Rietveld Refinement protocol – SKK Lab, IISER Pune

Priyank Shyam, Dr. Smita Chaturvedi and Dr. Mandar Shirolkar

Running the Refinement:

1. Make Folder with CIF and DAT files. Open Fullprof Suite. ED-PCR. CIF-PCR. Open CIF file. Save.
PCR file is created.
2. Go to Editor. Open PCR file. Change job value from 2 to 0. Save. Close.
3. Cycle of refinement to 3, force termination to 0.3 (0.1 is only for Synchrotron sources. For lab
sources, it should be 0.3); Check Profile Matching Mode in the ‘Others’ option. For pure
material, enable ‘only first cycle’.
4. Instrumental: Zero.
5. Profile: Scale Factor.
6. Background: Refine 1st background parameter. In case of sloppy background, it is wise to
refine 2-3 parameters. Save the last 3 parameters for the end.
7. Profile: Lattice constants (a,b,c, alpha, beta, gamma).
8. Atoms: Refine atomic positions for the individual atoms in the unit cell.
9. Profile: Peak shape parameters (U,X,V,W and Y) individually.
10. Atoms: B factors for the individual atoms followed by the Occupancies (or vice versa).
11. Background: Add the additional background parameters.
12. The refinement strategy is now modified on a ‘case-to-case’ basis for including effects like
anisotropic thermal movements, asymmetric peaks, preferred orientations in the samples etc.

Upon attaining a good enough value of 2 (< 10), perform the following checks:

 The values of the R-factors are at least below 20. Rexp should ideally be a single digit value.
 The values of U,W,X and Y should be positive and V should be negative.
 Confirm that the B-factors (Overall or B_iso) are positive – a negative value is incorrect!
 Check the occupancies – make sure that the values are non-negative and make sense in
terms of the particular sample.
 Inspect the residual curve carefully – it can provide valuable information about the quality of
the fit and the errors made.

Obtaining the Output information:

1. Go to Output. In ‘Output Files’ section, select option of ‘CIF’ and ‘SYM’

2. Change Correlation output matrix to ‘Correlation Matrix’. Also, enable all options in the table
below.
3. Don’t check ‘Simulation Diffraction Pattern’.
4. Check ‘Analysis of Goodness of Refinement’.
5. In second tab, enable ‘Background File’ in BAC and GFourier in FOU.
6. In HKL, enable 2nd option (because it gives all information about the refinement).
7. In ‘Refinement Plot on Screen’, don’t change anything.
8. In ‘PRF’, select 2nd option (for getting a .bat text file).
9. In ‘SUV’, enable ‘Calculate profile + background for each plane’.
10. In 3rd tab, in ‘SCH’ select 2nd option.
11. In ‘DIS’, select ‘GC’. Max distance is 3.4 and Max distance angle is 2.7. Enable ‘BVS’. In BFO,
we have 2 cations and 1 anion, so put the numbers accordingly. However, there’s a bug here.
Tolerance is 10.
12. In ‘ATM’, select the last option ‘atoms inside a conventional cell’ – this is required for XRD.

28th Jun, 2016 ©SKK Lab, IISER Pune 1

 13. Go to Output once again. Go to ‘DIS’ once again. Put the element symbols in the cations and
anions cells – this is the bug mentioned earlier!
14. Save the file. Make a copy of the PCR file in the same folder.
15. Now do Refinement again. All the information that we enabled in the previous exercise is now
available (This should create a .INP, .CIF and a .PRF file, amongst others).

Obtaining Fourier Maps:

1. Open GFourier. Open this INP file.

2. In ‘Calculation’, select ‘Fourier Program’. This will plot the electron density map as a contour
plot.
3. In the ‘Limits to Fourier map’, put a value limits as 0 and 1 or 2 for all X, Y and Z (If you make
it 3, then the software will not be able to make a data without errors – a software limitation).
4. Select ‘Create ASCII file of the original version’ option. This software has its limitation – you
cannot exceed more than [0, 2] as the Fourier limits of the X, Y and Z coordinates.
5. The obtained ASCII file can be now plotted in Origin as a contour plot of the electron density.

Bond Lengths and Bond Angles Calculation:

1. Run BondSTR.
2. There’s a bug here. In ‘File’, select ‘Import CIF’. Select the CIF that has been generated. Our
refinement program overwrote the original CIF.
3. In ‘File’, now ‘Open’ the CFL file (that has now been mysteriously generated – some bug, eh?)
4. Enable the ‘restraints output’ as well.
5. For ‘Dist. Angl’, change the values to (3.4, 2.7)
6. Make the default Tolerance to 10.
7. Put the respective valencies of the ions in the unit cell in front of the respective labels in the
table.
8. Run the BondSTR program by clicking the icon located below the ‘Help’ button on top.
9. This will generate a .BVS file with all bond angle information.

Obtaining Rietveld fitted profile:

1. Run WinPlotr.
2. In the ‘File’ menu – choose the ‘Open Rietveld/profile file’.
3. From the pop-up menu, choose ‘101: FullProf PRF file’ and open the PRF file generated from
the refinement.
4. The fitted profile will be visible in the WinPlotr window.
5. In the ‘File’ menu – choose ‘Save data as…’ and ‘Save data as XYY file.’ Ensure that all 4
checkboxes are ticked.
6. This should generate an XYY file that can be then plotted in Origin.

This is the end of Rietveld Refinement using FullProf Suite. You now have all the information (five
important parameters – structural information (from XRD), electron density, atomic coordination,
bond angle and bond lengths. Success!

28th Jun, 2016 ©SKK Lab, IISER Pune 2