wip: VTK DataRepo and VTKMeshGenerator

src/coreComponents/mesh/generators/VTKHierarchicalDataRepository.cpp

@@ -18,7 +18,7 @@
  */
 
 #include "mesh/generators/VTKHierarchicalDataRepository.hpp"
-
+#include "mesh/generators/VTKUtilities.hpp"
 #include <vtkXMLPartitionedDataSetCollectionReader.h>
 
 namespace geos
@@ -38,6 +38,9 @@ VTKHierarchicalDataRepository::VTKHierarchicalDataRepository( string const & nam
 
 void VTKHierarchicalDataRepository::open()
 {
+  string const extension = m_filePath.extension();
+  GEOS_ERROR_IF( extension != "vtpc", "Unsupported vtk extension. File must be a vtpc file" );
+
   vtkNew< vtkXMLPartitionedDataSetCollectionReader > reader;
   reader->SetFileName( m_filePath.c_str());
   reader->Update();
@@ -46,15 +49,22 @@ void VTKHierarchicalDataRepository::open()
   m_dataAssembly = vtkSmartPointer< vtkDataAssembly >( m_collection->GetDataAssembly() );
 }
 
-vtkSmartPointer< vtkDataSet >
+vtkSmartPointer< vtkPartitionedDataSet >
 VTKHierarchicalDataRepository::search( string const & path )
 {
   int node = m_dataAssembly->GetFirstNodeByPath( path.c_str());
-  GEOS_ERROR_IF( node == -1, "" );
+  GEOS_ERROR_IF( node == -1, "Node doesn't exist" );
+  GEOS_ERROR_IF( m_dataAssembly->GetNumberOfChildren( node ) > 0, "only leaf nodes can be queried." );
 
-  // for sub_node : m_dataAssembly->GetChildNodes(node, False)
+  return m_collection->GetPartitionedDataSet( node );
+
+  // for(auto & sub_node : m_dataAssembly->GetChildNodes(node, false))
+  // {
+  //   std::vector<unsigned int> datasets = m_dataAssembly->GetDataSetIndices(sub_node, false);
+  //   dataset = pdsc.GetPartitionedDataSet(node)
+  // }
   // {
-  //   datasets = m_dataAssembly->GetDataSetIndices(sub_node, False)
+  //   d
   //   for d in datasets
   //   {
   //     dataset = pdsc.GetPartitionedDataSet(d)
@@ -64,8 +74,9 @@ VTKHierarchicalDataRepository::search( string const & path )
   //   }
   // }
   //TODO
+}
+
+REGISTER_CATALOG_ENTRY( ExternalDataRepositoryBase, VTKHierarchicalDataRepository, string const &, Group * const )
 
-  return {};
 
-}
 }

src/coreComponents/mesh/generators/VTKHierarchicalDataRepository.hpp

@@ -26,6 +26,7 @@
 #include <vtkSmartPointer.h>
 #include <vtkDataSet.h>
 #include <vtkDataAssembly.h>
+#include <vtkPartitionedDataSet.h>
 #include <vtkPartitionedDataSetCollection.h>
 
 namespace geos
@@ -56,7 +57,7 @@ class VTKHierarchicalDataRepository : public ExternalDataRepositoryBase
 
   void open() override;
 
-  vtkSmartPointer< vtkDataSet > search( string const & path );
+  vtkSmartPointer< vtkPartitionedDataSet > search( string const & path );
 
 private:
 

src/coreComponents/mesh/generators/VTKMeshGenerator.cpp

@@ -19,6 +19,7 @@
 
 #include "VTKMeshGenerator.hpp"
 
+#include "mesh/ExternalDataRepositoryManager.hpp"
 #include "mesh/generators/VTKFaceBlockUtilities.hpp"
 #include "mesh/generators/VTKMeshGeneratorTools.hpp"
 #include "mesh/generators/CellBlockManager.hpp"
@@ -33,10 +34,11 @@ using namespace dataRepository;
 
 VTKMeshGenerator::VTKMeshGenerator( string const & name,
                                     Group * const parent )
-  : ExternalMeshGeneratorBase( name, parent )
+  : ExternalMeshGeneratorBase( name, parent ),
+  m_repository( nullptr )
 {
-  // getWrapperBase(ExternalMeshGeneratorBase::viewKeyStruct::filePathString()).
-  //   setInputFlag( InputFlags::OPTIONAL );
+  getWrapperBase( ExternalMeshGeneratorBase::viewKeyStruct::filePathString()).
+    setInputFlag( InputFlags::OPTIONAL );
 
   registerWrapper( viewKeyStruct::regionAttributeString(), &m_attributeName ).
     setRTTypeName( rtTypes::CustomTypes::groupNameRef ).
@@ -78,12 +80,38 @@ VTKMeshGenerator::VTKMeshGenerator( string const & name,
                     " If set to 0 (default value), the GlobalId arrays in the input mesh are used if available, and generated otherwise."
                     " If set to a negative value, the GlobalId arrays in the input mesh are not used, and generated global Ids are automatically generated."
                     " If set to a positive value, the GlobalId arrays in the input mesh are used and required, and the simulation aborts if they are not available" );
+
+  registerWrapper( viewKeyStruct::repositoryString(), &m_repositoryName ).
+    setInputFlag( InputFlags::OPTIONAL ).
+    setDescription( "Name of the VTK Repository" );
+
+  registerWrapper( viewKeyStruct::meshPathString(), &m_meshPath ).
+    setInputFlag( InputFlags::OPTIONAL ).
+    setDescription( "path of the VTK mesh in the repository" );
 }
 
 void VTKMeshGenerator::postInputInitialization()
 {
-  // if(this->m_filePath && m_meshPath)
-  // GEOS_ERROR( "Could not import field \"" << meshFieldName << "\" from cell block \"" << cellBlockName << "\"." );
+  GEOS_ERROR_IF( !this->m_filePath.empty() && (!m_repositoryName.empty() || !m_meshPath.empty()),
+                 getName() << ": Access to the mesh via file or repository are mutually exclusive. "
+                              "You can't set " << viewKeyStruct::repositoryString() << " or " << viewKeyStruct::meshPathString() << " and " <<
+                 ExternalMeshGeneratorBase::viewKeyStruct::filePathString() );
+
+  GEOS_ERROR_IF ( !m_repositoryName.empty() && m_meshPath.empty(),
+                  getName() << ": using the repository mode, you must supply a path in the repository for the mesh." );
+
+  GEOS_ERROR_IF ( m_repositoryName.empty() && !m_meshPath.empty(),
+                  getName() << ": using a path in the repository for the mesh, you must supply a repository mode." );
+
+  ExternalDataRepositoryManager & externalDataManager = this->getGroupByPath< ExternalDataRepositoryManager >( "/Problem/ExternalDataRepository" );
+  // objectRepository.
+  m_repository = externalDataManager.getGroupPointer< VTKHierarchicalDataRepository >( m_repositoryName );
+
+  GEOS_THROW_IF( m_repository == nullptr,
+                 getName() << ": VTK Data Object Repository not found: " << m_repositoryName,
+                 InputError );
+
+
 }
 
 void VTKMeshGenerator::fillCellBlockManager( CellBlockManager & cellBlockManager, SpatialPartition & partition )
@@ -98,7 +126,20 @@ void VTKMeshGenerator::fillCellBlockManager( CellBlockManager & cellBlockManager
   GEOS_LOG_RANK_0( GEOS_FMT( "{} '{}': reading mesh from {}", catalogName(), getName(), m_filePath ) );
   {
     GEOS_LOG_LEVEL_RANK_0( 2, "  reading the dataset..." );
-    vtk::AllMeshes allMeshes = vtk::loadAllMeshes( m_filePath, m_mainBlockName, m_faceBlockNames );
+
+    vtk::AllMeshes allMeshes;
+
+    if( !m_filePath.empty())
+    {
+      allMeshes = vtk::loadAllMeshes( m_filePath, m_mainBlockName, m_faceBlockNames );
+    }
+    else if( !m_repositoryName.empty())
+    {
+      vtkSmartPointer< vtkPartitionedDataSet > partitions  = m_repository->search( m_meshPath );
+      // allMeshes = vtk::loadPartitions(partitions);
+    }
+
+
     GEOS_LOG_LEVEL_RANK_0( 2, "  redistributing mesh..." );
     vtk::AllMeshes redistributedMeshes =
       vtk::redistributeMeshes( getLogLevel(), allMeshes.getMainMesh(), allMeshes.getFaceBlocks(), comm, m_partitionMethod, m_partitionRefinement, m_useGlobalIds );

src/coreComponents/mesh/generators/VTKMeshGenerator.hpp

@@ -22,6 +22,7 @@
 
 #include "mesh/generators/ExternalMeshGeneratorBase.hpp"
 #include "mesh/generators/VTKUtilities.hpp"
+#include "mesh/generators/VTKHierarchicalDataRepository.hpp"
 #include "mesh/mpiCommunications/SpatialPartition.hpp"
 
 #include <vtkDataSet.h>
@@ -88,15 +89,15 @@ class VTKMeshGenerator : public ExternalMeshGeneratorBase
    * surfaces of interest, with triangles and/or quads holding an attribute value
    * of 1, 2 or 3, three node sets named "1", "2" and "3" will be instantiated by this method
    */
-  virtual void fillCellBlockManager( CellBlockManager & cellBlockManager, SpatialPartition & partition ) override;
+  void fillCellBlockManager( CellBlockManager & cellBlockManager, SpatialPartition & partition ) override;
 
   void importFieldOnArray( Block block,
                            string const & blockName,
                            string const & meshFieldName,
                            bool isMaterialField,
                            dataRepository::WrapperBase & wrapper ) const override;
 
-  virtual void freeResources() override;
+  void freeResources() override;
 
 protected:
   void postInputInitialization() override;
@@ -113,6 +114,8 @@ class VTKMeshGenerator : public ExternalMeshGeneratorBase
     constexpr static char const * partitionRefinementString() { return "partitionRefinement"; }
     constexpr static char const * partitionMethodString() { return "partitionMethod"; }
     constexpr static char const * useGlobalIdsString() { return "useGlobalIds"; }
+    constexpr static char const * repositoryString() { return "repositoryName"; }
+    constexpr static char const * meshPathString() { return "meshPath"; }
   };
   /// @endcond
 
@@ -158,6 +161,15 @@ class VTKMeshGenerator : public ExternalMeshGeneratorBase
 
   /// Lists of VTK cell ids, organized by element type, then by region
   vtk::CellMapType m_cellMap;
+
+  /// Repository name
+  string m_repositoryName;
+
+  /// path to the mesh in the repository
+  string m_meshPath;
+
+  /// Repository of VTK objects
+  VTKHierarchicalDataRepository * m_repository;
 };
 
 } // namespace geos

src/coreComponents/schema/docs/ExternalDataRepository.rst

@@ -1,9 +1,9 @@
 
 
-==== ==== ============================ 
-Name Type Description                  
-==== ==== ============================ 
-          (no documentation available) 
-==== ==== ============================ 
+============================= ==== ======= ======================================== 
+Name                          Type Default Description                              
+============================= ==== ======= ======================================== 
+VTKHierarchicalDataRepository node         :ref:`XML_VTKHierarchicalDataRepository` 
+============================= ==== ======= ======================================== 
 
 

src/coreComponents/schema/docs/ExternalDataRepository_other.rst

@@ -1,9 +1,9 @@
 
 
-==== ==== ============================ 
-Name Type Description                  
-==== ==== ============================ 
-          (no documentation available) 
-==== ==== ============================ 
+============================= ==== ================================================== 
+Name                          Type Description                                        
+============================= ==== ================================================== 
+VTKHierarchicalDataRepository node :ref:`DATASTRUCTURE_VTKHierarchicalDataRepository` 
+============================= ==== ================================================== 
 
 

src/coreComponents/schema/docs/VTKHierarchicalDataRepository.rst

@@ -0,0 +1,11 @@
+
+
+============================= ============ ======== =========================================== 
+Name                          Type         Default  Description                                 
+============================= ============ ======== =========================================== 
+file                          groupNameRef required Path to the mesh file                       
+name                          groupName    required A name is required for any non-unique nodes 
+VTKHierarchicalDataRepository node                  :ref:`XML_VTKHierarchicalDataRepository`    
+============================= ============ ======== =========================================== 
+
+

src/coreComponents/schema/docs/VTKHierarchicalDataRepository_other.rst

@@ -0,0 +1,9 @@
+
+
+============================= ==== ================================================== 
+Name                          Type Description                                        
+============================= ==== ================================================== 
+VTKHierarchicalDataRepository node :ref:`DATASTRUCTURE_VTKHierarchicalDataRepository` 
+============================= ==== ================================================== 
+
+