started merging master

.gitignore

@@ -321,7 +321,7 @@ TSWLatexianTemp*
 
 ### Python ###
 # Byte-compiled / optimized / DLL files
-__pycache__/
+__pycache__/*
 *.py[cod]
 *$py.class
 
@@ -387,6 +387,9 @@ target/
 # pyenv
 .python-version
 
+# pycharm 
+.idea/
+
 # pipenv
 #   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
 #   However, in case of collaboration, if having platform-specific dependencies or dependencies
@@ -432,6 +435,9 @@ dmypy.json
 
 # Qt Creator autogenerated files
 
+# other
+*.cflags
+*.cxxflags
 
 # A listing of all the files included in the project
 *.files

.gitlab-ci.yml

 image: rtsn/test:latest
 
 stages:
-  - build
   - unit_tests
 
-build:
-  stage: build
-  script:
-    - git submodule update --init --recursive
-    - cd code/build/debug
-    - cmake -G Ninja -DCMAKE_BUILD_TYPE=Debug -DBUILD_TESTING=True ../../
-    - ninja
-  timeout: 2h
-  only:
-    refs:
-      - master
-      - merge_requests
-    changes:
-      - "code/include/**/*"
-      - "code/tests/**/*"
-      - "code/src/**/*"
-      - "code/CMakeLists.txt"
-      - "scripts/Dockerfile"
-      - ".gitmodules"
-      
 unit_tests:
   stage: unit_tests
   script:
     - git submodule update --init --recursive
     - cd code/build/release
-    - cmake -G Ninja -DCMAKE_BUILD_TYPE=Release -DBUILD_TESTING=True ../../
+    - cmake -G Ninja -DCMAKE_BUILD_TYPE=Debug ../../
     - ninja
-    - cd ../../bin
-    - ./unit_tests
-  timeout: 2h
-  only:
-    refs:
-      - master
-      - merge_requests
-    changes:
-      - "code/include/**/*"
-      - "code/tests/**/*"
-      - "code/src/**/*"
-      - "code/CMakeLists.txt"
-      - "scripts/Dockerfile"
-      - ".gitmodules"
+    - OMP_NUM_THREADS=1 ./unit_tests -r junit > unit_tests_report.xml
+    - gcovr -e ../../ext/ -e ../../tests/ -r ../../
+  artifacts:
+    when: always
+    paths:
+      - code/build/release/unit_tests_report.xml
+    reports:
+      junit: code/build/release/unit_tests_report.xml
+  timeout: 4h
+  rules:
+    - if: $CI_PIPELINE_SOURCE == "merge_request_event" || $CI_COMMIT_BRANCH == "master" || $CI_COMMIT_BRANCH == "develop"
+      changes:
+        - "code/include/**/*"
+        - "code/tests/**/*"
+        - "code/src/**/*"
+        - "code/CMakeLists.txt"
+        - "scripts/Dockerfile"
+        - ".gitmodules"
+    - if: $CI_PIPELINE_SOURCE == "web"

README.md

-# RTSN - an HPC Radio Therapy $`S_n`$ framework
+[![pipeline status](https://git.scc.kit.edu/rtsn/rtsn/badges/master/pipeline.svg)](https://git.scc.kit.edu/rtsn/rtsn/-/commits/master) [![coverage report](https://git.scc.kit.edu/rtsn/rtsn/badges/master/coverage.svg)](https://git.scc.kit.edu/rtsn/rtsn/-/commits/master)
+
+# KiT-RT - an HPC Radio Therapy $`S_n`$ framework
 TBD 
-## What RTSN is capable of
+## What KiT-RT is capable of
 ### Theory
 TBD
 ### Examples
@@ -52,17 +54,17 @@ The resulting executable will automatically be placed in the `code/bin` folder.
 
 ## Run
 ### Local
-Execute the compiled binary and hand over a valid *TOML*-styled config file.
+Execute the compiled binary from the `bin` folder and hand over a valid *TOML*-styled config file.
 Example from inside the `code` directory:
 
 ```bash
-./bin/RTSN input/example.cfg
+./KiT-RT ../input/example.cfg
 ```
 
 In order to run the code in parallel execute:
 
 ```bash
-OMP_NUM_THREADS=N mpirun -np J ./bin/RTSN input/example.cfg
+OMP_NUM_THREADS=N mpirun -np J ./KiT-RT ../input/example.cfg
 ```
 
 with `N` equal to the number of shared memory threads and `J` equal to the number of distrubuted memory threads.
@@ -86,8 +88,8 @@ rm -r VTK-8.2.0 VTK-build
 Example for build and run on bwUniCluster:
 Get the code
 ```bash
-git clone https://git.scc.kit.edu/rtsn/rtsn.git
-cd rtsn/
+git clone https://git.scc.kit.edu/rtsn/rtsn.git KiT-RT
+cd KiT-RT/
 git submodule init
 git submodule update
 ```
@@ -109,13 +111,13 @@ make -j
 ---
 
 ## Tests
-In order to also compile the unit tests, add `-DBUILD_TESTING=True` to the cmake command, e.g.:
+After compiling the framework as described above just run:
 
 ```bash
-cmake -DCMAKE_BUILD_TYPE=Release -DBUILD_TESTING=True ../../
+make test
 ```
 
-The resulting `unit_tests` executable will also be placed in `/bin`.
+The `unit_tests` executable will also be placed in in the build folder.
 
 ## Continuous Integration (CI)
 Every commit on the master branch will trigger a build test and unit tests.
@@ -145,13 +147,13 @@ This last step requires a preceeding `docker login`. Ask Jannick for login crede
 ## Code structure
 **WARNING: is not created automatically - might be out of date!**
 Reverse engineered plantuml diagram of the current code structure: 
-![Can't load image](doc/rtsn.svg "UML diagram")
+![Can't load image](doc/KiT-RT.svg "UML diagram")
 <br/><br/>
 Was created using [hpp2plantuml](https://github.com/thibaultmarin/hpp2plantuml) and [plantuml](https://plantuml.com/), e.g.:
 ```bash
 cd doc 
-hpp2plantuml -i "../code/include/*.h" -i "../code/include/*/*.h" -o rtsn.puml
-plantuml rtsn.puml -tsvg
+hpp2plantuml -i "../code/include/*.h" -i "../code/include/*/*.h" -o KiT-RT.puml
+plantuml KiT-RT.puml -tsvg
 ```
 
 ---

code/CMakeLists.txt

 cmake_minimum_required( VERSION 3.12.4 )
-project( RTSN VERSION 0.1.0 LANGUAGES CXX )
+project( KiT-RT VERSION 0.1.0 LANGUAGES CXX )
+
+
+### COMPILER ####################################
 set( CMAKE_CXX_STANDARD 17 )
 set( CMAKE_CXX_STANDARD_REQUIRED ON )
+set( KITRT_RELEASE_OPTIONS -march=native -w )
+set( KITRT_RELWITHDEBINFO_OPTIONS -march=native -pg -no-pie )
+set( KITRT_DEBUG_OPTIONS -Wall -Wextra -Wpedantic )
+#################################################
 
-set( CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -march=native -Wno-dev" )
-set( CMAKE_CXX_FLAGS_RELWITHDEBINFO "${CMAKE_CXX_FLAGS_RELWITHDEBINFO} -march=native -pg -no-pie" )
-set( CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -O0 -Wall" )
 
-set( CMAKE_RUNTIME_OUTPUT_DIRECTORY "${CMAKE_SOURCE_DIR}/bin" )
-
-file( GLOB_RECURSE SRCS RELATIVE ${CMAKE_SOURCE_DIR} "src/*.cpp" "include/*.h" )
-include_directories( ${CMAKE_SOURCE_DIR}/include )
-add_executable( ${CMAKE_PROJECT_NAME} ${SRCS} )
-
-find_package( Python3 COMPONENTS Interpreter Development NumPy REQUIRED )
-include_directories( ${Python3_INCLUDE_DIRS} ${Python3_NumPy_INCLUDE_DIRS} )
-add_compile_definitions( RTSN_PYTHON_PATH="${CMAKE_SOURCE_DIR}/python" )
+### LIBRARIES ###################################
+set(CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/cmake)
 
 find_package( OpenMP REQUIRED )
-if( OPENMP_FOUND )
-    set( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}" )
-    set( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}" )
-endif()
 
 find_package( MPI REQUIRED )
 include_directories( ${MPI_INCLUDE_PATH} )
@@ -30,6 +23,15 @@ find_package( LAPACK REQUIRED )
 include_directories( ${LAPACK_INCLUDE_DIR} )
 
 find_package( BLAS )
+
+find_package( VTK REQUIRED COMPONENTS vtkIOGeometry vtkFiltersCore )
+
+find_package( Python3 COMPONENTS Interpreter Development NumPy REQUIRED )
+include_directories( ${Python3_INCLUDE_DIRS} ${Python3_NumPy_INCLUDE_DIRS} )
+add_compile_definitions( KITRT_PYTHON_PATH="${CMAKE_SOURCE_DIR}/python" )
+
+add_compile_definitions( BLAZE_USE_SHARED_MEMORY_PARALLELIZATION=0 )
+message( STATUS "Blaze: Shared memory parallelization disabled" )
 if( BLAS_FOUND )
     message( STATUS "Blaze: BLAS mode enabled" )
     add_compile_definitions( BLAZE_BLAS_MODE=1 )
@@ -38,80 +40,7 @@ else()
     message( STATUS "Blaze: BLAS mode disabled" )
     add_compile_definitions( BLAZE_BLAS_MODE=0 )
 endif()
-
-add_compile_definitions( BLAZE_USE_SHARED_MEMORY_PARALLELIZATION=0 )
-
-set(flag 1)
-if (WIN32)
-    execute_process(COMMAND wmic cpu get L3CacheSize
-        OUTPUT_VARIABLE tmp
-        RESULT_VARIABLE flag
-        ERROR_QUIET)
-    if (flag)
-        execute_process(COMMAND wmic cpu get L2CacheSize
-            OUTPUT_VARIABLE tmp
-            RESULT_VARIABLE flag
-            ERROR_QUIET)
-    endif (flag)
-    if (flag)
-        execute_process(COMMAND wmic cpu get L1CacheSize
-            OUTPUT_VARIABLE tmp
-            RESULT_VARIABLE flag
-            ERROR_QUIET)
-    endif (flag)
-endif (WIN32)
-
-if (UNIX)
-    execute_process(COMMAND cat /sys/devices/system/cpu/cpu0/cache/index3/size
-        OUTPUT_VARIABLE tmp
-        RESULT_VARIABLE flag
-        ERROR_QUIET)
-    if (flag)
-        execute_process(COMMAND cat /sys/devices/system/cpu/cpu0/cache/index2/size
-            OUTPUT_VARIABLE tmp
-            RESULT_VARIABLE flag
-            ERROR_QUIET)
-    endif (flag)
-    if (flag)
-        execute_process(COMMAND cat /sys/devices/system/cpu/cpu0/cache/index1/size
-            OUTPUT_VARIABLE tmp
-            RESULT_VARIABLE flag
-            ERROR_QUIET)
-    endif (flag)
-endif (UNIX)
-
-if (APPLE)
-    execute_process(COMMAND sysctl -n hw.l3cachesize
-        OUTPUT_VARIABLE tmp
-        RESULT_VARIABLE flag
-        ERROR_QUIET)
-    if (flag)
-        execute_process(COMMAND sysctl -n hw.l2cachesize
-            OUTPUT_VARIABLE tmp
-            RESULT_VARIABLE flag
-            ERROR_QUIET)
-    endif (flag)
-    if (flag)
-        execute_process(COMMAND sysctl -n hw.l1icachesize
-            OUTPUT_VARIABLE tmp
-            RESULT_VARIABLE flag
-            ERROR_QUIET)
-    endif (flag)
-
-    if (flag EQUAL 0)
-        math(EXPR tmp ${tmp}/1024)  # If successful convert to kibibytes to comply with rest
-    endif (flag EQUAL 0)
-endif (APPLE)
-
-if (flag)
-    message(WARNING "Cache size not found automatically. Using default value as cache size.")
-    set(tmp "3072")
-endif (flag)
-
-string( REGEX MATCH "([0-9][0-9]+)" tmp ${tmp} )
-math( EXPR BLAZE_CACHE_SIZE ${tmp}*1024 )
-add_compile_definitions( BLAZE_CACHE_SIZE=${BLAZE_CACHE_SIZE}UL )
-message( STATUS "Blaze: Automatic Cache Size Configuration = ${BLAZE_CACHE_SIZE} KiB" )
+include( blaze-cache-config )
 include_directories( ${CMAKE_SOURCE_DIR}/ext/blaze )
 
 add_compile_definitions( METIS_EXPORT= )
@@ -121,12 +50,14 @@ include_directories( ${ParMETIS_PATH}/include )
 include_directories( ${ParMETIS_PATH}/metis/include )
 add_subdirectory( ${ParMETIS_PATH} )
 
-find_package( VTK REQUIRED COMPONENTS vtkIOGeometry vtkFiltersCore HINTS /home/pia/vtk-inst/include/vtk-8.2)
-include(${VTK_USE_FILE})
-
 include_directories( ${CMAKE_SOURCE_DIR}/ext/cpptoml/include )
 include_directories( ${CMAKE_SOURCE_DIR}/ext/spdlog/include )
 
+set( CORE_LIBRARIES ${Python3_LIBRARIES} ${LAPACK_LIBRARIES} ${BLAS_LIBRARIES} ${MPI_LIBRARIES} ${VTK_LIBRARIES} OpenMP::OpenMP_CXX parmetis -lstdc++fs )
+#################################################
+
+
+### MISC ########################################
 execute_process(
     COMMAND git rev-parse HEAD
     WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
@@ -134,17 +65,40 @@ execute_process(
     OUTPUT_STRIP_TRAILING_WHITESPACE
 )
 add_compile_definitions( GIT_HASH="${GIT_HASH}" )
+#################################################
 
-set( CORE_LIBRARIES ${Python3_LIBRARIES} ${LAPACK_LIBRARIES} ${BLAS_LIBRARIES} ${MPI_LIBRARIES} ${VTK_LIBRARIES} OpenMP::OpenMP_CXX parmetis -lstdc++fs )
 
+### BUILD KIT-RT ################################
+file( GLOB_RECURSE SRCS RELATIVE ${CMAKE_SOURCE_DIR} "src/*.cpp" "include/*.h" )
+include_directories( ${CMAKE_SOURCE_DIR}/include )
+add_executable( ${CMAKE_PROJECT_NAME} ${SRCS} ${EXT_SRCS} )
 target_link_libraries( ${CMAKE_PROJECT_NAME} ${CORE_LIBRARIES} )
-
-if( BUILD_TESTING )
-    add_compile_definitions( BUILD_TESTING=1 )
-    add_subdirectory( ${CMAKE_SOURCE_DIR}/ext/Catch2 )
-    include_directories( ${CMAKE_SOURCE_DIR}/ext/Catch2/single_include/catch2 )
-    file( GLOB_RECURSE TEST_SRCS RELATIVE ${CMAKE_SOURCE_DIR} "tests/*.cpp" )
-    list( REMOVE_ITEM SRCS "src/main.cpp" )
-    add_executable( unit_tests ${SRCS} ${TEST_SRCS} )
-    target_link_libraries( unit_tests ${CORE_LIBRARIES} )
+set_target_properties( ${CMAKE_PROJECT_NAME} PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${CMAKE_SOURCE_DIR}/bin" )
+target_compile_options( ${CMAKE_PROJECT_NAME} PUBLIC "$<$<CONFIG:DEBUG>:${KITRT_DEBUG_OPTIONS}>" )
+target_compile_options( ${CMAKE_PROJECT_NAME} PUBLIC "$<$<CONFIG:RELWITHDEBINFO>:${KITRT_RELWITHDEBINFO_OPTIONS}>" )
+target_compile_options( ${CMAKE_PROJECT_NAME} PUBLIC "$<$<CONFIG:RELEASE>:${KITRT_RELEASE_OPTIONS}>" )
+#################################################
+
+
+### BUILD UNIT TESTS ############################
+include( CTest )
+set( CATCH_INCLUDE_DIR ${CMAKE_SOURCE_DIR}/ext/Catch2/single_include/catch2 )
+add_compile_definitions( BUILD_TESTING )
+add_compile_definitions( TESTS_PATH="${CMAKE_SOURCE_DIR}/tests/" )
+add_library( Catch INTERFACE )
+target_include_directories( Catch INTERFACE ${CATCH_INCLUDE_DIR} )
+file( GLOB_RECURSE TEST_SRCS RELATIVE ${CMAKE_SOURCE_DIR} "tests/*.cpp" )
+list( REMOVE_ITEM SRCS "src/main.cpp" )
+add_executable( unit_tests ${TEST_SRCS} ${SRCS} ${EXT_SRCS} )
+target_link_libraries( unit_tests Catch ${CORE_LIBRARIES} )
+target_compile_options( unit_tests PUBLIC "$<$<CONFIG:DEBUG>:${KITRT_DEBUG_OPTIONS}>" )
+if( CMAKE_COMPILER_IS_GNUCXX )
+    set( CODE_COVERAGE_OPTIONS --coverage -g -O0 -w )
+    target_compile_options( unit_tests PUBLIC "$<$<CONFIG:DEBUG>:${CODE_COVERAGE_OPTIONS}>" )
+    target_link_libraries( unit_tests Catch gcov )
 endif()
+target_compile_options( unit_tests PUBLIC "$<$<CONFIG:RELWITHDEBINFO>:${KITRT_RELWITHDEBINFO_OPTIONS}>" )
+target_compile_options( unit_tests PUBLIC "$<$<CONFIG:RELEASE>:${KITRT_RELEASE_OPTIONS}>" )
+add_test( NAME unit_tests COMMAND unit_tests )
+enable_testing()
+#################################################

code/cmake/blaze-cache-config.cmake

+set(flag 1)
+if (WIN32)
+    execute_process(COMMAND wmic cpu get L3CacheSize
+        OUTPUT_VARIABLE tmp
+        RESULT_VARIABLE flag
+        ERROR_QUIET)
+    if (flag)
+        execute_process(COMMAND wmic cpu get L2CacheSize
+            OUTPUT_VARIABLE tmp
+            RESULT_VARIABLE flag
+            ERROR_QUIET)
+    endif (flag)
+    if (flag)
+        execute_process(COMMAND wmic cpu get L1CacheSize
+            OUTPUT_VARIABLE tmp
+            RESULT_VARIABLE flag
+            ERROR_QUIET)
+    endif (flag)
+endif (WIN32)
+
+if (UNIX)
+    execute_process(COMMAND cat /sys/devices/system/cpu/cpu0/cache/index3/size
+        OUTPUT_VARIABLE tmp
+        RESULT_VARIABLE flag
+        ERROR_QUIET)
+    if (flag)
+        execute_process(COMMAND cat /sys/devices/system/cpu/cpu0/cache/index2/size
+            OUTPUT_VARIABLE tmp
+            RESULT_VARIABLE flag
+            ERROR_QUIET)
+    endif (flag)
+    if (flag)
+        execute_process(COMMAND cat /sys/devices/system/cpu/cpu0/cache/index1/size
+            OUTPUT_VARIABLE tmp
+            RESULT_VARIABLE flag
+            ERROR_QUIET)
+    endif (flag)
+endif (UNIX)
+
+if (APPLE)
+    execute_process(COMMAND sysctl -n hw.l3cachesize
+        OUTPUT_VARIABLE tmp
+        RESULT_VARIABLE flag
+        ERROR_QUIET)
+    if (flag)
+        execute_process(COMMAND sysctl -n hw.l2cachesize
+            OUTPUT_VARIABLE tmp
+            RESULT_VARIABLE flag
+            ERROR_QUIET)
+    endif (flag)
+    if (flag)
+        execute_process(COMMAND sysctl -n hw.l1icachesize
+            OUTPUT_VARIABLE tmp
+            RESULT_VARIABLE flag
+            ERROR_QUIET)
+    endif (flag)
+
+    if (flag EQUAL 0)
+        math(EXPR tmp ${tmp}/1024)  # If successful convert to kibibytes to comply with rest
+    endif (flag EQUAL 0)
+endif (APPLE)
+
+if (flag)
+    message(WARNING "Cache size not found automatically. Using default value as cache size.")
+    set(tmp "3072")
+endif (flag)
+
+string( REGEX MATCH "([0-9][0-9]+)" tmp ${tmp} )
+math( EXPR BLAZE_CACHE_SIZE ${tmp}*1024 )
+add_compile_definitions( BLAZE_CACHE_SIZE=${BLAZE_CACHE_SIZE}UL )
+message( STATUS "Blaze: Automatic Cache Size Configuration = ${BLAZE_CACHE_SIZE} KiB" )

code/include/common/config.h

@@ -34,12 +34,13 @@ class Config
 
     // --- Options ---
     // File Structure
-    std::string _inputDir;   /*!< @brief Directory for input files*/
-    std::string _outputDir;  /*!< @brief Directory for output files*/
-    std::string _outputFile; /*!< @brief Name of output file*/
-    std::string _logDir;     /*!< @brief Directory of log file*/
-    std::string _meshFile;   /*!< @brief Name of mesh file*/
-    std::string _ctFile;     /*!< @brief Name of CT file*/
+    std::string _inputDir;    /*!< @brief Directory for input files*/
+    std::string _outputDir;   /*!< @brief Directory for output files*/
+    std::string _outputFile;  /*!< @brief Name of output file*/
+    std::string _logDir;      /*!< @brief Directory of log file*/
+    std::string _logFileName; /*!< @brief Name of log file*/
+    std::string _meshFile;    /*!< @brief Name of mesh file*/
+    std::string _ctFile;      /*!< @brief Name of CT file*/
 
     // Quadrature
     QUAD_NAME _quadName;       /*!< @brief Quadrature Name*/
@@ -58,9 +59,13 @@ class Config
     unsigned short _maxMomentDegree; /*!< @brief Maximal Order of Moments for PN and MN Solver */
     unsigned short _reconsOrder;     /*!< @brief Spatial Order of Accuracy for Solver */
 
+    // Linesource
+    double _sigmaS; /*!< @brief Scattering coeffient for Linesource test case */
+
     /*!< @brief If true, very low entries (10^-10 or smaller) of the flux matrices will be set to zero,
      * to improve floating point accuracy */
     bool _cleanFluxMat;
+    bool _allGaussPts; /*!< @brief If true, the SN Solver uses all Gauss pts in the quadrature */
 
     bool _csd;                 /*!< @brief If true, continuous slowing down approximation will be used */
     std::string _hydrogenFile; /*!< @brief Name of hydrogen cross section file */
@@ -86,6 +91,19 @@ class Config
     unsigned short _newtonLineSearchIter; /*!< @brief Maximal Number of line search iterations for newton optimizer */
     bool _newtonFastMode;                 /*!< @brief If true, we skip the NewtonOptimizer for quadratic entropy and assign alpha = u */
 
+    // Output Options
+    unsigned short _nVolumeOutput;            /*!< @brief Number of volume outputs */
+    std::vector<VOLUME_OUTPUT> _volumeOutput; /*!< @brief Output groups for volume output*/
+    unsigned short _volumeOutputFrequency;    /*!< @brief Frequency of vtk write of volume output*/
+
+    unsigned short _nScreenOutput;            /*!< @brief Number of screen outputs */
+    std::vector<SCALAR_OUTPUT> _screenOutput; /*!< @brief Output groups for screen output*/
+    unsigned short _screenOutputFrequency;    /*!< @brief Frequency of screen output*/
+
+    unsigned short _nHistoryOutput;            /*!< @brief Number of screen outputs */
+    std::vector<SCALAR_OUTPUT> _historyOutput; /*!< @brief Output groups for screen output*/
+    unsigned short _historyOutputFrequency;    /*!< @brief Frequency of screen output*/
+
     // --- Parsing Functionality and Initializing of Options ---
     /*!
      * @brief Set default values for all options not yet set.
@@ -175,7 +193,13 @@ class Config
     void AddEnumOption( const std::string name, Tenum& option_field, const std::map<std::string, Tenum>& enum_map, Tenum default_value );
 
     // List Options
-    void AddStringListOption( const std::string name, unsigned short& num_marker, std::vector<std::string>& option_field );
+    void AddStringListOption( const std::string name, unsigned short& input_size, std::vector<std::string>& option_field );
+
+    template <class Tenum>
+    void AddEnumListOption( const std::string name,
+                            unsigned short& num_marker,
+                            std::vector<Tenum>& option_field,
+                            const std::map<std::string, Tenum>& enum_map );
 
     // Initialize the cmdline and file logger
     void InitLogger();
@@ -198,43 +222,45 @@ class Config
      *        Please keep alphabetical order within each subcategory
      */
     // File structure
+    std::string inline GetCTFile() const { return std::filesystem::path( _ctFile ).lexically_normal(); }
+    std::string inline GetHydrogenFile() const { return std::filesystem::path( _hydrogenFile ).lexically_normal(); }
+    std::string inline GetLogDir() const { return std::filesystem::path( _logDir ).lexically_normal(); }
+    std::string inline GetLogFile() const { return std::filesystem::path( _logFileName ).lexically_normal(); }
     std::string inline GetMeshFile() const { return std::filesystem::path( _meshFile ).lexically_normal(); }
     std::string inline GetOutputDir() const { return std::filesystem::path( _outputDir ).lexically_normal(); }
     std::string inline GetOutputFile() const { return std::filesystem::path( _outputFile ).lexically_normal(); }
-    std::string inline GetLogDir() const { return std::filesystem::path( _logDir ).lexically_normal(); }
-    std::string inline GetCTFile() const { return std::filesystem::path( _ctFile ).lexically_normal(); }
-    std::string inline GetHydrogenFile() const { return std::filesystem::path( _hydrogenFile ).lexically_normal(); }
     std::string inline GetOxygenFile() const { return std::filesystem::path( _oxygenFile ).lexically_normal(); }
 
     // Quadrature Structure
+    unsigned GetNQuadPoints() { return _nQuadPoints; }
     QUAD_NAME inline GetQuadName() const { return _quadName; }
     unsigned short inline GetQuadOrder() const { return _quadOrder; }
-    void SetNQuadPoints( unsigned nq ) { _nQuadPoints = nq; }
-    unsigned GetNQuadPoints() { return _nQuadPoints; }
 
     // Mesh Structure
-    void SetNCells( unsigned nCells ) { _nCells = nCells; }
     unsigned GetNCells() { return _nCells; }
 
     // Solver Structure
-    unsigned short inline GetMaxMomentDegree() const { return _maxMomentDegree; }
     double inline GetCFL() const { return _CFL; }
-    double inline GetTEnd() const { return _tEnd; }
+    bool inline GetCleanFluxMat() const { return _cleanFluxMat; }
+    ENTROPY_NAME inline GetEntropyName() const { return _entropyName; }
+    unsigned short inline GetMaxMomentDegree() const { return _maxMomentDegree; }
     PROBLEM_NAME inline GetProblemName() const { return _problemName; }
+    unsigned inline GetReconsOrder() { return _reconsOrder; }
     SOLVER_NAME inline GetSolverName() const { return _solverName; }
-    ENTROPY_NAME inline GetEntropyName() const { return _entropyName; }
-    bool inline GetCleanFluxMat() const { return _cleanFluxMat; }
-    unsigned GetReconsOrder() { return _reconsOrder; }
-    bool inline IsCSD() const { return _csd; }
-    unsigned inline GetMaxMomentDegree() { return _maxMomentDegree; }
+    double inline GetTEnd() const { return _tEnd; }
+    bool inline GetSNAllGaussPts() const { return _allGaussPts; }
+    bool inline GetIsCSD() const { return _csd; }
+
+    // Linesource
+    double inline GetSigmaS() const { return _sigmaS; }
 
     //  Optimizer
-    OPTIMIZER_NAME inline GetOptimizerName() const { return _entropyOptimizerName; }
     double inline GetNewtonOptimizerEpsilon() const { return _optimizerEpsilon; }
     unsigned inline GetNewtonIter() const { return _newtonIter; }
     double inline GetNewtonStepSize() const { return _newtonStepSize; }
-    unsigned inline GetMaxLineSearches() const { return _newtonLineSearchIter; }
+    unsigned inline GetNewtonMaxLineSearches() const { return _newtonLineSearchIter; }
     bool inline GetNewtonFastMode() const { return _newtonFastMode; }
+    OPTIMIZER_NAME inline GetOptimizerName() const { return _entropyOptimizerName; }
 
     // Boundary Conditions
     BOUNDARY_TYPE GetBoundaryType( std::string nameMarker ) const; /*! @brief Get Boundary Type of given marker */
@@ -243,6 +269,26 @@ class Config
     KERNEL_NAME inline GetKernelName() const { return _kernelName; }
 
     // Output Structure
+    std::vector<VOLUME_OUTPUT> inline GetVolumeOutput() { return _volumeOutput; }
+    unsigned short inline GetNVolumeOutput() { return _nVolumeOutput; }
+    unsigned short inline GetVolumeOutputFrequency() { return _volumeOutputFrequency; }
+
+    std::vector<SCALAR_OUTPUT> inline GetScreenOutput() { return _screenOutput; }
+    unsigned short inline GetNScreenOutput() { return _nScreenOutput; }
+    unsigned short inline GetScreenOutputFrequency() { return _screenOutputFrequency; }
+
+    std::vector<SCALAR_OUTPUT> inline GetHistoryOutput() { return _historyOutput; }
+    unsigned short inline GetNHistoryOutput() { return _nHistoryOutput; }
+    unsigned short inline GetHistoryOutputFrequency() { return _historyOutputFrequency; }
+    // ---- Setters for option structure
+
+    // Quadrature Structure
+    void SetNQuadPoints( unsigned nq ) { _nQuadPoints = nq; }
+    void SetQuadName( QUAD_NAME quadName ) { _quadName = quadName; }    /*! @brief Never change the quadName! This is only for the test framework. */
+    void SetQuadOrder( unsigned quadOrder ) { _quadOrder = quadOrder; } /*! @brief Never change the quadOrder! This is only for the test framework. */
+    void SetSNAllGaussPts( bool useall ) { _allGaussPts = useall; }     /*! @brief Never change the this! This is only for the test framework. */
+    // Mesh Structure
+    void SetNCells( unsigned nCells ) { _nCells = nCells; }
 };
 
 #endif    // CONFIG_H

code/include/common/globalconstants.h

@@ -119,13 +119,26 @@ inline std::map<std::string, SOLVER_NAME> Solver_Map{ { "SN_SOLVER", SN_SOLVER }
                                                       { "MN_SOLVER", MN_SOLVER } };
 
 // Entropy functional
-enum ENTROPY_NAME { QUADRATIC, MAXWELL_BOLZMANN, BOSE_EINSTEIN, FERMI_DIRAC };
+enum ENTROPY_NAME { QUADRATIC, MAXWELL_BOLTZMANN, BOSE_EINSTEIN, FERMI_DIRAC };
 
 inline std::map<std::string, ENTROPY_NAME> Entropy_Map{
-    { "QUADRATIC", QUADRATIC }, { "MAXWELL_BOLZMANN", MAXWELL_BOLZMANN }, { "BOSE_EINSTEIN", BOSE_EINSTEIN }, { "FERMI_DIRAC", FERMI_DIRAC } };
+    { "QUADRATIC", QUADRATIC }, { "MAXWELL_BOLTZMANN", MAXWELL_BOLTZMANN }, { "BOSE_EINSTEIN", BOSE_EINSTEIN }, { "FERMI_DIRAC", FERMI_DIRAC } };
 
-// Otpimizer
+// Optimizer