Merge branch 'develop'

.gitignore

@@ -42,6 +42,10 @@ externals/autotools/share
 *.err
 
 # configuration sets
-REVERSE/
-NORMAL/
-DIRECTDIFF/
+SU2_AD/
+SU2_BASE/
+SU2_DIRECTDIFF/
+
+# ignore the bin/ directory
+bin/
+

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 4.1.3 "Cardinal"
+ * \version 4.2.0 "Cardinal"
  *
  * SU2 Lead Developers: Dr. Francisco Palacios (Francisco.D.Palacios@boeing.com).
  *                      Dr. Thomas D. Economon (economon@stanford.edu).

Common/include/config_structure.hpp

@@ -3,7 +3,7 @@
  * \brief All the information about the definition of the physical problem.
  *        The subroutines and functions are in the <i>config_structure.cpp</i> file.
  * \author F. Palacios, T. Economon, B. Tracey
- * \version 4.1.3 "Cardinal"
+ * \version 4.2.0 "Cardinal"
  *
  * SU2 Lead Developers: Dr. Francisco Palacios (Francisco.D.Palacios@boeing.com).
  *                      Dr. Thomas D. Economon (economon@stanford.edu).
@@ -55,7 +55,7 @@ using namespace std;
  * \brief Main class for defining the problem; basically this class reads the configuration file, and
  *        stores all the information.
  * \author F. Palacios
- * \version 4.1.3 "Cardinal"
+ * \version 4.2.0 "Cardinal"
  */
 
 class CConfig {
@@ -228,7 +228,7 @@ class CConfig {
 	su2double *NRBC_Var1, *NRBC_Var2;    /*!< \brief Specified values for NRBC boundary. */
 	su2double **NRBC_FlowDir;  /*!< \brief Specified flow direction vector (unit vector) for NRBC boundaries. */
 	su2double *Inlet_Ptotal;    /*!< \brief Specified total pressures for inlet boundaries. */
-	su2double **Inlet_FlowDir;  /*!< \brief Specified flow direction vector (unit vector) for inlet boundaries. */
+    su2double **Inlet_FlowDir;  /*!< \brief Specified flow direction vector (unit vector) for inlet boundaries. */
 	su2double *Inlet_Temperature;    /*!< \brief Specified temperatures for a supersonic inlet boundaries. */
 	su2double *Inlet_Pressure;    /*!< \brief Specified static pressures for supersonic inlet boundaries. */
 	su2double **Inlet_Velocity;  /*!< \brief Specified flow velocity vectors for supersonic inlet boundaries. */
@@ -281,6 +281,7 @@ class CConfig {
 	unsigned long Dyn_nIntIter;			/*!< \brief Number of internal iterations (Newton-Raphson Method for nonlinear structural analysis). */
   long Unst_RestartIter;			/*!< \brief Iteration number to restart an unsteady simulation (Dual time Method). */
   long Unst_AdjointIter;			/*!< \brief Iteration number to begin the reverse time integration in the direct solver for the unsteady adjoint. */
+  long Iter_Avg_Objective;			/*!< \brief Iteration the number of time steps to be averaged, counting from the back */
   long Dyn_RestartIter;			/*!< \brief Iteration number to restart a dynamic structural analysis. */
   unsigned short nRKStep;			/*!< \brief Number of steps of the explicit Runge-Kutta method. */
 	su2double *RK_Alpha_Step;			/*!< \brief Runge-Kutta beta coefficients. */
@@ -418,6 +419,7 @@ class CConfig {
   unsigned short Deform_Stiffness_Type; /*!< \brief Type of element stiffness imposed for FEA mesh deformation. */
   bool Deform_Output;  /*!< \brief Print the residuals during mesh deformation to the console. */
   su2double Deform_Tol_Factor; /*!< Factor to multiply smallest volume for deform tolerance (0.001 default) */
+  su2double Deform_Coeff; /*!< Deform coeffienct */
   unsigned short Deform_Linear_Solver; /*!< Numerical method to deform the grid */
   unsigned short FFD_Continuity; /*!< Surface continuity at the intersection with the FFD */
   su2double Deform_ElasticityMod, Deform_PoissonRatio; /*!< young's modulus and poisson ratio for volume deformation stiffness model */
@@ -529,7 +531,9 @@ class CConfig {
 	ObjFunc_Value_FileName,			/*!< \brief Objective function. */
 	SurfFlowCoeff_FileName,			/*!< \brief Output file with the flow variables on the surface. */
 	SurfAdjCoeff_FileName,			/*!< \brief Output file with the adjoint variables on the surface. */
-	New_SU2_FileName;        		/*!< \brief Output SU2 mesh file converted from CGNS format. */
+  New_SU2_FileName,       		/*!< \brief Output SU2 mesh file converted from CGNS format. */
+  SurfSens_FileName,			/*!< \brief Output file for the sensitivity on the surface (discrete adjoint). */
+  VolSens_FileName;			/*!< \brief Output file for the sensitivity in the volume (discrete adjoint). */
 	bool Low_MemoryOutput,      /*!< \brief Write a volume solution file */
   Wrt_Vol_Sol,                /*!< \brief Write a volume solution file */
 	Wrt_Srf_Sol,                /*!< \brief Write a surface solution file */
@@ -701,6 +705,8 @@ class CConfig {
   su2double Static_Time;			/*!< \brief Time while the structure is not loaded in FSI applications. */
   unsigned short Pred_Order;  /*!< \brief Order of the predictor for FSI applications. */
   unsigned short Kind_Interpolation; /*!\brief type of interpolation to use for FSI applications. */
+  bool Prestretch;             /*!< Read a reference geometry for optimization purposes. */
+  string Prestretch_FEMFileName;         /*!< \brief File name for reference geometry. */
   unsigned long Nonphys_Points, /*!< \brief Current number of non-physical points in the solution. */
   Nonphys_Reconstr;      /*!< \brief Current number of non-physical reconstructions for 2nd-order upwinding. */
   bool ParMETIS;      /*!< \brief Boolean for activating ParMETIS mode (while testing). */
@@ -1570,6 +1576,19 @@ class CConfig {
 	 */
 	unsigned short GetElas2D_Formulation(void);
 
+  /*!
+    * \brief Decide whether it's necessary to read a reference geometry.
+    * \return <code>TRUE</code> if it's necessary to read a reference geometry, <code>FALSE</code> otherwise.
+    */
+
+  bool GetPrestretch(void);
+
+  /*!
+   * \brief Get the name of the file with the reference geometry of the structural problem.
+   * \return Name of the file with the reference geometry of the structural problem.
+   */
+  string GetPrestretch_FEMFileName(void);
+
 	/*!
 	 * \brief Get the Poisson's ratio.
 	 * \return Value of the Poisson's ratio.
@@ -2177,7 +2196,13 @@ class CConfig {
   long GetUnst_AdjointIter(void);
 
   /*!
-	 * \brief Get the restart iteration number for dynamic structural simulations.
+  * \brief Number of iterations to average (reverse time integration).
+  * \return Starting direct iteration number for the unsteady adjoint.
+  */
+  unsigned long GetIter_Avg_Objective(void);
+
+  /*!
+   * \brief Get the restart iteration number for dynamic structural simulations.
 	 * \return Restart iteration number for dynamic structural simulations.
 	 */
   long GetDyn_RestartIter(void);
@@ -2389,7 +2414,7 @@ class CConfig {
 	 */
 	string GetMarker_EngineExhaust(unsigned short val_marker);
 
-    /*!
+  /*!
 	 * \brief Get the name of the surface defined in the geometry file.
 	 * \param[in] val_marker - Value of the marker in which we are interested.
 	 * \return Name that is in the geometry file for the surface that
@@ -2904,6 +2929,12 @@ class CConfig {
 	 * \return Factor to multiply smallest volume for deform tolerance.
 	 */
 	su2double GetDeform_Tol_Factor(void);
+
+  /*!
+   * \brief Get factor to multiply smallest volume for deform tolerance.
+   * \return Factor to multiply smallest volume for deform tolerance.
+   */
+  su2double GetDeform_Coeff(void);
 
   /*!
    * \brief Get Young's modulus for deformation (constant stiffness deformation)
@@ -3904,6 +3935,18 @@ class CConfig {
 	 */
 	string GetSurfAdjCoeff_FileName(void);
 
+  /*!
+   * \brief Get the name of the file with the surface sensitivity (discrete adjoint).
+   * \return Name of the file with the surface sensitivity (discrete adjoint).
+   */
+  string GetSurfSens_FileName(void);
+
+  /*!
+   * \brief Get the name of the file with the volume sensitivity (discrete adjoint).
+   * \return Name of the file with the volume sensitivity (discrete adjoint).
+   */
+  string GetVolSens_FileName(void);
+
   /*!
 	 * \brief Augment the input filename with the iteration number for an unsteady file.
    * \param[in] val_filename - String value of the base filename.

Common/include/config_structure.inl

@@ -2,7 +2,7 @@
  * \file config_structure.inl
  * \brief In-Line subroutines of the <i>config_structure.hpp</i> file.
  * \author F. Palacios, T. Economon
- * \version 4.1.3 "Cardinal"
+ * \version 4.2.0 "Cardinal"
  *
  * SU2 Lead Developers: Dr. Francisco Palacios (Francisco.D.Palacios@boeing.com).
  *                      Dr. Thomas D. Economon (economon@stanford.edu).
@@ -89,6 +89,8 @@ inline long CConfig::GetUnst_RestartIter(void) { return Unst_RestartIter; }
 
 inline long CConfig::GetUnst_AdjointIter(void) { return Unst_AdjointIter; }
 
+inline unsigned long CConfig::GetIter_Avg_Objective(void) { return Iter_Avg_Objective ; }
+
 inline long CConfig::GetDyn_RestartIter(void) { return Dyn_RestartIter; }
 
 inline string CConfig::GetPlaneTag(unsigned short index) { return PlaneTag[index]; }
@@ -137,7 +139,6 @@ inline unsigned short CConfig::GetElas2D_Formulation(void) { return Kind_2DElasF
 
 inline su2double CConfig::GetPoissonRatio(void) { return PoissonRatio; }
 
-
 inline su2double CConfig::GetMaterialDensity(void) { return MaterialDensity; }
 
 inline unsigned short CConfig::GetMaterialCompressibility(void) { return Kind_Material_Compress; }
@@ -146,6 +147,10 @@ inline unsigned short CConfig::GetMaterialModel(void) { return Kind_Material; }
 
 inline unsigned short CConfig::GetGeometricConditions(void) { return Kind_Struct_Solver; }
 
+inline bool CConfig::GetPrestretch(void) { return Prestretch; }
+
+inline string CConfig::GetPrestretch_FEMFileName(void) { return Prestretch_FEMFileName; }
+
 inline su2double CConfig::GetRefLengthMoment(void) { return RefLengthMoment; }
 
 inline su2double CConfig::GetRefElemLength(void) { return RefElemLength; }
@@ -610,6 +615,8 @@ inline bool CConfig::GetDeform_Output(void) { return Deform_Output; }
 
 inline su2double CConfig::GetDeform_Tol_Factor(void) { return Deform_Tol_Factor; }
 
+inline su2double CConfig::GetDeform_Coeff(void) { return Deform_Coeff; }
+
 inline su2double CConfig::GetDeform_ElasticityMod(void) { return Deform_ElasticityMod; }
 
 inline su2double CConfig::GetDeform_PoissonRatio(void) { return Deform_PoissonRatio; }
@@ -918,6 +925,10 @@ inline string CConfig::GetSurfFlowCoeff_FileName(void) { return SurfFlowCoeff_Fi
 
 inline string CConfig::GetSurfAdjCoeff_FileName(void) { return SurfAdjCoeff_FileName; }
 
+inline string CConfig::GetSurfSens_FileName(void) { return SurfSens_FileName; }
+
+inline string CConfig::GetVolSens_FileName(void) { return VolSens_FileName; }
+
 inline unsigned short CConfig::GetResidual_Func_Flow(void) { return Residual_Func_Flow; }
 
 inline unsigned short CConfig::GetCauchy_Func_Flow(void) { return Cauchy_Func_Flow; }

Common/include/datatype_structure.hpp

@@ -3,7 +3,7 @@
  * \brief Headers for generalized datatypes.
  *        The subroutines and functions are in the <i>datatype_structure.cpp</i> file.
  * \author T. Albring
- * \version 4.1.3 "Cardinal"
+ * \version 4.2.0 "Cardinal"
  *
  * SU2 Lead Developers: Dr. Francisco Palacios (Francisco.D.Palacios@boeing.com).
  *                      Dr. Thomas D. Economon (economon@stanford.edu).
@@ -64,7 +64,7 @@ typedef double passivedouble;
  * \brief Namespace for defining the datatype wrapper routines; this class features as a base class for
  * type interfaces for non-primitive dataypes e.g. used by AD, complex etc.
  * \author T. Albring
- * \version 4.1.3 "Cardinal"
+ * \version 4.2.0 "Cardinal"
  */
 namespace SU2_TYPE{
   /*!

Common/include/datatype_structure.inl

@@ -2,7 +2,7 @@
  * \file datatype_structure.inl
  * \brief In-Line subroutines of the <i>datatype_structure.hpp</i> file.
  * \author T. Albring
- * \version 4.1.3 "Cardinal"
+ * \version 4.2.0 "Cardinal"
  *
  * SU2 Lead Developers: Dr. Francisco Palacios (Francisco.D.Palacios@boeing.com).
  *                      Dr. Thomas D. Economon (economon@stanford.edu).

Common/include/datatypes/codi_forward_structure.hpp

@@ -2,7 +2,7 @@
  * \file codi_forward_structure.hpp
  * \brief Header for codi forward type definition.
  * \author T. Albring
- * \version 4.1.3 "Cardinal"
+ * \version 4.2.0 "Cardinal"
  *
  * SU2 Lead Developers: Dr. Francisco Palacios (Francisco.D.Palacios@boeing.com).
  *                      Dr. Thomas D. Economon (economon@stanford.edu).

Common/include/datatypes/codi_forward_structure.inl

@@ -2,7 +2,7 @@
  * \file codi_forward_structure.inl
  * \brief Inline subroutines for <i>codi_forward_structure.hpp<i>.
  * \author T. Albring
- * \version 4.1.3 "Cardinal"
+ * \version 4.2.0 "Cardinal"
  *
  * SU2 Lead Developers: Dr. Francisco Palacios (Francisco.D.Palacios@boeing.com).
  *                      Dr. Thomas D. Economon (economon@stanford.edu).

Common/include/datatypes/codi_reverse_structure.hpp

@@ -2,7 +2,7 @@
  * \file codi_reverse_structure.hpp
  * \brief Header for codi reverse type definition.
  * \author T. Albring
- * \version 4.1.3 "Cardinal"
+ * \version 4.2.0 "Cardinal"
  *
  * SU2 Lead Developers: Dr. Francisco Palacios (Francisco.D.Palacios@boeing.com).
  *                      Dr. Thomas D. Economon (economon@stanford.edu).

Common/include/datatypes/codi_reverse_structure.inl

@@ -2,7 +2,7 @@
  * \file codi_reverse_structure.inl
  * \brief Inline subroutines for <i>datatype_structure.hpp<i>.
  * \author T. Albring
- * \version 4.1.3 "Cardinal"
+ * \version 4.2.0 "Cardinal"
  *
  * SU2 Lead Developers: Dr. Francisco Palacios (Francisco.D.Palacios@boeing.com).
  *                      Dr. Thomas D. Economon (economon@stanford.edu).

Common/include/datatypes/complex_structure.hpp

@@ -2,7 +2,7 @@
  * \file complex_structure.hpp
  * \brief Headers for complex datatype definition.
  * \author T. Albring
- * \version 4.1.3 "Cardinal"
+ * \version 4.2.0 "Cardinal"
  *
  * SU2 Lead Developers: Dr. Francisco Palacios (Francisco.D.Palacios@boeing.com).
  *                      Dr. Thomas D. Economon (economon@stanford.edu).
@@ -43,7 +43,7 @@ inline double real(const double& r);
  * \brief Class for defining the complex datatype for complex step gradient computation.
  * Based on complexify.h by Peter Sturdza.
  * \author T. Albring
- * \version 4.1.3 "Cardinal"
+ * \version 4.2.0 "Cardinal"
  */
 
 class CComplexType : public std::complex<double> {

Common/include/datatypes/complex_structure.inl

@@ -2,7 +2,7 @@
  * \file complex_structure.inl
  * \brief In-Line subroutines of the <i>datatype_structure.hpp</i> file.
  * \author T. Albring
- * \version 4.1.3 "Cardinal"
+ * \version 4.2.0 "Cardinal"
  *
  * SU2 Lead Developers: Dr. Francisco Palacios (Francisco.D.Palacios@boeing.com).
  *                      Dr. Thomas D. Economon (economon@stanford.edu).

Common/include/datatypes/primitive_structure.hpp

@@ -2,7 +2,7 @@
  * \file primitive_structure.hpp
  * \brief Header for the primitive datatype.
  * \author T. Albring
- * \version 4.1.3 "Cardinal"
+ * \version 4.2.0 "Cardinal"
  *
  * SU2 Lead Developers: Dr. Francisco Palacios (Francisco.D.Palacios@boeing.com).
  *                      Dr. Thomas D. Economon (economon@stanford.edu).

Common/include/datatypes/primitive_structure.inl

@@ -2,7 +2,7 @@
  * \file primitive_structure.inl
  * \brief Inline subroutines for <i>datatype_structure.hpp<i>.
  * \author T. Albring
- * \version 4.1.3 "Cardinal"
+ * \version 4.2.0 "Cardinal"
  *
  * SU2 Lead Developers: Dr. Francisco Palacios (Francisco.D.Palacios@boeing.com).
  *                      Dr. Thomas D. Economon (economon@stanford.edu).

Common/include/dual_grid_structure.hpp

@@ -3,7 +3,7 @@
  * \brief Headers of the main subroutines for doing the complete dual grid structure.
  *        The subroutines and functions are in the <i>dual_grid_structure.cpp</i> file.
  * \author F. Palacios, T. Economon
- * \version 4.1.3 "Cardinal"
+ * \version 4.2.0 "Cardinal"
  *
  * SU2 Lead Developers: Dr. Francisco Palacios (Francisco.D.Palacios@boeing.com).
  *                      Dr. Thomas D. Economon (economon@stanford.edu).
@@ -48,7 +48,7 @@ using namespace std;
  * \brief Class for controlling the dual volume definition. The dual volume is compose by 
  *        three main elements: points, edges, and vertices.
  * \author F. Palacios
- * \version 4.1.3 "Cardinal"
+ * \version 4.2.0 "Cardinal"
  */
 class CDualGrid{
 protected:
@@ -133,7 +133,7 @@ class CDualGrid{
  * \class CPoint
  * \brief Class for point definition (including control volume definition).
  * \author F. Palacios
- * \version 4.1.3 "Cardinal"
+ * \version 4.2.0 "Cardinal"
  */
 class CPoint : public CDualGrid {
 private:
@@ -740,7 +740,7 @@ class CPoint : public CDualGrid {
  * \class CEdge
  * \brief Class for defining an edge.
  * \author F. Palacios
- * \version 4.1.3 "Cardinal"
+ * \version 4.2.0 "Cardinal"
  */
 class CEdge : public CDualGrid {
 private:
@@ -877,7 +877,7 @@ class CEdge : public CDualGrid {
  * \class CVertex
  * \brief Class for vertex definition (equivalent to edges, but for the boundaries).
  * \author F. Palacios
- * \version 4.1.3 "Cardinal"
+ * \version 4.2.0 "Cardinal"
  */
 class CVertex : public CDualGrid {
 private:

Common/include/dual_grid_structure.inl

@@ -2,7 +2,7 @@
  * \file dual_grid_structure.inl
  * \brief In-Line subroutines of the <i>dual_grid_structure.hpp</i> file.
  * \author F. Palacios, T. Economon
- * \version 4.1.3 "Cardinal"
+ * \version 4.2.0 "Cardinal"
  *
  * SU2 Lead Developers: Dr. Francisco Palacios (Francisco.D.Palacios@boeing.com).
  *                      Dr. Thomas D. Economon (economon@stanford.edu).