Changes between Version 5 and Version 6 of DemoAutoIndex


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Timestamp:
Jul 30, 2011 5:56:59 PM (12 years ago)
Author:
toby
Comment:

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  • DemoAutoIndex

    v5 v6  
    1919=== Step 3: read in the data file ===
    2020
    21  Use the Data/Read powder data menu item to read the data file into the current GSAS-II project.
     21 Use the '''Data/Read powder data''' menu item to read the data file into the current GSAS-II project.
    2222 
    23  Select the 11bmb_3844.fxye data file in the first dialog and press Open.
     23 Select the {{{11bmb_3844.fxye}}} data file in the first dialog and press Open.
    2424
    25  Select the 11bmb_3844.prm instrument parameter file in the second dialog and press Open.
     25 Select the {{{11bmb_3844.prm}}} instrument parameter file in the second dialog and press Open.
    2626
    2727    At this point the data tree window will have several entries
    … …  
    3434 This pattern has much more data than we need, so it is helpful to cut down the range. Click on the Limits item in the data tree. A new window is created. Use the "changed" row of entry boxes to set Tmin and Tmax to 4 and 30
    3535 ([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d3w3.png view]).
    36  Note the green and red lines in the plot window move.
     36 Note the green and red vertical lines in the plot window move.
    3737
    3838
    … …  
    6262=== Step 6: Refine Peak Positions ===
    6363
    64 First, refine the peak intensities and the background. These parameters have their refinement flag turned on by default. Use the menu item Peak Fitting/LSQ !PeakFit. A window will show the progress of the refinement and will close when the least squares is complete.
     64First, refine the peak intensities and the background. These parameters have their refinement flag turned on by default. Use the menu item '''Peak Fitting/LSQ !PeakFit'''. A window will show the progress of the refinement and will close when the least squares is complete.
    6565
    6666Second, add refinement of the peak positions. This can be done by clicking on all the refinement flags for the individual peaks or it is possible to set them all at the same time using this recipe:
    … …  
    6868 * double-click on the refine label above the peak position check-boxes. The entire column of checkboxes is highlighted in blue. Press the y key to turn on all refinement flags (n would turn them off).
    6969 
    70 Third, repeat the refinement using the Peak Fitting/LSQ !PeakFit menu item.
     70Third, repeat the refinement using the '''Peak Fitting/LSQ !PeakFit''' menu item.
    7171 
    7272Fourth, select peak widths for refinement. This can be done by refining sigma (Gaussian width) and/or gamma (Lorentzian width) for individual peaks, but here we constrain the peaks to follow an instrumental broadening equation. Select the Instrumental Parameters item in the data tree.
    … …  
    7575Select the refine flag checkbox for Gaussian U, V, W, Lorentzian X, Y and the asymmetry parameter SH/L.
    7676
    77 Fifth, repeat the refinement. First click on the Peak List item in the data tree and then refine using the Peak Fitting/LSQ !PeakFit menu item. At this point a good fit should be seen by zooming in on individual peaks. (For example see
     77Fifth, repeat the refinement. First click on the Peak List item in the data tree and then refine using the '''Peak Fitting/LSQ !PeakFit''' menu item. At this point a good fit should be seen by zooming in on individual peaks. (For example see
    7878[https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d3w7.png this]). The Rwp is ~6%.
    7979
    8080=== Prepare Indexing Peak List ===
    8181
    82 A separate list of peaks is kept for use in autoindexing. This list is manipulated by clicking on the Index Peak List item in the data tree. In the initially empty window created by this action, use menu item Index Peaks Operations/Load to copy over the fitted peaks from the Peak List tree entry
     82A separate list of peaks is kept for use in autoindexing. This list is manipulated by clicking on the Index Peak List item in the data tree. In the initially empty window created by this action, use menu item '''Index Peaks Operations/Load''' to copy over the fitted peaks from the Peak List tree entry
    8383([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d4w1.png view]).
    8484Note that by default all peaks are selected to be used.
    … …  
    8787
    8888Select the Unit Cells List data item. This brings up a window for indexing and cell refinement options
    89 ([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d4w2.png view]). For the most rapid search (since we know the right answer), select Cubic-P and launch the search using menu item Cell Index/Index Cell. The search then
    90 runs and a list of possible matching cells is shown in the window
     89([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d4w2.png view]). For the most rapid search (since we know the right answer), select Cubic-P and launch the search using menu item '''Cell Index/Index Cell'''. The search then runs and a list of possible matching cells is shown in the window
    9190([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d4w3.png view]).
    9291
    … …  
    10099=== Select/Refine Cell ===
    101100
    102 Select the top option, a 4.1568 A cell with M20 figure of merit of 2700. This indexes all peaks, though peak positions are not exactly perfect if one zooms in enough. Import the cell information using the Cell Index/Copy Cell menu option. Then optimize the cell by refining the lattice parameters and the two-theta zero: click on the refine checkbox next to the Zero offset value and then the Cell Index/Refine Cell menu option. The a cell parameter value shifts from 4.15679 to 4.15684 when zero is refined.
     101Select the top option, a 4.1568 A cell with M20 figure of merit of 2700. This indexes all peaks, though peak positions are not exactly perfect if one zooms in enough. Import the cell information using the '''Cell Index/Copy Cell''' menu option. Then optimize the cell by refining the lattice parameters and the two-theta zero: click on the refine checkbox next to the Zero offset value and then the '''Cell Index/Refine Cell''' menu option. The a cell parameter value shifts from 4.15679 to 4.15684 when zero is refined.
    103102
    104 (Optional) Finally, use of the Cell Index/New phase menu option allows one to assign a phase with these lattice parameters to the data set (histogram). A name for the new phase is then requested. This adds a Phases entry to the data tree, as well as an entry for the new phase. This new phase can be used in future code.
     103(Optional) Finally, use of the '''Cell Index/New phase''' menu option allows one to assign a phase with these lattice parameters to the data set (histogram). A name for the new phase is then requested. This adds a Phases entry to the data tree, as well as an entry for the new phase. This new phase can be used in future code.