Insert new header comment block, remove old one, manually improve file...

Insert new header comment block, remove old one, manually improve file comments (defines / implements), change brief function description to doxygen format, remove some outcommented code

Core/Fitting/inc/AttFitting.h

@@ -21,10 +21,8 @@
 #include <iostream>
 #include <iomanip>
 
-//- -------------------------------------------------------------------
-//! @class AttFitting
-//! @brief Defines general fitting attributes
-//- -------------------------------------------------------------------
+//! General fitting attributes.
+
 class AttFitting
 {
 public:

Core/Fitting/inc/AttLimits.h

@@ -21,10 +21,8 @@
 #include <iostream>
 #include <iomanip>
 
-//- -------------------------------------------------------------------
-//! @class AttLimits
-//! @brief Defines limits for fit parameters
-//- -------------------------------------------------------------------
+//! Limits for fit parameters
+
 class AttLimits
 {
 public:

Core/Fitting/inc/FitObject.h

@@ -23,11 +23,8 @@
 #include "OutputData.h"
 #include "ChiSquaredModule.h"
 
-//- -------------------------------------------------------------------
-//! @class FitObject
-//! @brief Class to hold single simulation description, real data and chi2 module
-//! Used by FitSuite
-//- -------------------------------------------------------------------
+//! Single simulation description, real data and chi2 module (used by FitSuite)
+
 class FitObject : public IParameterized
 {
 public:

Core/Fitting/inc/FitParameter.h

@@ -23,10 +23,8 @@
 #include <string>
 #include <vector>
 
-//- -------------------------------------------------------------------
-//! @class FitParameter
-//! @brief Parameter with value, error and limits for fitting routines
-//- -------------------------------------------------------------------
+//! Parameter with value, error and limits for fitting routines.
+
 class FitParameter : public INamed, public AttLimits
 {
 public:

Core/Fitting/inc/FitParameterLinked.h

@@ -25,11 +25,8 @@
 #include <vector>
 #include <iostream>
 
-//- -------------------------------------------------------------------
-//! @class FitParameterLinked
-//! @brief Provide simultaneous access for several real parameters from
-//! parameter pool
-//- -------------------------------------------------------------------
+//! Provide simultaneous access for several real parameters from parameter pool
+
 class FitParameterLinked : public FitParameter
 {
 public:

Core/Fitting/inc/FitSuite.h

@@ -31,10 +31,8 @@
 class Simulation;
 class ParameterPool;
 
-//- -------------------------------------------------------------------
-//! @class FitSuite
-//! @brief Main class to perform fitting
-//- -------------------------------------------------------------------
+//! Main class to perform fitting
+
 class FitSuite : public IObservable
 {
 public:

Core/Fitting/inc/FitSuiteFunctions.h

@@ -24,10 +24,8 @@ using std::size_t;
 
 class FitSuite;
 
-//- -------------------------------------------------------------------
-//! @class IFitSuiteFunction
-//! @brief Fitting functions interface to be used by Minimizer.
-//- -------------------------------------------------------------------
+//! Fitting functions interface to be used by Minimizer.
+
 class IFitSuiteFunction
 {
 public:
@@ -40,10 +38,8 @@ protected:
     size_t m_ncall;
 };
 
-//- -------------------------------------------------------------------
-//! @class FitSuiteChiSquaredFunction
-//! @brief Chi squared fitting function for minimizer
-//- -------------------------------------------------------------------
+//! Chi squared fitting function for minimizer
+
 class FitSuiteChiSquaredFunction : public IFitSuiteFunction
 {
 public:
@@ -53,11 +49,8 @@ public:
     double evaluate(const double *pars);
 };
 
+//! Gradient fitting function for minimizer
 
-//- -------------------------------------------------------------------
-//! @class FitSuiteChiSquaredFunction
-//! @brief Gradient fitting function for minimizer
-//- -------------------------------------------------------------------
 class FitSuiteGradientFunction : public IFitSuiteFunction
 {
 public:

Core/Fitting/inc/FitSuiteObjects.h

@@ -26,10 +26,8 @@
 
 #include <vector>
 
-//- -------------------------------------------------------------------
-//! @class FitSuiteObjects
-//! @brief Class containing vector FitObject's (simulation and real data) to fit
-//- -------------------------------------------------------------------
+//! class containing vector FitObject's (simulation and real data) to fit
+
 class FitSuiteObjects : public IParameterized
 {
 public:

Core/Fitting/inc/FitSuiteParameters.h

@@ -25,10 +25,8 @@
 
 class ParameterPool;
 
-//- -------------------------------------------------------------------
-//! @class FitSuiteParameters
-//! @brief Class holds vector of parameters for FitSuite
-//- -------------------------------------------------------------------
+//! Holds vector of parameters for FitSuite
+
 class FitSuiteParameters
 {
 public:

Core/Fitting/inc/FitSuiteStrategies.h

@@ -23,10 +23,8 @@
 
 class FitSuite;
 
-//- -------------------------------------------------------------------
-//! @class FitSuiteStrategies
-//! @brief Collection of strategies to fit
-//- -------------------------------------------------------------------
+//! Collection of strategies to fit
+
 class FitSuiteStrategies
 {
 public:

Core/Fitting/inc/IFitSuiteStrategy.h

@@ -27,12 +27,10 @@ class FitSuite;
 #include <vector>
 #include <map>
 
-//- -------------------------------------------------------------------
-//! @class IFitSuiteStrategy
-//! @brief Interface to concrete fit strategy.
-//! Concrete implementation should manipulate with fit parameters/data
-//! and then call minimizer.
-//- -------------------------------------------------------------------
+//! Interface to concrete fit strategy.
+//  Concrete implementation should manipulate with fit parameters/data
+//  and then call minimizer.
+
 class IFitSuiteStrategy : public INamed
 {
 public:
@@ -48,10 +46,8 @@ protected:
     FitSuite *m_fit_suite;
 };
 
-//- -------------------------------------------------------------------
-//! @class FitSuiteStrategyDefault
-//! @brief Default fit strategy just let FitSuite to run it's minimization round
-//- -------------------------------------------------------------------
+//! Default fit strategy just let FitSuite to run it's minimization round
+
 class FitSuiteStrategyDefault : public IFitSuiteStrategy
 {
 public:
@@ -59,10 +55,8 @@ public:
     virtual void execute();
 };
 
-//- -------------------------------------------------------------------
-//! @class FitSuiteStrategyAdjustData
-//! @brief Strategy modifies data before running minimization round
-//- -------------------------------------------------------------------
+//! Strategy modifies data before running minimization round
+
 class FitSuiteStrategyAdjustData : public IFitSuiteStrategy
 {
 public:
@@ -76,10 +70,8 @@ private:
     bool m_call_minimize; //! if it's true, modify data and then call FitSuite's minimizer, if false - simply modify the data
 };
 
-//- -------------------------------------------------------------------
-//! @class FitSuiteStrategyAdjustParameters
-//! @brief Strategy which fixes/releases fit parameters and call minimizer
-//- -------------------------------------------------------------------
+//! Strategy which fixes/releases fit parameters and call minimizer
+
 class FitSuiteStrategyAdjustParameters : public IFitSuiteStrategy
 {
 public:
@@ -100,10 +92,8 @@ private:
     bool m_preserve_original_values; //! if it's true, strategy will set back values of parameters as they were before minimization round
 };
 
-//- -------------------------------------------------------------------
-//! @class FitSuiteStrategyBootstrap
-//! @brief Helps minimizer get out of local minima by disturbing real data
-//- -------------------------------------------------------------------
+//! Helps minimizer get out of local minima by disturbing real data
+
 class FitSuiteStrategyBootstrap : public IFitSuiteStrategy
 {
 public:

Core/Fitting/inc/IMinimizer.h

@@ -25,10 +25,8 @@
 class FitParameter;
 class FitSuiteParameters;
 
-//- -------------------------------------------------------------------
-//! @class IMinimizer
-//! @brief Common interface for all kind minimizer's
-//- -------------------------------------------------------------------
+//! Common interface for all kind minimizer's
+
 class IMinimizer
 {
 public:

Core/Fitting/inc/MinimizerScan.h

@@ -22,10 +22,8 @@
 #include "FitSuiteParameters.h"
 #include "OutputData.h"
 
-//- -------------------------------------------------------------------
-//! @class MinimizerScan
-//! @brief Simple scan minimizer looks for minimum of chi2 function on the grid
-//- -------------------------------------------------------------------
+//! Simple scan minimizer looks for minimum of chi2 function on the grid
+
 class MinimizerScan : public IMinimizer
 {
 public:

Core/Fitting/inc/MinimizerTest.h

@@ -22,10 +22,8 @@
 #include "FitSuiteParameters.h"
 #include <map>
 
-//- -------------------------------------------------------------------
-//! @class MinimizerTest
-//! @brief Minimizer which calls minimization function once to test whole chain
-//- -------------------------------------------------------------------
+//! Minimizer which calls minimization function once to test whole chain
+
 class MinimizerTest : public IMinimizer
 {
 public:

Core/Samples/inc/Crystal.h

+// ************************************************************************** //
+//                                                                           
+//  BornAgain: simulate and fit scattering at grazing incidence
+//
+//! @copyright Forschungszentrum Jülich GmbH 2013
+//             
+//  Homepage:  apps.jcns.fz-juelich.de/BornAgain
+//  License:   GNU General Public License v3 or higher (see COPYING)
+//
+//! @authors   Scientific Computing Group at MLZ Garching
+//! @authors   C. Durniak, G. Pospelov, W. Van Herck, J. Wuttke 
+//
+//! @file      Samples/Crystal.h 
+//! @brief     Defines class Crystal.
+//
+// ************************************************************************** //
+
 #ifndef CRYSTAL_H_
 #define CRYSTAL_H_
-// ********************************************************************
-// * The BornAgain project                                            *
-// * Simulation of neutron and x-ray scattering at grazing incidence  *
-// *                                                                  *
-// * LICENSE AND DISCLAIMER                                           *
-// * Lorem ipsum dolor sit amet, consectetur adipiscing elit.  Mauris *
-// * eget quam orci. Quisque  porta  varius  dui,  quis  posuere nibh *
-// * mollis quis. Mauris commodo rhoncus porttitor.                   *
-// ********************************************************************
-//! @file   Crystal.h
-//! @brief  Definition of Crystal class
-//! @author Scientific Computing Group at FRM II
-//! @date   Jul 12, 2012
 
 #include "IClusteredParticles.h"
 #include "Particle.h"
 #include "Lattice.h"
 #include "LatticeBasis.h"
 
-//- -------------------------------------------------------------------
-//! @class Crystal
-//! @brief Definition of a crystal structure with a form factor as a basis
-//- -------------------------------------------------------------------
+//! A crystal structure with a form factor as a basis
+
 class Crystal : public IClusteredParticles
 {
 public:
@@ -58,5 +60,4 @@ private:
     double m_dw_factor;
 };
 
-
 #endif /* CRYSTAL_H_ */

Core/Samples/inc/DiffuseParticleInfo.h

+// ************************************************************************** //
+//                                                                           
+//  BornAgain: simulate and fit scattering at grazing incidence
+//
+//! @copyright Forschungszentrum Jülich GmbH 2013
+//             
+//  Homepage:  apps.jcns.fz-juelich.de/BornAgain
+//  License:   GNU General Public License v3 or higher (see COPYING)
+//
+//! @authors   Scientific Computing Group at MLZ Garching
+//! @authors   C. Durniak, G. Pospelov, W. Van Herck, J. Wuttke 
+//
+//! @file      Samples/DiffuseParticleInfo.h 
+//! @brief     Defines class DiffuseParticleInfo.
+//
+// ************************************************************************** //
+
 #ifndef DIFFUSEPARTICLEINFO_H_
 #define DIFFUSEPARTICLEINFO_H_
-// ********************************************************************
-// * The BornAgain project                                            *
-// * Simulation of neutron and x-ray scattering at grazing incidence  *
-// *                                                                  *
-// * LICENSE AND DISCLAIMER                                           *
-// * Lorem ipsum dolor sit amet, consectetur adipiscing elit.  Mauris *
-// * eget quam orci. Quisque  porta  varius  dui,  quis  posuere nibh *
-// * mollis quis. Mauris commodo rhoncus porttitor.                   *
-// ********************************************************************
-//! @file   DiffuseParticleInfo.h
-//! @brief  Definition of
-//! @author Scientific Computing Group at FRM II
-//! @date   Sep 4, 2012
 
 #include "ParticleInfo.h"
 
+//! ?
+
 class DiffuseParticleInfo: public ParticleInfo
 {
 public:
@@ -44,7 +50,6 @@ public:
 protected:
     double m_number_per_meso;
     double m_height_range;
-
 };
 
 #endif /* DIFFUSEPARTICLEINFO_H_ */

Core/Samples/inc/HomogeneousMaterial.h

+// ************************************************************************** //
+//                                                                           
+//  BornAgain: simulate and fit scattering at grazing incidence
+//
+//! @copyright Forschungszentrum Jülich GmbH 2013
+//             
+//  Homepage:  apps.jcns.fz-juelich.de/BornAgain
+//  License:   GNU General Public License v3 or higher (see COPYING)
+//
+//! @authors   Scientific Computing Group at MLZ Garching
+//! @authors   C. Durniak, G. Pospelov, W. Van Herck, J. Wuttke 
+//
+//! @file      Samples/HomogeneousMaterial.h 
+//! @brief     Defines class HomogeneousMaterial.
+//
+// ************************************************************************** //
+
 #ifndef HOMOGENEOUSMATERIAL_H
 #define HOMOGENEOUSMATERIAL_H
-// ********************************************************************
-// * The BornAgain project                                            *
-// * Simulation of neutron and x-ray scattering at grazing incidence  *
-// *                                                                  *
-// * LICENSE AND DISCLAIMER                                           *
-// * Lorem ipsum dolor sit amet, consectetur adipiscing elit.  Mauris *
-// * eget quam orci. Quisque  porta  varius  dui,  quis  posuere nibh *
-// * mollis quis. Mauris commodo rhoncus porttitor.                   *
-// ********************************************************************
-//! @file   HomogeneousMaterial.h
-//! @brief  Definition of HomogeneousMaterial class
-//! @author Scientific Computing Group at FRM II
-//! @date   01.04.2012
 
 #include "IMaterial.h"
 #include "Types.h"
 
+//! A homogeneous material with refraction index
 
-//- -------------------------------------------------------------------
-/// @class HomogeneousMaterial
-/// @brief Definition of homogeneous material with refraction index
-//- -------------------------------------------------------------------
 class HomogeneousMaterial : public IMaterial
 {
 public:

Core/Samples/inc/IClusteredParticles.h

+// ************************************************************************** //
+//                                                                           
+//  BornAgain: simulate and fit scattering at grazing incidence
+//
+//! @copyright Forschungszentrum Jülich GmbH 2013
+//             
+//  Homepage:  apps.jcns.fz-juelich.de/BornAgain
+//  License:   GNU General Public License v3 or higher (see COPYING)
+//
+//! @authors   Scientific Computing Group at MLZ Garching
+//! @authors   C. Durniak, G. Pospelov, W. Van Herck, J. Wuttke 
+//
+//! @file      Samples/IClusteredParticles.h 
+//! @brief     Defines class IClusteredParticles.
+//
+// ************************************************************************** //
+
 #ifndef ICLUSTEREDPARTICLES_H_
 #define ICLUSTEREDPARTICLES_H_
-// ********************************************************************
-// * The BornAgain project                                            *
-// * Simulation of neutron and x-ray scattering at grazing incidence  *
-// *                                                                  *
-// * LICENSE AND DISCLAIMER                                           *
-// * Lorem ipsum dolor sit amet, consectetur adipiscing elit.  Mauris *
-// * eget quam orci. Quisque  porta  varius  dui,  quis  posuere nibh *
-// * mollis quis. Mauris commodo rhoncus porttitor.                   *
-// ********************************************************************
-//! @file   IClusteredParticles.h
-//! @brief  Definition of IClusteredParticles interface
-//! @author Scientific Computing Group at FRM II
-//! @date   Jul 12, 2012
 
 #include "IFormFactor.h"
 #include "ICompositeSample.h"
@@ -21,10 +25,8 @@
 #include "Exceptions.h"
 #include "DiffuseParticleInfo.h"
 
-//- -------------------------------------------------------------------
-//! @class IClusteredParticles
-//! @brief Definition of an interface, representing an ordered assembly of particles
-//- -------------------------------------------------------------------
+//! An ordered assembly of particles
+
 class IClusteredParticles : public ICompositeSample
 {
 public:
@@ -61,5 +63,4 @@ public:
 
 };
 
-
 #endif /* ICLUSTEREDNANOPARTICLES_H_ */

Core/Samples/inc/ICompositeIterator.h

+// ************************************************************************** //
+//                                                                           
+//  BornAgain: simulate and fit scattering at grazing incidence
+//
+//! @copyright Forschungszentrum Jülich GmbH 2013
+//             
+//  Homepage:  apps.jcns.fz-juelich.de/BornAgain
+//  License:   GNU General Public License v3 or higher (see COPYING)
+//
+//! @authors   Scientific Computing Group at MLZ Garching
+//! @authors   C. Durniak, G. Pospelov, W. Van Herck, J. Wuttke 
+//
+//! @file      Samples/ICompositeIterator.h 
+//! @brief     Defines class ICompositeIterator.
+//
+// ************************************************************************** //
+
 #ifndef ICOMPOSITEITERATOR_H
 #define ICOMPOSITEITERATOR_H
-// ********************************************************************
-// * The BornAgain project                                            *
-// * Simulation of neutron and x-ray scattering at grazing incidence  *
-// *                                                                  *
-// * LICENSE AND DISCLAIMER                                           *
-// * Lorem ipsum dolor sit amet, consectetur adipiscing elit.  Mauris *
-// * eget quam orci. Quisque  porta  varius  dui,  quis  posuere nibh *
-// * mollis quis. Mauris commodo rhoncus porttitor.                   *
-// ********************************************************************
-//! @file   ICompositeIterator.h
-//! @brief  Definition of ICompositeIterator class and surroundings
-//! @author Scientific Computing Group at FRM II
-//! @date   18.06.2012
 
 #include "ISample.h"
 #include "ICompositeSample.h"
@@ -20,11 +24,8 @@
 #include <stack>
 #include <list>
 
+//! Holds state of IComositeSample iterator
 
-//- -------------------------------------------------------------------
-//! @class MementoState
-//! @brief Definition of MementoState to hold state of IComositeSample iterator
-//- -------------------------------------------------------------------
 class MementoState
 {
 public:
@@ -59,11 +60,8 @@ private:
     MementoState();
 };
 
+//! Holds state of IComositeSample iterator
 
-//- -------------------------------------------------------------------
-//! @class MementoIterator
-//! @brief Definition of MementoIterator to hold state of IComositeSample iterator
-//- -------------------------------------------------------------------
 class MementoIterator
 {
 public:
@@ -82,8 +80,6 @@ protected:
     std::stack<MementoState > m_state_stack;
 };
 
-
-//- -------------------------------------------------------------------
 //! @class ICompositeIterator
 //! @brief Definition of ICompositeIterator to walk through ISample tree
 //! of objects inside ICompositeSample object.
@@ -95,7 +91,7 @@ protected:
 //!        ISample *child = it.get_current();
 //!        it.next();
 //!     }
-//- -------------------------------------------------------------------
+
 class ICompositeIterator
 {
 public:
@@ -113,6 +109,4 @@ protected:
     bool m_done;
 };
 
-
-
 #endif // ICOMPOSITEITERATOR_H

Core/Samples/inc/ICompositeSample.h

+// ************************************************************************** //
+//                                                                           
+//  BornAgain: simulate and fit scattering at grazing incidence
+//
+//! @copyright Forschungszentrum Jülich GmbH 2013
+//             
+//  Homepage:  apps.jcns.fz-juelich.de/BornAgain
+//  License:   GNU General Public License v3 or higher (see COPYING)
+//
+//! @authors   Scientific Computing Group at MLZ Garching
+//! @authors   C. Durniak, G. Pospelov, W. Van Herck, J. Wuttke 
+//
+//! @file      Samples/ICompositeSample.h 
+//! @brief     Defines class ICompositeSample.
+//
+// ************************************************************************** //
+
 #ifndef ICOMPOSITESAMPLE_H
 #define ICOMPOSITESAMPLE_H
-// ********************************************************************
-// * The BornAgain project                                            *
-// * Simulation of neutron and x-ray scattering at grazing incidence  *
-// *                                                                  *
-// * LICENSE AND DISCLAIMER                                           *
-// * Lorem ipsum dolor sit amet, consectetur adipiscing elit.  Mauris *
-// * eget quam orci. Quisque  porta  varius  dui,  quis  posuere nibh *
-// * mollis quis. Mauris commodo rhoncus porttitor.                   *
-// ********************************************************************
-//! @file   ICompositeSample
-//! @brief  Definition of ICompositeSample class
-//! @author Scientific Computing Group at FRM II
-//! @date   16.06.2012
 
 #include "ISample.h"
 #include <list>
 
-
 class ICompositeIterator;
 
-//- -------------------------------------------------------------------
-//! @class ICompositeSample
-//! @brief Definition of ICompositeSample which compose ISample objects
-//! into tree structure
-//- -------------------------------------------------------------------
+//! Compose ISample objects into tree structure
+
 class ICompositeSample : public ISample
 {
 public: