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https://github.com/TREX-CoE/trexio.git
synced 2024-12-22 20:35:44 +01:00
Merge pull request #78 from TREX-CoE/add-inquire-functionality
Add trexio_info function
This commit is contained in:
Evgeny Posenitskiy
GitHub
commit
d46d4adab8
@ -32,8 +32,25 @@ if(EXISTS "${CMAKE_SOURCE_DIR}/.git/config")
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else()
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message(FATAL_ERROR "EMACS not found. It is required to produce TREXIO source code from org-mode files.")
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endif()
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# in case Git is not available, we default to "unknown"
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set(GIT_HASH "unknown")
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# find Git and if available set GIT_HASH variable
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find_package(Git QUIET)
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if(GIT_FOUND)
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execute_process(
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COMMAND ${GIT_EXECUTABLE} --no-pager show -s --pretty=format:%H -n 1
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OUTPUT_VARIABLE GIT_HASH
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OUTPUT_STRIP_TRAILING_WHITESPACE
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WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
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ERROR_QUIET)
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endif()
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# get the user name from the ${USER} env variable
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set(TREXIO_USER_NAME $ENV{USER})
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# replace placeholders in the templace config.h.in file to produce config.h
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# config.h is needed to insert TREXIO_PACKAGE_VERSION and TREXIO_GIT_HASH into trexio.h
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configure_file(${CMAKE_SOURCE_DIR}/include/cmake_config.h.in
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${CMAKE_SOURCE_DIR}/include/config.h)
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${CMAKE_SOURCE_DIR}/include/config.h
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@ONLY)
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endif()
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# Set directories to be included at build time.
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@ -3,3 +3,5 @@
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#define VERSION_MAJOR @PROJECT_VERSION_MAJOR@
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#define VERSION_MINOR @PROJECT_VERSION_MINOR@
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#define VERSION_PATCH @PROJECT_VERSION_PATCH@
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#define GIT_HASH "@GIT_HASH@"
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#define TREXIO_USER_NAME "@TREXIO_USER_NAME@"
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@ -38,6 +38,8 @@ except:
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#============ WRITE THE DATA IN THE TEST FILE ============#
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#=========================================================#
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trexio.info()
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# create TREXIO file and open it for writing
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test_file = trexio.File(output_filename, mode='w', back_end=TEST_TREXIO_BACKEND)
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assert test_file.exists
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@ -1,13 +1,26 @@
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# ========= DEFINE TREXIO C LIBRARY =========
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# ============= THREADS SUPPORT ==============
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# the two options below add preference for the pthread library over other system-wide threads implementations
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set(CMAKE_THREAD_PREFER_PTHREAD TRUE)
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set(THREADS_PREFER_PTHREAD_FLAG TRUE)
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# find thread library
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find_package(Threads REQUIRED)
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# ============= STDINT SUPPORT ===============
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include(CheckIncludeFile)
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check_include_file(stdint.h HAVE_STDINT_H)
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# ========= DEFINE TREXIO C LIBRARY =========
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# Set a list of TREXIO source and header files that are always compiled.
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set(TREXIO_SOURCES
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set(TREXIO_SOURCES
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${CMAKE_CURRENT_SOURCE_DIR}/trexio.c
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${CMAKE_CURRENT_SOURCE_DIR}/trexio_text.c
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)
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set(TREXIO_PUBLIC_HEADERS ${CMAKE_SOURCE_DIR}/include/trexio.h)
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set(TREXIO_PRIVATE_HEADERS
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set(TREXIO_PRIVATE_HEADERS
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${CMAKE_CURRENT_SOURCE_DIR}/trexio_s.h
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${CMAKE_CURRENT_SOURCE_DIR}/trexio_private.h
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${CMAKE_CURRENT_SOURCE_DIR}/trexio_text.h
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@ -29,7 +42,7 @@ if(BUILD_SHARED_LIBS AND NOT BUILD_STATIC_LIBS)
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add_library(trexio SHARED)
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elseif(NOT BUILD_SHARED_LIBS AND BUILD_STATIC_LIBS)
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message(STATUS "TREXIO :: static C library will be built")
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add_library(trexio STATIC)
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# Static TREXIO has to be compiled with -fPIC flag. For Shared it is done by default.
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@ -40,12 +53,12 @@ else()
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endif()
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# Set TREXIO version and include files.
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set_target_properties(trexio PROPERTIES
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set_target_properties(trexio PROPERTIES
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VERSION ${PROJECT_VERSION}
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PUBLIC_HEADER ${TREXIO_PUBLIC_HEADERS}
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)
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# ============= CONFIGURE HDF5 ==============
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# ============= CONFIGURE HDF5 ==============
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# By defaulti, TREXIO is configured with the HDF5 support.
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# To change this, append -DENABLE_HDF5=OFF to the cmake call.
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@ -74,8 +87,8 @@ if(ENABLE_HDF5)
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# - include directories with HDF5 header files
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target_include_directories(trexio PRIVATE ${HDF5_C_INCLUDE_DIRS})
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# - link to HDF5 C libraries
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target_link_libraries(trexio PRIVATE
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${HDF5_C_HL_LIBRARIES}
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target_link_libraries(trexio PRIVATE
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${HDF5_C_HL_LIBRARIES}
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${HDF5_C_LIBRARIES})
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endif()
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@ -110,7 +123,7 @@ if(TREXIO_DEVEL)
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list(APPEND ORG_FILES templates_hdf5/templator_hdf5.org)
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endif()
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add_custom_command(OUTPUT
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add_custom_command(OUTPUT
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${TREXIO_SOURCES}
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${TREXIO_PUBLIC_HEADERS}
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${TREXIO_PRIVATE_HEADERS}
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@ -129,7 +142,7 @@ if(TREXIO_DEVEL)
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endif()
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# ============= INSTALL TREXIO ==============
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# ============= INSTALL TREXIO ==============
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include(GNUInstallDirs)
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# Use standard GNU directories for installation of TREXIO (e.g. /usr/local/lib|include).
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@ -153,4 +166,4 @@ if(NOT TARGET uninstall)
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COMMAND ${CMAKE_COMMAND} -P ${CMAKE_CURRENT_BINARY_DIR}/cmake_uninstall.cmake)
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endif()
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# ===========================================
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# ===========================================
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@ -4,18 +4,22 @@
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cat prefix_front.c > trexio.c
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cat prefix_front.h > trexio.h
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# parse the config-defined version attributes to pass them to Fortran module file
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# parse the config-defined version attributes to pass them to the header files
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VERSION_VAL=`grep "PACKAGE_VERSION" ../../include/config.h | cut -d " " -f 3`
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VERSION_MAJOR_VAL=`grep "VERSION_MAJOR" ../../include/config.h | cut -d " " -f 3`
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VERSION_MINOR_VAL=`grep "VERSION_MINOR" ../../include/config.h | cut -d " " -f 3`
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VERSION_PATCH_VAL=`grep "VERSION_PATCH" ../../include/config.h | cut -d " " -f 3`
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# parse the config-defined GIT_HASH to pass them to the header files
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GIT_HASH_STR=`grep "GIT_HASH" ../../include/config.h | cut -d " " -f 3`
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# grep some usefull constants from the config.h
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echo "" >> trexio.h
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echo "#define TREXIO_PACKAGE_VERSION ${VERSION_VAL:='0.0.0'}" >> trexio.h
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echo "#define TREXIO_VERSION_MAJOR ${VERSION_MAJOR_VAL:=0}" >> trexio.h
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echo "#define TREXIO_VERSION_MINOR ${VERSION_MINOR_VAL:=0}" >> trexio.h
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echo "#define TREXIO_VERSION_PATCH ${VERSION_PATCH_VAL:=0}" >> trexio.h
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echo "#define TREXIO_GIT_HASH ${GIT_HASH_STR:='0000'}" >> trexio.h
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echo "" >> trexio.h
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cat prefix_s_front.h > trexio_s.h
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@ -24,10 +28,11 @@ cat prefix_python.py > trexio.py
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# append version string and attributes to the Fortran module file
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echo "" >> trexio_f.f90
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echo "character(len = 12) :: TREXIO_PACKAGE_VERSION = ${VERSION_VAL}" >> trexio_f.f90
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echo "character(len = 12) :: TREXIO_PACKAGE_VERSION = ${VERSION_VAL:='0.0.0'}" >> trexio_f.f90
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echo "integer :: TREXIO_VERSION_MAJOR = ${VERSION_MAJOR_VAL}" >> trexio_f.f90
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echo "integer :: TREXIO_VERSION_MINOR = ${VERSION_MINOR_VAL}" >> trexio_f.f90
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echo "integer :: TREXIO_VERSION_PATCH = ${VERSION_PATCH_VAL}" >> trexio_f.f90
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echo "character(len = 64) :: TREXIO_GIT_HASH = ${GIT_HASH_STR:='0000'}" >> trexio_f.f90
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echo "" >> trexio_f.f90
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# c front end
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@ -1201,6 +1201,18 @@ def _close(trexio_file):
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output:
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~trexio_exit_code~ exit code.
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It returns:
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- ~TREXIO_SUCCESS~ if the ~file_name~ exists and if it correspond to a valid TREXIO file (i.e. a directory OR an HDF5 file)
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- ~TREXIO_FILE_ERROR~ if ~file_name~ exists but it is not a TREXIO file
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- ~TREXIO_FAILURE~ otherwise
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Also, there is an implicit way to have the aforementioned functionality.
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Attempt to open a non-existing file with ~trexio_open~ function will result in a ~TREXIO_OPEN_ERROR~ exit code
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(see the modified value that has been passed as a 4-th argument to ~trexio_open~).
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You can see examples of both functionalities in =test_f.f90= (search for calls with ~_void~ suffix).
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*** C
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#+begin_src c :tangle prefix_front.h :exports none
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@ -1387,6 +1399,7 @@ trexio_exit_code
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trexio_read_$group_num$_64 (trexio_t* const file, $group_num_dtype_double$* const num)
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{
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if (file == NULL) return TREXIO_INVALID_ARG_1;
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if (num == NULL) return TREXIO_INVALID_ARG_2;
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if (trexio_has_$group_num$(file) != TREXIO_SUCCESS) return TREXIO_ATTR_MISSING;
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switch (file->back_end) {
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@ -1446,6 +1459,7 @@ trexio_exit_code
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trexio_read_$group_num$_32 (trexio_t* const file, $group_num_dtype_single$* const num)
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{
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if (file == NULL) return TREXIO_INVALID_ARG_1;
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if (num == NULL) return TREXIO_INVALID_ARG_2;
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if (trexio_has_$group_num$(file) != TREXIO_SUCCESS) return TREXIO_ATTR_MISSING;
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$group_num_dtype_double$ num_64 = 0;
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@ -2670,6 +2684,7 @@ trexio_exit_code
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trexio_read_$group_dset$_size(trexio_t* const file, int64_t* const size_max)
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{
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if (file == NULL) return TREXIO_INVALID_ARG_1;
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if (size_max == NULL) return TREXIO_INVALID_ARG_2;
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if (trexio_has_$group_dset$(file) != TREXIO_SUCCESS) return TREXIO_DSET_MISSING;
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switch (file->back_end) {
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@ -3894,6 +3909,70 @@ def has_$group_str$(trexio_file) -> bool:
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return False
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#+end_src
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* General helper functions
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This section contains general helper functions like ~trexio_info~.
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~trexio_info~ prints information about the TREXIO configuration (see =config.h= file).
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In particular:
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1) ~TREXIO_PACKAGE_VERSION~ [string]
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2) ~HAVE_HDF5~ [bool]
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3) ~HDF5_VERSION~ [string] (optional, only if ~HAVE_HDF5~ is ~true~)
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4) ~TREXIO_GIT_HASH~ [string]
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** C
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#+begin_src c :tangle prefix_front.h :exports none
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trexio_exit_code trexio_info(void);
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#+end_src
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#+begin_src c :tangle prefix_front.c
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trexio_exit_code
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trexio_info (void)
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{
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printf("TREXIO_PACKAGE_VERSION : %s\n", TREXIO_PACKAGE_VERSION);
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#ifdef TREXIO_GIT_HASH
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printf("TREXIO_GIT_HASH : %s\n", TREXIO_GIT_HASH);
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#else
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printf("GIT_HASH is stored in the config.h file, which is missing.");
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#endif
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#ifdef HAVE_HDF5
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printf("HAVE_HDF5 : true\n");
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printf("%s\n", H5_VERS_INFO);
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#else
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printf("HAVE_HDF5 : false\n");
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printf("TREXIO configured without the HDF5 library\n");
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#endif
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return TREXIO_SUCCESS;
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}
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#+end_src
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** Fortran
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#+begin_src f90 :tangle prefix_fortran.f90
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interface
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integer function trexio_info () bind(C)
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use, intrinsic :: iso_c_binding
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end function trexio_info
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end interface
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#+end_src
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** Python
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#+begin_src python :tangle basic_python.py
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def info():
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"""Print the info about the installed TREXIO library.
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"""
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rc = pytr.trexio_info()
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if rc != TREXIO_SUCCESS:
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raise Error(rc)
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#+end_src
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* Fortran helper/wrapper functions
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The function below adapts the original C-based ~trexio_open~ for Fortran.
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@ -14,6 +14,8 @@ int main() {
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int rc;
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trexio_info();
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bool have_hdf5 = trexio_has_backend(TREXIO_HDF5);
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if(have_hdf5) {
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rc = system("rm -f -- test_all.h5");
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@ -72,7 +74,7 @@ int test_write(const char* file_name, const back_end_t backend) {
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"H 999asdasd" ,
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"H" ,
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"H" };
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const char* sym = "B3U with some comments";
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/*================= START OF TEST ==================*/
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@ -96,11 +98,11 @@ int test_write(const char* file_name, const back_end_t backend) {
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assert (rc == TREXIO_SUCCESS);
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rc = trexio_write_nucleus_point_group(file, sym, 32);
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assert (rc == TREXIO_SUCCESS);
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// close current session
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rc = trexio_close(file);
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assert (rc == TREXIO_SUCCESS);
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// reopen file in 'write' mode
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file = trexio_open(file_name, 'w', backend, &rc);
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assert (file != NULL);
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@ -188,7 +190,7 @@ int test_read(const char* file_name, const back_end_t backend) {
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assert (rc == TREXIO_SUCCESS);
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assert (strcmp(label[0], "C") == 0);
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assert (strcmp(label[1], "Na") == 0);
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for (int i=0; i<num; i++){
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free(label[i]);
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}
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@ -220,8 +222,6 @@ int test_read(const char* file_name, const back_end_t backend) {
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assert (file2 == NULL);
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/*================= END OF TEST =====================*/
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return 0;
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}
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@ -3,6 +3,7 @@ program test_trexio
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use, intrinsic :: iso_c_binding
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implicit none
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integer :: rc
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logical :: have_hdf5
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print * , "============================================"
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@ -11,6 +12,8 @@ program test_trexio
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print'(a,i3)', " TREXIO MINOR VERSION : ", TREXIO_VERSION_MINOR
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print * , "============================================"
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rc = trexio_info()
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call system('rm -rf -- test_write_f.dir')
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print *, 'call test_write(''test_write_f.dir'', TREXIO_TEXT)'
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call test_write('test_write_f.dir', TREXIO_TEXT)
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