feat: Add ExternalDataRepository

inputFiles/singlePhaseFlow/FieldCaseTutorial3_composite_smoke.xml

@@ -0,0 +1,47 @@
+<?xml version="1.0" ?>
+
+<Problem>
+  <Included>
+    <File name="./FieldCaseTutorial3_base.xml" />
+  </Included>
+
+  <!-- SPHINX_FIELD_CASE_COMPOSITE_MESH -->
+  <ExternalDataSource>
+    <VTKHierarchicalDataSource
+      name="synthetic"
+      file="synthetic.vtpc"/>
+  </ExternalDataSource>
+
+  <Mesh>
+    <VTKMesh
+      name="SyntheticMesh"
+      repositoryName="synthetic">
+      <Region
+        name="Region1"
+        id="1"
+        pathInRepository="/Root/Mesh/Region1"/>
+      <Region
+        name="Region2"
+        id="2"
+        pathInRepository="/Root/Mesh/Region2"/>
+      <Region
+        name="Region3"
+        id="3"
+        pathInRepository="/Root/Mesh/Region3"/>
+    </VTKMesh>
+  </Mesh>
+  <!-- SPHINX_FIELD_CASE_COMPOSITE_MESH -->
+
+  <!-- SPHINX_FIELD_CASE_EVENTS -->
+  <Events maxTime="100.0e6">
+    <PeriodicEvent name="solverApplications"
+                   forceDt="10.0e6"
+                   target="/Solvers/SinglePhaseFlow" />
+
+    <PeriodicEvent name="outputs"
+                   timeFrequency="10.0e6"
+                   target="/Outputs/reservoir_with_properties" />
+  </Events>
+  <!-- SPHINX_FIELD_CASE_EVENTS_END -->
+
+</Problem>

inputFiles/singlePhaseFlow/synthetic.vtpc

@@ -0,0 +1,17 @@
+<?xml version="1.0"?>
+<VTKFile type="vtkPartitionedDataSetCollection" version="1.0" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
+  <vtkPartitionedDataSetCollection>
+    <Partitions index="0" name="Region1">
+      <DataSet index="0" file="synthetic/synthetic_0_0.vtu"/>
+    </Partitions>
+    <Partitions index="1" name="Region2">
+      <DataSet index="0" file="synthetic/synthetic_1_0.vtu"/>
+    </Partitions>
+    <Partitions index="2" name="Region3">
+      <DataSet index="0" file="synthetic/synthetic_2_0.vtu"/>
+    </Partitions>
+    <DataAssembly encoding="base64">
+      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
+    </DataAssembly>
+  </vtkPartitionedDataSetCollection>
+</VTKFile>

src/CMakeLists.txt

@@ -80,7 +80,7 @@ add_subdirectory( thirdparty )
 ################################
 # Add components
 ################################
-unset( externalComponentsLinkList )
+# unset( externalComponentsLinkList )
 add_subdirectory( coreComponents )
 add_subdirectory( externalComponents )
 add_subdirectory( main )

src/coreComponents/fileIO/vtk/VTKPolyDataWriterInterface.cpp

@@ -1078,7 +1078,6 @@ void VTKPolyDataWriterInterface::writeParticleRegions( real64 const time,
     writeTimestamp( ug.GetPointer(), time );
     writeParticleFields( region, ug->GetCellData() );
 
-    // string const regionDir = joinPath( path, region.getName() );
     writeUnstructuredGrid( path, region, ug.GetPointer() );
   } );
 }
@@ -1185,8 +1184,6 @@ void VTKPolyDataWriterInterface::writeVtmFile( integer const cycle,
 
       string const meshPath = joinPath( getCycleSubFolder( cycle ), meshBodyName, meshLevelName );
 
-      // int const mpiSize = MpiWrapper::commSize();
-
       auto addElementRegion = [&]( ElementRegionBase const & region )
       {
         std::vector< string > const blockPath{ meshBody.getName(), meshLevel.getName(), region.getCatalogName(), region.getName() };

src/coreComponents/fileIO/vtk/VTKPolyDataWriterInterface.hpp

@@ -219,7 +219,7 @@ class VTKPolyDataWriterInterface
   void clearData();
 
 
-private:
+protected:
 
   /**
    * @brief Check if plotting is enabled for this field
@@ -234,20 +234,29 @@ class VTKPolyDataWriterInterface
    * @param[in] time the time-step
    * @param[in] elemManager the ElementRegionManager containing the CellElementRegions to be output
    * @param[in] nodeManager the NodeManager containing the nodes of the domain to be output
-   * @param[in] path the root path where the mesh will be written
+   * @param[in] path the path to the file to output
    */
   void writeCellElementRegions( real64 time,
                                 ElementRegionManager const & elemManager,
                                 NodeManager const & nodeManager,
                                 string const & path );
+  /**
+   * @brief Writes the files for all the ParticleRegions.
+   * @param[in] time the time-step
+   * @param[in] particleManager the ParticleManager containing the ParticleRegions to be output
+   * @param[in] path The path to the file to output
+   */
+  void writeParticleRegions( real64 const time,
+                             ParticleManager const & particleManager,
+                             string const & path ) const;
 
   /**
    * @brief Writes the files containing the well representation
    * @details There will be one file written per WellElementRegion and per rank
    * @param[in] time the time-step
    * @param[in] elemManager the ElementRegionManager containing the WellElementRegions to be output
    * @param[in] nodeManager the NodeManager containing the nodes of the domain to be output
-   * @param[in] path the root path where the mesh will be written
+   * @param[in] path The path to the file to output
    */
   void writeWellElementRegions( real64 time,
                                 ElementRegionManager const & elemManager,
@@ -289,7 +298,6 @@ class VTKPolyDataWriterInterface
    * @param[in] domain the DomainPartition containing all the regions to be output and referred to in the VTM file
    * @param[in] vtmWriter a writer specialized for the VTM file format
    */
-
   void writeVtmFile( integer const cycle,
                      DomainPartition const & domain,
                      VTKVTMWriter const & vtmWriter ) const;
@@ -312,7 +320,7 @@ class VTKPolyDataWriterInterface
                            vtkCellData * cellData ) const;
 
   /**
-   * @brief Writes all the fields associated to the elements of \p er if their plotlevel is <= m_plotLevel
+   * @brief Writes all the fields associated to the elements of \p region if their plotlevel is <= m_plotLevel
    * @param[in] region ParticleRegion being written
    * @param[in] cellData a VTK object containing all the fields associated with the elements
    */
@@ -332,7 +340,7 @@ class VTKPolyDataWriterInterface
                               ObjectManagerBase const & region,
                               vtkUnstructuredGrid * ug );
 
-private:
+protected:
 
   /// Output directory name
   string m_outputDir;

src/coreComponents/mainInterface/ProblemManager.cpp

@@ -39,6 +39,7 @@
 #include "fileIO/Outputs/OutputBase.hpp"
 #include "fileIO/Outputs/OutputManager.hpp"
 #include "functions/FunctionManager.hpp"
+#include "mesh/ExternalDataSourceManager.hpp"
 #include "mesh/DomainPartition.hpp"
 #include "mesh/MeshBody.hpp"
 #include "mesh/MeshManager.hpp"
@@ -73,6 +74,8 @@ ProblemManager::ProblemManager( conduit::Node & root ):
 
   setInputFlags( InputFlags::PROBLEM_ROOT );
 
+  registerGroup< ExternalDataSourceManager >( groupKeys.externalDataSourceManager );
+
   m_fieldSpecificationManager = &registerGroup< FieldSpecificationManager >( groupKeys.fieldSpecificationManager );
 
   m_eventManager = &registerGroup< EventManager >( groupKeys.eventManager );

src/coreComponents/mainInterface/ProblemManager.hpp

@@ -243,6 +243,7 @@ class ProblemManager : public dataRepository::Group
     dataRepository::GroupKey constitutiveManager = { "Constitutive" };                    ///< Constitutive key
     dataRepository::GroupKey domain    = { "domain" };                                    ///< Domain key
     dataRepository::GroupKey eventManager = { "Events" };                                 ///< Events key
+    dataRepository::GroupKey externalDataSourceManager = { "ExternalDataSource" };        ///< External Data Source key
     dataRepository::GroupKey fieldSpecificationManager = { "FieldSpecifications" };       ///< Field specification key
     dataRepository::GroupKey functionManager = { "Functions" };                           ///< Functions key
     dataRepository::GroupKey geometricObjectManager = { "Geometry" };                     ///< Geometry key

src/coreComponents/mesh/CMakeLists.txt

@@ -35,6 +35,8 @@ set( mesh_headers
      ElementRegionManager.hpp
      ElementSubRegionBase.hpp
      ElementType.hpp
+     ExternalDataSourceBase.hpp
+     ExternalDataSourceManager.hpp
      EmbeddedSurfaceNodeManager.hpp
      EmbeddedSurfaceSubRegion.hpp
      MeshFields.hpp
@@ -80,12 +82,13 @@ set( mesh_headers
      generators/InternalMeshGenerator.hpp
      generators/InternalWellGenerator.hpp
      generators/InternalWellboreGenerator.hpp
+     generators/MeshComponentBase.hpp
      generators/MeshGeneratorBase.hpp
      generators/ParMETISInterface.hpp
      generators/ParticleMeshGenerator.hpp
      generators/PartitionDescriptor.hpp
      generators/PrismUtilities.hpp
-     generators/WellGeneratorABC.hpp
+     generators/Region.hpp
      generators/WellGeneratorBase.hpp
      mpiCommunications/CommID.hpp
      mpiCommunications/CommunicationTools.hpp
@@ -124,6 +127,8 @@ set( mesh_sources
      ElementSubRegionBase.cpp
      EmbeddedSurfaceNodeManager.cpp
      EmbeddedSurfaceSubRegion.cpp
+     ExternalDataSourceBase.cpp
+     ExternalDataSourceManager.cpp
      FaceElementSubRegion.cpp
      FaceManager.cpp
      MeshBody.cpp
@@ -156,9 +161,11 @@ set( mesh_sources
      generators/InternalMeshGenerator.cpp
      generators/InternalWellGenerator.cpp
      generators/InternalWellboreGenerator.cpp
+     generators/MeshComponentBase.cpp
      generators/MeshGeneratorBase.cpp
      generators/ParMETISInterface.cpp
      generators/ParticleMeshGenerator.cpp
+     generators/Region.cpp
      generators/WellGeneratorBase.cpp
      mpiCommunications/CommID.cpp
      mpiCommunications/CommunicationTools.cpp
@@ -184,6 +191,7 @@ if( ENABLE_VTK )
     set( mesh_headers ${mesh_headers}
          generators/CollocatedNodes.hpp
          generators/VTKFaceBlockUtilities.hpp
+         generators/VTKHierarchicalDataSource.hpp
          generators/VTKMeshGenerator.hpp
          generators/VTKMeshGeneratorTools.hpp
          generators/VTKWellGenerator.hpp
@@ -192,6 +200,7 @@ if( ENABLE_VTK )
     set( mesh_sources ${mesh_sources}
          generators/CollocatedNodes.cpp
          generators/VTKFaceBlockUtilities.cpp
+         generators/VTKHierarchicalDataSource.cpp
          generators/VTKMeshGenerator.cpp
          generators/VTKMeshGeneratorTools.cpp
          generators/VTKWellGenerator.cpp

src/coreComponents/mesh/ExternalDataSourceBase.cpp

@@ -0,0 +1,54 @@
+/*
+ * ------------------------------------------------------------------------------------------------------------
+ * 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 "ExternalDataSourceBase.hpp"
+
+namespace geos
+{
+using namespace dataRepository;
+
+ExternalDataSourceBase::ExternalDataSourceBase( string const & name, Group * const parent ):
+  Group( name, parent )
+{
+  setInputFlags( InputFlags::OPTIONAL_NONUNIQUE );
+}
+
+Group * ExternalDataSourceBase::createChild( string const & childKey, string const & childName )
+{
+  GEOS_LOG_RANK_0( "Adding External Data Source: " << childKey << ", " << childName );
+  std::unique_ptr< ExternalDataSourceBase > event = ExternalDataSourceBase::CatalogInterface::factory( childKey, childName, this );
+  return &this->registerGroup< ExternalDataSourceBase >( childName, std::move( event ) );
+}
+
+void ExternalDataSourceBase::expandObjectCatalogs()
+{
+  // Only add children if the parent is of type EventManager
+  // otherwise, this would fall into a loop
+  if( strcmp( this->getParent().getName().c_str(), "ExternalDataSource" ) == 0 )
+  {
+    for( auto & catalogIter: ExternalDataSourceBase::getCatalog())
+    {
+      createChild( catalogIter.first, catalogIter.first );
+    }
+  }
+}
+
+ExternalDataSourceBase::CatalogInterface::CatalogType & ExternalDataSourceBase::getCatalog()
+{
+  static ExternalDataSourceBase::CatalogInterface::CatalogType catalog;
+  return catalog;
+}
+
+
+}

src/coreComponents/mesh/ExternalDataSourceBase.hpp

@@ -0,0 +1,77 @@
+/*
+ * ------------------------------------------------------------------------------------------------------------
+ * 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 ExternalDataSourceBase.hpp
+ */
+
+#ifndef GEOS_MESH_EXTERNALDATASOURCEBASE_HPP
+#define GEOS_MESH_EXTERNALDATASOURCEBASE_HPP
+
+#include "dataRepository/Group.hpp"
+#include "dataRepository/WrapperBase.hpp"
+#include "codingUtilities/Utilities.hpp"
+#include "common/DataTypes.hpp"
+
+
+namespace geos
+{
+
+/**
+ *  @class ExternalDataSourceBase
+ *  @brief The ExternalDataSourceBase class provides an abstract base class implementation for different mesh types.
+ *	   The ExternalDataSourceBase is the Group specialization for different type of mesh handling.
+ */
+class ExternalDataSourceBase : public dataRepository::Group
+{
+public:
+
+  /**
+   * @brief Main constructor for ExternalDataSourceBase base class.
+   * @param[in] name of the ExternalDataSourceBase object
+   * @param[in] parent the parent Group pointer for the ExternalDataSourceBase object
+   */
+  explicit ExternalDataSourceBase( string const & name,
+                                   Group * const parent );
+
+  /// This function is used to expand any catalogs in the data structure
+  virtual void expandObjectCatalogs() override;
+
+  /// using alias for templated Catalog ExternalDataSourceBase type
+  using CatalogInterface = dataRepository::CatalogInterface< ExternalDataSourceBase, 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();
+
+  /**
+   * @brief This function provides the capability to open an external data repository
+   * from another component whatever its format.
+   */
+  virtual void open() = 0;
+};
+
+}
+
+#endif /* GEOS_MESH_EXTERNALDATASOURCEBASE_HPP */