Single crystal structure refinement with TOF data in GSAS-II


In these exercises you will use GSAS-II to refine the structure of sapphire (really corundum, Al2O3) from single crystal diffraction data collected at the SNS on the TOPAZ instrument at room temperature. The data consists of a suite of exposures with the crystal in 31 different orientations. If you have not done so already, start GSAS-II.

Step 1. Setup the phase information for sapphire

1.      Use the Data/Add phase menu item add a new phase into the current GSAS-II project. A popup window will appear asking for a phase name; I entered sapphire; press OK when done. Select Loaded Data/Phases/sapphire from the GSAS-II Data tree window. The General tab for Phase Data will appear.


2.      Enter R -3 c (don’t forget the spaces between axial fields) & press Return. A Space Group Information popup window will appear; press OK. The General window will be refreshed showing only the needed lattice parameters for R -3 c.


3.      Enter 4.7613 for a and 12.9846 for c; a new cell volume will be calculated.

4.      Select the Atoms tab; it will be empty. Do Edit/Append atom from the Phase Data for sapphire menu twice. There will be two UNK entries in the table.

5.      Double click the first entry under Type (H); a periodic table will appear. Select Al. Do the same for the second one and pick O. The Atom list should look like

6.      Change the Al(z) to 0. 352, the O(x) to -0.306 and the O(z) to ¼ (it will be changed to 0.2500). Site symmetries and multiplicities will automatically change for these positions.


This completes the initial phase setup for sapphire. An alternative would be to read the phase information from another GSAS-II gpx file, a cif file or an old GSAS exp file; these are all accessed from the Import/Phase menu item on the main GSAS-II Data tree window. It may be useful to save your project at this point; select File/Save project as… from the main GSAS-II Data tree window menu. A file dialog box will appear; select the directory and give a file name (no extension – I chose sapphire).

Step 2. Import the diffraction data

The diffraction data collected on TOPAZ has been processed (absorption corrections, wavelength and geometric corrections) to give a single file with 31 embedded histograms as a space delimited multicolumn text file (sapphire_sphere.hkl). To read this file select Import/Structure Factor/from Neutron TOF HKL F2 file; a file dialog box will appear. Change the directory to the location of this exercise (exercises/TOF Single Crystal Refinement – yours might be different), select sapphire_sphere.hkl and press Open. A popup will show a bit of the file and ask if you want to read this file; press Yes. Another popup will appear with a suggested name for the data; this will be used for the GSAS-II Data tree. Press OK. The console will show messages as each histogram is read; when done a new popup will appear

This makes the connection between the data you just read and the phase (sapphire) you entered in Step 1. Select it (or Set All) and press OK. The GSAS-II data tree window will show all the new histograms, expanding the last one.

The plot window shows a not very interesting 2D view of the l=0 layer of reciprocal space for the last data set. If you select Commands/Plot 3D HKLs from the data window you’ll see a 3D view of the reflection set; press i after selecting the plot (I’ve zoomed in a bit)


The save as/key commands give you control on the appearance of the plot; the plot responds to zoom/rotate commands from the mouse. Left mouse button to rotate, right mouse button to translate, center wheel to rotate about view direction and the wheel to zoom in or out. One cursor is the view point and the other is the 000 reciprocal space origin.

Step 3. Initial least squares refinement

By default the scale factors for all 31 data set are set to be refined so you can immediately do a refinement. Select Calculate/Refine from the main GSAS-II data tree window menu. This will do an F2 refinement by default; probably better is an F refinement. Select Controls from the tree

Uncheck the Refine HKLF as F^2? Box and set the Min obs/sig to 1.0.