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


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