Merge kintera

CMakeLists.txt

@@ -7,6 +7,7 @@ set(CMAKE_CXX_EXTENSIONS OFF)
 project(canoe
   LANGUAGES CXX C Fortran
 	)
+
 # search for <Package>_ROOT
 cmake_policy(SET CMP0074 NEW)
 
@@ -27,11 +28,12 @@ endif()
 add_compile_definitions(_GLIBCXX_USE_CXX11_ABI=${_ABI_OUTPUT})
 
 # Set MacOS deployment target
-set(CMAKE_OSX_DEPLOYMENT_TARGET "15.0")
+set(CMAKE_OSX_DEPLOYMENT_TARGET "14.0")
 
 string(ASCII 27 Esc)
 set(ColorReset "${Esc}[m")
 set(Green      "${Esc}[32m")
+set(Blue       "${Esc}[34m")
 
 message(STATUS "")
 message(STATUS "${Green}==== ${PROJECT_NAME} configure begin ====${ColorReset}")
@@ -54,12 +56,12 @@ foreach(_file ${_macro_files})
 endforeach()
 
 ## 1. set up compiler flags ##
-message(STATUS "${PROJECT_NAME}-1. Setting up project compiler flags ...")
+message(STATUS "${Blue}${PROJECT_NAME}-1. Setting up project compiler flags ...${ColorReset}")
 message(STATUS "Include ${CMAKE_SOURCE_DIR}/cmake/compilers.cmake")
 include(${CMAKE_SOURCE_DIR}/cmake/compilers.cmake)
 
 ## 2. set up project specific configuration ##
-message(STATUS "${PROJECT_NAME}-2. Setting up project parameters ...")
+message(STATUS "${Blue}${PROJECT_NAME}-2. Setting up project parameters ...${ColorReset}")
 
 # load custom task
 message(STATUS "Load custom task = ${TASK}")
@@ -80,17 +82,21 @@ message(STATUS "Include ${CMAKE_CURRENT_SOURCE_DIR}/cmake/parameters.cmake")
 include(${CMAKE_CURRENT_SOURCE_DIR}/cmake/parameters.cmake)
 
 ## 3. set up project system libraries ##
-message(STATUS "${PROJECT_NAME}-3. Setting up system libraries")
+message(STATUS "${Blue}${PROJECT_NAME}-3. Setting up system libraries ...${ColorReset}")
+find_package(Torch REQUIRED)
 find_package(Eigen3 REQUIRED)
-find_package(Cantera)
-find_package(Torch)
+find_package(Disort REQUIRED)
+find_package(Harp REQUIRED)
+find_package(Kintera REQUIRED)
+find_package(Snap REQUIRED)
+
+include(${CMAKE_CURRENT_SOURCE_DIR}/cmake/fmt.cmake)
+include(${CMAKE_CURRENT_SOURCE_DIR}/cmake/gtest.cmake)
+include(${CMAKE_CURRENT_SOURCE_DIR}/cmake/yamlpp.cmake)
 
-include(${CMAKE_SOURCE_DIR}/cmake/yamlpp.cmake)
-include(${CMAKE_SOURCE_DIR}/cmake/gtest.cmake)
 include(${CMAKE_SOURCE_DIR}/cmake/athena.cmake)
 include(${CMAKE_SOURCE_DIR}/cmake/application.cmake)
 include(${CMAKE_SOURCE_DIR}/cmake/rfm.cmake)
-include(${CMAKE_SOURCE_DIR}/cmake/disort.cmake)
 include(${CMAKE_SOURCE_DIR}/cmake/rrtmg.cmake)
 include(${CMAKE_SOURCE_DIR}/cmake/pvfmm.cmake)
 include(${CMAKE_SOURCE_DIR}/cmake/minichem.cmake)
@@ -99,20 +105,20 @@ include(${CMAKE_SOURCE_DIR}/cmake/pybind11.cmake)
 include(${CMAKE_SOURCE_DIR}/cmake/c3m.cmake)
 
 ## 4. set up project configure file and library ##
-message(STATUS "${PROJECT_NAME}-4. Setting up project libraries")
-configure_file(${CMAKE_SOURCE_DIR}/configure.hpp.in configure.hpp @ONLY)
+message(STATUS "${Blue}${PROJECT_NAME}-4. Setting up project libraries ...${ColorReset}")
+configure_file(${CMAKE_SOURCE_DIR}/configure.h.in configure.h @ONLY)
 add_subdirectory(src)
 add_subdirectory(tools)
 add_subdirectory(data)
 
 ## 5. set up examples and tests
-message(STATUS "${PROJECT_NAME}-5. Setting up unit tests")
+message(STATUS "${Blue}${PROJECT_NAME}-5. Setting up unit tests ..${ColorReset}")
 
 add_subdirectory(examples)
-add_subdirectory(tests)
+#add_subdirectory(tests)
 
 ## 6. set up python binding ##
-add_subdirectory(python)
+#add_subdirectory(python)
 
 ## 7. add uninstall targets ##
 configure_file(

cmake/athena.cmake

@@ -19,5 +19,5 @@ set(patch_command
 
 set(PACKAGE_NAME athenapp)
 set(REPO_URL "https://github.com/chengcli/athenapp")
-set(REPO_TAG "6a612f4039ac08eacf92ce1644657fd0f340834f")
+set(REPO_TAG "f9d3ae8bb84cac6954e6a224cb84bc917450e43d")
 add_package(${PACKAGE_NAME} ${REPO_URL} ${REPO_TAG} "${patch_command}" ON)

cmake/fmt.cmake

@@ -0,0 +1,11 @@
+include(FetchContent)
+set(FETCHCONTENT_QUIET TRUE)
+
+set(PACKAGE_NAME fmt)
+set(REPO_URL "https://github.com/fmtlib/fmt")
+set(REPO_TAG "11.1.2")
+
+add_package(${PACKAGE_NAME} ${REPO_URL} ${REPO_TAG} "" ON)
+set(FMT_INCLUDE_DIR
+    "${CMAKE_CURRENT_BINARY_DIR}/_deps/${PACKAGE_NAME}-src/include"
+    CACHE PATH "fmt include directory")

cmake/gtest.cmake

@@ -7,3 +7,5 @@ set(REPO_TAG "v1.13.0")
 set(INSTALL_GTEST OFF)
 
 add_package(${PACKAGE_NAME} ${REPO_URL} ${REPO_TAG} "" ON)
+include_directories(${gtest_SOURCE_DIR}/include
+                    ${gtest_SOURCE_DIR}/googletest/include)

cmake/macros/macro_setup_problem.cmake

@@ -19,16 +19,24 @@ macro(setup_problem namel)
     ${namel}.${buildl}
     PRIVATE ${CMAKE_BINARY_DIR}
             ${CANOE_INCLUDE_DIR}
-            SYSTEM
             ${CANTERA_INCLUDE_DIR}
+            ${EIGEN3_INCLUDE_DIR}
+            ${MPI_CXX_HEADER_DIR}
+            ${MPI_CXX_INCLUDE_PATH}
+            ${NETCDF_INCLUDES}
+            ${PNETCDF_INCLUDE_DIR}
+            SYSTEM
+            ${TORCH_API_INCLUDE_DIR}
+            SYSTEM
+            ${TORCH_INCLUDE_DIR}
             SYSTEM
             ${EIGEN3_INCLUDE_DIR}
             SYSTEM
-            ${MPI_CXX_HEADER_DIR}
+            ${DISORT_INCLUDE_DIR}
             SYSTEM
-            ${MPI_CXX_INCLUDE_PATH}
+            ${HARP_INCLUDE_DIR}
             SYSTEM
-            ${NETCDF_INCLUDES}
+            ${KINTERA_INCLUDE_DIR}
             SYSTEM
-            ${PNETCDF_INCLUDE_DIR})
+            ${SNAP_INCLUDE_DIR})
 endmacro()

cmake/macros/macro_setup_test.cmake

@@ -6,15 +6,14 @@ macro(setup_test namel)
   string(TOLOWER ${CMAKE_BUILD_TYPE} buildl)
   string(TOUPPER ${CMAKE_BUILD_TYPE} buildu)
 
-  add_executable(${namel}.${buildl} ${namel}.cpp globals.cpp)
+  add_executable(${namel}.${buildl} ${namel}.cpp)
 
   set_target_properties(${namel}.${buildl}
                         PROPERTIES COMPILE_FLAGS ${CMAKE_CXX_FLAGS_${buildu}})
 
   target_include_directories(
     ${namel}.${buildl}
-    PRIVATE $<$<BOOL:${PVFMM}>:${PVFMM_SOURCE_DIR}/SCTL/include>
-            ${CMAKE_BINARY_DIR}
+    PRIVATE ${CMAKE_BINARY_DIR}
             ${CANOE_INCLUDE_DIR}
             ${EIGEN3_INCLUDE_DIR}
             ${MPI_CXX_INCLUDE_PATH}
@@ -23,16 +22,12 @@ macro(setup_test namel)
             ${PNETCDF_INCLUDE_DIR}
             ${OpenMP_CXX_INCLUDE_DIR}
             ${FFTW_INCLUDE_DIRS}
-            SYSTEM
             ${CANTERA_INCLUDE_DIR}
-            SYSTEM
             ${TORCH_INCLUDE_DIR}
-            SYSTEM
             ${TORCH_API_INCLUDE_DIR})
 
-  target_link_libraries(
-    ${namel}.${buildl} gtest_main $<$<BOOL:${PVFMM}>:pvfmmStatic>
-    ${CANOE_LIBRARY_${buildu}})
+  target_link_libraries(${namel}.${buildl} gtest_main
+                        ${CANOE_LIBRARY_${buildu}})
 
   add_test(NAME ${namel}.${buildl} COMMAND ${namel}.${buildl})
 endmacro()

cmake/modules/FindDisort.cmake

@@ -0,0 +1,103 @@
+# Find the disort includes and library
+#
+# DISORT_INCLUDE_DIR  - where to find disort.hpp
+#
+# DISORT_LIBRARY      - Link these libraries when using DISORT
+#
+# DISORT_FOUND        - True if DISORT found
+#
+# Normal usage would be:
+#
+# find_package(Disort REQUIRED) include_directories(${DISORT_INCLUDE_DIR})
+# target_link_libraries(${DISORT_LIBRARY})
+
+include(FindPackageHandleStandardArgs)
+
+macro(__disort_determine_version)
+  execute_process(
+    COMMAND ${Python3_EXECUTABLE} -c
+            "import pydisort; print(pydisort.__version__)"
+    OUTPUT_VARIABLE DISORT_PEP440_VERSION
+    OUTPUT_STRIP_TRAILING_WHITESPACE
+    RESULT_VARIABLE result)
+
+  if(result GREATER 0)
+    message(FATAL_ERROR "cannot determine PEP 440 version of Pydisort!")
+  endif()
+
+  if(DISORT_PEP440_VERSION MATCHES "^[0-9]+\.[0-9]+(\.[0-9]+)?")
+    set(DISORT_VERSION ${CMAKE_MATCH_0})
+  endif()
+
+  unset(result)
+endmacro()
+
+# Find Python
+set(Python3_FIND_VIRTUALENV ONLY)
+find_package(Python3 QUIET COMPONENTS Interpreter)
+if(Python3_Interpreter_FOUND)
+  execute_process(
+    COMMAND ${Python3_EXECUTABLE} -c "import pydisort; print(pydisort.__file__)"
+    OUTPUT_VARIABLE disort_init_file
+    OUTPUT_STRIP_TRAILING_WHITESPACE ERROR_QUIET)
+
+  cmake_path(CONVERT ${disort_init_file} TO_CMAKE_PATH_LIST disort_init_file
+             NORMALIZE)
+
+  cmake_path(REPLACE_FILENAME disort_init_file lib OUTPUT_VARIABLE
+             disort_lib_dir)
+  cmake_path(REPLACE_FILENAME disort_init_file disort OUTPUT_VARIABLE
+             disort_include_dir)
+
+  unset(disort_init_file)
+endif()
+
+# Step 1: Find header
+find_path(
+  _DISORT_HEADER_DIR disort.hpp
+  HINTS ${disort_include_dir}
+        /opt/homebrew/include
+        /usr/include
+        DISORT_DIR/include
+        DISORT_INC
+        $ENV{DISORT_INC}
+        $ENV{DISORT_DIR}/include
+        $ENV{DISORT_ROOT}/include)
+
+# Step 2: Go one level up from the header location
+get_filename_component(DISORT_INCLUDE_DIR ${_DISORT_HEADER_DIR} DIRECTORY)
+
+# Step 3: Save to cache
+set(DISORT_INCLUDE_DIR
+    "${DISORT_INCLUDE_DIR}"
+    CACHE FILEPATH "Path to a file.")
+
+# Step 4: unset the internal temp variable
+unset(_DISORT_HEADER_DIR CACHE)
+
+find_library(
+  DISORT_LIBRARY disort_release
+  HINTS ${disort_lib_dir}
+        /opt/homebrew/lib
+        /usr/lib/x86_64-linux-gnu/
+        DISORT_DIR/lib
+        DISORT_LIB
+        $ENV{DISORT_LIB}
+        $ENV{DISORT_DIR}/lib
+        $ENV{DISORT_ROOT}/lib)
+
+set(disort_required_vars DISORT_LIBRARY DISORT_INCLUDE_DIR)
+mark_as_advanced(${disort_required_vars})
+
+if(DISORT_LIBRARY)
+  __disort_determine_version()
+endif()
+
+find_package_handle_standard_args(
+  Disort
+  REQUIRED_VARS ${disort_required_vars}
+  VERSION_VAR DISORT_VERSION)
+
+unset(disort_lib_dir)
+unset(disort_include_dir)
+unset(disort_required_vars)