Files needed: d5_05005.raw
Learning outcomes: How to obtain accurate 2-theta values for reflections suitable for indexing. In this example a single peak shape is used to fit all reflections. This method lets you spot easily if certain reflections are broader than others. This could indicate they're from a different phase or that what looks like one reflection is actually two closely spaced reflections. There are lots of ways of fitting peaks with individual fwhm's which you can explore.
Methodology: The easiest way to do this in topas academic is to read a data file into topas and let it perform an automatic peak search to obtain approximate 2-theta values. These values are then copied and pasted into an input file in jedit and positions/areas refined.
1. Save the files listed above in your directory.
2. Launch topas and use "file/load scan file" from its menus to read in data.
3. Use "View/Search Peaks" to search for peaks. Lines should appear on the screen showing where peaks have been found. Click on the "Add Peaks" button and the approximate 2-theta positions will be saved to the topas grid.
4. Click on the "+" sign next to the d5_05005.raw filename in the topas grid. Then click on "Peaks Phase". A list of peak positions should appear. Click on the "Position" and "Area" columns to highlight them. Right click on the yellow highlighted columns and select "copy all/selection".
5. In jedit work your way through the menus under "Peak Fitting".
6. Click on "Select Data File" and navigate to select d5_05005.raw.
7. In Instruments/Corrections select "Durham_d5000" as the instrument.
8. Click on the peak information icon.
9. Paste the approximate 2-theta and Area values from the clipboard to the relevant part of the input file (there is text to tell you where!). Delete or comment out the line saying "Position Area".
10. Click on the save/send to topas icon. The default filename is fine.
11. Launch topas if not already running and run the refinement. You should get Rwp of 600+% initially. You may get the error "Expecting Numeric at Area" when you try and refine in topas. If so it's because you've left the text "Position Area" in your input file. Return to jedit and either delete or comment this line out and try again.
12. Try refining the peak areas by putting an @ symbol in front of each. Remember this is a single keystroke if you use the column editting feature of jedit (hold down ctrl key when dragging mouse). You should now get a Rwp of ~ 16.4%.
13. Try refining 2-theta values. You should now get an Rwp of ~ 15.1%.
14. Extra work: you might want to compare this Rwp and quality of fit to that obtained in the Rietveld tutorial of the same data set (Rwp ~15.5%); you might want to introduce a term to describe peak asymmetry by adding a line immediately after the peak shape line:
TCHZ_Peak_Type(pku,-0.00666`,pkv, 0.01240`,pkw, -0.00542`,!pkx,
0.0000,pky, 0.16322`,!pkz, 0.0000)
[Modified 10-Apr-2021 by John S.O. Evans. Pages checked for Google Chrome.]