Tutorial pdf sno2

PDF fitting of SnO₂ and SnO₂/MoO₃ mixture – topas-editor

Files needed: sno2_dofr.xye; sno2_baur.cif; SnO2_2MoO3_dofr.xye; moo3.cif

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. This tutorial uses the topas-editor templates approach. The original tutorial using jEdit pdf menus is here.

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 pdf.inc TOPAS macros if you don’t already have them. They are on Phil’s git site and should go into your main topas folder (something like c:\topas_v7). They’re distributed as part of v8+.

2. Edit your local.inc to include the following line (if it’s not already there): #include pdf.inc.

SnO₂ small box PDF fitting

1. Save sno2_dofr.xye and sno2_baur.cif file in your working directory.

2. From the TOPAS_Durham menus/PDF fitting read in the PDF template. Save the file as sno2_dof_te_01.inp or similar.

3. Go through the template and change all the purple text following arrows (->). Filename should be sno2_dofr.xye. dQ_damping should be set to 0.08 and fixed. convolute_SuperLorch should be set to 0.06 and fixed.

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. Other parameters can be left at their defaults.

5. Delete all the str information then click on “Structure from CIF for PDF” 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 include 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. Send INP to TOPAS then refine. You should get an Rwp value of around 35%.

8. Allow the tetragonal cell parameters to refine by setting appropriate flags. You should get Rwp ~26% 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 15.2%.

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 ~13.9%. 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

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. You should get Rwp ~18.7% and weight percentages of 33 and 67 %.

4. If you need a hint look at the file here.