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 manual [2009/08/27 10:09]clare manual [2020/07/16 11:29] Line 1: Line 1: - ====== Manual ====== - - This text comes directly from the topas academic technical reference and therefore it is a read only page. To find specific parts of this file, please use the search box on the left of this page. - - \\ - [[manual part 1]] - sections 2,3,4,5,6,7 - - \\ - [[manual part 2]] - sections 8,9,10 - - \\ - [[manual part 3]] - sections 11,12,13,14 - - \\ - ==== 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**