Merge pull request #11580 from KratosMultiphysics/med/fixes

[MEDApp] Minor Fixes

applications/MedApplication/README.md

@@ -5,8 +5,17 @@ The Med Application an interface to the MED-library. This library writes med-fil
 ## Installation
 The MED-library is an external library, which must be installed before the application can be compiled
 
+### Ubuntu
+
 On Ubuntu, it can be installed with `sudo apt-get install libmedc-dev`. This installs all required dependencies, including HDF5
 
 The source code is available on the Salome website for a manual installation. In this case also HDF5 needs to be installed separately.
 
 Use `MED_ROOT` to specify the path to the MED installation in the CMake of Kratos.
+
+### Arch / Manjaro
+
+Packages related to *Salome* and *MED* for arch-based distros can be installed from the [AUR](https://en.wikipedia.org/wiki/Arch_Linux#Arch_User_Repository_(AUR)). The MedApplication requires [med-serial](https://aur.archlinux.org/packages/med-serial) (for non-MPI builds) or [med-openmpi](https://archlinux.org/packages/extra/x86_64/med-openmpi/) (for MPI builds with OpenMPI).
+```
+sudo pacman -S med-serial med-openmpi
+```

applications/MedApplication/custom_io/med_model_part_io.cpp

@@ -86,7 +86,11 @@ std::function<void(std::vector<T>&)> GetReorderFunction(const med_geometry_type
         };
 
     case MED_TRIA6:
-        KRATOS_ERROR << "MED_TRIA6 is not implemented!" << std::endl;
+        return [](auto& rConnectivities) -> void {
+            CheckConnectivitiesSize(6, rConnectivities);
+            std::swap(rConnectivities[1], rConnectivities[2]);
+            std::swap(rConnectivities[3], rConnectivities[5]);
+        };
 
     case MED_QUAD4:
         return [](auto& Connectivities){
@@ -100,6 +104,14 @@ std::function<void(std::vector<T>&)> GetReorderFunction(const med_geometry_type
     case MED_QUAD9: // should be same as MED_QUAD8
         KRATOS_ERROR << "MED_QUAD9 is not implemented!" << std::endl;
 
+    case MED_TETRA10:
+        return [](auto& rConnectivities) -> void {
+            CheckConnectivitiesSize(10, rConnectivities);
+            std::swap(rConnectivities[1], rConnectivities[2]);
+            std::swap(rConnectivities[4], rConnectivities[6]);
+            std::swap(rConnectivities[8], rConnectivities[9]);
+        };
+
     case MED_PYRA5:
         KRATOS_ERROR << "MED_PYRA5 is not implemented!" << std::endl;
 
@@ -311,11 +323,7 @@ class MedModelPartIO::MedFileHandler
 
     ~MedFileHandler()
     {
-        KRATOS_TRY
-
         KRATOS_WARNING_IF("MedModelPartIO", MEDfileClose(mFileHandle) < 0) << "Closing of file " << mFileName << " failed!" << std::endl;
-
-        KRATOS_CATCH("")
     }
 
 private:
@@ -340,8 +348,6 @@ void MedModelPartIO::ReadModelPart(ModelPart& rThisModelPart)
 {
     KRATOS_TRY
 
-    using NodePointerType = ModelPart::NodeType::Pointer;
-
     KRATOS_ERROR_IF_NOT(mpFileHandler->IsReadMode()) << "MedModelPartIO needs to be created in read mode to read a ModelPart!" << std::endl;
 
     // reading nodes
@@ -430,16 +436,19 @@ void MedModelPartIO::ReadModelPart(ModelPart& rThisModelPart)
 
         std::vector<IndexType> geom_node_ids(num_nodes_geo_type);
 
-        for (std::size_t i=0; i<num_geometries; ++i) {
+        for (std::size_t i=0; i<static_cast<std::size_t>(num_geometries); ++i) {
             for (int j=0; j<num_nodes_geo_type; ++j) {
                 const int node_idx = i*num_nodes_geo_type + j;
                 geom_node_ids[j] = connectivity[node_idx];
             }
             reorder_fct(geom_node_ids);
-            rThisModelPart.CreateNewGeometry(kratos_geo_name, geom_node_ids);
-        }
 
-        num_geometries_total += num_geometries;
+            KRATOS_ERROR_IF(std::numeric_limits<decltype(num_geometries_total)>::max() == num_geometries_total)
+                << "number of geometries read (" << num_geometries_total << ") exceeds the capacity of the index type";
+            rThisModelPart.CreateNewGeometry(kratos_geo_name,
+                                             num_geometries_total++,
+                                             geom_node_ids);
+        }
 
         KRATOS_INFO("MedModelPartIO") << "Read " << num_geometries << " geometries of type " << kratos_geo_name << std::endl;
     }

applications/MedApplication/med_inc.h

@@ -14,8 +14,10 @@
 
 // Those dummy structs are necessary when the MED-library is compiled with MPI support.
 // Then the header also contains functions which use those MPI-types
+#ifndef KRATOS_USING_MPI
 struct MPI_Comm;
 struct MPI_Info;
+#endif
 
 // External includes
 #include "med.h"

applications/MedApplication/tests/cpp_tests/test_med_model_part_io.cpp

@@ -23,22 +23,22 @@ namespace Kratos::Testing {
 KRATOS_TEST_CASE_IN_SUITE(MedModelpartIO_NonExistingFile_read, KratosMedFastSuite)
 {
     const std::filesystem::path file_path(this->Name() + ".txt");
-    KRATOS_CHECK_IS_FALSE(std::filesystem::exists(file_path)); // make sure there are no leftovers
+    KRATOS_EXPECT_FALSE(std::filesystem::exists(file_path)); // make sure there are no leftovers
 
-    KRATOS_CHECK_EXCEPTION_IS_THROWN(
+    KRATOS_EXPECT_EXCEPTION_IS_THROWN(
         MedModelPartIO dummy(file_path),
         "File \""+file_path.string()+"\" does not exist!");
 
-    KRATOS_CHECK_IS_FALSE(std::filesystem::exists(file_path));
+    KRATOS_EXPECT_FALSE(std::filesystem::exists(file_path));
 }
 
 KRATOS_TEST_CASE_IN_SUITE(MedModelpartIO_NonExistingFile_write, KratosMedFastSuite)
 {
     const std::filesystem::path file_path(this->Name() + ".txt");
-    KRATOS_CHECK_IS_FALSE(std::filesystem::exists(file_path)); // make sure there are no leftovers
+    KRATOS_EXPECT_FALSE(std::filesystem::exists(file_path)); // make sure there are no leftovers
 
     MedModelPartIO(file_path, IO::WRITE);
-    KRATOS_CHECK(std::filesystem::exists(file_path));
+    KRATOS_EXPECT_TRUE(std::filesystem::exists(file_path));
 
     std::filesystem::remove(file_path); // clean leftover
 }
@@ -48,7 +48,7 @@ KRATOS_TEST_CASE_IN_SUITE(MedModelpartIO_TextFile, KratosMedFastSuite)
     const std::filesystem::path file_path(this->Name() + ".txt");
     std::ofstream output(file_path); // create a dummy file (that is not a hdf file)
 
-    KRATOS_CHECK_EXCEPTION_IS_THROWN(
+    KRATOS_EXPECT_EXCEPTION_IS_THROWN(
         MedModelPartIO dummy(file_path),
         "A problem with HDF occured while trying to open file \""+file_path.string()+"\"!");