Changeset 586


Ignore:
Timestamp:
May 5, 2012 10:26:06 AM (11 years ago)
Author:
vondreele
Message:

tutorial stuff

Location:
trunk/help
Files:
15 added
8 edited

Legend:

Unmodified
Added
Removed

  • trunk/help/Fit Peaks.htm

    r585 r586  
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    591 
    592 <p class=MsoTitle><span style='mso-spacerun:yes'> </span>Fit Peaks/<span
    593 class=SpellE>Autoindexing</span> in GSAS-II <o:p></o:p></p>
    594 
    595 </div>
     690<h1><span style='mso-spacerun:yes'> </span>Fit Peaks/<span class=SpellE>Autoindexing</span>
     691in GSAS-II </h1>
    596692
    597693<p class=MsoNormal>In this exercise you will use the GSAS-II program to search
    598694for a unit cell that matches a set of diffraction peaks -- a process known as
    599 auto-indexing. First peaks must be located and optimized and then indexing can
    600 be done.<o:p></o:p></p>
    601 
    602 <p class=MsoNormal>Step 1: read in data<o:p></o:p></p>
     695auto-indexing. First peaks must be located and optimized and then indexing can be
     696done.</p>
     697
     698<h2>Step 1: read in data</h2>
    603699
    604700<p class=MsoNormal>Download the sample data file and matching instrument
    605 parameter file from these links:<o:p></o:p></p>
     701parameter file from these links:</p>
    606702
    607703<p class=MsoNormal><span style='mso-spacerun:yes'>   
    608 </span>https://subversion.xor.aps.anl.gov/trac/pyGSAS/browser/Examples/powder%20data/11bmb_3844.fxye?format=raw<o:p></o:p></p>
     704</span>https://subversion.xor.aps.anl.gov/trac/pyGSAS/browser/Examples/powder%20data/11bmb_3844.fxye?format=raw</p>
    609705
    610706<p class=MsoNormal><span style='mso-spacerun:yes'>   
    611 </span>https://subversion.xor.aps.anl.gov/trac/pyGSAS/browser/Examples/powder%20data/11bmb_3844.prm?format=raw<o:p></o:p></p>
     707</span>https://subversion.xor.aps.anl.gov/trac/pyGSAS/browser/Examples/powder%20data/11bmb_3844.prm?format=raw</p>
    612708
    613709<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    614710
    615711<p class=MsoNormal><span style='mso-spacerun:yes'>    </span>(One can also use
    616 this links<span style='mso-spacerun:yes'>    </span><o:p></o:p></p>
     712this links<span style='mso-spacerun:yes'>    </span></p>
    617713
    618714<p class=MsoNormal><span style='mso-spacerun:yes'>   
    619715</span>https://subversion.xor.aps.anl.gov/pyGSAS/Examples/powder%20data/11bmb_3844.fxye
    620 and <o:p></o:p></p>
     716and </p>
    621717
    622718<p class=MsoNormal><span style='mso-spacerun:yes'>   
    623 </span>https://subversion.xor.aps.anl.gov/pyGSAS/Examples/powder%20data/11bmb_3844.prm<o:p></o:p></p>
    624 
    625 <p class=MsoNormal><span style='mso-spacerun:yes'>    </span><span class=GramE>to</span>
    626 obtain the file, but this is more complex).<o:p></o:p></p>
    627 
    628 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    629 
    630 <p class=MsoNormal>=== Step 2: Start GSAS-II ===<o:p></o:p></p>
     719</span>https://subversion.xor.aps.anl.gov/pyGSAS/Examples/powder%20data/11bmb_3844.prm</p>
     720
     721<p class=MsoNormal><span style='mso-spacerun:yes'>    </span>to obtain the
     722file, but this is more complex).</p>
     723
     724<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     725
     726<h2>Step 2: Start GSAS-II </h2>
    631727
    632728<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    633729
    634730<p class=MsoNormal><span style='mso-spacerun:yes'> </span>This is done in
    635 different ways, depending on your OS and how GSAS-II is installed.<o:p></o:p></p>
    636 
    637 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    638 
    639 <p class=MsoNormal>=== Step 3: read in the data file ===<o:p></o:p></p>
     731different ways, depending on your OS and how GSAS-II is installed.</p>
     732
     733<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     734
     735<p class=MsoNormal>=== Step 3: read in the data file ===</p>
    640736
    641737<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    … …  
    643739<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Use the '''Data/Read
    644740powder data''' menu item to read the data file into the current GSAS-II
    645 project. <o:p></o:p></p>
    646 
    647 <p class=MsoNormal><span style='mso-spacerun:yes'> </span><o:p></o:p></p>
     741project. </p>
     742
     743<p class=MsoNormal><span style='mso-spacerun:yes'> </span></p>
    648744
    649745<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Select the
    650 {{{11bmb_3844.fxye}}} data file in the first dialog and press Open.<o:p></o:p></p>
     746{{{11bmb_3844.fxye}}} data file in the first dialog and press Open.</p>
    651747
    652748<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    … …  
    654750<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Select the
    655751{{{11bmb_3844.prm}}} instrument parameter file in the second dialog and press
    656 Open.<o:p></o:p></p>
     752Open.</p>
    657753
    658754<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    659755
    660756<p class=MsoNormal><span style='mso-spacerun:yes'>    </span>At this point the
    661 data tree window will have several entries <o:p></o:p></p>
     757data tree window will have several entries </p>
    662758
    663759<p class=MsoNormal><span style='mso-spacerun:yes'>   
    664760</span>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d3w2.png
    665 view]);<o:p></o:p></p>
    666 
    667 <p class=MsoNormal><span style='mso-spacerun:yes'>    </span><span class=GramE>and</span>
    668 the plot window will show the powder pattern<o:p></o:p></p>
    669 
    670 <p class=MsoNormal><span style='mso-spacerun:yes'>    </span><span class=GramE>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d3w1.png
    671 view]).</span><o:p></o:p></p>
    672 
    673 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    674 
    675 <p class=MsoNormal>=== Step 4: Select Data Range ===<o:p></o:p></p>
     761view]);</p>
     762
     763<p class=MsoNormal><span style='mso-spacerun:yes'>    </span>and the plot
     764window will show the powder pattern</p>
     765
     766<p class=MsoNormal><span style='mso-spacerun:yes'>   
     767</span>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d3w1.png
     768view]).</p>
     769
     770<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     771
     772<p class=MsoNormal>=== Step 4: Select Data Range ===</p>
    676773
    677774<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    678775
    679776<p class=MsoNormal><span style='mso-spacerun:yes'> </span>This pattern has much
    680 more data than we need, so it is helpful to cut down the range. Click on the
    681 Limits item in the data tree. A new window is created. Use the
    682 &quot;changed&quot; row of entry boxes to set <span class=SpellE>Tmin</span>
    683 and <span class=SpellE>Tmax</span> to 4 and 30. You may also drag the limits lines
    684 to the desired location or place them by a left mouse click on a data point for
    685 the lower limit or a right click on a data point for the upper limit.<o:p></o:p></p>
    686 
    687 <p class=MsoNormal><span style='mso-spacerun:yes'> </span><span class=GramE>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d3w3.png
    688 view]).</span> <o:p></o:p></p>
     777more data than we need, so it is helpful to cut down the range. Click on the Limits
     778item in the data tree. A new window is created. Use the &quot;changed&quot; row
     779of entry boxes to set <span class=SpellE>Tmin</span> and <span class=SpellE>Tmax</span>
     780to 4 and 30. You may also drag the limits lines to the desired location or
     781place them by a left mouse click on a data point for the lower limit or a right
     782click on a data point for the upper limit.</p>
     783
     784<p class=MsoNormal><span
     785style='mso-spacerun:yes'> </span>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d3w3.png
     786view]). </p>
    689787
    690788<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Note the green and
    691 red vertical lines in the plot window move. <o:p></o:p></p>
    692 
    693 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    694 
    695 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    696 
    697 <p class=MsoNormal>=== Step 5: Determine Peak Positions ===<o:p></o:p></p>
     789red vertical lines in the plot window move. </p>
     790
     791<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     792
     793<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     794
     795<p class=MsoNormal>=== Step 5: Determine Peak Positions ===</p>
    698796
    699797<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    … …  
    701799<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Click on the Peak
    702800List item in the data tree. This creates an empty window of peak positions. At
    703 this point it is wise to <o:p></o:p></p>
    704 
    705 <p class=MsoNormal><span style='mso-spacerun:yes'> </span><span class=GramE>zoom</span>
    706 in on the data that will be used for indexing. This can be done by clicking on
    707 this button:<o:p></o:p></p>
     801this point it is wise to </p>
     802
     803<p class=MsoNormal><span style='mso-spacerun:yes'> </span>zoom in on the data
     804that will be used for indexing. This can be done by clicking on this button:</p>
    708805
    709806<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    … …  
    712809magnification button: [[Image(d3z1.png)]], then press the left mouse in one
    713810corner of the region to be used; holding the mouse button down, drag over the
    714 region to the opposite corner. <o:p></o:p></p>
     811region to the opposite corner. </p>
    715812
    716813<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    717814
    718815<p class=MsoNormal><span style='mso-spacerun:yes'> </span>'''Important:'''
    719 Click on the magnification [[<span class=GramE>Image(</span>d3z1.png)]] button
    720 again to turn off the zoom mode. <o:p></o:p></p>
    721 
    722 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    723 
    724 <p class=MsoNormal><span style='mso-spacerun:yes'>  </span><span class=GramE>Using
    725 the left mouse button click on a data point near the top of each peak to be
    726 added to the peak list.</span> As this is done, a line is <o:p></o:p></p>
    727 
    728 <p class=MsoNormal><span style='mso-spacerun:yes'>  </span><span class=GramE>drawn</span>
    729 in the plot window<o:p></o:p></p>
     816Click on the magnification [[Image(d3z1.png)]] button again to turn off the
     817zoom mode. </p>
     818
     819<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     820
     821<p class=MsoNormal><span style='mso-spacerun:yes'>  </span>Using the left mouse
     822button click on a data point near the top of each peak to be added to the peak
     823list. As this is done, a line is </p>
     824
     825<p class=MsoNormal><span style='mso-spacerun:yes'>  </span>drawn in the plot
     826window</p>
    730827
    731828<p class=MsoNormal><span style='mso-spacerun:yes'> 
    732829</span>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d3w4.png
    733 view]) and<o:p></o:p></p>
    734 
    735 <p class=MsoNormal><span style='mso-spacerun:yes'>  </span><span class=GramE>peaks</span>
    736 are added to the Peak List window<o:p></o:p></p>
    737 
    738 <p class=MsoNormal><span style='mso-spacerun:yes'>  </span><span class=GramE>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d3w5.png
    739 view]).</span> Note that if peaks are <o:p></o:p></p>
    740 
    741 <p class=MsoNormal><span style='mso-spacerun:yes'>  </span><span class=GramE>not</span>
    742 being added, you probably have not exited zoom mode.<o:p></o:p></p>
     830view]) and</p>
     831
     832<p class=MsoNormal><span style='mso-spacerun:yes'>  </span>peaks are added to
     833the Peak List window</p>
     834
     835<p class=MsoNormal><span style='mso-spacerun:yes'> 
     836</span>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d3w5.png
     837view]). Note that if peaks are </p>
     838
     839<p class=MsoNormal><span style='mso-spacerun:yes'>  </span>not being added, you
     840probably have not exited zoom mode.</p>
    743841
    744842<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    … …  
    746844<p class=MsoNormal><span style='mso-spacerun:yes'>  </span>Once peaks in that
    747845region have been added, move to a new region of the pattern. This can be done
    748 by clicking on the shift button: [[<span class=GramE>Image(</span>d3z2.png)]].
    749 Dragging with the left mouse will shift the data to follow the mouse. <span
    750 class=GramE>Clicking with the right button (on the Mac, control + mouse) and
    751 moving up increases the vertical scale and to the right increases the
    752 horizontal scale.</span><span style='mso-spacerun:yes'> 
    753 </span>'''Important:''' Click on the shift [[<span class=GramE>Image(</span>d3z2.png)]]
    754 button again to turn off this mode. <o:p></o:p></p>
     846by clicking on the shift button: [[Image(d3z2.png)]]. Dragging with the left
     847mouse will shift the data to follow the mouse. Clicking with the right button (on
     848the Mac, control + mouse) and moving up increases the vertical scale and to the
     849right increases the horizontal scale.<span style='mso-spacerun:yes'> 
     850</span>'''Important:''' Click on the shift [[Image(d3z2.png)]] button again to
     851turn off this mode. </p>
    755852
    756853<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    … …  
    758855<p class=MsoNormal><span style='mso-spacerun:yes'>  </span>Again, using the
    759856left mouse button, click on the tops of more peaks to be added to the peak
    760 list. Note that if peaks are <o:p></o:p></p>
    761 
    762 <p class=MsoNormal><span style='mso-spacerun:yes'>  </span><span class=GramE>not</span>
    763 being added, you probably have not exited shift mode.<o:p></o:p></p>
     857list. Note that if peaks are </p>
     858
     859<p class=MsoNormal><span style='mso-spacerun:yes'>  </span>not being added, you
     860probably have not exited shift mode.</p>
    764861
    765862<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    … …  
    769866visible in the plot. You may drag a peak position as needed; be sure the
    770867zoom/shift buttons are off. A position may be deleted with a right click with
    771 the mouse on the blue line.<o:p></o:p></p>
    772 
    773 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    774 
    775 <p class=MsoNormal>=== Step 6: Refine Peak Positions ===<o:p></o:p></p>
     868the mouse on the blue line.</p>
     869
     870<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     871
     872<p class=MsoNormal>=== Step 6: Refine Peak Positions ===</p>
    776873
    777874<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    … …  
    779876<p class=MsoNormal>First, refine the peak intensities and the background. These
    780877parameters have their refinement flag turned on by default. Use the menu item
    781 '''Peak Fitting/<span class=GramE>LSQ !<span class=SpellE>PeakFit</span>'''</span>.
    782 A window will show the progress of the refinement and will close when the least
    783 <span class=GramE>squares is</span> complete. A summary of the refinement is
    784 shown on the console window as well.<o:p></o:p></p>
     878'''Peak Fitting/LSQ !<span class=SpellE>PeakFit</span>'''. A window will show
     879the progress of the refinement and will close when the least squares is
     880complete. A summary of the refinement is shown on the console window as well.</p>
    785881
    786882<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    … …  
    788884<p class=MsoNormal>Second, add refinement of the peak positions. This can be
    789885done by clicking on all the refinement flags for the individual peaks or it is
    790 possible to set them all at the same time using this recipe: <o:p></o:p></p>
    791 
    792 <p class=MsoNormal><span style='mso-spacerun:yes'> </span>* <span class=GramE>single-click</span>
    793 on any value in the table to select it, for example the first peak position. A
    794 black box appears around the value. If the field if opened for editing (the box
    795 turns to blue), select a different item in the table.<o:p></o:p></p>
     886possible to set them all at the same time using this recipe: </p>
     887
     888<p class=MsoNormal><span style='mso-spacerun:yes'> </span>* single-click on any
     889value in the table to select it, for example the first peak position. A black
     890box appears around the value. If the field if opened for editing (the box turns
     891to blue), select a different item in the table.</p>
    796892
    797893<p class=MsoNormal><span style='mso-spacerun:yes'> </span>* double-click on the
    798894refine label above the peak position check-boxes. The entire column of
    799895checkboxes is highlighted in blue. Press the y key to turn on all refinement
    800 flags (n would turn them off).<o:p></o:p></p>
    801 
    802 <p class=MsoNormal><span style='mso-spacerun:yes'> </span><o:p></o:p></p>
    803 
    804 <p class=MsoNormal>Third, repeat the refinement using the '''Peak Fitting/<span
    805 class=GramE>LSQ !<span class=SpellE>PeakFit</span>'''</span> menu item.<o:p></o:p></p>
    806 
    807 <p class=MsoNormal><span style='mso-spacerun:yes'> </span><o:p></o:p></p>
     896flags (n would turn them off).</p>
     897
     898<p class=MsoNormal><span style='mso-spacerun:yes'> </span></p>
     899
     900<p class=MsoNormal>Third, repeat the refinement using the '''Peak Fitting/LSQ !<span
     901class=SpellE>PeakFit</span>''' menu item.</p>
     902
     903<p class=MsoNormal><span style='mso-spacerun:yes'> </span></p>
    808904
    809905<p class=MsoNormal>Fourth, select peak widths for refinement. This can be done
    810906by refining sigma (Gaussian width) and/or gamma (Lorentzian width) for
    811907individual peaks, but here we constrain the peaks to follow an instrumental
    812 broadening equation. Select the Instrumental Parameters item in the data tree. <o:p></o:p></p>
    813 
    814 <p class=MsoNormal>This opens a window for peak profile terms<o:p></o:p></p>
    815 
    816 <p class=MsoNormal><span class=GramE>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d3w6.png
    817 view]).</span> <o:p></o:p></p>
     908broadening equation. Select the Instrumental Parameters item in the data tree. </p>
     909
     910<p class=MsoNormal>This opens a window for peak profile terms</p>
     911
     912<p class=MsoNormal>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d3w6.png
     913view]). </p>
    818914
    819915<p class=MsoNormal>Select the refine flag checkbox for Gaussian U, V, W,
    820 Lorentzian X, Y and the asymmetry parameter SH/L. <o:p></o:p></p>
     916Lorentzian X, Y and the asymmetry parameter SH/L. </p>
    821917
    822918<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    823919
    824920<p class=MsoNormal>Fifth, repeat the refinement. First click on the Peak List
    825 item in the data tree and then refine using the '''Peak Fitting/<span
    826 class=GramE>LSQ !<span class=SpellE>PeakFit</span>'''</span> menu item. At this
    827 point a good fit should be seen by zooming in on individual peaks. (For example
    828 see <o:p></o:p></p>
    829 
    830 <p class=MsoNormal><span class=GramE>[https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d3w7.png
    831 this]).</span> The <span class=SpellE>Rwp</span> is ~6% as shown on the console
    832 window.<o:p></o:p></p>
    833 
    834 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    835 
    836 <p class=MsoNormal>=== Prepare Indexing Peak List ===<o:p></o:p></p>
     921item in the data tree and then refine using the '''Peak Fitting/LSQ !<span
     922class=SpellE>PeakFit</span>''' menu item. At this point a good fit should be
     923seen by zooming in on individual peaks. (For example see </p>
     924
     925<p class=MsoNormal>[https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d3w7.png
     926this]). The <span class=SpellE>Rwp</span> is ~6% as shown on the console
     927window.</p>
     928
     929<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     930
     931<p class=MsoNormal>=== Prepare Indexing Peak List ===</p>
    837932
    838933<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    … …  
    842937Index Peak List item in the data tree. In the initially empty window created by
    843938this action, use menu item '''Index Peaks Operations/Load''' to copy over the
    844 fitted peaks from the Peak List tree entry<o:p></o:p></p>
    845 
    846 <p class=MsoNormal><span class=GramE>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d4w1.png
    847 view]).</span> <o:p></o:p></p>
    848 
    849 <p class=MsoNormal>Note that by default all peaks are selected to be used. <o:p></o:p></p>
    850 
    851 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    852 
    853 <p class=MsoNormal>=== Run <span class=SpellE>Autoindexing</span> ===<o:p></o:p></p>
     939fitted peaks from the Peak List tree entry</p>
     940
     941<p class=MsoNormal>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d4w1.png
     942view]). </p>
     943
     944<p class=MsoNormal>Note that by default all peaks are selected to be used. </p>
     945
     946<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     947
     948<p class=MsoNormal>=== Run <span class=SpellE>Autoindexing</span> ===</p>
    854949
    855950<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    856951
    857952<p class=MsoNormal>Select the Unit Cells List data item. This brings up a
    858 window for indexing and cell refinement options<o:p></o:p></p>
    859 
    860 <p class=MsoNormal><span class=GramE>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d4w2.png
    861 view]).</span> For the most rapid search (since we know the right answer),
    862 select Cubic-P and launch the search using menu item '''Cell Index/Index
    863 Cell'''. The search then runs and he console shows a running list of possible
    864 cells as they are found; the sorted by M20 list of possible matching cells is
    865 shown in the window<o:p></o:p></p>
    866 
    867 <p class=MsoNormal><span class=GramE>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d4w3.png
    868 view]).</span> <o:p></o:p></p>
    869 
    870 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    871 
    872 <p class=MsoNormal>=== Review Cell Choices === <o:p></o:p></p>
     953window for indexing and cell refinement options</p>
     954
     955<p class=MsoNormal>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d4w2.png
     956view]). For the most rapid search (since we know the right answer), select
     957Cubic-P and launch the search using menu item '''Cell Index/Index Cell'''. The
     958search then runs and he console shows a running list of possible cells as they
     959are found; the sorted by M20 list of possible matching cells is shown in the
     960window</p>
     961
     962<p class=MsoNormal>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d4w3.png
     963view]). </p>
     964
     965<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     966
     967<p class=MsoNormal>=== Review Cell Choices === </p>
    873968
    874969<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    875970
    876971<p class=MsoNormal>Review the list of cells associated with the Unit Cells List
    877 data item. Note that as one selects a unit cell, the generated reflections for
    878 that cell are shown in the plot with dashed red lines. Sliding the cursor over
    879 these lines shows a small popup window with the indexed <span class=SpellE>hkl</span>
    880 for them. Note how the 8.312 <span class=GramE>A</span> cell generates very
    881 many lines with no corresponding peaks <o:p></o:p></p>
     972data item. Note that as one selects a unit cell, the generated reflections for that
     973cell are shown in the plot with dashed red lines. Sliding the cursor over these
     974lines shows a small popup window with the indexed <span class=SpellE>hkl</span>
     975for them. Note how the 8.312 A cell generates very many lines with no
     976corresponding peaks </p>
    882977
    883978<p class=MsoNormal>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d4w4.png
    884 view])<o:p></o:p></p>
    885 
    886 <p class=MsoNormal><span class=GramE>while</span> the 2.939 A cell generates
    887 not enough lines to match all the peaks<o:p></o:p></p>
    888 
    889 <p class=MsoNormal><span class=GramE>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d4w5.png
    890 view]).</span> <o:p></o:p></p>
    891 
    892 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    893 
    894 <p class=MsoNormal>=== Select/Refine Cell === <o:p></o:p></p>
    895 
    896 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    897 
    898 <p class=MsoNormal>Select the top option, a 4.1568 <span class=GramE>A</span>
    899 cell with M20 figure of merit of 2700. This indexes all peaks, though peak
    900 positions are not exactly perfect if one zooms in enough. Import the cell
    901 information using the '''Cell Index/Copy Cell''' menu option. Then optimize the
    902 cell by refining the lattice parameters and the two-theta zero: click on the
    903 refine checkbox next to the Zero offset value and then the '''Cell Index/Refine
    904 Cell''' menu option. <span class=GramE>The a</span> cell parameter value shifts
    905 from 4.15679 to 4.15684 when zero is refined. <o:p></o:p></p>
     979view])</p>
     980
     981<p class=MsoNormal>while the 2.939 A cell generates not enough lines to match
     982all the peaks</p>
     983
     984<p class=MsoNormal>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d4w5.png
     985view]). </p>
     986
     987<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     988
     989<p class=MsoNormal>=== Select/Refine Cell === </p>
     990
     991<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     992
     993<p class=MsoNormal>Select the top option, a 4.1568 A cell with M20 figure of
     994merit of 2700. This indexes all peaks, though peak positions are not exactly
     995perfect if one zooms in enough. Import the cell information using the '''Cell
     996Index/Copy Cell''' menu option. Then optimize the cell by refining the lattice
     997parameters and the two-theta zero: click on the refine checkbox next to the
     998Zero offset value and then the '''Cell Index/Refine Cell''' menu option. The a
     999cell parameter value shifts from 4.15679 to 4.15684 when zero is refined. </p>
    9061000
    9071001<p class=MsoNormal><o:p>&nbsp;</o:p></p>

  • trunk/help/Integration of area detector data in GSAS.htm

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    389         mso-bidi-theme-font:minor-bidi;}
     371        margin:0in;
     372        margin-bottom:.0001pt;
     373        mso-pagination:widow-orphan;
     374        font-size:12.0pt;
     375        font-family:"Times New Roman","serif";
     376        mso-fareast-font-family:"Times New Roman";
     377        mso-fareast-theme-font:minor-fareast;}
    390378h1
    391379        {mso-style-priority:9;
    … …  
    393381        mso-style-qformat:yes;
    394382        mso-style-link:"Heading 1 Char";
    395         mso-style-next:Normal;
    396         margin-top:24.0pt;
     383        mso-margin-top-alt:auto;
    397384        margin-right:0in;
    398         margin-bottom:0in;
     385        mso-margin-bottom-alt:auto;
    399386        margin-left:0in;
    400         margin-bottom:.0001pt;
    401         line-height:115%;
    402         mso-pagination:widow-orphan lines-together;
    403         page-break-after:avoid;
     387        mso-pagination:widow-orphan;
    404388        mso-outline-level:1;
    405         font-size:14.0pt;
    406         font-family:"Cambria","serif";
    407         mso-ascii-font-family:Cambria;
    408         mso-ascii-theme-font:major-latin;
    409         mso-fareast-font-family:"Times New Roman";
    410         mso-fareast-theme-font:major-fareast;
    411         mso-hansi-font-family:Cambria;
    412         mso-hansi-theme-font:major-latin;
    413         mso-bidi-font-family:"Times New Roman";
    414         mso-bidi-theme-font:major-bidi;
    415         color:#365F91;
    416         mso-themecolor:accent1;
    417         mso-themeshade:191;
    418         mso-font-kerning:0pt;}
     389        font-size:24.0pt;
     390        font-family:"Times New Roman","serif";
     391        mso-fareast-font-family:"Times New Roman";
     392        mso-fareast-theme-font:minor-fareast;
     393        font-weight:bold;}
    419394h2
     395        {mso-style-priority:9;
     396        mso-style-unhide:no;
     397        mso-style-qformat:yes;
     398        mso-style-link:"Heading 2 Char";
     399        mso-margin-top-alt:auto;
     400        margin-right:0in;
     401        mso-margin-bottom-alt:auto;
     402        margin-left:0in;
     403        mso-pagination:widow-orphan;
     404        mso-outline-level:2;
     405        font-size:18.0pt;
     406        font-family:"Times New Roman","serif";
     407        mso-fareast-font-family:"Times New Roman";
     408        mso-fareast-theme-font:minor-fareast;
     409        font-weight:bold;}
     410h3
     411        {mso-style-priority:9;
     412        mso-style-unhide:no;
     413        mso-style-qformat:yes;
     414        mso-style-link:"Heading 3 Char";
     415        mso-margin-top-alt:auto;
     416        margin-right:0in;
     417        mso-margin-bottom-alt:auto;
     418        margin-left:0in;
     419        mso-pagination:widow-orphan;
     420        mso-outline-level:3;
     421        font-size:13.5pt;
     422        font-family:"Times New Roman","serif";
     423        mso-fareast-font-family:"Times New Roman";
     424        mso-fareast-theme-font:minor-fareast;
     425        font-weight:bold;}
     426h4
    420427        {mso-style-noshow:yes;
    421428        mso-style-priority:9;
    422429        mso-style-qformat:yes;
    423         mso-style-link:"Heading 2 Char";
     430        mso-style-link:"Heading 4 Char";
    424431        mso-style-next:Normal;
    425432        margin-top:10.0pt;
    … …  
    428435        margin-left:0in;
    429436        margin-bottom:.0001pt;
    430         line-height:115%;
    431437        mso-pagination:widow-orphan lines-together;
    432438        page-break-after:avoid;
    433         mso-outline-level:2;
     439        mso-outline-level:4;
    434440        font-size:13.0pt;
    435441        font-family:"Cambria","serif";
    … …  
    443449        mso-bidi-theme-font:major-bidi;
    444450        color:#4F81BD;
    445         mso-themecolor:accent1;}
    446 h3
     451        mso-themecolor:accent1;
     452        font-weight:bold;
     453        font-style:italic;}
     454h5
    447455        {mso-style-noshow:yes;
    448456        mso-style-priority:9;
    449457        mso-style-qformat:yes;
    450         mso-style-link:"Heading 3 Char";
    451         mso-style-next:Normal;
    452         margin-top:10.0pt;
     458        mso-style-link:"Heading 5 Char";
     459        mso-margin-top-alt:auto;
    453460        margin-right:0in;
    454         margin-bottom:0in;
     461        mso-margin-bottom-alt:auto;
    455462        margin-left:0in;
    456         margin-bottom:.0001pt;
    457         line-height:115%;
    458         mso-pagination:widow-orphan lines-together;
    459         page-break-after:avoid;
    460         mso-outline-level:3;
    461         font-size:11.0pt;
    462         font-family:"Cambria","serif";
    463         mso-ascii-font-family:Cambria;
    464         mso-ascii-theme-font:major-latin;
    465         mso-fareast-font-family:"Times New Roman";
    466         mso-fareast-theme-font:major-fareast;
    467         mso-hansi-font-family:Cambria;
    468         mso-hansi-theme-font:major-latin;
    469         mso-bidi-font-family:"Times New Roman";
    470         mso-bidi-theme-font:major-bidi;
    471         color:#4F81BD;
    472         mso-themecolor:accent1;}
     463        mso-pagination:widow-orphan;
     464        mso-outline-level:5;
     465        font-size:12.0pt;
     466        font-family:"Times New Roman","serif";
     467        mso-fareast-font-family:"Times New Roman";
     468        mso-fareast-theme-font:minor-fareast;
     469        color:#4F4FFF;
     470        font-weight:bold;}
    473471p.MsoTitle, li.MsoTitle, div.MsoTitle
    474472        {mso-style-priority:10;
    … …  
    602600        mso-style-priority:99;
    603601        color:blue;
    604         mso-themecolor:hyperlink;
    605602        text-decoration:underline;
    606603        text-underline:single;}
    … …  
    609606        mso-style-priority:99;
    610607        color:purple;
    611         mso-themecolor:followedhyperlink;
    612608        text-decoration:underline;
    613609        text-underline:single;}
     610p.MsoDocumentMap, li.MsoDocumentMap, div.MsoDocumentMap
     611        {mso-style-noshow:yes;
     612        mso-style-priority:99;
     613        mso-style-link:"Document Map Char";
     614        margin:0in;
     615        margin-bottom:.0001pt;
     616        mso-pagination:widow-orphan;
     617        font-size:8.0pt;
     618        font-family:"Tahoma","sans-serif";
     619        mso-fareast-font-family:"Times New Roman";
     620        mso-fareast-theme-font:minor-fareast;}
     621p
     622        {mso-style-noshow:yes;
     623        mso-style-priority:99;
     624        mso-margin-top-alt:auto;
     625        margin-right:0in;
     626        mso-margin-bottom-alt:auto;
     627        margin-left:0in;
     628        mso-pagination:widow-orphan;
     629        font-size:12.0pt;
     630        font-family:"Times New Roman","serif";
     631        mso-fareast-font-family:"Times New Roman";
     632        mso-fareast-theme-font:minor-fareast;}
     633pre
     634        {mso-style-noshow:yes;
     635        mso-style-priority:99;
     636        mso-style-link:"HTML Preformatted Char";
     637        margin:0in;
     638        margin-bottom:.0001pt;
     639        mso-pagination:widow-orphan;
     640        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;
     641        font-size:10.0pt;
     642        font-family:"Courier New";
     643        mso-fareast-font-family:"Times New Roman";}
    614644p.MsoAcetate, li.MsoAcetate, div.MsoAcetate
    615645        {mso-style-noshow:yes;
    … …  
    621651        font-size:8.0pt;
    622652        font-family:"Tahoma","sans-serif";
    623         mso-fareast-font-family:Calibri;
    624         mso-fareast-theme-font:minor-latin;}
     653        mso-fareast-font-family:"Times New Roman";
     654        mso-fareast-theme-font:minor-fareast;}
     655span.MsoPlaceholderText
     656        {mso-style-noshow:yes;
     657        mso-style-priority:99;
     658        mso-style-unhide:no;
     659        color:gray;}
     660p.MsoNoSpacing, li.MsoNoSpacing, div.MsoNoSpacing
     661        {mso-style-priority:1;
     662        mso-style-unhide:no;
     663        mso-style-qformat:yes;
     664        mso-style-parent:"";
     665        margin:0in;
     666        margin-bottom:.0001pt;
     667        mso-pagination:widow-orphan;
     668        font-size:12.0pt;
     669        font-family:"Times New Roman","serif";
     670        mso-fareast-font-family:"Times New Roman";
     671        mso-fareast-theme-font:minor-fareast;}
     672p.MsoListParagraph, li.MsoListParagraph, div.MsoListParagraph
     673        {mso-style-priority:34;
     674        mso-style-unhide:no;
     675        mso-style-qformat:yes;
     676        margin-top:0in;
     677        margin-right:0in;
     678        margin-bottom:0in;
     679        margin-left:.5in;
     680        margin-bottom:.0001pt;
     681        mso-add-space:auto;
     682        mso-pagination:widow-orphan;
     683        font-size:12.0pt;
     684        font-family:"Times New Roman","serif";
     685        mso-fareast-font-family:"Times New Roman";
     686        mso-fareast-theme-font:minor-fareast;}
     687p.MsoListParagraphCxSpFirst, li.MsoListParagraphCxSpFirst, div.MsoListParagraphCxSpFirst
     688        {mso-style-priority:34;
     689        mso-style-unhide:no;
     690        mso-style-qformat:yes;
     691        mso-style-type:export-only;
     692        margin-top:0in;
     693        margin-right:0in;
     694        margin-bottom:0in;
     695        margin-left:.5in;
     696        margin-bottom:.0001pt;
     697        mso-add-space:auto;
     698        mso-pagination:widow-orphan;
     699        font-size:12.0pt;
     700        font-family:"Times New Roman","serif";
     701        mso-fareast-font-family:"Times New Roman";
     702        mso-fareast-theme-font:minor-fareast;}
     703p.MsoListParagraphCxSpMiddle, li.MsoListParagraphCxSpMiddle, div.MsoListParagraphCxSpMiddle
     704        {mso-style-priority:34;
     705        mso-style-unhide:no;
     706        mso-style-qformat:yes;
     707        mso-style-type:export-only;
     708        margin-top:0in;
     709        margin-right:0in;
     710        margin-bottom:0in;
     711        margin-left:.5in;
     712        margin-bottom:.0001pt;
     713        mso-add-space:auto;
     714        mso-pagination:widow-orphan;
     715        font-size:12.0pt;
     716        font-family:"Times New Roman","serif";
     717        mso-fareast-font-family:"Times New Roman";
     718        mso-fareast-theme-font:minor-fareast;}
     719p.MsoListParagraphCxSpLast, li.MsoListParagraphCxSpLast, div.MsoListParagraphCxSpLast
     720        {mso-style-priority:34;
     721        mso-style-unhide:no;
     722        mso-style-qformat:yes;
     723        mso-style-type:export-only;
     724        margin-top:0in;
     725        margin-right:0in;
     726        margin-bottom:0in;
     727        margin-left:.5in;
     728        margin-bottom:.0001pt;
     729        mso-add-space:auto;
     730        mso-pagination:widow-orphan;
     731        font-size:12.0pt;
     732        font-family:"Times New Roman","serif";
     733        mso-fareast-font-family:"Times New Roman";
     734        mso-fareast-theme-font:minor-fareast;}
     735span.MsoIntenseReference
     736        {mso-style-priority:32;
     737        mso-style-unhide:no;
     738        mso-style-qformat:yes;
     739        font-variant:small-caps;
     740        color:#C0504D;
     741        mso-themecolor:accent2;
     742        letter-spacing:.25pt;
     743        font-weight:bold;
     744        text-decoration:underline;
     745        text-underline:single;}
    625746span.Heading1Char
    626747        {mso-style-name:"Heading 1 Char";
    … …  
    629750        mso-style-locked:yes;
    630751        mso-style-link:"Heading 1";
    631         mso-ansi-font-size:14.0pt;
    632         mso-bidi-font-size:14.0pt;
    633         font-family:"Cambria","serif";
    634         mso-ascii-font-family:Cambria;
    635         mso-ascii-theme-font:major-latin;
    636         mso-fareast-font-family:"Times New Roman";
    637         mso-fareast-theme-font:major-fareast;
    638         mso-hansi-font-family:Cambria;
    639         mso-hansi-theme-font:major-latin;
    640         mso-bidi-font-family:"Times New Roman";
    641         mso-bidi-theme-font:major-bidi;
    642         color:#365F91;
    643         mso-themecolor:accent1;
    644         mso-themeshade:191;
     752        mso-ansi-font-size:24.0pt;
     753        mso-bidi-font-size:24.0pt;
     754        font-family:"Times New Roman","serif";
     755        mso-ascii-font-family:"Times New Roman";
     756        mso-fareast-font-family:"Times New Roman";
     757        mso-fareast-theme-font:minor-fareast;
     758        mso-hansi-font-family:"Times New Roman";
     759        mso-bidi-font-family:"Times New Roman";
     760        mso-font-kerning:18.0pt;
    645761        font-weight:bold;}
    646762span.Heading2Char
    647763        {mso-style-name:"Heading 2 Char";
    648         mso-style-noshow:yes;
    649764        mso-style-priority:9;
    650765        mso-style-unhide:no;
    651766        mso-style-locked:yes;
    652767        mso-style-link:"Heading 2";
    653         mso-ansi-font-size:13.0pt;
    654         mso-bidi-font-size:13.0pt;
    655         font-family:"Cambria","serif";
    656         mso-ascii-font-family:Cambria;
    657         mso-ascii-theme-font:major-latin;
    658         mso-fareast-font-family:"Times New Roman";
    659         mso-fareast-theme-font:major-fareast;
    660         mso-hansi-font-family:Cambria;
    661         mso-hansi-theme-font:major-latin;
    662         mso-bidi-font-family:"Times New Roman";
    663         mso-bidi-theme-font:major-bidi;
    664         color:#4F81BD;
    665         mso-themecolor:accent1;
     768        mso-ansi-font-size:18.0pt;
     769        mso-bidi-font-size:18.0pt;
     770        font-family:"Times New Roman","serif";
     771        mso-ascii-font-family:"Times New Roman";
     772        mso-fareast-font-family:"Times New Roman";
     773        mso-fareast-theme-font:minor-fareast;
     774        mso-hansi-font-family:"Times New Roman";
     775        mso-bidi-font-family:"Times New Roman";
    666776        font-weight:bold;}
    667777span.Heading3Char
    668778        {mso-style-name:"Heading 3 Char";
    669         mso-style-noshow:yes;
    670779        mso-style-priority:9;
    671780        mso-style-unhide:no;
    672781        mso-style-locked:yes;
    673782        mso-style-link:"Heading 3";
    674         font-family:"Cambria","serif";
    675         mso-ascii-font-family:Cambria;
    676         mso-ascii-theme-font:major-latin;
    677         mso-fareast-font-family:"Times New Roman";
    678         mso-fareast-theme-font:major-fareast;
    679         mso-hansi-font-family:Cambria;
    680         mso-hansi-theme-font:major-latin;
    681         mso-bidi-font-family:"Times New Roman";
    682         mso-bidi-theme-font:major-bidi;
    683         color:#4F81BD;
    684         mso-themecolor:accent1;
     783        mso-ansi-font-size:13.5pt;
     784        mso-bidi-font-size:13.5pt;
     785        font-family:"Times New Roman","serif";
     786        mso-ascii-font-family:"Times New Roman";
     787        mso-fareast-font-family:"Times New Roman";
     788        mso-fareast-theme-font:minor-fareast;
     789        mso-hansi-font-family:"Times New Roman";
     790        mso-bidi-font-family:"Times New Roman";
    685791        font-weight:bold;}
    686792span.TitleChar
    … …  
    717823        font-family:"Tahoma","sans-serif";
    718824        mso-ascii-font-family:Tahoma;
     825        mso-fareast-font-family:"Times New Roman";
     826        mso-fareast-theme-font:minor-fareast;
    719827        mso-hansi-font-family:Tahoma;
    720828        mso-bidi-font-family:Tahoma;}
     829span.DocumentMapChar
     830        {mso-style-name:"Document Map Char";
     831        mso-style-noshow:yes;
     832        mso-style-priority:99;
     833        mso-style-unhide:no;
     834        mso-style-locked:yes;
     835        mso-style-link:"Document Map";
     836        mso-ansi-font-size:8.0pt;
     837        mso-bidi-font-size:8.0pt;
     838        font-family:"Tahoma","sans-serif";
     839        mso-ascii-font-family:Tahoma;
     840        mso-fareast-font-family:"Times New Roman";
     841        mso-fareast-theme-font:minor-fareast;
     842        mso-hansi-font-family:Tahoma;
     843        mso-bidi-font-family:Tahoma;}
     844span.Heading4Char
     845        {mso-style-name:"Heading 4 Char";
     846        mso-style-noshow:yes;
     847        mso-style-priority:9;
     848        mso-style-unhide:no;
     849        mso-style-locked:yes;
     850        mso-style-link:"Heading 4";
     851        mso-ansi-font-size:13.0pt;
     852        mso-bidi-font-size:13.0pt;
     853        font-family:"Cambria","serif";
     854        mso-ascii-font-family:Cambria;
     855        mso-ascii-theme-font:major-latin;
     856        mso-fareast-font-family:"Times New Roman";
     857        mso-fareast-theme-font:major-fareast;
     858        mso-hansi-font-family:Cambria;
     859        mso-hansi-theme-font:major-latin;
     860        mso-bidi-font-family:"Times New Roman";
     861        mso-bidi-theme-font:major-bidi;
     862        color:#4F81BD;
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    789 
    790 <p class=MsoTitle>Integration of area detector data in GSAS-II</p>
    791 
    792 </div>
     958<h1>Integration of area detector data in GSAS-II</h1>
    793959
    794960<p class=MsoNormal>In this demo, data collected with a Perkin-Elmer area
    … …  
    801967normal'>About GSAS-II</b>).</p>
    802968
    803 <h1>Prerequisite:<span style='mso-spacerun:yes'>  </span><a
    804 href="Calibration%20of%20an%20area%20detector%20in%20GSAS.htm">Calibration Demo</a></h1>
     969<h2>Prerequisite:<span style='mso-spacerun:yes'>  </span><a
     970href="Calibration%20of%20an%20area%20detector%20in%20GSAS.htm">Calibration Demo</a></h2>
    805971
    806972<p class=MsoNormal>This assumes that an image data set has been read in and
    807 calibration results have been derived, see <span class=GramE>the<span
    808 style='mso-spacerun:yes'>  </span></span><a
    809 href="Calibration%20of%20an%20area%20detector%20in%20GSAS.htm">Calibration Demo</a></p>
     973calibration results have been derived, see the<span style='mso-spacerun:yes'> 
     974</span><a href="Calibration%20of%20an%20area%20detector%20in%20GSAS.htm">Calibration
     975Demo</a></p>
    810976
    811977<h2>Step 1: Clear calibration plot</h2>
    … …  
    821987
    822988<p class=MsoNormal>In the simplest case, all that is needed is to click on the <b
    823 style='mso-bidi-font-weight:normal'>Do full integration?</b> <span class=GramE>check</span>
    824 box and adjust the inner and outer 2-theta values with the <b style='mso-bidi-font-weight:
     989style='mso-bidi-font-weight:normal'>Do full integration?</b> check box and
     990adjust the inner and outer 2-theta values with the <b style='mso-bidi-font-weight:
    825991normal'>Inner 2-theta</b> and<b style='mso-bidi-font-weight:normal'> Outer
    8269922-theta</b> controls. Change the limits to 1 and 7 for this data. Note that
    … …  
    831997<p class=MsoNormal>It is helpful to see the two-theta limits on the plot
    832998visually, while adjusting the two-theta range. This is done by clicking on the <b
    833 style='mso-bidi-font-weight:normal'>Show integration limits?</b> <span
    834 class=GramE>check</span> box. Note that inner limit is shown as a green ellipse
    835 at 2deg and the outer is shown as a red ellipse at 5deg by default. These
    836 limits may also be dragged to the desired values; a small popup window shows
    837 the value. </p>
     999style='mso-bidi-font-weight:normal'>Show integration limits?</b> check box.
     1000Note that inner limit is shown as a green ellipse at 2deg and the outer is
     1001shown as a red ellipse at 5deg by default. These limits may also be dragged to
     1002the desired values; a small popup window shows the value. </p>
    8381003
    8391004<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
    … …  
    8621027  o:title=""/>
    8631028</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=370
    864 src="Integration%20of%20area%20detector%20data%20in%20GSAS_files/image002.png"
     1029src="Integration%20of%20area%20detector%20data%20in%20GSAS_files/image008.png"
    8651030v:shapes="Picture_x0020_2"><![endif]></span></p>
    8661031
    8671032<h3>Other useful controls:</h3>
    8681033
    869 <p class=MsoNormal><span style='mso-spacerun:yes'> </span><b style='mso-bidi-font-weight:
    870 normal'>Azimuth offset</b>: The image vertical axis (from the beam center,
    871 going down) is labeled with the azimuth value placed in the <b
    872 style='mso-bidi-font-weight:normal'>Azimuth offset</b> box. This is usually
    873 zero.</p>
    874 
    875 <p class=MsoNormal><span style='mso-spacerun:yes'> </span><b style='mso-bidi-font-weight:
    876 normal'>Start/End azimuth</b>: The integration is started at the Start azimuth
    877 angle in the left box, and when the <b style='mso-bidi-font-weight:normal'>Do
    878 full integration?</b> checkbox is not checked, the integration will be run only
    879 to the maximum value specified. When the range is less than 360 degrees, the
    880 integration range will be shown (if selected) with the high and low limits
    881 plotted and only segments of the max and min ellipses drawn. These limits may
    882 also be dragged on the plot to desired locations.</p>
     1034<p class=MsoNormal><b style='mso-bidi-font-weight:normal'>Azimuth offset</b>:
     1035The image vertical axis (from the beam center, going down) is labeled with the
     1036azimuth value placed in the <b style='mso-bidi-font-weight:normal'>Azimuth
     1037offset</b> box. This is usually zero.</p>
     1038
     1039<p class=MsoNormal><b style='mso-bidi-font-weight:normal'>Start/End azimuth</b>:
     1040The integration is started at the Start azimuth angle in the left box, and when
     1041the <b style='mso-bidi-font-weight:normal'>Do full integration?</b> checkbox is
     1042not checked, the integration will be run only to the maximum value specified.
     1043When the range is less than 360 degrees, the integration range will be shown
     1044(if selected) with the high and low limits plotted and only segments of the max
     1045and min ellipses drawn. These limits may also be dragged on the plot to desired
     1046locations.</p>
    8831047
    8841048<p class=MsoNormal><b style='mso-bidi-font-weight:normal'>Number of 2-theta
    … …  
    8921056pattern to be useful for further analysis.</p>
    8931057
    894 <p class=MsoNormal><span style='mso-spacerun:yes'> </span><b style='mso-bidi-font-weight:
    895 normal'>Number of azimuth bins</b>: In cases where the diffraction experiment
    896 shows changes as a function of azimuthal angle, the integration can be
    897 performed as a function of angle. This number specifies the number of bins to
    898 use by azimuthal angle. The process of breaking up the integration in this way
    899 is sometimes called &quot;caking&quot; since the integration region grows with
    900 distance from the beam-center, with a shape like a slice of cake or pie. When
    901 more than one azimuthal bin is used, the regions are shown in the plot with
    902 dashed lines, when the Show integration limits?&quot; check box is checked. </p>
     1058<p class=MsoNormal><b style='mso-bidi-font-weight:normal'>Number of azimuth
     1059bins</b>: In cases where the diffraction experiment shows changes as a function
     1060of azimuthal angle, the integration can be performed as a function of angle.
     1061This number specifies the number of bins to use by azimuthal angle. The process
     1062of breaking up the integration in this way is sometimes called
     1063&quot;caking&quot; since the integration region grows with distance from the
     1064beam-center, with a shape like a slice of cake or pie. When more than one
     1065azimuthal bin is used, the regions are shown in the plot with dashed lines,
     1066when the Show integration limits?&quot; check box is checked. </p>
    9031067
    9041068<p class=MsoNormal><b style='mso-bidi-font-weight:normal'>Background Image </b>and<b
    … …  
    9161080  o:title=""/>
    9171081</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=535
    918 src="Integration%20of%20area%20detector%20data%20in%20GSAS_files/image004.png"
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    9201084
    … …  
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    9441108
    945 <p class=MsoNormal><span class=GramE>two</span> plots are added to the plot
    946 window: One (with tab 2D Integration) shows the diffraction intensity as a
    947 function of both 2-theta and (when there is more than one azimuthal integration
    948 region) azimuthal angle</p>
     1109<p class=MsoNormal>two plots are added to the plot window: One (with tab 2D
     1110Integration) shows the diffraction intensity as a function of both 2-theta and
     1111(when there is more than one azimuthal integration region) azimuthal angle</p>
    9491112
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    960 <p class=MsoNormal><span class=GramE>and</span> a conventional 1-D powder
    961 pattern(s) for each &quot;slice&quot;</p>
     1121style='mso-spacerun:yes'> </span>c</p>
     1122
     1123<p class=MsoNormal>and a conventional 1-D powder pattern(s) for each
     1124&quot;slice&quot;</p>
    9621125
    9631126<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape

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     901span.TitleChar
     902        {mso-style-name:"Title Char";
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    774923span.SpellE
    775924        {mso-style-name:"";
    776925        mso-spl-e:yes;}
    777 span.GramE
    778         {mso-style-name:"";
    779         mso-gram-e:yes;}
    780926.MsoChpDefault
    781927        {mso-style-type:export-only;
    … …  
    17671913        mso-style-noshow:yes;
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    17701917        mso-padding-alt:0in 5.4pt 0in 5.4pt;
    … …  
    17781925<link href=gsasIIfav.png rel="SHORTCUT ICON">
    17791926<!--[if gte mso 9]><xml>
    1780  <o:shapedefaults v:ext="edit" spidmax="1027"/>
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    17821929 <o:shapelayout v:ext="edit">
    … …  
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    1814  visibility:visible;mso-wrap-style:square;mso-width-percent:0;
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     1964 mso-position-vertical:absolute;mso-position-vertical-relative:line'
     1965 o:allowoverlap="f">
    18211966 <v:imagedata src="gsas2logo.png"/>
    18221967 <w:wrap type="square" anchory="line"/>
    … …  
    18391984<h2><strong>GSAS-II tutorials:<o:p></o:p></strong></h2>
    18401985
    1841 <p class=MsoNormal><strong><a href="Calibration%20of%20an%20area%20detector%20in%20GSAS.htm"><span
     1986<p class=MsoNormal><strong>Starting GSAS-II<o:p></o:p></strong></p>
     1987
     1988<p class=MsoNormal><strong><a
     1989href="Calibration%20of%20an%20area%20detector%20in%20GSAS.htm"><span
    18421990style='font-weight:normal'>2-D Image calibration</span></a><o:p></o:p></strong></p>
    18431991
    … …  
    18491997normal'>Powder pattern peak picking, fitting and indexing</span></a><o:p></o:p></strong></p>
    18501998
    1851 <p class=MsoNormal><strong>Powder pattern Rietveld refinement (future)<o:p></o:p></strong></p>
    1852 
    1853 <p class=MsoNormal><strong>Crystal structure drawing (future)<o:p></o:p></strong></p>
    1854 
    1855 <p class=MsoNormal><strong>Distance/Angle/Torsion <span class=GramE>calculations(</span>future)<o:p></o:p></strong></p>
     1999<p class=MsoNormal><strong>Lab X-ray powder pattern <span class=SpellE>Rietveld</span>
     2000refinement (future)<o:p></o:p></strong></p>
     2001
     2002<p class=MsoNormal><strong>CW Neutron powder pattern <span class=SpellE>Rietveld</span>
     2003refinement (future)<o:p></o:p></strong></p>
     2004
     2005<p class=MsoNormal><strong>Synchrotron X-ray powder pattern <span class=SpellE>Rietveld</span>
     2006refinement (future)<o:p></o:p></strong></p>
     2007
     2008<p class=MsoNormal><strong>Crystal structure drawing (balls &amp; sticks, etc.)
     2009(future)<o:p></o:p></strong></p>
     2010
     2011<p class=MsoNormal><strong>Crystal structure drawing (<span class=SpellE>polyhedra</span>)
     2012(future)<o:p></o:p></strong></p>
     2013
     2014<p class=MsoNormal><strong>Distance/Angle/Torsion calculations(future)<o:p></o:p></strong></p>
    18562015
    18572016<p class=MsoNormal><strong>Charge flipping structure solution(future)<o:p></o:p></strong></p>
    18582017
    1859 <p class=MsoNormal><span class=GramE><strong>etc., etc.</strong></span><strong><o:p></o:p></strong></p>
     2018<p class=MsoNormal><strong>etc., etc.<o:p></o:p></strong></p>
    18602019
    18612020<div class=MsoNormal align=center style='text-align:center'><span
    … …  
    19272086style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Save
    19282087As&#8230;</span></b><span style='mso-fareast-font-family:"Times New Roman"'> -
    1929 Save the current project to a new file. A file dialog will be shown to enter
    1930 the name (and change directory if desired). If the file exists, you will be
    1931 asked if it OK to overwrite.</span></p>
     2088Save the current project to a new file. A file dialog will be shown to enter the
     2089name (and change directory if desired). If the file exists, you will be asked
     2090if it OK to overwrite.</span></p>
    19322091
    19332092<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    … …  
    19472106style='mso-fareast-font-family:"Times New Roman"'> &#8211; Exit the GSAS-II
    19482107program; if there is a current project you will be asked if you want to save it
    1949 first. Pressing the red X in the upper right (Windows) also exits (no save option)
    1950 GSAS-II; useful for escaping from GSAS-II if needed.</span></p>
     2108first. Pressing the red X in the upper right (Windows) also exits (no save
     2109option) GSAS-II; useful for escaping from GSAS-II if needed.</span></p>
    19512110
    19522111<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l11 level1 lfo1'><![if !supportLists]><span
    … …  
    19592118style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
    19602119style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    1961 style='mso-bidi-font-weight:normal'>Read powder data&#8230;</b> - Read in
    1962 powder diffraction patterns (multiple patterns can be selected). GSAS-II can
    1963 read most of the old GSAS powder format files with the position in <span
    1964 class=SpellE>centidegrees</span> 2-theta. It can also read &#8220;<span
    1965 class=SpellE>xye</span>&#8221; format files used by <span class=SpellE>topas</span>
    1966 where the position is in degrees 2-theta. As each file is read, an old GSAS
    1967 style &#8220;instrument parameter file&#8221; is searched for; if not found a <span
    1968 class=SpellE>CuK</span><span style='font-family:Symbol'>a</span> laboratory
    1969 data set is assumed. </p>
     2120style='mso-bidi-font-weight:normal'>Read powder data&#8230;</b> - Read in powder
     2121diffraction patterns (multiple patterns can be selected). GSAS-II can read most
     2122of the old GSAS powder format files with the position in <span class=SpellE>centidegrees</span>
     21232-theta. It can also read &#8220;<span class=SpellE>xye</span>&#8221; format
     2124files used by <span class=SpellE>topas</span> where the position is in degrees
     21252-theta. As each file is read, an old GSAS style &#8220;instrument parameter
     2126file&#8221; is searched for; if not found a <span class=SpellE>CuK</span><span
     2127style='font-family:Symbol'>a</span> laboratory data set is assumed. </p>
    19702128
    19712129<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    … …  
    20702228The total number of refined parameters is also shown at the top of the list.
    20712229The value of each parameter is also given. The parameter names are of the form
    2072 &#8216;p<span class=GramE>:h:name:id&#8217;</span> where &#8216;p&#8217; is the
    2073 phase index, &#8216;h&#8217; is the histogram index and &#8216;id&#8217; is the
    2074 item index (if needed). Indexes all begin with &#8216;0&#8217; (zero). Note
    2075 that for atom positions the value is not a <span class=SpellE>refinable</span>
    2076 parameter, but the shift in the value is. Position names are, e.g. &#8216;0:<span
    2077 class=GramE>:Ax:0&#8217;</span> for the x-position of the <span class=SpellE>zeroth</span>
    2078 atom in the <span class=SpellE>zeroth</span> phase while shift names have a
    2079 &#8216;d&#8217; in then, e.g. &#8216;0::dAx:0&#8217;. </p>
     2230&#8216;p:h:name:id&#8217; where &#8216;p&#8217; is the phase index,
     2231&#8216;h&#8217; is the histogram index and &#8216;id&#8217; is the item index
     2232(if needed). Indexes all begin with &#8216;0&#8217; (zero). Note that for atom
     2233positions the value is not a <span class=SpellE>refinable</span> parameter, but
     2234the shift in the value is. Position names are, e.g. &#8216;0::Ax:0&#8217; for
     2235the x-position of the <span class=SpellE>zeroth</span> atom in the <span
     2236class=SpellE>zeroth</span> phase while shift names have a &#8216;d&#8217; in
     2237then, e.g. &#8216;0::dAx:0&#8217;. </p>
    20802238
    20812239<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    … …  
    20832241style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span
    20842242style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    2085 style='mso-bidi-font-weight:normal'>Refine</b> &#8211; This performs the refinement
    2086 (Pawley/Rietveld or single crystal) according to the controls set in the <b
    2087 style='mso-bidi-font-weight:normal'><a href="#Controls">Controls</a></b> data
    2088 tree item.</p>
     2243style='mso-bidi-font-weight:normal'>Refine</b> &#8211; This performs the
     2244refinement (Pawley/Rietveld or single crystal) according to the controls set in
     2245the <b style='mso-bidi-font-weight:normal'><a href="#Controls">Controls</a></b>
     2246data tree item.</p>
    20892247
    20902248<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    … …  
    22552413
    22562414<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Two
    2257 of the main refinement tools are the <span class=SpellE><span class=GramE>fortran</span></span>
    2258 MINPACK <span class=SpellE>lmdif</span> and <span class=SpellE>lmder</span>
    2259 algorithms wrapped in python as provided in the <span class=SpellE>Scipy</span>
    2260 package and a third one is a python version utilizing only the <span
    2261 class=SpellE>numpy</span> package. The purpose is to </span>minimize the sum of
    2262 the squares of M<span style='mso-fareast-font-family:"Times New Roman"'>
    2263 nonlinear functions in N variables by a modification of the <span class=SpellE>Levenberg</span>-Marquardt
     2415of the main refinement tools are the <span class=SpellE>fortran</span> MINPACK <span
     2416class=SpellE>lmdif</span> and <span class=SpellE>lmder</span> algorithms
     2417wrapped in python as provided in the <span class=SpellE>Scipy</span> package
     2418and a third one is a python version utilizing only the <span class=SpellE>numpy</span>
     2419package. The purpose is to </span>minimize the sum of the squares of M<span
     2420style='mso-fareast-font-family:"Times New Roman"'> nonlinear functions in N
     2421variables by a modification of the <span class=SpellE>Levenberg</span>-Marquardt
    22642422algorithm. The <span class=SpellE>lmdif</span> and <span class=SpellE>lmder</span>
    22652423routines were written by </span>Burton S. <span class=SpellE>Garbow</span>,
    2266 Kenneth E. <span class=SpellE>Hillstrom</span>, <span class=GramE>Jorge</span>
    2267 J. <span class=GramE>More (Argonne National Laboratory, 1980).</span> The
    2268 python/numpy version was developed by us based on the material in Numerical
    2269 Recipes (Press, Flannery, <span class=SpellE><span class=GramE>Teulosky</span></span>
     2424Kenneth E. <span class=SpellE>Hillstrom</span>, Jorge J. More (Argonne National
     2425Laboratory, 1980). The python/numpy version was developed by us based on the
     2426material in Numerical Recipes (Press, Flannery, <span class=SpellE>Teulosky</span>
    22702427&amp; <span class=SpellE>Vetterling</span>) for the <span class=SpellE>Levenberg</span>-Marquardt
    22712428algorithm.<span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
    … …  
    23022459the first cycle of refinement. This value is modified by the least squares
    23032460routine. The allowed range is 10<sup>-5</sup> to 100. Smaller values may be
    2304 needed if your initial <span class=GramE>refinement</span> trials immediately diverge,
    2305 however make sure your starting parameter values are &#8216;reasonable&#8217;.
    2306 The selected default (=1.0) normally gives good performance.<o:p></o:p></span></p>
     2461needed if your initial refinement trials immediately diverge, however make sure
     2462your starting parameter values are &#8216;reasonable&#8217;. The selected
     2463default (=1.0) normally gives good performance.<o:p></o:p></span></p>
    23072464
    23082465<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l15 level1 lfo2'><![if !supportLists]><span
    … …  
    23442501"Times New Roman"'>m</span><span style='mso-fareast-font-family:"Times New Roman"'>strain
    23452502and crystallite size parameters). &#8216;Histogram constraints&#8217; are those
    2346 that depend only on the data set (e.g. profile coefficients U<span class=GramE>,V,W,X</span>
    2347 and Y).<o:p></o:p></span></p>
     2503that depend only on the data set (e.g. profile coefficients U,V,W,X and Y).<o:p></o:p></span></p>
    23482504
    23492505<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
    … …  
    23652521auto;text-indent:-.25in;mso-list:l17 level2 lfo3'><![if !supportLists]><span
    23662522style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
    2367 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    2368 class=GramE><b style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:
    2369 "Times New Roman"'>Add</span></b></span><b style='mso-bidi-font-weight:normal'><span
    2370 style='mso-fareast-font-family:"Times New Roman"'> Hold</span></b><span
    2371 style='mso-fareast-font-family:"Times New Roman"'> &#8211; select a parameter
    2372 that you wish to remain fixed although other parameters of the same type may be
    2373 selected as a group for refinement. For example, if the space group for a phase
    2374 has a polar axis (e.g. the b-axis in P2<sub>1</sub>), then one atom y-parameter
    2375 is arbitrary and should be selected for a Hold to keep the structure from
    2376 drifting up or down the y-axis during refinement. If selected, a dialog box
    2377 will appear showing the list of available parameters; select one and then OK to
    2378 implement it, Cancel will cancel the operation. The held parameter will be
    2379 shown in the constraint window with the keyword &#8216;FIXED&#8217;. A Delete
    2380 button can be used to remove it.<o:p></o:p></span></p>
     2523style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     2524style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Add
     2525Hold</span></b><span style='mso-fareast-font-family:"Times New Roman"'> &#8211;
     2526select a parameter that you wish to remain fixed although other parameters of
     2527the same type may be selected as a group for refinement. For example, if the
     2528space group for a phase has a polar axis (e.g. the b-axis in P2<sub>1</sub>),
     2529then one atom y-parameter is arbitrary and should be selected for a Hold to
     2530keep the structure from drifting up or down the y-axis during refinement. If
     2531selected, a dialog box will appear showing the list of available parameters;
     2532select one and then OK to implement it, Cancel will cancel the operation. The
     2533held parameter will be shown in the constraint window with the keyword
     2534&#8216;FIXED&#8217;. A Delete button can be used to remove it.<o:p></o:p></span></p>
    23812535
    23822536<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    … …  
    23892543with a non-unitary multiplier for some). Examples are a list of atoms with the
    23902544same thermal motion <span class=SpellE>Uiso</span>, sets of profile
    2391 coefficients U<span class=GramE>,V,W</span> across multiple data sets. If
    2392 selected, a dialog box will appear with a list of the available parameters.
    2393 Select one and press OK; a second dialog box will appear with only those
    2394 parameters that can be made equivalent to the first one. Choose those and press
    2395 OK. Cancel in either dialog will cancel the operation. The equivalenced
    2396 parameters will show as an equation of the form M<sub>1</sub>*P<sub>1</sub>+M<sub>2</sub>*P<sub>2</sub>=0;
    2397 usually M1=1.0 and M2=-1.0, but can be changed via the &#8216;Edit&#8217;
    2398 button. The keyword &#8216;EQUIV&#8217; marks it as <span class=GramE>an
    2399 equivalence</span>. A Delete button can be used to remove it.<o:p></o:p></span></p>
     2545coefficients U,V,W across multiple data sets. If selected, a dialog box will
     2546appear with a list of the available parameters. Select one and press OK; a
     2547second dialog box will appear with only those parameters that can be made
     2548equivalent to the first one. Choose those and press OK. Cancel in either dialog
     2549will cancel the operation. The equivalenced parameters will show as an equation
     2550of the form M<sub>1</sub>*P<sub>1</sub>+M<sub>2</sub>*P<sub>2</sub>=0; usually
     2551M1=1.0 and M2=-1.0, but can be changed via the &#8216;Edit&#8217; button. The
     2552keyword &#8216;EQUIV&#8217; marks it as an equivalence. A Delete button can be
     2553used to remove it.<o:p></o:p></span></p>
    24002554
    24012555<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    … …  
    24132567the operation. The equivalenced parameters will show as an equation of the form
    24142568M<sub>1</sub>*P<sub>1</sub>+M<sub>2</sub>*P<sub>2</sub>+&#8230;=C; the
    2415 multipliers M1, <span class=GramE>M2, &#8230;</span> and C can be changed via
    2416 the &#8216;Edit&#8217; button. The keyword &#8216;CONSTR&#8217; marks it as a
    2417 constraint. A Delete button can be used to remove it.<o:p></o:p></span></p>
     2569multipliers M1, M2, &#8230; and C can be changed via the &#8216;Edit&#8217;
     2570button. The keyword &#8216;CONSTR&#8217; marks it as a constraint. A Delete
     2571button can be used to remove it.<o:p></o:p></span></p>
    24182572
    24192573<p class=MsoListParagraphCxSpLast style='margin-left:1.0in;mso-add-space:auto;
    … …  
    24452599<p class=MsoNormal>In this window is tabulated the results of your sequential
    24462600refinement. The columns are the parameter names; the naming convention is
    2447 &#8216;p<span class=GramE>:h:name:n&#8217;</span> where p is the phase number,
    2448 h is the histogram number, name is the parameter name, and num (if needed) is
    2449 the item number (e.g. atom number). The rows are the data sets used in the
    2450 sequential refinement.</p>
     2601&#8216;p:h:name:n&#8217; where p is the phase number, h is the histogram
     2602number, name is the parameter name, and num (if needed) is the item number
     2603(e.g. atom number). The rows are the data sets used in the sequential
     2604refinement.</p>
    24512605
    24522606<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
    … …  
    24872641style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Analyze</span></b></span><span
    24882642style='mso-bookmark:Comments'><span style='mso-fareast-font-family:"Times New Roman"'>
    2489 &#8211; this produces a &#8216;normal probability&#8217; plot for the refinement
    2490 result as bounded by the limits. The slope and intercept of the curve in the
    2491 central region (-1 &lt; </span></span><span style='mso-bookmark:Comments'><span
    2492 style='font-family:Symbol;mso-fareast-font-family:"Times New Roman"'>D</span></span><span
     2643&#8211; this produces a &#8216;normal probability&#8217; plot for the
     2644refinement result as bounded by the limits. The slope and intercept of the
     2645curve in the central region (-1 &lt; </span></span><span style='mso-bookmark:
     2646Comments'><span style='font-family:Symbol;mso-fareast-font-family:"Times New Roman"'>D</span></span><span
    24932647style='mso-bookmark:Comments'><span style='mso-fareast-font-family:"Times New Roman"'>/</span></span><span
    24942648style='mso-bookmark:Comments'><span style='font-family:Symbol;mso-fareast-font-family:
    … …  
    25522706style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    25532707style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Copy</span></b><span
    2554 style='mso-fareast-font-family:"Times New Roman"'> &#8211; this copies the
    2555 limits shown to other selected powder patterns. If used, a dialog box (Copy
     2708style='mso-fareast-font-family:"Times New Roman"'> &#8211; this copies the limits
     2709shown to other selected powder patterns. If used, a dialog box (Copy
    25562710Parameters) will appear showing the list of available powder patterns, you can
    25572711copy the limits parameters to any or all of them; select &#8216;All&#8217; to
    … …  
    25652719<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
    25662720window shows the choice of background functions and coefficients to be used in
    2567 fitting this powder pattern. There are three types of contributions available for
    2568 the background:<o:p></o:p></span></p>
    2569 
    2570 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>1).
    2571 A continuous empirical function (&#8216;<span class=SpellE>chebyschev</span>&#8217;,
    2572 &#8216;cosine&#8217;, &#8216;<span class=SpellE><span class=GramE>lin</span></span>
    2573 interpolate&#8217;, &#8216;inv interpolate&#8217; &amp; &#8216;log
    2574 interpolate&#8217;). The latter three select fixed points with spacing that is <span
    2575 class=GramE>either equal</span>, inversely equal or equal on a log scale of the
    2576 x-coordinate. The set of magnitudes at each point then comprise the background
    2577 variables. All are refined when refine is selected.<o:p></o:p></span></p>
     2721fitting this powder pattern. There are three types of contributions available
     2722for the background:<o:p></o:p></span></p>
     2723
     2724<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>1). A
     2725continuous empirical function (&#8216;<span class=SpellE>chebyschev</span>&#8217;,
     2726&#8216;cosine&#8217;, &#8216;<span class=SpellE>lin</span> interpolate&#8217;,
     2727&#8216;inv interpolate&#8217; &amp; &#8216;log interpolate&#8217;). The latter
     2728three select fixed points with spacing that is either equal, inversely equal or
     2729equal on a log scale of the x-coordinate. The set of magnitudes at each point
     2730then comprise the background variables. All are refined when refine is
     2731selected.<o:p></o:p></span></p>
    25782732
    25792733<p class=MsoNormal style='tab-stops:0in'><span style='mso-fareast-font-family:
    … …  
    262027741'>&nbsp;&nbsp;&nbsp;&nbsp; </span><o:p></o:p></span></p>
    26212775
    2622 <p class=MsoNormal><span class=GramE><span style='mso-fareast-font-family:"Times New Roman"'>where</span></span><span
    2623 style='mso-fareast-font-family:"Times New Roman"'> A,R &amp; U are the possible
    2624 variables and can be individually selected as desired; Q = 2</span><span
    2625 style='font-family:Symbol;mso-fareast-font-family:"Times New Roman"'>p</span><span
    2626 style='mso-fareast-font-family:"Times New Roman"'>/d.<o:p></o:p></span></p>
     2776<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>where
     2777A,R &amp; U are the possible variables and can be individually selected as
     2778desired; Q = 2</span><span style='font-family:Symbol;mso-fareast-font-family:
     2779"Times New Roman"'>p</span><span style='mso-fareast-font-family:"Times New Roman"'>/d.<o:p></o:p></span></p>
    26272780
    26282781<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>3).
    26292782A set of individual Bragg peaks using the pseudo-Voigt profile function as
    2630 their shapes. Their parameters are &#8216;<span class=SpellE>pos</span>&#8217;,
    2631 &#8217;<span class=SpellE>int</span>&#8217;, &#8216;sig&#8217; &amp;
    2632 &#8216;gam&#8217;; each can be selected for refinement. The default values for
    2633 sig &amp; gam (=0.10) are for very sharp peaks, you may adjust them accordingly
    2634 to the kind of peak you are trying to fit before trying to refine them.<o:p></o:p></span></p>
     2783their shapes. Their parameters are &#8216;pos&#8217;, &#8217;<span
     2784class=SpellE>int</span>&#8217;, &#8216;sig&#8217; &amp; &#8216;<span
     2785class=SpellE>gam</span>&#8217;; each can be selected for refinement. The
     2786default values for sig &amp; gam (=0.10) are for very sharp peaks, you may
     2787adjust them accordingly to the kind of peak you are trying to fit before trying
     2788to refine them.<o:p></o:p></span></p>
    26352789
    26362790<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
    … …  
    28252979profile coefficients. <b style='mso-bidi-font-weight:normal'>NB</b>: In certain
    28262980circumstances some choices are ignored e.g. Zero is not refined during peak
    2827 fitting. Also some choices may lead to unstable refinement, e.g. <span
    2828 class=GramE>Lam</span> refinement and lattice parameter refinement. Examine the
    2829 &#8216;</span><a href="#Covariance"><span style='mso-fareast-font-family:"Times New Roman"'>Covariance&#8217;</span></a><span
    2830 style='mso-fareast-font-family:"Times New Roman"'> display for highly correlated
    2831 parameters.<o:p></o:p></span></p>
     2981fitting. Also some choices may lead to unstable refinement, e.g. Lam refinement
     2982and lattice parameter refinement. Examine the &#8216;</span><a
     2983href="#Covariance"><span style='mso-fareast-font-family:"Times New Roman"'>Covariance&#8217;</span></a><span
     2984style='mso-fareast-font-family:"Times New Roman"'> display for highly
     2985correlated parameters.<o:p></o:p></span></p>
    28322986
    28332987<h4><a name="Sample_Parameters"></a><u><span style='mso-fareast-font-family:
    … …  
    28843038appear showing the list of available powder patterns, you can copy the sample
    28853039parameter refinement flags to any or all of them; select &#8216;All&#8217; to
    2886 copy them to all patterns. Then select &#8216;OK&#8217; to do the copy; &#8216;Cancel&#8217;
    2887 to cancel the operation. <o:p></o:p></span></span></span></p>
     3040copy them to all patterns. Then select &#8216;OK&#8217; to do the copy;
     3041&#8216;Cancel&#8217; to cancel the operation. <o:p></o:p></span></span></span></p>
    28883042
    28893043<h4><span style='mso-bookmark:Peak_List'><span style='mso-bookmark:Powder_Peaks'><span
    … …  
    29733127style='mso-fareast-font-family:"Times New Roman";color:windowtext;font-weight:
    29743128normal;mso-bidi-font-weight:bold'>&#8211; this resets the values of sigma and
    2975 gamma to those computed from the instrument parameters U, V, W, <span
    2976 class=GramE>X</span> &amp; Y.<o:p></o:p></span></span></h5>
     3129gamma to those computed from the instrument parameters U, V, W, X &amp; Y.<o:p></o:p></span></span></h5>
    29773130
    29783131<h5 style='margin-left:1.0in;text-indent:-.25in;mso-list:l9 level2 lfo12;
    … …  
    29943147peaks to the Peak list using the mouse on the plot by: 1) position the pointer
    29953148near to the top point on a peak, 2) press the left mouse button. The selected
    2996 peak will be added to the Peak List in its correct sorted order and a blue vertical
    2997 line will be plotted on that position. Be sure that the Zoom/Pan buttons are
    2998 not selected on the Plot window. We recommend that you begin picking peaks from
    2999 the right side of the pattern; that way the tool tip won&#8217;t be in your way
    3000 as you select peaks.<o:p></o:p></span></span></h5>
     3149peak will be added to the Peak List in its correct sorted order and a blue
     3150vertical line will be plotted on that position. Be sure that the Zoom/Pan
     3151buttons are not selected on the Plot window. We recommend that you begin
     3152picking peaks from the right side of the pattern; that way the tool tip
     3153won&#8217;t be in your way as you select peaks.<o:p></o:p></span></span></h5>
    30013154
    30023155<h5 style='margin-left:.5in;text-indent:-.25in;mso-list:l9 level1 lfo12'><span
    … …  
    31043257<p class=MsoNormal>This window </p>
    31053258
    3106 <h4><a name="I_Q"></a><span class=GramE><span style='mso-fareast-font-family:
    3107 "Times New Roman"'>I(</span></span><span style='mso-fareast-font-family:"Times New Roman"'>Q),
     3259<h4><a name="I_Q"></a><span style='mso-fareast-font-family:"Times New Roman"'>I(Q),
    31083260<a name="S_Q"></a>S(Q), <a name="F_Q"></a>F(Q) &amp; <a name="G_R"></a>G(R)<o:p></o:p></span></h4>
    31093261
    … …  
    32073359style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Space
    32083360group</span></b><span style='mso-fareast-font-family:"Times New Roman"'>
    3209 &#8211; this should be set when the phase is initialized; it can be changed
    3210 later. Be careful about the impact on Atom site symmetry and multiplicity if
    3211 you do. GSAS-II will recognize any legal space group symbol using the short
    3212 Hermann-<span class=SpellE>Mauguin</span> forms; put a space between the axial
    3213 fields (e.g. &#8216;F d 3 m&#8217; not &#8216;Fd3m&#8217;). For space groups
    3214 with a choice of origin (e.g. F d 3 m), GSAS-II always uses the 2<sup>nd</sup>
    3215 setting where the center of inversion is located at the origin. The choice of
    3216 space group will set the available unit cell parameters.<u><o:p></o:p></u></span></p>
     3361&#8211; this should be set when the phase is initialized; it can be changed later.
     3362Be careful about the impact on Atom site symmetry and multiplicity if you do.
     3363GSAS-II will recognize any legal space group symbol using the short Hermann-<span
     3364class=SpellE>Mauguin</span> forms; put a space between the axial fields (e.g.
     3365&#8216;F d 3 m&#8217; not &#8216;Fd3m&#8217;). For space groups with a choice
     3366of origin (e.g. F d 3 m), GSAS-II always uses the 2<sup>nd</sup> setting where
     3367the center of inversion is located at the origin. The choice of space group
     3368will set the available unit cell parameters.<u><o:p></o:p></u></span></p>
    32173369
    32183370<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    … …  
    32223374style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Refine
    32233375unit cell</span></b><span style='mso-fareast-font-family:"Times New Roman"'>
    3224 &#8211; set this flag to refine the unit cell parameters in a Rietveld or Pawley
    3225 refinement. The actual parameters refined are the symmetry allowed terms (A<sub>0</sub>-A<sub>5</sub>)
    3226 in the expression</span><i style='mso-bidi-font-style:normal'><span
    3227 style='font-family:"Cambria Math","serif";mso-fareast-font-family:"Times New Roman"'><br>
     3376&#8211; set this flag to refine the unit cell parameters in a Rietveld or
     3377Pawley refinement. The actual parameters refined are the symmetry allowed terms
     3378(A<sub>0</sub>-A<sub>5</sub>) in the expression</span><i style='mso-bidi-font-style:
     3379normal'><span style='font-family:"Cambria Math","serif";mso-fareast-font-family:
     3380"Times New Roman"'><br>
    32283381</span></i><!--[if gte msEquation 12]><m:oMathPara><m:oMath><m:sSup><m:sSupPr><span
    32293382    style='font-family:"Cambria Math","serif";mso-ascii-font-family:"Cambria Math";
    … …  
    33233476auto;text-indent:-.25in;mso-list:l0 level2 lfo14'><![if !supportLists]><span
    33243477style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>e.<span
    3325 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    3326 class=GramE><b style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:
    3327 "Times New Roman"'>a</span></b></span><b style='mso-bidi-font-weight:normal'><span
    3328 style='mso-fareast-font-family:"Times New Roman"'>, b, c, alpha, beta, gamma</span></b><span
    3329 style='mso-fareast-font-family:"Times New Roman"'> &#8211; lattice parameters;
    3330 only those permitted by the space group are shown. The volume is computed from
    3331 the values entered.<u><o:p></o:p></u></span></p>
     3478style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     3479style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>a,
     3480b, c, alpha, beta, gamma</span></b><span style='mso-fareast-font-family:"Times New Roman"'>
     3481&#8211; lattice parameters; only those permitted by the space group are shown.
     3482The volume is computed from the values entered.<u><o:p></o:p></u></span></p>
    33323483
    33333484<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l0 level1 lfo14'><![if !supportLists]><span
    … …  
    34213572style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Double
    34223573left click a Style, Label or Color column: a dialog box is shown that allows
    3423 you to select a rendering option for all the atoms. For Color a color choice
    3424 dialog is displayed that covers the entire color spectrum. Choose a color by
    3425 any of the means available, press the &#8220;Add to Custom Colors&#8221;,
    3426 select that color in the Custom colors display and then press OK. <b
    3427 style='mso-bidi-font-weight:normal'>NB</b>: selecting Color will make all atoms
    3428 have the same color and for Style &#8220;blank&#8221; means the atoms
    3429 aren&#8217;t rendered and thus the plot will not show any atoms or bonds!</p>
     3574you to select a rendering option for all the atoms. For Color a color choice dialog
     3575is displayed that covers the entire color spectrum. Choose a color by any of
     3576the means available, press the &#8220;Add to Custom Colors&#8221;, select that
     3577color in the Custom colors display and then press OK. <b style='mso-bidi-font-weight:
     3578normal'>NB</b>: selecting Color will make all atoms have the same color and for
     3579Style &#8220;blank&#8221; means the atoms aren&#8217;t rendered and thus the
     3580plot will not show any atoms or bonds!</p>
    34303581
    34313582<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l10 level1 lfo15'><![if !supportLists]><span
    … …  
    35343685style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    35353686style='mso-bidi-font-weight:normal'>Dist. Ang.</b> <b style='mso-bidi-font-weight:
    3536 normal'>Tors. </b>&#8211; <span class=GramE>when</span> 2-4 atoms are selected,
    3537 a distance, angle or torsion angle will be found for them. The angles are
    3538 computed for the atoms in their selection order. The torsion angle is a right
    3539 hand angle about the A2-A3 vector for the sequence of atoms A1-A2-A3-A4. An
    3540 estimated standard deviation is given for the calculated value if a current
    3541 variance-covariance matrix is available. The result is shown on the console
    3542 window; it may be cut &amp; pasted to another application (e.g. Microsoft
    3543 Word).</p>
     3687normal'>Tors. </b>&#8211; when 2-4 atoms are selected, a distance, angle or
     3688torsion angle will be found for them. The angles are computed for the atoms in
     3689their selection order. The torsion angle is a right hand angle about the A2-A3
     3690vector for the sequence of atoms A1-A2-A3-A4. An estimated standard deviation
     3691is given for the calculated value if a current variance-covariance matrix is
     3692available. The result is shown on the console window; it may be cut &amp;
     3693pasted to another application (e.g. Microsoft Word).</p>
    35443694
    35453695<p class=MsoListParagraphCxSpLast style='margin-left:1.0in;mso-add-space:auto;
    … …  
    35853735set as &#8216;Pawley <span class=SpellE>dmin</span>&#8217; in the General tab
    35863736for this phase. By default the refine flags are not set and the <span
    3587 class=SpellE><span class=GramE>Fsq</span></span><span class=GramE>(</span><span
    3588 class=SpellE>hkl</span>) = 100.0.</p>
     3737class=SpellE>Fsq</span>(<span class=SpellE>hkl</span>) = 100.0.</p>
    35893738
    35903739<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    … …  
    35933742style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    35943743style='mso-bidi-font-weight:normal'>Pawley estimate</b> &#8211; this attempts
    3595 an estimate of <span class=SpellE><span class=GramE>Fsq</span></span><span
    3596 class=GramE>(</span><span class=SpellE>hkl</span>) from the peak heights of the
    3597 reflection as seen in the 1<sup>st</sup> powder pattern of those selected in
    3598 the <a href="#Data">Data</a> tab.</p>
     3744an estimate of <span class=SpellE>Fsq</span>(<span class=SpellE>hkl</span>)
     3745from the peak heights of the reflection as seen in the 1<sup>st</sup> powder
     3746pattern of those selected in the <a href="#Data">Data</a> tab.</p>
    35993747
    36003748<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    … …  
    36183766style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
    36193767style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>You
    3620 can change the individual <span class=SpellE><span class=GramE>Fsq</span></span><span
    3621 class=GramE>(</span><span class=SpellE>hkl</span>) values by selecting it,
    3622 typing in the new value and then pressing enter or selecting somewhere else in
    3623 the table.</p>
     3768can change the individual <span class=SpellE>Fsq</span>(<span class=SpellE>hkl</span>)
     3769values by selecting it, typing in the new value and then pressing enter or
     3770selecting somewhere else in the table.</p>
    36243771
    36253772<p class=MsoListParagraphCxSpLast><o:p>&nbsp;</o:p></p>
    … …  
    36293776<span style='mso-bookmark:Map_peaks'></span>
    36303777
    3631 <p class=MsoNormal>This gives the list (magnitude, x y &amp; z) of all peaks
    3632 found within the unit cell from the last Fourier map search sorted in order of
     3778<p class=MsoNormal>This gives the list (magnitude, x y &amp; z) of all peaks found
     3779within the unit cell from the last Fourier map search sorted in order of
    36333780decreasing peak magnitude. The crystal structure plot shows each peak position
    36343781as a white 3-D cross.</p>
    … …  
    36583805name &#8216;UNK&#8217; and the atom type as &#8216;H&#8217;. They will also be
    36593806drawn as small white spheres at their respective positions in the structure
    3660 drawing. You should next go to the <a href="gsasII.html">Atoms</a> page and change
    3661 the atom type to whatever element you desire; it will be renamed automatically.</p>
     3807drawing. You should next go to the <a href="gsasII.html">Atoms</a> page and
     3808change the atom type to whatever element you desire; it will be renamed
     3809automatically.</p>
    36623810
    36633811<p class=MsoListParagraphCxSpLast style='margin-left:1.0in;mso-add-space:auto;
    … …  
    36903838<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
    36913839window presents all the graphical material as a multipage tabbed set of plots
    3692 utilizing the <span class=SpellE>matplotlib</span> python package. Each page has
    3693 a tool bar (at bottom in Windows) with the controls<o:p></o:p></span></p>
     3840utilizing the <span class=SpellE>matplotlib</span> python package. Each page
     3841has a tool bar (at bottom in Windows) with the controls<o:p></o:p></span></p>
    36943842
    36953843<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
    … …  
    37463894
    37473895<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>The
    3748 powder patterns that are part of your project are shown on this page. They can
    3749 be displayed as a stack of powder patterns, just a single pattern or as a
    3750 contour image of the peak intensities. What can be done here will depend on
    3751 which is displayed and on which item in the GSAS-II data tree you have
    3752 selected.<o:p></o:p></span></p>
     3896powder patterns that are part of your project are shown on this page. They can be
     3897displayed as a stack of powder patterns, just a single pattern or as a contour
     3898image of the peak intensities. What can be done here will depend on which is
     3899displayed and on which item in the GSAS-II data tree you have selected.<o:p></o:p></span></p>
    37533900
    37543901<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
    … …  
    37753922auto;text-indent:-.25in;mso-list:l4 level2 lfo22;tab-stops:list 1.0in'><![if !supportLists]><span
    37763923style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
    3777 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    3778 class=GramE><b style='mso-bidi-font-weight:normal'>l</b></span><b
    3779 style='mso-bidi-font-weight:normal'>: offset left</b> &#8211; for a waterfall
     3924style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     3925style='mso-bidi-font-weight:normal'>l: offset left</b> &#8211; for a waterfall
    37803926plot of multiple powder profiles, increase the offset to the left. Does not
    37813927apply if only one pattern.</p>
    … …  
    37843930auto;text-indent:-.25in;mso-list:l4 level2 lfo22;tab-stops:list 1.0in'><![if !supportLists]><span
    37853931style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
    3786 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    3787 class=GramE><b style='mso-bidi-font-weight:normal'>r</b></span><b
    3788 style='mso-bidi-font-weight:normal'>: offset right</b> - for a waterfall plot
     3932style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     3933style='mso-bidi-font-weight:normal'>r: offset right</b> - for a waterfall plot
    37893934of multiple powder profiles, increase the offset to the left. Does not apply if
    37903935only one pattern.</p>
    … …  
    37933938auto;text-indent:-.25in;mso-list:l4 level2 lfo22;tab-stops:list 1.0in'><![if !supportLists]><span
    37943939style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span
    3795 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    3796 class=GramE><b style='mso-bidi-font-weight:normal'>d</b></span><b
    3797 style='mso-bidi-font-weight:normal'>: offset down</b> - for a waterfall plot of
    3798 multiple powder profiles, increase the offset down. Does not apply if only one
    3799 pattern.</p>
     3940style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     3941style='mso-bidi-font-weight:normal'>d: offset down</b> - for a waterfall plot
     3942of multiple powder profiles, increase the offset down. Does not apply if only
     3943one pattern.</p>
    38003944
    38013945<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    38023946auto;text-indent:-.25in;mso-list:l4 level2 lfo22;tab-stops:list 1.0in'><![if !supportLists]><span
    38033947style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>d.<span
    3804 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    3805 class=GramE><b style='mso-bidi-font-weight:normal'>u</b></span><b
    3806 style='mso-bidi-font-weight:normal'>: offset up</b> - for a waterfall plot of
    3807 multiple powder profiles, increase the offset up. Does not apply if only one
    3808 pattern.</p>
     3948style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     3949style='mso-bidi-font-weight:normal'>u: offset up</b> - for a waterfall plot of multiple
     3950powder profiles, increase the offset up. Does not apply if only one pattern.</p>
    38093951
    38103952<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    38113953auto;text-indent:-.25in;mso-list:l4 level2 lfo22;tab-stops:list 1.0in'><![if !supportLists]><span
    38123954style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>e.<span
    3813 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    3814 class=GramE><b style='mso-bidi-font-weight:normal'>o</b></span><b
    3815 style='mso-bidi-font-weight:normal'>: reset offset</b> - for a waterfall plot
     3955style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     3956style='mso-bidi-font-weight:normal'>o: reset offset</b> - for a waterfall plot
    38163957of multiple powder profiles, reset to no offset. Does not apply if only one
    38173958pattern.</p>
    … …  
    38203961auto;text-indent:-.25in;mso-list:l4 level2 lfo22;tab-stops:list 1.0in'><![if !supportLists]><span
    38213962style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>f.<span
    3822 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    3823 class=GramE><b style='mso-bidi-font-weight:normal'>n</b></span><b
    3824 style='mso-bidi-font-weight:normal'>: log(I) on/off</b> &#8211; changes the
     3963style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     3964style='mso-bidi-font-weight:normal'>n: log(I) on/off</b> &#8211; changes the
    38253965y-axis to be the log10 of the intensity; difference curve is not shown for
    38263966log(I) on.</p>
    … …  
    38293969auto;text-indent:-.25in;mso-list:l4 level2 lfo22;tab-stops:list 1.0in'><![if !supportLists]><span
    38303970style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>g.<span
    3831 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    3832 class=GramE><b style='mso-bidi-font-weight:normal'>c</b></span><b
    3833 style='mso-bidi-font-weight:normal'>: contour on/off</b> &#8211; if multiple
     3971style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     3972style='mso-bidi-font-weight:normal'>c: contour on/off</b> &#8211; if multiple
    38343973powder profiles, then a contour plot is shown of the observed intensities. All
    3835 data sets must be the same length as the first one to be included in the
    3836 contour plot.</p>
     3974data sets must be the same length as the first one to be included in the contour
     3975plot.</p>
    38373976
    38383977<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    … …  
    38493988style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>i.<span
    38503989style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    3851 </span></span></span><![endif]><span class=GramE><b style='mso-bidi-font-weight:
    3852 normal'>s</b></span><b style='mso-bidi-font-weight:normal'>: toggle single plot</b>
    3853 &#8211; for multiple powder profiles, this will show only the one selected from
    3854 the data tree. The offset options are not active.</p>
     3990</span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>s: toggle
     3991single plot</b> &#8211; for multiple powder profiles, this will show only the
     3992one selected from the data tree. The offset options are not active.</p>
    38553993
    38563994<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    … …  
    38583996style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>j.<span
    38593997style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    3860 </span></span></span><![endif]><span class=GramE><b style='mso-bidi-font-weight:
    3861 normal'>w</b></span><b style='mso-bidi-font-weight:normal'>: toggle divide by
    3862 sig</b> &#8211; for the pattern selected from the data tree, this will divide
    3863 the observed, calculated and difference curves by the <span class=SpellE>esd</span>
    3864 for the data points. Other data sets are not shown.</p>
     3998</span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>w: toggle
     3999divide by sig</b> &#8211; for the pattern selected from the data tree, this
     4000will divide the observed, calculated and difference curves by the <span
     4001class=SpellE>esd</span> for the data points. Other data sets are not shown.</p>
    38654002
    38664003<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    … …  
    38804017auto;text-indent:-.25in;mso-list:l4 level2 lfo22;tab-stops:list 1.0in'><![if !supportLists]><span
    38814018style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
    3882 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    3883 class=GramE><b style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:
    3884 "Times New Roman"'>d</span></b></span><b style='mso-bidi-font-weight:normal'><span
    3885 style='mso-fareast-font-family:"Times New Roman"'>: lower contour max</span></b><span
    3886 style='mso-fareast-font-family:"Times New Roman"'> &#8211; this lowers the
    3887 level chosen for the highest contour color.<o:p></o:p></span></p>
     4019style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     4020style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>d:
     4021lower contour max</span></b><span style='mso-fareast-font-family:"Times New Roman"'>
     4022&#8211; this lowers the level chosen for the highest contour color.<o:p></o:p></span></p>
    38884023
    38894024<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    … …  
    38984033auto;text-indent:-.25in;mso-list:l4 level2 lfo22;tab-stops:list 1.0in'><![if !supportLists]><span
    38994034style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span
    3900 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    3901 class=GramE><b style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:
    3902 "Times New Roman"'>i</span></b></span><b style='mso-bidi-font-weight:normal'><span
    3903 style='mso-fareast-font-family:"Times New Roman"'>: interpolation method</span></b><span
    3904 style='mso-fareast-font-family:"Times New Roman"'> &#8211; this changes the
    3905 method used to represent the contours. If selected a dialog box appears with
    3906 all the possible choices. Default is &#8216;nearest&#8217;; the other useful
    3907 choice is &#8216;bilinear&#8217;, this will smooth out the contours. <o:p></o:p></span></p>
     4035style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     4036style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>i:
     4037interpolation method</span></b><span style='mso-fareast-font-family:"Times New Roman"'>
     4038&#8211; this changes the method used to represent the contours. If selected a
     4039dialog box appears with all the possible choices. Default is
     4040&#8216;nearest&#8217;; the other useful choice is &#8216;bilinear&#8217;, this
     4041will smooth out the contours. <o:p></o:p></span></p>
    39084042
    39094043<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    39104044auto;text-indent:-.25in;mso-list:l4 level2 lfo22;tab-stops:list 1.0in'><![if !supportLists]><span
    39114045style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>d.<span
    3912 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    3913 class=GramE><b style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:
    3914 "Times New Roman"'>s</span></b></span><b style='mso-bidi-font-weight:normal'><span
    3915 style='mso-fareast-font-family:"Times New Roman"'>: color scheme</span></b><span
    3916 style='mso-fareast-font-family:"Times New Roman"'> &#8211; this changes the
    3917 color scheme for the contouring. Default is <span class=GramE>&#8216;Paired&#8217;,</span>
    3918 black/ white options are &#8216;Greys&#8217; and &#8216;binary&#8217; (for
    3919 black on white) or &#8216;gray&#8217; (for white on black). Others can be very
    3920 colorful (but not useful)!<o:p></o:p></span></p>
     4046style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     4047style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>s:
     4048color scheme</span></b><span style='mso-fareast-font-family:"Times New Roman"'>
     4049&#8211; this changes the color scheme for the contouring. Default is
     4050&#8216;Paired&#8217;, black/ white options are &#8216;Greys&#8217; and
     4051&#8216;binary&#8217; (for black on white) or &#8216;gray&#8217; (for white on
     4052black). Others can be very colorful (but not useful)!<o:p></o:p></span></p>
    39214053
    39224054<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    39234055auto;text-indent:-.25in;mso-list:l4 level2 lfo22;tab-stops:list 1.0in'><![if !supportLists]><span
    39244056style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>e.<span
    3925 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    3926 class=GramE><b style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:
    3927 "Times New Roman"'>c</span></b></span><b style='mso-bidi-font-weight:normal'><span
    3928 style='mso-fareast-font-family:"Times New Roman"'>: contour off/on</span></b><span
    3929 style='mso-fareast-font-family:"Times New Roman"'> &#8211; this turns off
    3930 contouring and returns to a waterfall plot with any offsets applied.<o:p></o:p></span></p>
     4057style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     4058style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>c:
     4059contour off/on</span></b><span style='mso-fareast-font-family:"Times New Roman"'>
     4060&#8211; this turns off contouring and returns to a waterfall plot with any
     4061offsets applied.<o:p></o:p></span></p>
    39314062
    39324063<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l4 level1 lfo22'><![if !supportLists]><span
    … …  
    39734104style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Move
    39744105the mouse cursor across the plot. If on a diagonal cell, the parameter name,
    3975 value and <span class=SpellE>esd</span> is shown both as a tool tip and in the
    3976 right hand portion of the status bar. If the cursor is off the diagonal, the
    3977 two parameter names and their covariance are shown in the tool tip and the
    3978 status bar.</p>
     4106value and <span class=SpellE>esd</span> is shown both as a tool tip and in the right
     4107hand portion of the status bar. If the cursor is off the diagonal, the two
     4108parameter names and their covariance are shown in the tool tip and the status
     4109bar.</p>
    39794110
    39804111<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l7 level1 lfo23'><![if !supportLists]><span
    … …  
    39864117<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l7 level1 lfo23'><![if !supportLists]><span
    39874118style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
    3988 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    3989 class=GramE>Type &#8216;s&#8217;</span> &#8211; A color scheme selection dialog
    3990 is shown. Select a color scheme and press <span class=GramE>OK,</span> the new
    3991 color scheme will be plotted. The default is &#8216;<span class=SpellE>RdYlGn</span>&#8217;.</p>
     4119style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Type
     4120&#8216;s&#8217; &#8211; A color scheme selection dialog is shown. Select a
     4121color scheme and press OK, the new color scheme will be plotted. The default is
     4122&#8216;<span class=SpellE>RdYlGn</span>&#8217;.</p>
    39924123
    39934124<h4><a name="Structure_Factors"><span style='mso-fareast-font-family:"Times New Roman"'>Structure
    … …  
    40234154style='font-family:Symbol;mso-fareast-font-family:"Times New Roman"'>D</span><span
    40244155style='mso-fareast-font-family:"Times New Roman"'>q/q) <span class=SpellE>vs</span>
    4025 <span class=GramE>q(</span>=2</span><span style='font-family:Symbol;mso-fareast-font-family:
    4026 "Times New Roman"'>p</span><span style='mso-fareast-font-family:"Times New Roman"'>/d)
    4027 from the Gaussian and Lorentzian parts of the profile function. The computed
    4028 curves are based on the values of U, V, W, X and Y shown in the Instrument
    4029 Parameters window in parentheses. These are the values for the instrument
    4030 contribution that were set when the powder pattern was first read in to
    4031 GSAS-II. If individual peak fitting has been performed, the values of
    4032 &#8216;sig&#8217; &amp; &#8216;gam&#8217; for the peaks are plotted as
    4033 &#8216;+&#8217;; these are computed from the fitted values of U, V, W, X and Y
    4034 as well as any sig or gam individually refined.<o:p></o:p></span></p>
     4156q(=2</span><span style='font-family:Symbol;mso-fareast-font-family:"Times New Roman"'>p</span><span
     4157style='mso-fareast-font-family:"Times New Roman"'>/d) from the Gaussian and
     4158Lorentzian parts of the profile function. The computed curves are based on the
     4159values of U, V, W, X and Y shown in the Instrument Parameters window in
     4160parentheses. These are the values for the instrument contribution that were set
     4161when the powder pattern was first read in to GSAS-II. If individual peak fitting
     4162has been performed, the values of &#8216;sig&#8217; &amp; &#8216;gam&#8217; for
     4163the peaks are plotted as &#8216;+&#8217;; these are computed from the fitted
     4164values of U, V, W, X and Y as well as any sig or gam individually refined.<o:p></o:p></span></p>
    40354165
    40364166<h4><span style='mso-fareast-font-family:"Times New Roman"'>Texture </span></h4>

  • trunk/help/gsasII_files/filelist.xml

    r585 r586  
    22 <o:MainFile HRef="../gsasII.html"/>
    33 <o:File HRef="item0010.xml"/>
    4  <o:File HRef="props011.xml"/>
     4 <o:File HRef="props0011.xml"/>
    55 <o:File HRef="themedata.thmx"/>
    66 <o:File HRef="colorschememapping.xml"/>
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