config constructor now deletes options proberly. shperical harmonics is now in...

config constructor now deletes options proberly. shperical harmonics is now in toolboxes. icru is now in problems.

code/include/common/optionstructure.h

@@ -22,7 +22,7 @@ class OptionBase
     std::vector<std::string> _value; /*! @brief: String name of the option */
 
   public:
-    OptionBase(){};
+    OptionBase() {}
     virtual ~OptionBase() = 0;
 
     virtual std::string SetValue( std::vector<std::string> value ); /*! @brief: Set string name of the option */
@@ -45,7 +45,7 @@ class OptionDouble : public OptionBase
   public:
     OptionDouble( std::string option_field_name, double& option_field, double default_value );
 
-    ~OptionDouble() override{};
+    ~OptionDouble() override {}
 
     std::string SetValue( std::vector<std::string> option_value ) override;
 
@@ -61,7 +61,7 @@ class OptionString : public OptionBase
   public:
     OptionString( std::string option_field_name, std::string& option_field, std::string default_value );
 
-    ~OptionString() override{};
+    ~OptionString() override {}
 
     std::string SetValue( std::vector<std::string> option_value ) override;
 
@@ -77,7 +77,7 @@ class OptionInt : public OptionBase
   public:
     OptionInt( std::string option_field_name, int& option_field, int default_value );
 
-    ~OptionInt() override{};
+    ~OptionInt() override {}
 
     std::string SetValue( std::vector<std::string> option_value ) override;
 
@@ -93,7 +93,7 @@ class OptionULong : public OptionBase
   public:
     OptionULong( std::string option_field_name, unsigned long& option_field, unsigned long default_value );
 
-    ~OptionULong() override{};
+    ~OptionULong() override {}
 
     std::string SetValue( std::vector<std::string> option_value ) override;
 
@@ -109,7 +109,7 @@ class OptionUShort : public OptionBase
   public:
     OptionUShort( std::string option_field_name, unsigned short& option_field, unsigned short default_value );
 
-    ~OptionUShort() override{};
+    ~OptionUShort() override {}
 
     std::string SetValue( std::vector<std::string> option_value ) override;
 
@@ -125,7 +125,7 @@ class OptionLong : public OptionBase
   public:
     OptionLong( std::string option_field_name, long& option_field, long default_value );
 
-    ~OptionLong() override{};
+    ~OptionLong() override {}
 
     std::string SetValue( std::vector<std::string> option_value ) override;
 
@@ -141,7 +141,7 @@ class OptionBool : public OptionBase
   public:
     OptionBool( std::string option_field_name, bool& option_field, bool default_value );
 
-    ~OptionBool() override{};
+    ~OptionBool() override {}
 
     std::string SetValue( std::vector<std::string> option_value ) override;
 
@@ -157,7 +157,7 @@ class OptionStringList : public OptionBase
   public:
     OptionStringList( std::string option_field_name, unsigned short& list_size, std::vector<std::string>& option_field );
 
-    ~OptionStringList() override{};
+    ~OptionStringList() override {}
 
     std::string SetValue( std::vector<std::string> option_value ) override;
 

code/include/icru.h → code/include/problems/icru.h

@@ -5,6 +5,7 @@
  * Disclaimer: This is copied from the code distributed with the ICRU 77 report
  * Link: https://icru.org/home/reports/elastic-scattering-of-electrons-and-positrons-icru-report-77
  */
+
 #ifndef ICRU_H
 #define ICRU_H
 

code/include/solvers/csdsnsolver.h

 #ifndef CSDSNSOLVER_H
 #define CSDSNSOLVER_H
 
-#include "icru.h"
 #include "solvers/snsolver.h"
 
 class CSDSNSolver : public SNSolver

code/include/solvers/csdsnsolverfp.h

 #ifndef CSDSNSOLVERFP_H
 #define CSDSNSOLVERFP_H
 
-#include "icru.h"
 #include "solvers/snsolver.h"
 
 class Physics;
@@ -22,9 +21,9 @@ class CSDSNSolverFP : public SNSolver
     Matrix _IL; /*!  @brief Laplace Beltrami Matrix */
 
     double _alpha; /*!  @brief  Coefficient of GFP operators (see Olbrant 2010, eq. (8)*/
-    double _beta; /*!  @brief  Coefficient of GFP operators (see Olbrant 2010, eq. (8)*/
+    double _beta;  /*!  @brief  Coefficient of GFP operators (see Olbrant 2010, eq. (8)*/
 
-    Matrix _xi;  /*!  @brief matrix of transport coefficients */
+    Matrix _xi; /*!  @brief matrix of transport coefficients */
 
     bool _RT; /*!  @brief radiotherapy application (on/off), if true use crosssections + stopping powers from database  */
 

code/include/solvers/csdsnsolvernotrafo.h

 #ifndef CSDSNSOLVERNOTRAFO_H
 #define CSDSNSOLVERNOTRAFO_H
 
-#include "icru.h"
 #include "solvers/snsolver.h"
 
 class Physics;

code/include/solvers/csdsolvertrafofp.h

 #ifndef CSDSOLVERTRAFOFP_H
 #define CSDSOLVERTRAFOFP_H
 
-#include "icru.h"
 #include "solvers/snsolver.h"
 
 class Physics;
@@ -21,15 +20,16 @@ class CSDSolverTrafoFP : public SNSolver
     Matrix _L;  /*!  @brief Laplace Beltrami Matrix */
     Matrix _IL; /*!  @brief Laplace Beltrami Matrix */
 
-    double _alpha; /*!  @brief  Coefficient of GFP operators (see Olbrant 2010, Appendix B)*/
+    double _alpha;  /*!  @brief  Coefficient of GFP operators (see Olbrant 2010, Appendix B)*/
     double _alpha2; /*!  @brief  Coefficient of GFP operators (see Olbrant 2010, Appendix B)*/
-    double _beta; /*!  @brief  Coefficient of GFP operators (see Olbrant 2010, Appendix B)*/
+    double _beta;   /*!  @brief  Coefficient of GFP operators (see Olbrant 2010, Appendix B)*/
 
-    Matrix _xi;  /*!  @brief matrix of transport coefficients */
+    Matrix _xi; /*!  @brief matrix of transport coefficients */
     Vector _xi1;
     Vector _xi2;
-    
-    unsigned _FPMethod; /*!  @brief Encodes different ways of computing coefficients alpha, alpha2 & beta, _FPMethod == 1, 2 ,3 stand for methods with increasing accuracy (see Olbrant 2010, Appendix B)*/
+
+    unsigned _FPMethod; /*!  @brief Encodes different ways of computing coefficients alpha, alpha2 & beta, _FPMethod == 1, 2 ,3 stand for methods with
+                           increasing accuracy (see Olbrant 2010, Appendix B)*/
 
     bool _RT; /*!  @brief radiotherapy application (on/off), if true use crosssections + stopping powers from database  */
 

code/include/solvers/csdsolvertrafofp2d.h

 #ifndef CSDSOLVERTRAFOFP2D_H
 #define CSDSOLVERTRAFOFP2D_H
 
-#include "icru.h"
 #include "solvers/snsolver.h"
 
 class Physics;

code/include/solvers/csdsolvertrafofpsh2d.h

@@ -8,12 +8,11 @@
 #include "common/config.h"
 #include "common/io.h"
 #include "fluxes/numericalflux.h"
-#include "icru.h"
 #include "kernels/scatteringkernelbase.h"
 #include "problems/problembase.h"
 #include "quadratures/quadraturebase.h"
 #include "solvers/snsolver.h"
-#include "sphericalharmonics.h"
+#include "toolboxes/sphericalharmonics.h"
 
 class Physics;
 

code/input/example_csd_1d.cfg

+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%  Checkerboard Benchmarking File SN   %
+%  Author <Jonas Kusch>     		   %
+%  Date   01.12.2020                   %
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+
 OUTPUT_DIR = ../result
 OUTPUT_FILE = example_csd_1d_10MeV_fine
 LOG_DIR = ../result/logs

code/src/common/config.cpp

@@ -16,7 +16,6 @@
 #include "spdlog/sinks/basic_file_sink.h"
 #include "spdlog/sinks/stdout_sinks.h"
 #include "spdlog/spdlog.h"
-#include <cassert>
 #include <filesystem>
 #include <fstream>
 #include <mpi.h>
@@ -74,6 +73,12 @@ Config::Config( string case_filename ) {
 
 Config::~Config( void ) {
     // Delete all introduced arrays!
+
+    // delete _option map values proberly
+    for( auto const& x : _optionMap ) {
+        delete x.second;
+        _optionMap.erase( x.first );
+    }
 }
 
 // ---- Add Options ----

code/src/main.cpp

+/*! @file: main.cpp
+ *  @brief: Main method to call the KiT-RT solver suite
+ *  @author: J. Kusch, S. Schotthöfer, P. Stammer, J. Wolters, T. Xiao
+ *  @version: 0.1
+ */
+
 #include <Python.h>
 #include <mpi.h>
+#include <string>
 
+#include "common/config.h"
 #include "common/io.h"
 #include "solvers/solverbase.h"
 
-#include "common/config.h"
-
-#include "solvers/sphericalharmonics.h"
-#include <fstream>
-#include <iostream>
-#include <string>
-
-// ----
-#include "optimizers/optimizerbase.h"
-#include "quadratures/qgausslegendretensorized.h"
-#include "quadratures/qmontecarlo.h"
-#include "solvers/sphericalharmonics.h"
-
-double testFunc( double my, double phi ) { return my * my + phi; }
-
-double testFunc2( double x, double y, double z ) { return x + y + z; }
-
 int main( int argc, char** argv ) {
     MPI_Init( &argc, &argv );
     wchar_t* program = Py_DecodeLocale( argv[0], NULL );

code/src/icru.cpp → code/src/problems/icru.cpp

-#include "icru.h"
+#include "problems/icru.h"
 
 void ICRU::angdcs( unsigned ncor, double e, std::vector<double>& dxse, std::vector<double>& dxsi, std::vector<double>& dxs ) {
 

code/src/solvers/csdsnsolver.cpp

@@ -3,6 +3,7 @@
 #include "common/io.h"
 #include "fluxes/numericalflux.h"
 #include "kernels/scatteringkernelbase.h"
+#include "problems/icru.h"
 #include "problems/problembase.h"
 
 // externals

code/src/solvers/csdsnsolverfp.cpp

@@ -4,6 +4,7 @@
 #include "common/mesh.h"
 #include "fluxes/numericalflux.h"
 #include "kernels/scatteringkernelbase.h"
+#include "problems/icru.h"
 #include "problems/problembase.h"
 #include "quadratures/quadraturebase.h"
 

code/src/solvers/csdsnsolvernotrafo.cpp

@@ -3,6 +3,7 @@
 #include "common/io.h"
 #include "fluxes/numericalflux.h"
 #include "kernels/scatteringkernelbase.h"
+#include "problems/icru.h"
 #include "problems/problembase.h"
 
 // externals

code/src/solvers/csdsolvertrafofp.cpp

@@ -3,6 +3,7 @@
 #include "common/io.h"
 #include "fluxes/numericalflux.h"
 #include "kernels/scatteringkernelbase.h"
+#include "problems/icru.h"
 #include "problems/problembase.h"
 #include "quadratures/quadraturebase.h"
 

code/src/solvers/csdsolvertrafofp2d.cpp

@@ -3,6 +3,7 @@
 #include "common/io.h"
 #include "fluxes/numericalflux.h"
 #include "kernels/scatteringkernelbase.h"
+#include "problems/icru.h"
 #include "problems/problembase.h"
 #include "quadratures/qproduct.h"
 #include "quadratures/quadraturebase.h"

code/src/solvers/csdsolvertrafofpsh2d.cpp

 #include "solvers/csdsolvertrafofpsh2d.h"
+#include "problems/icru.h"
 
 CSDSolverTrafoFPSH2D::CSDSolverTrafoFPSH2D( Config* settings ) : SNSolver( settings ) {
     _dose = std::vector<double>( _settings->GetNCells(), 0.0 );

code/src/solvers/mnsolver.cpp

@@ -7,8 +7,8 @@
 #include "optimizers/optimizerbase.h"
 #include "problems/problembase.h"
 #include "quadratures/quadraturebase.h"
-#include "solvers/sphericalharmonics.h"
 #include "toolboxes/errormessages.h"
+#include "toolboxes/sphericalharmonics.h"
 #include "toolboxes/textprocessingtoolbox.h"
 
 // externals