Durham Topas Tutorials

Various tutorials on the use of topas/jEdit are given below. They’ve been collated from various schools and user meetings. There’s more background/theory on many of them in the TOPAS Rietveld book.

Please note that these tutorials have been created over several years in Topas version from v4 to v7. In some cases there may now be better ways of tackling the problem or setting up the input file. Most tutorials will run in v4.2 onwards, but some need functionality only available in later releases.

Several jEdit menus were updated in June 2020 for TOPAS v7and jEdit5.5 not all tutorials have been tested. Please tell me if you find problems. They will definitely all work if you go back to jEdit 4.3.

Peak Positions/Indexing

Peak positions are one of the fundamental aspects of a diffraction pattern and are determined by the cell size and shape. These tutorials look at how unknown unit cells are obtained/refined from powder data. You can try these procedures on any of the other data sets provided. If you’ve never used topas/jEdit before you might want to try e.g. tutorial 8 or tutorial 9 first which go through some of the mechanics of using jEdit in a bit more detail.

Tutorial 6 – Peak Fitting: How to perform individual peak fitting in topas, often the first step before indexing.

Tutorial 7 – Indexing: How to index a powder pattern in topas.

TA/Simple Rietveld refinement in jedit/Topas Academic

The tutorials below are intended to give you an introduction to Rietveld and Pawley refinement using the topas academic/jEdit interface. The aim of the tutorials is not to necessarily fully understand what your doing, but to make sure you’re happy with the “mechanics” of the overall process of Rietveld refinement.

If you want even more basic tutorials on topas/jEdit then take a look at the introductory tutorials on the web. The examples there have more step-by-step detail and contain screen shots of (approximately) what you should see at each stage.

Tutorial 8 – How to run a prewritten input file.

Tutorial 9 – TiO₂ Rietveld: A simple Rietveld refinement using lab data starting from scratch.

Tutorial 10 – TiO₂ Rietveld starting from a template file.

Tutorial 11 – Pawley Fitting: Pawley fitting is a structure-independent whole-pattern fitting method. It’s a good way of finding if a unit cell is correct and also finding the “best possible” fit you’d get in a Rietveld refinement.

Tutorial 12 – ZrW₂O₈ Rietveld: Simple Rietveld refinements using lab data, constant wavelength neutron and time of flight neutron data – make sure you have John’s local.inc on your computer.

Tutorial 13 – Multiphase Rietveld refinement.

Tutorial 13.5 – LaMnO₃ Rietveld with no detailed instructions.

Neutron/Synchrotron/Combined Refinement

How to perform Rietveld/Pawley refinements using neutron/sychrotron data.

Tutorial 14 – Y₂O₃ data recorded on id31 at the esrf

Tutorial 15 – ZrW₂O₈ Rietveld: Simple Rietveld refinements using lab data, constant wavelength neutron and time of flight neutron data – make sure you have john’s local.inc on your computer. Note this is the same as tutorial 12 above.

Tutorial 16 – PbSO₄ constant wavelength neutron data from Jeremy Cockcroft that have been used in several Rietveld schoools.

Tutorial 17 – Combined Refinement: Builds from earlier tutorial on ZrW₂O₈ and shows how to simultaneously fit X-ray and neutron data. Also discusses ab-inition structure solution from X-ray and neutron data. See also gsas 3 and gsas 4.

Peak Shapes

Peak shapes are another fundamental aspect of a diffraction pattern. These tutorials investigate some of the functions used in Rietveld packages and how peak shapes can be used to give sample size/strain information.

Tutorial 18 – This tutorial explores convolutions to fit a single peak in a pattern using the convolution approach discussed in Rietveld school lectures.

Tutorial 19 – In this tutorial you’ll investigate the various peak shape functions that are used in Rietveld refinement packages. You’ll use experimental fwhm vs 2-theta data in excel to come up with functions that might describe a real data set. You’ll then try these functions in topas.

Tutorial 20 – Fundamental Parameters peak shape fitting – modelling peak shapes in terms of instrumental and sample contributions.

Tutorial 21 – Size/Strain Analysis: Shows how size/strain can be determined in topas using the CeO₂ round robin data using an empirical instrumental resoultion function.

Tutorial 22 – Nanoparticle Sizing: Determines the size of ~2 nm nanoparticles from diffraction data.

Restraints/Rigid Bodies

Use of extra chemical information such as restraints and rigid bodies is often important when analysing powder data. Several of the tutorials (e.g. the one on ZrW₂O₈ Rietveld) use bond distance and angle restraints. Tutorials in this section provide more examples.

Tutorial 23 – Rietveld refinement of an organic molecule using restraints and rigid bodies. See also gsas 7.

Tutorial 24 – A complex use of rigid bodies to refine 3 molecules in asymmetric unit with z-matrix description of local bodies to constrain internal symmetry. Data recorded on id31.

Neutron and X-ray Combined Refinement

How to perform a combined refinement using neutron and X-ray data.

Tutorial 17 – Combined Refinement: Builds from the earlier tutorial on ZrW₂O₈ and shows how to simultaneously fit X-ray and neutron data. Also discusses structure solution from X-ray and neutron data. See also gsas 3 and gsas 4.

Structure Solution

Structure solution is not formally part of the Rietveld School, but you could try the tutorials below if you’re interested. The tutorial on compbined refinement of ZrW₂O₈ also explores these ideas.

Tutorial 26 – Structure Solution of an inorganic oxide: Takes the information from earlier tutorials and solves the structure of TiO₂ using simulated annealing.

Tutorial 27 – Structure solution of a rigid organic molecule and other examples.

Tutorial 28 – Structure solution of inorganic materials.

Miscellaneous Examples

Tutorial 29 – Quantitative Rietveld refinement. This is extremely important in many industries. This example uses the Round Robin data of Ian Madsen and Nikki Scarlett.

Tutorial 30 – Size/Strain Analysis: Shows how size/strain can be determined in topas using the CeO₂ round robin data.

Tutorial 31 – Nanoparticle Sizing: Determines the size of ~2 nm particles from diffraction data.

Tutorial 32 – Solving a structure from single crystal data using charge flipping

Tutorial 33 – Single crystal: How to do a simple single crystal refinement in topas.

Tutorial 33.5 – Using functions in topas v5 and above to explore the fundamental equations used in crystallographic refinement.

Sequential and Parametric/Surface Refinement

Tutorial 33.7 – How to refine against multiple datasets sequentially in v6 with #list format or v4/v5 with command files.

Tutorial 34 – Parametric or surface Rietveld refinement – how to use surface fitting to analyse 100 patterns simultaneously to follow phase transitions in WO₃. Tutorials linked from this one show several different ways of setting up input files.

Tutorial 35 – Parametric or surface Rietveld refinement – how to refine sample temperature using the ZrP₂O₇ example.

Symmetry Mode Refinements

Tutorial 36 – Structural transformations. Directly refine symmetry-mode amplitudes rather than traditional atomic xyz coordinates of a distorted subgroup structure. Example based on simulated lab x-ray diffraction data from low-temperature orthorhombic LaMnO₃. The symmetry modes are obtained using the ISODISTORT software.

Tutorial 37 – Structural transformations. Directly refine symmetry-mode amplitudes rather than traditional atomic xyz coordinates of a distorted subgroup structure. Example based on laboratory x-ray diffraction data from room-temperature monoclinic WO₃. The symmetry modes are obtained using the ISODISTORT software.

Tutorial 38 – Structural transformations. A more advanced symmetry-mode refinement example based on room-temperature WO₃. Fit both neutron and X-ray data. Try to determine space-group symmetry at high temperature using ISODISTORT.

Tutorial 39 – By combining topas, ISODISTORT and some python scripts you can automatically search through different space group possibilities for samples which undergo symmetry-lowering phase transitions.

Tutorial 39.5 – This is an update of Tutorial 39 and shows how you can use a single TOPAS INP file to search through different space group possibilities for samples which undergo symmetry-lowering phase transitions – no external Python scripts are needed.

Tutorial 40 – This tutorial teaches you how to use a Genetic Algorithm with a P1 distortion mode model of a structure to decide which modes are actually important in fitting the data. This lets you simultaneously determine the space group and structure of a material. The tutorial uses WO₃ as an example. See also the magnetic example below.

Magnetic Refinements

Tutorial 41 – Topas v5 onwards will perform magnetic Rietveld refinement. This tutorial takes you through three different ways of describing the low temperature magnetic structure of LaMnO₃.

Tutorial 42 – This tutorial teaches you how to use a Genetic Algorithm in P1 1.1 symmetry to determine the magnetic structure and true magnetic symmetry of a material..

Stacking Fault Refinements

Tutorial 43 – Topas v6 lets you calculate the diffraction of materials with stacking faults. This tutorial takes you through this type of analysis using examples from the DIFFaX software package.

PDF Refinement

Tutorial 44 – PDF small box fitting in Topas v6. Tutorial fits data on SnO2 and a 2-phase mixture of SnO₂ and MoO₃.