Merge branch 'develop' into feature_improved_cauchy_convergence

su2code · May 10, 2022 · c59ed24 · c59ed24
2 parents 0e3c09d + fa910a0
commit c59ed24
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diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
@@ -7,14 +7,18 @@ assignees: ''
 
 ---
 
-**Describe the bug**
-*A clear and concise description of what the bug is and what you expect the behavior to be instead. If applicable, add screenshots to help explain your problem.*
+*If this is a general question or difficulty building/using the code, please open a "Discussion" instead.*
 
+**Describe the bug**
+*Give a clear and concise description of what the bug is and what you expect the behavior to be instead. Please provide enough instructions and data for a developer to reproduce the problem (config, mesh, commands, etc.). Please provide the smallest working example that reproduces the problem.*
 
 
-**To Reproduce**
-*Please provide a config file and mesh for a minimal example that recreates the problem.*
+**Bug report checklist**
+*Please make sure that you have followed the checklist below, many common problems can be solved by:*
 
+- [ ] Consulting the build instructions (https://su2code.github.io/docs_v7/Build-SU2-Linux-MacOS/).
+- [ ] Looking for similar problems on GitHub or CFD-Online (https://www.cfd-online.com/Forums/su2/).
+- [ ] Updating to the newest version of SU2 (either develop, master, or the pre-built executables https://su2code.github.io/download.html).
 
 
 **Desktop (please complete the following information):**

diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md
@@ -12,7 +12,7 @@
 *Put an X by all that apply. You can fill this out after submitting the PR. If you have any questions, don't hesitate to ask! We want to help. These are a guide for you to know what the reviewers will be looking for in your contribution.*
 
 - [ ] I am submitting my contribution to the develop branch.
-- [ ] My contribution generates no new compiler warnings (try with the '-Wall -Wextra -Wno-unused-parameter -Wno-empty-body' compiler flags, or simply --warnlevel=2 when using meson).
-- [ ] My contribution is commented and consistent with SU2 style.
+- [ ] My contribution generates no new compiler warnings (try with --warnlevel=3 when using meson).
+- [ ] My contribution is commented and consistent with SU2 style (https://su2code.github.io/docs_v7/Style-Guide/).
 - [ ] I have added a test case that demonstrates my contribution, if necessary.
-- [ ] I have updated appropriate documentation (Tutorials, Docs Page, config_template.cpp) , if necessary.
+- [ ] I have updated appropriate documentation (Tutorials, Docs Page, config_template.cpp), if necessary.
diff --git a/.github/workflows/regression.yml b/.github/workflows/regression.yml
@@ -31,7 +31,7 @@ jobs:
           - config_set: ForwardNoMPI
             flags: '-Denable-directdiff=true -Denable-normal=false -Dwith-mpi=disabled -Denable-tests=true --warnlevel=3 --werror'
           - config_set: BaseOMP
-            flags: '-Dwith-omp=true -Denable-mixedprec=true -Denable-tecio=false --warnlevel=3 --werror'
+            flags: '-Dwith-omp=true -Denable-mixedprec=true -Denable-pywrapper=true -Denable-tecio=false --warnlevel=3 --werror'
           - config_set: ReverseOMP
             flags: '-Denable-autodiff=true -Denable-normal=false -Dwith-omp=true -Denable-mixedprec=true -Denable-tecio=false --warnlevel=3 --werror'
           - config_set: ForwardOMP

diff --git a/Common/doc/docmain.hpp b/Common/doc/docmain.hpp
@@ -2,7 +2,7 @@
  * \file docmain.hpp
  * \brief This file contains documentation for Doxygen and does not have any significance with respect to C++.
  * \author F. Palacios
- * \version 7.3.0 "Blackbird"
+ * \version 7.3.1 "Blackbird"
  *
  * SU2 Project Website: https://su2code.github.io
  *
@@ -26,7 +26,7 @@
  */
 
 /*! 
- * \mainpage SU2 version 7.3.0 "Blackbird"
+ * \mainpage SU2 version 7.3.1 "Blackbird"
  * SU2 suite is an open-source collection of C++ based software tools
  * to perform PDE analysis and PDE constrained optimization problems.  The toolset is designed with 
  * computational fluid dynamics and aerodynamic shape optimization in mind, but is extensible to

diff --git a/Common/include/CConfig.hpp b/Common/include/CConfig.hpp
@@ -3,7 +3,7 @@
  * \brief All the information about the definition of the physical problem.
  *        The subroutines and functions are in the <i>CConfig.cpp</i> file.
  * \author F. Palacios, T. Economon, B. Tracey
- * \version 7.3.0 "Blackbird"
+ * \version 7.3.1 "Blackbird"
  *
  * SU2 Project Website: https://su2code.github.io
  *
@@ -387,10 +387,6 @@ class CConfig {
   su2double **Periodic_RotCenter;            /*!< \brief Rotational center for each periodic boundary. */
   su2double **Periodic_RotAngles;            /*!< \brief Rotation angles for each periodic boundary. */
   su2double **Periodic_Translation;          /*!< \brief Translation vector for each periodic boundary. */
-  unsigned short nPeriodic_Index;            /*!< \brief Number of SEND_RECEIVE periodic transformations. */
-  su2double **Periodic_Center;               /*!< \brief Rotational center for each SEND_RECEIVE boundary. */
-  su2double **Periodic_Rotation;             /*!< \brief Rotation angles for each SEND_RECEIVE boundary. */
-  su2double **Periodic_Translate;            /*!< \brief Translation vector for each SEND_RECEIVE boundary. */
   string *Marker_CfgFile_TagBound;           /*!< \brief Global index for markers using config file. */
   unsigned short *Marker_All_KindBC,         /*!< \brief Global index for boundaries using grid information. */
   *Marker_CfgFile_KindBC;                    /*!< \brief Global index for boundaries using config file. */
@@ -1123,9 +1119,10 @@ class CConfig {
 
   unsigned long HistoryWrtFreq[3],    /*!< \brief Array containing history writing frequencies for timer iter, outer iter, inner iter */
                 ScreenWrtFreq[3];     /*!< \brief Array containing screen writing frequencies for timer iter, outer iter, inner iter */
-  unsigned long VolumeWrtFreq;        /*!< \brief Writing frequency for solution files. */
   OUTPUT_TYPE* VolumeOutputFiles;     /*!< \brief File formats to output */
-  unsigned short nVolumeOutputFiles;  /*!< \brief Number of File formats to output */
+  unsigned short nVolumeOutputFiles=0;/*!< \brief Number of File formats to output */
+  unsigned short nVolumeOutputFrequencies; /*!< \brief Number of frequencies for the volume outputs */
+  unsigned long *VolumeOutputFrequencies; /*!< \brief list containing the writing frequencies */
 
   bool Multizone_Mesh;            /*!< \brief Determines if the mesh contains multiple zones. */
   bool SinglezoneDriver;          /*!< \brief Determines if the single-zone driver is used. (TEMPORARY) */
@@ -1260,6 +1257,8 @@ class CConfig {
 
   void addUShortListOption(const string name, unsigned short & size, unsigned short * & option_field);
 
+  void addULongListOption(const string name, unsigned short & size, unsigned long * & option_field);
+
   void addStringListOption(const string name, unsigned short & num_marker, string* & option_field);
 
   void addConvectOption(const string name, unsigned short & space_field, unsigned short & centered_field, unsigned short & upwind_field);
@@ -6602,13 +6601,6 @@ class CConfig {
    */
   const su2double* GetInlet_Velocity(string val_index) const;
 
-  /*!
-   * \brief Get the mass fraction vector at a supersonic inlet boundary.
-   * \param[in] val_index - Index corresponding to the inlet boundary.
-   * \return The inlet mass fraction vector - NEMO only.
-   */
-  const su2double* GetInlet_MassFrac(string val_index) const;
-
   /*!
    * \brief Get the total pressure at an inlet boundary.
    * \param[in] val_index - Index corresponding to the inlet boundary.
@@ -6638,8 +6630,8 @@ class CConfig {
   su2double GetExhaust_Pressure_Target(string val_index) const;
 
   /*!
-   * \brief Value of the CFL reduction in LevelSet problems.
-   * \return Value of the CFL reduction in LevelSet problems.
+   * \brief Value of the CFL reduction in turbulence problems.
+   * \return Value of the CFL reduction in turbulence problems.
    */
   su2double GetCFLRedCoeff_Turb(void) const { return CFLRedCoeff_Turb; }
 
@@ -8137,11 +8129,6 @@ class CConfig {
    */
   void SetConfig_Options();
 
-  /*!
-   * \brief Set the config options.
-   */
-  void SetRunTime_Options(void);
-
   /*!
    * \brief Set the config file parsing.
    */
@@ -9454,11 +9441,6 @@ class CConfig {
    */
   void SetScreen_Wrt_Freq(unsigned short iter, unsigned long nIter) { ScreenWrtFreq[iter] = nIter; }
 
-  /*!
-   * \brief GetScreen_Wrt_Freq_Inner
-   */
-  unsigned long GetVolume_Wrt_Freq() const { return VolumeWrtFreq; }
-
   /*!
    * \brief GetVolumeOutputFiles
    */
@@ -9469,6 +9451,12 @@ class CConfig {
    */
   unsigned short GetnVolumeOutputFiles() const { return nVolumeOutputFiles; }
 
+  /*!
+   * \brief GetVolumeOutputFrequency
+   * \param[in] iFile: index of file number for which the writing frequency needs to be returned.
+   */
+  unsigned long GetVolumeOutputFrequency(unsigned short iFile) const { return VolumeOutputFrequencies[iFile]; }
+
   /*!
    * \brief Get the desired factorization frequency for PaStiX
    * \return Number of calls to 'Build' that trigger re-factorization.

diff --git a/Common/include/adt/CADTBaseClass.hpp b/Common/include/adt/CADTBaseClass.hpp
@@ -2,7 +2,7 @@
  * \file CADTBaseClass.hpp
  * \brief Base class for storing an ADT in an arbitrary number of dimensions.
  * \author E. van der Weide
- * \version 7.3.0 "Blackbird"
+ * \version 7.3.1 "Blackbird"
  *
  * SU2 Project Website: https://su2code.github.io
  *

diff --git a/Common/include/adt/CADTComparePointClass.hpp b/Common/include/adt/CADTComparePointClass.hpp
@@ -2,7 +2,7 @@
  * \file CADTComparePointClass.hpp
  * \brief subroutines for comparing two points in an alternating digital tree (ADT).
  * \author E. van der Weide
- * \version 7.3.0 "Blackbird"
+ * \version 7.3.1 "Blackbird"
  *
  * SU2 Project Website: https://su2code.github.io
  *

diff --git a/Common/include/adt/CADTElemClass.hpp b/Common/include/adt/CADTElemClass.hpp
@@ -2,7 +2,7 @@
  * \file CADTElemClass.hpp
  * \brief Class for storing an ADT of (linear) elements in an arbitrary number of dimensions.
  * \author E. van der Weide
- * \version 7.3.0 "Blackbird"
+ * \version 7.3.1 "Blackbird"
  *
  * SU2 Project Website: https://su2code.github.io
  *
@@ -35,7 +35,7 @@
  * \class CADTElemClass
  * \brief  Class for storing an ADT of (linear) elements in an arbitrary number of dimensions.
  * \author E. van der Weide
- * \version 7.3.0 "Blackbird"
+ * \version 7.3.1 "Blackbird"
  */
 class CADTElemClass : public CADTBaseClass {
 private:
@@ -97,7 +97,7 @@ class CADTElemClass : public CADTBaseClass {
    * \param[out] rankID           Rank on which element containing the coordinate is stored.
    * \param[out] parCoor          Parametric coordinates of coor inside the element,
                                   which contains the coordinate.
-   * \param[out] weightsInterpol  Interpolation weigts of of coor inside the element,
+   * \param[out] weightsInterpol  Interpolation weights of coor inside the element,
                                   which contains the coordinate.
    * \return                      True if an element is found, false if not.
    */

diff --git a/Common/include/adt/CADTNodeClass.hpp b/Common/include/adt/CADTNodeClass.hpp
@@ -2,7 +2,7 @@
  * \file CADTNodeClass.hpp
  * \brief Class for storing the information needed in a node of an ADT.
  * \author E. van der Weide
- * \version 7.3.0 "Blackbird"
+ * \version 7.3.1 "Blackbird"
  *
  * SU2 Project Website: https://su2code.github.io
  *

diff --git a/Common/include/adt/CADTPointsOnlyClass.hpp b/Common/include/adt/CADTPointsOnlyClass.hpp
@@ -2,7 +2,7 @@
  * \file CADTPointsOnlyClass.hpp
  * \brief Class for storing an ADT of only points in an arbitrary number of dimensions.
  * \author E. van der Weide
- * \version 7.3.0 "Blackbird"
+ * \version 7.3.1 "Blackbird"
  *
  * SU2 Project Website: https://su2code.github.io
  *

diff --git a/Common/include/adt/CBBoxTargetClass.hpp b/Common/include/adt/CBBoxTargetClass.hpp
@@ -3,7 +3,7 @@
  * \brief Class for storing the information of a possible bounding box candidate
            during a minimum distance search.
  * \author E. van der Weide
- * \version 7.3.0 "Blackbird"
+ * \version 7.3.1 "Blackbird"
  *
  * SU2 Project Website: https://su2code.github.io
  *
@@ -34,7 +34,7 @@
  * \brief  Class for storing the information of a possible bounding box candidate
            during a minimum distance search.
  * \author E. van der Weide
- * \version 7.3.0 "Blackbird"
+ * \version 7.3.1 "Blackbird"
  */
 struct CBBoxTargetClass {
 

diff --git a/Common/include/basic_types/ad_structure.hpp b/Common/include/basic_types/ad_structure.hpp
@@ -2,7 +2,7 @@
  * \file ad_structure.hpp
  * \brief Main routines for the algorithmic differentiation (AD) structure.
  * \author T. Albring, J. Blühdorn
- * \version 7.3.0 "Blackbird"
+ * \version 7.3.1 "Blackbird"
  *
  * SU2 Project Website: https://su2code.github.io
  *

diff --git a/Common/include/basic_types/datatype_structure.hpp b/Common/include/basic_types/datatype_structure.hpp
@@ -2,7 +2,7 @@
  * \file datatype_structure.hpp
  * \brief Headers for generalized datatypes, defines an interface for AD types.
  * \author T. Albring
- * \version 7.3.0 "Blackbird"
+ * \version 7.3.1 "Blackbird"
  *
  * SU2 Project Website: https://su2code.github.io
  *

diff --git a/Common/include/code_config.hpp b/Common/include/code_config.hpp
@@ -2,7 +2,7 @@
  * \file code_config.hpp
  * \brief Header file for collecting common macros, definitions and type configurations.
  * \author T. Albring, P. Gomes, J. Blühdorn
- * \version 7.3.0 "Blackbird"
+ * \version 7.3.1 "Blackbird"
  *
  * SU2 Project Website: https://su2code.github.io
  *

diff --git a/Common/include/containers/C2DContainer.hpp b/Common/include/containers/C2DContainer.hpp
@@ -2,7 +2,7 @@
  * \file C2DContainer.hpp
  * \brief A templated vector/matrix object.
  * \author P. Gomes
- * \version 7.3.0 "Blackbird"
+ * \version 7.3.1 "Blackbird"
  *
  * SU2 Project Website: https://su2code.github.io
  *

diff --git a/Common/include/containers/CFastFindAndEraseQueue.hpp b/Common/include/containers/CFastFindAndEraseQueue.hpp
@@ -3,7 +3,7 @@
  * \brief A queue-type container (push back, pop front), but with
  *        fast deletion of arbitrary items (possibly in the middle).
  * \author P. Gomes
- * \version 7.3.0 "Blackbird"
+ * \version 7.3.1 "Blackbird"
  *
  * SU2 Project Website: https://su2code.github.io
  *

diff --git a/Common/include/containers/CVertexMap.hpp b/Common/include/containers/CVertexMap.hpp
@@ -2,7 +2,7 @@
  * \file CVertexMap.hpp
  * \brief An index to index lookup vector.
  * \author P. Gomes
- * \version 7.3.0 "Blackbird"
+ * \version 7.3.1 "Blackbird"
  *
  * SU2 Project Website: https://su2code.github.io
  *

diff --git a/Common/include/containers/container_decorators.hpp b/Common/include/containers/container_decorators.hpp
@@ -3,7 +3,7 @@
  * \brief Collection of small classes that decorate C2DContainer to
  * augment its functionality, e.g. give it extra dimensions.
  * \author P. Gomes
- * \version 7.3.0 "Blackbird"
+ * \version 7.3.1 "Blackbird"
  *
  * SU2 Project Website: https://su2code.github.io
  *

diff --git a/Common/include/fem/fem_cgns_elements.hpp b/Common/include/fem/fem_cgns_elements.hpp
@@ -4,7 +4,7 @@
  *        with high order elements.
  *        The functions are in the <i>cgns_elements.cpp</i> file.
  * \author E. van der Weide
- * \version 7.3.0 "Blackbird"
+ * \version 7.3.1 "Blackbird"
  *
  * SU2 Project Website: https://su2code.github.io
  *

diff --git a/Common/include/fem/fem_gauss_jacobi_quadrature.hpp b/Common/include/fem/fem_gauss_jacobi_quadrature.hpp
@@ -6,7 +6,7 @@
           All the functions in this class are based on the program JACOBI_RULE
           of John Burkardt.
  * \author E. van der Weide
- * \version 7.3.0 "Blackbird"
+ * \version 7.3.1 "Blackbird"
  *
  * SU2 Project Website: https://su2code.github.io
  *
@@ -95,7 +95,7 @@ using namespace std;
  * \brief Class used to determine the quadrature points of the Gauss Jacobi
           integration rules.
  * \author E. van der Weide
- * \version 7.3.0 "Blackbird"
+ * \version 7.3.1 "Blackbird"
  */
 class CGaussJacobiQuadrature {
 public: