use Claude ai to generate doxygen documentation.
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@@ -37,49 +37,109 @@
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#include "PMsrHandler.h"
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#include "PUserFcnBase.h"
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// --------------------------------------------------------
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// function handling tags
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// --------------------------------------------------------
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//-------------------------------------------------------------
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/**
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* <p>Theory function type tags.
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*
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* <p>These constants identify the built-in theory functions available in
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* the THEORY block of MSR files. Each function represents a specific physical
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* model for muon spin relaxation, precession, or depolarization.
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*
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* <p>Theory functions can be combined using addition (+) and multiplication (*):
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* - <b>Addition:</b> Independent relaxation channels (e.g., 1/3 fast + 2/3 slow)
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* - <b>Multiplication:</b> Multiple relaxation mechanisms (e.g., precession * damping)
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*
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* <p><b>Categories:</b>
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* - <b>Basic:</b> Constants, asymmetries, simple exponentials
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* - <b>Static relaxation:</b> Gaussian, Lorentzian (Kubo-Toyabe)
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* - <b>Dynamic relaxation:</b> Motional narrowing, spin fluctuations
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* - <b>Precession:</b> Cosine, Bessel functions for oscillations
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* - <b>Vortex lattice:</b> Internal field distributions in superconductors
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* - <b>Special:</b> Spin glass, Abragam, mu-minus, polynomials, user functions
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*/
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// function tags
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/// Undefined or invalid theory function
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#define THEORY_UNDEFINED -1
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/// Constant value (baseline, background)
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#define THEORY_CONST 0
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/// Initial asymmetry (multiplicative factor)
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#define THEORY_ASYMMETRY 1
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/// Simple exponential relaxation: exp(-λt)
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#define THEORY_SIMPLE_EXP 2
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/// General exponential relaxation: exp(-(λt)^β)
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#define THEORY_GENERAL_EXP 3
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/// Simple Gaussian relaxation: exp(-σ²t²/2)
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#define THEORY_SIMPLE_GAUSS 4
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/// Static Gaussian Kubo-Toyabe (zero-field)
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#define THEORY_STATIC_GAUSS_KT 5
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/// Static Gaussian Kubo-Toyabe in longitudinal field
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#define THEORY_STATIC_GAUSS_KT_LF 6
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/// Dynamic Gaussian Kubo-Toyabe in longitudinal field
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#define THEORY_DYNAMIC_GAUSS_KT_LF 7
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/// Static Lorentzian Kubo-Toyabe (zero-field)
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#define THEORY_STATIC_LORENTZ_KT 8
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/// Static Lorentzian Kubo-Toyabe in longitudinal field
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#define THEORY_STATIC_LORENTZ_KT_LF 9
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/// Dynamic Lorentzian Kubo-Toyabe in longitudinal field
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#define THEORY_DYNAMIC_LORENTZ_KT_LF 10
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/// Fast dynamic Gauss-Lorentz Kubo-Toyabe (zero-field)
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#define THEORY_DYNAMIC_GAULOR_FAST_KT_ZF 11
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/// Fast dynamic Gauss-Lorentz Kubo-Toyabe in longitudinal field
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#define THEORY_DYNAMIC_GAULOR_FAST_KT_LF 12
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/// Dynamic Gauss-Lorentz Kubo-Toyabe in longitudinal field
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#define THEORY_DYNAMIC_GAULOR_KT_LF 13
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/// Combined Lorentzian-Gaussian Kubo-Toyabe
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#define THEORY_COMBI_LGKT 14
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/// Stretched Kubo-Toyabe relaxation
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#define THEORY_STR_KT 15
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/// Spin glass order parameter function
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#define THEORY_SPIN_GLASS 16
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/// Random anisotropic hyperfine coupling
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#define THEORY_RANDOM_ANISOTROPIC_HYPERFINE 17
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/// Abragam relaxation function (diffusion)
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#define THEORY_ABRAGAM 18
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/// Transverse field cosine precession
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#define THEORY_TF_COS 19
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/// Internal magnetic field distribution (superconductors)
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#define THEORY_INTERNAL_FIELD 20
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/// Internal field (Kornilov vortex lattice model)
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#define THEORY_INTERNAL_FIELD_KORNILOV 21
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/// Internal field (Larkin-Ovchinnikov model)
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#define THEORY_INTERNAL_FIELD_LARKIN 22
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/// Bessel function (modulated precession)
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#define THEORY_BESSEL 23
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/// Internal Bessel (field distribution with Bessel)
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#define THEORY_INTERNAL_BESSEL 24
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/// Skewed Gaussian relaxation (asymmetric rates)
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#define THEORY_SKEWED_GAUSS 25
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/// Static Nakajima zero-field function
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#define THEORY_STATIC_ZF_NK 26
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/// Static Nakajima transverse field function
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#define THEORY_STATIC_TF_NK 27
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/// Dynamic Nakajima zero-field function
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#define THEORY_DYNAMIC_ZF_NK 28
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/// Dynamic Nakajima transverse field function
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#define THEORY_DYNAMIC_TF_NK 29
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/// F-μ-F (μ-fluorine) oscillation
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#define THEORY_F_MU_F 30
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/// Negative muon (μ-) exponential TF decay
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#define THEORY_MU_MINUS_EXP 31
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/// Polynomial function (arbitrary order)
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#define THEORY_POLYNOM 32
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/// User-defined external function (shared library)
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#define THEORY_USER_FCN 33
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// function parameter tags, i.e. how many parameters has a specific function
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// if there is a comment with a (tshift), the number of parameters is increased by one
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//-------------------------------------------------------------
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/**
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* <p>Number of parameters for each theory function.
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*
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* <p>These constants define how many parameters each theory function requires,
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* <b>excluding</b> optional time shift. If a function includes time shift,
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* add 1 to the parameter count.
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*
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* <p>Parameters typically include: rates (λ, σ), frequencies (ω, ν),
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* phases (φ), fractions, exponents (β), hopping rates (ν_hop), etc.
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*/
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#define THEORY_PARAM_CONST 1 // const
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#define THEORY_PARAM_ASYMMETRY 1 // asymmetry
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#define THEORY_PARAM_SIMPLE_EXP 1 // damping (tshift)
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@@ -113,31 +173,64 @@
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#define THEORY_PARAM_F_MU_F 1 // frequency (tshift)
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#define THEORY_PARAM_MU_MINUS_EXP 6 // N0, tau, A, damping, phase, frequency (tshift)
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// number of available user functions
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//-------------------------------------------------------------
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/**
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* <p>Maximum number of theory functions in database.
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*
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* <p>This is the total number of built-in theory functions available,
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* including all relaxation, precession, and special functions.
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*/
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#define THEORY_MAX 34
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// maximal number of parameters. Needed in the contents of LF
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//-------------------------------------------------------------
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/**
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* <p>Maximum number of parameters for any theory function.
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*
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* <p>Used to allocate arrays for longitudinal field calculations where
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* parameter values from previous iterations must be cached.
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*/
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#define THEORY_MAX_PARAM 10
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// deg -> rad factor
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//-------------------------------------------------------------
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/**
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* <p>Conversion factor from degrees to radians.
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*
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* <p>Value: π/180 = 0.017453292519943295
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* <p>Used for phase parameters which are specified in degrees in MSR files
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* but converted to radians for calculations.
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*/
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#define DEG_TO_RAD 0.0174532925199432955
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// 2 pi
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/**
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* <p>Mathematical constant 2π.
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*
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* <p>Used extensively in frequency-to-angular-frequency conversions:
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* ω = 2πν
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*/
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#define TWO_PI 6.28318530717958623
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class PTheory;
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//--------------------------------------------------------------------------------------
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/**
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* <p>Structure holding the infos of a the available internally defined functions.
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* <p>Database entry for a theory function definition.
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*
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* <p>This structure stores metadata about each built-in theory function,
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* including its identifier, parameter count, name, abbreviation, and
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* help text. The database is used for:
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* - Parsing THEORY block entries in MSR files
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* - Validating parameter counts
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* - Generating help text and documentation
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* - Writing theory blocks with correct syntax
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*/
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typedef struct theo_data_base {
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UInt_t fType; ///< function tag
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UInt_t fNoOfParam; ///< number of parameters for this function
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Bool_t fTable; ///< table flag, indicating if the function is generate from a table
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TString fName; ///< name of the function as written into the msr-file
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TString fAbbrev; ///< abbreviation of the function name
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TString fComment; ///< comment added in the msr-file theory block to help the used
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TString fCommentTimeShift; ///< comment added in the msr-file theory block if there is a time shift
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UInt_t fType; ///< Theory function type tag (THEORY_CONST, THEORY_SIMPLE_EXP, etc.)
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UInt_t fNoOfParam; ///< Number of parameters (excluding optional time shift)
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Bool_t fTable; ///< True if function requires pre-calculated lookup table (e.g., LF Kubo-Toyabe)
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TString fName; ///< Full function name for MSR files (e.g., "simplExpo", "statGssKt")
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TString fAbbrev; ///< Short abbreviation (e.g., "se", "stg")
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TString fComment; ///< Parameter list shown as help text in MSR file
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TString fCommentTimeShift; ///< Parameter list with time shift included
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} PTheoDataBase;
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//--------------------------------------------------------------------------------------
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@@ -251,15 +344,62 @@ static PTheoDataBase fgTheoDataBase[THEORY_MAX] = {
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//--------------------------------------------------------------------------------------
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/**
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* <p>Class handling a theory of a msr-file.
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* <p>Theory function evaluator and manager.
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*
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* <p>This class parses, validates, and evaluates theory functions specified
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* in the THEORY block of MSR files. It handles:
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* - Parsing theory syntax (function names, parameters, operators)
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* - Building theory expression trees (addition/multiplication)
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* - Resolving parameter mappings and user functions
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* - Evaluating theory at specific time points
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* - Caching longitudinal field calculations
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* - Loading and managing user-defined shared library functions
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*
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* <p><b>Theory syntax:</b>
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* - Single function: <tt>asymmetry simpleExp 1 3</tt>
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* - Addition: <tt>func1 par1... + func2 par1...</tt>
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* - Multiplication: <tt>func1 par1... * func2 par1...</tt>
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* - Nested: <tt>(func1 + func2) * func3</tt>
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*
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* <p><b>Parameter resolution:</b>
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* Parameters can be direct numbers, parameter references (1, 2, 3, ...),
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* map references (map1, map2, ...), or function references (fun1, fun2, ...).
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*
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* <p><b>Example:</b>
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* @code
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* THEORY
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* asymmetry 1
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* TFieldCos 2 3 (phase, freq)
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* +
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* simpleExp 4 (rate)
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* @endcode
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* This evaluates to: par1 * cos(par2 + 2π*par3*t) + exp(-par4*t)
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*/
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class PTheory
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{
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public:
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/**
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* <p>Constructor for theory handler.
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*
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* @param msrInfo Pointer to MSR file handler
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* @param runNo Run number for this theory (0-based)
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* @param hasParent True if this is a sub-theory (for +/* operators)
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*/
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PTheory(PMsrHandler *msrInfo, UInt_t runNo, const Bool_t hasParent = false);
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virtual ~PTheory();
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/// Returns true if theory is valid and ready for evaluation
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virtual Bool_t IsValid();
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/**
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* <p>Evaluates the theory function at time t.
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*
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* @param t Time in microseconds (μs)
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* @param paramValues Vector of fit parameter values
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* @param funcValues Vector of evaluated user function values
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* @return Theory value at time t
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*/
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virtual Double_t Func(Double_t t, const PDoubleVector& paramValues, const PDoubleVector& funcValues) const;
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private:
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