Exodus Mesh, boundary condition, and block data transfer functionality implementation.

.gitignore

@@ -245,4 +245,10 @@ conf_vars.mk
 *docker/**/*.tar.gz
 
 # MFEM Joule outputs
-*Joule_000*
+*Joule_000*
+
+# Ignoring all of OutputData 
+*/OutputData/
+
+#Ignore output mfem meshes
+*.mesh

docker/apollo-ubuntu/Dockerfile

@@ -59,12 +59,14 @@ RUN cd /$WORKDIR && \
     ln -s ../build/Linux-x86_64/libmetis/libmetis.so lib
 
 # Install MUMPS
+# Install MUMPS
+
 RUN cd /$WORKDIR && \
     git clone https://github.com/scivision/mumps && \
     cd mumps/ && \
     mkdir build && \
     cd build && \
-    cmake --preset=build -DBUILD_SHARED_LIBS=on -Dscotch=true -Dintsize64=false -Darith="s;d;c;z" -Dautobuild=true  \
+    cmake -DBUILD_SHARED_LIBS=on -Dscotch=true -Dintsize64=false -Darith="s;d;c;z"  \
     -DCMAKE_INSTALL_PREFIX=/usr/local/ .. && \
     make && \
     make install

examples/MFEM/rod/joule_rod_coupled_mesh.i

@@ -0,0 +1,75 @@
+[Mesh]
+  type = ExclusiveMFEMMesh
+  file = ./cylinder-hex-q2.e
+  dim = 3
+[]
+
+[Problem]
+  type = MFEMProblem
+  formulation = Joule
+  order = 2
+  dt = 0.5
+  end_time = 2.5
+[]
+
+[Functions]
+  [./p_bc]
+    type = ParsedFunction
+    value = (z/abs(z))*cos(2.0*pi*freq*t)
+    vars = 'freq'
+    vals = '0.01666667'
+  [../]
+[]
+
+[BCs]
+  [./tangential_dEdt]
+    type = MFEMBoundaryCondition
+    variable = tangential_dEdt
+    boundary = '1 2 3'
+  [../]
+  [./thermal_flux]
+    type = MFEMBoundaryCondition
+    variable = thermal_flux
+    boundary = '1 2'
+  []
+  [./electric_potential]
+    type = MFEMFunctionDirichletBC
+    variable = electric_potential
+    boundary = '1 2'
+    function = p_bc
+  [../]
+[]
+
+[Materials]
+  [./copper]
+    type = MFEMConductor
+    electrical_conductivity = 62.83185
+    thermal_conductivity = 0.01
+    heat_capacity = 1.0
+    block = 1
+  [../]
+  [./air]
+    type = MFEMConductor
+    electrical_conductivity = 62.83185e-6
+    thermal_conductivity = 1e4
+    heat_capacity = 1.0
+    block = 2
+  [../]
+[]
+
+[Executioner]
+  type = Steady
+[]
+
+[Outputs]
+  [VisItDataCollection]
+    type = MFEMVisItDataCollection
+    file_base = OutputData/JouleRodVisIt
+  []
+  [ParaViewDataCollection]
+    type = MFEMParaViewDataCollection
+    file_base = OutputData/JouleRodParaView
+    refinements = 1
+    high_order_output = true
+  []
+[]

include/mesh/CoupledMFEMMesh.h

@@ -19,17 +19,55 @@ class CoupledMFEMMesh : public ExclusiveMFEMMesh {
 
   CoupledMFEMMesh(const InputParameters& parameters);
 
+  virtual ~CoupledMFEMMesh();
+
+  virtual std::unique_ptr<MooseMesh> safeClone() const override;
+
   virtual void buildMesh() override;
+
+  void getElementInfo();
 
-  // Builds the corresponding MOOSE mesh
-  void buildRealMesh();
+  void getBdrLists(int** elem_ss, int** side_ss);
 
-  // Function that maps vtk element types to libmesh element types
-  int map_elems_vtk_to_libmesh(int VTKElemType);
+  int getNumSidesets();
+
+  void createMFEMMesh();
 
-  // Boolean value determining whether the user wants the corresponding MOOSE
-  // mesh built
-  bool CreateMOOSEMesh;
+  void create_ss_node_id(int** elem_ss, int** side_ss, int** ss_node_id);
 
-  virtual std::unique_ptr<MooseMesh> safeClone() const override;
+ protected:
+
+  int curved = 0;
+  int read_gf = 0;
+  bool topo = false;
+
+  unsigned int num_node_per_el;
+  int libmesh_element_type;
+  int libmesh_face_type;
+  int num_element_linear_nodes;
+  int num_face_nodes;
+  int num_face_linear_nodes;
+  int num_side_sets;
+  int bdrElems;
+  std::vector<int> num_sides_in_ss;
+
+  enum CubitFaceType {
+    FACE_EDGE2,
+    FACE_EDGE3,
+    FACE_TRI3,
+    FACE_TRI6,
+    FACE_QUAD4,
+    FACE_QUAD9
+  };
+
+  enum CubitElementType {
+    ELEMENT_TRI3,
+    ELEMENT_TRI6,
+    ELEMENT_QUAD4,
+    ELEMENT_QUAD9,
+    ELEMENT_TET4,
+    ELEMENT_TET10,
+    ELEMENT_HEX8,
+    ELEMENT_HEX27
+  };
 };

include/mesh/ExclusiveMFEMMesh.h

@@ -10,6 +10,7 @@
 #pragma once
 #include "FileMesh.h"
 #include "MFEMMesh.h"
+#include "memory"
 #include "libmesh/elem.h"
 #include "libmesh/enum_io_package.h"
 #include "libmesh/equation_systems.h"
@@ -42,5 +43,5 @@ class ExclusiveMFEMMesh : public FileMesh {
   void buildDummyMesh();
 
   // The object holding our MFEM mesh. Needs renaming as to avoid confusion
-  MFEMMesh* mfem_mesh;
+  std::shared_ptr<MFEMMesh> mfem_mesh;
 };

include/mesh/MFEMMesh.h

@@ -1,17 +1,28 @@
 #pragma once
 
+#include "libmesh/elem.h"
+#include "libmesh/enum_io_package.h"
+#include "libmesh/exodusII_io.h"
+#include "libmesh/nemesis_io.h"
+#include "libmesh/node.h"
+#include "libmesh/parallel_mesh.h"
 #include "mfem.hpp"
 
 class MFEMMesh : public mfem::Mesh {
  public:
-  MFEMMesh(const mfem::Vector &points, const mfem::Array<int> &cell_data,
-           const mfem::Array<int> &cell_offsets,
-           const mfem::Array<int> &cell_types,
-           const mfem::Array<int> &cell_attributes, int &curved, int &read_gf,
-           bool &finalize_topo);
+  MFEMMesh(int num_elem, std::vector<double> &coordx,
+                    std::vector<double> &coordy, std::vector<double> &coordz,
+                    std::map<int, int> &cubitToMFEMVertMap,
+                    std::vector<int> uniqueVertexID, int libmesh_element_type,
+                    int libmesh_face_type, int **elem_blk, int num_el_blk,
+                    int num_node_per_el, size_t *num_el_in_blk,
+                    int num_element_linear_nodes, int num_face_nodes,
+                    int num_face_linear_nodes, int num_side_sets,
+                    std::vector<int> num_side_in_ss, int **ss_node_id,
+                    int *eb_prop, int *ss_prop, int dim_num, int* start_of_block);
 
-  MFEMMesh(std::string afilename, int generate_edges = 0, int refine = 1,
-           bool fix_orientation = true);
+  MFEMMesh(std::string cpp_filename, int generate_edges = 0,
+                    int refine = 1, bool fix_orientation = true);
 
   void get_mesh_nodes();
 
@@ -21,8 +32,34 @@ class MFEMMesh : public mfem::Mesh {
 
   int get_num_nodes();
 
+  void create_boundary(int **ss_node_id, int *num_sides_in_sidesets,
+                       int num_side_sets,
+                       std::vector<libMesh::boundary_id_type> ssprop,
+                       int num_face_linear_nodes, int num_face_nodes,
+                       int libmesh_face_type);
+
   std::vector<int> connectivityVec;
   std::vector<double> pointsVec;
   std::vector<int> cellTypeVec;
   std::vector<int> verticesVec;
+
+  enum CubitFaceType {
+    FACE_EDGE2,
+    FACE_EDGE3,
+    FACE_TRI3,
+    FACE_TRI6,
+    FACE_QUAD4,
+    FACE_QUAD9
+  };
+
+  enum CubitElementType {
+    ELEMENT_TRI3,
+    ELEMENT_TRI6,
+    ELEMENT_QUAD4,
+    ELEMENT_QUAD9,
+    ELEMENT_TET4,
+    ELEMENT_TET10,
+    ELEMENT_HEX8,
+    ELEMENT_HEX27
+  };
 };