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--- manual [2009/08/27 16:34] – johnsoevans
+++ manual [2022/11/03 15:08] (current) – external edit 127.0.0.1
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+====== 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 It's now slightly out of date so please refer to the Technical_Reference.pdf in your topas directory for more up to date information.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.
+**
+        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**