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Manual
This page contains links to the topas technical reference manual and is a read only page. The pages are converted from an original word document so some of the formatting may be slightly strange - refer to 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