Merge pull request #11419 from KratosMultiphysics/med-application

MedApplication

applications/MedApplication/CMakeLists.txt

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+set(CMAKE_INCLUDE_CURRENT_DIR ON)
+
+message("**** configuring KratosMedApplication ****")
+
+################### PYBIND11
+include(pybind11Tools)
+
+list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}) # for FindMED
+find_package(MED REQUIRED)
+
+# MED uses HDF
+# TODO check interoperability with the HDFapp, both in serial and parallel
+if (NOT HDF5_FOUND)
+    find_package(HDF5 REQUIRED COMPONENTS C)
+endif()
+
+include_directories(${MED_INCLUDE_DIR} ${HDF5_INCLUDE_DIRS})
+
+include_directories( ${KRATOS_SOURCE_DIR}/kratos )
+
+## Med Core sources
+file(GLOB_RECURSE KRATOS_MED_APPLICATION_CORE
+    ${CMAKE_CURRENT_SOURCE_DIR}/med_application.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/custom_io/*.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/custom_utilities/*.cpp
+)
+
+## Med testing sources
+if(${KRATOS_BUILD_TESTING} MATCHES ON)
+    file(GLOB_RECURSE KRATOS_MED_APPLICATION_TESTING_SOURCES ${CMAKE_CURRENT_SOURCE_DIR}/tests/*.cpp)
+endif(${KRATOS_BUILD_TESTING} MATCHES ON)
+
+## Med python interface sources
+file(GLOB_RECURSE KRATOS_MED_APPLICATION_PYTHON_INTERFACE ${CMAKE_CURRENT_SOURCE_DIR}/custom_python/*.cpp)
+
+add_library(KratosMedCore SHARED ${KRATOS_MED_APPLICATION_CORE} ${KRATOS_MED_APPLICATION_TESTING_SOURCES})
+target_link_libraries(KratosMedCore PUBLIC KratosCore ${MED_LIBRARIES} ${HDF5_C_LIBRARIES})
+set_target_properties(KratosMedCore PROPERTIES COMPILE_DEFINITIONS "MED_APPLICATION=EXPORT,API")
+target_include_directories(KratosMedCore SYSTEM PRIVATE hdf5::hdf5)
+
+
+###############################################################
+## define library Kratos which defines the basic python interface
+pybind11_add_module(KratosMedApplication MODULE THIN_LTO ${KRATOS_MED_APPLICATION_PYTHON_INTERFACE})
+target_link_libraries(KratosMedApplication PRIVATE KratosMedCore)
+set_target_properties(KratosMedApplication PROPERTIES PREFIX "")
+
+# changing the .dll suffix to .pyd (Windows)
+if(${CMAKE_SYSTEM_NAME} MATCHES "Windows")
+    set_target_properties(KratosMedApplication PROPERTIES SUFFIX .pyd)
+endif(${CMAKE_SYSTEM_NAME} MATCHES "Windows")
+
+# changing the .dylib suffix to .so (OS X)
+if(${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
+    set_target_properties(KratosMedApplication PROPERTIES SUFFIX .so)
+endif(${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
+
+# Add to the KratosMultiphisics Python module
+kratos_python_install(${INSTALL_PYTHON_USING_LINKS} ${CMAKE_CURRENT_SOURCE_DIR}/MedApplication.py KratosMultiphysics/MedApplication/__init__.py )
+
+# Install python files
+get_filename_component (CURRENT_DIR_NAME ${CMAKE_CURRENT_SOURCE_DIR} NAME)
+kratos_python_install_directory(${INSTALL_PYTHON_USING_LINKS} ${CMAKE_CURRENT_SOURCE_DIR}/python_scripts KratosMultiphysics/${CURRENT_DIR_NAME} )
+
+# Kratos Testing. Install everything except sources to ensure that reference and configuration files are copied.
+if(${INSTALL_TESTING_FILES} MATCHES ON )
+    get_filename_component (CURRENT_DIR_NAME ${CMAKE_CURRENT_SOURCE_DIR} NAME)
+    install(DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/tests DESTINATION applications/${CURRENT_DIR_NAME}
+        PATTERN "*.git" EXCLUDE
+        PATTERN "*.c" EXCLUDE
+        PATTERN "*.h" EXCLUDE
+        PATTERN "*.cpp" EXCLUDE
+        PATTERN "*.hpp" EXCLUDE
+  )
+endif(${INSTALL_TESTING_FILES} MATCHES ON)
+
+# Install targets
+install(TARGETS KratosMedCore DESTINATION libs )
+install(TARGETS KratosMedApplication DESTINATION libs )
+
+# Define custom targets
+set(KRATOS_KERNEL "${KRATOS_KERNEL};KratosMedCore" PARENT_SCOPE)
+set(KRATOS_PYTHON_INTERFACE "${KRATOS_PYTHON_INTERFACE};KratosMedApplication" PARENT_SCOPE)

applications/MedApplication/FindMED.cmake

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+
+# include(FindPackageHandleStandardArgs)
+# find_package_handle_standard_args
+
+
+
+
+
+
+# Find the MED includes and libraries
+#
+# MED_INCLUDE_DIR - where to find autopack.h
+# MED_LIBRARIES   - List of fully qualified libraries to link against.
+# MED_FOUND       - Do not attempt to use if "no" or undefined.
+
+FIND_PATH(MED_INCLUDE_DIR "med.h"
+  PATHS
+  "${MED_ROOT}/include"
+  /usr/local/include
+  /usr/include
+)
+
+FIND_LIBRARY(MED_LIBRARY medC
+  PATHS
+  "${MED_ROOT}/lib"
+  /usr/local/lib/*
+  /usr/lib/*
+)
+
+IF(MED_INCLUDE_DIR AND MED_LIBRARY)
+  SET( MED_LIBRARIES ${MED_LIBRARY})
+  SET( MED_FOUND "YES" )
+  message(STATUS "MED found!")
+  message(STATUS "MED includes: ${MED_INCLUDE_DIR}")
+  message(STATUS "MED libraries: ${MED_LIBRARY}")
+else()
+  message(WARNING "finding MED failed, please try to set the var MED_ROOT")
+ENDIF()

applications/MedApplication/MedApplication.py

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+# Application dependent names and paths
+from KratosMultiphysics import _ImportApplication
+from KratosMedApplication import *
+application = KratosMedApplication()
+application_name = "KratosMedApplication"
+
+_ImportApplication(application, application_name)

applications/MedApplication/README.md

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+# MedApplication
+
+The Med Application an interface to the MED-library. This library writes med-files, which contain mesh, field results and other data, and is based on [HDF5](https://www.hdfgroup.org/solutions/hdf5/). This format is used by [Salome](https://www.salome-platform.org/) and [Code_Aster](https://code-aster.org).
+
+## Installation
+The MED-library is an external library, which must be installed before the application can be compiled
+
+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.