Durham Topas Tutorials

Various tutorials on use of topas/jedit are given below. They're a collection of various tutorials from recent schools and user meetings.

Please note that these tutorials have been created over several years in Topas v4 and up. In several cases there may now be better ways of tackling the problem or setting up the input file. Some topics will need topas v5 or v6.

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. 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 tutorial session 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 far more 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 of lab data.

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 by Rietveld.

Tutorial 12 - ZrW2O8 Rietveld: Simple Rietveld refinements of 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. As well as these examples you might want to repeat/complete the exercises from session 14.

Tutorial 14 - Y2O3 data recorded on id31 at the esrf

Tutorial 15 - ZrW2O8 Rietveld: Simple Rietveld refinements of 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 neutron data Jeremy discussed are here.

Tutorial 17 - Combined Refinement: Builds from 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.

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 size/strain information.

Tutorial 18 - This tutorial explores convolutions to fit a single peak in a pattern using the convolution approach discussed in 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.

Tutorial 21 - Size/Strain Analysis: Shows how size/strain can be determined in topas using the CeO2 round robin data.

Tutorial 22 - Nanoparticle Sizing: Determines the size of ~2 nm particles 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 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 course, but you could try the tutorials below if you're interested. The tutorial on combined 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 to explore the fundamental equations used in crystallographic refinement.

Sequential and Parametric/Surface Refinement

Tutorial 33.7 - How to refine 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.

Tutorial 35 - Parametric or surface Rietveld refinement - how to refine 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 superstructure. 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 superstructure. 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 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 dta on SnO2 and a 2-phase mixture of SnO2 and MoO3.

 

 

 

 

 

 

[Modified 01-Oct-2017 by John S.O. Evans. Pages checked for Google Chrome.]