Merge branch 'develop' into feature_signal_handling

.github/workflows/regression.yml

@@ -52,12 +52,12 @@ jobs:
           key: ${{ matrix.config_set }}-${{ github.sha }}
           restore-keys: ${{ matrix.config_set }}
       - name: Pre Cleanup
-        uses: docker://ghcr.io/su2code/su2/build-su2:230813-0103
+        uses: docker://ghcr.io/su2code/su2/build-su2:240320-1536
         with:
           entrypoint: /bin/rm
           args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
       - name: Build
-        uses: docker://ghcr.io/su2code/su2/build-su2:230813-0103
+        uses: docker://ghcr.io/su2code/su2/build-su2:240320-1536
         with:
           args: -b ${{github.ref}} -f "${{matrix.flags}}"
       - name: Compress binaries
@@ -68,7 +68,7 @@ jobs:
           name: ${{ matrix.config_set }}
           path: install_bin.tgz
       - name: Post Cleanup
-        uses: docker://ghcr.io/su2code/su2/build-su2:230813-0103
+        uses: docker://ghcr.io/su2code/su2/build-su2:240320-1536
         with:
           entrypoint: /bin/rm
           args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
@@ -97,12 +97,12 @@ jobs:
           key: ${{ matrix.config_set }}-${{ github.sha }}
           restore-keys: ${{ matrix.config_set }}
       - name: Pre Cleanup
-        uses: docker://ghcr.io/su2code/su2/build-su2-tsan:230813-0103
+        uses: docker://ghcr.io/su2code/su2/build-su2-tsan:240320-1536
         with:
           entrypoint: /bin/rm
           args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
       - name: Build
-        uses: docker://ghcr.io/su2code/su2/build-su2-tsan:230813-0103
+        uses: docker://ghcr.io/su2code/su2/build-su2-tsan:240320-1536
         with:
           args: -b ${{github.ref}} -f "${{matrix.flags}}"
       - name: Compress binaries
@@ -113,7 +113,47 @@ jobs:
           name: ${{ matrix.config_set }}
           path: install_bin.tgz
       - name: Post Cleanup
-        uses: docker://ghcr.io/su2code/su2/build-su2-tsan:230813-0103
+        uses: docker://ghcr.io/su2code/su2/build-su2-tsan:240320-1536
+        with:
+          entrypoint: /bin/rm
+          args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
+  build_asan:
+    name: Build SU2 (asan)
+    strategy:
+      fail-fast: false
+      matrix:
+        config_set: [BaseNoMPI-asan, ReverseNoMPI-asan]
+        include:
+          - config_set: BaseNoMPI-asan
+            flags: '--buildtype=debugoptimized -Denable-openblas=true -Dwith-mpi=disabled -Denable-mlpcpp=true --warnlevel=3 --werror'
+          - config_set: ReverseNoMPI-asan
+            flags: '--buildtype=debugoptimized -Denable-autodiff=true -Denable-normal=false -Dwith-mpi=disabled --warnlevel=3 --werror'
+    runs-on: ${{ inputs.runner || 'ubuntu-latest' }}
+    steps:
+      - name: Reduce ASLR entropy for asan
+        run: sudo sysctl -w vm.mmap_rnd_bits=28
+      - name: Cache Object Files
+        uses: actions/cache@v4
+        with:
+          path: ccache
+          key: ${{ matrix.config_set }}-${{ github.sha }}
+          restore-keys: ${{ matrix.config_set }}
+      - name: Pre Cleanup
+        uses: docker://ghcr.io/su2code/su2/build-su2-asan:240320-1536
+        with:
+          entrypoint: /bin/rm
+          args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
+      - name: Build
+        run: docker run --rm --cap-add SYS_PTRACE -v $(pwd):${{ github.workspace }} -w ${{ github.workspace }} ghcr.io/su2code/su2/build-su2-asan:240320-1536 -b ${{github.ref}} -f "${{matrix.flags}}"
+      - name: Compress binaries
+        run: tar -zcvf install_bin.tgz install/*
+      - name: Upload Binaries
+        uses: actions/upload-artifact@v4
+        with:
+          name: ${{ matrix.config_set }}
+          path: install_bin.tgz
+      - name: Post Cleanup
+        uses: docker://ghcr.io/su2code/su2/build-su2-asan:240320-1536
         with:
           entrypoint: /bin/rm
           args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
@@ -144,7 +184,7 @@ jobs:
             tag: OMP
     steps:
       - name: Pre Cleanup
-        uses: docker://ghcr.io/su2code/su2/test-su2:230813-0103
+        uses: docker://ghcr.io/su2code/su2/test-su2:240320-1536
         with:
           entrypoint: /bin/rm
           args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
@@ -170,12 +210,12 @@ jobs:
           chmod a+x $BIN_FOLDER/*
           ls -lahR $BIN_FOLDER
       - name: Run Tests in Container
-        uses: docker://ghcr.io/su2code/su2/test-su2:230813-0103
+        uses: docker://ghcr.io/su2code/su2/test-su2:240320-1536
         with:
           # -t <Tutorials-branch> -c <Testcases-branch>
           args: -b ${{github.ref}} -t develop -c develop -s ${{matrix.testscript}}
       - name: Cleanup
-        uses: docker://ghcr.io/su2code/su2/test-su2:230813-0103
+        uses: docker://ghcr.io/su2code/su2/test-su2:240320-1536
         with:
           entrypoint: /bin/rm
           args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
@@ -192,7 +232,7 @@ jobs:
       - name: Reduce ASLR entropy for tsan
         run: sudo sysctl -w vm.mmap_rnd_bits=28
       - name: Pre Cleanup
-        uses: docker://ghcr.io/su2code/su2/test-su2-tsan:230813-0103
+        uses: docker://ghcr.io/su2code/su2/test-su2-tsan:240320-1536
         with:
           entrypoint: /bin/rm
           args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
@@ -218,12 +258,59 @@ jobs:
           chmod a+x $BIN_FOLDER/*
           ls -lahR $BIN_FOLDER
       - name: Run Tests in Container
-        uses: docker://ghcr.io/su2code/su2/test-su2-tsan:230813-0103
+        uses: docker://ghcr.io/su2code/su2/test-su2-tsan:240320-1536
         with:
           # -t <Tutorials-branch> -c <Testcases-branch>
           args: -b ${{github.ref}} -t develop -c develop -s ${{matrix.testscript}} -a "--tsan"
       - name: Cleanup
-        uses: docker://ghcr.io/su2code/su2/test-su2-tsan:230813-0103
+        uses: docker://ghcr.io/su2code/su2/test-su2-tsan:240320-1536
+        with:
+          entrypoint: /bin/rm
+          args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
+  address_sanitizer_tests:
+    runs-on: ${{ inputs.runner || 'ubuntu-latest' }}
+    name: Address Sanitizer Tests
+    needs: build_asan
+    strategy:
+      fail-fast: false
+      matrix:
+        testscript: ['serial_regression.py', 'serial_regression_AD.py']
+    steps:
+      - name: Reduce ASLR entropy for asan
+        run: sudo sysctl -w vm.mmap_rnd_bits=28
+      - name: Pre Cleanup
+        uses: docker://ghcr.io/su2code/su2/test-su2-asan:240320-1536
+        with:
+          entrypoint: /bin/rm
+          args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
+      - name: Download All artifacts
+        uses: actions/download-artifact@v4
+      - name: Uncompress and Move Binaries
+        run: |
+          BIN_FOLDER="$PWD/install/bin"
+          mkdir -p $BIN_FOLDER
+          ls -lah $BIN_FOLDER
+          for type in Base Reverse Forward; do
+            TYPE_FOLDER="${type}NoMPI-asan"
+            echo "Processing '$TYPE_FOLDER' ..."
+            if [ -d $TYPE_FOLDER ]; then
+              pushd $TYPE_FOLDER
+              ls -lah
+              tar -zxvf install_bin.tgz
+              ls -lah install/bin/
+              cp -r install/* $BIN_FOLDER/../
+              popd;
+            fi
+          done
+          chmod a+x $BIN_FOLDER/*
+          ls -lahR $BIN_FOLDER
+      - name: Run Tests in Container
+        uses: docker://ghcr.io/su2code/su2/test-su2-asan:240320-1536
+        with:
+          # -t <Tutorials-branch> -c <Testcases-branch>
+          args: -b ${{github.ref}} -t develop -c develop -s ${{matrix.testscript}} -a "--asan"
+      - name: Cleanup
+        uses: docker://ghcr.io/su2code/su2/test-su2-asan:240320-1536
         with:
           entrypoint: /bin/rm
           args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
@@ -244,7 +331,7 @@ jobs:
             tag: MPI
     steps:
       - name: Pre Cleanup
-        uses: docker://ghcr.io/su2code/su2/test-su2:230813-0103
+        uses: docker://ghcr.io/su2code/su2/test-su2:240320-1536
         with:
           entrypoint: /bin/rm
           args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
@@ -305,11 +392,11 @@ jobs:
           echo $PWD
           ls -lahR
       - name: Run Unit Tests
-        uses: docker://ghcr.io/su2code/su2/test-su2:230813-0103
+        uses: docker://ghcr.io/su2code/su2/test-su2:240320-1536
         with:
           entrypoint: install/bin/${{matrix.testdriver}}
       - name: Post Cleanup
-        uses: docker://ghcr.io/su2code/su2/test-su2:230813-0103
+        uses: docker://ghcr.io/su2code/su2/test-su2:240320-1536
         with:
           entrypoint: /bin/rm
           args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}

Common/include/CConfig.hpp

@@ -1224,7 +1224,13 @@ class CConfig {
   unsigned short nSpecies_Init;    /*!< \brief Number of entries of SPECIES_INIT */
 
   /*--- Additional flamelet solver options ---*/
-  su2double flame_init[8];       /*!< \brief Initial solution parameters for flamelet solver.*/
+  ///TODO: Add python wrapper initialization option
+  FLAMELET_INIT_TYPE flame_init_type = FLAMELET_INIT_TYPE::NONE; /*!< \brief Method for solution ignition for flamelet problems. */
+  std::array<su2double,8> flame_init;       /*!< \brief Flame front initialization parameters. */
+  std::array<su2double,6> spark_init;       /*!< \brief Spark ignition initialization parameters. */
+  su2double* spark_reaction_rates; /*!< \brief Source terms for flamelet spark ignition option. */
+  unsigned short nspark;           /*!< \brief Number of source terms for spark initialization. */
+  bool preferential_diffusion = false;  /*!< \brief Preferential diffusion physics for flamelet solver.*/
 
   /*--- lookup table ---*/
   unsigned short n_scalars = 0;       /*!< \brief Number of transported scalars for flamelet LUT approach. */
@@ -2138,13 +2144,44 @@ class CConfig {
 
   /*!
    * \brief Get the flame initialization.
-   *        (x1,x2,x3) = flame offset.
-   *        (x4,x5,x6) = flame normal, separating unburnt from burnt.
+   *        (x1,x2,x3) = flame offset/spark center location.
+   *        (x4,x5,x6) = flame normal, separating unburnt from burnt or
+   *                     spark radius, spark start iteration, spark duration.
    *        (x7) = flame thickness, the length from unburnt to burnt conditions.
    *        (x8) = flame burnt thickness, the length to stay at burnt conditions.
-   * \return Flame initialization for the flamelet model.
+   * \return Ignition initialization parameters for the flamelet model.
+   */
+  const su2double* GetFlameInit() const {
+    switch (flame_init_type)
+    {
+    case FLAMELET_INIT_TYPE::FLAME_FRONT:
+      return flame_init.data();
+      break;
+    case FLAMELET_INIT_TYPE::SPARK:
+      return spark_init.data();
+      break;
+    default:
+      return nullptr;
+      break;
+    }
+  }
+
+  /*!
+   * \brief Get species net reaction rates applied during spark ignition.
+   */
+  const su2double* GetSpark() const {
+    return spark_reaction_rates;
+  }
+
+  /*!
+   * \brief Preferential diffusion combustion problem.
+   */
+  bool GetPreferentialDiffusion() const { return preferential_diffusion; }
+
+  /*!
+   * \brief Define preferential diffusion combustion problem.
    */
-  const su2double* GetFlameInit() const { return flame_init; }
+  inline void SetPreferentialDiffusion(bool input) { preferential_diffusion = input; }
 
   /*!
    * \brief Get the number of control variables for flamelet model.
@@ -2190,6 +2227,11 @@ class CConfig {
     if (n_user_sources > 0) return user_source_names[i_user_source]; else return none;
   }
 
+  /*!
+   * \brief Get the ignition method used for combustion problems.
+   */
+  FLAMELET_INIT_TYPE GetFlameletInitType() const { return flame_init_type; }
+
   /*!
    * \brief Get the number of transported scalars for combustion.
    */

Common/include/containers/CLookUpTable.hpp

@@ -389,7 +389,6 @@ class CLookUpTable {
   /*!
    * \brief Find the table levels with constant z-values directly above and below query val_z.
    * \param[in] val_CV3 - Value of controlling variable 3.
-   * \param[in] within_limits - Whether query point lies within table bounds.
    * \returns Pair of inclusion level indices (first = lower level index, second = upper level index).
    */
   std::pair<unsigned long, unsigned long> FindInclusionLevels(const su2double val_CV3);
@@ -410,6 +409,11 @@ class CLookUpTable {
     return limits_table_x[i_level];
   }
 
+  /*!
+   * \brief Check whether requested set of variables are included in the table.
+   */
+  bool CheckForVariables(const std::vector<std::string>& vars_to_check) const;
+
   /*!
    * \brief Returns the index to the variable in the lookup table.
    * \param[in] nameVar - Variable name for which to retrieve the column index.

Common/include/geometry/CGeometry.hpp

@@ -426,7 +426,7 @@ class CGeometry {
    * \param[out] COUNT_PER_POINT - Number of communicated variables per point.
    * \param[out] MPI_TYPE - Enumerated type for the datatype of the quantity to be communicated.
    */
-  void GetCommCountAndType(const CConfig* config, unsigned short commType, unsigned short& COUNT_PER_POINT,
+  void GetCommCountAndType(const CConfig* config, MPI_QUANTITIES commType, unsigned short& COUNT_PER_POINT,
                            unsigned short& MPI_TYPE) const;
 
   /*!
@@ -436,14 +436,14 @@ class CGeometry {
    * \param[in] config   - Definition of the particular problem.
    * \param[in] commType - Enumerated type for the quantity to be communicated.
    */
-  void InitiateComms(CGeometry* geometry, const CConfig* config, unsigned short commType) const;
+  void InitiateComms(CGeometry* geometry, const CConfig* config, MPI_QUANTITIES commType) const;
 
   /*!
    * \brief Routine to complete the set of non-blocking communications launched by InitiateComms() and unpacking of the
    * data into the geometry class. \param[in] geometry - Geometrical definition of the problem. \param[in] config   -
    * Definition of the particular problem. \param[in] commType - Enumerated type for the quantity to be unpacked.
    */
-  void CompleteComms(CGeometry* geometry, const CConfig* config, unsigned short commType);
+  void CompleteComms(CGeometry* geometry, const CConfig* config, MPI_QUANTITIES commType);
 
   /*!
    * \brief Get number of coordinates.

Common/include/linear_algebra/CSysMatrix.hpp

@@ -92,7 +92,7 @@ struct CSysMatrixComms {
    */
   template <class T>
   static void Initiate(const CSysVector<T>& x, CGeometry* geometry, const CConfig* config,
-                       unsigned short commType = SOLUTION_MATRIX);
+                       MPI_QUANTITIES commType = MPI_QUANTITIES::SOLUTION_MATRIX);
 
   /*!
    * \brief Routine to complete the set of non-blocking communications launched by
@@ -104,7 +104,7 @@ struct CSysMatrixComms {
    */
   template <class T>
   static void Complete(CSysVector<T>& x, CGeometry* geometry, const CConfig* config,
-                       unsigned short commType = SOLUTION_MATRIX);
+                       MPI_QUANTITIES commType = MPI_QUANTITIES::SOLUTION_MATRIX);
 };
 
 /*!

Common/include/option_structure.hpp

@@ -1333,11 +1333,38 @@ enum FLAMELET_SCALAR_SOURCES {
  * \brief Look-up operations for the flamelet scalar solver.
  */
 enum FLAMELET_LOOKUP_OPS {
-  TD,       /*!< \brief Thermochemical properties (temperature, density, diffusivity, etc.). */
+  THERMO,   /*!< \brief Thermochemical properties (temperature, density, diffusivity, etc.). */
+  PREFDIF,  /*!< \brief Preferential diffusion scalars. */
   SOURCES,  /*!< \brief Scalar source terms (controlling variables, passive species).*/
   LOOKUP,   /*!< \brief Passive look-up variables specified in config. */
 };
 
+/*!
+ * \brief The preferential diffusion scalar indices for the preferential diffusion model.
+ */
+enum FLAMELET_PREF_DIFF_SCALARS {
+  I_BETA_PROGVAR,       /*!< \brief Preferential diffusion scalar for the progress variable. */
+  I_BETA_ENTH_THERMAL,  /*!< \brief Preferential diffusion scalar for temperature. */
+  I_BETA_ENTH,          /*!< \brief Preferential diffusion scalar for total enthalpy. */
+  I_BETA_MIXFRAC,       /*!< \brief Preferential diffusion scalar for mixture fraction. */
+  N_BETA_TERMS,         /*!< \brief Total number of preferential diffusion scalars. */
+};
+
+/*!
+ * \brief Flame initialization options for the flamelet solver.
+ */
+enum class FLAMELET_INIT_TYPE {
+  FLAME_FRONT,  /*!< \brief Straight flame front. */
+  SPARK,        /*!< \brief Species reaction rate in a set location. */
+  NONE,         /*!< \brief No ignition, cold flow only. */
+};
+
+static const MapType<std::string, FLAMELET_INIT_TYPE> Flamelet_Init_Map = {
+  MakePair("NONE", FLAMELET_INIT_TYPE::NONE)
+  MakePair("FLAME_FRONT", FLAMELET_INIT_TYPE::FLAME_FRONT)
+  MakePair("SPARK", FLAMELET_INIT_TYPE::SPARK)
+};
+
 /*!
  * \brief Types of subgrid scale models
  */
@@ -2471,7 +2498,7 @@ enum PERIODIC_QUANTITIES {
 /*!
  * \brief Vertex-based quantities exchanged in MPI point-to-point communications.
  */
-enum MPI_QUANTITIES {
+enum class MPI_QUANTITIES {
   SOLUTION             ,  /*!< \brief Conservative solution communication. */
   SOLUTION_OLD         ,  /*!< \brief Conservative solution old communication. */
   SOLUTION_GRADIENT    ,  /*!< \brief Conservative solution gradient communication. */