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/src/common/config.cpp

/*!
 * \file config.cpp
 * \brief Class for different Options in rtsn
 * \author S. Schotthoefer
 *
 * Disclaimer: This class structure was copied and modifed with open source permission from SU2 v7.0.3 https://su2code.github.io/
 */
#ifdef IMPORT_MPI
#include <mpi.h>
#endif
#include "common/config.hpp"
#include "common/globalconstants.hpp"
#include "common/optionstructure.hpp"
#include "quadratures/quadraturebase.hpp"
#include "toolboxes/errormessages.hpp"
#include "toolboxes/textprocessingtoolbox.hpp"

// externals
#include "spdlog/sinks/basic_file_sink.h"
#include "spdlog/sinks/stdout_sinks.h"
#include "spdlog/spdlog.h"
#include <filesystem>
#include <fstream>

using namespace std;

Config::Config( string case_filename ) {

    /*--- Set the case name to the base config file name without extension ---*/

    auto cwd     = std::filesystem::current_path();
    auto relPath = std::filesystem::relative( std::filesystem::path( case_filename ), cwd );
    _fileName    = relPath.filename().string();
    _inputDir    = cwd.string() + "/" + relPath.parent_path().string();

    _baseConfig = true;

    /*--- Store MPI rank and size ---*/
    // TODO with MPI implementation

    /*--- Initialize pointers to Null---*/

    SetPointersNull();

    /*--- Reading config options  ---*/

    SetConfigOptions();

    /*--- Parsing the config file  ---*/

    SetConfigParsing( case_filename );

    /*--- Set the default values for all of the options that weren't set ---*/

    SetDefault();

    /*--- Get the Mesh Value--- */

    // val_nDim = GetnDim(Mesh_FileName, Mesh_FileFormat);
    // TODO

    /*--- Configuration file postprocessing ---*/

    SetPostprocessing();

    /*--- Configuration file boundaries/markers setting ---*/

    // SetBoundary(); IDK how boundaries are implemented, but i think this should be treated here

    /*--- Configuration file output ---*/

    // if ((rank == MASTER_NODE))
    SetOutput();
}

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 ----

// Simple Options
void Config::AddBoolOption( const string name, bool& option_field, bool default_value ) {
    // Check if the key is already in the map. If this fails, it is coder error
    // and not user error, so throw.
    assert( _optionMap.find( name ) == _optionMap.end() );

    // Add this option to the list of all the options
    _allOptions.insert( pair<string, bool>( name, true ) );

    // Create the parser for a bool option with a reference to the option_field and the desired
    // default value. This will take the string in the config file, convert it to a bool, and
    // place that bool in the memory location specified by the reference.
    OptionBase* val = new OptionBool( name, option_field, default_value );

    // Create an association between the option name ("CFL") and the parser generated above.
    // During configuration, the parsing script will get the option name, and use this map
    // to find how to parse that option.
    _optionMap.insert( pair<string, OptionBase*>( name, val ) );
}

void Config::AddDoubleOption( const string name, double& option_field, double default_value ) {
    assert( _optionMap.find( name ) == _optionMap.end() );
    _allOptions.insert( pair<string, bool>( name, true ) );
    OptionBase* val = new OptionDouble( name, option_field, default_value );
    _optionMap.insert( pair<string, OptionBase*>( name, val ) );
}

void Config::AddIntegerOption( const string name, int& option_field, int default_value ) {
    assert( _optionMap.find( name ) == _optionMap.end() );
    _allOptions.insert( pair<string, bool>( name, true ) );
    OptionBase* val = new OptionInt( name, option_field, default_value );
    _optionMap.insert( pair<string, OptionBase*>( name, val ) );
}

void Config::AddLongOption( const string name, long& option_field, long default_value ) {
    assert( _optionMap.find( name ) == _optionMap.end() );
    _allOptions.insert( pair<string, bool>( name, true ) );
    OptionBase* val = new OptionLong( name, option_field, default_value );
    _optionMap.insert( pair<string, OptionBase*>( name, val ) );
}

void Config::AddStringOption( const string name, string& option_field, string default_value ) {
    assert( _optionMap.find( name ) == _optionMap.end() );
    _allOptions.insert( pair<string, bool>( name, true ) );
    OptionBase* val = new OptionString( name, option_field, default_value );
    _optionMap.insert( pair<string, OptionBase*>( name, val ) );
}

void Config::AddUnsignedLongOption( const string name, unsigned long& option_field, unsigned long default_value ) {
    assert( _optionMap.find( name ) == _optionMap.end() );
    _allOptions.insert( pair<string, bool>( name, true ) );
    OptionBase* val = new OptionULong( name, option_field, default_value );
    _optionMap.insert( pair<string, OptionBase*>( name, val ) );
}

void Config::AddUnsignedShortOption( const string name, unsigned short& option_field, unsigned short default_value ) {
    assert( _optionMap.find( name ) == _optionMap.end() );
    _allOptions.insert( pair<string, bool>( name, true ) );
    OptionBase* val = new OptionUShort( name, option_field, default_value );
    _optionMap.insert( pair<string, OptionBase*>( name, val ) );
}

// enum types work differently than all of the others because there are a small number of valid
// string entries for the type. One must also provide a list of all the valid strings of that type.
template <class Tenum> void Config::AddEnumOption( const string name, Tenum& option_field, const map<string, Tenum>& enum_map, Tenum default_value ) {
    assert( _optionMap.find( name ) == _optionMap.end() );
    _allOptions.insert( pair<string, bool>( name, true ) );
    OptionBase* val = new OptionEnum<Tenum>( name, enum_map, option_field, default_value );
    _optionMap.insert( pair<string, OptionBase*>( name, val ) );
    return;
}

// List Options
void Config::AddStringListOption( const string name, unsigned short& num_marker, std::vector<std::string>& option_field ) {
    assert( _optionMap.find( name ) == _optionMap.end() );
    _allOptions.insert( pair<string, bool>( name, true ) );
    OptionBase* val = new OptionStringList( name, num_marker, option_field );
    _optionMap.insert( pair<string, OptionBase*>( name, val ) );
}

void Config::AddDoubleListOption( const string name, unsigned short& num_marker, std::vector<double>& option_field ) {
    assert( _optionMap.find( name ) == _optionMap.end() );
    _allOptions.insert( pair<string, bool>( name, true ) );
    OptionBase* val = new OptionDoubleList( name, num_marker, option_field );
    _optionMap.insert( pair<string, OptionBase*>( name, val ) );
}

template <class Tenum>
void Config::AddEnumListOption( const std::string name,
                                unsigned short& input_size,
                                std::vector<Tenum>& option_field,
                                const map<std::string, Tenum>& enum_map ) {
    input_size = 0;
    assert( _optionMap.find( name ) == _optionMap.end() );
    _allOptions.insert( pair<string, bool>( name, true ) );
    OptionBase* val = new OptionEnumList<Tenum>( name, enum_map, option_field, input_size );
    _optionMap.insert( pair<string, OptionBase*>( name, val ) );
}

// ---- Getter Functions ----

BOUNDARY_TYPE Config::GetBoundaryType( std::string name ) const {
    for( unsigned i = 0; i < _boundaries.size(); ++i ) {
        if( name == _boundaries[i].first ) return _boundaries[i].second;
    }
    return BOUNDARY_TYPE::INVALID;
}

// ---- Setter Functions ----

void Config::SetDefault() {
    /*--- Set the default values for all of the options that weren't set ---*/

    for( map<string, bool>::iterator iter = _allOptions.begin(); iter != _allOptions.end(); ++iter ) {
        if( _optionMap[iter->first]->GetValue().size() == 0 ) _optionMap[iter->first]->SetDefault();
    }
}

void Config::SetConfigOptions() {

    /* BEGIN_CONFIG_OPTIONS */

    /*! @par CONFIG_CATEGORY: Problem Definition \ingroup Config */
    /*--- Options related to problem definition and partitioning ---*/

    // File Structure related options
    /*! @brief OUTPUT_DIR \n DESCRIPTION: Relative Directory of output files \n DEFAULT "/out" @ingroup Config.*/
    AddStringOption( "OUTPUT_DIR", _outputDir, string( "/out" ) );
    /*! @brief OUTPUT_FILE \n DESCRIPTION: Name of output file \n DEFAULT "output" @ingroup Config.*/
    AddStringOption( "OUTPUT_FILE", _outputFile, string( "output" ) );
    /*! @brief LOG_DIR \n DESCRIPTION: Relative Directory of log files \n DEFAULT "/out" @ingroup Config.*/
    AddStringOption( "LOG_DIR", _logDir, string( "/out/logs" ) );
    /*! @brief LOG_DIR \n DESCRIPTION: Name of log files \n DEFAULT "/out" @ingroup Config.*/
    AddStringOption( "LOG_FILE", _logFileName, string( "use_date" ) );
    /*! @brief MESH_FILE \n DESCRIPTION: Name of mesh file \n DEFAULT "" \ingroup Config.*/
    AddStringOption( "MESH_FILE", _meshFile, string( "mesh.su2" ) );
    /*! @brief MESH_FILE \n DESCRIPTION: Name of mesh file \n DEFAULT "" \ingroup Config.*/
    AddStringOption( "CT_FILE", _ctFile, string( "/home/pia/kitrt/examples/meshes/phantom.png" ) );
    /*! @brief FORCE_CONNECTIVITY_RECOMPUTE \n DESCRIPTION:If true, mesh recomputes connectivity instead of loading from file \n DEFAULT false
     * \ingroup Config.*/
    AddBoolOption( "FORCE_CONNECTIVITY_RECOMPUTE", _forcedConnectivityWrite, false );
    /*! @brief RESTART_SOLUTION \n DESCRIPTION:If true, simulation loads a restart solution from file \n DEFAULT false
     * \ingroup Config.*/
    AddBoolOption( "LOAD_RESTART_SOLUTION", _loadrestartSolution, false );
    AddUnsignedLongOption( "SAVE_RESTART_SOLUTION_FREQUENCY", _saveRestartSolutionFrequency, false );

    // Quadrature relatated options
    /*! @brief QUAD_TYPE \n DESCRIPTION: Type of Quadrature rule \n Options: see @link QUAD_NAME \endlink \n DEFAULT: QUAD_MonteCarlo
     * \ingroup Config
     */
    AddEnumOption( "QUAD_TYPE", _quadName, Quadrature_Map, QUAD_MonteCarlo );
    /*!\brief QUAD_ORDER \n DESCRIPTION: Order of Quadrature rule \n DEFAULT 2 \ingroup Config.*/
    AddUnsignedShortOption( "QUAD_ORDER", _quadOrder, 1 );

    // Solver related options
    /*! @brief HPC_SOLVER \n DESCRIPTION: If true, the SN Solver uses hpc implementation. \n DEFAULT false \ingroup Config */
    AddBoolOption( "HPC_SOLVER", _HPC, false );

    /*! @brief MAX_MOMENT_ORDER \n: DESCRIPTON: Specifies the maximal order of Moments for PN and SN Solver */
    AddUnsignedShortOption( "MAX_MOMENT_SOLVER", _maxMomentDegree, 1 );
    /*! @brief CFL \n DESCRIPTION: CFL number \n DEFAULT 1.0 @ingroup Config.*/
    AddDoubleOption( "CFL_NUMBER", _CFL, 1.0 );
    /*! @brief TIME_FINAL \n DESCRIPTION: Final time for simulation \n DEFAULT 1.0 @ingroup Config.*/
    AddDoubleOption( "TIME_FINAL", _tEnd, 1.0 );
    /*! @brief Problem \n DESCRIPTION: Type of problem setting \n DEFAULT PROBLEM_ElectronRT @ingroup Config.*/
    AddEnumOption( "PROBLEM", _problemName, Problem_Map, PROBLEM_Linesource );
    /*! @brief Solver \n DESCRIPTION: Solver used for problem \n DEFAULT SN_SOLVER @ingroup Config. */
    AddEnumOption( "SOLVER", _solverName, Solver_Map, SN_SOLVER );
    /*! @brief RECONS_ORDER \n DESCRIPTION: Reconstruction order for solver (spatial flux) \n DEFAULT 1 \ingroup Config.*/
    AddUnsignedShortOption( "RECONS_ORDER", _reconsOrder, 1 );
    /*! @brief CleanFluxMatrices \n DESCRIPTION:  If true, very low entries (10^-10 or smaller) of the flux matrices will be set to zero,
     * to improve floating point accuracy \n DEFAULT false \ingroup Config */
    AddBoolOption( "CLEAN_FLUX_MATRICES", _cleanFluxMat, false );
    /*! @brief Realizability Step for MN solver \n DESCRIPTION: If true, MN solvers use a realizability reconstruction step in each time step. Also
     * applicable in regression sampling \n DEFAULT false \ingroup Config */
    AddBoolOption( "REALIZABILITY_RECONSTRUCTION", _realizabilityRecons, false );
    /*! @brief Runge Kutta Staes  \n DESCRIPTION: Sets number of Runge Kutta Stages for time integration \n DEFAULT 1 \ingroup Config */
    AddUnsignedShortOption( "TIME_INTEGRATION_ORDER", _rungeKuttaStages, 1 );

    // Problem Related Options
    /*! @brief MaterialDir \n DESCRIPTION: Relative Path to the data directory (used in the ICRU database class), starting from the directory of the
     * cfg file . \n DEFAULT "../data/material/" \ingroup Config */
    AddStringOption( "DATA_DIR", _dataDir, string( "../data/" ) );
    /*! @brief HydogenFile \n DESCRIPTION: If the continuous slowing down approximation is used, this referes to the cross section file for hydrogen.
     * . \n DEFAULT "h.dat" \ingroup Config */
    AddStringOption( "HYDROGEN_FILE", _hydrogenFile, string( "ENDL_H.txt" ) );
    /*! @brief OxygenFile \n DESCRIPTION: If the continuous slowing down approximation is used, this referes to the cross section file for oxygen.
     * . \n DEFAULT "o.dat" \ingroup Config */
    AddStringOption( "OXYGEN_FILE", _oxygenFile, string( "ENDL_O.txt" ) );
    /*! @brief StoppingPowerFile \n DESCRIPTION: Only temporary added. \ingroup Config */
    AddStringOption( "STOPPING_POWER_FILE", _stoppingPowerFile, string( "stopping_power.txt" ) );
    /*! @brief SN_ALL_GAUSS_PTS \n DESCRIPTION: If true, the SN Solver uses all Gauss Quadrature Points for 2d. \n DEFAULT false \ingroup Config */
    AddBoolOption( "SN_ALL_GAUSS_PTS", _allGaussPts, false );

    // Linesource Testcase Options
    /*! @brief SCATTER_COEFF \n DESCRIPTION: Sets the scattering coefficient for the Linesource test case. \n DEFAULT 1.0 \ingroup Config */
    AddDoubleOption( "SCATTER_COEFF", _sigmaS, 1.0 );

    // Checkerboard Testcase Options
    /*! @brief SCATTER_COEFF \n DESCRIPTION: Sets the Source magnitude for the checkerboard testcase. \n DEFAULT 1.0 \ingroup Config */
    AddDoubleOption( "SOURCE_MAGNITUDE", _magQ, 1.0 );

    // CSD related options
    /*! @brief MAX_ENERGY_CSD \n DESCRIPTION: Sets maximum energy for the CSD simulation.\n DEFAULT \ingroup Config */
    AddDoubleOption( "MAX_ENERGY_CSD", _maxEnergyCSD, 5.0 );

    // Lattice related options
    /*! @brief LATTICE_DSGN_ABSORPTION_BLUE \n DESCRIPTION: Sets absorption rate for the blue blocks (absorption blocks) in the lattice test case. \n
     * DEFAULT  10.0 \ingroup Config */
    AddDoubleOption( "LATTICE_DSGN_ABSORPTION_BLUE", _dsgnAbsBlue, 10.0 );
    /*! @brief LATTICE_DSGN_SCATTER_WHITE \n DESCRIPTION: Sets absorption rate for the white blocks (scattering blocks) in the lattice test case. \n
     * DEFAULT 1.0 \ingroup Config */
    AddDoubleOption( "LATTICE_DSGN_SCATTER_WHITE", _dsgnScatterWhite, 1.0 );
    /*! @brief LATTICE_DSGN_ABSORPTION_INDIVIDUAL \n DESCRIPTION: Sets absorption rate all 7x7 blocks in the lattice test case. Order from upper left
     * to lower right (row major). \n DEFAULT \ingroup Config */
    AddDoubleListOption( "LATTICE_DSGN_ABSORPTION_INDIVIDUAL", _nDsgnAbsIndividual, _dsgnAbsIndividual );
    /*! @brief LATTICE_DSGN_SCATTER_INDIVIDUAL \n DESCRIPTION: Sets scattering rate all 7x7 blocks in the lattice test case. Order from upper left to
     * lower right (row major). \n DEFAULT \ingroup Config */
    AddDoubleListOption( "LATTICE_DSGN_SCATTER_INDIVIDUAL", _nDsgnScatterIndividual, _dsgnScatterIndividual );

    // Hohlraum related options
    AddUnsignedShortOption( "N_SAMPLING_PTS_LINE_GREEN", _nProbingCellsLineGreenHohlraum, 4 );
    AddDoubleOption( "POS_CENTER_X", _posCenterXHohlraum, 0.0 );
    AddDoubleOption( "POS_CENTER_Y", _posCenterYHohlraum, 0.0 );
    AddDoubleOption( "POS_RED_RIGHT_TOP", _posRedRightTop, 0.4 );
    AddDoubleOption( "POS_RED_RIGHT_BOTTOM", _posRedRightBottom, -0.4 );
    AddDoubleOption( "POS_RED_LEFT_TOP", _posRedLeftTop, 0.4 );
    AddDoubleOption( "POS_RED_LEFT_BOTTOM", _posRedLeftBottom, -0.4 );
    AddDoubleOption( "POS_BORDER_RED_LEFT", _posRedLeftBorder, -0.65 );
    AddDoubleOption( "POS_BORDER_RED_RIGHT", _posRedRightBorder, 0.65 );
    // Entropy related options
    /*! @brief Entropy Functional \n DESCRIPTION: Entropy functional used for the MN_Solver \n DEFAULT QUADRTATIC @ingroup Config. */
    AddEnumOption( "ENTROPY_FUNCTIONAL", _entropyName, Entropy_Map, QUADRATIC );
    /*! @brief Optimizer Name \n DESCRIPTION:  Optimizer used to determine the minimal Entropy reconstruction \n DEFAULT NEWTON \ingroup Config */
    AddEnumOption( "ENTROPY_OPTIMIZER", _entropyOptimizerName, Optimizer_Map, NEWTON );
    /*! @brief Sets Flag for dynamic ansatz for normalized mn entropy closure \n DESCRIPTION:  True = enable ansatz, False = disable ansatz \n DEFAULT
     * false \ingroup Config */
    AddBoolOption( "ENTROPY_DYNAMIC_CLOSURE", _entropyDynamicClosure, true );

    // Newton optimizer related options
    /*! @brief Regularization Parameter \n DESCRIPTION:  Regularization Parameter for the regularized entropy closure. Must not be negative \n DEFAULT
     * 1e-2 \ingroup Config */
    AddDoubleOption( "REGULARIZER_GAMMA", _regularizerGamma, 1e-2 );
    /*! @brief Newton Optimizer Epsilon \n DESCRIPTION:  Convergencce Epsilon for Newton Optimizer \n DEFAULT 1e-3 \ingroup Config */
    AddDoubleOption( "NEWTON_EPSILON", _optimizerEpsilon, 0.001 );
    /*! @brief Max Iter Newton Optmizers \n DESCRIPTION: Max number of newton iterations \n DEFAULT 10 \ingroup Config */
    AddUnsignedLongOption( "NEWTON_ITER", _newtonIter, 1000 );
    /*! @brief Step Size Newton Optmizers \n DESCRIPTION: Step size for Newton optimizer \n DEFAULT 10 \ingroup Config */
    AddDoubleOption( "NEWTON_STEP_SIZE", _newtonStepSize, 1 );
    /*! @brief Max Iter for line search in Newton Optmizers \n DESCRIPTION: Max number of line search iter for newton optimizer \n DEFAULT 10
     * \ingroup Config */
    AddUnsignedLongOption( "NEWTON_LINE_SEARCH_ITER", _newtonLineSearchIter, 1000 );
    /*! @brief Newton Fast mode \n DESCRIPTION:  If true, we skip the Newton optimizer for Quadratic entropy and set alpha = u \n DEFAULT false
     * \ingroup Config */
    AddBoolOption( "NEWTON_FAST_MODE", _newtonFastMode, false );
    // Neural Entropy Closure options
    /*! @brief Neural Model \n DESCRIPTION:  Specifies the neural netwok architecture \n DEFAULT 11 (values: 11=input convex, 12 non-convex)
     * \ingroup Config */
    AddUnsignedShortOption( "NEURAL_MODEL_MK", _neuralModel, 11 );
    /*! @brief Neural Model Gamma \n DESCRIPTION:  Specifies regularization parameter for neural networks \n DEFAULT 0 (values: 0,1,2,3)
    \ingroup Config */
    AddUnsignedShortOption( "NEURAL_MODEL_GAMMA", _neuralGamma, 0 );
    /*! @brief NEURAL_MODEL_ENFORCE_ROTATION_SYMMETRY \n DESCRIPTION:  Flag to enforce rotational symmetry \n DEFAULT false \ingroup Config */
    AddBoolOption( "NEURAL_MODEL_ENFORCE_ROTATION_SYMMETRY", _enforceNeuralRotationalSymmetry, false );

    // Mesh related options
    // Boundary Markers
    /*!\brief BC_DIRICHLET\n DESCRIPTION: Dirichlet wall boundary marker(s) \ingroup Config*/
    AddStringListOption( "BC_DIRICHLET", _nMarkerDirichlet, _MarkerDirichlet );
    AddStringListOption( "BC_NEUMANN", _nMarkerNeumann, _MarkerNeumann );
    AddUnsignedShortOption( "SPATIAL_DIM", _dim, 3 );

    /*! @brief Scattering kernel \n DESCRIPTION: Describes used scattering kernel \n DEFAULT KERNEL_Isotropic \ingroup Config */
    AddEnumOption( "KERNEL", _kernelName, Kernel_Map, KERNEL_Isotropic );

    /*! @brief Spherical Basis \n DESCRIPTION: Describes the chosen set of basis functions for on the unit sphere (e.g. for Moment methods) \n DEFAULT
     * SPHERICAL_HARMONICS \ingroup Config */
    AddEnumOption( "SPHERICAL_BASIS", _sphericalBasisName, SphericalBasis_Map, SPHERICAL_HARMONICS );

    // Output related options
    /*! @brief Volume output \n DESCRIPTION: Describes output groups to write to vtk \ingroup Config */
    AddEnumListOption( "VOLUME_OUTPUT", _nVolumeOutput, _volumeOutput, VolOutput_Map );
    /*! @brief Volume output Frequency \n DESCRIPTION: Describes output write frequency \n DEFAULT 0 ,i.e. only last value \ingroup Config */
    AddUnsignedShortOption( "VOLUME_OUTPUT_FREQUENCY", _volumeOutputFrequency, 0 );
    /*! @brief Screen output \n DESCRIPTION: Describes screen output fields \ingroup Config */
    AddEnumListOption( "SCREEN_OUTPUT", _nScreenOutput, _screenOutput, ScalarOutput_Map );
    /*! @brief Screen output Frequency \n DESCRIPTION: Describes screen output write frequency \n DEFAULT 1 \ingroup Config */
    AddUnsignedShortOption( "SCREEN_OUTPUT_FREQUENCY", _screenOutputFrequency, 1 );
    /*! @brief History output \n DESCRIPTION: Describes history output fields \ingroup Config */
    AddEnumListOption( "HISTORY_OUTPUT", _nHistoryOutput, _historyOutput, ScalarOutput_Map );
    /*! @brief History output Frequency \n DESCRIPTION: Describes history output write frequency \n DEFAULT 1 \ingroup Config */
    AddUnsignedShortOption( "HISTORY_OUTPUT_FREQUENCY", _historyOutputFrequency, 1 );

    // Data generator related options
    /*! @brief Choice of sampling method \n DESCRIPTION:  Choose between creating a regression and a classification dataset. \ingroup Config */
    AddEnumOption( "SAMPLER_NAME", _sampler, SamplerName_MAP, REGRESSION_SAMPLER );
    /*! @brief Size of training data set \n DESCRIPTION: Size of training data set  \n DEFAULT 1 \ingroup Config */
    AddUnsignedLongOption( "TRAINING_SET_SIZE", _tainingSetSize, 1 );
    /*! @brief Determines, if TRAINING_SET_SIZE is counted by dimension \n DESCRIPTION: Determines, if TRAINING_SET_SIZE is counted by dimension   \n
     * DEFAULT true \ingroup Config */
    AddBoolOption( "SIZE_BY_DIMENSION", _sizeByDimension, true );
    /*! @brief Size of training data set \n DESCRIPTION: Size of training data set  \n DEFAULT 10 \ingroup Config */
    AddUnsignedLongOption( "MAX_VALUE_FIRST_MOMENT", _maxValFirstMoment, 10 );
    /*! @brief Data generator mode \n DESCRIPTION: Check, if data generator mode is active. If yes, no solver is called, but instead the data
     *         generator is executed \n DEFAULT false \ingroup Config */
    AddBoolOption( "DATA_GENERATOR_MODE", _dataGeneratorMode, false );
    /*! @brief Distance to 0 of the sampled moments to the boundary of the realizable set  \n DESCRIPTION: Distance to the boundary of the
     * realizable set  \n DEFAULT 0.1 \ingroup Config */
    AddDoubleOption( "REALIZABLE_SET_EPSILON_U0", _RealizableSetEpsilonU0, 0.1 );
    /*! @brief norm(u_1)/u_0 is enforced to be smaller than _RealizableSetEpsilonU1 \n DESCRIPTION: Distance to the boundary of the realizable set  \n
     * DEFAULT 0.1 \ingroup Config */
    AddDoubleOption( "REALIZABLE_SET_EPSILON_U1", _RealizableSetEpsilonU1, 0.9 );
    /*! @brief Flag for sampling of normalized moments, i.e. u_0 =1  \n DESCRIPTION: Flag for sampling of normalized moments, i.e. u_0 =1  \n
     * DEFAULT False \ingroup Config */
    AddBoolOption( "NORMALIZED_SAMPLING", _normalizedSampling, false );
    /*! @brief Flag for sampling the space of Legendre multipliers instead of the moments  \n DESCRIPTION: Sample alpha instead of u \n DEFAULT False
     * \ingroup Config */
    AddBoolOption( "ALPHA_SAMPLING", _alphaSampling, false );
    /*! @brief Switch for sampling distribution  \n DESCRIPTION: Uniform (true) or trunctaded normal (false) \n DEFAULT true
     * \ingroup Config */
    AddBoolOption( "UNIFORM_SAMPLING", _sampleUniform, true );
    /*! @brief Boundary for the sampling region of the Lagrange multipliers  \n DESCRIPTION: Norm sampling boundary for alpha \n DEFAULT 20.0
     * \ingroup Config */
    AddDoubleOption( "ALPHA_SAMPLING_BOUND", _alphaBound, 20.0 );
    /*! @brief Rejection sampling threshold based on the minimal Eigenvalue of the Hessian of the entropy functions  \n DESCRIPTION: Rejection
     * sampling threshold \n DEFAULT 1e-8 \ingroup Config */
    AddDoubleOption( "MIN_EIGENVALUE_THRESHOLD", _minEVAlphaSampling, 1e-8 );
    /*! @brief Boundary for the velocity integral  \n DESCRIPTION: Upper boundary for the velocity integral \n DEFAULT 5.0  * \ingroup Config */
    AddDoubleOption( "MAX_VELOCITY", _maxSamplingVelocity, 5.0 );
    ///*! @brief Boundary for the velocity integral  \n DESCRIPTION: Lower boundary for the velocity integral \n DEFAULT 5.0  * \ingroup Config */
    // AddDoubleOption( "MIN_VELOCITY", _minSamplingVelocity, -5.0 );
    /*! @brief Boundary for the sampling temperature  \n DESCRIPTION: Upper boundary for the sampling temperature \n DEFAULT 1.0  * \ingroup Config */
    AddDoubleOption( "MAX_TEMPERATURE", _maxSamplingTemperature, 1 );
    /*! @brief Boundary for the sampling temperature  \n DESCRIPTION: Lower boundary for the sampling temperature \n DEFAULT 0.1  * \ingroup Config */
    AddDoubleOption( "MIN_TEMPERATURE", _minSamplingTemperature, 0.1 );
    /*! @brief Number of temperature samples  \n DESCRIPTION: Number of temperature samples for the sampler \n DEFAULT 10  * \ingroup Config */
    AddUnsignedShortOption( "N_TEMPERATURES", _nTemperatures, 10 );
}

void Config::SetConfigParsing( string case_filename ) {
    string text_line, option_name;
    ifstream case_file;
    vector<string> option_value;

    /*--- Read the configuration file ---*/

    case_file.open( case_filename, ios::in );

    if( case_file.fail() ) {
        ErrorMessages::Error( "The configuration file (.cfg) is missing!!", CURRENT_FUNCTION );
    }

    string errorString;

    int err_count     = 0;     // How many errors have we found in the config file
    int max_err_count = 30;    // Maximum number of errors to print before stopping

    map<string, bool> included_options;

    /*--- Parse the configuration file and set the options ---*/

    while( getline( case_file, text_line ) ) {

        if( err_count >= max_err_count ) {
            errorString.append( "too many errors. Stopping parse" );

            cout << errorString << endl;
            throw( 1 );
        }

        if( TokenizeString( text_line, option_name, option_value ) ) {

            /*--- See if it's a python option ---*/

            if( _optionMap.find( option_name ) == _optionMap.end() ) {
                string newString;
                newString.append( option_name );
                newString.append( ": invalid option name" );
                newString.append( ". Check current KiT-RT options in config_template.cfg." );
                newString.append( "\n" );
                errorString.append( newString );
                err_count++;
                continue;
            }

            /*--- Option exists, check if the option has already been in the config file ---*/

            if( included_options.find( option_name ) != included_options.end() ) {
                string newString;
                newString.append( option_name );
                newString.append( ": option appears twice" );
                newString.append( "\n" );
                errorString.append( newString );
                err_count++;
                continue;
            }

            /*--- New found option. Add it to the map, and delete from all options ---*/

            included_options.insert( pair<string, bool>( option_name, true ) );
            _allOptions.erase( option_name );

            /*--- Set the value and check error ---*/

            string out = _optionMap[option_name]->SetValue( option_value );
            if( out.compare( "" ) != 0 ) {
                errorString.append( out );
                errorString.append( "\n" );
                err_count++;
            }
        }
    }

    /*--- See if there were any errors parsing the config file ---*/

    if( errorString.size() != 0 ) {
        ErrorMessages::ParsingError( errorString, CURRENT_FUNCTION );
    }

    case_file.close();
}

void Config::SetPointersNull( void ) {
    // All pointer valued options should be set to NULL here
}

void Config::SetPostprocessing() {

    // append '/' to all dirs to allow for simple path addition
    if( _logDir[_logDir.size() - 1] != '/' ) _logDir.append( "/" );
    if( _outputDir[_outputDir.size() - 1] != '/' ) _outputDir.append( "/" );
    if( _inputDir[_inputDir.size() - 1] != '/' ) _inputDir.append( "/" );

    // setup relative paths
    _logDir            = std::filesystem::path( _inputDir ).append( _logDir ).lexically_normal();
    _outputDir         = std::filesystem::path( _inputDir ).append( _outputDir ).lexically_normal();
    _meshFile          = std::filesystem::path( _inputDir ).append( _meshFile ).lexically_normal();
    _outputFile        = std::filesystem::path( _outputDir ).append( _outputFile ).lexically_normal();
    _ctFile            = std::filesystem::path( _inputDir ).append( _ctFile ).lexically_normal();
    _hydrogenFile      = std::filesystem::path( _inputDir ).append( _hydrogenFile ).lexically_normal();
    _oxygenFile        = std::filesystem::path( _inputDir ).append( _oxygenFile ).lexically_normal();
    _stoppingPowerFile = std::filesystem::path( _inputDir ).append( _stoppingPowerFile ).lexically_normal();
    _dataDir           = std::filesystem::path( _inputDir ).append( _dataDir ).lexically_normal();

    // create directories if they dont exist
    if( !std::filesystem::exists( _outputDir ) ) std::filesystem::create_directories( _outputDir );

    // init logger
    InitLogger();

    // Regroup Boundary Conditions to  std::vector<std::pair<std::string, BOUNDARY_TYPE>> _boundaries;
    for( int i = 0; i < _nMarkerDirichlet; i++ ) {
        _boundaries.push_back( std::pair<std::string, BOUNDARY_TYPE>( _MarkerDirichlet[i], DIRICHLET ) );
    }
    for( int i = 0; i < _nMarkerNeumann; i++ ) {
        _boundaries.push_back( std::pair<std::string, BOUNDARY_TYPE>( _MarkerNeumann[i], NEUMANN ) );
    }

    // Set option ISCSD
    switch( _solverName ) {
        case CSD_SN_SOLVER:    // Fallthrough
        case CSD_PN_SOLVER:    // Fallthrough
        case CSD_MN_SOLVER:    // Fallthrough
            _csd = true;
            break;
        default: _csd = false;
    }

    // Set option MomentSolver
    switch( _solverName ) {
        case MN_SOLVER:
        case MN_SOLVER_NORMALIZED:
        case CSD_MN_SOLVER:
        case PN_SOLVER:
        case CSD_PN_SOLVER: _isMomentSolver = true; break;
        default: _isMomentSolver = false;
    }

    // Quadrature Postprocessing
    {
        QuadratureBase* quad                      = QuadratureBase::Create( this );
        std::vector<unsigned short> supportedDims = quad->GetSupportedDims();

        if( std::find( supportedDims.begin(), supportedDims.end(), _dim ) == supportedDims.end() ) {
            // Dimension not supported
            std::string msg = "Chosen spatial dimension not supported for this Quadrature.\nChosen spatial dimension " + std::to_string( _dim ) + ".";
            ErrorMessages::Error( msg, CURRENT_FUNCTION );
        }
        delete quad;
    }

    // Optimizer Postprocessing
    {
        if( ( _entropyOptimizerName == REDUCED_NEWTON || _entropyOptimizerName == REDUCED_PART_REGULARIZED_NEWTON ) &&
            _entropyName != MAXWELL_BOLTZMANN ) {
            std::string msg = "Reduction of the optimization problen only possible with Maxwell Boltzmann Entropy" + std::to_string( _dim ) + ".";
            ErrorMessages::Error( msg, CURRENT_FUNCTION );
        }
    }

    // --- Solver setup ---
    {
        if( GetSolverName() == PN_SOLVER && GetSphericalBasisName() != SPHERICAL_HARMONICS ) {
            ErrorMessages::Error(
                "PN Solver only works with spherical harmonics basis.\nThis should be the default setting for option SPHERICAL_BASIS.",
                CURRENT_FUNCTION );
        }

        if( GetSolverName() == CSD_MN_SOLVER && GetSphericalBasisName() != SPHERICAL_HARMONICS ) {
            ErrorMessages::Error( "CSD_MN_SOLVER only works with Spherical Harmonics currently.", CURRENT_FUNCTION );
        }

        if( GetSpatialOrder() > 2 ) {
            ErrorMessages::Error( "Solvers only work with 1st and 2nd order spatial fluxes.", CURRENT_FUNCTION );
        }

        if( GetOptimizerName() == ML && GetSolverName() != MN_SOLVER_NORMALIZED ) {
            ErrorMessages::Error( "ML Optimizer only works with normalized MN Solver.", CURRENT_FUNCTION );
        }

        if( GetSolverName() == PN_SOLVER || GetSolverName() == CSD_PN_SOLVER ) {
            _dim        = 3;
            auto log    = spdlog::get( "event" );
            auto logCSV = spdlog::get( "tabular" );
            log->info(
                "| Spherical harmonics based solver currently use 3D Spherical functions and a projection. Thus spatial dimension is set to 3." );
            logCSV->info(
                "| Spherical harmonics based solver currently use 3D Spherical functions and a projection. Thus spatial dimension is set to 3." );
        }
    }

    // --- Output Postprocessing ---

    // Volume Output Postprocessing
    {
        // Check for doublicates in VOLUME OUTPUT
        std::map<VOLUME_OUTPUT, int> dublicate_map;

        for( unsigned short idx_volOutput = 0; idx_volOutput < _nVolumeOutput; idx_volOutput++ ) {
            std::map<VOLUME_OUTPUT, int>::iterator it = dublicate_map.find( _volumeOutput[idx_volOutput] );
            if( it == dublicate_map.end() ) {
                dublicate_map.insert( std::pair<VOLUME_OUTPUT, int>( _volumeOutput[idx_volOutput], 0 ) );
            }
            else {
                it->second++;
            }
        }
        for( auto& e : dublicate_map ) {
            if( e.second > 0 ) {
                ErrorMessages::Error( "Each output group for option VOLUME_OUTPUT can only be set once.\nPlease check your .cfg file.",
                                      CURRENT_FUNCTION );
            }
        }

        // Check, if the choice of volume output is compatible to the solver
        std::vector<VOLUME_OUTPUT> supportedGroups;

        for( unsigned short idx_volOutput = 0; idx_volOutput < _nVolumeOutput; idx_volOutput++ ) {
            switch( _solverName ) {
                case SN_SOLVER:
                    if( _problemName == PROBLEM_Linesource )
                        supportedGroups = { MINIMAL, ANALYTIC };
                    else {
                        supportedGroups = { MINIMAL };
                        if( _HPC ) supportedGroups = { MINIMAL, MOMENTS };
                    }

                    if( supportedGroups.end() == std::find( supportedGroups.begin(), supportedGroups.end(), _volumeOutput[idx_volOutput] ) ) {
                        ErrorMessages::Error(
                            "SN_SOLVER only supports volume output MINIMAL and ANALYTIC (and experimentally MOMENTS).\nPlease check your .cfg file.",
                            CURRENT_FUNCTION );
                    }
                    if( _volumeOutput[idx_volOutput] == ANALYTIC && _problemName != PROBLEM_Linesource ) {
                        ErrorMessages::Error( "Analytical solution (VOLUME_OUTPUT=ANALYTIC) is only available for the PROBLEM=LINESOURCE.\nPlease "
                                              "check your .cfg file.",
                                              CURRENT_FUNCTION );
                    }
                    break;
                case MN_SOLVER:    // Fallthrough
                case MN_SOLVER_NORMALIZED:
                    if( _problemName == PROBLEM_SymmetricHohlraum )
                        supportedGroups = { MINIMAL, MOMENTS, DUAL_MOMENTS };
                    else if( _problemName == PROBLEM_Linesource )
                        supportedGroups = { MINIMAL, ANALYTIC, MOMENTS, DUAL_MOMENTS };
                    else
                        supportedGroups = { MINIMAL, MOMENTS, DUAL_MOMENTS };
                    if( supportedGroups.end() == std::find( supportedGroups.begin(), supportedGroups.end(), _volumeOutput[idx_volOutput] ) ) {
                        std::string supportedGroupStr = "";
                        for( unsigned i = 0; i < supportedGroups.size(); i++ ) {
                            supportedGroupStr += findKey( VolOutput_Map, supportedGroups[i] ) + ", ";
                        }
                        ErrorMessages::Error( "MN_SOLVER supports volume outputs" + supportedGroupStr + ".\nPlease check your .cfg file.",
                                              CURRENT_FUNCTION );
                    }
                    break;
                case PN_SOLVER:
                    supportedGroups = { MINIMAL, MOMENTS, ANALYTIC };
                    if( supportedGroups.end() == std::find( supportedGroups.begin(), supportedGroups.end(), _volumeOutput[idx_volOutput] ) ) {

                        ErrorMessages::Error( "PN_SOLVER only supports volume output ANALYTIC, MINIMAL and MOMENTS.\nPlease check your .cfg file.",
                                              CURRENT_FUNCTION );
                    }
                    if( _volumeOutput[idx_volOutput] == ANALYTIC && _problemName != PROBLEM_Linesource ) {
                        ErrorMessages::Error( "Analytical solution (VOLUME_OUTPUT=ANALYTIC) is only available for the PROBLEM=LINESOURCE.\nPlease "
                                              "check your .cfg file.",
                                              CURRENT_FUNCTION );
                    }
                    break;
                case CSD_SN_SOLVER:
                    supportedGroups = { MINIMAL, MEDICAL };
                    if( supportedGroups.end() == std::find( supportedGroups.begin(), supportedGroups.end(), _volumeOutput[idx_volOutput] ) ) {

                        ErrorMessages::Error( "CSD_SN_SOLVER types only supports volume output MEDICAL and MINIMAL.\nPlease check your .cfg file.",
                                              CURRENT_FUNCTION );
                    }
                    break;
                case CSD_PN_SOLVER:
                    supportedGroups = { MINIMAL, MEDICAL, MOMENTS };
                    if( supportedGroups.end() == std::find( supportedGroups.begin(), supportedGroups.end(), _volumeOutput[idx_volOutput] ) ) {

                        ErrorMessages::Error(
                            "CSD_PN_SOLVER types only supports volume output MEDICAL, MOMENTS and MINIMAL.\nPlease check your .cfg file.",
                            CURRENT_FUNCTION );
                    }
                    break;
                case CSD_MN_SOLVER:
                    supportedGroups = { MINIMAL, MEDICAL, MOMENTS, DUAL_MOMENTS };
                    if( supportedGroups.end() == std::find( supportedGroups.begin(), supportedGroups.end(), _volumeOutput[idx_volOutput] ) ) {

                        ErrorMessages::Error( "CSD_MN_SOLVER types only supports volume output MEDICAL, MOMENTS, DUAL_MOMENTS and MINIMAL.\nPlease "
                                              "check your .cfg file.",
                                              CURRENT_FUNCTION );
                    }
                    break;
                default:
                    ErrorMessages::Error( "Solver output check not implemented for this Solver.\nThis is the fault of the coder.", CURRENT_FUNCTION );
            }
        }

        // Set default volume output
        if( _nVolumeOutput == 0 ) {    // If no specific output is chosen,  use "MINIMAL"
            _nVolumeOutput = 1;
            _volumeOutput.push_back( MINIMAL );
        }
    }

    // Screen Output Postprocessing
    {
        // Check for doublicates in SCALAR OUTPUT
        std::map<SCALAR_OUTPUT, int> dublicate_map;

        for( unsigned short idx_screenOutput = 0; idx_screenOutput < _nScreenOutput; idx_screenOutput++ ) {
            std::map<SCALAR_OUTPUT, int>::iterator it = dublicate_map.find( _screenOutput[idx_screenOutput] );
            if( it == dublicate_map.end() ) {
                dublicate_map.insert( std::pair<SCALAR_OUTPUT, int>( _screenOutput[idx_screenOutput], 0 ) );
            }
            else {
                it->second++;
            }
        }
        for( auto& e : dublicate_map ) {
            if( e.second > 0 ) {
                ErrorMessages::Error( "Each output field for option SCREEN_OUTPUT can only be set once.\nPlease check your .cfg file.",
                                      CURRENT_FUNCTION );
            }
        }
        // Check if the choice of screen output is compatible to the problem
        for( unsigned short idx_screenOutput = 0; idx_screenOutput < _nScreenOutput; idx_screenOutput++ ) {
            std::vector<SCALAR_OUTPUT> legalOutputs;
            std::vector<SCALAR_OUTPUT>::iterator it;
            switch( _problemName ) {
                case PROBLEM_HalfLattice:
                case PROBLEM_Lattice:
                    legalOutputs = { ITER,
                                     WALL_TIME,
                                     SIM_TIME,
                                     MASS,
                                     RMS_FLUX,
                                     VTK_OUTPUT,
                                     CSV_OUTPUT,
                                     CUR_OUTFLOW,
                                     TOTAL_OUTFLOW,
                                     CUR_OUTFLOW_P1,
                                     TOTAL_OUTFLOW_P1,
                                     CUR_OUTFLOW_P2,
                                     TOTAL_OUTFLOW_P2,
                                     MAX_OUTFLOW,
                                     CUR_PARTICLE_ABSORPTION,
                                     TOTAL_PARTICLE_ABSORPTION,
                                     MAX_PARTICLE_ABSORPTION };
                    it           = std::find( legalOutputs.begin(), legalOutputs.end(), _screenOutput[idx_screenOutput] );
                    if( it == legalOutputs.end() ) {
                        std::string foundKey = findKey( ScalarOutput_Map, _screenOutput[idx_screenOutput] );
                        ErrorMessages::Error(
                            "Illegal output field <" + foundKey +
                                "> for option SCREEN_OUTPUT for this test case.\n"
                                "Supported fields are: ITER, SIM_TIME, WALL_TIME, MASS, RMS_FLUX, VTK_OUTPUT, CSV_OUTPUT, FINAL_TIME_OUTFLOW, TOTAL_OUTFLOW, MAX_OUTFLOW, "
                                "FINAL_TIME_PARTICLE_ABSORPTION, TOTAL_PARTICLE_ABSORPTION, MAX_PARTICLE_ABSORPTION\n"
                                "Please check your .cfg file.",
                            CURRENT_FUNCTION );
                    }
                    break;
                case PROBLEM_QuarterHohlraum:
                case PROBLEM_SymmetricHohlraum:
                    legalOutputs = {
                        ITER,
                        SIM_TIME,
                        WALL_TIME,
                        MASS,
                        RMS_FLUX,
                        VTK_OUTPUT,
                        CSV_OUTPUT,
                        CUR_OUTFLOW,
                        TOTAL_OUTFLOW,
                        MAX_OUTFLOW,
                        TOTAL_PARTICLE_ABSORPTION_CENTER,
                        TOTAL_PARTICLE_ABSORPTION_VERTICAL,
                        TOTAL_PARTICLE_ABSORPTION_HORIZONTAL,
                        TOTAL_PARTICLE_ABSORPTION,
                        PROBE_MOMENT_TIME_TRACE,
                        VAR_ABSORPTION_GREEN,
                        AVG_ABSORPTION_GREEN_BLOCK_INTEGRATED,
                        VAR_ABSORPTION_GREEN_BLOCK_INTEGRATED,
                    };

                    it = std::find( legalOutputs.begin(), legalOutputs.end(), _screenOutput[idx_screenOutput] );

                    if( it == legalOutputs.end() ) {
                        std::string foundKey = findKey( ScalarOutput_Map, _screenOutput[idx_screenOutput] );
                        ErrorMessages::Error(
                                "Illegal output field <" + foundKey +
                                "> for option SCREEN_OUTPUT for this test case.\n"
                                "Supported fields are: ITER, SIM_TIME, WALL_TIME, MASS, RMS_FLUX, VTK_OUTPUT, CSV_OUTPUT, TOTAL_PARTICLE_ABSORPTION_CENTER, \n"
                                "TOTAL_PARTICLE_ABSORPTION_VERTICAL, TOTAL_PARTICLE_ABSORPTION_HORIZONTAL, PROBE_MOMENT_TIME_TRACE, CUR_OUTFLOW, \n "
                                "TOTAL_OUTFLOW, MAX_OUTFLOW, VAR_ABSORPTION_GREEN, AVG_ABSORPTION_GREEN_BLOCK_INTEGRATED, "
                                "VAR_ABSORPTION_GREEN_BLOCK_INTEGRATED \n"
                                "Please check your .cfg file.",
                            CURRENT_FUNCTION );
                    }
                    break;

                default:
                    legalOutputs = { ITER, SIM_TIME, WALL_TIME, MASS, RMS_FLUX, VTK_OUTPUT, CSV_OUTPUT, CUR_OUTFLOW, TOTAL_OUTFLOW, MAX_OUTFLOW };
                    it           = std::find( legalOutputs.begin(), legalOutputs.end(), _screenOutput[idx_screenOutput] );

                    if( it == legalOutputs.end() ) {
                        std::string foundKey = findKey( ScalarOutput_Map, _screenOutput[idx_screenOutput] );
                        ErrorMessages::Error(
                            "Illegal output field <" + foundKey +
                                "> for option SCREEN_OUTPUT for this test case.\n"
                                "Supported fields are: ITER, SIM_TIME, WALL_TIME, MASS RMS_FLUX, VTK_OUTPUT, CSV_OUTPUT, CUR_OUTFLOW, TOTAL_OUTFLOW, MAX_OUTFLOW \n"
                                "Please check your .cfg file.",
                            CURRENT_FUNCTION );
                    }
                    break;
            }
        }
        // Set ITER always to index 0 . Assume only one instance of iter is chosen
        if( _nScreenOutput > 0 ) {
            std::vector<SCALAR_OUTPUT>::iterator it;
            it = find( _screenOutput.begin(), _screenOutput.end(), ITER );
            _screenOutput.erase( it );
            _screenOutput.insert( _screenOutput.begin(), ITER );
        }
        // Set default screen output
        if( _nScreenOutput == 0 ) {
            _nScreenOutput = 4;
            _screenOutput.push_back( ITER );
            _screenOutput.push_back( RMS_FLUX );
            _screenOutput.push_back( MASS );
            _screenOutput.push_back( VTK_OUTPUT );
        }

        // Postprocessing for probing moments in symmetric Hohlraum. Make it four outputs
        if( _problemName == PROBLEM_SymmetricHohlraum ) {
            std::vector<SCALAR_OUTPUT>::iterator it;

            it = find( _screenOutput.begin(), _screenOutput.end(), PROBE_MOMENT_TIME_TRACE );

            if( it != _screenOutput.end() ) {
                _screenOutput.erase( it );
                _nScreenOutput += 3;    // extend the screen output by the number of probing points
                for( unsigned i = 0; i < 4; i++ ) _screenOutput.push_back( PROBE_MOMENT_TIME_TRACE );
            }
        }
        if( _problemName == PROBLEM_QuarterHohlraum ) {
            std::vector<SCALAR_OUTPUT>::iterator it;

            it = find( _screenOutput.begin(), _screenOutput.end(), PROBE_MOMENT_TIME_TRACE );

            if( it != _screenOutput.end() ) {
                _screenOutput.erase( it );
                _nScreenOutput += 1;    // extend the screen output by the number of probing points
                for( unsigned i = 0; i < 2; i++ ) _screenOutput.push_back( PROBE_MOMENT_TIME_TRACE );
            }
        }
    }

    // History Output Postprocessing
    {
        // Check for doublicates in HISTORY OUTPUT
        std::map<SCALAR_OUTPUT, int> dublicate_map;

        for( unsigned idx_historyOutput = 0; idx_historyOutput < _nHistoryOutput; idx_historyOutput++ ) {
            std::map<SCALAR_OUTPUT, int>::iterator it = dublicate_map.find( _historyOutput[idx_historyOutput] );
            if( it == dublicate_map.end() ) {
                dublicate_map.insert( std::pair<SCALAR_OUTPUT, int>( _historyOutput[idx_historyOutput], 0 ) );
            }
            else {
                it->second++;
            }
        }
        for( auto& e : dublicate_map ) {
            if( e.second > 0 ) {
                ErrorMessages::Error( "Each output field for option HISTORY_OUTPUT can only be set once.\nPlease check your .cfg file.",
                                      CURRENT_FUNCTION );
            }
        }

        // Check if the choice of history output is compatible to the problem
        for( unsigned short idx_historyOutput = 0; idx_historyOutput < _nHistoryOutput; idx_historyOutput++ ) {
            std::vector<SCALAR_OUTPUT> legalOutputs;
            std::vector<SCALAR_OUTPUT>::iterator it;

            switch( _problemName ) {
                case PROBLEM_HalfLattice:
                case PROBLEM_Lattice:
                    legalOutputs = { ITER,
                                     WALL_TIME,
                                     SIM_TIME,
                                     MASS,
                                     RMS_FLUX,
                                     VTK_OUTPUT,
                                     CSV_OUTPUT,
                                     CUR_OUTFLOW,
                                     TOTAL_OUTFLOW,
                                     CUR_OUTFLOW_P1,
                                     TOTAL_OUTFLOW_P1,
                                     CUR_OUTFLOW_P2,
                                     TOTAL_OUTFLOW_P2,
                                     MAX_OUTFLOW,
                                     CUR_PARTICLE_ABSORPTION,
                                     TOTAL_PARTICLE_ABSORPTION,
                                     MAX_PARTICLE_ABSORPTION };
                    it           = std::find( legalOutputs.begin(), legalOutputs.end(), _historyOutput[idx_historyOutput] );
                    if( it == legalOutputs.end() ) {
                        std::string foundKey = findKey( ScalarOutput_Map, _historyOutput[idx_historyOutput] );
                        ErrorMessages::Error(
                            "Illegal output field <" + foundKey +
                                "> for option HISTORY_OUTPUT for this test case.\n"
                                "Supported fields are: ITER, SIM_TIME, WALL_TIME, MASS, RMS_FLUX, VTK_OUTPUT, CSV_OUTPUT, FINAL_TIME_OUTFLOW,\n"
                                "TOTAL_OUTFLOW, MAX_OUTFLOW, FINAL_TIME_PARTICLE_ABSORPTION, TOTAL_PARTICLE_ABSORPTION, MAX_PARTICLE_ABSORPTION\n"
                                "Please check your .cfg file.",
                            CURRENT_FUNCTION );
                    }
                    break;
                case PROBLEM_QuarterHohlraum:
                case PROBLEM_SymmetricHohlraum:
                    legalOutputs = { ITER,
                                     WALL_TIME,
                                     SIM_TIME,
                                     MASS,
                                     RMS_FLUX,
                                     VTK_OUTPUT,
                                     CSV_OUTPUT,
                                     CUR_OUTFLOW,
                                     TOTAL_OUTFLOW,
                                     MAX_OUTFLOW,
                                     TOTAL_PARTICLE_ABSORPTION_CENTER,
                                     TOTAL_PARTICLE_ABSORPTION_VERTICAL,
                                     TOTAL_PARTICLE_ABSORPTION_HORIZONTAL,
                                     TOTAL_PARTICLE_ABSORPTION,
                                     PROBE_MOMENT_TIME_TRACE,
                                     VAR_ABSORPTION_GREEN,
                                     ABSORPTION_GREEN_BLOCK,
                                     AVG_ABSORPTION_GREEN_BLOCK_INTEGRATED,
                                     VAR_ABSORPTION_GREEN_BLOCK_INTEGRATED,
                                     ABSORPTION_GREEN_LINE };

                    it = std::find( legalOutputs.begin(), legalOutputs.end(), _historyOutput[idx_historyOutput] );

                    if( it == legalOutputs.end() ) {
                        std::string foundKey = findKey( ScalarOutput_Map, _historyOutput[idx_historyOutput] );
                        ErrorMessages::Error(
                            "Illegal output field <" + foundKey +
                                "> for option HISTORY_OUTPUT for this test case.\n"
                                "Supported fields are: ITER, SIM_TIME, WALL_TIME, MASS RMS_FLUX, VTK_OUTPUT, CSV_OUTPUT, TOTAL_PARTICLE_ABSORPTION_CENTER, \n "
                                "TOTAL_PARTICLE_ABSORPTION_VERTICAL, TOTAL_PARTICLE_ABSORPTION_HORIZONTAL,PROBE_MOMENT_TIME_TRACE,  CUR_OUTFLOW, \n"
                                "TOTAL_OUTFLOW, MAX_OUTFLOW , VAR_ABSORPTION_GREEN, ABSORPTION_GREEN_BLOCK, "
                                "AVG_ABSORPTION_GREEN_BLOCK_INTEGRATED, VAR_ABSORPTION_GREEN_BLOCK_INTEGRATED, ABSORPTION_GREEN_LINE \n"
                                "Please check your .cfg file.",
                            CURRENT_FUNCTION );
                    }
                    break;

                default:
                    legalOutputs = { ITER, WALL_TIME, SIM_TIME, MASS, RMS_FLUX, VTK_OUTPUT, CSV_OUTPUT, CUR_OUTFLOW, TOTAL_OUTFLOW, MAX_OUTFLOW };
                    it           = std::find( legalOutputs.begin(), legalOutputs.end(), _historyOutput[idx_historyOutput] );

                    if( it == legalOutputs.end() ) {
                        std::string foundKey = findKey( ScalarOutput_Map, _historyOutput[idx_historyOutput] );
                        ErrorMessages::Error(
                            "Illegal output field <" + foundKey +
                                "> for option SCREEN_OUTPUT for this test case.\n"
                                "Supported fields are: ITER, SIM_TIME, WALL_TIME, MASS RMS_FLUX, VTK_OUTPUT, CSV_OUTPUT, CUR_OUTFLOW, TOTAL_OUTFLOW, MAX_OUTFLOW \n"
                                "Please check your .cfg file.",
                            CURRENT_FUNCTION );
                    }
                    break;
            }
        }

        // Set ITER always to index 0 . Assume only one instance of iter is chosen
        if( _nHistoryOutput > 0 ) {
            std::vector<SCALAR_OUTPUT>::iterator it;
            it = find( _historyOutput.begin(), _historyOutput.end(), ITER );
            _historyOutput.erase( it );
            _historyOutput.insert( _historyOutput.begin(), ITER );
        }
        // Set default screen output
        if( _nHistoryOutput == 0 ) {
            _nHistoryOutput = 5;
            _historyOutput.push_back( ITER );
            _historyOutput.push_back( MASS );
            _historyOutput.push_back( RMS_FLUX );
            _historyOutput.push_back( VTK_OUTPUT );
            _historyOutput.push_back( CSV_OUTPUT );
        }

        // Postprocessing for probing moments in symmetric Hohlraum. Make it four outputs
        if( _problemName == PROBLEM_SymmetricHohlraum ) {
            std::vector<SCALAR_OUTPUT>::iterator it;
            it = find( _historyOutput.begin(), _historyOutput.end(), PROBE_MOMENT_TIME_TRACE );
            if( it != _historyOutput.end() ) {
                _historyOutput.erase( it );
                _nHistoryOutput += 11;    // extend the screen output by the number of probing points
                for( unsigned i = 0; i < 12; i++ ) _historyOutput.push_back( PROBE_MOMENT_TIME_TRACE );
            }
        }
        if( _problemName == PROBLEM_QuarterHohlraum ) {
            std::vector<SCALAR_OUTPUT>::iterator it;
            it = find( _historyOutput.begin(), _historyOutput.end(), PROBE_MOMENT_TIME_TRACE );
            if( it != _historyOutput.end() ) {
                _historyOutput.erase( it );
                _nHistoryOutput += 5;    // extend the screen output by the number of probing points
                for( unsigned i = 0; i < 6; i++ ) _historyOutput.push_back( PROBE_MOMENT_TIME_TRACE );
            }
        }

        if( _problemName == PROBLEM_SymmetricHohlraum || _problemName == PROBLEM_QuarterHohlraum ) {
            std::vector<SCALAR_OUTPUT>::iterator it;
            it = find( _historyOutput.begin(), _historyOutput.end(), ABSORPTION_GREEN_LINE );
            if( it != _historyOutput.end() ) {
                _historyOutput.erase( it );
                _nHistoryOutput += _nProbingCellsLineGreenHohlraum - 1;    // extend the screen output by the number of probing points
                for( unsigned i = 0; i < _nProbingCellsLineGreenHohlraum; i++ ) _historyOutput.push_back( ABSORPTION_GREEN_LINE );
            }

            it = find( _historyOutput.begin(), _historyOutput.end(), ABSORPTION_GREEN_BLOCK );
            if( it != _historyOutput.end() ) {
                _historyOutput.erase( it );
                _nHistoryOutput += 44 - 1;    // extend the screen output by the number of probing points
                for( unsigned i = 0; i < 44; i++ ) _historyOutput.push_back( ABSORPTION_GREEN_BLOCK );
            }

        }
    }

    // Mesh postprocessing
    {
        if( _dim < (unsigned short)1 || _dim > (unsigned short)3 ) {
            std::string msg = "Dimension " + std::to_string( _dim ) + "not supported.\n";
            ErrorMessages::Error( msg, CURRENT_FUNCTION );
        }
    }

    // Data generator postprocessing
    {
        if( _alphaBound <= 0 ) {
            std::string msg = "Norm boundary for alpha sampling must be positive.\n Current choice: " + std::to_string( _alphaSampling ) +
                              ". Check choice of ALPHA_SAMPLING_BOUND.";
            ErrorMessages::Error( msg, CURRENT_FUNCTION );
        }
        if( _minEVAlphaSampling <= 0 ) {
            std::string msg =
                "Minimal Eigenvalue threshold of the entropy hession must be positive.\n Current choice: " + std::to_string( _alphaSampling ) +
                ". Check choice of MIN_EIGENVALUE_THRESHOLD.";
            ErrorMessages::Error( msg, CURRENT_FUNCTION );
        }
    }

    // Optimizer postprocessing
    {
        if( _regularizerGamma <= 0.0 ) {
            ErrorMessages::Error( "REGULARIZER_GAMMA must be positive.", CURRENT_FUNCTION );
        }

        if( _entropyOptimizerName == ML ) {
            // set regularizer gamma to the correct value
            switch( _neuralGamma ) {
                case 0: _regularizerGamma = 0; break;
                case 1: _regularizerGamma = 0.1; break;
                case 2: _regularizerGamma = 0.01; break;
                case 3: _regularizerGamma = 0.001; break;
            }
        }
        if( _entropyOptimizerName == NEWTON ) {
            _regularizerGamma = 0.0;
        }
    }
}

void Config::SetOutput() {
    // Set Output for settings, i.e. feedback on what has been chosen
}

bool Config::TokenizeString( string& str, string& option_name, vector<string>& option_value ) {
    const string delimiters( " (){}:,\t\n\v\f\r" );
    // check for comments or empty string
    string::size_type pos, last_pos;
    pos = str.find_first_of( "%" );
    if( ( str.length() == 0 ) || ( pos == 0 ) ) {
        // str is empty or a comment line, so no option here
        return false;
    }
    if( pos != string::npos ) {
        // remove comment at end if necessary
        str.erase( pos );
    }

    // look for line composed on only delimiters (usually whitespace)
    pos = str.find_first_not_of( delimiters );
    if( pos == string::npos ) {
        return false;
    }

    // find the equals sign and split string
    string name_part, value_part;
    pos = str.find( "=" );
    if( pos == string::npos ) {
        string errmsg = "Error in Config::TokenizeString(): line in the configuration file with no \"=\" sign.  ";
        errmsg += "\nLook for: \n  str.length() = " + std::to_string( str.length() );
        spdlog::error( errmsg );
        throw( -1 );
    }
    name_part  = str.substr( 0, pos );
    value_part = str.substr( pos + 1, string::npos );

    // the first_part should consist of one string with no interior delimiters
    last_pos = name_part.find_first_not_of( delimiters, 0 );
    pos      = name_part.find_first_of( delimiters, last_pos );
    if( ( name_part.length() == 0 ) || ( last_pos == string::npos ) ) {
        string errmsg = "Error in Config::TokenizeString(): ";
        errmsg += "line in the configuration file with no name before the \"=\" sign.\n";
        spdlog::error( errmsg );
        throw( -1 );
    }
    if( pos == string::npos ) pos = name_part.length();
    option_name = name_part.substr( last_pos, pos - last_pos );
    last_pos    = name_part.find_first_not_of( delimiters, pos );
    if( last_pos != string::npos ) {
        string errmsg = "Error in  Config::TokenizeString(): ";
        errmsg += "two or more options before an \"=\" sign in the configuration file.";
        spdlog::error( errmsg );
        throw( -1 );
    }
    TextProcessingToolbox::StringToUpperCase( option_name );

    // now fill the option value vector
    option_value.clear();
    last_pos = value_part.find_first_not_of( delimiters, 0 );
    pos      = value_part.find_first_of( delimiters, last_pos );
    while( string::npos != pos || string::npos != last_pos ) {
        // add token to the vector<string>
        option_value.push_back( value_part.substr( last_pos, pos - last_pos ) );
        // skip delimiters
        last_pos = value_part.find_first_not_of( delimiters, pos );
        // find next "non-delimiter"
        pos = value_part.find_first_of( delimiters, last_pos );
    }
    if( option_value.size() == 0 ) {
        string errmsg = "Error in  Config::TokenizeString(): ";
        errmsg += "option " + option_name + " in configuration file with no value assigned.\n";
        spdlog::error( errmsg );
        throw( -1 );
    }

    // look for ';' DV delimiters attached to values
    vector<string>::iterator it;
    it = option_value.begin();
    while( it != option_value.end() ) {
        if( it->compare( ";" ) == 0 ) {
            it++;
            continue;
        }

        pos = it->find( ';' );
        if( pos != string::npos ) {
            string before_semi = it->substr( 0, pos );
            string after_semi  = it->substr( pos + 1, string::npos );
            if( before_semi.empty() ) {
                *it = ";";
                it++;
                option_value.insert( it, after_semi );
            }
            else {
                *it = before_semi;
                it++;
                vector<string> to_insert;
                to_insert.push_back( ";" );
                if( !after_semi.empty() ) to_insert.push_back( after_semi );
                option_value.insert( it, to_insert.begin(), to_insert.end() );
            }
            it = option_value.begin();    // go back to beginning; not efficient
            continue;
        }
        else {
            it++;
        }
    }

    // remove any consecutive ";"
    it                = option_value.begin();
    bool semi_at_prev = false;
    while( it != option_value.end() ) {
        if( semi_at_prev ) {
            if( it->compare( ";" ) == 0 ) {
                option_value.erase( it );
                it           = option_value.begin();
                semi_at_prev = false;
                continue;
            }
        }
        if( it->compare( ";" ) == 0 ) {
            semi_at_prev = true;
        }
        else {
            semi_at_prev = false;
        }
        it++;
    }

    return true;
}

void Config::InitLogger() {
    int rank = 0;
#ifdef IMPORT_MPI
    MPI_Comm_rank( MPI_COMM_WORLD, &rank );    // Initialize MPI
#endif

    if( rank == 0 ) {

        // Declare Logger
        spdlog::level::level_enum terminalLogLvl;
        spdlog::level::level_enum fileLogLvl;

        // Choose Logger
#ifdef BUILD_TESTING
        terminalLogLvl = spdlog::level::err;
        fileLogLvl     = spdlog::level::info;
#elif NDEBUG
        terminalLogLvl = spdlog::level::info;
        fileLogLvl     = spdlog::level::info;
#else
        terminalLogLvl = spdlog::level::debug;
        fileLogLvl     = spdlog::level::debug;
#endif

        // create log dir if not existent
        if( !std::filesystem::exists( _logDir ) ) {
            std::filesystem::create_directories( _logDir );
        }

        if( !spdlog::get( "event" ) ) {
            // create sinks if level is not off
            std::vector<spdlog::sink_ptr> sinks;
            if( terminalLogLvl != spdlog::level::off ) {
                // create spdlog terminal sink
                auto terminalSink = std::make_shared<spdlog::sinks::stdout_sink_mt>();
                terminalSink->set_level( terminalLogLvl );
                terminalSink->set_pattern( "%v" );
                sinks.push_back( terminalSink );
            }
            if( fileLogLvl != spdlog::level::off ) {
                // define filename on root
                // int pe = 0;
                // MPI_Comm_rank( MPI_COMM_WORLD, &pe );
                // char cfilename[1024];

                // if( pe == 0 ) {
                //  get date and time
                time_t now = time( nullptr );
                struct tm tstruct;
                char buf[80];
                tstruct = *localtime( &now );
                strftime( buf, sizeof( buf ), "%Y-%m-%d_%X", &tstruct );

                // set filename
                std::string filepathStr;
                if( _logFileName.compare( "use_date" ) == 0 ) {
                    _logFileName = buf;    // set filename to date and time
                    filepathStr  = _logDir + _logFileName;
                }
                else {
                    std::filesystem::path filePath( _logDir + _logFileName );
                    std::string baseFilename( _logDir + _logFileName );
                    filepathStr = _logDir + _logFileName;
                    // Check if the file with the original name exists
                    if( std::filesystem::exists( filePath ) ) {
                        // Extract the stem and extension
                        std::string stem      = filePath.stem().string();
                        std::string extension = filePath.extension().string();

                        // Counter for incrementing the filename
                        int counter = 1;

                        // Keep incrementing the counter until a unique filename is found
                        while( std::filesystem::exists( filePath ) ) {
                            stem = baseFilename + std::to_string( counter );
                            filePath.replace_filename( stem + extension );
                            counter++;
                        }
                    }
                    filepathStr = filePath.string();
                }
                //}
                // MPI_Bcast( &cfilename, sizeof( cfilename ), MPI_CHAR, 0, MPI_COMM_WORLD );
                // MPI_Barrier( MPI_COMM_WORLD );

                // create spdlog file sink
                auto fileSink = std::make_shared<spdlog::sinks::basic_file_sink_mt>( filepathStr );
                fileSink->set_level( fileLogLvl );
                fileSink->set_pattern( "%Y-%m-%d %H:%M:%S.%f | %v" );
                sinks.push_back( fileSink );
            }

            // register all sinks
            auto event_logger = std::make_shared<spdlog::logger>( "event", begin( sinks ), end( sinks ) );
            spdlog::register_logger( event_logger );
            spdlog::flush_every( std::chrono::seconds( 5 ) );
        }

        if( !spdlog::get( "tabular" ) ) {
            // create sinks if level is not off
            std::vector<spdlog::sink_ptr> sinks;
            if( fileLogLvl != spdlog::level::off ) {
                // define filename on root
                // int pe = 0;
                // MPI_Comm_rank( MPI_COMM_WORLD, &pe );
                // char cfilename[1024];

                // if( pe == 0 ) {
                //  get date and time
                time_t now = time( nullptr );
                struct tm tstruct;
                char buf[80];
                tstruct = *localtime( &now );
                strftime( buf, sizeof( buf ), "%Y-%m-%d_%X.csv", &tstruct );

                // set filename
                // set filename
                std::string filepathStr;
                if( _logFileName.compare( "use_date" ) == 0 ) {
                    _logFileName = buf;    // set filename to date and time
                    filepathStr  = _logDir + _logFileName + ".csv";
                }
                else {
                    std::filesystem::path filePath( _logDir + _logFileName + ".csv" );
                    std::string baseFilename( _logDir + _logFileName );
                    filepathStr = _logDir + _logFileName + ".csv";
                    // Check if the file with the original name exists
                    if( std::filesystem::exists( filePath ) ) {
                        // Extract the stem and extension
                        std::string stem      = filePath.stem().string();
                        std::string extension = filePath.extension().string();

                        // Counter for incrementing the filename
                        int counter = 1;

                        // Keep incrementing the counter until a unique filename is found
                        while( std::filesystem::exists( filePath ) ) {
                            stem = baseFilename + std::to_string( counter );
                            filePath.replace_filename( stem + extension );
                            counter++;
                        }
                    }
                    filepathStr = filePath.string();
                }
                //}
                // MPI_Bcast( &cfilename, sizeof( cfilename ), MPI_CHAR, 0, MPI_COMM_WORLD );
                // MPI_Barrier( MPI_COMM_WORLD );

                // create spdlog file sink
                auto fileSink = std::make_shared<spdlog::sinks::basic_file_sink_mt>( filepathStr );
                fileSink->set_level( fileLogLvl );
                fileSink->set_pattern( "%Y-%m-%d %H:%M:%S.%f ,%v" );
                sinks.push_back( fileSink );
            }

            // register all sinks
            auto tabular_logger = std::make_shared<spdlog::logger>( "tabular", begin( sinks ), end( sinks ) );
            spdlog::register_logger( tabular_logger );
            spdlog::flush_every( std::chrono::seconds( 5 ) );
        }
    }
#ifdef IMPORT_MPI
    MPI_Barrier( MPI_COMM_WORLD );
#endif
}

// Function to find the key for a given value in a map
template <typename K, typename V> K Config::findKey( const std::map<K, V>& myMap, const V& valueToFind ) {
    for( const auto& pair : myMap ) {
        if( pair.second == valueToFind ) {
            return pair.first;    // Return the key if the value is found
        }
    }
    // If the value is not found, you can return a default value or throw an exception
    throw std::out_of_range( "Value not found in the map" );
}

CSMMLab / KiT-RT / #143

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