Y2O3 fullprof
Fullprof Refinement – Y2O3
Files needed: y2o3_demo.txt (save as y2o3_demo.dat); y2o3.cif
Learning Outcomes: This example shows a simple Rietveld refinement of Y2O3 in FullProf. You may have used the same dataset in topas/gsas. I’m not a FullProf expert so it’s set up to give you a first idea of how FullProf works.
0. Fullprof hasn’t been installed by default on your computer. To install it go to: https://www.ill.eu/sites/fullprof/downloads.html . I selected the ifort/Winteracter FullProf Suite (with the newer ifx PySide6_Winteracter FP wouldn’t run on my computer). Save the .exe to your c:\users\username area, then run it. You should be able to install FullProfSuite in your c:\users\username area. Note that it may be wiped either when you logout or overnight. If you want to use FullProf in a later session save a copy of the setup.exe to your J: drive.
1. Create a new folder and save the data file y2o3_demo.txt as y2o3_demo.dat and the Y2O3.cif fileb. Start FP_Suite and press the Red/blue EdPCR button on the bar below. Press the green cif-pcr arrow in the EDPCR, select Y2O3.cif and press OK in the window that appears. The next steps are to work down each of the buttons on the screen that appears
2. Press General and type in a title.
3.1 Press Patterns, Data file/peak shape and select the data file y2o3_demo.dat. Select X,Y,sigma (XYdata) as data format then OK.
3.2 In the Refinement/simulation tab select X-ray; make sure, the correct radiation/wavelength is chosen. You’ll need to set the second wavelength to zero and have an I2/I1 ratio of 0.0 as it’s Cu Ka1 data.
3.3 In the Pattern calculation/Peak Shape tab: select e.g. Thompson-Cox_Hastings pseudo-Voigt (scroll to find this); change the range of calculation to a reasonable cut-off value. Higher values will result in longer calculation times, too low values will lead to poor fits. Try with a value of e.g. 15*FWHM. Compare the result to that using a value of 2*FWHM. Click OK.
3.4. Select the Background Type, chose e.g. 6-coefficient polynomial.
3.4. You can use Excluded Regions to exclude 0 to 15 and 90 to 150 degrees for speed.
3.5 In the Geometry/IRF box go to the Corrections tab and enter the monochromator polarisation correction as 0.79. Enter the 2-Theta limit for the asymmetry correction as 90 degrees.
4. Return to the main EDPCR window by clicking OK and click on Phases. Type in the phase name, e.g. Y2O3. Select the Method of calculation, e.g. Structural Model (Rietveld Method) for Rietveld, Profile matching with constant scale factor for LeBail fits.
4.1 Press Contribution to patterns and select X-ray. Select TCHZ Peak shape.
5. Return to the main window and press Refinement in the main window. Chose an adequate number of Refinement cycles. Start with e.g. 10 cycles. Tick the parameters you want to refine in the different sections of this Refinement menu. Decide a reasonable order for refining the parameters and make sure to gradually increase the number of parameters. Selecting too many parameters in one step will lead to divergence of the refinement.
You could start this refinement by selecting the lattice parameters, profile parameter W, Scale factor (all in the “Profile” box) and the first two background polynomial coefficients (in Background box), and the zero point (in the Instrumental box). If you are happy with your selection press OK, and close the Refinement window.
6. Back in the main EDPCR Editor window, save the instructions file (file/save) into the same folder as the data file. It will be written as y2o3.pcr. There is no need to close the EDPCR window. N.B. if you don’t select save the pcr file will not be updated.
9. It’s might be worth going through the pcr file to check all your changes have been made at this stage. In particular check that all three atoms in the cif file (2*Y and 1*O) have been loaded. You might like to open the .pcr file in VS Code to see how the information compares to a TOPAS input file.
10. Press the Run FP icon in the FullProf toolbar It’s next to the EDPCR icon. Load the PCR file and select the data file if prompted. The refinement will start and inform you about the residuals, chi^2 and the parameter with the largest shift in each cycle. Continue refining until convergence is reached (keep clicking on Run). If the refinement diverges, think of a different refinement strategy.
11. You can look at the refinement by zooming in the plot window. A right click returns you to an unzoomed picture.
12. After convergence, go back to the EdPCR and do File/reload. N.B. if you don’t do this you won’t get the refined values.
13. Visually inspect the refinement result and think of a strategy to improve the fit. Select additional parameters to refine, e.g. U and V and/or more background coefficients. Save the PCR file and redo the refinement (You can just press “Run” in the FullProf window). Continue until you are satisfied with the refinement result. Regularly check the parameter values to identify fit artefacts quickly. If the parameters have physically meaningless values, think of another refinement strategy. Pretty often, a different order of refining the parameters does the trick. Make sure to reset the parameters to reasonable values before trying out a different strategy.
14. With atomic coordinates, isotropic temperature factors and peak shape parameters refined I got Rwp 19.8% and RBragg 7.04%.
14. Try refining peak asymmetry in the Refinement/Profile box. Go to the “Asymmetry Parameters” tab and enter e.g. 0.05 for S_L. You may find that you need to fix other peak shape parameters when you first refine this value.
15. Try adding a <111> preferred orientation parameter in the “Preferred Orientation” tab of the Profile parameters box.
16. Play with the output options to check, what information is obtained. If you want to do some Fourier-map calculation to e.g., find missing atoms, select Patterns output – Structure factors file (FOU) and tick GFOURIER. You can then use the program GFOURIER to calculate different Fourier-maps.
16. I gave up at Rwp 16 %. If you’re a FullProf expert try and match the final fit obtained in the corresponding TOPAS tutorial. My pcr file is here.