Merge pull request #31761 from miaoyinb/transitionXYZD

XYZDelaunay Hole Conversion and Stitching Improvements

Author: miaoyinb

framework/doc/content/source/meshgenerators/BoundaryElementConversionGenerator.md

@@ -20,6 +20,9 @@ There are four types of linear 3D elements supported by this mesh generator: `HE
 
 The most common application of this mesh generator is applied to external boundaries of the [!param](/Mesh/BoundaryElementConversionGenerator/input) mesh. The mesh generator can also be applied to internal boundaries, in which case both sides of the internal boundary are converted. Users can enable [!param](/Mesh/BoundaryElementConversionGenerator/external_boundaries_checking) to enforce that the specified boundaries are external to avert unintended behavior.
 
+!alert note
+In distributed mesh mode, the mesh is temporarily serialized to enable some essential methods.
+
 ### HEX8
 
 All the six sides of a `HEX8` elements are `QUAD4`. Any sides involved in the given boundaries will need to be divided into two `TRI3` sides that belong to two different new elements. To keep the other `QUAD4` sides unchanged, a simple strategy is adopted. First, the `HEX8` elements are divided into six `PYRAMID5` elements, each of which is defined by one of the `QUAD4` sides and the centroid of the `HEX8` element. For those `QUAD4` sides involved in the given boundaries, the `PYRAMID5` elements are further divided into two `TET4` elements (see the top row of [boundary_transition] as an example).

framework/doc/content/source/meshgenerators/XYZDelaunayGenerator.md

@@ -43,6 +43,11 @@ volume elements with non-Tri3 surface sides, it cannot be stitched
 with the output mesh without modifications. 
 [!param](/Mesh/XYZDelaunayGenerator/convert_holes_for_stitching) needs to
 be set as `true` to allow the stitching of such hole meshes after modifications.
+These hole meshes can either be converted into pure Tet4 meshes, or they can be
+converted using boundary element conversion
+(see [`BoundaryElementConversionGenerator`](/BoundaryElementConversionGenerator.md))
+to only convert elements near the external boundaries. This can be controlled
+by the [!param](/Mesh/XYZDelaunayGenerator/conversion_method) parameter.
 
 !alert note
 In distributed mesh mode, the [!param](/Mesh/XYZDelaunayGenerator/boundary) input mesh is temporarily serialized when it is set to be stitched with at least one of the [!param](/Mesh/XYZDelaunayGenerator/holes) input meshes. Additionally, the [!param](/Mesh/XYZDelaunayGenerator/holes) input meshes are always temporarily serialized to ensure compatibility with required processing methods.

framework/include/meshgenerators/CombinerGenerator.h

@@ -29,11 +29,6 @@ class CombinerGenerator : public MeshGenerator
   void fillPositions();
 
 protected:
-  /**
-   * Helper funciton for copying one mesh into another
-   */
-  void copyIntoMesh(UnstructuredMesh & destination, const UnstructuredMesh & source);
-
   // Holds pointers to the mesh smart pointers (to be populated later).
   const std::vector<std::unique_ptr<MeshBase> *> _meshes;
 

framework/include/meshgenerators/XYZDelaunayGenerator.h

@@ -44,9 +44,15 @@ class XYZDelaunayGenerator : public MeshGenerator
   /// Whether to stitch to the mesh defining each hole
   const std::vector<bool> _stitch_holes;
 
-  /// Whether to convert 3D hole meshes with non-TRI3 surface elements into all-TET4 meshes
+  /// Whether to convert 3D hole meshes with non-TRI3 surface elements into a compatible form
   const bool _convert_holes_for_stitching;
 
+  /// Method to convert 3D hole meshes into compatible meshes
+  const MooseEnum _conversion_method;
+
+  /// Whether to stitch all holes in one combined stitching step
+  const bool _combined_stitching;
+
   /// Type of algorithm used to find matching nodes (binary or exhaustive)
   const MooseEnum _algorithm;
 

framework/include/utils/MooseMeshElementConversionUtils.h

@@ -35,7 +35,7 @@ struct BCTupleKeyComp
  * @param elem_id The id of the element to be split
  * @param converted_elems_ids a vector to record the ids of the newly created TET4 elements
  */
-void hexElemSplitter(ReplicatedMesh & mesh,
+void hexElemSplitter(MeshBase & mesh,
                      const std::vector<libMesh::BoundaryInfo::BCTuple> & bdry_side_list,
                      const dof_id_type elem_id,
                      std::vector<dof_id_type> & converted_elems_ids);
@@ -47,7 +47,7 @@ void hexElemSplitter(ReplicatedMesh & mesh,
  * @param elem_id The id of the element to be split
  * @param converted_elems_ids a vector to record the ids of the newly created TET4 elements
  */
-void pyramidElemSplitter(ReplicatedMesh & mesh,
+void pyramidElemSplitter(MeshBase & mesh,
                          const std::vector<libMesh::BoundaryInfo::BCTuple> & bdry_side_list,
                          const dof_id_type elem_id,
                          std::vector<dof_id_type> & converted_elems_ids);
@@ -59,7 +59,7 @@ void pyramidElemSplitter(ReplicatedMesh & mesh,
  * @param elem_id The id of the element to be split
  * @param converted_elems_ids a vector to record the ids of the newly created TET4 elements
  */
-void prismElemSplitter(ReplicatedMesh & mesh,
+void prismElemSplitter(MeshBase & mesh,
                        const std::vector<libMesh::BoundaryInfo::BCTuple> & bdry_side_list,
                        const dof_id_type elem_id,
                        std::vector<dof_id_type> & converted_elems_ids);
@@ -207,7 +207,7 @@ pyramidNodesToTetNodesDeterminer(std::vector<const Node *> & pyramid_nodes,
  * @param delete_block_to_remove A bool indicating whether the block to be removed will be
  * deleted in this method
  */
-void convert3DMeshToAllTet4(ReplicatedMesh & mesh,
+void convert3DMeshToAllTet4(MeshBase & mesh,
                             const std::vector<std::pair<dof_id_type, bool>> & elems_to_process,
                             std::vector<dof_id_type> & converted_elems_ids_to_track,
                             const subdomain_id_type block_id_to_remove,
@@ -217,7 +217,7 @@ void convert3DMeshToAllTet4(ReplicatedMesh & mesh,
  * Convert all the elements in a 3D mesh consisting of only linear elements into TET4 elements.
  * @param mesh The mesh to be converted
  */
-void convert3DMeshToAllTet4(ReplicatedMesh & mesh);
+void convert3DMeshToAllTet4(MeshBase & mesh);
 
 /**
  * Collect the boundary information of the given element in a mesh.
@@ -241,7 +241,7 @@ elementBoundaryInfoCollector(const std::vector<libMesh::BoundaryInfo::BCTuple> &
  * @param elem_side_info The boundary IDs associated with the sides of the element
  * @param subdomain_id_shift_base the reference id used to shift the subdomain ID for new elements
  */
-void convertElem(ReplicatedMesh & mesh,
+void convertElem(MeshBase & mesh,
                  const dof_id_type & elem_id,
                  const std::vector<unsigned int> & side_indices,
                  const std::vector<std::vector<boundary_id_type>> & elem_side_info,
@@ -255,7 +255,7 @@ void convertElem(ReplicatedMesh & mesh,
  * @param elem_side_info The boundary IDs associated with the sides of the HEX8 element
  * @param subdomain_id_shift_base the reference id used to shift the subdomain ID for new elements
  */
-void convertHex8Elem(ReplicatedMesh & mesh,
+void convertHex8Elem(MeshBase & mesh,
                      const dof_id_type & elem_id,
                      const std::vector<unsigned int> & side_indices,
                      const std::vector<std::vector<boundary_id_type>> & elem_side_info,
@@ -270,7 +270,7 @@ void convertHex8Elem(ReplicatedMesh & mesh,
  * @param side_info The boundary IDs associated with the side of the HEX8 element
  * @param subdomain_id_shift_base the reference id used to shift the subdomain ID for new elements
  */
-void createUnitPyramid5FromHex8(ReplicatedMesh & mesh,
+void createUnitPyramid5FromHex8(MeshBase & mesh,
                                 const dof_id_type & elem_id,
                                 const unsigned int & side_index,
                                 const Node * new_node,
@@ -286,7 +286,7 @@ void createUnitPyramid5FromHex8(ReplicatedMesh & mesh,
  * @param side_info The boundary IDs associated with the side of the HEX8 element
  * @param subdomain_id_shift_base the reference id used to shift the subdomain ID for new elements
  */
-void createUnitTet4FromHex8(ReplicatedMesh & mesh,
+void createUnitTet4FromHex8(MeshBase & mesh,
                             const dof_id_type & elem_id,
                             const unsigned int & side_index,
                             const Node * new_node,
@@ -301,7 +301,7 @@ void createUnitTet4FromHex8(ReplicatedMesh & mesh,
  * @param elem_side_info The boundary IDs associated with the sides of the PRISM6 element
  * @param subdomain_id_shift_base the reference id used to shift the subdomain ID for new elements
  */
-void convertPrism6Elem(ReplicatedMesh & mesh,
+void convertPrism6Elem(MeshBase & mesh,
                        const dof_id_type & elem_id,
                        const std::vector<unsigned int> & side_indices,
                        const std::vector<std::vector<boundary_id_type>> & elem_side_info,
@@ -315,7 +315,7 @@ void convertPrism6Elem(ReplicatedMesh & mesh,
  * @param side_info The boundary IDs associated with the side of the PRISM6 element
  * @param subdomain_id_shift_base the reference id used to shift the subdomain ID for new elements
  */
-void createUnitTet4FromPrism6(ReplicatedMesh & mesh,
+void createUnitTet4FromPrism6(MeshBase & mesh,
                               const dof_id_type & elem_id,
                               const unsigned int & side_index,
                               const Node * new_node,
@@ -332,7 +332,7 @@ void createUnitTet4FromPrism6(ReplicatedMesh & mesh,
  * @param side_info The boundary IDs associated with the side of the PRISM6 element
  * @param subdomain_id_shift_base the reference id used to shift the subdomain ID for new elements
  */
-void createUnitPyramid5FromPrism6(ReplicatedMesh & mesh,
+void createUnitPyramid5FromPrism6(MeshBase & mesh,
                                   const dof_id_type & elem_id,
                                   const unsigned int & side_index,
                                   const Node * new_node,
@@ -346,7 +346,7 @@ void createUnitPyramid5FromPrism6(ReplicatedMesh & mesh,
  * @param elem_side_info The boundary IDs associated with the sides of the PYRAMID
  * @param subdomain_id_shift_base the reference id used to shift the subdomain ID for new elements
  */
-void convertPyramid5Elem(ReplicatedMesh & mesh,
+void convertPyramid5Elem(MeshBase & mesh,
                          const dof_id_type & elem_id,
                          const std::vector<std::vector<boundary_id_type>> & elem_side_info,
                          const SubdomainID & subdomain_id_shift_base);
@@ -357,7 +357,7 @@ void convertPyramid5Elem(ReplicatedMesh & mesh,
  * @param elem_id The ID of the original element
  * @param new_elem_ptr The pointer to the new element that will retain the extra integer
  */
-void retainEEID(ReplicatedMesh & mesh, const dof_id_type & elem_id, Elem * new_elem_ptr);
+void retainEEID(MeshBase & mesh, const dof_id_type & elem_id, Elem * new_elem_ptr);
 
 /**
  * Generate a transition layer of elements with TRI3 surfaces on the given boundaries.
@@ -369,10 +369,11 @@ void retainEEID(ReplicatedMesh & mesh, const dof_id_type & elem_id, Elem * new_e
  * @param external_boundaries_checking Whether to check if the provided boundaries are external
  * boundaries
  */
-void transitionLayerGenerator(ReplicatedMesh & mesh,
+void transitionLayerGenerator(MeshBase & mesh,
                               const std::vector<BoundaryName> & boundary_names,
                               const unsigned int conversion_element_layer_number,
                               const bool external_boundaries_checking);
+
 /**
  * Assign a subdomain name suffix to the converted elements created during transition layer
  * generation.
@@ -385,7 +386,7 @@ void transitionLayerGenerator(ReplicatedMesh & mesh,
  * elements
  */
 void assignConvertedElementsSubdomainNameSuffix(
-    ReplicatedMesh & mesh,
+    MeshBase & mesh,
     const std::set<subdomain_id_type> & original_subdomain_ids,
     const subdomain_id_type sid_shift_base,
     const SubdomainName & tet_suffix,

framework/include/utils/MooseMeshUtils.h

@@ -15,6 +15,7 @@
 #include "MooseUtils.h"
 #include "MooseTypes.h"
 #include "FaceInfo.h"
+#include "MeshGenerator.h"
 
 namespace MooseMeshUtils
 {
@@ -451,4 +452,22 @@ void createSubdomainFromSidesets(std::unique_ptr<MeshBase> & mesh,
 void convertBlockToMesh(std::unique_ptr<MeshBase> & source_mesh,
                         std::unique_ptr<MeshBase> & target_mesh,
                         const std::vector<SubdomainName> & target_blocks);
+
+/**
+ * Helper function for copying one mesh into another
+ * @param mg The mesh generator calling this function
+ * @param destination The mesh to copy into
+ * @param source The mesh to copy from
+ * @param avoid_merging_subdomains If true, subdomain IDs in the source mesh will
+ * be offset to avoid merging with subdomain IDs in the destination mesh
+ * @param avoid_merging_boundaries If true, boundary IDs in the source mesh will
+ * be offset to avoid merging with boundary IDs in the destination mesh
+ * @param communicator The communicator for parallel operations
+ */
+void copyIntoMesh(MeshGenerator & mg,
+                  UnstructuredMesh & destination,
+                  const UnstructuredMesh & source,
+                  const bool avoid_merging_subdomains,
+                  const bool avoid_merging_boundaries,
+                  const Parallel::Communicator & communicator);
 }

framework/src/meshgenerators/BoundaryElementConversionGenerator.C

@@ -12,6 +12,8 @@
 #include "CastUniquePointer.h"
 #include "MooseMeshUtils.h"
 
+#include "libmesh/mesh_serializer.h"
+
 registerMooseObject("MooseApp", BoundaryElementConversionGenerator);
 
 InputParameters
@@ -62,11 +64,9 @@ BoundaryElementConversionGenerator::BoundaryElementConversionGenerator(
 std::unique_ptr<MeshBase>
 BoundaryElementConversionGenerator::generate()
 {
-  auto replicated_mesh_ptr = dynamic_cast<ReplicatedMesh *>(_input.get());
-  if (!replicated_mesh_ptr)
-    paramError("input", "Input is not a replicated mesh, which is required");
+  UnstructuredMesh & mesh = dynamic_cast<UnstructuredMesh &>(*_input);
 
-  ReplicatedMesh & mesh = *replicated_mesh_ptr;
+  libMesh::MeshSerializer serial_mesh(mesh);
 
   // collect the subdomain ids of the original mesh
   std::set<subdomain_id_type> original_subdomain_ids;
@@ -75,7 +75,6 @@ BoundaryElementConversionGenerator::generate()
   {
     original_subdomain_ids.emplace((*elem_it)->subdomain_id());
   }
-
   try
   {
     MooseMeshElementConversionUtils::transitionLayerGenerator(
@@ -93,7 +92,6 @@ BoundaryElementConversionGenerator::generate()
     else
       paramError("input", e.what());
   }
-
   try
   {
     MooseMeshElementConversionUtils::assignConvertedElementsSubdomainNameSuffix(
@@ -111,5 +109,11 @@ BoundaryElementConversionGenerator::generate()
       paramError("converted_pyramid_element_subdomain_name_suffix", e.what());
   }
 
+  // MeshSerializer's destructor calls delete_remote_elements()
+  if (!mesh.is_replicated())
+    mesh.prepare_for_use();
+  else
+    mesh.set_isnt_prepared();
+
   return std::move(_input);
 }