Merge remote-tracking branch 'upstream/develop' into feature_Sobolev_smoothing_solver

Author: thomasdick

.github/workflows/regression.yml

@@ -90,7 +90,7 @@ jobs:
         uses: docker://su2code/test-su2:20200303
         with:
           # -t <Tutorials-branch> -c <Testcases-branch>
-          args: -b ${{github.ref}} -t develop -c feature_Sobolev_smoothing_solver -s ${{matrix.testscript}}
+          args: -b ${{github.ref}} -t develop -c develop -s ${{matrix.testscript}}
   unit_tests:
     runs-on: ubuntu-latest
     name: Unit Tests

.lgtm.yml

@@ -1,3 +1,15 @@
+extraction:
+  cpp:
+     prepare:
+        packages: 
+          - libboost-all-dev
+     configure:
+        command:
+        - ./meson.py build --optimization=1
+     index:
+        build_command:
+        - ./ninja -C build
+
 path_classifiers:
   test:
     - TestCases/*

Common/include/CConfig.hpp

@@ -4285,7 +4285,7 @@ class CConfig {
   unsigned short GetRef_Inc_NonDim(void) const { return Ref_Inc_NonDim; }
 
   /*!
-   * \brief Get the kind of SU2 software component.
+   * \brief Set the kind of SU2 software component.
    * \return Kind of the SU2 software component.
    */
   void SetKind_SU2(SU2_COMPONENT val_kind_su2) { Kind_SU2 = val_kind_su2 ; }

SU2_CFD/src/drivers/CDiscAdjSinglezoneDriver.cpp

@@ -434,9 +434,8 @@ void CDiscAdjSinglezoneDriver::DirectRun(RECORDING kind_recording){
 }
 
 void CDiscAdjSinglezoneDriver::MainRecording(){
-
-  /*--- SetRecording stores the computational graph on one iteration of the direct problem. Calling it with NONE
-   *    as argument ensures that all information from a previous recording is removed. ---*/
+  /*--- SetRecording stores the computational graph on one iteration of the direct problem. Calling it with
+   *    RECORDING::CLEAR_INDICES as argument ensures that all information from a previous recording is removed. ---*/
 
   SetRecording(RECORDING::CLEAR_INDICES);
 
@@ -447,9 +446,8 @@ void CDiscAdjSinglezoneDriver::MainRecording(){
 }
 
 void CDiscAdjSinglezoneDriver::SecondaryRecording(){
-
-  /*--- SetRecording stores the computational graph on one iteration of the direct problem. Calling it with NONE
-   *    as argument ensures that all information from a previous recording is removed. ---*/
+  /*--- SetRecording stores the computational graph on one iteration of the direct problem. Calling it with
+   *    RECORDING::CLEAR_INDICES as argument ensures that all information from a previous recording is removed. ---*/
 
   SetRecording(RECORDING::CLEAR_INDICES);
 

SU2_CFD/src/fluid/CMutationTCLib.cpp

@@ -59,8 +59,15 @@ CMutationTCLib::CMutationTCLib(const CConfig* config, unsigned short val_nDim):
 
   for(iSpecies = 0; iSpecies < nSpecies; iSpecies++) MolarMass[iSpecies] = 1000* mix->speciesMw(iSpecies); // x1000 to have Molar Mass in kg/kmol
 
-  if (mix->hasElectrons()) { nHeavy = nSpecies-1; nEl = 1; }
-  else                     { nHeavy = nSpecies;   nEl = 0; }
+  if (mix->hasElectrons()) { 
+    if (config->GetViscous()) {
+      SU2_MPI::Error("Ionization is not yet operational for a viscous flow in the NEMO solver.", CURRENT_FUNCTION);
+    } else {
+      nHeavy = nSpecies-1;
+      nEl = 1;
+    }
+  }
+  else { nHeavy = nSpecies;   nEl = 0; }
 
 }
 

SU2_CFD/src/iteration/CDiscAdjFluidIteration.cpp

@@ -507,7 +507,7 @@ void CDiscAdjFluidIteration::RegisterInput(CSolver***** solver, CGeometry**** ge
     }
   }
 
-  if (kind_recording == RECORDING::MESH_COORDS) {
+  if (kind_recording == RECORDING::MESH_COORDS || kind_recording == RECORDING::SOLUTION_AND_MESH) {
     /*--- Register node coordinates as input ---*/
 
     geometry[iZone][iInst][MESH_0]->RegisterCoordinates();

externals/cgns/README

@@ -1,6 +1,6 @@
 **********************************************************************
 https://github.com/CGNS/CGNS/releases, 
-the source files for CGNS v3.3.0 are bundled and build directly into SU2
+the source files for CGNS v4.2.0 are bundled and build directly into SU2
 
 From the CGNS webpage:
 

externals/cgns/adf/ADF.h

@@ -58,6 +58,7 @@ File:	ADF.h
 	ADF core code.  These sizes are provided for reference only!
 ***********************************************************************/
 #define ADF_DATA_TYPE_LENGTH        32
+#define ADF_CGIO_DATA_TYPE_LENGTH    2
 #define ADF_DATE_LENGTH             32
 #define ADF_FILENAME_LENGTH       1024
 #define ADF_FORMAT_LENGTH           20
@@ -249,6 +250,7 @@ EXTERN	void	ADF_Put_Name(
 
 EXTERN	void	ADF_Read_All_Data(
 			const double ID,
+                        const char *m_data_type,
 			char *data,
 			int *error_return ) ;
 
@@ -269,6 +271,7 @@ EXTERN	void	ADF_Read_Data(
 			const cgsize_t m_start[],
 			const cgsize_t m_end[],
 			const cgsize_t m_stride[],
+                        const char *m_data_type,
 			char *data,
 			int *error_return ) ;
 

externals/cgns/adf/ADF_interface.c

@@ -1371,7 +1371,7 @@ ADFI_chase_link( ID, &LID, &file_index,  &block_offset, &node, error_return ) ;
 CHECK_ADF_ABORT( *error_return ) ;
 
 	/** Copy the blank-filled data-type into a C string **/
-ADFI_string_2_C_string( node.data_type, ADF_DATA_TYPE_LENGTH, data_type,
+ADFI_string_2_C_string( node.data_type, ADF_CGIO_DATA_TYPE_LENGTH, data_type,
 		error_return ) ;
 CHECK_ADF_ABORT( *error_return ) ;
 
@@ -2601,6 +2601,7 @@ output: int *error_return	Error return.
 ***********************************************************************/
 void	ADF_Read_All_Data(
 		const double ID,
+                const char *m_data_type,
 		char *data,
 		int *error_return )
 {
@@ -2629,7 +2630,16 @@ if( data == NULL ) {
 ADFI_chase_link( ID, &LID, &file_index,  &block_offset, &node, error_return ) ;
 CHECK_ADF_ABORT( *error_return ) ;
 
+/* if it was provided, check to make sure the data types match */
+if( m_data_type != NULL ) {
+  if(strncmp(m_data_type, node.data_type, 2) != 0){
+    *error_return = INVALID_DATA_TYPE;
+    CHECK_ADF_ABORT( *error_return );
+  }
+}
+
 	/** Get datatype size **/
+
 ADFI_evaluate_datatype( file_index, node.data_type, &file_bytes, &memory_bytes,
 	tokenized_data_type, &file_format, &machine_format, error_return ) ;
 CHECK_ADF_ABORT( *error_return ) ;
@@ -2916,6 +2926,7 @@ void	ADF_Read_Data(
 		const cgsize_t m_start[],
 		const cgsize_t m_end[],
 		const cgsize_t m_stride[],
+                const char *m_data_type,
 		char *data,
 		int *error_return )
 {
@@ -2952,6 +2963,14 @@ if( (s_start == NULL) || (s_end == NULL) || (s_stride == NULL) ||
 ADFI_chase_link( ID, &LID, &file_index,  &block_offset, &node, error_return ) ;
 CHECK_ADF_ABORT( *error_return ) ;
 
+/* if it was provided, check to make sure the data types match */
+if( m_data_type != NULL ) {
+  if(strncmp(m_data_type, node.data_type, 2) != 0){
+    *error_return = INVALID_DATA_TYPE;
+    CHECK_ADF_ABORT( *error_return );
+  }
+}
+
 	/** Get datatype length **/
 ADFI_evaluate_datatype( file_index, node.data_type, &file_bytes, &memory_bytes,
 	tokenized_data_type, &disk_format, &machine_format, error_return ) ;

externals/cgns/adf/ADF_internals.c

@@ -482,7 +482,7 @@ static void ADFI_convert_integers(
 	}
     }
     else {
-        memcpy(to_data, from_data, size * count);
+        memcpy(to_data, from_data, (size_t)size * (size_t)count);
     }
 }
 /*------------------------------------------------------------------------------------*/