make style

(cherry picked from commit 4c111d6f9198f418d32df98fd5e711455f73170a)

CHANGELOG

@@ -35,6 +35,9 @@ Meshing improvements
 
 - Added support for internal boundary elements in nonconforming meshes.
 
+- Added ExodusII output capability. The writer can handle first-order (Pyramid5, 
+  Wedge6, Hex8, Tet4) and second-order FE types (Pyramid14, Wedge18, Hex27, Tet10).
+
 - The ReadCubit Genesis mesh importer has been rewritten to improve readability.
 
 Discretization improvements

mesh/CMakeLists.txt

@@ -12,6 +12,7 @@
 set(SRCS
   attribute_sets.cpp
   element.cpp
+  exodus_writer.cpp
   face_nbr_geom.cpp
   gmsh.cpp
   hexahedron.cpp

mesh/mesh.hpp

@@ -2331,6 +2331,11 @@ public:
                     bool high_order_output=false,
                     int compression_level=0);
 
+#ifdef MFEM_USE_NETCDF
+   /// @brief Export a mesh to an Exodus II file.
+   void PrintExodusII(const std::string fpath);
+#endif
+
    /** @brief Prints the mesh with boundary elements given by the boundary of
        the subdomains, so that the boundary of subdomain i has boundary
        attribute i+1. */

miniapps/meshing/mesh-explorer.cpp

@@ -386,6 +386,9 @@ int main (int argc, char *argv[])
            "S) Save in MFEM serial format\n"
            "T) Save in MFEM parallel format using the current partitioning\n"
            "V) Save in VTK format (only linear and quadratic meshes)\n"
+#ifdef MFEM_USE_NETCDF
+           "X) Save in Exodus II format (only linear and quadratic meshes)\n"
+#endif
            "D) Save as a DataCollection\n"
            "q) Quit\n"
 #ifdef MFEM_USE_ZLIB
@@ -1288,6 +1291,15 @@ int main (int argc, char *argv[])
          cout << "New VTK mesh file: " << omesh_file << endl;
       }
 
+#ifdef MFEM_USE_NETCDF
+      if (mk == 'X')
+      {
+         const char omesh_file[] = "mesh-explorer.e";
+         mesh->PrintExodusII(omesh_file);
+         cout << "New Exodus II mesh file: " << omesh_file << endl;
+      }
+#endif
+
       if (mk == 'D')
       {
          cout << "What type of DataCollection?\n"

tests/unit/CMakeLists.txt

@@ -56,6 +56,7 @@ set(UNIT_TESTS_SRCS
   mesh/test_submesh.cpp
   mesh/test_vtu.cpp
   mesh/test_nurbs.cpp
+  mesh/test_exodus_writer.cpp
   fem/test_1d_bilininteg.cpp
   fem/test_2d_bilininteg.cpp
   fem/test_3d_bilininteg.cpp

tests/unit/mesh/test_exodus_writer.cpp

@@ -0,0 +1,273 @@
+// Copyright (c) 2010-2024, Lawrence Livermore National Security, LLC. Produced
+// at the Lawrence Livermore National Laboratory. All Rights reserved. See files
+// LICENSE and NOTICE for details. LLNL-CODE-806117.
+//
+// This file is part of the MFEM library. For more information and source code
+// availability visit https://mfem.org.
+//
+// MFEM is free software; you can redistribute it and/or modify it under the
+// terms of the BSD-3 license. We welcome feedback and contributions, see file
+// CONTRIBUTING.md for details.
+
+#include "mfem.hpp"
+#include "unit_tests.hpp"
+
+using namespace mfem;
+
+#ifdef MFEM_USE_NETCDF
+static void CompareMeshes(Mesh & mesh1, Mesh & mesh2)
+{
+   REQUIRE(mesh1.GetNE() == mesh2.GetNE());
+   REQUIRE(mesh1.GetNV() == mesh2.GetNV());
+   REQUIRE(mesh1.GetNBE() == mesh2.GetNBE());
+   REQUIRE(mesh1.GetNFaces() == mesh2.GetNFaces());
+
+   const FiniteElementSpace * fespace1 = mesh1.GetNodalFESpace();
+   const FiniteElementSpace * fespace2 = mesh2.GetNodalFESpace();
+
+   // Check elements.
+   Array<int> element_faces1, element_faces2;
+   Array<int> element_orient1, element_orient2;
+   Array<int> dofs1, dofs2;
+
+   for (int ielement = 0; ielement < mesh1.GetNE(); ielement++)
+   {
+      int attr1 = mesh1.GetAttribute(ielement);
+      int attr2 = mesh2.GetAttribute(ielement);
+
+      REQUIRE(attr1 == attr2);
+
+      Element::Type type1 = mesh1.GetElementType(ielement);
+      Element::Type type2 = mesh2.GetElementType(ielement);
+
+      REQUIRE(type1 == type2);
+
+      mesh1.GetElementFaces(ielement, element_faces1, element_orient1);
+      mesh2.GetElementFaces(ielement, element_faces2, element_orient2);
+
+      REQUIRE(element_faces1 == element_faces2);
+      REQUIRE(element_orient1 == element_orient2);
+
+      if (fespace1 && fespace2)
+      {
+         fespace1->GetElementDofs(ielement, dofs1);
+         fespace2->GetElementDofs(ielement, dofs2);
+      }
+      else
+      {
+         mesh1.GetElementVertices(ielement, dofs1);
+         mesh2.GetElementVertices(ielement, dofs2);
+      }
+
+      REQUIRE(dofs1 == dofs2);
+   }
+
+   // Check bdr elements.
+   for (int ibdr_element = 0; ibdr_element < mesh1.GetNBE(); ibdr_element++)
+   {
+      int attr1 = mesh1.GetBdrAttribute(ibdr_element);
+      int attr2 = mesh2.GetBdrAttribute(ibdr_element);
+
+      REQUIRE(attr1 == attr2);
+
+      Element::Type type1 = mesh1.GetBdrElementType(ibdr_element);
+      Element::Type type2 = mesh2.GetBdrElementType(ibdr_element);
+
+      REQUIRE(type1 == type2);
+
+      int face_index1 = mesh1.GetBdrElementFaceIndex(ibdr_element);
+      int face_index2 = mesh2.GetBdrElementFaceIndex(ibdr_element);
+
+      REQUIRE(face_index1 == face_index2);
+   }
+
+   // Check face vertices.
+   Array<int> face_vertices1, face_vertices2;
+   for (int iface_index = 0; iface_index < mesh1.GetNFaces(); iface_index++)
+   {
+      mesh1.GetFaceVertices(iface_index, face_vertices1);
+      mesh2.GetFaceVertices(iface_index, face_vertices2);
+
+      REQUIRE(face_vertices1 == face_vertices2);
+   }
+}
+#endif
+
+TEST_CASE("ExodusII Write Hex8", "[Mesh]")
+{
+#ifdef MFEM_USE_NETCDF
+   // Load Exodus II mesh from file.
+   std::string fpath_original = "data/simple-cube-hex8.e";
+   Mesh original_mesh = Mesh::LoadFromFile(fpath_original, 0, 0, true);
+
+   // Write generated Exodus II mesh to file.
+   std::string fpath_generated = "simple-cube-hex8-out.e";
+   original_mesh.PrintExodusII(fpath_generated);
+
+   // Load generated Exodus II mesh.
+   Mesh generated_mesh = Mesh::LoadFromFile(fpath_generated, 0, 0, true);
+
+   CompareMeshes(original_mesh, generated_mesh);
+
+   // Remove temporary file.
+   REQUIRE(remove(fpath_generated.c_str()) == 0);
+#endif
+}
+
+TEST_CASE("ExodusII Write Hex27", "[Mesh]")
+{
+#ifdef MFEM_USE_NETCDF
+   // Load Exodus II mesh from file.
+   std::string fpath_original = "data/simple-cube-hex27.e";
+   Mesh original_mesh = Mesh::LoadFromFile(fpath_original, 0, 0, true);
+
+   // Write generated Exodus II mesh to file.
+   std::string fpath_generated = "simple-cube-hex27-out.e";
+   original_mesh.PrintExodusII(fpath_generated);
+
+   // Load generated Exodus II mesh.
+   Mesh generated_mesh = Mesh::LoadFromFile(fpath_generated, 0, 0, true);
+
+   CompareMeshes(original_mesh, generated_mesh);
+
+   REQUIRE(remove(fpath_generated.c_str()) == 0);
+#endif
+}
+
+TEST_CASE("ExodusII Write Tet4", "[Mesh]")
+{
+#ifdef MFEM_USE_NETCDF
+   // Load Exodus II mesh from file. NB: - Do NOT refine as this changes vertex ordering!
+   std::string fpath_original = "data/simple-cube-tet4.e";
+   Mesh original_mesh = Mesh::LoadFromFile(fpath_original, 0, 0, true);
+
+   // Write generated Exodus II mesh to file.
+   std::string fpath_generated = "simple-cube-tet4-out.e";
+   original_mesh.PrintExodusII(fpath_generated);
+
+   // Load generated Exodus II mesh.
+   Mesh generated_mesh = Mesh::LoadFromFile(fpath_generated, 0, 0, true);
+
+   CompareMeshes(original_mesh, generated_mesh);
+
+   REQUIRE(remove(fpath_generated.c_str()) == 0);
+#endif
+}
+
+TEST_CASE("ExodusII Write Tet10", "[Mesh]")
+{
+#ifdef MFEM_USE_NETCDF
+   // Load Exodus II mesh from file.
+   std::string fpath_original = "data/simple-cube-tet10.e";
+   Mesh original_mesh = Mesh::LoadFromFile(fpath_original, 0, 0, true);
+
+   // Write generated Exodus II mesh to file.
+   std::string fpath_generated = "simple-cube-tet10-out.e";
+   original_mesh.PrintExodusII(fpath_generated);
+
+   // Load generated Exodus II mesh.
+   Mesh generated_mesh = Mesh::LoadFromFile(fpath_generated, 0, 0, true);
+
+   CompareMeshes(original_mesh, generated_mesh);
+
+   REQUIRE(remove(fpath_generated.c_str()) == 0);
+#endif
+}
+
+// TEST_CASE("ExodusII Write Wedge6", "[Mesh]")
+// {
+// #ifdef MFEM_USE_NETCDF
+//    std::string fpath_original = "data/simple-cube-wedge6.e";
+//    Mesh original_mesh = Mesh::LoadFromFile(fpath_original, 0, 0, true);
+
+//    std::string fpath_generated = "simple-cube-wedge6-out.e";
+//    original_mesh.PrintExodusII(fpath_generated);
+
+//    Mesh generated_mesh = Mesh::LoadFromFile(fpath_generated, 0, 0, true);
+//    CompareMeshes(original_mesh, generated_mesh);
+//
+//    REQUIRE(remove(fpath_generated.c_str()) == 0);
+// #endif
+// }
+
+// TEST_CASE("ExodusII Write Wedge18", "[Mesh]")
+// {
+// #ifdef MFEM_USE_NETCDF
+//    std::string fpath_original = "data/simple-cube-wedge18.e";
+//    Mesh original_mesh = Mesh::LoadFromFile(fpath_original, 0, 0, true);
+
+//    std::string fpath_generated = "simple-cube-wedge18-out.e";
+//    original_mesh.PrintExodusII(fpath_generated);
+
+//    Mesh generated_mesh = Mesh::LoadFromFile(fpath_generated, 0, 0, true);
+//    CompareMeshes(original_mesh, generated_mesh);
+
+//    REQUIRE(remove(fpath_generated.c_str()) == 0);
+// #endif
+// }
+
+// TEST_CASE("ExodusII Write Pyramid5", "[Mesh]")
+// {
+// #ifdef MFEM_USE_NETCDF
+//    std::string fpath_original = "data/simple-cube-pyramid5.e";
+//    Mesh original_mesh = Mesh::LoadFromFile(fpath_original, 0, 0, true);
+
+//    std::string fpath_generated = "simple-cube-pyramid5-out.e";
+//    original_mesh.PrintExodusII(fpath_generated);
+
+//    Mesh generated_mesh = Mesh::LoadFromFile(fpath_generated, 0, 0, true);
+//    CompareMeshes(original_mesh, generated_mesh);
+
+//    REQUIRE(remove(fpath_generated.c_str()) == 0);
+// #endif
+// }
+
+// TEST_CASE("ExodusII Write Pyramid14", "[Mesh]")
+// {
+// #ifdef MFEM_USE_NETCDF
+//    std::string fpath_original = "data/simple-cube-pyramid14.e";
+//    Mesh original_mesh = Mesh::LoadFromFile(fpath_original, 0, 0, true);
+
+//    std::string fpath_generated = "simple-cube-pyramid14-out.e";
+//    original_mesh.PrintExodusII(fpath_generated);
+
+//    Mesh generated_mesh = Mesh::LoadFromFile(fpath_generated, 0, 0, true);
+//    CompareMeshes(original_mesh, generated_mesh);
+
+//    REQUIRE(remove(fpath_generated.c_str()) == 0);
+// #endif
+// }
+
+// TEST_CASE("ExodusII Write Mixed First-Order", "[Mesh]")
+// {
+// #ifdef MFEM_USE_NETCDF
+//    // Contains Hex8, Tet4, Wedge6, Pyramid5 elements.
+//    std::string fpath_original = "data/simple-cube-multi-element-order1.e";
+//    Mesh original_mesh = Mesh::LoadFromFile(fpath_original, 0, 0, true);
+
+//    std::string fpath_generated = "simple-cube-multi-element-order1-out.e";
+//    original_mesh.PrintExodusII(fpath_generated);
+
+//    Mesh generated_mesh = Mesh::LoadFromFile(fpath_generated, 0, 0, true);
+//    CompareMeshes(original_mesh, generated_mesh);
+
+//    REQUIRE(remove(fpath_generated.c_str()) == 0);
+// #endif
+// }
+
+// TEST_CASE("ExodusII Write Mixed Second-Order", "[Mesh]")
+// {
+// #ifdef MFEM_USE_NETCDF
+//    // Contains Hex27 and Tet10 elements.
+//    std::string fpath_original = "data/simple-cube-multi-element-order2.e";
+//    Mesh original_mesh = Mesh::LoadFromFile(fpath_original, 0, 0, true);
+
+//    std::string fpath_generated = "simple-cube-multi-element-order2-out.e";
+//    original_mesh.PrintExodusII(fpath_generated);
+
+//    Mesh generated_mesh = Mesh::LoadFromFile(fpath_generated, 0, 0, true);
+//    CompareMeshes(original_mesh, generated_mesh);
+
+//    REQUIRE(remove(fpath_generated.c_str()) == 0);
+// #endif
+// }