Changeset 5344


Ignore:
Timestamp:
Oct 6, 2022 1:08:47 PM (12 months ago)
Author:
vondreele
Message:

Add new plot to cluster analysis that shows serial distances across selected data; update help for it.

Location:
trunk
Files:
20 edited

Legend:

Unmodified
Added
Removed

  • trunk/GSASIIplot.py

    r5342 r5344  
    5353:func:`PlotLayers`            show layer structures as balls & sticks
    5454:func:`PlotFPAconvolutors`    plots the convolutors from Fundamental Parameters
     55:func:'PlotClusterYYZ'plots the result of cluster analysis
    5556============================  ===========================================================================
    5657
    … …  
    1161711618    Imin = np.min(YM)
    1161811619    Imax = np.max(YM)
     11620    Ndata = len(CLuDict['Files'])
     11621    neighD = [YM[i][i+1] for i in range(Ndata-1)]
    1161911622    if CLuDict['CLuZ'] is None and CLuDict['plots'] == 'Dendrogram':
    1162011623        CLuDict['plots'] = 'All'
    … …  
    1163211635        Plot.set_xlabel(r''+'data set no.',fontsize=12)
    1163311636        Plot.set_ylabel(r''+CLuDict['Method']+' distance',fontsize=12)
     11637    elif CLuDict['plots'] == 'Diffs':
     11638        Plot.plot(neighD)
     11639        Plot.set_title('Distance to next data set')
     11640        Plot.set_xlabel('Data no.',fontsize=12)
     11641        Plot.set_ylabel('dist to next',fontsize=12)
    1163411642    elif CLuDict['plots'] == '3D PCA':
    1163511643        if CLuDict['codes'] is not None:
    … …  
    1164411652    else:         
    1164511653        Plot.set_visible(False)         #hide old plot frame, will get replaced below
    11646         if CLuDict['CLuZ'] is not None:
    11647             gs = mpl.gridspec.GridSpec(2,2,figure=Page.figure)
    11648             ax1 = Page.figure.add_subplot(gs[0,0])
    11649             ax2 = Page.figure.add_subplot(gs[1,1],projection='3d')
    11650             ax3 = Page.figure.add_subplot(gs[0,1])
    11651             ax4 = Page.figure.add_subplot(gs[1,0])
    11652         else:
    11653             ax1 = Page.figure.add_subplot(211)
    11654             ax2 = Page.figure.add_subplot(212,projection='3d')
    11655             Page.figure.tight_layout()           
     11654        gs = mpl.gridspec.GridSpec(2,2,figure=Page.figure)
     11655        ax1 = Page.figure.add_subplot(gs[0,0])
     11656        ax2 = Page.figure.add_subplot(gs[1,1],projection='3d')
     11657        ax3 = Page.figure.add_subplot(gs[0,1])
     11658        ax4 = Page.figure.add_subplot(gs[1,0])
    1165611659        Page.ImgObj = ax1.imshow(YM,interpolation='nearest',vmin=Imin,vmax=Imax,origin='lower')
    1165711660        cax = inset_axes(ax1,width="5%",height="100%",loc='lower left',bbox_to_anchor=(1.05, 0., 1, 1),
    … …  
    1167011673        ax2.set_ylabel('PCA axis-2',fontsize=12)
    1167111674        ax2.set_zlabel('PCA axis-3',fontsize=12)
     11675        ax4.plot(neighD)
     11676        ax4.set_xlabel('Data no.',fontsize=12)
     11677        ax4.set_ylabel('dist to next',fontsize=12)
    1167211678        if CLuDict['CLuZ'] is not None:
    1167311679            CLR = SCH.dendrogram(CLuDict['CLuZ'],orientation='right',ax=ax3)
    … …  
    1167511681            ax3.set_ylabel(r''+'data set no.',fontsize=12)
    1167611682            ax3.set_xlabel(r''+CLuDict['Method']+' distance',fontsize=12)
    11677             ax4.plot(100.*CLuDict['PCA'][:10]/np.sum(CLuDict['PCA']))
    11678             ax4.set_xlabel('PCA index',fontsize=12)
    11679             ax4.set_ylabel('% of total',fontsize=12)
     11683        else:
     11684            ax3.plot(100.*CLuDict['PCA'][:10]/np.sum(CLuDict['PCA']))
     11685            ax3.set_xlabel('PCA index',fontsize=12)
     11686            ax3.set_ylabel('% of total',fontsize=12)
    1168011687    Page.canvas.draw()
    1168111688       

  • trunk/GSASIIseqGUI.py

    r5336 r5344  
    20472047            plotSizer.Add(wx.StaticText(G2frame.dataWindow,label='Plot selection: '),0,WACV)
    20482048            if ClusData['CLuZ'] is None:
    2049                 choice = ['All','Distances','3D PCA',]
     2049                choice = ['All','Distances','3D PCA','Diffs']
    20502050            else:
    2051                 choice = ['All','Distances','Dendrogram','3D PCA',]
     2051                choice = ['All','Distances','Dendrogram','3D PCA','Diffs']
    20522052            plotsel = wx.ComboBox(G2frame.dataWindow,choices=choice,style=wx.CB_READONLY|wx.CB_DROPDOWN)
    20532053            plotsel.SetValue(str(ClusData['plots']))

  • trunk/help/gsasII.html

    r5333 r5344  
    2424 <o:DocumentProperties>
    2525  <o:Author>Von Dreele</o:Author>
    26   <o:LastAuthor>Robert Von Dreele</o:LastAuthor>
    27   <o:Revision>227</o:Revision>
    28   <o:TotalTime>8347</o:TotalTime>
     26  <o:LastAuthor>Von Dreele, Robert B.</o:LastAuthor>
     27  <o:Revision>228</o:Revision>
     28  <o:TotalTime>8353</o:TotalTime>
    2929  <o:Created>2011-11-28T16:49:00Z</o:Created>
    30   <o:LastSaved>2022-09-14T16:10:00Z</o:LastSaved>
    31   <o:Pages>1</o:Pages>
    32   <o:Words>18329</o:Words>
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     30  <o:LastSaved>2022-10-06T18:08:00Z</o:LastSaved>
     31  <o:Pages>44</o:Pages>
     32  <o:Words>18360</o:Words>
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    3434  <o:Company>Argonne National Laboratory</o:Company>
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    … …  
    4747 <w:WordDocument>
    4848  <w:View>Print</w:View>
    49   <w:GrammarState>Clean</w:GrammarState>
    5049  <w:TrackMoves>false</w:TrackMoves>
    5150  <w:TrackFormatting/>
    … …  
    13021301        {mso-style-name:mjx_assistive_mathml;
    13031302        mso-style-unhide:no;}
    1304 span.GramE
    1305         {mso-style-name:"";
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    … …  
    51405136<p class=MsoNormal>This is where to find help on various GSAS-II windows and
    51415137plots. Note that GSAS-II operates with three windows: the main <a
    5142 href="#_1._GSAS-II_Data">GSAS-II data tree</a> section, which provides a hierarchical
    5143 view of the current project on the left and the <a href="#Data_Frame">GSAS-II
    5144 data editing</a> section, which shows the contents of a particular section of
    5145 the project, where values can be examined and changed; The second is the <a
    5146 href="#_3._GSAS-II_Plots">GSAS-II Plots</a> window, which shows graphical
    5147 representations of the results. The third is a console window, which has
    5148 printout information that can be selected, cut &amp; pasted into a document. </p>
     5138href="#_1._GSAS-II_Data">GSAS-II data tree</a> section, which provides a
     5139hierarchical view of the current project on the left and the <a
     5140href="#Data_Frame">GSAS-II data editing</a> section, which shows the contents
     5141of a particular section of the project, where values can be examined and
     5142changed; The second is the <a href="#_3._GSAS-II_Plots">GSAS-II Plots</a>
     5143window, which shows graphical representations of the results. The third is a
     5144console window, which has printout information that can be selected, cut &amp;
     5145pasted into a document. </p>
    51495146
    51505147<h2><a name=Index><span style='mso-fareast-font-family:"Times New Roman"'>Help
    … …  
    52435240Window</span></span><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h2>
    52445241
    5245 <p class=MsoNormal>This window presents all the graphical material as a multipage
    5246 tabbed set of plots utilizing the matplotlib python package. Each page
    5247 containing a graph or plot has a tool bar with the controls</p>
     5242<p class=MsoNormal>This window presents all the graphical material as a
     5243multipage tabbed set of plots utilizing the matplotlib python package. Each
     5244page containing a graph or plot has a tool bar with the controls</p>
    52485245
    52495246<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    … …  
    52535250  cropbottom="2353f" cropleft="535f" cropright="28388f"/>
    52545251</v:shape><![endif]--><![if !vml]><img border=0 width=480 height=24
    5255 src="gsasII_files/image002.png" alt="GSAS-II plots: NiTi-C.gpx" v:shapes="Picture_x0020_1"><![endif]></span><span
     5252src="gsasII_files/image003.png" alt="GSAS-II plots: NiTi-C.gpx" v:shapes="Picture_x0020_1"><![endif]></span><span
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    53055302style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
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    5307 </span></span></span><![endif]>Save - allows you to save the currently
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    5309 insertion in a document. </p>
     5304</span></span></span><![endif]>Save - allows you to save the currently displayed
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    … …  
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    57205724" filled="f" stroked="f">
    57215725 <o:lock v:ext="edit" aspectratio="t"/>
    … …  
    573857423-dimensional structure drawings there will be below the toolbar may be a
    57395743status bar that on the left may show either an instruction for a keyed input or
    5740 a <span class=GramE>pull down</span> selection of keyed input; on the right may
    5741 be displayed position dependent information that is updated as the mouse is
    5742 moved over the plot region.<span style='mso-fareast-font-family:"Times New Roman";
    5743 mso-fareast-theme-font:minor-fareast'><o:p></o:p></span></p>
     5744a pull down selection of keyed input; on the right may be displayed position
     5745dependent information that is updated as the mouse is moved over the plot
     5746region.<span style='mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:
     5747minor-fareast'><o:p></o:p></span></p>
    57445748
    57455749<p class=MsoListParagraphCxSpLast><span style='mso-fareast-font-family:"Times New Roman";
    … …  
    57715775style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    57725776Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5773 </span></span></span><![endif]><b>Open project…</b> - Open a previously saved
    5774 GSAS-II project file ({project}.gpx). If you currently have a project file
    5775 open, you are asked if it is OK to overwrite it; Cancel will cancel the read
    5776 process. </p>
     5777</span></span></span><![endif]><b>Open project…</b> - Open a previously saved GSAS-II
     5778project file ({project}.gpx). If you currently have a project file open, you
     5779are asked if it is OK to overwrite it; Cancel will cancel the read process. </p>
    57775780
    57785781<p class=MsoListParagraphCxSpMiddle>Note that as files are saved during a
    57795782structure refinement, copies of the previous version are saved as backup files,
    57805783named as {project}.bak{<i>i</i>}.gpx, where <i>i</i> starts as 0 and is
    5781 increased after each save operation. NB: you may open a backup .gpx file (<span
    5782 class=GramE>e.g.</span> name.bak3.gpx) to return to a previous version of your
    5783 project, but if you do so, it is best to immediately use the <b'>Save As...
    5784 menu command (you may wish to use name.gpx to overwrite the current version or
    5785 select a new name.) If you forget <span class=GramE>specify</span> a project
    5786 name, then name.bak3 will be considered the project name and backups will then
    5787 be named name.bak3.bak0.gpx, etc.</p>
     5784increased after each save operation. NB: you may open a backup .gpx file (e.g.
     5785name.bak3.gpx) to return to a previous version of your project, but if you do
     5786so, it is best to immediately use the <b'>Save As... menu command (you may wish
     5787to use name.gpx to overwrite the current version or select a new name.) If you
     5788forget specify a project name, then name.bak3 will be considered the project
     5789name and backups will then be named name.bak3.bak0.gpx, etc.</p>
    57885790
    57895791<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l37 level1 lfo3'><![if !supportLists]><span
    57905792style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    57915793Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5792 </span></span></span><![endif]><b>Save <span class=GramE>project<span
    5793 style='mso-spacerun:yes'>  </span>-</span> </b>Save the current project. If
    5794 this is a new project that has not yet been saved, you will be prompted for a
    5795 new name in a file dialog (you may optionally change the directory in that
    5796 dialog). If the file exists, you will be asked if it is OK to overwrite it.
    5797 Once a file name has been used to read or save a project, the name is shown
    5798 after ‘Loaded Data:’ in the first item in the data tree. </p>
     5794</span></span></span><![endif]><b>Save project<span style='mso-spacerun:yes'> 
     5795</span>- </b>Save the current project. If this is a new project that has not
     5796yet been saved, you will be prompted for a new name in a file dialog (you may
     5797optionally change the directory in that dialog). If the file exists, you will be
     5798asked if it is OK to overwrite it. Once a file name has been used to read or
     5799save a project, the name is shown after ‘Loaded Data:’ in the first item in the
     5800data tree. </p>
    57995801
    58005802<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l37 level1 lfo3'><![if !supportLists]><span
    … …  
    58115813style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    58125814Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5813 </span></span></span><![endif]><b>New <span class=GramE>Project<span
    5814 style='mso-spacerun:yes'>  </span>-</span> </b>Discards any changes made to the
    5815 current project since the last save and creates a new empty project. </p>
     5815</span></span></span><![endif]><b>New Project<span style='mso-spacerun:yes'> 
     5816</span>- </b>Discards any changes made to the current project since the last
     5817save and creates a new empty project. </p>
    58165818
    58175819<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l37 level1 lfo3'><![if !supportLists]><span
    58185820style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    58195821Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5820 </span></span></span><![endif]><span class=GramE><b>Preferences<span
    5821 style='mso-spacerun:yes'>  </span>-</b></span><b> </b>Provides access to
    5822 GSAS-II configuration settings, as described in the <a href="#Preferences">Configuration
    5823 Variables</a> section. </p>
     5822</span></span></span><![endif]><b>Preferences<span style='mso-spacerun:yes'> 
     5823</span>- </b>Provides access to GSAS-II configuration settings, as described in
     5824the <a href="#Preferences">Configuration Variables</a> section. </p>
    58245825
    58255826<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l37 level1 lfo3'><![if !supportLists]><span
    … …  
    58385839style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    58395840Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5840 </span></span></span><![endif]><span class=GramE><b>wx.inspection</b></span><b>
    5841 tool - </b>Debugging tool.</p>
     5841</span></span></span><![endif]><b>wx.inspection tool - </b>Debugging tool.</p>
    58425842
    58435843<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l37 level1 lfo3'><![if !supportLists]><span
    58445844style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    58455845Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5846 </span></span></span><![endif]><span class=GramE><b>Quit<span
    5847 style='mso-spacerun:yes'>  </span>-</b></span><b> </b>Exit the GSAS-II program.
    5848 You will be asked if the project should be saved or not (Cancel aborts the
    5849 quit). 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
    5851 GSAS-II run without any save.</p>
     5846</span></span></span><![endif]><b>Quit<span style='mso-spacerun:yes'>  </span>-
     5847</b>Exit the GSAS-II program. You will be asked if the project should be saved
     5848or not (Cancel aborts the quit). You can also exit GSAS-II by pressing the red
     5849X in the upper right (Windows) or left (Mac). Pressing the red X on the console
     5850will kill the GSAS-II run without any save.</p>
    58525851
    58535852<p class=MsoListParagraphCxSpMiddle style='margin-left:.25in;mso-add-space:
    … …  
    59015900
    59025901<p class=MsoListParagraphCxSpMiddle>Note that nonstandard space group symbols
    5903 are permitted; space group names must have spaces between the axial fields (<span
    5904 class=GramE>e.g.</span> use ‘P n a 21’ not ‘Pna21’). </p>
     5902are permitted; space group names must have spaces between the axial fields
     5903(e.g. use ‘P n a 21’ not ‘Pna21’). </p>
    59055904
    59065905<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l38 level1 lfo4'><![if !supportLists]><span
    … …  
    59155914Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    59165915</span></span></span><![endif]><b>Rename tree entry - </b>Rename a histogram
    5917 entry. This should only be done before the histogram is used in any phases: <span
    5918 class=GramE>e.g.</span> only rename data immediately after reading. </p>
     5916entry. This should only be done before the histogram is used in any phases:
     5917e.g. only rename data immediately after reading. </p>
    59195918
    59205919<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l38 level1 lfo4'><![if !supportLists]><span
    … …  
    59225921Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    59235922</span></span></span><![endif]><b>Delete data entries - </b>This will remove a
    5924 data (<span class=GramE>e.g.</span> PWDR) item from the data tree. A dialog box
    5925 with a list of choices for histograms is presented; it has filter capability to
    5926 ease this process. Be sure to remove histograms from all phases before deleting
    5927 them from the tree. </p>
     5923data (e.g. PWDR) item from the data tree. A dialog box with a list of choices
     5924for histograms is presented; it has filter capability to ease this process. Be
     5925sure to remove histograms from all phases before deleting them from the tree. </p>
    59285926
    59295927<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l38 level1 lfo4'><![if !supportLists]><span
    … …  
    59825980
    59835981<p class=MsoListParagraphCxSpMiddle>Note that for atom positions, the
    5984 coordinate values (named as ‘<span class=GramE>p::</span>A<i>w</i>:n’, where p
    5985 is the phase number, n is the atom number and <i>w</i> is x, y or z) is not a
    5986 refinable 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
    5988 treating 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
    5990 refined rather than the x,y, or z values is that this simplifies symmetry
     5982coordinate values (named as ‘p::A<i>w</i>:n’, where p is the phase number, n is
     5983the atom number and <i>w</i> is x, y or z) is not a refinable parameter, but
     5984the shift in the value is. The refined parameters are ‘p::A<i>w</i>:n’. The
     5985reason this is done is that by treating an atom position as x+dx,y+dy,z+dz
     5986where the “d” values indicate shifts from the starting position and the shifts
     5987are refined rather than the x,y, or z values is that this simplifies symmetry
    59915988constraints. As an example, suppose we have an atom on a symmetry constrained
    5992 site, x,1/2-<span class=GramE>x,z.</span> The process needed to define this
    5993 constraint, so that if x moves positively y <span class=GramE>has to</span> move
    5994 negatively by the same amount would be messy. With refinement of shifts, all we
    5995 need to do is constrain dy (‘<span class=GramE>0::</span>dAy:n’) to be equal to
    5996 -dx (-1*‘0::dAx:n’). </p>
     5989site, x,1/2-x,z. The process needed to define this constraint, so that if x
     5990moves positively y has to move negatively by the same amount would be messy.
     5991With refinement of shifts, all we need to do is constrain dy (‘0::dAy:n’) to be
     5992equal to -dx (-1*‘0::dAx:n’). </p>
    59975993
    59985994<p class=MsoListParagraphCxSpMiddle>Press the window exit button to exit this
    … …  
    60156011refinement where the contributions from each phase (phase partial intensities)
    60166012are written for each histogram and each phase in that histogram into a single
    6017 file named <span class=GramE><tt><i><span style='font-size:10.0pt'>project</span></i></tt><tt><span
    6018 style='font-size:10.0pt'>.partials</span></tt></span> where <tt><i><span
     6013file named <tt><i><span style='font-size:10.0pt'>project</span></i></tt><tt><span
     6014style='font-size:10.0pt'>.partials</span></tt> where <tt><i><span
    60196015style='font-size:10.0pt'>project</span></i></tt> is the GSAS-II project (.gpx)
    6020 name. This file is intended for internal use in GSAS-II and will be deleted if
    6021 additional refinements are performed (making the information in them obsolete;
    6022 use this menu command to recreate them if needed.) When <span class=GramE>the <tt><span
    6023 style='font-size:10.0pt'>.partials</span></tt></span> file is created, the user
    6024 can optionally choose to export the intensity information in a series of ASCII
    6025 files named <tt><i><span style='font-size:10.0pt'>prefix</span></i></tt><tt><span
    6026 style='font-size:10.0pt'>_part_</span></tt><i>N</i><tt><span style='font-size:
    6027 10.0pt'>.csv</span></tt>, which can be read by spreadsheets and most scientific
    6028 software. </p>
     6016name. This file is intended for internal use in GSAS-II and will be deleted if additional
     6017refinements are performed (making the information in them obsolete; use this
     6018menu command to recreate them if needed.) When the <tt><span style='font-size:
     601910.0pt'>.partials</span></tt> file is created, the user can optionally choose
     6020to export the intensity information in a series of ASCII files named <tt><i><span
     6021style='font-size:10.0pt'>prefix</span></i></tt><tt><span style='font-size:10.0pt'>_part_</span></tt><i>N</i><tt><span
     6022style='font-size:10.0pt'>.csv</span></tt>, which can be read by spreadsheets
     6023and most scientific software. </p>
    60296024
    60306025<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l2 level1 lfo5'><![if !supportLists]><span
    … …  
    60746069import of data. Each entry when selected with the mouse shows further submenus
    60756070with specific imports that are available. Any of these files can be accessed
    6076 from a zip file. GSAS-II can read many different <span class=GramE>image</span>
    6077 file formats including MAR345 files, Quantum ADSC files, and tiff files from
    6078 Perkin-Elmer, Pilatus, and GE. Although many of these formats have data fields
    6079 that should contain relevant information for the exposure (<span class=GramE>e.g.</span>
    6080 wavelength), these are rarely filled in correctly by the data acquisition
    6081 software. Thus, you should have separately noted this information as it will be
    6082 needed. In some cases, this information may be in a separate “metadata” file;
    6083 GSAS-II will look for this and attempt to open it as well as the image file. <br>
     6071from a zip file. GSAS-II can read many different image file formats including
     6072MAR345 files, Quantum ADSC files, and tiff files from Perkin-Elmer, Pilatus,
     6073and GE. Although many of these formats have data fields that should contain
     6074relevant information for the exposure (e.g. wavelength), these are rarely
     6075filled in correctly by the data acquisition software. Thus, you should have
     6076separately noted this information as it will be needed. In some cases, this
     6077information may be in a separate “metadata” file; GSAS-II will look for this
     6078and attempt to open it as well as the image file. <br>
    60846079NB: gain maps can be imported but they must be 1000*the gain value (typically
    60856080~1) as integers; if used, GSAS-II will rescale the gain map by 1/1000 and apply
    … …  
    60976092style='font-family:"Courier New";mso-fareast-font-family:"Courier New"'><span
    60986093style='mso-list:Ignore'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
    6099 </span></span></span><![endif]><span class=GramE><b>GSAS .EXP</b></span> - This
    6100 reads one phase from a (old) gsas experiment file (name.EXP). The file name is
    6101 found in a directory dialog; you can change directories as needed. <span
    6102 class=GramE>Only .EXP</span> (or .exp) file names are shown. If the selected
    6103 file has more than one phase, a dialog is shown with the <span class=GramE>choices;</span>
    6104 only one can be chosen. If you want more than one, redo this command. After
    6105 selecting a phase, a dialog box is shown with the proposed phase name. You can
    6106 change it if desired. </p>
     6094</span></span></span><![endif]><b>GSAS .EXP</b> - This reads one phase from a
     6095(old) gsas experiment file (name.EXP). The file name is found in a directory
     6096dialog; you can change directories as needed. Only .EXP (or .exp) file names
     6097are shown. If the selected file has more than one phase, a dialog is shown with
     6098the choices; only one can be chosen. If you want more than one, redo this
     6099command. After selecting a phase, a dialog box is shown with the proposed phase
     6100name. You can change it if desired. </p>
    61076101
    61086102<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    … …  
    61136107phase information from a Protein Data Base file (name.PDB or name.ENT). The
    61146108file name is found in a directory dialog; you can change directories as needed.
    6115 Only .PDB (or .pdb) <span class=GramE>or .ENT</span> (or .ent) file names are
    6116 shown. Be careful that the space group symbol on the ‘CRYST1’ record in the PDB
    6117 file follows the GSAS-II conventions (<span class=GramE>e.g.</span> with spaces
    6118 between axial fields). A dialog box is shown with the proposed phase name. You
    6119 can change it if desired. </p>
     6109Only .PDB (or .pdb) or .ENT (or .ent) file names are shown. Be careful that the
     6110space group symbol on the ‘CRYST1’ record in the PDB file follows the GSAS-II
     6111conventions (e.g. with spaces between axial fields). A dialog box is shown with
     6112the proposed phase name. You can change it if desired. </p>
    61206113
    61216114<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    … …  
    61246117style='mso-list:Ignore'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
    61256118</span></span></span><![endif]><b>CIF file</b> - This reads one phase from a
    6126 Crystallographic Information File ({name<span class=GramE>}.CIF</span> (or
    6127 .cif). The file name is found in a directory dialog; you can change directories
    6128 as needed. If the selected file has more than one phase, a dialog is shown with
    6129 the <span class=GramE>choices;</span> only one can be chosen. If you want more
    6130 than one, redo this command. After selecting a phase, a dialog box is shown
    6131 with the proposed phase name. You can change it if desired. </p>
     6119Crystallographic Information File ({name}.CIF (or .cif). The file name is found
     6120in a directory dialog; you can change directories as needed. If the selected
     6121file has more than one phase, a dialog is shown with the choices; only one can
     6122be chosen. If you want more than one, redo this command. After selecting a
     6123phase, a dialog box is shown with the proposed phase name. You can change it if
     6124desired. </p>
    61326125
    61336126<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    … …  
    61646157data set, such as data type, calibration constants (such as wavelength) and
    61656158default profile parameters are read from a separate file, either a (old) GSAS
    6166 instrument parameter file (<span class=GramE>usually .prm</span>, .ins or .inst
    6167 extension) 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>
     6159instrument parameter file (usually .prm, .ins or .inst extension) or a new
     6160GSAS-II .instparm file. <span style='mso-fareast-font-family:"Times New Roman";
     6161mso-fareast-theme-font:minor-fareast'><o:p></o:p></span></p>
    61696162
    61706163<p class=MsoListParagraphCxSpMiddle>Note that it is possible to apply
    61716164corrections to the 2-theta, intensity or weight values by adding a Python
    6172 command(s) to the instrument <span class=GramE>(.instprm</span>) parameter with
    6173 a variable named CorrectionCode. See the <tt><span style='font-size:10.0pt'>CorrectionCode.instprm.sample</span></tt>
     6165command(s) to the instrument (.instprm) parameter with a variable named
     6166CorrectionCode. See the <tt><span style='font-size:10.0pt'>CorrectionCode.instprm.sample</span></tt>
    61746167file provided in the GSAS-II source directory for an example of how this is
    61756168done. <span style='mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:
    … …  
    61816174style='mso-list:Ignore'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
    61826175</span></span></span><![endif]><b>CIF file</b> - This reads one powder pattern
    6183 (histogram) from a Crystallographic Information File ({name<span class=GramE>}.CIF</span>).
    6184 The file name is found in a directory dialog; you can change directories as
    6185 needed. Only <span class=GramE>one .cif</span> can be chosen. If you want more
    6186 than one, redo this command. </p>
     6176(histogram) from a Crystallographic Information File ({name}.CIF). The file
     6177name is found in a directory dialog; you can change directories as needed. Only
     6178one .cif can be chosen. If you want more than one, redo this command. </p>
    61876179
    61886180<p class=MsoListParagraphCxSpMiddle style='margin-left:.75in;mso-add-space:
    … …  
    62026194</span></span></span><![endif]><b>GSAS .fxye files</b> - This reads powder
    62036195patterns (histograms) from the defined GSAS format powder data files. GSAS file
    6204 <span class=GramE>types</span> STD, ESD, FXY and FXYE are recognized. Neutron
    6205 TOF data with a ‘TIME-MAP’ are also recognized. The file names are found in a
    6206 directory dialog; you can change directories as needed. If the selected files
    6207 have more than one powder pattern, a dialog is shown with the choice(s). </p>
     6196types STD, ESD, FXY and FXYE are recognized. Neutron TOF data with a ‘TIME-MAP’
     6197are also recognized. The file names are found in a directory dialog; you can
     6198change directories as needed. If the selected files have more than one powder
     6199pattern, a dialog is shown with the choice(s). </p>
    62086200
    62096201<p class=MsoListParagraphCxSpMiddle style='margin-left:.75in;mso-add-space:
    … …  
    62286220style='font-family:"Courier New";mso-fareast-font-family:"Courier New"'><span
    62296221style='mso-list:Ignore'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
    6230 </span></span></span><![endif]><i>other supported formats</i> – <span
    6231 class=GramE>Bruker .RAW</span>; FullProf .dat; Panalytical .xrdml;
    6232 Comma-separated .csv; Rigaku .ras &amp; .txt </p>
     6222</span></span></span><![endif]><i>other supported formats</i> – Bruker .RAW;
     6223FullProf .dat; Panalytical .xrdml; Comma-separated .csv; Rigaku .ras &amp; .txt
     6224</p>
    62336225
    62346226<p class=MsoNormal style='text-indent:.5in'>Other formats that are supported,
    … …  
    62486240histogram with all zero intensity values in it using a set of instrument
    62496241parameters that are read in from a file or one of the default sets provided
    6250 when Cancel is pressed at the prompt to select a file. The user <span
    6251 class=GramE>is able to</span> specify the data range and step size. One or more
    6252 crystalline phases must also be provided to perform a crystallographic
    6253 simulation. When the &quot;Refine&quot; menu command is initially used, the
    6254 intensities are computed from these phases and the &quot;observed&quot;
    6255 intensity 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
    6258 refinements 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
    6261 by this option. </p>
     6242when Cancel is pressed at the prompt to select a file. The user is able to
     6243specify the data range and step size. One or more crystalline phases must also
     6244be provided to perform a crystallographic simulation. When the
     6245&quot;Refine&quot; menu command is initially used, the intensities are computed
     6246from these phases and the &quot;observed&quot; intensity values are set from
     6247these computed values, with superimposed &quot;random&quot; noise added based
     6248on the calculated values as σ=sqrt(I) (increase the histogram scale factor to
     6249change this, if desired). Further refinements can then be used to fit to these
     6250simulated data. To reset the &quot;observed&quot; intensity values back to
     6251zero, to recompute them, use the &quot;Edit range&quot; button on the
     6252&quot;PWDR&quot; tree item that is created by this option. </p>
    62626253
    62636254<p class=MsoListParagraphCxSpMiddle style='margin-left:.75in;mso-add-space:
    … …  
    62696260file extension must determine the importer that will be used and a filter
    62706261pattern is specified to determine which files will be read (e.g. use &quot;<tt><span
    6271 style='font-size:10.0pt'>*June23<span class=GramE>*.fxye</span></span></tt>&quot;
    6272 so that only files that contain the string &quot;June23&quot; will be read. </p>
     6262style='font-size:10.0pt'>*June23*.fxye</span></tt>&quot; so that only files
     6263that contain the string &quot;June23&quot; will be read. </p>
    62736264
    62746265<p class=MsoListParagraphCxSpMiddle style='margin-left:.75in;mso-add-space:
    … …  
    62806271fundamental parameters that describe a constant wavelength (most likely
    62816272Bragg-Brentano) powder diffraction instrument. The user must first specify the
    6282 data 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
    6284 supplied using a nomenclature <span class=GramE>similar to</span> Topas
    6285 (described further below). They will then be converted to the SI units and
    6286 parameter names used in the NIST FPA code. Alternately a file can be supplied
    6287 with the parameter values used directly in that program. With this input, a
    6288 series of peaks are computed across the specified data range and the <a
     6273data range to be used and then a set of FP (fundamental parameter) values. The
     6274FP values and a source spectrum can be supplied using a nomenclature similar to
     6275Topas (described further below). They will then be converted to the SI units
     6276and parameter names used in the NIST FPA code. Alternately a file can be
     6277supplied with the parameter values used directly in that program. With this
     6278input, a series of peaks are computed across the specified data range and the <a
    62896279href="gsasII-pwdr.html#PWDR_Instrument_Parameters">Instrumental Parameters</a>
    62906280that determine the instrumental profile (U, V, W, X, Y and SH/L) are determined
    … …  
    62976287
    62986288<p class=MsoListParagraphCxSpLast style='margin-left:.75in;mso-add-space:auto'><span
    6299 style='mso-bookmark:FPAinput'>Description of the Topas-style fundamental
    6300 parameters used as FPA input for GSAS-II</span> </p>
     6289style='mso-bookmark:FPAinput'>Description of the Topas-style fundamental parameters
     6290used as FPA input for GSAS-II</span> </p>
    63016291
    63026292<div align=center>
    … …  
    64256415  mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt;
    64266416  mso-border-alt:solid windowtext .5pt;padding:0in 5.4pt 0in 5.4pt'>
    6427   <p class=MsoNormal>Illuminated sample length in axial direction. <span
    6428   class=GramE>Typically</span> the same as filament_length.</p>
     6417  <p class=MsoNormal>Illuminated sample length in axial direction. Typically
     6418  the same as filament_length.</p>
    64296419  </td>
    64306420 </tr>
    … …  
    64456435  mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt;
    64466436  mso-border-alt:solid windowtext .5pt;padding:0in 5.4pt 0in 5.4pt'>
    6447   <p class=MsoNormal>Length of the receiving slit in axial direction. <span
    6448   class=GramE>Typically</span> the same as filament_length.</p>
     6437  <p class=MsoNormal>Length of the receiving slit in axial direction. Typically
     6438  the same as filament_length.</p>
    64496439  </td>
    64506440 </tr>
    … …  
    64596449  mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt;
    64606450  mso-border-alt:solid windowtext .5pt;padding:0in 5.4pt 0in 5.4pt'>
    6461   <p class=MsoNormal><span class=GramE>cm<sup>-1</sup></span></p>
     6451  <p class=MsoNormal>cm<sup>-1</sup></p>
    64626452  </td>
    64636453  <td width=354 valign=top style='width:265.6pt;border-top:none;border-left:
    … …  
    67576747  mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt;
    67586748  mso-border-alt:solid windowtext .5pt;padding:0in 5.4pt 0in 5.4pt'>
    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>
     6749  <p class=MsoNormal>Width of transition region from high-intensity, roughly flat
     6750  region of the x-ray tube output to the to the tube tails region as a fraction
     6751  of the IBM bandwidth</p>
    67626752  </td>
    67636753 </tr>
    … …  
    68086798</div>
    68096799
    6810 <p class=MsoNormal style='margin-left:.75in'>If you use this, please cite M.H.
    6811 Mendenhall, K. Mullen &amp; J.P. Cline (2015), <i>J. Res. of NIST</i>, <b>120</b>,
     6800<p class=MsoNormal style='margin-left:.75in'><span style='color:white;
     6801mso-color-alt:windowtext'>If you use this, please cite M.H. Mendenhall, K.
     6802Mullen &amp; J.P. Cline (2015), </span><i>J. Res. of NIST</i>, <b>120</b>,
    68126803p223. DOI: 10.6028/jres.120.014. If the incident beam monochromator model is
    68136804used, please also cite: M.H. Mendenhall, D. Black &amp; J.P. Cline (2019), <i>J.
    … …  
    68206811style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    68216812Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    6822 </span></span></span><![endif]><b>Structure Factor</b> - Reads single crystal
    6823 input from a variety of file types. Results are placed in the GSAS-II data tree
    6824 as ‘HKLF file name’ </p>
     6813</span></span></span><![endif]><b>Structure Factor</b> - Reads single crystal input
     6814from a variety of file types. Results are placed in the GSAS-II data tree as
     6815‘HKLF file name’ </p>
    68256816
    68266817<p class=MsoListParagraphCxSpMiddle style='margin-left:.75in;mso-add-space:
    … …  
    68286819style='font-family:"Courier New";mso-fareast-font-family:"Courier New"'><span
    68296820style='mso-list:Ignore'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
    6830 </span></span></span><![endif]><b>F**2 HKL file</b> - <span class=GramE>This
    6831 reads</span> squared structure factors (as F**2) and sig(F**2) from a SHELX
    6832 format .hkl file. The file names are found in a directory dialog; you can
    6833 change 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>
     6821</span></span></span><![endif]><b>F**2 HKL file</b> - This reads squared
     6822structure factors (as F**2) and sig(F**2) from a SHELX format .hkl file. The
     6823file names are found in a directory dialog; you can change directories as
     6824needed. You must know the file contains structure factors (as F**2) as the file
     6825itself has no internal indication of this. </p>
    68356826
    68366827<p class=MsoListParagraphCxSpMiddle style='margin-left:.75in;mso-add-space:
    … …  
    68496840style='mso-list:Ignore'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
    68506841</span></span></span><![endif]><b>CIF file</b> - This reads structure factors
    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
    6853 dialog; you can change directories as needed. The internal structure of this
    6854 file indicates in which form the structure factors are used. </p>
     6842(as F**2 or F) and sig(F**2 or F) from a .CIF (or .cif) or .FCF (or .fcf)
     6843format file. The file names are found in a directory dialog; you can change
     6844directories as needed. The internal structure of this file indicates in which
     6845form the structure factors are used. </p>
    68556846
    68566847<p class=MsoListParagraphCxSpLast style='margin-left:.75in;mso-add-space:auto;
    … …  
    68606851</span></span></span><![endif]><b>guess format from file</b> - This attempts to
    68616852read one data set from a file trying the formats as described above. However,
    6862 since it cannot be determined if SHELX <span class=GramE>format .hkl</span>
    6863 contains F or F**2 values, do not use this command for those files. On
    6864 occasion, this command may not succeed in correctly determining a file format.
    6865 If it fails, retry by selecting the correct format from the list.</p>
     6853since it cannot be determined if SHELX format .hkl contains F or F**2 values,
     6854do not use this command for those files. On occasion, this command may not
     6855succeed in correctly determining a file format. If it fails, retry by selecting
     6856the correct format from the list.</p>
    68666857
    68676858<p class=MsoNormal style='margin-left:.25in;text-indent:.25in'>There are
    … …  
    69216912auto'>GSAS-II uses separate routines to write out files with information inside
    69226913GSAS-II. These routines can be created and customized easily. See the <a
    6923 href="https://gsas-ii.readthedocs.io/en/latest/exports.html">GSAS-II Export
    6924 Modules section</a> of the <a href="#Programmers"><strong>Programmers
    6925 documentation</strong></a> for more information on this. Since it is easy to
    6926 support new formats, the documentation below may not list all supported
    6927 formats. <span style='mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:
    6928 minor-fareast'><o:p></o:p></span></p>
     6914href="https://gsas-ii.readthedocs.io/en/latest/exports.html">GSAS-II Export Modules
     6915section</a> of the <a href="#Programmers"><strong>Programmers documentation</strong></a>
     6916for more information on this. Since it is easy to support new formats, the
     6917documentation below may not list all supported formats. <span style='mso-fareast-font-family:
     6918"Times New Roman";mso-fareast-theme-font:minor-fareast'><o:p></o:p></span></p>
    69296919
    69306920<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l30 level1 lfo14'><![if !supportLists]><span
    … …  
    69666956style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    69676957Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    6968 </span></span></span><![endif]><b>Single crystal data as</b> - Single crystal reflection
    6969 lists can be exported as text files or as a simplified CIF file that contains
    6970 only structure factors. </p>
     6958</span></span></span><![endif]><b>Single crystal data as</b> - Single crystal
     6959reflection lists can be exported as text files or as a simplified CIF file that
     6960contains only structure factors. </p>
    69716961
    69726962<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l30 level1 lfo14'><![if !supportLists]><span
    69736963style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    69746964Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    6975 </span></span></span><![endif]><b>Image data</b> - <span class=GramE>This
    6976 exports</span> selected images as a portable networks graphics format (PNG)
    6977 file. Alternately, the image controls and masks can be written for selected
    6978 images. If strain analysis has been performed on images, the results can also
    6979 be exported here as a spreadsheet (.csv file). </p>
     6965</span></span></span><![endif]><b>Image data</b> - This exports selected images
     6966as a portable networks graphics format (PNG) file. Alternately, the image
     6967controls and masks can be written for selected images. If strain analysis has
     6968been performed on images, the results can also be exported here as a
     6969spreadsheet (.csv file). </p>
    69806970
    69816971<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l30 level1 lfo14'><![if !supportLists]><span
    … …  
    70117001</span></span></span><![endif]><b>Export PDF...</b> - This allows computed PDFs
    70127002peak lists from selected histograms to be written as two simple text files,
    7013 {name}.gr and {name<span class=GramE>}.sq</span>, containing g(r) and s(q),
    7014 respectively as 2 columns of data; a header on each indicated the source file
    7015 name and the column headings. The file name comes from the PDF entry in the
    7016 GSAS-II data tree. </p>
     7003{name}.gr and {name}.sq, containing g(r) and s(q), respectively as 2 columns of
     7004data; a header on each indicated the source file name and the column headings.
     7005The file name comes from the PDF entry in the GSAS-II data tree. </p>
    70177006
    70187007<div class=MsoNormal align=center style='text-align:center'><span
    … …  
    70917080style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>analytic
    70927081Jacobian: This uses a numpy-provided <i>leastsq</i> minimizer, which not
    7093 applicable for problem with <span class=GramE>a large number of</span>
    7094 histograms as it requires much more memory than the Hessian routines. This
    7095 because it creates a Jacobian matrix (J) that is shaped N x M (N parameters x M
    7096 observations) while the Hessian method create a Jacobian matrix only for each
    7097 histogram; the N x N Hessian is the made from summing the J x J<sup>T</sup>
    7098 products across the histograms</p>
     7082applicable for problem with a large number of histograms as it requires much
     7083more memory than the Hessian routines. This because it creates a Jacobian
     7084matrix (J) that is shaped N x M (N parameters x M observations) while the
     7085Hessian method create a Jacobian matrix only for each histogram; the N x N
     7086Hessian is the made from summing the J x J<sup>T</sup> products across the
     7087histograms</p>
    70997088
    71007089<p class=MsoListParagraphCxSpMiddle style='margin-left:.75in;mso-add-space:
    … …  
    71077096derivatives are computed rather than use the analytical derivatives that are
    71087097coded directly into GSAS-II. This will be slower than the analytical
    7109 derivatives and will is often less accurate which results in slower
    7110 convergence. <i>It is typically used for code development to check the accuracy
    7111 of the analytical derivative formulations. </i></p>
     7098derivatives and will is often less accurate which results in slower convergence.
     7099<i>It is typically used for code development to check the accuracy of the
     7100analytical derivative formulations. </i></p>
    71127101
    71137102<p class=MsoListParagraphCxSpLast style='margin-left:.75in;mso-add-space:auto;
    … …  
    71547143elements of the Hessian. When λ is large, this down-weights the significance of
    71557144the off-diagonal terms in the Hessian. Thus, when λ is large, the refinement is
    7156 effectively one of <span class=GramE>steepest-descents</span>, where
    7157 correlation between variables is ignored. Note that steepest-descents
    7158 minimization is typically slow and may not always find the local minimum. This
    7159 is only used when with the &quot;analytical Hessian&quot; minimizer is
    7160 selected. </p>
     7145effectively one of steepest-descents, where correlation between variables is
     7146ignored. Note that steepest-descents minimization is typically slow and may not
     7147always find the local minimum. This is only used when with the &quot;analytical
     7148Hessian&quot; minimizer is selected. </p>
    71617149
    71627150<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l18 level1 lfo17'><![if !supportLists]><span
    … …  
    71997187style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    72007188Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    7201 </span></span></span><![endif]><b>Min extinct.</b> – Reflections with
    7202 extinction corrections larger than this value are ignored.</p>
     7189</span></span></span><![endif]><b>Min extinct.</b> – Reflections with extinction
     7190corrections larger than this value are ignored.</p>
    72037191
    72047192<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l27 level1 lfo19'><![if !supportLists]><span
    … …  
    72067194Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    72077195</span></span></span><![endif]><b>Max delt-F/sig</b> - Removes reflections that
    7208 are very poorly fit. Should be used only with extreme care, since <span
    7209 class=GramE>poorly-fit</span> reflections could be an indication that the
    7210 structure is wrong. </p>
     7196are very poorly fit. Should be used only with extreme care, since poorly-fit reflections
     7197could be an indication that the structure is wrong. </p>
    72117198
    72127199<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l27 level1 lfo19'><![if !supportLists]><span
    … …  
    72497236style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    72507237Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    7251 </span></span></span><![endif]><b>Reverse order?</b> - Normally, in <span
    7252 class=GramE>a sequential refinement histograms</span> are fit in the order they
    7253 are in the data tree (which can be reordered by dragging tree items), but when
    7254 this option is selected, the sequential fit is performed with the last tree
    7255 entry first. </p>
     7238</span></span></span><![endif]><b>Reverse order?</b> - Normally, in a
     7239sequential refinement histograms are fit in the order they are in the data tree
     7240(which can be reordered by dragging tree items), but when this option is
     7241selected, the sequential fit is performed with the last tree entry first. </p>
    72567242
    72577243<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l8 level1 lfo20'><![if !supportLists]><span
    … …  
    72777263<p style='margin-left:.25in;text-indent:-.25in;mso-list:l23 level1 lfo16'><![if !supportLists]><span
    72787264style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    7279 </span></span><![endif]><b><u>Global Settings</u></b><u>:</u> This is a
    7280 location for parameters that apply to an entire project. At present there is
    7281 only one. <span style='mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:
    7282 minor-fareast'><o:p></o:p></span></p>
     7265</span></span><![endif]><b><u>Global Settings</u></b><u>:</u> This is a location
     7266for parameters that apply to an entire project. At present there is only one. <span
     7267style='mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast'><o:p></o:p></span></p>
    72837268
    72847269<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l22 level1 lfo21'><![if !supportLists]><span
    … …  
    73597344style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    73607345</span></span></span><![endif]>those pertaining to quantities in each phase
    7361 (naming pattern &quot;<span class=GramE><tt><i><span style='font-size:10.0pt'>p</span></i></tt><tt><span
    7362 style='font-size:10.0pt'>::</span></tt></span><tt><i><span style='font-size:
    7363 10.0pt'>name</span></i></tt>&quot;); examples include atom coordinates, thermal
    7364 motion and site fraction parameters; </p>
     7346(naming pattern &quot;<tt><i><span style='font-size:10.0pt'>p</span></i></tt><tt><span
     7347style='font-size:10.0pt'>::<i>name</i></span></tt>&quot;); examples include
     7348atom coordinates, thermal motion and site fraction parameters; </p>
    73657349
    73667350<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l26 level1 lfo22;
    … …  
    73737357style='font-size:10.0pt'>:<i>name</i></span></tt>&quot;); such parameters are
    73747358those that depend only on the data set: the scale factor and profile
    7375 coefficients (<span class=GramE>e.g.</span> U, V, W, X and Y); </p>
     7359coefficients (e.g. U, V, W, X and Y); </p>
    73767360
    73777361<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l26 level1 lfo22;
    … …  
    73957379style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    73967380Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    7397 </span></span></span><![endif]><b>Holds</b> - Use this to prevent a parameter from
    7398 being refined. Most valuable when refinement of a parameter is selected in a
    7399 group for refinement (such as x, y &amp; z for an atom or unit cell parameters)
    7400 and one must be fixed. For example, if the space group for a phase has a polar
    7401 axis (e.g., the <i>b</i>-axis in P2<sub>1</sub>), then the origin with respect
    7402 to <i>b</i> is arbitrary and it is not possible to refine the y coordinates for
    7403 all atoms. Place a Hold on any one atom y coordinate to keep the structure from
    7404 drifting up or down the y-axis during refinement. </p>
     7381</span></span></span><![endif]><b>Holds</b> - Use this to prevent a parameter
     7382from being refined. Most valuable when refinement of a parameter is selected in
     7383a group for refinement (such as x, y &amp; z for an atom or unit cell
     7384parameters) and one must be fixed. For example, if the space group for a phase
     7385has a polar axis (e.g., the <i>b</i>-axis in P2<sub>1</sub>), then the origin
     7386with respect to <i>b</i> is arbitrary and it is not possible to refine the y
     7387coordinates for all atoms. Place a Hold on any one atom y coordinate to keep
     7388the structure from drifting up or down the y-axis during refinement. </p>
    74057389
    74067390<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l43 level1 lfo23'><![if !supportLists]><span
    … …  
    74127396the actual coordinate values) Examples for typical use are sets of atoms that
    74137397should be constrained to have the same displacement parameters (aka thermal
    7414 motion, Uiso, etc.) or sets of profile coefficients <span class=GramE>U,V</span>,W
    7415 across multiple data sets. Note that the first selected parameter is treated as
    7416 independent, and the remainder are &quot;slaved&quot; to that parameter as
    7417 &quot;dependent parameters.&quot; All parameters in an equivalence must be
    7418 varied. If any parameter is not varied or is given a &quot;hold,&quot; a
    7419 warning is displayed and none of the parameters are refined. </p>
     7398motion, Uiso, etc.) or sets of profile coefficients U,V,W across multiple data
     7399sets. Note that the first selected parameter is treated as independent, and the
     7400remainder are &quot;slaved&quot; to that parameter as &quot;dependent
     7401parameters.&quot; All parameters in an equivalence must be varied. If any
     7402parameter is not varied or is given a &quot;hold,&quot; a warning is displayed
     7403and none of the parameters are refined. </p>
    74207404
    74217405<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l43 level1 lfo23'><![if !supportLists]><span
    … …  
    74367420style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    74377421Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    7438 </span></span></span><![endif]><b>New Var assignment</b> - These are <span
    7439 class=GramE>similar to</span> constraint equations in that they define a set of
    7440 parameters and multipliers, but rather than specifying a value for the
    7441 expression, a new parameter is assigned to that sum and these constraints have
    7442 a very different function. This replaces a degree of freedom from the original
    7443 variables with a new one that modifies the parameters where the shift is
    7444 applied according to the ratio specified in the expression. This can be used to
    7445 create new parameters that redefine the relationships between items such as
    7446 coordinates or magnetic moments. The new parameter may optionally be named by
    7447 the user. The new var expression creates a new global parameter, where that new
    7448 parameter is independent, while all the parameters in the expression are
    7449 considered as dependent. The setting of the refine flags for the dependent
    7450 parameters is not used. Only if the new var parameter is marked as refine then
    7451 it will be refined. However, if any dependent variable is set as
    7452 &quot;hold,&quot; the new var parameter will not be refined. </p>
     7422</span></span></span><![endif]><b>New Var assignment</b> - These are similar to
     7423constraint equations in that they define a set of parameters and multipliers,
     7424but rather than specifying a value for the expression, a new parameter is
     7425assigned to that sum and these constraints have a very different function. This
     7426replaces a degree of freedom from the original variables with a new one that
     7427modifies the parameters where the shift is applied according to the ratio
     7428specified in the expression. This can be used to create new parameters that
     7429redefine the relationships between items such as coordinates or magnetic
     7430moments. The new parameter may optionally be named by the user. The new var
     7431expression creates a new global parameter, where that new parameter is
     7432independent, while all the parameters in the expression are considered as
     7433dependent. The setting of the refine flags for the dependent parameters is not
     7434used. Only if the new var parameter is marked as refine then it will be
     7435refined. However, if any dependent variable is set as &quot;hold,&quot; the new
     7436var parameter will not be refined. </p>
    74537437
    74547438<p class=MsoNormal>Note that when new var and constraint equation constraints
    … …  
    74627446<p class=MsoNormal>New Var constraints are generated when <a
    74637447href="https://iso.byu.edu/iso/isodistort.php">ISODISTORT</a> is used to develop
    7464 mode distortions from a comparison of a high symmetry parent structure (<span
    7465 class=GramE>e.g.</span> cubic perovskite) with a distorted child substructure.
    7466 They are developed for the phase imported from the special cif file produced by
    7467 ISODISTORT from a mode distortion analysis. </p>
     7448mode distortions from a comparison of a high symmetry parent structure (e.g.
     7449cubic perovskite) with a distorted child substructure. They are developed for
     7450the phase imported from the special cif file produced by ISODISTORT from a mode
     7451distortion analysis. </p>
    74687452
    74697453<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
    … …  
    74907474OK. Cancel in either dialog will cancel the operation. The equivalenced
    74917475parameters 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;
    7492 usually M1=1.0 and M2=-1.0 but can be changed via the ‘Edit’ button. The
    7493 equation(s) are shown in the window tagged by ‘EQUIV’ to mark it as an
    7494 equivalence assignment. </p>
     7476usually M1=1.0 and M2=-1.0 but can be changed via the ‘Edit’ button. The equation(s)
     7477are shown in the window tagged by ‘EQUIV’ to mark it as an equivalence
     7478assignment. </p>
    74957479
    74967480<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l3 level1 lfo24'><![if !supportLists]><span
    … …  
    75327516normal modes from representational analysis from the coordinates. </p>
    75337517
    7534 <p>In addition to menu commands, this window also offer the following actions by
    7535 pressing buttons:<span style='mso-fareast-font-family:"Times New Roman";
     7518<p>In addition to menu commands, this window also offer the following actions
     7519by pressing buttons:<span style='mso-fareast-font-family:"Times New Roman";
    75367520mso-fareast-theme-font:minor-fareast'><o:p></o:p></span></p>
    75377521
    … …  
    75617545mso-bidi-font-family:Symbol'><span style='mso-list:Ignore'>·<span
    75627546style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    7563 </span></span></span><![endif]><b>Show Generated Constraints</b> - After constraints
    7564 have been processed, a series of relationships are developed to determine new
    7565 variables from the current parameters and &quot;inverse&quot; equations that
    7566 determine dependent parameters from the new variables and independent
    7567 parameters. This shows the resulting relationships, as well as any
     7547</span></span></span><![endif]><b>Show Generated Constraints</b> - After
     7548constraints have been processed, a series of relationships are developed to
     7549determine new variables from the current parameters and &quot;inverse&quot;
     7550equations that determine dependent parameters from the new variables and
     7551independent parameters. This shows the resulting relationships, as well as any
    75687552&quot;Hold&quot; variables. </p>
    75697553
    … …  
    75857569a particular constraint number. When sequential refinement is selected (via the
    75867570<a href="#Controls">Controls tree item</a>), it becomes possible to define
    7587 constraints of form &quot;<span class=GramE><tt><i><span style='font-size:10.0pt'>p</span></i></tt>:*</span>:<tt><i><span
     7571constraints of form &quot;<tt><i><span style='font-size:10.0pt'>p</span></i></tt>:*:<tt><i><span
    75887572style='font-size:10.0pt'>name</span></i></tt>&quot; and &quot;:*:<tt><i><span
    75897573style='font-size:10.0pt'>name</span></i></tt>&quot; (where &quot;<tt><i><span
    … …  
    76147598previously specified with a specific histogram number will be ignored and
    76157599constraints with a &quot;*&quot; where for a histogram number will be used.
    7616 Note that constraints on phase parameters (of form &quot;<span class=GramE><tt><i><span
    7617 style='font-size:10.0pt'>p</span></i></tt>::</span><tt><i><span
    7618 style='font-size:10.0pt'>name</span></i></tt>&quot; -- without a histogram number
    7619 specified) will be used normally. Note that this was the normal operating mode
    7620 for GSAS-II in earlier versions. </p>
     7600Note that constraints on phase parameters (of form &quot;<tt><i><span
     7601style='font-size:10.0pt'>p</span></i></tt>::<tt><i><span style='font-size:10.0pt'>name</span></i></tt>&quot;
     7602-- without a histogram number specified) will be used normally. Note that this
     7603was the normal operating mode for GSAS-II in earlier versions. </p>
    76217604
    76227605<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l12 level1 lfo26'><![if !supportLists]><span
    … …  
    76967679style='mso-list:Ignore'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
    76977680</span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Add
    7698 restraints</b> – this takes you through a sequence of dialog boxes which ask
    7699 for the identities of the atoms involved in the restraint and the value to be
     7681restraints</b> – this takes you through a sequence of dialog boxes which ask for
     7682the identities of the atoms involved in the restraint and the value to be
    77007683assigned to the restraint. The esd is given a default value which can be
    77017684changed after the restraints are created.</p>
    … …  
    77957778</span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Add rigid
    77967779body</b> – (Vector rigid bodies) this creates a vector description of a rigid
    7797 body. A dialog box asks the number of atoms (&gt;2) and the number of vectors
    7798 required to create the rigid body. An entry will be created showing a magnitude
    7799 with the vector set to be applied for each vector needed to develop the rigid
    7800 body.<b style='mso-bidi-font-weight:normal'><o:p></o:p></b></p>
     7780body. A dialog box asks the number of atoms (&gt;2) and the number of vectors required
     7781to create the rigid body. An entry will be created showing a magnitude with the
     7782vector set to be applied for each vector needed to develop the rigid body.<b
     7783style='mso-bidi-font-weight:normal'><o:p></o:p></b></p>
    78017784
    78027785<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    … …  
    78067789</span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Import
    78077790XYZ</b> – (Residue rigid bodies) this reads a text file containing a set of
    7808 Cartesian coordinates describing a rigid body model. Each line has atom type (<span
    7809 class=GramE>e.g.</span> C, Na, etc.) and Cartesian X, Y and Z.</p>
     7791Cartesian coordinates describing a rigid body model. Each line has atom type
     7792(e.g. C, Na, etc.) and Cartesian X, Y and Z.</p>
    78107793
    78117794<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    … …  
    78487831has been run. (See the <a href="#Controls">Controls tree item</a> to set the
    78497832histograms to be used in a sequential refinement and use the
    7850 Calculate/Sequential refine menu command to run the refinement.) <span
    7851 class=GramE>A number of</span> other fitting processes within GSAS-II can be
    7852 done sequentially, each will have its own differently named set of sequential
    7853 results When any one is selected, the window tabulates the sequential
    7854 refinement results. The columns are the parameter names; the naming convention
    7855 is generally ‘p:h:<span class=GramE>name:n</span>’ where ‘p’ is the phase
    7856 number,’ h’ is the histogram number, ‘name’ is the parameter name, and ‘n’ (if
    7857 needed) is the item number (e.g. atom number). The rows are the data sets used
    7858 in the sequential refinement.</p>
     7833Calculate/Sequential refine menu command to run the refinement.) A number of
     7834other fitting processes within GSAS-II can be done sequentially, each will have
     7835its own differently named set of sequential results When any one is selected,
     7836the window tabulates the sequential refinement results. The columns are the
     7837parameter names; the naming convention is generally ‘p:h:name:n’ where ‘p’ is
     7838the phase number,’ h’ is the histogram number, ‘name’ is the parameter name,
     7839and ‘n’ (if needed) is the item number (e.g. atom number). The rows are the
     7840data sets used in the sequential refinement.</p>
    78597841
    78607842<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
    … …  
    78927874style='font-family:"Courier New";mso-fareast-font-family:"Courier New"'><span
    78937875style='mso-list:Ignore'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
    7894 </span></span></span><![endif]><b>Update phase from row</b> – <span
    7895 class=GramE>this updates</span> the phase parameters from the entries in the
    7896 selected row. Normally the phase parameters at the end of a sequential fit are
    7897 those obtained from the last histogram.</p>
     7876</span></span></span><![endif]><b>Update phase from row</b> – this updates the
     7877phase parameters from the entries in the selected row. Normally the phase
     7878parameters at the end of a sequential fit are those obtained from the last
     7879histogram.</p>
    78987880
    78997881<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    … …  
    79587940Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    79597941</span></span></span><![endif]><span style='mso-bidi-font-weight:bold'>Menu</span>
    7960 ‘<b>Pseudo Vars</b>’ –<span style='mso-bidi-font-weight:bold'> this is used to create
    7961 derived results from sequentially refined parameters; new columns are the
    7962 result.</span></p>
     7942‘<b>Pseudo Vars</b>’ –<span style='mso-bidi-font-weight:bold'> this is used to
     7943create derived results from sequentially refined parameters; new columns are
     7944the result.</span></p>
    79637945
    79647946<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    … …  
    81008082</span></span></span><![endif]>Press ‘s’ – this presents a choice of parameters
    81018083from the table columns to be used for the x-axis. Typically, this is used to
    8102 show parameter variation with <span class=GramE>e.g.</span> temperature.</p>
     8084show parameter variation with e.g. temperature.</p>
    81038085
    81048086<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l1 level1 lfo30;
    … …  
    81198101<p class=MsoNormal>Cluster analysis is a suite of data survey techniques where
    81208102data are grouped by some measure of their similarity. Thus, it can be used as a
    8121 preliminary survey of a large number of data sets in <span class=GramE>e.g.</span>
    8122 preparation of detailed examination of representative members. In the case of
    8123 powder diffraction pattern (PWDR) data or pair distribution (PDF) data, their
     8103preliminary survey of a large number of data sets in e.g. preparation of
     8104detailed examination of representative members. In the case of powder
     8105diffraction pattern (PWDR) data or pair distribution (PDF) data, their
    81248106similarity is determined by considering each pattern as a hyper-dimensional
    81258107vector with one dimension for each data point and then computing some measure
    81268108of how parallel pairs of these vectors are. Consequently, it can be used to
    8127 survey PWDR data entries that have identical scan characteristics (<span
    8128 class=GramE>e.g.</span> instrument type, step size, radiation type, wavelength)
    8129 or multiple PDF G(R) entries created with the same step sizes and using the
    8130 same radiation from data collected with identical instrument configurations.
    8131 Cluster analysis is available in GSAS-II after it is initiated by the main menu
    8132 command <b><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    8133 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Calculate/Setup
     8109survey PWDR data entries that have identical scan characteristics (e.g.
     8110instrument type, step size, radiation type, wavelength) or multiple PDF G(R)
     8111entries created with the same step sizes and using the same radiation from data
     8112collected with identical instrument configurations. Cluster analysis is
     8113available in GSAS-II after it is initiated by the main menu command <b><span
     8114style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     8115mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Calculate/Setup
    81348116Cluster Analysis. </span></b>The cluster analysis routines used here are from
    81358117the scipy library and (if available) the scikit-learn library.<span
    … …  
    81648146style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    81658147Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    8166 </span></span></span><![endif]><b>Select datasets</b> – this brings up a
    8167 selection tool for PWDR (&amp; PDF, if present) entries in the GSAS-II data
    8168 tree. Your selection must be either PWDR or PDF data; otherwise, there is no
    8169 check on data similarity so be careful with your selections. Multi-bank TOF
    8170 data should not be mixed for cluster analysis nor should laboratory and
    8171 synchrotron data. Cluster analysis on fewer than 5-10 data sets is probably not
    8172 useful but should be used when you have dozens or even hundreds of data sets.</p>
     8148</span></span></span><![endif]><b>Select datasets</b> – this brings up a selection
     8149tool for PWDR (&amp; PDF, if present) entries in the GSAS-II data tree. Your
     8150selection must be either PWDR or PDF data; otherwise, there is no check on data
     8151similarity so be careful with your selections. Multi-bank TOF data should not
     8152be mixed for cluster analysis nor should laboratory and synchrotron data.
     8153Cluster analysis on fewer than 5-10 data sets is probably not useful but should
     8154be used when you have dozens or even hundreds of data sets.</p>
    81738155
    81748156<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l39 level1 lfo31'><![if !supportLists]><span
    … …  
    82878269mso-ansi-language:EN-US;mso-fareast-language:EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape
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    82908272</v:shape><![endif]--><![if !vml]><img width=145 height=59
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    82928274style='font-family:"Cambria Math",serif;color:#4A4A4A'><o:p></o:p></span></p>
    82938275
    … …  
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    83718353</v:shape><![endif]--><![if !vml]><img width=163 height=47
    8372 src="gsasII_files/image006.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
     8354src="gsasII_files/image007.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
    83738355style='color:#4A4A4A'><o:p></o:p></span></p>
    83748356
    … …  
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     8404 <v:imagedata src="gsasII_files/image008.png" o:title="" chromakey="white"/>
    84238405</v:shape><![endif]--><![if !vml]><img width=158 height=19
    8424 src="gsasII_files/image008.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
     8406src="gsasII_files/image009.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
    84258407style='color:#4A4A4A'><o:p></o:p></span></p>
    84268408
    … …  
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    84808462</v:shape><![endif]--><![if !vml]><img width=150 height=43
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     8463src="gsasII_files/image011.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
    84828464style='color:#4A4A4A'><o:p></o:p></span></p>
    84838465
    … …  
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    85678549</v:shape><![endif]--><![if !vml]><img width=225 height=45
    8568 src="gsasII_files/image012.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
     8550src="gsasII_files/image013.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
    85698551style='color:#4A4A4A'><br style='mso-special-character:line-break'>
    85708552<![if !supportLineBreakNewLine]><br style='mso-special-character:line-break'>
    … …  
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    86168598</v:shape><![endif]--><![if !vml]><img width=141 height=37
    8617 src="gsasII_files/image014.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
     8599src="gsasII_files/image015.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
    86188600style='color:#4A4A4A'><br style='mso-special-character:line-break'>
    86198601<![if !supportLineBreakNewLine]><br style='mso-special-character:line-break'>
    … …  
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     8665src="gsasII_files/image017.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
    86848666style='color:#4A4A4A'><o:p></o:p></span></p>
    86858667
    … …  
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     8738 <v:imagedata src="gsasII_files/image018.png" o:title="" chromakey="white"/>
    87578739</v:shape><![endif]--><![if !vml]><img width=173 height=57
    8758 src="gsasII_files/image018.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
     8740src="gsasII_files/image019.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
    87598741style='color:#4A4A4A'><o:p></o:p></span></p>
    87608742
    … …  
    87628744auto'><span style='color:#4A4A4A'>where the exponent, p, = 2 by default; this
    87638745is identical to the Euclidian formula. Some choices for p: 1 is the same as
    8764 city 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)
    8766 give distance results that are between Euclidian (p=2) and Chebyschev (p=10 ~
    8767 ∞).<o:p></o:p></span></p>
     8746city block, and 10 (~<span style='mso-spacerun:yes'>  </span>∞) is essentially
     8747the same as Chebyschev. The others (3 &amp; 4) give distance results that are
     8748between Euclidian (p=2) and Chebyschev (p=10 ~ ∞).<o:p></o:p></span></p>
    87688749
    87698750<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    … …  
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     8822 <v:imagedata src="gsasII_files/image020.png" o:title="" chromakey="white"/>
    88428823</v:shape><![endif]--><![if !vml]><img width=220 height=57
    8843 src="gsasII_files/image020.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
     8824src="gsasII_files/image021.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
    88448825style='color:#4A4A4A'><o:p></o:p></span></p>
    88458826
    … …  
    88478828auto'><span style='color:#4A4A4A'>where the variance, <i>V</i>[<i>x<sub>i</sub></i>],
    88488829is computed automatically as the variance in the data point values for each
    8849 data position (<span class=GramE>i.e.</span> 2</span><span style='font-family:
    8850 Symbol;mso-ascii-font-family:"Times New Roman";mso-hansi-font-family:"Times New Roman";
    8851 color:#4A4A4A;mso-char-type:symbol;mso-symbol-font-family:Symbol'><span
    8852 style='mso-char-type:symbol;mso-symbol-font-family:Symbol'>Q</span></span><span
    8853 style='color:#4A4A4A'>) across the entire data array.<o:p></o:p></span></p>
     8830data position (i.e. 2</span><span style='font-family:Symbol;mso-ascii-font-family:
     8831"Times New Roman";mso-hansi-font-family:"Times New Roman";color:#4A4A4A;
     8832mso-char-type:symbol;mso-symbol-font-family:Symbol'><span style='mso-char-type:
     8833symbol;mso-symbol-font-family:Symbol'>Q</span></span><span style='color:#4A4A4A'>)
     8834across the entire data array.<o:p></o:p></span></p>
    88548835
    88558836<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    … …  
    89068887mso-ansi-language:EN-US;mso-fareast-language:EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape
    89078888 id="_x0000_i1025" type="#_x0000_t75" style='width:120.75pt;height:32.25pt'>
    8908  <v:imagedata src="gsasII_files/image021.png" o:title="" chromakey="white"/>
     8889 <v:imagedata src="gsasII_files/image022.png" o:title="" chromakey="white"/>
    89098890</v:shape><![endif]--><![if !vml]><img width=161 height=43
    8910 src="gsasII_files/image022.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
     8891src="gsasII_files/image023.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
    89118892style='color:#4A4A4A'><o:p></o:p></span></p>
    89128893
    … …  
    89188899tab is a 3D plot of the result of a Principal Component Analysis (PCA) of the
    89198900distance data; it shows the location of each data set in this space. Clusters
    8920 may be evident from this plot; variable temperature scans tend to show a complex
    8921 path of distance points with cluster grouping corresponding to phases. The GUI
    8922 will be extended to show more steps in cluster analysis.<o:p></o:p></span></p>
     8901may be evident from this plot; variable temperature scans tend to show a
     8902complex path of distance points with cluster grouping corresponding to phases. Since
     8903data sets may be in a series, a plot of the serial distances across the suite
     8904of data is shown; spikes in a temperature series may indicate phase changes. The
     8905GUI will be extended to show more steps in cluster analysis.<o:p></o:p></span></p>
    89238906
    89248907<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l28 level1 lfo32'><![if !supportLists]><span
    … …  
    89338916single cluster is obtained. A dendrogram is displayed showing the progression
    89348917of this clustering. Each cluster is given a mean position, <i>s</i> or <i>t</i>,
    8935 to compare to the others. The linkage methods for calculating the distance
    8936 (using the distance method, <i>dist</i>, as selected above) between each pair
    8937 of clusters are:<o:p></o:p></span></p>
     8918to compare to the others. The linkage methods for calculating the distance (using
     8919the distance method, <i>dist</i>, as selected above) between each pair of
     8920clusters are:<o:p></o:p></span></p>
    89388921
    89398922<p class=MsoListParagraphCxSpMiddle style='margin-left:.75in;mso-add-space:
    … …  
    89488931
    89498932<p class=MsoListParagraphCxSpMiddle style='margin-left:.75in;mso-add-space:
    8950 auto'><i><span style='color:#4A4A4A'>d</span></i><span style='color:#4A4A4A'>(<span
    8951 class=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>
     8933auto'><i><span style='color:#4A4A4A'>d</span></i><span style='color:#4A4A4A'>(<i>s,t</i>)<i>
     8934= 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>
    89528935
    89538936<p class=MsoListParagraphCxSpMiddle style='margin-left:.75in;mso-add-space:
    … …  
    89648947
    89658948<p class=MsoNormal style='margin-left:.75in'><i><span style='color:#4A4A4A'>d</span></i><span
    8966 style='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>
     8949style='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>
    89678950
    89688951<p class=MsoNormal style='margin-left:.75in'><span style='color:#4A4A4A'><o:p>&nbsp;</o:p></span></p>
    … …  
    90359018mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape id="_x0000_i1025" type="#_x0000_t75"
    90369019 style='width:159pt;height:39pt'>
    9037  <v:imagedata src="gsasII_files/image023.png" o:title="" chromakey="white"/>
     9020 <v:imagedata src="gsasII_files/image024.png" o:title="" chromakey="white"/>
    90389021</v:shape><![endif]--><![if !vml]><img width=212 height=52
    9039 src="gsasII_files/image024.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
     9022src="gsasII_files/image025.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
    90409023style='color:#4A4A4A'><o:p></o:p></span></p>
    90419024
    … …  
    90479030color:#4A4A4A'><span style='mso-list:Ignore'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
    90489031</span></span></span><![endif]><b><span style='color:#4A4A4A'>weighted</span></b><span
    9049 style='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>
     9032style='color:#4A4A4A'> – computes the linkage when <i>s</i> is formed with
     9033clusters <i>u</i> &amp; <i>v</i> and <i>t</i> is another cluster as:<o:p></o:p></span></p>
    90519034
    90529035<p class=MsoListParagraphCxSpMiddle style='margin-left:.75in;mso-add-space:
    … …  
    90819064mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape id="_x0000_i1025" type="#_x0000_t75"
    90829065 style='width:180.75pt;height:14.25pt'>
    9083  <v:imagedata src="gsasII_files/image025.png" o:title="" chromakey="white"/>
     9066 <v:imagedata src="gsasII_files/image026.png" o:title="" chromakey="white"/>
    90849067</v:shape><![endif]--><![if !vml]><img width=241 height=19
    9085 src="gsasII_files/image026.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
     9068src="gsasII_files/image027.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
    90869069style='color:#4A4A4A'><o:p></o:p></span></p>
    90879070
    … …  
    91319114mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape id="_x0000_i1025" type="#_x0000_t75"
    91329115 style='width:103.5pt;height:14.25pt'>
    9133  <v:imagedata src="gsasII_files/image027.png" o:title="" chromakey="white"/>
     9116 <v:imagedata src="gsasII_files/image028.png" o:title="" chromakey="white"/>
    91349117</v:shape><![endif]--><![if !vml]><img width=138 height=19
    9135 src="gsasII_files/image028.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
     9118src="gsasII_files/image029.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
    91369119style='color:#4A4A4A'><o:p></o:p></span></p>
    91379120
    … …  
    91809163mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape id="_x0000_i1025" type="#_x0000_t75"
    91819164 style='width:113.25pt;height:14.25pt'>
    9182  <v:imagedata src="gsasII_files/image029.png" o:title="" chromakey="white"/>
     9165 <v:imagedata src="gsasII_files/image030.png" o:title="" chromakey="white"/>
    91839166</v:shape><![endif]--><![if !vml]><img width=151 height=19
    9184 src="gsasII_files/image030.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
     9167src="gsasII_files/image031.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
    91859168style='color:#4A4A4A'><o:p></o:p></span></p>
    91869169
    … …  
    93049287mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape id="_x0000_i1025" type="#_x0000_t75"
    93059288 style='width:350.25pt;height:42.75pt'>
    9306  <v:imagedata src="gsasII_files/image031.png" o:title="" chromakey="white"/>
     9289 <v:imagedata src="gsasII_files/image032.png" o:title="" chromakey="white"/>
    93079290</v:shape><![endif]--><![if !vml]><img width=467 height=57
    9308 src="gsasII_files/image032.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
     9291src="gsasII_files/image033.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
    93099292style='color:#4A4A4A'><o:p></o:p></span></p>
    93109293
    … …  
    93839366style='color:#4A4A4A'> – Only the hierarchical dendrogram is shown.<o:p></o:p></span></p>
    93849367
    9385 <p class=MsoListParagraphCxSpLast style='margin-left:.75in;mso-add-space:auto;
    9386 text-indent:-.25in;mso-list:l28 level2 lfo32'><![if !supportLists]><span
     9368<p class=MsoListParagraphCxSpMiddle style='margin-left:.75in;mso-add-space:
     9369auto;text-indent:-.25in;mso-list:l28 level2 lfo32'><![if !supportLists]><span
    93879370style='font-family:"Courier New";mso-fareast-font-family:"Courier New";
    93889371color:#4A4A4A'><span style='mso-list:Ignore'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
    … …  
    93909373style='color:#4A4A4A'> – Only the 3D representation of the Principal Component
    93919374Analysis is shown.<o:p></o:p></span></p>
     9375
     9376<p class=MsoListParagraphCxSpLast style='margin-left:.75in;mso-add-space:auto;
     9377text-indent:-.25in;mso-list:l28 level2 lfo32'><![if !supportLists]><span
     9378style='font-family:"Courier New";mso-fareast-font-family:"Courier New";
     9379color:#4A4A4A'><span style='mso-list:Ignore'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
     9380</span></span></span><![endif]><b><span style='color:#4A4A4A'>Diffs </span></b><span
     9381style='color:#4A4A4A'>– Only the serial differences are shown.<o:p></o:p></span></p>
    93929382
    93939383<h4>Cluster Analysis with scikit-learn</h4>
    … …  
    94709460different in the resulting 3D PCA plot from all others that would be in
    94719461clusters. Although the chosen distance method affects the appearance of the 3D
    9472 PCA plot, the three outlier methods all use the original data, thus are independent
    9473 of any selected distance method. The GUI is refreshed showing a listing of the
    9474 outlier data; selection of any, displays that data item in the powder pattern
    9475 plot tab. Any previous cluster identification, e. g. by K-means, is erased. The
    9476 outlier detection methods are:<o:p></o:p></span></p>
     9462PCA plot, the three outlier methods all use the original data, thus are
     9463independent of any selected distance method. The GUI is refreshed showing a
     9464listing of the outlier data; selection of any, displays that data item in the
     9465powder pattern plot tab. Any previous cluster identification, e. g. by K-means,
     9466is erased. The outlier detection methods are:<o:p></o:p></span></p>
    94779467
    94789468<p class=MsoListParagraphCxSpMiddle style='margin-left:.25in;mso-add-space:
    … …  
    95159505
    95169506<p class=MsoNormal><span style='color:#4A4A4A'>For each selection of distance
    9517 method, <span class=GramE>i.e.</span> “Euclidian”, a plot tab is created with 2
    9518 or 4 plots. They are: 1) the distance matrix displayed in the same way the
    9519 refinement covariance matrix is displayed (default coloring is “paired” – same
    9520 parameter as the powder pattern contour plot); 2) the 3D PCA analysis plot; 3) the
    9521 hierarchical dendrogram plot and 4) the PCA percent contribution plot. Each can
    9522 be zoomed independent of the others and the 1<sup>st</sup> three can be
    9523 selected to show as a single plot in the tab (see <b>Plot selection</b> above).
    9524 A LB mouse selection (&amp; hold button down) of a 3D PCA point will show the
    9525 data set name in the plot status line. If clusters are determined by e. g.
    9526 K-means, the 3D PCA points will be colored by cluster membership.<o:p></o:p></span></p>
     9507method, i.e. “Euclidian”, a plot tab is created with 2 or 4 plots. They are: 1)
     9508the distance matrix displayed in the same way the refinement covariance matrix
     9509is displayed (default coloring is “paired” – same parameter as the powder
     9510pattern contour plot); 2) the 3D PCA analysis plot; 3) the hierarchical
     9511dendrogram plot and 4) the PCA percent contribution plot. Each can be zoomed
     9512independent of the others and the 1<sup>st</sup> three can be selected to show
     9513as a single plot in the tab (see <b>Plot selection</b> above). A LB mouse
     9514selection (&amp; hold button down) of a 3D PCA point will show the data set
     9515name in the plot status line. If clusters are determined by e. g. K-means, the
     95163D PCA points will be colored by cluster membership.<o:p></o:p></span></p>
    95279517
    95289518<p class=MsoListParagraph style='margin-left:.75in;mso-add-space:auto'><span
    … …  
    95499539</span></div>
    95509540
    9551 <h2><span style='mso-fareast-font-family:"Times New Roman";color:#4A4A4A'>6. Histogram
    9552 data tree items<o:p></o:p></span></h2>
     9541<h2><span style='mso-fareast-font-family:"Times New Roman";color:#4A4A4A'>6.
     9542Histogram data tree items<o:p></o:p></span></h2>
    95539543
    95549544<p class=MsoNormal><span style='color:#4A4A4A'>These are shown in the data tree
    … …  
    95749564
    95759565<p class=MsoNormal><span style='color:#4A4A4A'>You can change the weight
    9576 factor. This is a multiplier on <span class=GramE>all of</span> the reflection
    9577 weights in this histogram. Rarely needs to be changed.<o:p></o:p></span></p>
     9566factor. This is a multiplier on all of the reflection weights in this
     9567histogram. Rarely needs to be changed.<o:p></o:p></span></p>
    95789568
    95799569<p><span style='color:#4A4A4A'>Menu Commands </span><span style='mso-fareast-font-family:
    … …  
    95949584Symbol;color:#4A4A4A'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    95959585</span></span></span><![endif]><b><span style='color:#4A4A4A'>Merge HKLs </span></b><span
    9596 style='color:#4A4A4A'>– this combines equivalent/duplicate reflections
    9597 according to space group and some options to make a unique and averaged set of
    9598 structure factors.<o:p></o:p></span></p>
     9586style='color:#4A4A4A'>– this combines equivalent/duplicate reflections according
     9587to space group and some options to make a unique and averaged set of structure
     9588factors.<o:p></o:p></span></p>
    95999589
    96009590<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l34 level1 lfo34'><![if !supportLists]><span
    … …  
    96109600</span></span></span><![endif]><b><span style='color:#4A4A4A'>Plot HKLs</span></b><span
    96119601style='color:#4A4A4A'> (the default plot)– shows a HKL layer with rings scaled
    9612 to F or F2 for Fo and Fc. +/- steps through the layers and <span class=GramE>h,k</span>
    9613 or l selects the orientation – see K box for all the possible commands.<o:p></o:p></span></p>
     9602to F or F2 for Fo and Fc. +/- steps through the layers and h,k or l selects the
     9603orientation – see K box for all the possible commands.<o:p></o:p></span></p>
    96149604
    96159605<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l34 level1 lfo34'><![if !supportLists]><span
    … …  
    96239613<h4><a name="HKLF_Instrument_Parameters">Instrument Parameters</a></h4>
    96249614
    9625 <p class=MsoNormal><span style='color:#4A4A4A'>This window shows the histogram
    9626 type (SXC or SNC) and the wavelength. You may change the wavelength or source
    9627 type but rarely will need to do so.<o:p></o:p></span></p>
     9615<p class=MsoNormal><span style='color:#4A4A4A'>This window shows the histogram type
     9616(SXC or SNC) and the wavelength. You may change the wavelength or source type
     9617but rarely will need to do so.<o:p></o:p></span></p>
    96289618
    96299619<h4><a name="HKLF_Reflection_List"></a><span style='mso-fareast-font-family:
    … …  
    96739663</span></span></span><![endif]><b><span style='color:#4A4A4A'>Plot HKLs</span></b><span
    96749664style='color:#4A4A4A'> (the default plot)– shows a HKL layer with rings scaled
    9675 to F or F2 for Fo and Fc. +/- steps through the layers and <span class=GramE>h,k</span>
    9676 or l selects the orientation – see K box for all the possible commands.<o:p></o:p></span></p>
     9665to F or F2 for Fo and Fc. +/- steps through the layers and h,k or l selects the
     9666orientation – see K box for all the possible commands.<o:p></o:p></span></p>
    96779667
    96789668<p class=MsoListParagraphCxSpMiddle style='margin-left:1.25in;mso-add-space:
    … …  
    96819671color:#4A4A4A'><span style='mso-list:Ignore'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
    96829672</span></span></span><![endif]><b><span style='color:#4A4A4A'>Plot 3D HKLs</span></b><span
    9683 style='color:#4A4A4A'> – shows a 3D representation of the unique part reciprocal
    9684 space points for this phase. The save as/key item in the plot status bar shows
    9685 the various commands for modifying this plot.<o:p></o:p></span></p>
     9673style='color:#4A4A4A'> – shows a 3D representation of the unique part
     9674reciprocal space points for this phase. The save as/key item in the plot status
     9675bar shows the various commands for modifying this plot.<o:p></o:p></span></p>
    96869676
    96879677<p class=MsoListParagraphCxSpMiddle style='margin-left:1.25in;mso-add-space:
    … …  
    96979687color:#4A4A4A'><span style='mso-list:Ignore'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
    96989688</span></span></span><![endif]><b><span style='color:#4A4A4A'>Show/hide extinct
    9699 reflections</span></b><span style='color:#4A4A4A'> – can exclude space group extinctions
    9700 from 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>
     9689reflections</span></b><span style='color:#4A4A4A'> – can exclude space group
     9690extinctions from the list (not valid for PWDR data).</span><span
     9691style='mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
     9692color:#4A4A4A'><o:p></o:p></span></p>
    97029693
    97039694<h5><a name=PDF><span style='mso-fareast-font-family:"Times New Roman"'>What is
    … …  
    97309721<h4><a name="PDF_Controls">PDF Controls</a></h4>
    97319722
    9732 <p class=MsoNormal><span style='color:#4A4A4A'>This window provides parameters for
    9733 computing the pair distribution function [PDF, G(r)] from the <a href="#PDF_I_Q">I(Q)
    9734 function</a>. This can only be done when a chemical formula and appropriate
    9735 control values are provided. If so, clicking on this menu item causes the <a
    9736 href="#PDF_I_Q">I(Q)</a>, <a href="#PDF_S_Q">S(Q)</a>, <a href="#PDF_F_Q">F(Q)</a>
    9737 and <a href="#PDF_G_R">G(R) functions</a> to be plotted, as described below. <o:p></o:p></span></p>
     9723<p class=MsoNormal><span style='color:#4A4A4A'>This window provides parameters
     9724for computing the pair distribution function [PDF, G(r)] from the <a
     9725href="#PDF_I_Q">I(Q) function</a>. This can only be done when a chemical
     9726formula and appropriate control values are provided. If so, clicking on this
     9727menu item causes the <a href="#PDF_I_Q">I(Q)</a>, <a href="#PDF_S_Q">S(Q)</a>, <a
     9728href="#PDF_F_Q">F(Q)</a> and <a href="#PDF_G_R">G(R) functions</a> to be
     9729plotted, as described below. <o:p></o:p></span></p>
    97389730
    97399731<p class=MsoNormal><span style='color:#4A4A4A'>The <b>Optimize PDF</b> button
    … …  
    97679759style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    97689760</span></span></span><![endif]><b><span style='color:#4A4A4A'>Delete element - </span></b><span
    9769 style='color:#4A4A4A'>Removes a <span class=GramE>previously-entered</span>
    9770 element from the chemical formula. <o:p></o:p></span></p>
     9761style='color:#4A4A4A'>Removes a previously-entered element from the chemical
     9762formula. <o:p></o:p></span></p>
    97719763
    97729764<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l25 level1 lfo36;
    … …  
    98469838style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    98479839</span></span></span><![endif]><b><span style='color:#4A4A4A'>m</span></b><span
    9848 style='color:#4A4A4A'>: toggle multiple plot - for multiple PDFs, this will
    9849 show only the one selected from the data tree. The offset options are not
    9850 active. Or all selected items will be plotted on a single axis. <o:p></o:p></span></p>
     9840style='color:#4A4A4A'>: toggle multiple plot - for multiple PDFs, this will show
     9841only the one selected from the data tree. The offset options are not active. Or
     9842all selected items will be plotted on a single axis. <o:p></o:p></span></p>
    98519843
    98529844<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l57 level1 lfo37;
    … …  
    98949886style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    98959887</span></span></span><![endif]><b><span style='color:#4A4A4A'>r</span></b><span
    9896 style='color:#4A4A4A'>: offset right - for a waterfall plot of multiple powder
    9897 profiles, increase the offset to the right (or decrease the left offset.) <o:p></o:p></span></p>
     9888style='color:#4A4A4A'>: offset right - for a waterfall plot of multiple powder profiles,
     9889increase the offset to the right (or decrease the left offset.) <o:p></o:p></span></p>
    98989890
    98999891<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l57 level1 lfo37;
    … …  
    1001210004"Times New Roman";color:#4A4A4A;mso-char-type:symbol;mso-symbol-font-family:
    1001310005Symbol'><span style='mso-char-type:symbol;mso-symbol-font-family:Symbol'>Q</span></span><span
    10014 style='color:#4A4A4A'> wide ring sampling area with and without an arc mask positioned
    10015 about 90° azimuth (top of image) with selected polarization values. The
    10016 integrations match with the correct polarization. You will be asked for a 2</span><span
     10006style='color:#4A4A4A'> wide ring sampling area with and without an arc mask
     10007positioned about 90° azimuth (top of image) with selected polarization values.
     10008The integrations match with the correct polarization. You will be asked for a 2</span><span
    1001710009style='font-family:Symbol;mso-ascii-font-family:"Times New Roman";mso-hansi-font-family:
    1001810010"Times New Roman";color:#4A4A4A;mso-char-type:symbol;mso-symbol-font-family:
    … …  
    1003510027style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    1003610028</span></span></span><![endif]><b><span style='color:#4A4A4A'>Make gain map … -
    10037 </span></b><span style='color:#4A4A4A'>This uses the same image (from a glass
    10038 slide) used for polarization analysis to determine a gain map for the detector.
    10039 The process uses the result of an integration of the glass pattern to normalize
    10040 the entire detector pixel array. The result (~1.0 for all pixels) is the scaled
    10041 by 1000, converted to integers and stored as a GSAS-II image file (NB: this is
    10042 a python pickle file and thus not usable by other programs) and entered in the
     10029</span></b><span style='color:#4A4A4A'>This uses the same image (from a glass slide)
     10030used for polarization analysis to determine a gain map for the detector. The
     10031process uses the result of an integration of the glass pattern to normalize the
     10032entire detector pixel array. The result (~1.0 for all pixels) is the scaled by
     100331000, converted to integers and stored as a GSAS-II image file (NB: this is a
     10034python pickle file and thus not usable by other programs) and entered in the
    1004310035GSAS-II data tree. You can view it to see what the map looks like (select its
    1004410036IMG entry). The gain map file can be imported into other projects using the
    10045 same detector. If selected in Image Controls, the image is immediately corrected
    10046 for the gain map.<o:p></o:p></span></p>
     10037same detector. If selected in Image Controls, the image is immediately
     10038corrected for the gain map.<o:p></o:p></span></p>
    1004710039
    1004810040<h4><a name="IMG_Comments">Comments</a></h4>
    … …  
    1010010092style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    1010110093</span></span></span><![endif]><b><span style='color:#4A4A4A'>Arc masks</span></b><span
    10102 style='color:#4A4A4A'>: occlude a section of a Bragg reflection, <span
    10103 class=GramE>similar to</span> a ring mask, except that in addition to the
    10104 location and thickness of the ring, the mask has a starting and ending
    10105 azimuthal angle. <o:p></o:p></span></p>
     10094style='color:#4A4A4A'>: occlude a section of a Bragg reflection, similar to a
     10095ring mask, except that in addition to the location and thickness of the ring,
     10096the mask has a starting and ending azimuthal angle. <o:p></o:p></span></p>
    1010610097
    1010710098<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l41 level1 lfo39;
    … …  
    1012110112style='color:#4A4A4A'>: occludes an arbitrary region created by line segments
    1012210113joining a series of points specified in image coordinates (mm). Typically, a
    10123 point is placed near each corner of the image. Only pixels inside the frame
    10124 mask are used for integration. Only one frame mask can be defined. <o:p></o:p></span></p>
     10114point is placed near each corner of the image. Only pixels inside the frame mask
     10115are used for integration. Only one frame mask can be defined. <o:p></o:p></span></p>
    1012510116
    1012610117<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?</span></h5>
    … …  
    1013510126
    1013610127<p><span style='color:#4A4A4A'>The image is shown, as described above. Note
    10137 that <span class=GramE>The</span> frame mask, if defined, is displayed in
    10138 green, while the other types of masks are shown in red.<o:p></o:p></span></p>
     10128that The frame mask, if defined, is displayed in green, while the other types
     10129of masks are shown in red.<o:p></o:p></span></p>
    1013910130
    1014010131<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do with
    … …  
    1016210153style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    1016310154</span></span></span><![endif]><span style='color:#4A4A4A'>Press the 's' key
    10164 and then <span class=GramE>left-click</span> successively on multiple locations
    10165 for spot masks. Press the 's' key again or <a href="#Mac_rightclick">right-click*</a>
    10166 to stop adding spot masks. <o:p></o:p></span></p>
     10155and then left-click successively on multiple locations for spot masks. Press
     10156the 's' key again or <a href="#Mac_rightclick">right-click*</a> to stop adding
     10157spot masks. <o:p></o:p></span></p>
    1016710158
    1016810159<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l35 level1 lfo41;
    … …  
    1017410165this can be used while the plot is in Zoom or Pan mode.) <o:p></o:p></span></p>
    1017510166
    10176 <p><span style='color:#4A4A4A'>The default size for <span class=GramE>newly-created</span>
    10177 spot masks is determined by the </span><tt><span style='font-size:10.0pt;
    10178 color:#4A4A4A'>Spot_mask_diameter</span></tt><span style='color:#4A4A4A'> <a
    10179 href="#Preferences">configuration variable</a> or 1.0 mm, if not specified. </span><span
    10180 style='mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
    10181 color:#4A4A4A'><o:p></o:p></span></p>
     10167<p><span style='color:#4A4A4A'>The default size for newly-created spot masks is
     10168determined by the </span><tt><span style='font-size:10.0pt;color:#4A4A4A'>Spot_mask_diameter</span></tt><span
     10169style='color:#4A4A4A'> <a href="#Preferences">configuration variable</a> or 1.0
     10170mm, if not specified. </span><span style='mso-fareast-font-family:"Times New Roman";
     10171mso-fareast-theme-font:minor-fareast;color:#4A4A4A'><o:p></o:p></span></p>
    1018210172
    1018310173<p><b><span style='color:#4A4A4A'>Edit Spot mask location</span></b><span
    10184 style='color:#4A4A4A'> by <span class=GramE>left-clicking</span> inside or on
    10185 the edge the of the mask and then drag the spot mask to a new location. <o:p></o:p></span></p>
     10174style='color:#4A4A4A'> by left-clicking inside or on the edge the of the mask
     10175and then drag the spot mask to a new location. <o:p></o:p></span></p>
    1018610176
    1018710177<p><b><span style='color:#4A4A4A'>Edit Spot mask radius</span></b><span
    … …  
    1019810188mso-symbol-font-family:Symbol'><span style='mso-char-type:symbol;mso-symbol-font-family:
    1019910189Symbol'>Q</span></span><span style='color:#4A4A4A'> as determined by the
    10200 calibration (<span class=GramE>e.g.</span> a Bragg diffraction ring).<o:p></o:p></span></p>
     10190calibration (e.g. a Bragg diffraction ring).<o:p></o:p></span></p>
    1020110191
    1020210192<p><b><span style='color:#4A4A4A'>Create Ring masks</span></b><span
    … …  
    1020710197color:#4A4A4A'><o:p></o:p></span></p>
    1020810198
    10209 <p><span style='color:#4A4A4A'>The default thickness for <span class=GramE>newly-created</span>
    10210 ring masks is determined by the </span><tt><span style='font-size:10.0pt;
    10211 color:#4A4A4A'>Ring_mask_thickness</span></tt><span style='color:#4A4A4A'> <a
    10212 href="#Preferences">configuration variable</a> or 0.1 degrees (2theta) if not
    10213 specified. <o:p></o:p></span></p>
     10199<p><span style='color:#4A4A4A'>The default thickness for newly-created ring
     10200masks is determined by the </span><tt><span style='font-size:10.0pt;color:#4A4A4A'>Ring_mask_thickness</span></tt><span
     10201style='color:#4A4A4A'> <a href="#Preferences">configuration variable</a> or 0.1
     10202degrees (2theta) if not specified. <o:p></o:p></span></p>
    1021410203
    1021510204<p><b><span style='color:#4A4A4A'>Edit Ring mask location</span></b><span
    10216 style='color:#4A4A4A'> by <span class=GramE>left-clicking</span> on either the
    10217 inner or outer circle and drag the circle to the new radius. <o:p></o:p></span></p>
     10205style='color:#4A4A4A'> by left-clicking on either the inner or outer circle and
     10206drag the circle to the new radius. <o:p></o:p></span></p>
    1021810207
    1021910208<p><b><span style='color:#4A4A4A'>Edit Ring mask thickness</span></b><span
    … …  
    1023010219"Times New Roman";color:#4A4A4A;mso-char-type:symbol;mso-symbol-font-family:
    1023110220Symbol'><span style='mso-char-type:symbol;mso-symbol-font-family:Symbol'>Q</span></span><span
    10232 style='color:#4A4A4A'>, <span class=GramE>similar to</span> a ring mask, except
    10233 that in addition to the location and thickness of the ring, the mask has a
    10234 starting and ending azimuthal angle. <o:p></o:p></span></p>
     10221style='color:#4A4A4A'>, similar to a ring mask, except that in addition to the
     10222location and thickness of the ring, the mask has a starting and ending
     10223azimuthal angle. <o:p></o:p></span></p>
    1023510224
    1023610225<p><b><span style='color:#4A4A4A'>Create Arc masks</span></b><span
    … …  
    1024110230color:#4A4A4A'><o:p></o:p></span></p>
    1024210231
    10243 <p><span style='color:#4A4A4A'>The default size for <span class=GramE>newly-created</span>
    10244 ring masks is determined by <a href="#Preferences">configuration variables</a><br>
     10232<p><span style='color:#4A4A4A'>The default size for newly-created ring masks is
     10233determined by <a href="#Preferences">configuration variables</a><br>
    1024510234thickness: </span><tt><span style='font-size:10.0pt;color:#4A4A4A'>Ring_mask_thickness</span></tt><span
    1024610235style='color:#4A4A4A'> (0.1 degrees 2theta if not specified) and <br>
    … …  
    1024910238
    1025010239<p><b><span style='color:#4A4A4A'>Edit Arc mask location</span></b><span
    10251 style='color:#4A4A4A'> by <span class=GramE>left-clicking</span> on either the
    10252 inner or outer circle and drag the circle to the new radius. Alternately, <span
    10253 class=GramE>left-click</span> on the upper or lower arc limit (the straight
    10254 lines) and drag them to rotate the center of the arc azimuthal range to a new
    10255 position. <o:p></o:p></span></p>
     10240style='color:#4A4A4A'> by left-clicking on either the inner or outer circle and
     10241drag the circle to the new radius. Alternately, left-click on the upper or
     10242lower arc limit (the straight lines) and drag them to rotate the center of the
     10243arc azimuthal range to a new position. <o:p></o:p></span></p>
    1025610244
    1025710245<p><b><span style='color:#4A4A4A'>Edit Arc mask thickness or range</span></b><span
    … …  
    1027110259
    1027210260<p><b><span style='color:#4A4A4A'>Create Polygon masks</span></b><span
    10273 style='color:#4A4A4A'> with a menu command and then by <span class=GramE>left-clicking</span>
     10261style='color:#4A4A4A'> with a menu command and then by left-clicking
    1027410262successively on the vertices of the polygon shape surrounding pixels to be
    1027510263excluded. After the last point is defined, <a href="#Mac_rightclick">right-click*</a>
    … …  
    1028010268
    1028110269<p><b><span style='color:#4A4A4A'>Edit Polygon mask</span></b><span
    10282 style='color:#4A4A4A'> by <span class=GramE>left-clicking</span> on any point
    10283 at a vertex in the polygon mask and drag that point to a new position. If the
    10284 vertex is dragged to the same position as any other vertex in the mask the
    10285 dragged point is deleted. <o:p></o:p></span></p>
     10270style='color:#4A4A4A'> by left-clicking on any point at a vertex in the polygon
     10271mask and drag that point to a new position. If the vertex is dragged to the
     10272same position as any other vertex in the mask the dragged point is deleted. <o:p></o:p></span></p>
    1028610273
    1028710274<p><b><span style='color:#4A4A4A'>Add a point to Polygon mask</span></b><span
    … …  
    1030010287
    1030110288<p><b><span style='color:#4A4A4A'>Create a Frame mask</span></b><span
    10302 style='color:#4A4A4A'> with a menu command and then by <span class=GramE>left-clicking</span>
     10289style='color:#4A4A4A'> with a menu command and then by left-clicking
    1030310290successively on the vertices of a polygon. After the last point is defined, <a
    10304 href="#Mac_rightclick">right-click*</a> anywhere to close the frame mask. Alternately,
    10305 press the 'f' key and then left-click, as before, to define the mask and <a
    10306 href="#Mac_rightclick">right-click*</a> anywhere to close the mask. Note that
    10307 if a Frame mask already exists, using the 'f' key or the &quot;Create
     10291href="#Mac_rightclick">right-click*</a> anywhere to close the frame mask.
     10292Alternately, press the 'f' key and then left-click, as before, to define the
     10293mask and <a href="#Mac_rightclick">right-click*</a> anywhere to close the mask.
     10294Note that if a Frame mask already exists, using the 'f' key or the &quot;Create
    1030810295Frame&quot; menu item causes the existing frame mask to be deleted. </span><span
    1030910296style='mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
    … …  
    1031110298
    1031210299<p><b><span style='color:#4A4A4A'>Edit the Frame mask</span></b><span
    10313 style='color:#4A4A4A'> by <span class=GramE>left-clicking</span> on any point
    10314 at a vertex in the frame mask and drag that point to a new position. If the
    10315 vertex is dragged to the same position as any other vertex in the mask the
    10316 dragged point is deleted. <o:p></o:p></span></p>
     10300style='color:#4A4A4A'> by left-clicking on any point at a vertex in the frame
     10301mask and drag that point to a new position. If the vertex is dragged to the
     10302same position as any other vertex in the mask the dragged point is deleted. <o:p></o:p></span></p>
    1031710303
    1031810304<p><b><span style='color:#4A4A4A'>Add a point to the Frame mask</span></b><span
    … …  
    1032910315
    1033010316<p class=MsoNormal><span style='color:#4A4A4A'>This allows one to evaluate
    10331 strain typically induced by a pure axial load (<span class=GramE>e.g.</span> no
    10332 shear) on a polycrystalline sample (e.g. a steel bar). This strain will distort
    10333 the Bragg diffraction rings seen by the 2D detector. This follows the method of
    10334 He &amp; Smith (Baoping Bob He &amp; Kingsley Smith, (1997). Adv. in X-Ray
    10335 Anal. 41, 501.) to determine the 3 unique terms of the axial strain tensor. One
    10336 can examine the results as a series of diffraction line d-spacings vs azimuth
     10317strain typically induced by a pure axial load (e.g. no shear) on a
     10318polycrystalline sample (e.g. a steel bar). This strain will distort the Bragg
     10319diffraction rings seen by the 2D detector. This follows the method of He &amp;
     10320Smith (Baoping Bob He &amp; Kingsley Smith, (1997). Adv. in X-Ray Anal. 41,
     10321501.) to determine the 3 unique terms of the axial strain tensor. One can
     10322examine the results as a series of diffraction line d-spacings vs azimuth
    1033710323angle; if no strain these are straight, otherwise they will show a single
    10338 sinusoidal variation with maxima at the maximum strain direction (90° &amp;
    10339 270°) for a tension load. The signs are reversed for a compression load. One
    10340 can also examine the local intensity variation as multiples of a random
    10341 distribution (MRD) due to texture. Before embarking on this analysis be sure
    10342 that your detector is carefully calibrated for orientation and position; you
    10343 are looking for very slight variations in ring shape which may be biased by
    10344 inadequate detector calibration. Commonly, the calibrant (typically CeO<sub>2</sub>)
    10345 is painted on one sample surface (be sure to note if in front or back of
    10346 sample!) and the sample ½ thickness is used in the <b>Sample delta-z</b> box
     10324sinusoidal variation with maxima at the maximum strain direction (90° &amp; 270°)
     10325for a tension load. The signs are reversed for a compression load. One can also
     10326examine the local intensity variation as multiples of a random distribution
     10327(MRD) due to texture. Before embarking on this analysis be sure that your
     10328detector is carefully calibrated for orientation and position; you are looking
     10329for very slight variations in ring shape which may be biased by inadequate
     10330detector calibration. Commonly, the calibrant (typically CeO<sub>2</sub>) is
     10331painted on one sample surface (be sure to note if in front or back of sample!)
     10332and the sample ½ thickness is used in the <b>Sample delta-z</b> box
    1034710333(significant only for residual stress analysis).<o:p></o:p></span></p>
    1034810334
    … …  
    1037910365style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    1038010366Symbol;color:#4A4A4A'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    10381 </span></span></span><![endif]><b><span style='color:#4A4A4A'>Save intensity
    10382 distribution</span></b><span style='color:#4A4A4A'> – this saves the intensity
    10383 distribution curves as a simple text file<o:p></o:p></span></p>
     10367</span></span></span><![endif]><b><span style='color:#4A4A4A'>Save intensity distribution</span></b><span
     10368style='color:#4A4A4A'> – this saves the intensity distribution curves as a
     10369simple text file<o:p></o:p></span></p>
    1038410370
    1038510371<p style='margin-left:.5in;text-indent:-.25in;mso-list:l6 level1 lfo42'><![if !supportLists]><span
    … …  
    1038710373Symbol;color:#4A4A4A'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    1038810374</span></span></span><![endif]><b><span style='color:#4A4A4A'>Update d-zero</span></b><span
    10389 style='color:#4A4A4A'> – <span class=GramE>this updates</span> the d-zero
    10390 values with the d-zero ave ones thus removing any effect of residual
    10391 stress/strain.<o:p></o:p></span></p>
     10375style='color:#4A4A4A'> – this updates the d-zero values with the d-zero ave
     10376ones thus removing any effect of residual stress/strain.<o:p></o:p></span></p>
    1039210377
    1039310378<p style='margin-left:.5in;text-indent:-.25in;mso-list:l6 level1 lfo42'><![if !supportLists]><span
    … …  
    1040610391stress/strain</span></b><span style='color:#4A4A4A'> – this copies the
    1040710392stress/strain data from the current image to other selected images in
    10408 preparation for doing an <span class=GramE><b>All image</b></span><b> fit</b>.<o:p></o:p></span></p>
     10393preparation for doing an <b>All image fit</b>.<o:p></o:p></span></p>
    1040910394
    1041010395<p style='margin-left:.5in;text-indent:-.25in;mso-list:l6 level1 lfo42'><![if !supportLists]><span
    … …  
    1041310398</span></span></span><![endif]><b><span style='color:#4A4A4A'>Save
    1041410399stress/strain</span></b><span style='color:#4A4A4A'> – this saves the current
    10415 stress/strain data to a file <span class=GramE>with .strsta</span> extension.<o:p></o:p></span></p>
     10400stress/strain data to a file with .strsta extension.<o:p></o:p></span></p>
    1041610401
    1041710402<p style='margin-left:.5in;text-indent:-.25in;mso-list:l6 level1 lfo42'><![if !supportLists]><span
    … …  
    1042010405</span></span></span><![endif]><b><span style='color:#4A4A4A'>Load
    1042110406stress/strain</span></b><span style='color:#4A4A4A'> – this loads previously
    10422 saved stress/strain data from a file <span class=GramE>with .strsta</span>
    10423 extension.<o:p></o:p></span></p>
     10407saved stress/strain data from a file with .strsta extension.<o:p></o:p></span></p>
    1042410408
    1042510409<p style='margin-left:.5in;text-indent:-.25in;mso-list:l6 level1 lfo42'><![if !supportLists]><span
    … …  
    1045710441
    1045810442<p class=MsoNormal><span style='color:#4A4A4A'>The Ring intensities plot will
    10459 respond to the following <span class=GramE>key strokes</span>:<o:p></o:p></span></p>
     10443respond to the following key strokes:<o:p></o:p></span></p>
    1046010444
    1046110445<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l9 level1 lfo43'><![if !supportLists]><span
    … …  
    1049210476style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    1049310477Symbol;color:#4A4A4A'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    10494 </span></span></span><![endif]><span style='color:#4A4A4A'>Key ‘<b>g</b>’ – <span
    10495 class=GramE>this toggles</span> display of a grid on the plot<o:p></o:p></span></p>
     10478</span></span></span><![endif]><span style='color:#4A4A4A'>Key ‘<b>g</b>’ –
     10479this toggles display of a grid on the plot<o:p></o:p></span></p>
    1049610480
    1049710481<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l9 level1 lfo43'><![if !supportLists]><span
    … …  
    1050510489"Times New Roman";color:#4A4A4A'><o:p></o:p></span></h2>
    1050610490
    10507 <p class=MsoNormal><span style='color:#4A4A4A'>Powder peaks can only be used for
    10508 indexing of the peak positions for possible unit cells.<o:p></o:p></span></p>
     10491<p class=MsoNormal><span style='color:#4A4A4A'>Powder peaks can only be used
     10492for indexing of the peak positions for possible unit cells.<o:p></o:p></span></p>
    1050910493
    1051010494<h4><span style='mso-fareast-font-family:"Times New Roman"'>Comments<o:p></o:p></span></h4>
    … …  
    1051210496<p class=MsoNormal><span style='color:#4A4A4A'>This window shows whatever
    1051310497comment lines (preceded by “#”) found when the peaks data file was read by
    10514 GSAS-II. If you are lucky, there will be useful information here (<span
    10515 class=GramE>e.g.</span> sample name, date collected, wavelength used, etc.). If
    10516 not, this window will be blank. The text is read-only.</span><span
    10517 style='mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
    10518 color:#4A4A4A'><o:p></o:p></span></p>
     10498GSAS-II. If you are lucky, there will be useful information here (e.g. sample
     10499name, date collected, wavelength used, etc.). If not, this window will be
     10500blank. The text is read-only.</span><span style='mso-fareast-font-family:"Times New Roman";
     10501mso-fareast-theme-font:minor-fareast;color:#4A4A4A'><o:p></o:p></span></p>
    1051910502
    1052010503<h4><a name="PKS_Limits">Limits</a></h4>
    … …  
    1052210505<p class=MsoNormal><span style='color:#4A4A4A'>This window shows the limits in
    1052310506position to be used in indexing from these peak positions. The ‘original’
    10524 values are obtained from the minimum &amp; maximum 1<sup>st</sup> &amp; last
    10525 position. The ‘new’ values determine the range of data that will be used in
    10526 fitting. Units are 2</span><span style='font-family:Symbol;mso-ascii-font-family:
    10527 "Times New Roman";mso-hansi-font-family:"Times New Roman";color:#4A4A4A;
    10528 mso-char-type:symbol;mso-symbol-font-family:Symbol'><span style='mso-char-type:
    10529 symbol;mso-symbol-font-family:Symbol'>Q</span></span><span style='color:#4A4A4A'>.<o:p></o:p></span></p>
     10507values are obtained from the minimum &amp; maximum 1<sup>st</sup> &amp; last position.
     10508The ‘new’ values determine the range of data that will be used in fitting.
     10509Units are 2</span><span style='font-family:Symbol;mso-ascii-font-family:"Times New Roman";
     10510mso-hansi-font-family:"Times New Roman";color:#4A4A4A;mso-char-type:symbol;
     10511mso-symbol-font-family:Symbol'><span style='mso-char-type:symbol;mso-symbol-font-family:
     10512Symbol'>Q</span></span><span style='color:#4A4A4A'>.<o:p></o:p></span></p>
    1053010513
    1053110514<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
    … …  
    1059710580</span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
    1059810581style='color:#4A4A4A'>Load profile… </span></b><span style='color:#4A4A4A'>-
    10599 loads a GSAS-II instrument parameter file (<span class=GramE>name.instprm</span>),
    10600 replacing the existing instrument parameter values. All refinement flags are
    10601 unset.</span><span class=MsoHyperlink><b style='mso-bidi-font-weight:normal'><span
     10582loads a GSAS-II instrument parameter file (name.instprm), replacing the
     10583existing instrument parameter values. All refinement flags are unset.</span><span
     10584class=MsoHyperlink><b style='mso-bidi-font-weight:normal'><span
    1060210585style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></b></span></span></p>
    1060310586
    … …  
    1060810591</span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
    1060910592style='color:#4A4A4A'>Save profile… - </span></b><span style='color:#4A4A4A'>saves
    10610 the current instrument parameter values in a simple text file (<span
    10611 class=GramE>name.instprm</span>); you will be prompted for the file name – do
    10612 not change the extension. This file may be edited but heed the warning to not
    10613 change the parameter names, the order of the parameter records or add new
    10614 parameter records as this will invalidate the file. You may only change the
    10615 numeric values if necessary. You can change or add comment records (begin with
    10616 ‘#’).</span></span><span style='mso-bookmark:PKS_Instrument_Parameters'><span
    10617 style='mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
    10618 color:#4A4A4A'><o:p></o:p></span></span></p>
     10593the current instrument parameter values in a simple text file (name.instprm);
     10594you will be prompted for the file name – do not change the extension. This file
     10595may be edited but heed the warning to not change the parameter names, the order
     10596of the parameter records or add new parameter records as this will invalidate
     10597the file. You may only change the numeric values if necessary. You can change
     10598or add comment records (begin with ‘#’).</span></span><span style='mso-bookmark:
     10599PKS_Instrument_Parameters'><span style='mso-fareast-font-family:"Times New Roman";
     10600mso-fareast-theme-font:minor-fareast;color:#4A4A4A'><o:p></o:p></span></span></p>
    1061910601
    1062010602<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l0 level1 lfo46'><span
    … …  
    1065910641style='mso-bookmark:PKS_Index_Peak_List'><b>Unit Cells List</b></span><span
    1066010642style='mso-bookmark:PKS_Index_Peak_List'></span></a><span style='mso-bookmark:
    10661 PKS_Index_Peak_List'><span class=GramE><span style='color:#4A4A4A'>. .</span></span><span
     10643PKS_Index_Peak_List'><span style='color:#4A4A4A'>. .</span><span
    1066210644class=MsoHyperlink><span style='color:windowtext;text-decoration:none;
    1066310645text-underline:none'><o:p></o:p></span></span></span></p>
    … …  
    1067010652text-indent:-.25in;mso-list:l10 level1 lfo48'><span style='mso-bookmark:PKS_Index_Peak_List'><![if !supportLists]><span
    1067110653style='color:#4A4A4A'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    10672 </span></span></span><![endif]><span style='color:#4A4A4A'>You may deselect individual
    10673 peaks from indexing by unchecking the corresponding ‘use’ box.</span></span><span
     10654</span></span></span><![endif]><span style='color:#4A4A4A'>You may deselect
     10655individual peaks from indexing by unchecking the corresponding ‘use’ box.</span></span><span
    1067410656style='mso-bookmark:PKS_Index_Peak_List'><span style='mso-fareast-font-family:
    1067510657"Times New Roman";mso-fareast-theme-font:minor-fareast;color:#4A4A4A'><o:p></o:p></span></span></p>
    … …  
    1068010662
    1068110663<p class=MsoNormal><span style='mso-bookmark:PKS_Unit_Cells_List'><span
    10682 style='color:#4A4A4A'>This tree item has several purposes, it can be used to perform
    10683 autoindexing and it can be used to show the positions of peaks from unit cells
    10684 which may be results from autoindexing or may be entered from a phase or
    10685 manually. It can be used to refine unit cell parameters. It can also be used to
    10686 search for cells/symmetry settings related to a specified unit cell &amp; space
    10687 group. <o:p></o:p></span></span></p>
     10664style='color:#4A4A4A'>This tree item has several purposes, it can be used to
     10665perform autoindexing and it can be used to show the positions of peaks from
     10666unit cells which may be results from autoindexing or may be entered from a
     10667phase or manually. It can be used to refine unit cell parameters. It can also
     10668be used to search for cells/symmetry settings related to a specified unit cell
     10669&amp; space group. <o:p></o:p></span></span></p>
    1068810670
    1068910671<h5><span style='mso-bookmark:PKS_Unit_Cells_List'><span style='mso-fareast-font-family:
    … …  
    1069610678style='mso-bookmark:PKS_Unit_Cells_List'>Index Peak List</span><span
    1069710679style='mso-bookmark:PKS_Unit_Cells_List'></span></a><span style='mso-bookmark:
    10698 PKS_Unit_Cells_List'><span style='color:#4A4A4A'> are used. Select one or more
    10699 Bravais lattice types to use and use the &quot;Cell Index/Refine&quot;/&quot;Index
     10680PKS_Unit_Cells_List'><span style='color:#4A4A4A'> are used. Select one or more Bravais
     10681lattice types to use and use the &quot;Cell Index/Refine&quot;/&quot;Index
    1070010682Cell&quot; menu command to start indexing. Output will appear on the console
    1070110683and a progress bar dialog will appear which tracks trial volume. A <b
    … …  
    1071210694solution to the Unit cell values; the Bravais lattice shown for the choice is
    1071310695copied. Press <b style='mso-bidi-font-weight:normal'>Show hkl positions</b> to
    10714 generate the allowed reflection positions, which are visually superimposed on the
    10715 displayed powder pattern to visually confirm the indexing. Pay particular
     10696generate the allowed reflection positions, which are visually superimposed on
     10697the displayed powder pattern to visually confirm the indexing. Pay particular
    1071610698attention to any unmatched peaks in the pattern. A <b style='mso-bidi-font-weight:
    1071710699normal'>Space group</b> can be selected from the pulldown box to remove
    10718 reflections based on space group extinctions and visually eliminate possibilities.
    10719 <o:p></o:p></span></span></p>
     10700reflections based on space group extinctions and visually eliminate
     10701possibilities. <o:p></o:p></span></span></p>
    1072010702
    1072110703<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l53 level1 lfo49;
    … …  
    1075110733PKS_Unit_Cells_List'>list below</span><span style='mso-bookmark:PKS_Unit_Cells_List'></span></a><span
    1075210734style='mso-bookmark:PKS_Unit_Cells_List'><span style='color:#4A4A4A'>),
    10753 optionally select a space group (by default the highest symmetry space group
    10754 for the class is selected) and enter the unit cell parameters. Or use the
     10735optionally select a space group (by default the highest symmetry space group for
     10736the class is selected) and enter the unit cell parameters. Or use the
    1075510737&quot;Cell Index/Refine&quot;/&quot;Load Phase&quot; menu command to read this
    1075610738information from a phase that has been read into a project or from a file (such
    … …  
    1085710839<h4><span style='mso-fareast-font-family:"Times New Roman"'>Comments<o:p></o:p></span></h4>
    1085810840
    10859 <p class=MsoNormal><span style='color:#4A4A4A'>This window shows whatever
    10860 comment lines found above the QIE table when the small angle data file was read
    10861 by GSAS-II. If you are lucky, there will be useful information here (<span
    10862 class=GramE>e.g.</span> sample name, date collected, wavelength used, etc.). If
    10863 not, this window will be blank. The text is read-only.</span><span
    10864 style='mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
    10865 color:#4A4A4A'><o:p></o:p></span></p>
     10841<p class=MsoNormal><span style='color:#4A4A4A'>This window shows whatever comment
     10842lines found above the QIE table when the small angle data file was read by
     10843GSAS-II. If you are lucky, there will be useful information here (e.g. sample
     10844name, date collected, wavelength used, etc.). If not, this window will be
     10845blank. The text is read-only.</span><span style='mso-fareast-font-family:"Times New Roman";
     10846mso-fareast-theme-font:minor-fareast;color:#4A4A4A'><o:p></o:p></span></p>
    1086610847
    1086710848<h4><a name="SASD_Limits">Limits</a></h4>
    … …  
    1089410875Symbol;color:#4A4A4A'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    1089510876</span></span></span><![endif]><b><span style='color:#4A4A4A'>Copy - </span></b><span
    10896 style='color:#4A4A4A'>this copies the limits shown to other selected small
    10897 angle patterns. If used, a dialog box (Copy Parameters) will appear showing the
    10898 list of available small angle patterns, you can copy the limits parameters to
    10899 any or all of them; select ‘All’ to copy them to all patterns. Then select ‘OK’
    10900 to do the copy; ‘Cancel’ to cancel the operation. <o:p></o:p></span></span></p>
     10877style='color:#4A4A4A'>this copies the limits shown to other selected small angle
     10878patterns. If used, a dialog box (Copy Parameters) will appear showing the list
     10879of available small angle patterns, you can copy the limits parameters to any or
     10880all of them; select ‘All’ to copy them to all patterns. Then select ‘OK’ to do
     10881the copy; ‘Cancel’ to cancel the operation. <o:p></o:p></span></span></p>
    1090110882
    1090210883<span style='mso-bookmark:SASD_Limits'></span>
    … …  
    1096610947style='color:#4A4A4A'> – select from a suite of various substance predefined by
    1096710948GSAS-II as defined in <b>GSASII/Substances.py</b>. You may add to this list by
    10968 adding a file, UserSubstances.py, by following the substance format as described
    10969 in Substances.py. Place your UserSubstances.py in the GSAS-II directory.<o:p></o:p></span></span></p>
     10949adding a file, UserSubstances.py, by following the substance format as
     10950described in Substances.py. Place your UserSubstances.py in the GSAS-II
     10951directory.<o:p></o:p></span></span></p>
    1097010952
    1097110953<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l5 level1 lfo53;
    … …  
    1098310965</span></span></span><![endif]><b><span style='color:#4A4A4A'>Add substance</span></b><span
    1098410966style='color:#4A4A4A'> – this allows one to enter a new substance that is not
    10985 among the previously defined ones. Give it a name, element composition and
    10986 volume/density; GSAS-II will compute the scattering contrast data for it.<o:p></o:p></span></span></p>
     10967among the previously defined ones. Give it a name, element composition and volume/density;
     10968GSAS-II will compute the scattering contrast data for it.<o:p></o:p></span></span></p>
    1098710969
    1098810970<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l5 level1 lfo53;
    … …  
    1102111003style='mso-bookmark:SASD_Substances'><![if !supportLists]><span
    1102211004style='color:#4A4A4A'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    11023 </span></span></span><![endif]><span style='color:#4A4A4A'>You can edit the
    11024 composition by changing the number of each kind of element and change the sum
    11025 of atomic volumes or the material density.<o:p></o:p></span></span></p>
     11005</span></span></span><![endif]><span style='color:#4A4A4A'>You can edit the composition
     11006by changing the number of each kind of element and change the sum of atomic
     11007volumes or the material density.<o:p></o:p></span></span></p>
    1102611008
    1102711009<span style='mso-bookmark:SASD_Substances'></span>
    … …  
    1103611018last three parameters (named FreePrm<i>X</i>, <i>X</i>=1,2,3) have labels that
    1103711019can be changed. If changed in one histogram, the same label is used for all
    11038 histograms. When a label is changed, the Comments tree item for each SASD
    11039 histogram is searched for a matching &quot;Label=value&quot; pair (differences
    11040 in letter case between the two label strings is ignored). When found, the value
    11041 is converted to a float and saved as the appropriate Sample Parameter. The last
     11020histograms. When a label is changed, the Comments tree item for each SASD histogram
     11021is searched for a matching &quot;Label=value&quot; pair (differences in letter
     11022case between the two label strings is ignored). When found, the value is
     11023converted to a float and saved as the appropriate Sample Parameter. The last
    1104211024two items define the two components of a small angle scattering sample. One
    1104311025comprises the objects of interest while the other is the marix they are
    … …  
    1104911031
    1105011032<p><span style='mso-bookmark:SASD_Models'><b><span style='color:#4A4A4A'>Command</span></b><span
    11051 style='color:#4A4A4A'> <span class=GramE>Menu<span style='mso-spacerun:yes'> 
    11052 </span>-</span> In this window you can change parameters associated with a
    11053 histogram. This histogram scale factor is ignored for SASD. Remaining
    11054 parameters are of use for parametric studies and may be changed with the menu
    11055 commands described here. <o:p></o:p></span></span></p>
     11033style='color:#4A4A4A'> Menu<span style='mso-spacerun:yes'>  </span>- In this
     11034window you can change parameters associated with a histogram. This histogram
     11035scale factor is ignored for SASD. Remaining parameters are of use for
     11036parametric studies and may be changed with the menu commands described here. <o:p></o:p></span></span></p>
    1105611037
    1105711038<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l50 level1 lfo54;
    … …  
    1106911050Symbol;color:#4A4A4A'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    1107011051</span></span></span><![endif]><b><span style='color:#4A4A4A'>Load - </span></b><span
    11071 style='color:#4A4A4A'>This loads sample parameters from a previously <span
    11072 class=GramE>saved .samprm</span> file. <o:p></o:p></span></span></p>
     11052style='color:#4A4A4A'>This loads sample parameters from a previously saved
     11053.samprm file. <o:p></o:p></span></span></p>
    1107311054
    1107411055<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l50 level1 lfo54;
    … …  
    1107711058Symbol;color:#4A4A4A'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    1107811059</span></span></span><![endif]><b><span style='color:#4A4A4A'>Save - </span></b><span
    11079 style='color:#4A4A4A'>This saves the sample parameters to a file with the <span
    11080 class=GramE>extension ’</span>.samprm’. A file dialog box will appear to ask
    11081 for the name of the file to be written. <o:p></o:p></span></span></p>
     11060style='color:#4A4A4A'>This saves the sample parameters to a file with the
     11061extension ’.samprm’. A file dialog box will appear to ask for the name of the
     11062file to be written. <o:p></o:p></span></span></p>
    1108211063
    1108311064<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l50 level1 lfo54;
    … …  
    1108511066style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    1108611067Symbol;color:#4A4A4A'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    11087 </span></span></span><![endif]><span class=GramE><b><span style='color:#4A4A4A'>Copy<span
    11088 style='mso-spacerun:yes'>  </span></span></b><span style='color:#4A4A4A'>This</span></span><span
    11089 style='color:#4A4A4A'> copies the sample parameters shown to other selected
    11090 SASD patterns. If used, a dialog box (Copy parameters) will appear showing the
    11091 list of available SASD patterns, you can copy the sample parameters to any or
    11092 all of them; select ‘All’ to copy them to all patterns. Then select ‘OK’ to do
    11093 the copy; ‘Cancel’ to cancel the operation. <o:p></o:p></span></span></p>
     11068</span></span></span><![endif]><b><span style='color:#4A4A4A'>Copy<span
     11069style='mso-spacerun:yes'>  </span></span></b><span style='color:#4A4A4A'>This
     11070copies the sample parameters shown to other selected SASD patterns. If used, a
     11071dialog box (Copy parameters) will appear showing the list of available SASD
     11072patterns, you can copy the sample parameters to any or all of them; select
     11073‘All’ to copy them to all patterns. Then select ‘OK’ to do the copy; ‘Cancel’
     11074to cancel the operation. <o:p></o:p></span></span></p>
    1109411075
    1109511076<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l50 level1 lfo54;
    … …  
    1109911080</span></span></span><![endif]><b><span style='color:#4A4A4A'>Copy selected...
    1110011081- </span></b><span style='color:#4A4A4A'>This copies only the sample parameter
    11101 that are selected to other selected SASD patterns but is otherwise <span
    11102 class=GramE>similar to</span> &quot;Copy&quot;. <o:p></o:p></span></span></p>
     11082that are selected to other selected SASD patterns but is otherwise similar to
     11083&quot;Copy&quot;. <o:p></o:p></span></span></p>
    1110311084
    1110411085<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l50 level1 lfo54;
    … …  
    1111511096</span></span></span><![endif]><b><span style='color:#4A4A4A'>Set one value - </span></b><span
    1111611097style='color:#4A4A4A'>This is used to set a single selected sample parameter
    11117 for a selected set of SASD histograms. The same value can be used for all <span
    11118 class=GramE>histograms</span> or a dialog can be used to provide a table where
    11119 you can set the values differently for each of selected histograms. <o:p></o:p></span></span></p>
     11098for a selected set of SASD histograms. The same value can be used for all
     11099histograms or a dialog can be used to provide a table where you can set the
     11100values differently for each of selected histograms. <o:p></o:p></span></span></p>
    1112011101
    1112111102<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l50 level1 lfo54;
    … …  
    1112911110
    1113011111<pre style='margin-left:.5in'><span style='mso-bookmark:SASD_Models'><span
    11131 style='color:#4A4A4A'>#filename<span style='mso-spacerun:yes'>       </span>temperature pressure ignore-<span
    11132 class=GramE>me<span style='mso-spacerun:yes'>  </span>humidity</span><o:p></o:p></span></span></pre><pre
     11112style='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
    1113311113style='margin-left:.5in'><span style='mso-bookmark:SASD_Models'><span
    1113411114style='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
    … …  
    1114111121marked with a hash (#). A header is not required. &quot;Columns&quot; in the
    1114211122table are separated by one or more delimiters (which may be a comma, tab or
    11143 space). Note that columns do not need to be aligned, <span class=GramE>as long
    11144 as</span> each entry is spaced by at least one delimiter. The first column in
    11145 the table is used to look up SASD entries where the initial space-delimited
    11146 string after the SASD tag (&quot;myfile&quot; in &quot;SASD myfile
    11147 AZM=180...&quot;) must match the table. Subsequent columns can then be mapped
    11148 to sample parameters or can be ignored, using a dialog window. <o:p></o:p></span></span></p>
     11123space). Note that columns do not need to be aligned, as long as each entry is
     11124spaced by at least one delimiter. The first column in the table is used to look
     11125up SASD entries where the initial space-delimited string after the SASD tag
     11126(&quot;myfile&quot; in &quot;SASD myfile AZM=180...&quot;) must match the table.
     11127Subsequent columns can then be mapped to sample parameters or can be ignored,
     11128using a dialog window. <o:p></o:p></span></span></p>
    1114911129
    1115011130<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l50 level1 lfo54;
    … …  
    1128211262style='color:#4A4A4A'>This window shows whatever comment lines found above the
    1128311263QIE table when the reflectometry data file was read by GSAS-II. If you are
    11284 lucky, there will be useful information here (<span class=GramE>e.g.</span>
    11285 sample name, date collected, wavelength used, etc.). If not, this window will
    11286 be 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>
     11264lucky, there will be useful information here (e.g. sample name, date collected,
     11265wavelength used, etc.). If not, this window will be blank. The text is
     11266read-only.</span><span style='mso-fareast-font-family:"Times New Roman";
     11267mso-fareast-theme-font:minor-fareast;color:#4A4A4A'><o:p></o:p></span></p>
    1128811268
    1128911269<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
    … …  
    1139911379style='color:#4A4A4A'> – select from a suite of various substance predefined by
    1140011380GSAS-II as defined in <b>GSASII/Substances.py</b>. You may add to this list by
    11401 adding a file, UserSubstances.py, by following the substance format as
    11402 described in Substances.py. Place your UserSubstances.py in the GSAS-II
    11403 directory.<o:p></o:p></span></span></p>
     11381adding a file, UserSubstances.py, by following the substance format as described
     11382in Substances.py. Place your UserSubstances.py in the GSAS-II directory.<o:p></o:p></span></span></p>
    1140411383
    1140511384<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l20 level1 lfo59;
    … …  
    1146511444
    1146611445<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'><a
    11467 name="REFD_Models"><span style='color:#4A4A4A'>This window shows the various sample-dependent
    11468 parameters for the selected reflectometry pattern. All values shown in this
    11469 window can be edited. Note that the last three parameters (named FreePrm<i>X</i>,
    11470 <i>X</i>=1,2,3) have labels that can be changed. If changed in one histogram,
    11471 the same label is used for all histograms. When a label is changed, the
    11472 Comments tree item for each REFD histogram is searched for a matching
    11473 &quot;Label=value&quot; pair (differences in letter case between the two label
    11474 strings is ignored). When found, the value is converted to a float and saved as
    11475 the appropriate Sample Parameter. <o:p></o:p></span></a></p>
     11446name="REFD_Models"><span style='color:#4A4A4A'>This window shows the various
     11447sample-dependent parameters for the selected reflectometry pattern. All values
     11448shown in this window can be edited. Note that the last three parameters (named
     11449FreePrm<i>X</i>, <i>X</i>=1,2,3) have labels that can be changed. If changed in
     11450one histogram, the same label is used for all histograms. When a label is
     11451changed, the Comments tree item for each REFD histogram is searched for a
     11452matching &quot;Label=value&quot; pair (differences in letter case between the
     11453two label strings is ignored). When found, the value is converted to a float
     11454and saved as the appropriate Sample Parameter. <o:p></o:p></span></a></p>
    1147611455
    1147711456<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
    … …  
    1150211481style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    1150311482</span></span></span><![endif]><b><span style='color:#4A4A4A'>Load - </span></b><span
    11504 style='color:#4A4A4A'>This loads sample parameters from a previously <span
    11505 class=GramE>saved .samprm</span> file. <o:p></o:p></span></span></p>
     11483style='color:#4A4A4A'>This loads sample parameters from a previously saved
     11484.samprm file. <o:p></o:p></span></span></p>
    1150611485
    1150711486<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l31 level1 lfo60;
    … …  
    1151111490style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    1151211491</span></span></span><![endif]><b><span style='color:#4A4A4A'>Save - </span></b><span
    11513 style='color:#4A4A4A'>This saves the sample parameters to a file with the <span
    11514 class=GramE>extension ’</span>.samprm’. A file dialog box will appear to ask
    11515 for the name of the file to be written. <o:p></o:p></span></span></p>
     11492style='color:#4A4A4A'>This saves the sample parameters to a file with the
     11493extension ’.samprm’. A file dialog box will appear to ask for the name of the
     11494file to be written. <o:p></o:p></span></span></p>
    1151611495
    1151711496<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l31 level1 lfo60;
    … …  
    1153411513</span></span></span><![endif]><b><span style='color:#4A4A4A'>Copy selected...
    1153511514- </span></b><span style='color:#4A4A4A'>This copies only the sample parameter
    11536 that are selected to other selected REFD patterns but is otherwise <span
    11537 class=GramE>similar to</span> &quot;Copy&quot;. <o:p></o:p></span></span></p>
     11515that are selected to other selected REFD patterns but is otherwise similar to
     11516&quot;Copy&quot;. <o:p></o:p></span></span></p>
    1153811517
    1153911518<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l31 level1 lfo60;
    … …  
    1155211531</span></span></span><![endif]><b><span style='color:#4A4A4A'>Set one value - </span></b><span
    1155311532style='color:#4A4A4A'>This is used to set a single selected sample parameter
    11554 for a selected set of REFD histograms. The same value can be used for all <span
    11555 class=GramE>histograms</span> or a dialog can be used to provide a table where
    11556 you can set the values differently for each of selected histograms. <o:p></o:p></span></span></p>
     11533for a selected set of REFD histograms. The same value can be used for all
     11534histograms or a dialog can be used to provide a table where you can set the
     11535values differently for each of selected histograms. <o:p></o:p></span></span></p>
    1155711536
    1155811537<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l31 level1 lfo60;
    … …  
    1156811547<pre><span style='mso-bookmark:REFD_Models'><span style='color:#4A4A4A'><o:p>&nbsp;</o:p></span></span></pre><pre
    1156911548style='margin-left:.5in'><span style='mso-bookmark:REFD_Models'><span
    11570 style='color:#4A4A4A'>#filename<span style='mso-spacerun:yes'>       </span>temperature pressure ignore-<span
    11571 class=GramE>me<span style='mso-spacerun:yes'>  </span>humidity</span><o:p></o:p></span></span></pre><pre
     11549style='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
    1157211550style='margin-left:.5in'><span style='mso-bookmark:REFD_Models'><span
    11573 style='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
     11551style='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
    1157411552style='margin-left:.5in'><span style='mso-bookmark:REFD_Models'><span
    1157511553style='color:#4A4A4A'>LaB6_dc300.tif<span style='mso-spacerun:yes'>      </span>150<span style='mso-spacerun:yes'>          </span>1<span style='mso-spacerun:yes'>      </span>test<span style='mso-spacerun:yes'>       </span>.25<o:p></o:p></span></span></pre>
    … …  
    1158011558marked with a hash (#). A header is not required. &quot;Columns&quot; in the
    1158111559table are separated by one or more delimiters (which may be a comma, tab or
    11582 space). Note that columns do not need to be aligned, <span class=GramE>as long
    11583 as</span> each entry is spaced by at least one delimiter. The first column in
    11584 the table is used to look up REFD entries where the initial space-delimited
    11585 string after the REFD tag (&quot;myfile&quot; in &quot; REFD myfile
    11586 AZM=180...&quot;) must match the table. Subsequent columns can then be mapped
    11587 to sample parameters or can be ignored, using a dialog window. <o:p></o:p></span></span></p>
     11560space). Note that columns do not need to be aligned, as long as each entry is
     11561spaced by at least one delimiter. The first column in the table is used to look
     11562up REFD entries where the initial space-delimited string after the REFD tag
     11563(&quot;myfile&quot; in &quot; REFD myfile AZM=180...&quot;) must match the
     11564table. Subsequent columns can then be mapped to sample parameters or can be
     11565ignored, using a dialog window. <o:p></o:p></span></span></p>
    1158811566
    1158911567<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l31 level1 lfo60;
    … …  
    1160311581<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
    1160411582style='mso-bookmark:REFD_Models'><span style='color:#4A4A4A'>A reflectometry
    11605 model is composed of a sequence of layers beginning with the medium (“superphase”)
    11606 as the top layer in which the incident and scattered radiation paths are
    11607 located (usually “vacuum” = air or other gasses) and ending with the bottom
    11608 layer (“substrate”) upon which the sample layers have been deposited. The
    11609 substrate <span class=GramE>is considered to be</span> “infinite” in thickness.
    11610 The sample layers in between are each defined as a particular substance with a
    11611 thickness and upper surface “roughness”. The surface roughness describes the
    11612 possibility of an interlayer mixing with the previous layer. Their scattering
    11613 density can also be scaled and could include polarized magnetic neutron
    11614 scatterers. The layer sequence is defined so that complex or multiple layers
    11615 can be defined.<o:p></o:p></span></span></p>
     11583model is composed of a sequence of layers beginning with the medium
     11584(“superphase”) as the top layer in which the incident and scattered radiation
     11585paths are located (usually “vacuum” = air or other gasses) and ending with the
     11586bottom layer (“substrate”) upon which the sample layers have been deposited.
     11587The substrate is considered to be “infinite” in thickness. The sample layers in
     11588between are each defined as a particular substance with a thickness and upper
     11589surface “roughness”. The surface roughness describes the possibility of an
     11590interlayer mixing with the previous layer. Their scattering density can also be
     11591scaled and could include polarized magnetic neutron scatterers. The layer
     11592sequence is defined so that complex or multiple layers can be defined.<o:p></o:p></span></span></p>
    1161611593
    1161711594<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
    … …  
    1162111598<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
    1162211599style='mso-bookmark:REFD_Models'><b><span style='color:#4A4A4A'>Command</span></b><span
    11623 style='color:#4A4A4A'> <span class=GramE>Menu<span style='mso-spacerun:yes'> 
    11624 </span>–</span><o:p></o:p></span></span></p>
     11600style='color:#4A4A4A'> Menu<span style='mso-spacerun:yes'>  </span>–<o:p></o:p></span></span></p>
    1162511601
    1162611602<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l31 level1 lfo60;
    … …  
    1170911685
    1171011686<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
    11711 style='color:#4A4A4A'>GSAS-II can be run on Windows, Linux and Macintosh/OS X computers,
    11712 but the GUI follows the native style of Mac OS X. On Windows and some versions
    11713 of Linux, the menu bars <span class=GramE>appears</span> on top of the main
    11714 window. On the Mac, the menu appears at the location that has been configured
    11715 for menus (usually at the top of the screen). GSAS-II defines actions for both
    11716 the left and right buttons on a two-button mouse, <span class=GramE>If</span> a
    11717 two or three-button mouse is used with a Mac, these mouse buttons will work as
    11718 intended. If using a Mac touchpad or single-button mouse, clicking the touchpad
    11719 or mouse button will generate a &quot;left button&quot; click. Hold down the
    11720 control-key to generate a &quot;right button&quot; click. </span></p>
     11687style='color:#4A4A4A'>GSAS-II can be run on Windows, Linux and Macintosh/OS X
     11688computers, but the GUI follows the native style of Mac OS X. On Windows and
     11689some versions of Linux, the menu bars appears on top of the main window. On the
     11690Mac, the menu appears at the location that has been configured for menus
     11691(usually at the top of the screen). GSAS-II defines actions for both the left
     11692and right buttons on a two-button mouse, If a two or three-button mouse is used
     11693with a Mac, these mouse buttons will work as intended. If using a Mac touchpad
     11694or single-button mouse, clicking the touchpad or mouse button will generate a
     11695&quot;left button&quot; click. Hold down the control-key to generate a
     11696&quot;right button&quot; click. </span></p>
    1172111697
    1172211698<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
    … …  
    1172611702
    1172711703<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
    11728 style='color:#4A4A4A'>GSAS-II provides <span class=GramE>a number of</span>
    11729 configuration settings that can be changed via variables that can be set and
    11730 saved. These are controlled in the File/Preferences menu item (on Mac the
    11731 Preferences menu is found in the usual place on Macs, in the main application
    11732 menu). These settings are optionally saved from for subsequent runs in a file
    11733 named </span><tt><span style='font-size:10.0pt;color:#4A4A4A'>config.py</span></tt><span
     11704style='color:#4A4A4A'>GSAS-II provides a number of configuration settings that
     11705can be changed via variables that can be set and saved. These are controlled in
     11706the File/Preferences menu item (on Mac the Preferences menu is found in the
     11707usual place on Macs, in the main application menu). These settings are
     11708optionally saved from for subsequent runs in a file named </span><tt><span
     11709style='font-size:10.0pt;color:#4A4A4A'>config.py</span></tt><span
    1173411710style='color:#4A4A4A'>. More information about this can be found in the <a
    1173511711href="https://gsas-ii.readthedocs.io/en/latest/GSASIIutil.html#module-config_example">appropriate

  • trunk/help/gsasII_files/filelist.xml

    r5333 r5344  
    44 <o:File HRef="colorschememapping.xml"/>
    55 <o:File HRef="image001.png"/>
    6  <o:File HRef="image002.png"/>
    76 <o:File HRef="image003.png"/>
    87 <o:File HRef="image004.png"/>
    … …  
    3534 <o:File HRef="image031.png"/>
    3635 <o:File HRef="image032.png"/>
     36 <o:File HRef="image033.png"/>
    3737 <o:File HRef="filelist.xml"/>
    3838</xml>
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