wiki:DemoAutoIndex

Fit Peaks/Autoindexing? in GSAS-II

The GSAS-II program will search for a unit cell that matches a set of diffraction peaks -- a process known as auto-indexing. First peaks must be located and optimized and then indexing can be done.

Step 1: read in data

Download the sample data file and matching instrument parameter file from these links:

https://subversion.xray.aps.anl.gov/trac/pyGSAS/browser/Examples/powder%20data/11bmb_3844.fxye?format=raw https://subversion.xray.aps.anl.gov/trac/pyGSAS/browser/Examples/powder%20data/11bmb_3844.prm?format=raw

(One can also use this links https://subversion.xray.aps.anl.gov/pyGSAS/Examples/powder%20data/11bmb_3844.fxye and https://subversion.xray.aps.anl.gov/pyGSAS/Examples/powder%20data/11bmb_3844.prm to obtain the file, but this is more complex).

Step 2: Start GSAS-II

This is done in different ways, depending on your OS and how GSAS-II is installed.

Step 3: read in the data file

Use the Data/Read? powder data menu item to read the data file into the current GSAS-II project.

Select the 11bmb_3844.fxye data file in the first dialog and press Open.

Select the 11bmb_3844.prm instrument parameter file in the second dialog and press Open.

At this point the data tree window will have several entries (view); and the plot window will show the powder pattern (view).

Step 4: Select Data Range

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. You may also drag the limits lines to the desired location or place them by a left mouse click on a data point for the lower limit or a right click on a data point for the upper limit. (view). Note the green and red vertical lines in the plot window move.

Step 5: Determine Peak Positions

Click on the Peak List item in the data tree. This creates an empty window of peak positions. At this point it is wise to zoom in on the data that will be used for indexing. This can be done by clicking on this button:

Click on the magnification button: , then press the left mouse in one corner of the region to be used; holding the mouse button down, drag over the region to the opposite corner.

Important: Click on the magnification button again to turn off the zoom mode.

Using the left mouse button click on a data point near the top of each peak to be added to the peak list. As this is done, a line is drawn in the plot window (view) and peaks are added to the Peak List window (view). Note that if peaks are not being added, you probably have not exited zoom mode.

Once peaks in that region have been added, move to a new region of the pattern. This can be done by clicking on the shift button: . Dragging with the left mouse will shift the data to follow the mouse. Clicking with the right button (on the Mac, control + mouse) and moving up increases the vertical scale and to the right increases the horizontal scale. Important: Click on the shift button again to turn off this mode.

Again, using the left mouse button, click on the tops of more peaks to be added to the peak list. Note that if peaks are not being added, you probably have not exited shift mode.

Add approximately 24 peaks total to the peak list. Be sure to add the lowest angle peaks that are visible in the plot. You may drag a peak position as needed; be sure the zoom/shift buttons are off. A position may be deleted with a right click with the mouse on the blue line.

Step 6: Refine Peak Positions

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. A summary of the refinement is shown on the console window as well.

Second, 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:

  • single-click on any value in the table to select it, for example the first peak position. A black box appears around the value. If the field if opened for editing (the box turns to blue), select a different item in the table.
  • 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).

Third, repeat the refinement using the Peak Fitting/LSQ PeakFit menu item. Fourth, 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. This opens a window for peak profile terms (view). Select the refine flag checkbox for Gaussian U, V, W, Lorentzian X, Y and the asymmetry parameter SH/L.

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 this). The Rwp is ~6% as shown on the console window.

Prepare Indexing Peak List

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 (view). Note that by default all peaks are selected to be used.

Run Autoindexing

Select the Unit Cells List data item. This brings up a window for indexing and cell refinement options (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 he console shows a running list of possible cells as they are found; the sorted by M20 list of possible matching cells is shown in the window (view).

Review Cell Choices

Review the list of cells associated with the Unit Cells List data item. Note that as one selects a unit cell, the generated reflections for that cell are shown in the plot with dashed red lines. Sliding the cursor over these lines shows a small popup window with the indexed hkl for them. Note how the 8.312 A cell generates very many lines with no corresponding peaks (view) while the 2.939 A cell generates not enough lines to match all the peaks (view).

Select/Refine? Cell

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.

(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.

Last modified 9 years ago Last modified on Sep 6, 2012 4:10:49 PM

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