Update LUT routine

Common/include/containers/CFileReaderLUT.hpp

@@ -63,7 +63,19 @@ class CFileReaderLUT {
 
   std::vector<unsigned long> hull;
 
-  std::string SkipToFlag(std::ifstream* file_stream, const std::string& flag);
+  /*! \brief Searches for the position of flag in file_stream and 
+   *         sets the stream position of file_stream to that position.
+   */
+  void SkipToFlag(std::ifstream& file_stream, const std::string& current_line, const std::string& flag) const;
+
+  /*! \brief Extracts the next non-empty characters from file_stream and stores them into line.
+   */
+  bool GetNextNonEmptyLine(std::ifstream& file_stream, std::string& line) const;
+
+  /*! \brief Extracts characters from file_stream, removes trailing control characters,
+   *         and stores them into line.
+   */
+  bool GetStrippedLine(std::ifstream& file_stream, std::string& line) const;
 
  public:
   CFileReaderLUT(){};
@@ -83,5 +95,5 @@ class CFileReaderLUT {
 
   inline const std::vector<unsigned long>& GetHull() const { return hull; };
 
-  void ReadRawDRG(const std::string& file_name);
+  void ReadRawLUT(const std::string& file_name);
 };

Common/src/CConfig.cpp

@@ -1095,7 +1095,7 @@ void CConfig::SetConfig_Options() {
   /*!\brief KIND_TRANS_MODEL \n DESCRIPTION: Specify transition model OPTIONS: see \link Trans_Model_Map \endlink \n DEFAULT: NONE \ingroup Config*/
   addEnumOption("KIND_TRANS_MODEL", Kind_Trans_Model, Trans_Model_Map, TURB_TRANS_MODEL::NONE);
 
-  /*!\brief KIND_SPECIES_MODEL \n DESCRIPTION: Specify scalar transport model \n Options: see \link Scalar_Model_Map \endlink \n DEFAULT: NONE \ingroup Config*/
+  /*!\brief KIND_SCALAR_MODEL \n DESCRIPTION: Specify scalar transport model \n Options: see \link Scalar_Model_Map \endlink \n DEFAULT: NONE \ingroup Config*/
   addEnumOption("KIND_SCALAR_MODEL", Kind_Species_Model, Species_Model_Map, SPECIES_MODEL::NONE);
 
   /*!\brief KIND_SGS_MODEL \n DESCRIPTION: Specify subgrid scale model OPTIONS: see \link SGS_Model_Map \endlink \n DEFAULT: NONE \ingroup Config*/
@@ -5339,7 +5339,7 @@ void CConfig::SetPostprocessing(SU2_COMPONENT val_software, unsigned short val_i
   }
 
   /*--- Checks for additional species transport. ---*/
-  if (Kind_Species_Model != SPECIES_MODEL::NONE) {
+  if (Kind_Species_Model == SPECIES_MODEL::SPECIES_TRANSPORT) {
     if (Kind_Solver != MAIN_SOLVER::INC_NAVIER_STOKES &&
         Kind_Solver != MAIN_SOLVER::INC_RANS &&
         Kind_Solver != MAIN_SOLVER::DISC_ADJ_INC_NAVIER_STOKES &&

Common/src/containers/CFileReaderLUT.cpp

@@ -33,8 +33,8 @@
 
 using namespace std;
 
-void CFileReaderLUT::ReadRawDRG(const string& file_name) {
-  version_reader = "1.0.0";
+void CFileReaderLUT::ReadRawLUT(const string& file_name) {
+  version_reader = "1.0.1";
 
   /*--- Store MPI rank. ---*/
   rank = SU2_MPI::GetRank();
@@ -46,8 +46,6 @@ void CFileReaderLUT::ReadRawDRG(const string& file_name) {
 
   ifstream file_stream;
 
-  int ixColon;
-
   bool eoHeader = false;
   bool eoData = false;
   bool eoConnectivity = false;
@@ -59,106 +57,104 @@ void CFileReaderLUT::ReadRawDRG(const string& file_name) {
     SU2_MPI::Error(string("There is no look-up-table file called ") + file_name, CURRENT_FUNCTION);
   }
 
-  /* Read header */
-  line = SkipToFlag(&file_stream, "<header>");
+  /*--- Read header ---*/
+  SkipToFlag(file_stream, line, "<Header>");
+
+  while (GetNextNonEmptyLine(file_stream, line) && !eoHeader) {
 
-  while (getline(file_stream, line) && !eoHeader) {
-    /* number of points in LUT */
-    if (line.compare("[version]") == 0) {
-      getline(file_stream, line);
+    /*--- number of points in LUT ---*/
+    if (line.compare("[Version]") == 0) {
+      GetNextNonEmptyLine(file_stream, line);
       version_lut = line;
     }
 
-    /* number of points in LUT */
-    if (line.compare("[number of points]") == 0) {
-      getline(file_stream, line);
+    /*--- number of points in LUT ---*/
+    if (line.compare("[Number of points]") == 0) {
+      GetNextNonEmptyLine(file_stream, line);
       n_points = stoi(line);
     }
 
-    /* number of triangles in LUT */
-    if (line.compare("[number of triangles]") == 0) {
-      getline(file_stream, line);
+    /*--- number of triangles in LUT ---*/
+    if (line.compare("[Number of triangles]") == 0) {
+      GetNextNonEmptyLine(file_stream, line);
       n_triangles = stoi(line);
     }
 
-    /* number of points on the hull */
-    if (line.compare("[number of hull points]") == 0) {
-      getline(file_stream, line);
+    /*--- number of points on the hull ---*/
+    if (line.compare("[Number of hull points]") == 0) {
+      GetNextNonEmptyLine(file_stream, line);
       n_hull_points = stoi(line);
     }
 
-    /* number of variables in LUT */
-    if (line.compare("[number of variables]") == 0) {
-      getline(file_stream, line);
+    /*--- number of variables in LUT ---*/
+    if (line.compare("[Number of variables]") == 0) {
+      GetNextNonEmptyLine(file_stream, line);
       n_variables = stoi(line);
     }
 
-    /* variable names */
-    if (line.compare("[variable names]") == 0) {
-      getline(file_stream, line);
-      stream_names_var.str(line);
-      while (stream_names_var) {
-        stream_names_var >> word;
-        ixColon = (int)word.find(":");
+    /*--- variable names ---*/
+    if (line.compare("[Variable names]") == 0) {
+
+      for (unsigned long i = 0; i < n_variables; i++){
 
-        names_var.push_back(word.substr(ixColon + 1, word.size() - 1));
+        /*--- grab a single line ---*/
+        GetNextNonEmptyLine(file_stream, line);
+        names_var.push_back(line.substr(line.find(":")+1)); 
       }
-      names_var.pop_back();  // removes last redundant element
     }
 
-    // check if end of header is reached
-    if (line.compare("</header>") == 0) eoHeader = true;
+    /*--- check if end of header is reached ---*/
+    if (line.compare("</Header>") == 0) eoHeader = true;
   }
 
-  // check version_lut
+  /*--- check version_lut ---*/
   if (version_lut.compare(version_reader) != 0)
-    SU2_MPI::Error("Version conflict between Dragon reader and Dragon library file.", CURRENT_FUNCTION);
+    SU2_MPI::Error("Version conflict between LUT reader and LUT library file.", CURRENT_FUNCTION);
 
-  // check header quantities
+  /*--- check header quantities ---*/
   if (n_points == 0 || n_triangles == 0 || n_variables == 0 || n_hull_points == 0)
     SU2_MPI::Error(
-        "Number of points, triangles, hull points, or variables in Dragon "
+        "Number of points, triangles, hull points, or variables in lookup table "
         "library header is zero.",
         CURRENT_FUNCTION);
 
-  // check if number of variables is consistent
+  /*--- check if number of variables is consistent ---*/
   if (n_variables != names_var.size())
     SU2_MPI::Error(
         "Number of read variables does not match number of "
-        "variables specified in Dragon "
+        "variables specified in lookup table "
         "library header.",
         CURRENT_FUNCTION);
 
-  /* now that n_variables, n_points, n_hull_points and n_variables is available,
-   * allocate memory */
-  if (rank == MASTER_NODE) cout << "allocating memory for the data" << endl;
+  /*--- now that n_variables, n_points, n_hull_points and n_variables are available, allocate memory ---*/
+  if (rank == MASTER_NODE) cout << "allocating memory for the data, size = ( " << GetNVariables() << " , " << GetNPoints() << " )" << endl;
   table_data.resize(GetNVariables(), GetNPoints());
 
-
-  if (rank == MASTER_NODE) cout << "allocating memory for the triangles" << endl;
+  if (rank == MASTER_NODE) cout << "allocating memory for the triangles, size = "<< GetNTriangles() << endl;
   triangles.resize(GetNTriangles(), 3);
 
-  if (rank == MASTER_NODE) cout << "allocating memory for the hull points" << endl;
+  if (rank == MASTER_NODE) cout << "allocating memory for the hull points, size = " << GetNHullPoints() << endl;
   hull.resize(GetNHullPoints());
 
-  /* flush any cout */
+  /*--- flush any cout ---*/
   if (rank == MASTER_NODE) cout << endl;
 
-  // read data block
+  /*--- read data block ---*/
   if (rank == MASTER_NODE) cout << "loading data block" << endl;
 
-  line = SkipToFlag(&file_stream, "<data>");
+  SkipToFlag(file_stream, line, "<Data>");
 
   unsigned long pointCounter = 0;
-  while (getline(file_stream, line) && !eoData) {
-    // check if end of data is reached
-    if (line.compare("</data>") == 0) eoData = true;
+  while (GetNextNonEmptyLine(file_stream, line) && !eoData) {
+
+    /*--- check if end of data is reached ---*/
+    if (line.compare("</Data>") == 0) eoData = true;
 
     if (!eoData) {
-      // one line contains values for one point for all variables
+      /*--- one line contains values for one point for all variables ---*/
       istringstream streamDataLine(line);
 
-      // add next line to table array
+      /*--- add next line to table array ---*/
       for (unsigned long iVar = 0; iVar < n_variables; iVar++) {
         streamDataLine >> word;
         passivedouble tmp = stod(word);
@@ -171,28 +167,32 @@ void CFileReaderLUT::ReadRawDRG(const string& file_name) {
   if (n_points != pointCounter - 1)
     SU2_MPI::Error(
         "Number of read points does not match number of points "
-        "specified in Dragon library header.",
+        "specified in lookup table library header.",
         CURRENT_FUNCTION);
 
-  // read connectivity
+  /*--- read connectivity ---*/
   if (rank == MASTER_NODE) cout << "loading connectivity block" << endl;
 
-  line = SkipToFlag(&file_stream, "<connectivity>");
+  SkipToFlag(file_stream, line, "<Connectivity>");
 
   unsigned long triCounter = 0;
-  while (getline(file_stream, line) && !eoConnectivity) {
-    // check if end of data is reached
-    if (line.compare("</connectivity>") == 0) eoConnectivity = true;
+  while (GetNextNonEmptyLine(file_stream, line) && !eoConnectivity) {
+    if (!line.empty() && (line[line.length()-1] == '\n' || line[line.length()-1] == '\r' )) {
+      line.erase(line.length()-1);
+    }
+    /*--- check if end of data is reached ---*/
+    if (line.compare("</Connectivity>") == 0) eoConnectivity = true;
 
     if (!eoConnectivity) {
-      // one line contains values for one triangle (3 points)
+      /*--- one line contains values for one triangle (3 points) ---*/
       istringstream streamTriLine(line);
 
-      // add next line to triangles
+      /*--- add next line to triangles ---*/
       for (int iPoint = 0; iPoint < 3; iPoint++) {
+
         streamTriLine >> word;
-        // Dragon table index starts with 1, convert to c++ indexing starting
-        // with 0:
+
+        /*--- lookup table index starts with 1, convert to c++ indexing starting with 0: ---*/
         triangles[triCounter][iPoint] = stol(word) - 1;
       }
     }
@@ -202,27 +202,29 @@ void CFileReaderLUT::ReadRawDRG(const string& file_name) {
   if (n_triangles != triCounter - 1)
     SU2_MPI::Error(
         "Number of read triangles does not match number of points "
-        "specified in Dragon library header.",
+        "specified in lookup table library header.",
         CURRENT_FUNCTION);
 
-  // read hull points
+  /*--- read hull points ---*/
   if (rank == MASTER_NODE) cout << "loading hull block" << endl;
 
-  line = SkipToFlag(&file_stream, "<hull>");
+  SkipToFlag(file_stream, line, "<Hull>");
 
   unsigned long hullCounter = 0;
-  while (getline(file_stream, line) && !eoHull) {
-    // check if end of data is reached
-    if (line.compare("</hull>") == 0) eoHull = true;
+  while (GetNextNonEmptyLine(file_stream, line) && !eoHull) {
+    if (!line.empty() && (line[line.length()-1] == '\n' || line[line.length()-1] == '\r' )) {
+      line.erase(line.length()-1);
+    }
+    /*--- check if end of data is reached ---*/
+    if (line.compare("</Hull>") == 0) eoHull = true;
 
     if (!eoHull) {
-      // one line contains one point ID for one point on the hull
+      /*--- one line contains one point ID for one point on the hull  ---*/
       istringstream streamHullLine(line);
 
       streamHullLine >> word;
 
-      // Dragon table indices start with 1, convert to c++ indexing starting
-      // with 0:
+      /*--- Lookup table indices start with 1, convert to c++ indexing starting with 0: ---*/
       hull[hullCounter] = stol(word) - 1;
     }
     hullCounter++;
@@ -231,22 +233,53 @@ void CFileReaderLUT::ReadRawDRG(const string& file_name) {
   if (n_hull_points != hullCounter - 1)
     SU2_MPI::Error(
         "Number of read hull points does not match number of points "
-        "specified in Dragon library header.",
+        "specified in lookup table library header.",
         CURRENT_FUNCTION);
 
   file_stream.close();
 
 }
 
-string CFileReaderLUT::SkipToFlag(ifstream* file_stream, const string& flag) {
-  string line;
-  getline(*file_stream, line);
+void CFileReaderLUT::SkipToFlag(ifstream& file_stream, const string& current_line, const string& flag) const {
+  string next_line = "";
+
+  /*--- compare current line to flag and return if equal ---*/
+  if (current_line.compare(flag) == 0) return;
 
-  while (line.compare(flag) != 0 && !(*file_stream).eof()) {
-    getline(*file_stream, line);
+  /*--- else, search for flag ---*/
+  while (next_line.find(flag) == string::npos && !(file_stream).eof()) {
+    GetStrippedLine(file_stream, next_line);
   }
 
-  if ((*file_stream).eof()) SU2_MPI::Error("Flag not found in file", CURRENT_FUNCTION);
+  /*--- throw error if end of file reached ---*/
+  if ((file_stream).eof()) SU2_MPI::Error("Flag " + flag + " not found in file", CURRENT_FUNCTION);
+}
+
+bool CFileReaderLUT::GetNextNonEmptyLine(ifstream& file_stream, string& line) const {
 
-  return line;
+  /*--- get next line and save return value ---*/
+  bool return_value = GetStrippedLine(file_stream, line);
+
+  /*--- skip empty lines ---*/
+  while (line.empty() && !(file_stream).eof()){
+    return_value = GetStrippedLine(file_stream, line);
+  }
+
+  /*--- return true if line is not empty, else return false ---*/
+  return return_value;
 }
+
+bool CFileReaderLUT::GetStrippedLine(ifstream& file_stream, string& line) const {
+
+    /*--- get next line and save return value ---*/
+    getline(file_stream, line);
+
+    /*--- find last non-control-character character ---*/
+    size_t end = line.find_last_not_of(" \n\r\t\f\v");
+
+    /*--- clean up line ---*/
+    line = (end == string::npos) ? "" : line.substr(0, end + 1);
+
+    /*--- return true if line is not empty, else return false ---*/
+    return !line.empty();
+  }

Common/src/containers/CLookUpTable.cpp

@@ -78,7 +78,7 @@ void CLookUpTable::LoadTableRaw(const string& var_file_name_lut) {
   if (rank == MASTER_NODE) 
     cout << "Loading lookup table, filename = " << var_file_name_lut << " ..." << endl;
 
-  file_reader.ReadRawDRG(var_file_name_lut);
+  file_reader.ReadRawLUT(var_file_name_lut);
 
   n_points = file_reader.GetNPoints();
   n_triangles = file_reader.GetNTriangles();