fixed neighbor to normal sorting; fixed index error; all fluxes of cell a to b...

fixed neighbor to normal sorting; fixed index error; all fluxes of cell a to b are equal to b to a everywhere

code/CMakeLists.txt

 cmake_minimum_required( VERSION 3.12.4 )
 project( RTSN LANGUAGES C CXX VERSION 0.0.1 )
-set( CMAKE_CXX_STANDARD 20 )
+set( CMAKE_CXX_STANDARD 17 )
 set( CMAKE_CXX_STANDARD_REQUIRED ON )
 
 set( CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -O3 -march=native -Wno-dev -DNDEBUG" )

code/config_template.cfg

-% This is a comment
-%%%%%%%%%%%%%%%%%%%%%%
-% Example config file
-%
-% ---- File specifications ----
-% 
-% Output directory
-OUTPUT_DIR = ../result
-% Output file
-OUTPUT_FILE = example
-% Log directory
-LOG_DIR = ../result/logs
-% Mesh File
-MESH_FILE = checkerboard.su2
-%
-% ---- Solver specifications ----
-%
-% CFL number
-CFL_NUMBER = 0.9
-% Final time for simulation
-TIME_FINAL = 0.3
-
-% ---- Boundary Conditions ----
-% Example: BC_DIRICLET = (dummyMarker1, dummyMarker2)
-% Dirichlet Boundary
-BC_DIRICHLET = ( void )
-%
-%% Quadrature Specifications
-% Quadrature Type
-QUAD_TYPE = MONTE_CARLO
-% Quadrature Order
-QUAD_ORDER = 42 

code/include/mesh.h

@@ -42,7 +42,6 @@ class Mesh
     void ComputeCellAreas();
     void ComputeCellMidpoints();
     void ComputeConnectivity();
-    void ComputeNormals();
     void ComputePartitioning();
     Vector ComputeOutwardFacingNormal( const Vector& nodeA, const Vector& nodeB, const Vector& cellCenter );
 

code/include/settings/CConfig.h

@@ -9,9 +9,10 @@
 #ifndef CONFIG_H
 #define CONFIG_H
 
-#include <map>
-#include "OptionStructure.h"
 #include "GlobalConstants.h"
+#include "OptionStructure.h"
+#include <filesystem>
+#include <map>
 
 /*!
  * \class CConfig
@@ -19,168 +20,167 @@
  *        stores all the information.
  */
 
-class CConfig {
-private:
-  std::string _fileName;                 /*!< \brief Name of the current file without extension */
-  bool _base_config;
-
-  int _comm_rank, _comm_size;                 /*!< \brief MPI rank and size.*/
-
-  // --- Options ---
-  // File Structure
-  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*/
-
-  // Quadrature
-  QUAD_NAME _quadName;   /*!< \brief Quadrature Name*/
-  unsigned short _quadOrder;  /*!< \brief Quadrature Order*/
-  // Solver
-  double _CFL;    /*!< \brief CFL Number for Solver*/
-  double _tEnd; /*!< \brief Final Time for Simulation */
-  // Boundary Conditions
-   /*!< \brief List of all Pairs (marker, BOUNDARY_TYPE), e.g. (farfield,DIRICHLET).
-        Each Boundary Conditions must have an entry in enum BOUNDARY_TYPE*/
-  std::vector<std::pair<std::string, BOUNDARY_TYPE>> _boundaries;
-  unsigned short _nMarkerDirichlet; /*!< \brief Number of Dirichlet BC markers. Enum entry: DIRICHLET */
-  std::string *_MarkerDirichlet;    /*!< \brief Dirichlet BC markers. */
-
-
-  // --- Parsing Functionality and Initializing of Options ---
-  /*!
-   * \brief Set default values for all options not yet set.
-   */
-  void SetDefault(void);
-
-  /*!
-   * \brief Set the config options.
-   *        ==> Set new config options here.
-   */
-  void SetConfigOptions(void);
-
-  /*!
-   * \brief Set the config file parsing.
-   */
-  void SetConfigParsing(char case_filename[MAX_STRING_SIZE]);
-
-  /*!
-   * \brief Config file screen output.
-   */
-  void SetOutput(void);
-
-  /*!
-   * \brief Initializes pointers to null
-   */
-  void SetPointersNull(void);
-
-  /*!
-   * \brief Config file postprocessing.
-   */
-  void SetPostprocessing(void);
-
-  /*!
-   * \brief breaks an input line from the config file into a set of tokens
-   * \param[in] str - the input line string
-   * \param[out] option_name - the name of the option found at the beginning of the line
-   * \param[out] option_value - the tokens found after the "=" sign on the line
-   * \return false if the line is empty or a commment, true otherwise
-   */
-  bool TokenizeString(std::string & str, std::string & option_name,
-                               std::vector<std::string> & option_value);
-
-
-
-  /*--- all_options is a map containing all of the options. This is used during config file parsing
-   to track the options which have not been set (so the default values can be used). Without this map
-   there would be no list of all the config file options. ---*/
-
-  std::map<std::string, bool> all_options;
-
-  /*--- brief param is a map from the option name (config file string) to its decoder (the specific child
-   class of COptionBase that turns the string into a value) ---*/
-
-  std::map<std::string, COptionBase*> option_map;
-
-
-  // ---- Option Types ----
-
-  // All of the addXxxOptions take in the name of the option, and a refernce to the field of that option
-  // in the option structure. Depending on the specific type, it may take in a default value, and may
-  // take in extra options. The addXxxOptions mostly follow the same pattern, so please see addDoubleOption
-  // for detailed comments.
-  //
-  // List options are those that can be an unknown number of elements, and also take in a reference to
-  // an integer. This integer will be populated with the number of elements of that type unmarshaled.
-  //
-  // Array options are those with a fixed number of elements.
-  //
-  // List and Array options should also be able to be specified with the string "NONE" indicating that there
-  // are no elements. This allows the option to be present in a config file but left blank.
-
-  /*!< \brief addDoubleOption creates a config file parser for an option with the given name whose
-   value can be represented by a su2double.*/
-
-  // Simple Options
-  void addBoolOption(const std::string name, bool & option_field, bool default_value);
-
-  void addDoubleOption(const std::string name, double & option_field, double default_value);
-
-  void addIntegerOption(const std::string name, int & option_field, int default_value);
-
-  void addLongOption(const std::string name, long & option_field, long default_value);
-
-  void addStringOption(const std::string name, std::string & option_field, std::string default_value);
-
-  void addUnsignedLongOption(const std::string name, unsigned long & option_field, unsigned long default_value);
-
-  void addUnsignedShortOption(const std::string name, unsigned short & option_field, unsigned short default_value);
-
-  // 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 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::string* & option_field);
-
-public:
-  /*!
-   * \brief Constructor of the class which reads the input file.
-   */
-  CConfig(char case_filename[MAX_STRING_SIZE]);
-
-  /*!
-   * \brief Destructor of the class.
-   */
-  ~CConfig(void);
-
-  // ---- Getters for option values ----
-
-  /*!
-   * \brief Get Value of this option.
-   *        Please keep alphabetical order within each subcategory
-   */
-  // File structure
-  std::string inline GetMeshFile() const { return _meshFile; }
-  std::string inline GetOutputDir() const { return _outputDir; }
-  std::string inline GetOutputFile() const { return _outputFile; }
-
-  // Quadrature Structure
-  QUAD_NAME inline GetQuadName()  const {return _quadName;}
-  unsigned short inline GetQuadOrder() const {return _quadOrder;}
-
-  // Solver Structure
-  double inline GetCFL() const { return _CFL; }
-  double inline GetTEnd() const { return _tEnd; }
-
-  // Boundary Conditions
-  BOUNDARY_TYPE GetBoundaryType( std::string nameMarker ) const; /*! \brief Get Boundary Type of given marker */
-
-  //Output Structure
+class CConfig
+{
+  private:
+    std::string _fileName; /*!< \brief Name of the current file without extension */
+    bool _base_config;
+
+    int _comm_rank, _comm_size; /*!< \brief MPI rank and size.*/
+
+    // --- 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*/
+
+    // Quadrature
+    QUAD_NAME _quadName;       /*!< \brief Quadrature Name*/
+    unsigned short _quadOrder; /*!< \brief Quadrature Order*/
+    // Solver
+    double _CFL;  /*!< \brief CFL Number for Solver*/
+    double _tEnd; /*!< \brief Final Time for Simulation */
+    // Boundary Conditions
+    /*!< \brief List of all Pairs (marker, BOUNDARY_TYPE), e.g. (farfield,DIRICHLET).
+         Each Boundary Conditions must have an entry in enum BOUNDARY_TYPE*/
+    std::vector<std::pair<std::string, BOUNDARY_TYPE>> _boundaries;
+    unsigned short _nMarkerDirichlet; /*!< \brief Number of Dirichlet BC markers. Enum entry: DIRICHLET */
+    std::string* _MarkerDirichlet;    /*!< \brief Dirichlet BC markers. */
+
+    // --- Parsing Functionality and Initializing of Options ---
+    /*!
+     * \brief Set default values for all options not yet set.
+     */
+    void SetDefault( void );
+
+    /*!
+     * \brief Set the config options.
+     *        ==> Set new config options here.
+     */
+    void SetConfigOptions( void );
+
+    /*!
+     * \brief Set the config file parsing.
+     */
+    void SetConfigParsing( char case_filename[MAX_STRING_SIZE] );
+
+    /*!
+     * \brief Config file screen output.
+     */
+    void SetOutput( void );
+
+    /*!
+     * \brief Initializes pointers to null
+     */
+    void SetPointersNull( void );
+
+    /*!
+     * \brief Config file postprocessing.
+     */
+    void SetPostprocessing( void );
+
+    /*!
+     * \brief breaks an input line from the config file into a set of tokens
+     * \param[in] str - the input line string
+     * \param[out] option_name - the name of the option found at the beginning of the line
+     * \param[out] option_value - the tokens found after the "=" sign on the line
+     * \return false if the line is empty or a commment, true otherwise
+     */
+    bool TokenizeString( std::string& str, std::string& option_name, std::vector<std::string>& option_value );
+
+    /*--- all_options is a map containing all of the options. This is used during config file parsing
+     to track the options which have not been set (so the default values can be used). Without this map
+     there would be no list of all the config file options. ---*/
+
+    std::map<std::string, bool> all_options;
+
+    /*--- brief param is a map from the option name (config file string) to its decoder (the specific child
+     class of COptionBase that turns the string into a value) ---*/
+
+    std::map<std::string, COptionBase*> option_map;
+
+    // ---- Option Types ----
+
+    // All of the addXxxOptions take in the name of the option, and a refernce to the field of that option
+    // in the option structure. Depending on the specific type, it may take in a default value, and may
+    // take in extra options. The addXxxOptions mostly follow the same pattern, so please see addDoubleOption
+    // for detailed comments.
+    //
+    // List options are those that can be an unknown number of elements, and also take in a reference to
+    // an integer. This integer will be populated with the number of elements of that type unmarshaled.
+    //
+    // Array options are those with a fixed number of elements.
+    //
+    // List and Array options should also be able to be specified with the string "NONE" indicating that there
+    // are no elements. This allows the option to be present in a config file but left blank.
+
+    /*!< \brief addDoubleOption creates a config file parser for an option with the given name whose
+     value can be represented by a su2double.*/
+
+    // Simple Options
+    void addBoolOption( const std::string name, bool& option_field, bool default_value );
+
+    void addDoubleOption( const std::string name, double& option_field, double default_value );
+
+    void addIntegerOption( const std::string name, int& option_field, int default_value );
+
+    void addLongOption( const std::string name, long& option_field, long default_value );
+
+    void addStringOption( const std::string name, std::string& option_field, std::string default_value );
+
+    void addUnsignedLongOption( const std::string name, unsigned long& option_field, unsigned long default_value );
+
+    void addUnsignedShortOption( const std::string name, unsigned short& option_field, unsigned short default_value );
+
+    // 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 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::string*& option_field );
+
+  public:
+    /*!
+     * \brief Constructor of the class which reads the input file.
+     */
+    CConfig( char case_filename[MAX_STRING_SIZE] );
+
+    /*!
+     * \brief Destructor of the class.
+     */
+    ~CConfig( void );
+
+    // ---- Getters for option values ----
+
+    /*!
+     * \brief Get Value of this option.
+     *        Please keep alphabetical order within each subcategory
+     */
+    // File structure
+    std::string inline GetMeshFile() const { return _inputDir + _meshFile; }
+    std::string inline GetOutputDir() const {
+        if( _outputDir.at( _outputDir.size() - 1 ) != '/' )
+            return _outputDir + "/";
+        else
+            return _outputDir;
+    }
+    std::string inline GetOutputFile() const { return _outputFile; }
+
+    // Quadrature Structure
+    QUAD_NAME inline GetQuadName() const { return _quadName; }
+    unsigned short inline GetQuadOrder() const { return _quadOrder; }
+
+    // Solver Structure
+    double inline GetCFL() const { return _CFL; }
+    double inline GetTEnd() const { return _tEnd; }
+
+    // Boundary Conditions
+    BOUNDARY_TYPE GetBoundaryType( std::string nameMarker ) const; /*! \brief Get Boundary Type of given marker */
 
+    // Output Structure
 };
 
-
-
-#endif // CONFIG_H
+#endif    // CONFIG_H

code/include/settings/GlobalConstants.h

@@ -9,43 +9,32 @@
 #ifndef GLOBAL_CONSTANTS_H
 #define GLOBAL_CONSTANTS_H
 
-#include <map>
 #include <cmath>
+#include <map>
+#include <string>
 
 // --- Definition for global constants goes here ---
 
-const double PI_NUMBER = 4.0 * std::atan(1.0);  /*!< \brief Pi number. */
-const unsigned int MAX_STRING_SIZE = 200;     /*!< \brief Maximum size for strings. */
-
+const double PI_NUMBER             = 4.0 * std::atan( 1.0 ); /*!< \brief Pi number. */
+const unsigned int MAX_STRING_SIZE = 200;                    /*!< \brief Maximum size for strings. */
 
 // --- Definition of enums goes here ---
 
-enum BOUNDARY_TYPE{
-  DIRICHLET,
-  INVALID
-};
+enum BOUNDARY_TYPE { DIRICHLET, INVALID };
 
 // --- Definition of enums for EnumOptions goes here ---
 
 /*! \brief Enum for all currently available quadratures in rtsn.
  *         Option enums are written in capital letters with underscores as spaces (e.g option "time integration" has option enum "TIME_INTEGRATION")
  */
-enum QUAD_NAME{
-    QUAD_MonteCarlo,
-    QUAD_GaussLegendreTensorized,
-    QUAD_LevelSymmetric,
-    QUAD_Lebedev,
-    QUAD_LDFESA
-};
+enum QUAD_NAME { QUAD_MonteCarlo, QUAD_GaussLegendreTensorized, QUAD_LevelSymmetric, QUAD_Lebedev, QUAD_LDFESA };
 
 /*! \brief Conversion Map String to enum
  */
-inline std::map <std::string,QUAD_NAME> Quadrature_Map {
-  { "MONTE_CARLO", QUAD_MonteCarlo },
-  { "GAUSS_LEGENDRE_TENSORIZED", QUAD_GaussLegendreTensorized },
-  { "LEVEL_SYMMETRIC", QUAD_LevelSymmetric },
-  { "LEBEDEV", QUAD_Lebedev },
-  { "LDFESA",QUAD_LDFESA }
-};
-
-#endif // GLOBAL_CONSTANTS_H
+inline std::map<std::string, QUAD_NAME> Quadrature_Map{ { "MONTE_CARLO", QUAD_MonteCarlo },
+                                                        { "GAUSS_LEGENDRE_TENSORIZED", QUAD_GaussLegendreTensorized },
+                                                        { "LEVEL_SYMMETRIC", QUAD_LevelSymmetric },
+                                                        { "LEBEDEV", QUAD_Lebedev },
+                                                        { "LDFESA", QUAD_LDFESA } };
+
+#endif    // GLOBAL_CONSTANTS_H

code/include/toolboxes/TextProcessingToolbox.h

@@ -11,8 +11,8 @@
  * \brief utility function for converting strings to uppercase
  * \param[in,out] str - string we want to convert
  */
-inline void StringToUpperCase(std::string & str) {
-  std::transform(str.begin(), str.end(), str.begin(), ::toupper);
+inline void StringToUpperCase( std::string& str ) {
+    for( auto& c : str ) c = std::toupper( c );
 }
 
-#endif // TEXTPROCESSINGTOOLBOX_H
+#endif    // TEXTPROCESSINGTOOLBOX_H

code/input/checkerboard.py

@@ -12,7 +12,7 @@ def add_block(x0,y0,length,char_length,geom):
     ])
     return geom.add_polygon(coords, char_length)
 
-char_length = 0.1
+char_length = 0.05
 geom = pg.opencascade.Geometry()
 domain = add_block(0, 0, 1.2, char_length, geom)
 xpos = ypos = [0.1, 0.3, 0.5, 0.7, 0.9]

code/src/io.cpp

@@ -18,7 +18,7 @@ void ExportVTK( const std::string fileName,
 
         auto writer                 = vtkUnstructuredGridWriterSP::New();
         std::string fileNameWithExt = fileName;
-        if( !fileNameWithExt.ends_with( ".vtk" ) ) {
+        if( fileNameWithExt.substr( fileNameWithExt.find_last_of( "." ) + 1 ) != ".vtk" ) {
             fileNameWithExt.append( ".vtk" );
         }
         writer->SetFileName( ( settings->GetOutputDir() + fileNameWithExt ).c_str() );
@@ -237,8 +237,8 @@ Mesh* LoadSU2MeshFromFile( const CConfig* settings ) {
                             markerTag.erase( end_pos, markerTag.end() );
                             btype = settings->GetBoundaryType( markerTag );
                             if( btype == BOUNDARY_TYPE::INVALID ) {
-                                std::string errorMsg = std::string("Invalid Boundary at marker \"" + markerTag + "\".");
-                                CRTSNError::Error(errorMsg,CURRENT_FUNCTION);
+                                std::string errorMsg = std::string( "Invalid Boundary at marker \"" + markerTag + "\"." );
+                                CRTSNError::Error( errorMsg, CURRENT_FUNCTION );
                             }
                         }
                         else if( line.find( "MARKER_ELEMS", 0 ) != std::string::npos ) {
@@ -411,7 +411,7 @@ Settings* ReadInputFile( std::string inputFile ) {
 
         auto cwd        = std::filesystem::current_path();
         std::string tmp = std::filesystem::path( inputFile ).parent_path().string();
-        if( !tmp.ends_with( "/" ) ) tmp.append( "/" );
+        if( tmp.substr( tmp.size() - 1 ) != "/" ) tmp.append( "/" );
         settings->_inputDir = tmp;
 
         // section IO
@@ -428,7 +428,7 @@ Settings* ReadInputFile( std::string inputFile ) {
         auto outputDir = io->get_as<std::string>( "outputDir" );
         if( outputDir ) {
             std::string tmp = *outputDir;
-            if( !tmp.ends_with( "/" ) ) tmp.append( "/" );
+            if( tmp.substr( tmp.size() - 1 ) != "/" ) tmp.append( "/" );
             settings->_outputDir = std::filesystem::path( tmp );
         }
         else {
@@ -448,7 +448,7 @@ Settings* ReadInputFile( std::string inputFile ) {
         auto logDir = io->get_as<std::string>( "logDir" );
         if( logDir ) {
             std::string tmp = *logDir;
-            if( !tmp.ends_with( "/" ) ) tmp.append( "/" );
+            if( tmp.substr( tmp.size() - 1 ) != "/" ) tmp.append( "/" );
             settings->_logDir = std::filesystem::path( tmp );
         }
         else {

code/src/main.cpp

@@ -9,7 +9,7 @@ int main( int argc, char** argv ) {
 
     MPI_Init( &argc, &argv );
 
-    /*std::string inputFile = ParseArguments( argc, argv );
+    /*
     Settings* settings    = ReadInputFile( inputFile );
     InitLogger( settings->GetLogDir(), spdlog::level::info, spdlog::level::info );
     PrintLogHeader( settings->GetInputFile() );
@@ -20,25 +20,22 @@ int main( int argc, char** argv ) {
     solver->Save();
     */
 
-    std::string filename = "default.cfg";
     char config_file_name[MAX_STRING_SIZE];
 
-    filename = ParseArguments( argc, argv );
+    std::string filename = ParseArguments( argc, argv );
 
     /*--- Load in the number of zones and spatial dimensions in the mesh file (If no config
      file is specified, default.cfg is used) ---*/
-    strcpy(config_file_name, filename.c_str());
-
-    //Load Settings from File
-    CConfig* config = new CConfig(config_file_name);
+    strcpy( config_file_name, filename.c_str() );
 
+    // Load Settings from File
+    CConfig* config = new CConfig( config_file_name );
 
     // build solver
     Solver* solver = Solver::Create( config );
     solver->Solve();
     solver->Save();
 
-
     // TODO: call solver
     MPI_Finalize();
     return EXIT_SUCCESS;

code/src/mesh.cpp

@@ -8,7 +8,6 @@ Mesh::Mesh( std::vector<Vector> nodes,
       _boundaries( boundaries ) {
     ComputeCellAreas();
     ComputeCellMidpoints();
-    ComputeNormals();
     ComputeConnectivity();
     ComputePartitioning();
 }
@@ -19,10 +18,17 @@ void Mesh::ComputeConnectivity() {
     int comm_size, comm_rank;
     MPI_Comm_size( MPI_COMM_WORLD, &comm_size );
     MPI_Comm_rank( MPI_COMM_WORLD, &comm_rank );
-    unsigned chunkSize    = std::ceil( static_cast<float>( _numCells ) / static_cast<float>( comm_size ) );
-    unsigned mpiCellStart = comm_rank * chunkSize;
-    unsigned mpiCellEnd   = std::min( ( comm_rank + 1 ) * chunkSize, _numCells );
-    std::vector<int> neighborsFlatPart( _numNodesPerCell * chunkSize, -1 );
+    // unsigned chunkSize    = std::ceil( static_cast<float>( _numCells ) / static_cast<float>( comm_size ) );
+    // unsigned mpiCellStart = comm_rank * chunkSize;
+    // unsigned mpiCellEnd   = std::min( ( comm_rank + 1 ) * chunkSize, _numCells );
+    // std::vector<int> neighborsFlatPart( _numNodesPerCell * chunkSize, -1 );
+    // std::vector<Vector> normalsFlatPart( _numNodesPerCell * chunkSize, Vect