Merge branch 'develop' into fix_damping_mass_outlet

Author: bigfooted

.github/workflows/codeql.yml

@@ -34,7 +34,7 @@ jobs:
 
       - name: Configure (cpp)
         if: ${{ matrix.language == 'cpp' }}
-        run: ./meson.py build --optimization=1
+        run: ./meson.py setup build --optimization=1
 
       - name: Initialize CodeQL
         uses: github/codeql-action/init@v3

.github/workflows/regression.yml

@@ -54,12 +54,12 @@ jobs:
           key: ${{ matrix.config_set }}-${{ github.sha }}
           restore-keys: ${{ matrix.config_set }}
       - name: Pre Cleanup
-        uses: docker://ghcr.io/su2code/su2/build-su2:240320-1536
+        uses: docker://ghcr.io/su2code/su2/build-su2:250717-1402
         with:
           entrypoint: /bin/rm
           args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
       - name: Build
-        uses: docker://ghcr.io/su2code/su2/build-su2:240320-1536
+        uses: docker://ghcr.io/su2code/su2/build-su2:250717-1402
         with:
           args: -b ${{github.ref}} -f "${{matrix.flags}}"
       - name: Compress binaries
@@ -70,7 +70,7 @@ jobs:
           name: ${{ matrix.config_set }}
           path: install_bin.tgz
       - name: Post Cleanup
-        uses: docker://ghcr.io/su2code/su2/build-su2:240320-1536
+        uses: docker://ghcr.io/su2code/su2/build-su2:250717-1402
         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:240320-1536
+        uses: docker://ghcr.io/su2code/su2/build-su2-tsan:250717-1402
         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:240320-1536
+        uses: docker://ghcr.io/su2code/su2/build-su2-tsan:250717-1402
         with:
           args: -b ${{github.ref}} -f "${{matrix.flags}}"
       - name: Compress binaries
@@ -113,7 +113,7 @@ jobs:
           name: ${{ matrix.config_set }}
           path: install_bin.tgz
       - name: Post Cleanup
-        uses: docker://ghcr.io/su2code/su2/build-su2-tsan:240320-1536
+        uses: docker://ghcr.io/su2code/su2/build-su2-tsan:250717-1402
         with:
           entrypoint: /bin/rm
           args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
@@ -137,12 +137,12 @@ jobs:
           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
+        uses: docker://ghcr.io/su2code/su2/build-su2-asan:250717-1402
         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}}"
+        run: docker run --rm --cap-add SYS_PTRACE -v $(pwd):${{ github.workspace }} -w ${{ github.workspace }} ghcr.io/su2code/su2/build-su2-asan:250717-1402 -b ${{github.ref}} -f "${{matrix.flags}}"
       - name: Compress binaries
         run: tar -zcvf install_bin.tgz install/*
       - name: Upload Binaries
@@ -151,7 +151,7 @@ jobs:
           name: ${{ matrix.config_set }}
           path: install_bin.tgz
       - name: Post Cleanup
-        uses: docker://ghcr.io/su2code/su2/build-su2-asan:240320-1536
+        uses: docker://ghcr.io/su2code/su2/build-su2-asan:250717-1402
         with:
           entrypoint: /bin/rm
           args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
@@ -182,7 +182,7 @@ jobs:
             tag: OMP
     steps:
       - name: Pre Cleanup
-        uses: docker://ghcr.io/su2code/su2/test-su2:240320-1536
+        uses: docker://ghcr.io/su2code/su2/test-su2:250717-1402
         with:
           entrypoint: /bin/rm
           args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
@@ -208,12 +208,12 @@ jobs:
           chmod a+x $BIN_FOLDER/*
           ls -lahR $BIN_FOLDER
       - name: Run Tests in Container
-        uses: docker://ghcr.io/su2code/su2/test-su2:240320-1536
+        uses: docker://ghcr.io/su2code/su2/test-su2:250717-1402
         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-su2:240320-1536
+        uses: docker://ghcr.io/su2code/su2/test-su2:250717-1402
         with:
           entrypoint: /bin/rm
           args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
@@ -231,7 +231,7 @@ jobs:
             tag: TagNoMPI
     steps:
       - name: Pre Cleanup
-        uses: docker://ghcr.io/su2code/su2/test-su2:240320-1536
+        uses: docker://ghcr.io/su2code/su2/test-su2:250717-1402
         with:
           entrypoint: /bin/rm
           args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
@@ -257,12 +257,12 @@ jobs:
           chmod a+x $BIN_FOLDER/*
           ls -lahR $BIN_FOLDER
       - name: Run Tests in Container
-        uses: docker://ghcr.io/su2code/su2/test-su2:240320-1536
+        uses: docker://ghcr.io/su2code/su2/test-su2:250717-1402
         with:
           # -t <Tutorials-branch> -c <Testcases-branch>
           args: -b ${{github.ref}} -t develop -c develop -s ${{matrix.testscript}} -a "--tapetests"
       - name: Cleanup
-        uses: docker://ghcr.io/su2code/su2/test-su2:240320-1536
+        uses: docker://ghcr.io/su2code/su2/test-su2:250717-1402
         with:
           entrypoint: /bin/rm
           args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
@@ -277,7 +277,7 @@ jobs:
         testscript: ['hybrid_regression.py', 'hybrid_regression_AD.py']
     steps:
       - name: Pre Cleanup
-        uses: docker://ghcr.io/su2code/su2/test-su2-tsan:240320-1536
+        uses: docker://ghcr.io/su2code/su2/test-su2-tsan:250717-1402
         with:
           entrypoint: /bin/rm
           args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
@@ -303,12 +303,12 @@ jobs:
           chmod a+x $BIN_FOLDER/*
           ls -lahR $BIN_FOLDER
       - name: Run Tests in Container
-        uses: docker://ghcr.io/su2code/su2/test-su2-tsan:240320-1536
+        uses: docker://ghcr.io/su2code/su2/test-su2-tsan:250717-1402
         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:240320-1536
+        uses: docker://ghcr.io/su2code/su2/test-su2-tsan:250717-1402
         with:
           entrypoint: /bin/rm
           args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
@@ -322,7 +322,7 @@ jobs:
         testscript: ['serial_regression.py', 'serial_regression_AD.py']
     steps:
       - name: Pre Cleanup
-        uses: docker://ghcr.io/su2code/su2/test-su2-asan:240320-1536
+        uses: docker://ghcr.io/su2code/su2/test-su2-asan:250717-1402
         with:
           entrypoint: /bin/rm
           args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
@@ -348,12 +348,12 @@ jobs:
           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
+        uses: docker://ghcr.io/su2code/su2/test-su2-asan:250717-1402
         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
+        uses: docker://ghcr.io/su2code/su2/test-su2-asan:250717-1402
         with:
           entrypoint: /bin/rm
           args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
@@ -374,7 +374,7 @@ jobs:
             tag: MPI
     steps:
       - name: Pre Cleanup
-        uses: docker://ghcr.io/su2code/su2/test-su2:240320-1536
+        uses: docker://ghcr.io/su2code/su2/test-su2:250717-1402
         with:
           entrypoint: /bin/rm
           args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
@@ -435,11 +435,11 @@ jobs:
           echo $PWD
           ls -lahR
       - name: Run Unit Tests
-        uses: docker://ghcr.io/su2code/su2/test-su2:240320-1536
+        uses: docker://ghcr.io/su2code/su2/test-su2:250717-1402
         with:
           entrypoint: install/bin/${{matrix.testdriver}}
       - name: Post Cleanup
-        uses: docker://ghcr.io/su2code/su2/test-su2:240320-1536
+        uses: docker://ghcr.io/su2code/su2/test-su2:250717-1402
         with:
           entrypoint: /bin/rm
           args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}

.github/workflows/release-management.yml

@@ -35,7 +35,7 @@ jobs:
           key: ${{ matrix.os_bin }}-${{ github.sha }}
           restore-keys: ${{ matrix.os_bin }}
       - name: Build
-        uses: docker://ghcr.io/su2code/su2/build-su2-cross:230813-0103
+        uses: docker://ghcr.io/su2code/su2/build-su2-cross:250717-1402
         with:
           args: -b ${{ github.sha }} -f "${{matrix.flags}}"
       - name: Create Archive

Common/include/CConfig.hpp

@@ -707,6 +707,7 @@ class CConfig {
   Wrt_Restart_Overwrite,              /*!< \brief Overwrite restart files or append iteration number.*/
   Wrt_Surface_Overwrite,              /*!< \brief Overwrite surface output files or append iteration number.*/
   Wrt_Volume_Overwrite,               /*!< \brief Overwrite volume output files or append iteration number.*/
+  PyCustomSource,                     /*!< \brief Use a user-defined custom source term .*/
   Restart_Flow;                       /*!< \brief Restart flow solution for adjoint and linearized problems. */
   unsigned short nMarker_Monitoring,  /*!< \brief Number of markers to monitor. */
   nMarker_Designing,                  /*!< \brief Number of markers for the objective function. */
@@ -3088,6 +3089,12 @@ class CConfig {
    */
   unsigned short GetnMarker_PyCustom(void) const { return nMarker_PyCustom; }
 
+  /*!
+   * \brief Get the Python custom source term activation.
+   * \return Custom source term is active or not.
+   */
+  bool GetPyCustomSource(void) const { return PyCustomSource; }
+
   /*!
    * \brief Get the total number of moving markers.
    * \return Total number of moving markers.

Common/include/basic_types/ad_structure.hpp

@@ -52,12 +52,12 @@ inline void StartRecording() {}
  * \brief Pause the recording of the operations and involved variables.
  * If called, all operations occuring after the call will not be stored on the computational graph.
  */
-inline void PauseRecording() {}
+inline bool PauseRecording() { return false; }
 
 /*!
  * \brief Resume the recording of the operations and variables after the recording had been paused.
  */
-inline void ResumeRecording() {}
+inline void ResumeRecording(bool wasActive) { (void)wasActive; }
 
 /*!
  * \brief Stops the recording of the operations and variables.
@@ -413,9 +413,19 @@ FORCEINLINE void ResetInput(su2double& data) { data = data.getValue(); }
 
 FORCEINLINE void StartRecording() { AD::getTape().setActive(); }
 
-FORCEINLINE void PauseRecording() { AD::getTape().setPassive(); }
+FORCEINLINE bool PauseRecording() {
+  if (AD::getTape().isActive()) {
+    AD::getTape().setPassive();
+    return true;
+  }
+  return false;
+}
 
-FORCEINLINE void ResumeRecording() { AD::getTape().setActive(); }
+FORCEINLINE void ResumeRecording(bool wasActive) {
+  if (wasActive) {
+    AD::getTape().setActive();
+  }
+}
 
 FORCEINLINE void StopRecording() { AD::getTape().setPassive(); }
 

Common/include/containers/CPyWrapperMatrixView.hpp

@@ -55,6 +55,9 @@
   /*! \brief Gets the value for a (row, column) pair. */                                                         \
   passivedouble operator()(unsigned long row, unsigned long col) const { return Get(row, col); }                 \
                                                                                                                  \
+  /*! \brief Gets the values for a row of the matrix. */                                                         \
+  std::vector<passivedouble> operator()(unsigned long row) const { return Get(row); }                            \
+                                                                                                                 \
   /*! \brief Gets the value for a (row, column) pair. */                                                         \
   passivedouble Get(unsigned long row, unsigned long col) const { return SU2_TYPE::GetValue(Access(row, col)); } \
                                                                                                                  \
@@ -163,3 +166,77 @@ class CPyWrapperMarkerMatrixView {
   /*--- Use the macro to generate the interface. ---*/
   PY_WRAPPER_MATRIX_INTERFACE
 };
+
+/*!
+ * \class CPyWrapper3DMatrixView
+ * \ingroup PySU2
+ * \brief This class wraps C3DDoubleMatrix for the python wrapper matrix interface.
+ * It is generaly used to wrap access to solver gradients defined for the entire volume.
+ */
+class CPyWrapper3DMatrixView {
+ protected:
+  static_assert(su2activematrix::IsRowMajor, "");
+  su2double* data_ = nullptr;
+  unsigned long rows_ = 0, cols_ = 0, dims_ = 0;
+  std::string name_;
+  bool read_only_ = false;
+
+  /*--- Define the functions required by the interface macro. ---*/
+  inline const su2double& Access(unsigned long row, unsigned long col, unsigned long dim) const {
+    if (row > rows_ || col > cols_ || dim > dims_) SU2_MPI::Error(name_ + " out of bounds", "CPyWrapper3DMatrixView");
+    return data_[row * (cols_ * dims_) + col * dims_ + dim];
+  }
+  inline su2double& Access(unsigned long row, unsigned long col, unsigned long dim) {
+    if (read_only_) SU2_MPI::Error(name_ + " is read-only", "CPyWrapper3DMatrixView");
+    const auto& const_me = *this;
+    return const_cast<su2double&>(const_me.Access(row, col, dim));
+  }
+
+ public:
+  CPyWrapper3DMatrixView() = default;
+
+  /*!
+   * \brief Construct the view of the matrix.
+   * \note "name" should be set to the variable name being returned to give better information to users.
+   * \note "read_only" can be set to true to prevent the data from being modified.
+   */
+  CPyWrapper3DMatrixView(C3DDoubleMatrix& mat, const std::string& name, bool read_only)
+      : data_(mat.data()),
+        rows_(mat.length()),
+        cols_(mat.rows()),
+        dims_(mat.cols()),
+        name_(name),
+        read_only_(read_only) {}
+
+  /*! \brief Returns the shape of the matrix. */
+  std::vector<unsigned long> Shape() const { return {rows_, cols_, dims_}; }
+
+  /*! \brief Returns whether the data is read-only [true] or if it can be modified [false]. */
+  bool IsReadOnly() const { return read_only_; }
+
+  /*! \brief Gets the value for a (row, column, dimension) triplet. */
+  passivedouble operator()(unsigned long row, unsigned long col, unsigned long dim) const { return Get(row, col, dim); }
+
+  /*! \brief Gets the values for a row and column of the matrix. */
+  std::vector<passivedouble> operator()(unsigned long row, unsigned long col) const { return Get(row, col); }
+
+  /*! \brief Gets the value for a (row, column, dimension) triplet. */
+  passivedouble Get(unsigned long row, unsigned long col, unsigned long dim) const {
+    return SU2_TYPE::GetValue(Access(row, col, dim));
+  }
+
+  /*! \brief Gets the values for a row and column of the matrix. */
+  std::vector<passivedouble> Get(unsigned long row, unsigned long col) const {
+    std::vector<passivedouble> vals(dims_);
+    for (unsigned long j = 0; j < dims_; ++j) vals[j] = Get(row, col, j);
+    return vals;
+  }
+  /*! \brief Sets the value for a (row, column, dimension) triplet. This clears derivative information. */
+  void Set(unsigned long row, unsigned long col, unsigned long dim, passivedouble val) { Access(row, col, dim) = val; }
+
+  /*! \brief Sets the values for a row and column of the matrix. */
+  void Set(unsigned long row, unsigned long col, std::vector<passivedouble> vals) {
+    unsigned long j = 0;
+    for (const auto& val : vals) Set(row, col, j++, val);
+  }
+};

Common/include/containers/container_decorators.hpp

@@ -165,6 +165,11 @@ class C3DContainerDecorator {
   FORCEINLINE StaticContainer get(Int i, Index j = 0) const noexcept {
     return m_storage.template get<StaticContainer>(i, j * m_innerSz);
   }
+
+  /*!
+   * \brief Raw data access, for Python wrapper.
+   */
+  FORCEINLINE Scalar* data() { return m_storage.data(); }
 };
 
 /*!

Common/include/geometry/dual_grid/CPoint.hpp

@@ -82,10 +82,9 @@ class CPoint {
   su2activematrix Coord; /*!< \brief vector with the coordinates of the node. */
   su2activematrix
       Coord_Old; /*!< \brief Old coordinates vector for primal solution reloading for Disc.Adj. with dynamic grid. */
-  su2activematrix Coord_Sum; /*!< \brief Sum of coordinates vector for geometry smoothing. */
-  su2activematrix Coord_n;   /*!< \brief Coordinates at time n for use with dynamic meshes. */
-  su2activematrix Coord_n1;  /*!< \brief Coordinates at time n-1 for use with dynamic meshes. */
-  su2activematrix Coord_p1;  /*!< \brief Coordinates at time n+1 for use with dynamic meshes. */
+  su2activematrix Coord_n;  /*!< \brief Coordinates at time n for use with dynamic meshes. */
+  su2activematrix Coord_n1; /*!< \brief Coordinates at time n-1 for use with dynamic meshes. */
+  su2activematrix Coord_p1; /*!< \brief Coordinates at time n+1 for use with dynamic meshes. */
 
   su2activematrix GridVel;      /*!< \brief Velocity of the grid for dynamic mesh cases. */
   CVectorOfMatrix GridVel_Grad; /*!< \brief Gradient of the grid velocity for dynamic meshes. */

Common/include/option_structure.hpp

@@ -550,7 +550,7 @@ enum ENUM_FLUIDMODEL {
   FLUID_MIXTURE = 9,      /*!< \brief Species mixture model. */
   COOLPROP = 10,          /*!< \brief Thermodynamics library. */
   FLUID_FLAMELET = 11,    /*!< \brief lookup table (LUT) method for premixed flamelets. */
-  DATADRIVEN_FLUID = 12,           /*!< \brief multi-layer perceptron driven fluid model. */
+  DATADRIVEN_FLUID = 12,  /*!< \brief multi-layer perceptron driven fluid model. */
 };
 static const MapType<std::string, ENUM_FLUIDMODEL> FluidModel_Map = {
   MakePair("STANDARD_AIR", STANDARD_AIR)