Added comments to problem files

code/include/problems/checkerboard.h

@@ -6,13 +6,13 @@
 class Checkerboard_SN : public ProblemBase
 {
   private:
-    Vector _scatteringXS;
-    Vector _totalXS;
+    Vector _scatteringXS;     /*! @brief Vector of scattering crosssections */
+    Vector _totalXS;      /*! @brief Vector of total crosssections */
 
     Checkerboard_SN() = delete;
 
-    bool isAbsorption( const Vector& pos ) const;
-    bool isSource( const Vector& pos ) const;
+    bool isAbsorption( const Vector& pos ) const; /*! @return True if pos is in absorption region, False otherwise */
+    bool isSource( const Vector& pos ) const; /*! @return True if pos is in source region, False otherwise */
 
   public:
     Checkerboard_SN( Config* settings, Mesh* mesh );
@@ -27,13 +27,22 @@ class Checkerboard_SN : public ProblemBase
 class Checkerboard_PN : public ProblemBase
 {
   private:
-    Vector _scatteringXS;
-    Vector _totalXS;
+    Vector _scatteringXS;     /*! @brief Vector of scattering crosssections */
+    Vector _totalXS;      /*! @brief Vector of total crosssections */
 
     Checkerboard_PN() = delete;
 
-    bool isAbsorption( const Vector& pos ) const;
-    bool isSource( const Vector& pos ) const;
+    bool isAbsorption( const Vector& pos ) const; /*! @return True if pos is in absorption region, False otherwise */
+    bool isSource( const Vector& pos ) const; /*! @return True if pos is in source region, False otherwise */
+
+    /**
+     * @brief Gets the global index for given order l of Legendre polynomials and given
+     *        order k of Legendre functions.
+     *        Note: This is code doubling from PNSolver::GlobalIndex
+     * @param l : order of Legendre polynomial
+     * @param k : order of Legendre function
+     * @returns global index
+     */
     int GlobalIndex( int l, int k ) const;
 
   public:

code/include/problems/problembase.h

@@ -16,8 +16,8 @@ class ProblemBase
     Mesh* _mesh;
     Physics* _physics;
 
-    std::vector<double> _density;
-    std::vector<double> _stoppingPower;
+    std::vector<double> _density; /*! @brief: vector with patient densities */
+    std::vector<double> _stoppingPower; /*! @brief: vector with stopping powers*/
 
     ProblemBase() = delete;
 
@@ -37,6 +37,7 @@ class ProblemBase
      * @param density is vector with patient densities (at different spatial cells)
      */
     virtual VectorVector GetTotalXS( const Vector& energies ) = 0;
+    
     /**
      * @brief GetTotalXSE gives back vector of total cross sections for
      *        energies in vector energy

code/src/problems/checkerboard.cpp

@@ -2,10 +2,16 @@
 #include "common/config.h"
 #include "common/mesh.h"
 
+// ---- Checkerboard Sn ----
+//Constructor for Ckeckerboard case with Sn
 Checkerboard_SN::Checkerboard_SN( Config* settings, Mesh* mesh ) : ProblemBase( settings, mesh ) {
     _physics      = nullptr;
+
+    // Initialise crosssections to 1
     _scatteringXS = Vector( _mesh->GetNumCells(), 1.0 );
     _totalXS      = Vector( _mesh->GetNumCells(), 1.0 );
+
+    // For absorption cells: set scattering XS to 0 and absorption to 10
     auto cellMids = _mesh->GetCellMidPoints();
     for( unsigned j = 0; j < cellMids.size(); ++j ) {
         if( isAbsorption( cellMids[j] ) ) {
@@ -36,6 +42,7 @@ VectorVector Checkerboard_SN::SetupIC() {
 }
 
 bool Checkerboard_SN::isAbsorption( const Vector& pos ) const {
+    // Check whether pos is inside absorbing squares
     std::vector<double> lbounds{ 1, 2, 3, 4, 5 };
     std::vector<double> ubounds{ 2, 3, 4, 5, 6 };
     for( unsigned k = 0; k < lbounds.size(); ++k ) {
@@ -50,6 +57,7 @@ bool Checkerboard_SN::isAbsorption( const Vector& pos ) const {
 }
 
 bool Checkerboard_SN::isSource( const Vector& pos ) const {
+    // Check whether pos is part of source region
     if( pos[0] >= 3 && pos[0] <= 4 && pos[1] >= 3 && pos[1] <= 4 )
         return true;
     else
@@ -58,10 +66,16 @@ bool Checkerboard_SN::isSource( const Vector& pos ) const {
 
 ////////////////////////////////////////////////////////////////////////////////////////////////////
 
+// ---- Checkerboard Pn ----
+//Constructor for checkerboard case with Pn
 Checkerboard_PN::Checkerboard_PN( Config* settings, Mesh* mesh ) : ProblemBase( settings, mesh ) {
     _physics      = nullptr;
+
+    //Initialise crosssections = 1 (scattering)
     _scatteringXS = Vector( _mesh->GetNumCells(), 1.0 );
     _totalXS      = Vector( _mesh->GetNumCells(), 1.0 );
+
+    // for absorption regions change crosssections to all absorption
     auto cellMids = _mesh->GetCellMidPoints();
     for( unsigned j = 0; j < cellMids.size(); ++j ) {
         if( isAbsorption( cellMids[j] ) ) {
@@ -93,6 +107,7 @@ VectorVector Checkerboard_PN::SetupIC() {
 }
 
 bool Checkerboard_PN::isAbsorption( const Vector& pos ) const {
+    // Check whether pos is in absorption region
     std::vector<double> lbounds{ 1, 2, 3, 4, 5 };
     std::vector<double> ubounds{ 2, 3, 4, 5, 6 };
     for( unsigned k = 0; k < lbounds.size(); ++k ) {
@@ -107,6 +122,7 @@ bool Checkerboard_PN::isAbsorption( const Vector& pos ) const {
 }
 
 bool Checkerboard_PN::isSource( const Vector& pos ) const {
+    // Check whether pos is in source region
     if( pos[0] >= 3 && pos[0] <= 4 && pos[1] >= 3 && pos[1] <= 4 )
         return true;
     else

code/src/problems/electronrt.cpp

@@ -2,6 +2,7 @@
 #include "common/config.h"
 #include "common/mesh.h"
 
+//Constructor: Legacy code, physics class is no longer used
 ElectronRT::ElectronRT( Config* settings, Mesh* mesh ) : ProblemBase( settings, mesh ) {
     _physics = new Physics( settings->GetHydrogenFile(), settings->GetOxygenFile(), "../input/stopping_power.txt" );
 }
@@ -9,37 +10,46 @@ ElectronRT::ElectronRT( Config* settings, Mesh* mesh ) : ProblemBase( settings,
 ElectronRT::~ElectronRT() { delete _physics; }
 
 VectorVector ElectronRT::GetScatteringXS( const Vector& energies ) {
-    // @TODO
+    // @TODO 
+    // Specified in subclasses 
     return VectorVector( energies.size(), Vector( _mesh->GetNumCells(), 0.0 ) );
 }
 
 VectorVector ElectronRT::GetTotalXS( const Vector& energies ) {
-    // @TODO
+    // @TODO 
+    // Specified in subclasses 
     return VectorVector( energies.size(), Vector( _mesh->GetNumCells(), 0.0 ) );
 }
 
 std::vector<Matrix> ElectronRT::GetScatteringXSE( const Vector& energies, const Matrix& angles ) {
-    // @TODO
+    // @TODO 
+    // Specified in subclasses 
     return _physics->GetScatteringXS( energies, angles );
 }
 
 Vector ElectronRT::GetTotalXSE( const Vector& energies ) {
-    // @TODO
+    // @TODO 
+    // Specified in subclasses 
     return _physics->GetTotalXSE( energies );
 }
 
 std::vector<VectorVector> ElectronRT::GetExternalSource( const Vector& energies ) {
-    // @TODO
+    // @TODO 
+    // Specified in subclasses 
     return std::vector<VectorVector>( energies.size(), std::vector<Vector>( _mesh->GetNumCells(), Vector( _settings->GetNQuadPoints(), 0.0 ) ) );
 }
 
 VectorVector ElectronRT::SetupIC() {
-    // @TODO
+    // @TODO 
+    // Specified in subclasses 
     return VectorVector( _mesh->GetNumCells(), Vector( _settings->GetNQuadPoints(), 1e-10 ) );
 }
 
 void ElectronRT::LoadXSH20( std::string fileSigmaS, std::string fileSigmaT ) {
-    // @TODO
+    // @TODO 
+    // Specified in subclasses 
 }
 
+
+// Default densities = 1, for patient files this is overwritten with "real" densities
 std::vector<double> ElectronRT::GetDensity( const VectorVector& cellMidPoints ) { return std::vector<double>( cellMidPoints.size(), 1.0 ); }

code/src/problems/musclebonelung.cpp

@@ -22,11 +22,12 @@ VectorVector MuscleBoneLung::SetupIC() {
 }
 
 std::vector<double>  MuscleBoneLung::GetDensity( const VectorVector& cellMidPoints ) { 
-    std::cout<<"Length of mesh "<< cellMidPoints.size() << std::endl;
     std::vector<double> densities ( 167, 1.04 ); //muscle layer
-    std::vector<double> bone( 167, 1.85  );
-    std::vector<double> lung ( 665, 0.3 ); //maybe this is just the lung tissue and after that there should be air?
+    std::vector<double> bone( 167, 1.85  ); // bone layer
+    std::vector<double> lung ( 665, 0.3 ); // lung layer (maybe this is just the lung tissue and after that there should be air?)
+
+    //Concatenate layers
     densities.insert(densities.end(),bone.begin(),bone.end());
     densities.insert(densities.end(),lung.begin(),lung.end());
-    std::cout<<"Length of densities "<< densities.size() << std::endl;
+    
     return densities; }

code/src/problems/problembase.cpp

@@ -18,6 +18,8 @@ ProblemBase::~ProblemBase() {}
 
 ProblemBase* ProblemBase::Create( Config* settings, Mesh* mesh ) {
     auto name = settings->GetProblemName();
+    
+    // Choose problem type
     switch( name ) {
         case PROBLEM_LineSource: {
             if( settings->GetSolverName() == PN_SOLVER || settings->GetSolverName() == MN_SOLVER )
@@ -42,10 +44,13 @@ ProblemBase* ProblemBase::Create( Config* settings, Mesh* mesh ) {
     }
 }
 
+// Default densities = 1
 std::vector<double> ProblemBase::GetDensity( const VectorVector& cellMidPoints ) { return std::vector<double>( cellMidPoints.size(), 1.0 ); }
 
+// Legacy code: Scattering crossection loaded from database ENDF with physics class -> later overwritten with ICRU data
 VectorVector ProblemBase::GetScatteringXSE( const Vector& energies, const Vector& angles ) { return _physics->GetScatteringXS( energies, angles ); }
 
+// Stopping powers from phyics class or default = -1
 Vector ProblemBase::GetStoppingPower( const Vector& energies ) {
     if( _physics ) {
         return _physics->GetStoppingPower( energies );

code/src/problems/waterphantom.cpp

@@ -15,4 +15,5 @@ VectorVector WaterPhantom::SetupIC() {
     return psi;
 }
 
+// Density of water = 1 everywhere
 std::vector<double> WaterPhantom::GetDensity( const VectorVector& cellMidPoints ) { return std::vector<double>( cellMidPoints.size(), 1.0 ); }