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| - | ====== Manual ====== | ||
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| - | 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. | ||
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| - | 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. | ||
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| - | [[Manual Part 1]] - Sections 2,3,4,5,6,7: Introduction, Parameters, Equations, Minimization, Peak Generation and Miscellaneous | ||
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| - | [[Manual Part 2]] - Sections 8,9,10: Keywords, Macros, File Types | ||
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| - | [[Manual Part 3]] - Sections 11,12,13,14: Charge-flipping, Indexing, Batch Mode, References | ||
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| - | ==== Contents: ==== | ||
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| - | **2 Introduction.** | ||
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| - | * 2.1 Conventions. | ||
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| - | * 2.2 Input file example (INP format) | ||
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| - | **3 Parameters. ** | ||
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| - | * 3.1 When is a parameter refined. | ||
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| - | * 3.2 User defined parameters - the prm keyword. | ||
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| - | * 3.3 Parameter constraints. | ||
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| - | * 3.4 The local keyword. | ||
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| - | * 3.5 Reporting on equation values. | ||
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| - | * 3.6 Naming of equations. | ||
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| - | * 3.7 Parameter errors and correlation matrix. | ||
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| - | * 3.8 Default parameter limits and LIMIT_MIN / LIMIT_MAX. | ||
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| - | * 3.9 Reserved parameter names. | ||
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| - | * 3.10 Val and Change reserved parameter names. | ||
| - | ** | ||
| - | 4 Equation Operators and Functions. ** | ||
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| - | * 4.1 'If' and nested 'if' statements. | ||
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| - | * 4.2 Floating point exceptions. | ||
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| - | **5 The Minimization Routines. ** | ||
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| - | * 5.1 The Marquardt method. | ||
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| - | * 5.2 Approximating the A matrix - the BFGS method. | ||
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| - | * 5.3 Line minimization and Parameter extrapolation. | ||
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| - | * 5.4 Minimizing on penalties only. | ||
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| - | * 5.5 Summary, Iteration and Refinement Cycle. | ||
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| - | * 5.6 quick_refine and computational issues. | ||
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| - | * 5.7 Auto_T and randomize_on_errors. | ||
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| - | * 5.8 Criteria of fit. | ||
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| - | **6 Peak Generation and "peak_type". ** | ||
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| - | * 6.1 Source emission profiles. | ||
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| - | * 6.2 Peak generation and peak types. | ||
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| - | * 6.3 Convolution and the peak generation stack. | ||
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| - | * 6.4 Speed / Accuracy and peak_buffer_step. | ||
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| - | **7 Miscellanous. ** | ||
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| - | * 7.1 Instrument and sample convolutions. | ||
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| - | * 7.2 Microstructure convolutions. | ||
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| - | * 7.3 Calculation of structure factors. | ||
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| - | * 7.4 Large refinements with tens of 1000s of parameters. | ||
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| - | * 7.5 Space groups, hkls and symmetry operators. | ||
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| - | * 7.6 Site identifying strings. | ||
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| - | * 7.7 Occupancies and symmetry operators. | ||
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| - | * 7.8 Pawley and Le Bail extraction. | ||
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| - | * 7.9 Anisotropic refinement models. | ||
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| - | * 7.10 Rigid bodies and bond length restraints. | ||
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| - | * 7.11 Simulated annealing and structure determination. | ||
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| - | **8 Keywords. ** | ||
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| - | * 8.1 Data structures. | ||
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| - | * 8.2 Alphabetical listing of keywords. | ||
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| - | * 8.3 Keywords to simplify User input. | ||
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| - | **9 Macros and Include Files. ** | ||
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| - | * 9.1 The macro directive. | ||
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| - | * 9.2 Overview.. | ||
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| - | **10 File types and formats. ** | ||
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| - | **11 Charge-flipping.. ** | ||
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| - | * 11.1 Charge-flipping usage. | ||
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| - | * 11.2 Charge-flipping Investigations / Tutorials. | ||
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| - | * 11.3 Charge-flipping Examples. | ||
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| - | * 11.4 Keywords in detail. | ||
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| - | **12 Indexing.. ** | ||
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| - | * 12.1 Reprocessing solutions - DET files. | ||
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| - | * 12.2 Keywords and data structures. | ||
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| - | * 12.3 Keywords in detail. | ||
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| - | * 12.4 Identifying dominant zones. | ||
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| - | * 12.5 *** Probable causes of Failure *** | ||
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| - | * 12.6 Unique space group hkls in Powder diffraction. | ||
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| - | * 12.7 Equations in Indexing - Background. | ||
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| - | **13 Batch mode operation – TC.EXE. ** | ||
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| - | **14 References** | ||
