add MeshBase

src/coreComponents/fileIO/vtk/VTKPolyDataWriterInterface.hpp

@@ -199,7 +199,7 @@ class VTKPolyDataWriterInterface
   void clearData();
 
 
-private:
+protected:
 
   /**
    * @brief Check if plotting is enabled for this field
@@ -299,7 +299,7 @@ class VTKPolyDataWriterInterface
   void writeUnstructuredGrid( string const & path,
                               vtkUnstructuredGrid * ug ) const;
 
-private:
+protected:
 
   /// Output directory name
   string m_outputDir;

src/coreComponents/mesh/CMakeLists.txt

@@ -16,6 +16,7 @@ set( mesh_headers
      FaceManager.hpp
      FieldIdentifiers.hpp
      InterObjectRelation.hpp
+     MeshBase.hpp
      MeshBody.hpp
      MeshForLoopInterface.hpp
      MeshLevel.hpp
@@ -96,6 +97,7 @@ set( mesh_sources
      EmbeddedSurfaceSubRegion.cpp
      FaceElementSubRegion.cpp
      FaceManager.cpp
+     MeshBase.cpp
      MeshBody.cpp
      MeshLevel.cpp
      MeshManager.cpp

src/coreComponents/mesh/MeshBase.cpp

@@ -0,0 +1,43 @@
+/*
+ * ------------------------------------------------------------------------------------------------------------
+ * SPDX-License-Identifier: LGPL-2.1-only
+ *
+ * Copyright (c) 2018-2020 Lawrence Livermore National Security LLC
+ * Copyright (c) 2018-2020 The Board of Trustees of the Leland Stanford Junior University
+ * Copyright (c) 2018-2020 TotalEnergies
+ * Copyright (c) 2019-     GEOSX Contributors
+ * All rights reserved
+ *
+ * See top level LICENSE, COPYRIGHT, CONTRIBUTORS, NOTICE, and ACKNOWLEDGEMENTS files for details.
+ * ------------------------------------------------------------------------------------------------------------
+ */
+
+#include "MeshBase.hpp"
+
+namespace geos
+{
+using namespace dataRepository;
+
+MeshBase::MeshBase( string const & name, Group * const parent ):
+  Group( name, parent )
+{
+  setInputFlags( InputFlags::OPTIONAL_NONUNIQUE );
+}
+
+// Group * MeshBase::createChild( string const & GEOS_UNUSED_PARAM(childKey), string const & GEOS_UNUSED_PARAM(childName) )
+// {
+//   return nullptr;
+// }
+
+// void MeshBase::expandObjectCatalogs()
+// {
+
+// }
+
+MeshBase::CatalogInterface::CatalogType & MeshBase::getCatalog()
+{
+  static MeshBase::CatalogInterface::CatalogType catalog;
+  return catalog;
+}
+
+}

src/coreComponents/mesh/MeshBase.hpp

@@ -0,0 +1,78 @@
+/*
+ * ------------------------------------------------------------------------------------------------------------
+ * SPDX-License-Identifier: LGPL-2.1-only
+ *
+ * Copyright (c) 2018-2020 Lawrence Livermore National Security LLC
+ * Copyright (c) 2018-2020 The Board of Trustees of the Leland Stanford Junior University
+ * Copyright (c) 2018-2020 TotalEnergies
+ * Copyright (c) 2019-     GEOSX Contributors
+ * All rights reserved
+ *
+ * See top level LICENSE, COPYRIGHT, CONTRIBUTORS, NOTICE, and ACKNOWLEDGEMENTS files for details.
+ * ------------------------------------------------------------------------------------------------------------
+ */
+
+/**
+ * @file MeshBase.hpp
+ */
+
+#ifndef GEOS_MESH_MESHBASE_HPP
+#define GEOS_MESH_MESHBASE_HPP
+
+#include "dataRepository/Group.hpp"
+#include "dataRepository/WrapperBase.hpp"
+#include "codingUtilities/Utilities.hpp"
+#include "common/DataTypes.hpp"
+
+
+namespace geos
+{
+
+/**
+ *  @class MeshBase
+ *  @brief The MeshBase class provides an abstract base class implementation for different mesh types.
+ *	   The MeshBase is the Group specialization for different type of mesh handling.
+ */
+class MeshBase : public dataRepository::Group
+{
+public:
+
+  /**
+   * @brief Main constructor for MeshBase base class.
+   * @param[in] name of the MeshBase object
+   * @param[in] parent the parent Group pointer for the MeshBase object
+   */
+  explicit MeshBase( string const & name,
+                     Group * const parent );
+
+  /**
+   * @brief Return the name of the MeshBase in object catalog.
+   * @return string that contains the catalog name of the MeshBase
+   */
+  static string catalogName() { return "MeshBase"; }
+
+  /// This function is used to expand any catalogs in the data structure
+//   virtual void expandObjectCatalogs() override;
+
+  /// using alias for templated Catalog MeshBase type
+  using CatalogInterface = dataRepository::CatalogInterface< MeshBase, string const &, Group * const >;
+
+  /**
+   * @brief Create a new geometric object (box, plane, etc) as a child of this group.
+   * @param childKey the catalog key of the new geometric object to create
+   * @param childName the name of the new geometric object in the repository
+   * @return the group child
+   */
+//   virtual Group * createChild( string const & childKey, string const & childName ) override;
+
+  /**
+   * @brief Accessor for the singleton Catalog object
+   * @return a static reference to the Catalog object
+   */
+  static CatalogInterface::CatalogType & getCatalog();
+
+};
+
+}
+
+#endif /* GEOS_MESH_MESHBASE_HPP */

src/coreComponents/mesh/MeshManager.cpp

@@ -43,15 +43,15 @@ MeshManager::~MeshManager()
 Group * MeshManager::createChild( string const & childKey, string const & childName )
 {
   GEOS_LOG_RANK_0( "Adding Mesh: " << childKey << ", " << childName );
-  std::unique_ptr< MeshGeneratorBase > solver = MeshGeneratorBase::CatalogInterface::factory( childKey, childName, this );
-  return &this->registerGroup< MeshGeneratorBase >( childName, std::move( solver ) );
+  std::unique_ptr< MeshBase > mesh = MeshBase::CatalogInterface::factory( childKey, childName, this );
+  return &this->registerGroup< MeshBase >( childName, std::move( mesh ) );
 }
 
 
 void MeshManager::expandObjectCatalogs()
 {
-  // During schema generation, register one of each type derived from MeshGeneratorBase here
-  for( auto & catalogIter: MeshGeneratorBase::getCatalog())
+  // During schema generation, register one of each type derived from MeshBase here
+  for( auto & catalogIter: MeshBase::getCatalog())
   {
     createChild( catalogIter.first, catalogIter.first );
   }

src/coreComponents/mesh/generators/ExternalMeshGeneratorBase.cpp

@@ -25,11 +25,6 @@ ExternalMeshGeneratorBase::ExternalMeshGeneratorBase( string const & name,
 {
   enableLogLevelInput();
 
-  registerWrapper( viewKeyStruct::filePathString(), &m_filePath ).
-    setInputFlag( InputFlags::REQUIRED ).
-    setRestartFlags( RestartFlags::NO_WRITE ).
-    setDescription( "Path to the mesh file" );
-
   registerWrapper( viewKeyStruct::translateString(), &m_translate ).
     setInputFlag( InputFlags::OPTIONAL ).
     setApplyDefaultValue( { 0.0, 0.0, 0.0 } ).

src/coreComponents/mesh/generators/ExternalMeshGeneratorBase.hpp

@@ -44,7 +44,6 @@ class ExternalMeshGeneratorBase : public MeshGeneratorBase
   ///@cond DO_NOT_DOCUMENT
   struct viewKeyStruct
   {
-    constexpr static char const * filePathString() { return "file"; }
     constexpr static char const * scaleString() { return "scale"; }
     constexpr static char const * translateString() { return "translate"; }
     constexpr static char const * volumicFieldsToImportString() { return "fieldsToImport"; }
@@ -56,9 +55,6 @@ class ExternalMeshGeneratorBase : public MeshGeneratorBase
 
   void postProcessInput() override;
 
-  /// Path to the mesh file
-  Path m_filePath;
-
   /// Translation vector that will be applied to the point coordinates (prior to scaling)
   R1Tensor m_translate;
 

src/coreComponents/mesh/generators/InternalMeshGenerator.cpp

@@ -998,5 +998,5 @@ InternalMeshGenerator::
   }
 }
 
-REGISTER_CATALOG_ENTRY( MeshGeneratorBase, InternalMeshGenerator, string const &, Group * const )
+REGISTER_CATALOG_ENTRY( MeshBase, InternalMeshGenerator, string const &, Group * const )
 } /* namespace geos */

src/coreComponents/mesh/generators/InternalWellboreGenerator.cpp

@@ -523,5 +523,5 @@ void InternalWellboreGenerator::coordinateTransformation( arrayView2d< real64, n
   }
 }
 
-REGISTER_CATALOG_ENTRY( MeshGeneratorBase, InternalWellboreGenerator, string const &, Group * const )
+REGISTER_CATALOG_ENTRY( MeshBase, InternalWellboreGenerator, string const &, Group * const )
 } /* namespace geos */

src/coreComponents/mesh/generators/MeshGeneratorBase.cpp

@@ -21,7 +21,7 @@ namespace geos
 using namespace dataRepository;
 
 MeshGeneratorBase::MeshGeneratorBase( string const & name, Group * const parent ):
-  Group( name, parent )
+  MeshBase( name, parent )
 {
   setInputFlags( InputFlags::OPTIONAL_NONUNIQUE );
 }
@@ -94,4 +94,5 @@ void MeshGeneratorBase::attachWellInfo( CellBlockManager & cellBlockManager )
 
   } );
 }
+
 }

src/coreComponents/mesh/generators/MeshGeneratorBase.hpp

@@ -19,13 +19,10 @@
 #ifndef GEOS_MESH_GENERATORS_MESHGENERATORBASE_HPP
 #define GEOS_MESH_GENERATORS_MESHGENERATORBASE_HPP
 
+#include "mesh/MeshBase.hpp"
 #include "mesh/mpiCommunications/SpatialPartition.hpp"
 #include "mesh/generators/CellBlockManagerABC.hpp"
 
-#include "dataRepository/Group.hpp"
-#include "dataRepository/WrapperBase.hpp"
-#include "codingUtilities/Utilities.hpp"
-#include "common/DataTypes.hpp"
 
 
 namespace geos
@@ -42,7 +39,7 @@ class CellBlockManager;
  *  @brief The MeshGeneratorBase class provides an abstract base class implementation for different mesh types.
  *	   The MeshGeneratorBase is the Group specialization for different type of mesh handling.
  */
-class MeshGeneratorBase : public dataRepository::Group
+class MeshGeneratorBase : public MeshBase
 {
 public:
 

src/coreComponents/mesh/generators/ParticleMeshGenerator.cpp

@@ -346,6 +346,6 @@ void ParticleMeshGenerator::importFieldOnArray( Block block,
   GEOS_UNUSED_VAR( wrapper );
 }
 
-REGISTER_CATALOG_ENTRY( MeshGeneratorBase, ParticleMeshGenerator, string const &, Group * const )
+REGISTER_CATALOG_ENTRY( MeshBase, ParticleMeshGenerator, string const &, Group * const )
 
 } /* namespace geos */

src/coreComponents/mesh/generators/VTKMeshGenerator.cpp

@@ -36,6 +36,11 @@ VTKMeshGenerator::VTKMeshGenerator( string const & name,
                                     Group * const parent )
   : ExternalMeshGeneratorBase( name, parent )
 {
+  registerWrapper( viewKeyStruct::filePathString(), &m_filePath ).
+    setInputFlag( InputFlags::REQUIRED ).
+    setRestartFlags( RestartFlags::NO_WRITE ).
+    setDescription( "Path to the mesh file" );
+
   registerWrapper( viewKeyStruct::regionAttributeString(), &m_attributeName ).
     setRTTypeName( rtTypes::CustomTypes::groupNameRef ).
     setInputFlag( InputFlags::OPTIONAL ).
@@ -216,6 +221,6 @@ void VTKMeshGenerator::freeResources()
   m_faceBlockMeshes.clear();
 }
 
-REGISTER_CATALOG_ENTRY( MeshGeneratorBase, VTKMeshGenerator, string const &, Group * const )
+REGISTER_CATALOG_ENTRY( MeshBase, VTKMeshGenerator, string const &, Group * const )
 
 } // namespace geos

src/coreComponents/mesh/generators/VTKMeshGenerator.hpp

@@ -101,6 +101,7 @@ class VTKMeshGenerator : public ExternalMeshGeneratorBase
   ///@cond DO_NOT_DOCUMENT
   struct viewKeyStruct
   {
+    constexpr static char const * filePathString() { return "file"; }
     constexpr static char const * regionAttributeString() { return "regionAttribute"; }
     constexpr static char const * mainBlockNameString() { return "mainBlockName"; }
     constexpr static char const * faceBlockNamesString() { return "faceBlocks"; }
@@ -120,6 +121,9 @@ class VTKMeshGenerator : public ExternalMeshGeneratorBase
                                    string const & meshFieldName,
                                    dataRepository::WrapperBase & wrapper ) const;
 
+  /// Path to the mesh file
+  Path m_filePath;
+
   /**
    * @brief The VTK mesh to be imported into GEOSX.
    * @note We keep this smart pointer as a member for use in @p importFields().

src/docs/doxygen/GeosxConfig.hpp

@@ -30,7 +30,7 @@
 #define GEOSX_USE_MPI
 
 /// Enables use of OpenMP (CMake option ENABLE_OPENMP)
-#define GEOSX_USE_OPENMP
+/* #undef GEOSX_USE_OPENMP */
 
 /// Enables use of CUDA (CMake option ENABLE_CUDA)
 /* #undef GEOS_USE_CUDA */
@@ -135,7 +135,7 @@
 /* #undef chai_VERSION */
 
 /// Version information for adiak
-#define adiak_VERSION ..
+/* #undef adiak_VERSION */
 
 /// Version information for caliper
 #define caliper_VERSION 2.10.0