PDF Fitting of SnO2 and SnO2/MoO3 mixture
Learning Outcomes: This tutorial will take you through simple fitting of PDF data for a crystalline sample of SnO2 and a mixture of crystalline SnO2 and MoO3. It will make use of the pdf menus that Phil Chater has created and his pdf.inc macros collection.
The data were collected with a wavelenght of 0.1616693 Angstroms at the I15-1 XPDF beamline at the Diamond Light Source by Luiza Rosa de Araujo, Matt Chambers, Phil Chater and John Evnas. The data were processed using GudrunX to produce a Gudrun dofr radial distribution. The SnO2 data were processed with a SoperLorch r-space broadening of 0.06 Angstroms and the data on the SnO2/MoO3 mixture with a broadening of 0.08.
To fully understand all the functions and corrections read the literature and GudrunX manuals.
Credits: tutorial by John Evans and Phil Chater.
Initial Setup for PDF
1. Install the pdf menus for jEdit if you don’t already have them. Go to Phil’s git site and save the file pdf.insert.xml in your jEdit xinsert folder. This should be at a location like c:\users\your_user_name\.jedit\xinsert. It’s the same folder where you’ll have durham.insert.xml.
2. Save Phil’s pdf.inc into your main topas folder (something like c:\topas_v6).
3. Edit your local.inc or topas.inc file to include the following line (if it’s not already there):#include pdf.inc.
SnO2 Small Box PDF Fitting
2. Work through the menus in the “Topas_for_PDF section. This process is similar to the Rietveld menus in other tutorials.
3. In menu “1. PDF data” click to “Select PDF Data File” and find sno2_dofr.xye. In the “file preparation menu” click the options to rebin data with a start value of 0.0 and a step of 0.02 then set a start_r of 0 and end_r of 50 Angstroms. Add the line “weighting = 1;” after the datafile name so that unit weights are used in the refinement.
4. In menu “2. Instrument parameters” select “dQ damping” with a value of 0.08 and a “Soper-Lorch” convolution with a value of 0.06.
5. In menu “3. Phase information” choose option 3b and read in sno2_baur.cif.
6. Gudrun defines peak positions in a slightly different way to Topas (centre of bin vs start of bin). To correct for this you need to add a zeropoint offset in each str in a pdf fit of half a bin. In the str section add the line: pdf_zero -0.01
7. Use the “to TA” button to save the file and run topas. You should get an Rwp value of around 32.2%.
8. Allow the tetragonal cell parameters to refine by setting appropriate flags. If you like you can use the command “set to tetragonal” in “ii. constrain lattice parameters” to set a and b cell parameters to refine with equal values. You should get Rwp=20.1% at this stage.
9. In a PDF fit the width of the peaks in r tells you about the spread of atomic distances. In a small box approach these are determined from the temperature factors on the atoms. Try refining the beq value on the Sn and O sites. You should get 15.3%.
10. In many materials the thermal motion of directly (strongly) bonded atoms will be highly correlated whereas it will be less correlated for atom pairs that are a long way apart. The width of peaks in a pdf therefore depends on r. There are various ways to model this using an r-dependent beq value. In this case we can use a relatively simple model. Try replacing the beq values with the macro below. Look in pdf.inc or topas.log to see the exact expression applied. You should get Rwp ~ 13.9%.
beq_spherical(beqloSn, 0.1,beqhiSn, 1.0,radius,8) beq_spherical(beqloOx, 0.1,beqhiOx, 1.0,radius, 8)
11. Try refining the free x/y coordinates on O. Try adding a scale factor on the SnO2 phase. You should get Rwp ~13.8%. The scale factor should refine to 1.02. This is very close to the ideal value of 1.0 suggesting that the data were well normalised in GudrunX. The final input file is linked here.
SnO2 and MoO3 Mixture Small Box PDF Fitting
SnO2 and MoO3 Mixture Small Box PDF Fitting
This dataset was recorded on a physical mixture made from 0.070 g of SnO2 and 0.131 g of MoO3 (a 1:2 molar ratio) on beamline I15-1 at Diamond. It was processed in GudrunX with a SoperLorch real space broadening of 0.08 Angstroms.
1. Save the SnO2_2MoO3_dofr.xye to your directory.
2. Start with your SnO2 input file. Set the SoperLorch r space broadening to 0.08. Add MoO3 as a second phase (use the cif file moo3.cif). Set the scale factors of the two phases to be frac and 1-frac. You may need to use the more complex peak width function below for each phase:
beq_rcut_rlo_spherical(!rcut,2.5, beqcutsn, 0.1,!rlo,2.0,beqlosn, 0.1,beqhisn, 0.5,radius, 10)
3. The topas gui doesn’t currently calculate the mass percentages correctly for pdf. In a 2-phase pdf the scale factor is proportional to the mole fraction. Write equations in your file to correctly calculate the mass percentage of SnO2 and MoO3.
4. If you need a hint look at the file here.