# Manual

This page contains information from the topas technical reference manual and is a read only page. It's now slightly out of date so please refer to the Technical_Reference.pdf in your topas directory for more up to date information. It's left online so there is an easily searchable version of the manual. You should also look at documents like “New7.pdf” which contains the updates from version 6 to version 7. The pages were converted from an original word document so some of the formatting may be slightly strange - look in Technical_Reference.pdf for a prettier format.

To find specific parts of this file, please use the search box on the left of this page. An alphabetical list of keywords is linked elsewhere.

Manual Part 1 - Sections 2,3,4,5,6,7: Introduction, Parameters, Equations, Minimization, Peak Generation and Miscellaneous

Manual Part 2 - Sections 8,9,10: Keywords, Macros, File Types

Manual Part 3 - Sections 11,12,13,14: Charge-flipping, Indexing, Batch Mode, References

### Contents:

2 Introduction.

• 2.1 Conventions.
• 2.2 Input file example (INP format)

3 Parameters.

• 3.1 When is a parameter refined.
• 3.2 User defined parameters - the prm keyword.
• 3.3 Parameter constraints.
• 3.4 The local keyword.
• 3.5 Reporting on equation values.
• 3.6 Naming of equations.
• 3.7 Parameter errors and correlation matrix.
• 3.8 Default parameter limits and LIMIT_MIN / LIMIT_MAX.
• 3.9 Reserved parameter names.
• 3.10 Val and Change reserved parameter names.

4 Equation Operators and Functions.

• 4.1 'If' and nested 'if' statements.
• 4.2 Floating point exceptions.

5 The Minimization Routines.

• 5.1 The Marquardt method.
• 5.2 Approximating the A matrix - the BFGS method.
• 5.3 Line minimization and Parameter extrapolation.
• 5.4 Minimizing on penalties only.
• 5.5 Summary, Iteration and Refinement Cycle.
• 5.6 quick_refine and computational issues.
• 5.7 Auto_T and randomize_on_errors.
• 5.8 Criteria of fit.

6 Peak Generation and “peak_type”.

• 6.1 Source emission profiles.
• 6.2 Peak generation and peak types.
• 6.3 Convolution and the peak generation stack.
• 6.4 Speed / Accuracy and peak_buffer_step.

7 Miscellanous.

• 7.1 Instrument and sample convolutions.
• 7.2 Microstructure convolutions.
• 7.3 Calculation of structure factors.
• 7.4 Large refinements with tens of 1000s of parameters.
• 7.5 Space groups, hkls and symmetry operators.
• 7.6 Site identifying strings.
• 7.7 Occupancies and symmetry operators.
• 7.8 Pawley and Le Bail extraction.
• 7.9 Anisotropic refinement models.
• 7.10 Rigid bodies and bond length restraints.
• 7.11 Simulated annealing and structure determination.

8 Keywords.

• 8.1 Data structures.
• 8.2 Alphabetical listing of keywords.
• 8.3 Keywords to simplify User input.

9 Macros and Include Files.

• 9.1 The macro directive.
• 9.2 Overview..

10 File types and formats.

11 Charge-flipping..

• 11.1 Charge-flipping usage.
• 11.2 Charge-flipping Investigations / Tutorials.
• 11.3 Charge-flipping Examples.
• 11.4 Keywords in detail.

12 Indexing..

• 12.1 Reprocessing solutions - DET files.
• 12.2 Keywords and data structures.
• 12.3 Keywords in detail.
• 12.4 Identifying dominant zones.
• 12.5 * Probable causes of Failure *
• 12.6 Unique space group hkls in Powder diffraction.
• 12.7 Equations in Indexing - Background.

13 Batch mode operation – TC.EXE.

14 References