level1 lfo54;
    1066011075tab-stops:list .5in'><span style='mso-bookmark:SASD_Models'><![if !supportLists]><span
    1066111076style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    1066211077Symbol;color:#4A4A4A'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    1066311078</span></span></span><![endif]><b><span style='color:#4A4A4A'>Save - </span></b><span
    10664 style='color:#4A4A4A'>This saves the sample parameters to a file with the
    10665 extension ’.samprm’. A file dialog box will appear to ask for the name of the
    10666 file to be written. <o:p></o:p></span></span></p>
    10667 
    10668 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l50 level1 lfo53;
     11079style='color:#4A4A4A'>This saves the sample parameters to a file with the <span
     11080class=GramE>extension ’</span>.samprm’. A file dialog box will appear to ask
     11081for the name of the file to be written. <o:p></o:p></span></span></p>
     11082
     11083<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l50 level1 lfo54;
    1066911084tab-stops:list .5in'><span style='mso-bookmark:SASD_Models'><![if !supportLists]><span
    1067011085style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    1067111086Symbol;color:#4A4A4A'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    10672 </span></span></span><![endif]><b><span style='color:#4A4A4A'>Copy<span
    10673 style='mso-spacerun:yes'>  </span></span></b><span style='color:#4A4A4A'>This copies
    10674 the sample parameters shown to other selected SASD patterns. If used, a dialog
    10675 box (Copy parameters) will appear showing the list of available SASD patterns,
    10676 you can copy the sample parameters to any or all of them; select ‘All’ to copy
    10677 them to all patterns. Then select ‘OK’ to do the copy; ‘Cancel’ to cancel the
    10678 operation. <o:p></o:p></span></span></p>
    10679 
    10680 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l50 level1 lfo53;
     11087</span></span></span><![endif]><span class=GramE><b><span style='color:#4A4A4A'>Copy<span
     11088style='mso-spacerun:yes'>  </span></span></b><span style='color:#4A4A4A'>This</span></span><span
     11089style='color:#4A4A4A'> copies the sample parameters shown to other selected
     11090SASD patterns. If used, a dialog box (Copy parameters) will appear showing the
     11091list of available SASD patterns, you can copy the sample parameters to any or
     11092all of them; select ‘All’ to copy them to all patterns. Then select ‘OK’ to do
     11093the copy; ‘Cancel’ to cancel the operation. <o:p></o:p></span></span></p>
     11094
     11095<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l50 level1 lfo54;
    1068111096tab-stops:list .5in'><span style='mso-bookmark:SASD_Models'><![if !supportLists]><span
    1068211097style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    … …  
    1068411099</span></span></span><![endif]><b><span style='color:#4A4A4A'>Copy selected...
    1068511100- </span></b><span style='color:#4A4A4A'>This copies only the sample parameter
    10686 that are selected to other selected SASD patterns but is otherwise similar to
    10687 &quot;Copy&quot;. <o:p></o:p></span></span></p>
    10688 
    10689 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l50 level1 lfo53;
     11101that are selected to other selected SASD patterns but is otherwise <span
     11102class=GramE>similar to</span> &quot;Copy&quot;. <o:p></o:p></span></span></p>
     11103
     11104<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l50 level1 lfo54;
    1069011105tab-stops:list .5in'><span style='mso-bookmark:SASD_Models'><![if !supportLists]><span
    1069111106style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    … …  
    1069411109style='color:#4A4A4A'>(Not valid for SASD). <o:p></o:p></span></span></p>
    1069511110
    10696 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l50 level1 lfo53;
     11111<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l50 level1 lfo54;
    1069711112tab-stops:list .5in'><span style='mso-bookmark:SASD_Models'><![if !supportLists]><span
    1069811113style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    … …  
    1070011115</span></span></span><![endif]><b><span style='color:#4A4A4A'>Set one value - </span></b><span
    1070111116style='color:#4A4A4A'>This is used to set a single selected sample parameter
    10702 for a selected set of SASD histograms. The same value can be used for all
    10703 histograms or a dialog can be used to provide a table where you can set the
    10704 values differently for each of selected histograms. <o:p></o:p></span></span></p>
    10705 
    10706 <p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l50 level1 lfo53;
     11117for a selected set of SASD histograms. The same value can be used for all <span
     11118class=GramE>histograms</span> or a dialog can be used to provide a table where
     11119you can set the values differently for each of selected histograms. <o:p></o:p></span></span></p>
     11120
     11121<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l50 level1 lfo54;
    1070711122tab-stops:list .5in'><span style='mso-bookmark:SASD_Models'><![if !supportLists]><span
    1070811123style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    … …  
    1071411129
    1071511130<pre style='margin-left:.5in'><span style='mso-bookmark:SASD_Models'><span
    10716 style='color:#4A4A4A'>#filename<span style='mso-spacerun:yes'>       </span>temperature pressure ignore-me<span style='mso-spacerun:yes'>  </span>humidity<o:p></o:p></span></span></pre><pre
     11131style='color:#4A4A4A'>#filename<span style='mso-spacerun:yes'>       </span>temperature pressure ignore-<span
     11132class=GramE>me<span style='mso-spacerun:yes'>  </span>humidity</span><o:p></o:p></span></span></pre><pre
    1071711133style='margin-left:.5in'><span style='mso-bookmark:SASD_Models'><span
    1071811134style='color:#4A4A4A'>LaB6_dc250.tif<span style='mso-spacerun:yes'>      </span>100<span style='mso-spacerun:yes'>          </span>1<span style='mso-spacerun:yes'>      </span>test<span style='mso-spacerun:yes'>       </span>.2<o:p></o:p></span></span></pre><pre
    … …  
    1072511141marked with a hash (#). A header is not required. &quot;Columns&quot; in the
    1072611142table are separated by one or more delimiters (which may be a comma, tab or
    10727 space). Note that columns do not need to be aligned, as long as each entry is
    10728 spaced by at least one delimiter. The first column in the table is used to look
    10729 up SASD entries where the initial space-delimited string after the SASD tag
    10730 (&quot;myfile&quot; in &quot;SASD myfile AZM=180...&quot;) must match the
    10731 table. Subsequent columns can then be mapped to sample parameters or can be
    10732 ignored, using a dialog window. <o:p></o:p></span></span></p>
    10733 
    10734 <p class=MsoListParagraph style='text-indent:-.25in;mso-list:l50 level1 lfo53;
     11143space). Note that columns do not need to be aligned, <span class=GramE>as long
     11144as</span> each entry is spaced by at least one delimiter. The first column in
     11145the table is used to look up SASD entries where the initial space-delimited
     11146string after the SASD tag (&quot;myfile&quot; in &quot;SASD myfile
     11147AZM=180...&quot;) must match the table. Subsequent columns can then be mapped
     11148to sample parameters or can be ignored, using a dialog window. <o:p></o:p></span></span></p>
     11149
     11150<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l50 level1 lfo54;
    1073511151tab-stops:list .5in left 45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    1073611152style='mso-bookmark:SASD_Models'><![if !supportLists]><span style='font-family:
    … …  
    1075011166scattering models in GSAS-II have four different forms:<o:p></o:p></span></span></p>
    1075111167
    10752 <p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l49 level1 lfo54;
     11168<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l49 level1 lfo55;
    1075311169tab-stops:list .5in left 45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    1075411170style='mso-bookmark:SASD_Models'><![if !supportLists]><span style='font-family:
    … …  
    1076311179style='color:#4A4A4A'>.<o:p></o:p></span></span></p>
    1076411180
    10765 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l49 level1 lfo54;
     11181<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l49 level1 lfo55;
    1076611182tab-stops:list .5in left 45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    1076711183style='mso-bookmark:SASD_Models'><![if !supportLists]><span style='font-family:
    … …  
    1077011186</span></span></span><![endif]><b><span style='color:#4A4A4A'>Particle Fit</span></b><span
    1077111187style='color:#4A4A4A'> – this gives the best fit of a suite of models for each
    10772 component of the sample. Each model is chosen from a suite of possible descriptions,
    10773 each with parameters that describe the shape, size (as a radius, </span></span><span
     11188component of the sample. Each model is chosen from a suite of possible
     11189descriptions, each with parameters that describe the shape, size (as a radius, </span></span><span
    1077411190style='mso-bookmark:SASD_Models'><span style='font-family:"Calibri",sans-serif;
    1077511191color:#4A4A4A'>Å)</span><span style='color:#4A4A4A'> and magnitude.<o:p></o:p></span></span></p>
    1077611192
    10777 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l49 level1 lfo54;
     11193<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l49 level1 lfo55;
    1077811194tab-stops:list .5in left 45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    1077911195style='mso-bookmark:SASD_Models'><![if !supportLists]><span style='font-family:
    … …  
    1078511201interatomic vectors within the protein.<o:p></o:p></span></span></p>
    1078611202
    10787 <p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l49 level1 lfo54;
     11203<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l49 level1 lfo55;
    1078811204tab-stops:list .5in left 45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    1078911205style='mso-bookmark:SASD_Models'><![if !supportLists]><span style='font-family:
    … …  
    1080711223–<o:p></o:p></span></span></p>
    1080811224
    10809 <p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l33 level1 lfo55;
     11225<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l33 level1 lfo56;
    1081011226tab-stops:list .5in'><span style='mso-bookmark:SASD_Models'><![if !supportLists]><span
    1081111227style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    … …  
    1081411230style='color:#4A4A4A'> – this adds a distribution to a Particle Fit model<o:p></o:p></span></span></p>
    1081511231
    10816 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l33 level1 lfo55;
     11232<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l33 level1 lfo56;
    1081711233tab-stops:list .5in'><span style='mso-bookmark:SASD_Models'><![if !supportLists]><span
    1081811234style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    … …  
    1082211238data or bead model to the Pair Distance distribution (Shapes only).<o:p></o:p></span></span></p>
    1082311239
    10824 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l33 level1 lfo55;
     11240<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l33 level1 lfo56;
    1082511241tab-stops:list .5in'><span style='mso-bookmark:SASD_Models'><![if !supportLists]><span
    1082611242style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    … …  
    1083011246for a given fit result.<o:p></o:p></span></span></p>
    1083111247
    10832 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l33 level1 lfo55;
     11248<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l33 level1 lfo56;
    1083311249tab-stops:list .5in'><span style='mso-bookmark:SASD_Models'><![if !supportLists]><span
    1083411250style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    … …  
    1083811254the same model description.<o:p></o:p></span></span></p>
    1083911255
    10840 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l33 level1 lfo55;
     11256<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l33 level1 lfo56;
    1084111257tab-stops:list .5in'><span style='mso-bookmark:SASD_Models'><![if !supportLists]><span
    1084211258style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    … …  
    1084611262SASD histograms<o:p></o:p></span></span></p>
    1084711263
    10848 <p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l33 level1 lfo55;
     11264<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l33 level1 lfo56;
    1084911265tab-stops:list .5in'><span style='mso-bookmark:SASD_Models'><![if !supportLists]><span
    1085011266style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    … …  
    1086611282style='color:#4A4A4A'>This window shows whatever comment lines found above the
    1086711283QIE table when the reflectometry data file was read by GSAS-II. If you are
    10868 lucky, there will be useful information here (e.g. sample name, date collected,
    10869 wavelength used, etc.). If not, this window will be blank. The text is
    10870 read-only.</span><span style='mso-fareast-font-family:"Times New Roman";
    10871 mso-fareast-theme-font:minor-fareast;color:#4A4A4A'><o:p></o:p></span></p>
     11284lucky, there will be useful information here (<span class=GramE>e.g.</span>
     11285sample name, date collected, wavelength used, etc.). If not, this window will
     11286be blank. The text is read-only.</span><span style='mso-fareast-font-family:
     11287"Times New Roman";mso-fareast-theme-font:minor-fareast;color:#4A4A4A'><o:p></o:p></span></p>
    1087211288
    1087311289<h4 style='tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><a
    … …  
    1089911315Limits</b>’ <o:p></o:p></span></span></p>
    1090011316
    10901 <p class=MsoListParagraph style='text-indent:-.25in;mso-list:l29 level1 lfo56;
     11317<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l29 level1 lfo57;
    1090211318tab-stops:list .5in left 45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    1090311319style='mso-bookmark:REFD_Limits'><![if !supportLists]><span style='font-family:
    … …  
    1093211348text-underline:none'><o:p></o:p></span></span></span></p>
    1093311349
    10934 <p class=MsoListParagraph style='text-indent:-.25in;mso-list:l29 level1 lfo56;
     11350<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l29 level1 lfo57;
    1093511351tab-stops:list .5in'><span style='mso-bookmark:REFD_Limits'><![if !supportLists]><span
    1093611352style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    … …  
    1097011386
    1097111387<p class=MsoListParagraphCxSpFirst style='margin-left:.25in;mso-add-space:auto;
    10972 text-indent:-.25in;mso-list:l54 level1 lfo57;tab-stops:list .25in left 45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
     11388text-indent:-.25in;mso-list:l54 level1 lfo58;tab-stops:list .25in left 45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    1097311389style='mso-bookmark:REFD_Sample_Parameters'><![if !supportLists]><span
    1097411390style='color:#4A4A4A'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    … …  
    1097611392substance’ –<o:p></o:p></span></span></p>
    1097711393
    10978 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l20 level1 lfo58;
     11394<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l20 level1 lfo59;
    1097911395tab-stops:list .5in'><span style='mso-bookmark:REFD_Sample_Parameters'><![if !supportLists]><span
    1098011396style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    … …  
    1098711403directory.<o:p></o:p></span></span></p>
    1098811404
    10989 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l20 level1 lfo58;
     11405<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l20 level1 lfo59;
    1099011406tab-stops:list .5in'><span style='mso-bookmark:REFD_Sample_Parameters'><![if !supportLists]><span
    1099111407style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    … …  
    1099511411substances.<o:p></o:p></span></span></p>
    1099611412
    10997 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l20 level1 lfo58;
     11413<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l20 level1 lfo59;
    1099811414tab-stops:list .5in'><span style='mso-bookmark:REFD_Sample_Parameters'><![if !supportLists]><span
    1099911415style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    … …  
    1100411420volume/density; GSAS-II will compute the scattering contrast data for it.<o:p></o:p></span></span></p>
    1100511421
    11006 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l20 level1 lfo58;
     11422<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l20 level1 lfo59;
    1100711423tab-stops:list .5in'><span style='mso-bookmark:REFD_Sample_Parameters'><![if !supportLists]><span
    1100811424style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    … …  
    1101211428other small angle data histograms.<o:p></o:p></span></span></p>
    1101311429
    11014 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l20 level1 lfo58;
     11430<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l20 level1 lfo59;
    1101511431tab-stops:list .5in'><span style='mso-bookmark:REFD_Sample_Parameters'><![if !supportLists]><span
    1101611432style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    … …  
    1102011436or unit scatterer.<o:p></o:p></span></span></p>
    1102111437
    11022 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l20 level1 lfo58;
     11438<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l20 level1 lfo59;
    1102311439tab-stops:list .5in'><span style='mso-bookmark:REFD_Sample_Parameters'><![if !supportLists]><span
    1102411440style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    … …  
    1102811444substance.<o:p></o:p></span></span></p>
    1102911445
    11030 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l20 level1 lfo58;
     11446<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l20 level1 lfo59;
    1103111447tab-stops:list .5in'><span style='mso-bookmark:REFD_Sample_Parameters'><![if !supportLists]><span
    1103211448style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    … …  
    1103611452
    1103711453<p class=MsoListParagraphCxSpLast style='margin-left:.25in;mso-add-space:auto;
    11038 text-indent:-.25in;mso-list:l54 level1 lfo57;tab-stops:list .25in left 45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
     11454text-indent:-.25in;mso-list:l54 level1 lfo58;tab-stops:list .25in left 45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    1103911455style='mso-bookmark:REFD_Sample_Parameters'><![if !supportLists]><span
    1104011456style='color:#4A4A4A'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    … …  
    1107011486the menu commands described here. <o:p></o:p></span></span></p>
    1107111487
    11072 <p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l31 level1 lfo59;
     11488<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l31 level1 lfo60;
    1107311489tab-stops:list .5in left 45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    1107411490style='mso-bookmark:REFD_Models'><![if !supportLists]><span style='font-family:
    … …  
    1108011496REFD scans<o:p></o:p></span></span></p>
    1108111497
    11082 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l31 level1 lfo59;
     11498<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l31 level1 lfo60;
    1108311499tab-stops:list .5in left 45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    1108411500style='mso-bookmark:REFD_Models'><![if !supportLists]><span style='font-family:
    … …  
    1108611502style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    1108711503</span></span></span><![endif]><b><span style='color:#4A4A4A'>Load - </span></b><span
    11088 style='color:#4A4A4A'>This loads sample parameters from a previously saved
    11089 .samprm file. <o:p></o:p></span></span></p>
    11090 
    11091 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l31 level1 lfo59;
     11504style='color:#4A4A4A'>This loads sample parameters from a previously <span
     11505class=GramE>saved .samprm</span> file. <o:p></o:p></span></span></p>
     11506
     11507<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l31 level1 lfo60;
    1109211508tab-stops:list .5in left 45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    1109311509style='mso-bookmark:REFD_Models'><![if !supportLists]><span style='font-family:
    … …  
    1109511511style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    1109611512</span></span></span><![endif]><b><span style='color:#4A4A4A'>Save - </span></b><span
    11097 style='color:#4A4A4A'>This saves the sample parameters to a file with the
    11098 extension ’.samprm’. A file dialog box will appear to ask for the name of the
    11099 file to be written. <o:p></o:p></span></span></p>
    11100 
    11101 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l31 level1 lfo59;
     11513style='color:#4A4A4A'>This saves the sample parameters to a file with the <span
     11514class=GramE>extension ’</span>.samprm’. A file dialog box will appear to ask
     11515for the name of the file to be written. <o:p></o:p></span></span></p>
     11516
     11517<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l31 level1 lfo60;
    1110211518tab-stops:list .5in left 45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    1110311519style='mso-bookmark:REFD_Models'><![if !supportLists]><span style='font-family:
    … …  
    1111111527the copy; ‘Cancel’ to cancel the operation. <o:p></o:p></span></span></p>
    1111211528
    11113 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l31 level1 lfo59;
     11529<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l31 level1 lfo60;
    1111411530tab-stops:list .5in left 45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    1111511531style='mso-bookmark:REFD_Models'><![if !supportLists]><span style='font-family:
    … …  
    1111811534</span></span></span><![endif]><b><span style='color:#4A4A4A'>Copy selected...
    1111911535- </span></b><span style='color:#4A4A4A'>This copies only the sample parameter
    11120 that are selected to other selected REFD patterns but is otherwise similar to
    11121 &quot;Copy&quot;. <o:p></o:p></span></span></p>
    11122 
    11123 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l31 level1 lfo59;
     11536that are selected to other selected REFD patterns but is otherwise <span
     11537class=GramE>similar to</span> &quot;Copy&quot;. <o:p></o:p></span></span></p>
     11538
     11539<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l31 level1 lfo60;
    1112411540tab-stops:list .5in left 45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    1112511541style='mso-bookmark:REFD_Models'><![if !supportLists]><span style='font-family:
    … …  
    1112911545style='color:#4A4A4A'>(Not valid for REFD). <o:p></o:p></span></span></p>
    1113011546
    11131 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l31 level1 lfo59;
     11547<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l31 level1 lfo60;
    1113211548tab-stops:list .5in left 45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    1113311549style='mso-bookmark:REFD_Models'><![if !supportLists]><span style='font-family:
    … …  
    1113611552</span></span></span><![endif]><b><span style='color:#4A4A4A'>Set one value - </span></b><span
    1113711553style='color:#4A4A4A'>This is used to set a single selected sample parameter
    11138 for a selected set of REFD histograms. The same value can be used for all
    11139 histograms or a dialog can be used to provide a table where you can set the
    11140 values differently for each of selected histograms. <o:p></o:p></span></span></p>
    11141 
    11142 <p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l31 level1 lfo59;
     11554for a selected set of REFD histograms. The same value can be used for all <span
     11555class=GramE>histograms</span> or a dialog can be used to provide a table where
     11556you can set the values differently for each of selected histograms. <o:p></o:p></span></span></p>
     11557
     11558<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l31 level1 lfo60;
    1114311559tab-stops:list .5in left 45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    1114411560style='mso-bookmark:REFD_Models'><![if !supportLists]><span style='font-family:
    … …  
    1115211568<pre><span style='mso-bookmark:REFD_Models'><span style='color:#4A4A4A'><o:p>&nbsp;</o:p></span></span></pre><pre
    1115311569style='margin-left:.5in'><span style='mso-bookmark:REFD_Models'><span
    11154 style='color:#4A4A4A'>#filename<span style='mso-spacerun:yes'>       </span>temperature pressure ignore-me<span style='mso-spacerun:yes'>  </span>humidity<o:p></o:p></span></span></pre><pre
     11570style='color:#4A4A4A'>#filename<span style='mso-spacerun:yes'>       </span>temperature pressure ignore-<span
     11571class=GramE>me<span style='mso-spacerun:yes'>  </span>humidity</span><o:p></o:p></span></span></pre><pre
    1115511572style='margin-left:.5in'><span style='mso-bookmark:REFD_Models'><span
    1115611573style='color:#4A4A4A'>LaB6_dc250.tif<span style='mso-spacerun:yes'>      </span>100<span style='mso-spacerun:yes'>          </span>1<span style='mso-spacerun:yes'>      </span>test<span style='mso-spacerun:yes'>       </span>.2<o:p></o:p></span></span></pre><pre
    … …  
    1116311580marked with a hash (#). A header is not required. &quot;Columns&quot; in the
    1116411581table are separated by one or more delimiters (which may be a comma, tab or
    11165 space). Note that columns do not need to be aligned, as long as each entry is
    11166 spaced by at least one delimiter. The first column in the table is used to look
    11167 up REFD entries where the initial space-delimited string after the REFD tag
    11168 (&quot;myfile&quot; in &quot; REFD myfile AZM=180...&quot;) must match the
    11169 table. Subsequent columns can then be mapped to sample parameters or can be
    11170 ignored, using a dialog window. <o:p></o:p></span></span></p>
    11171 
    11172 <p class=MsoListParagraph style='text-indent:-.25in;mso-list:l31 level1 lfo59;
     11582space). Note that columns do not need to be aligned, <span class=GramE>as long
     11583as</span> each entry is spaced by at least one delimiter. The first column in
     11584the table is used to look up REFD entries where the initial space-delimited
     11585string after the REFD tag (&quot;myfile&quot; in &quot; REFD myfile
     11586AZM=180...&quot;) must match the table. Subsequent columns can then be mapped
     11587to sample parameters or can be ignored, using a dialog window. <o:p></o:p></span></span></p>
     11588
     11589<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l31 level1 lfo60;
    1117311590tab-stops:list .5in left 45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    1117411591style='mso-bookmark:REFD_Models'><![if !supportLists]><span style='font-family:
    … …  
    1119011607located (usually “vacuum” = air or other gasses) and ending with the bottom
    1119111608layer (“substrate”) upon which the sample layers have been deposited. The
    11192 substrate is considered to be “infinite” in thickness. The sample layers in
    11193 between are each defined as a particular substance with a thickness and upper
    11194 surface “roughness”. The surface roughness describes the possibility of an
    11195 interlayer mixing with the previous layer. Their scattering density can also be
    11196 scaled and could include polarized magnetic neutron scatterers. The layer
    11197 sequence is defined so that complex or multiple layers can be defined.<o:p></o:p></span></span></p>
     11609substrate <span class=GramE>is considered to be</span> “infinite” in thickness.
     11610The sample layers in between are each defined as a particular substance with a
     11611thickness and upper surface “roughness”. The surface roughness describes the
     11612possibility of an interlayer mixing with the previous layer. Their scattering
     11613density can also be scaled and could include polarized magnetic neutron
     11614scatterers. The layer sequence is defined so that complex or multiple layers
     11615can be defined.<o:p></o:p></span></span></p>
    1119811616
    1119911617<h5 style='tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    … …  
    1120311621<p style='tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    1120411622style='mso-bookmark:REFD_Models'><b><span style='color:#4A4A4A'>Command</span></b><span
    11205 style='color:#4A4A4A'> Menu<span style='mso-spacerun:yes'>  </span>–<o:p></o:p></span></span></p>
    11206 
    11207 <p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l31 level1 lfo59;
     11623style='color:#4A4A4A'> <span class=GramE>Menu<span style='mso-spacerun:yes'> 
     11624</span>–</span><o:p></o:p></span></span></p>
     11625
     11626<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l31 level1 lfo60;
    1120811627tab-stops:list .5in'><span style='mso-bookmark:REFD_Models'><![if !supportLists]><span
    1120911628style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    … …  
    1121311632methods of the reflectometry model to the data.<o:p></o:p></span></span></p>
    1121411633
    11215 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l31 level1 lfo59;
     11634<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l31 level1 lfo60;
    1121611635tab-stops:list .5in'><span style='mso-bookmark:REFD_Models'><![if !supportLists]><span
    1121711636style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    … …  
    1122111640be done once.<o:p></o:p></span></span></p>
    1122211641
    11223 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l31 level1 lfo59;
     11642<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l31 level1 lfo60;
    1122411643tab-stops:list .5in'><span style='mso-bookmark:REFD_Models'><![if !supportLists]><span
    1122511644style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    … …  
    1122911648each has their own model description so one should ensure they are all similar.<o:p></o:p></span></span></p>
    1123011649
    11231 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l31 level1 lfo59;
     11650<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l31 level1 lfo60;
    1123211651tab-stops:list .5in'><span style='mso-bookmark:REFD_Models'><![if !supportLists]><span
    1123311652style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    … …  
    1123611655style='color:#4A4A4A'> – Copy the present model to other REFD patterns.<o:p></o:p></span></span></p>
    1123711656
    11238 <p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l31 level1 lfo59;
     11657<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l31 level1 lfo60;
    1123911658tab-stops:list .5in'><span style='mso-bookmark:REFD_Models'><![if !supportLists]><span
    1124011659style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    … …  
    1129211711style='color:#4A4A4A'>GSAS-II can be run on Windows, Linux and Macintosh/OS X computers,
    1129311712but the GUI follows the native style of Mac OS X. On Windows and some versions
    11294 of Linux, the menu bars appears on top of the main window. On the Mac, the menu
    11295 appears at the location that has been configured for menus (usually at the top
    11296 of the screen). GSAS-II defines actions for both the left and right buttons on
    11297 a two-button mouse, If a two or three-button mouse is used with a Mac, these
    11298 mouse buttons will work as intended. If using a Mac touchpad or single-button
    11299 mouse, clicking the touchpad or mouse button will generate a &quot;left
    11300 button&quot; click. Hold down the control-key to generate a &quot;right
    11301 button&quot; click. </span></p>
     11713of Linux, the menu bars <span class=GramE>appears</span> on top of the main
     11714window. On the Mac, the menu appears at the location that has been configured
     11715for menus (usually at the top of the screen). GSAS-II defines actions for both
     11716the left and right buttons on a two-button mouse, <span class=GramE>If</span> a
     11717two or three-button mouse is used with a Mac, these mouse buttons will work as
     11718intended. If using a Mac touchpad or single-button mouse, clicking the touchpad
     11719or mouse button will generate a &quot;left button&quot; click. Hold down the
     11720control-key to generate a &quot;right button&quot; click. </span></p>
    1130211721
    1130311722<h3 style='tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><a
    … …  
    1130711726
    1130811727<p class=MsoNormal style='tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    11309 style='color:#4A4A4A'>GSAS-II provides a number of configuration settings that can
    11310 be changed via variables that can be set and saved. These are controlled in the
    11311 File/Preferences menu item (on Mac the Preferences menu is found in the usual
    11312 place on Macs, in the main application menu). These settings are optionally
    11313 saved from for subsequent runs in a file named </span><tt><span
    11314 style='font-size:10.0pt;color:#4A4A4A'>config.py</span></tt><span
     11728style='color:#4A4A4A'>GSAS-II provides <span class=GramE>a number of</span>
     11729configuration settings that can be changed via variables that can be set and
     11730saved. These are controlled in the File/Preferences menu item (on Mac the
     11731Preferences menu is found in the usual place on Macs, in the main application
     11732menu). These settings are optionally saved from for subsequent runs in a file
     11733named </span><tt><span style='font-size:10.0pt;color:#4A4A4A'>config.py</span></tt><span
    1131511734style='color:#4A4A4A'>. More information about this can be found in the <a
    1131611735href="https://gsas-ii.readthedocs.io/en/latest/GSASIIutil.html#module-config_example">appropriate

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