[codex] Embed CoLM2024 as MPAS land model

.gitignore

@@ -61,3 +61,4 @@ stream_list.*
 *.i90
 
 src/core_*/inc
+/build-cmake-colm-debug

CMakeLists.txt

@@ -22,13 +22,19 @@ option(MPAS_PROFILE "Enable GPTL profiling" OFF)
 option(MPAS_OPENMP "Enable OpenMP" OFF)
 option(BUILD_SHARED_LIBS "Build shared libraries" ON)
 option(MPAS_USE_PIO "Build with PIO I/O library" OFF)
+option(MPAS_COLM2024 "Build atmosphere core with embedded CoLM2024 land-surface physics" OFF)
+
+if(MPAS_COLM2024 AND NOT DO_PHYSICS)
+    message(FATAL_ERROR "MPAS_COLM2024 requires DO_PHYSICS=ON because CoLM2024 is built into the atmosphere physics driver.")
+endif()
 
 message(STATUS "[OPTION] MPAS_CORES: ${MPAS_CORES}")
 message(STATUS "[OPTION] MPAS_DOUBLE_PRECISION: ${MPAS_DOUBLE_PRECISION}")
 message(STATUS "[OPTION] MPAS_PROFILE: ${MPAS_PROFILE}")
 message(STATUS "[OPTION] MPAS_OPENMP: ${MPAS_OPENMP}")
 message(STATUS "[OPTION] BUILD_SHARED_LIBS: ${BUILD_SHARED_LIBS}")
 message(STATUS "[OPTION] MPAS_USE_PIO: ${MPAS_USE_PIO}")
+message(STATUS "[OPTION] MPAS_COLM2024: ${MPAS_COLM2024}")
 
 # Build product output locations
 set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
@@ -43,8 +49,11 @@ if(NOT CMAKE_BUILD_TYPE)
 endif()
 
 # Detect MPAS git version
+if(DEFINED GIT_EXECUTABLE AND NOT EXISTS "${GIT_EXECUTABLE}")
+    unset(GIT_EXECUTABLE CACHE)
+endif()
+find_package(Git QUIET)
 if(NOT MPAS_GIT_VERSION)
-    find_package(Git QUIET)
     if(GIT_FOUND)
         execute_process(COMMAND ${GIT_EXECUTABLE} describe --dirty
                         WORKING_DIRECTORY "${CMAKE_SOURCE_DIR}"
@@ -68,9 +77,11 @@ endif()
 find_package(MPI REQUIRED COMPONENTS Fortran)
 
 find_package(PnetCDF REQUIRED COMPONENTS Fortran)
+if(MPAS_USE_PIO OR MPAS_COLM2024)
+    find_package(NetCDF REQUIRED COMPONENTS Fortran C)
+endif()
 if(MPAS_USE_PIO)
     find_package(PIO REQUIRED COMPONENTS Fortran C)
-    find_package(NetCDF REQUIRED COMPONENTS Fortran C)
 endif()
 if(MPAS_PROFILE)
     find_package(GPTL REQUIRED)

Makefile

@@ -1029,6 +1029,13 @@ endif # END OF GIT DESCRIBE VERSION
 ####################################################
 # Section for adding external libraries and includes
 ####################################################
+ifeq "$(COLM2024)" "true"
+COLM2024_DIR ?= $(PWD)/src/core_atmosphere/physics/physics_colm2024
+override CPPFLAGS += -DMPAS_COLM2024
+COLM2024_MESSAGE = "MPAS was built with CoLM2024 from $(COLM2024_DIR)."
+else
+COLM2024_MESSAGE = "MPAS was not built with CoLM2024."
+endif
 ifdef MPAS_EXTERNAL_LIBS
 	override LIBS += $(MPAS_EXTERNAL_LIBS)
 endif
@@ -1573,6 +1580,7 @@ mpas_main: $(MAIN_DEPS)
 	@echo $(OPENMP_OFFLOAD_MESSAGE)
 	@echo $(OPENACC_MESSAGE)
 	@echo $(MUSICA_MESSAGE)
+	@echo $(COLM2024_MESSAGE)
 	@echo $(SCOTCH_MESSAGE)
 	@echo $(SHAREDLIB_MESSAGE)
 ifeq "$(AUTOCLEAN)" "true"
@@ -1648,4 +1656,3 @@ errmsg:
 ifdef CORE
 	exit 1
 endif
-

cmake/Functions/MPAS_Functions.cmake

@@ -148,7 +148,8 @@ function(mpas_fortran_target target)
 endfunction()
 
 
-# mpas_core_target(CORE <core-name> TARGET <cmake-target-name> INCLUDE <file1.inc, ...> )
+# mpas_core_target(CORE <core-name> TARGET <cmake-target-name>
+#                  INCLUDES <file1.inc, ...> REGISTRY_DEPENDS <file1.xml, ...> )
 #
 # Common configuration and properties for `MPAS::core::<core_name>` targets.
 # * Calls mpas_fortran_target() for common Fortran target configuration.
@@ -164,9 +165,10 @@ endfunction()
 #   CORE - Name of core
 #   TARGET - Name of core_target (without namespace)
 #   INCLUDES - List of generated include files
+#   REGISTRY_DEPENDS - Files included by the core Registry.xml preprocessor input
 #
 function(mpas_core_target)
-    cmake_parse_arguments(ARG "" "CORE;TARGET" "INCLUDES" ${ARGN})
+    cmake_parse_arguments(ARG "" "CORE;TARGET" "INCLUDES;REGISTRY_DEPENDS" ${ARGN})
 
     mpas_fortran_target(${ARG_TARGET})
 
@@ -214,25 +216,26 @@ function(mpas_core_target)
     if (${DO_PHYSICS})
         set(CPP_EXTRA_FLAGS ${CPP_EXTRA_FLAGS} -DDO_PHYSICS)
     endif()
+    set(REGISTRY_PROCESSED_XML ${CMAKE_CURRENT_BINARY_DIR}/Registry_processed.xml)
 
-add_custom_command(OUTPUT Registry_processed.xml
-            COMMAND ${CPP_EXECUTABLE} -E -P ${CPP_EXTRA_FLAGS} ${CMAKE_CURRENT_SOURCE_DIR}/Registry.xml > Registry_processed.xml
+add_custom_command(OUTPUT ${REGISTRY_PROCESSED_XML}
+            COMMAND ${CPP_EXECUTABLE} -E -P ${CPP_EXTRA_FLAGS} ${CMAKE_CURRENT_SOURCE_DIR}/Registry.xml > ${REGISTRY_PROCESSED_XML}
             COMMENT "CORE ${ARG_CORE}: Pre-Process Registry"
-            DEPENDS Registry.xml)
+            DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/Registry.xml ${ARG_REGISTRY_DEPENDS})
     add_custom_command(OUTPUT ${ARG_INCLUDES}
-            COMMAND mpas_parse_${ARG_CORE} Registry_processed.xml ${CPP_EXTRA_FLAGS}
+            COMMAND mpas_parse_${ARG_CORE} ${REGISTRY_PROCESSED_XML} ${CPP_EXTRA_FLAGS}
             COMMENT "CORE ${ARG_CORE}: Parse Registry"
-            DEPENDS mpas_parse_${ARG_CORE} Registry_processed.xml)
+            DEPENDS mpas_parse_${ARG_CORE} ${REGISTRY_PROCESSED_XML})
     add_custom_command(OUTPUT namelist.${ARG_CORE}
             WORKING_DIRECTORY ${CORE_DATADIR}
-            COMMAND mpas_namelist_gen ${CMAKE_CURRENT_BINARY_DIR}/Registry_processed.xml namelist.${ARG_CORE} in_defaults=true
+            COMMAND mpas_namelist_gen ${REGISTRY_PROCESSED_XML} namelist.${ARG_CORE} in_defaults=true
             COMMENT "CORE ${ARG_CORE}: Generate Namelist"
-            DEPENDS mpas_namelist_gen Registry_processed.xml)
+            DEPENDS mpas_namelist_gen ${REGISTRY_PROCESSED_XML})
     add_custom_command(OUTPUT streams.${ARG_CORE}
             WORKING_DIRECTORY ${CORE_DATADIR}
-            COMMAND mpas_streams_gen ${CMAKE_CURRENT_BINARY_DIR}/Registry_processed.xml streams.${ARG_CORE} stream_list.${ARG_CORE}. listed
+            COMMAND mpas_streams_gen ${REGISTRY_PROCESSED_XML} streams.${ARG_CORE} stream_list.${ARG_CORE}. listed
             COMMENT "CORE ${ARG_CORE}: Generate Streams"
-            DEPENDS mpas_streams_gen Registry_processed.xml)
+            DEPENDS mpas_streams_gen ${REGISTRY_PROCESSED_XML})
     add_custom_target(gen_${ARG_CORE} DEPENDS ${ARG_INCLUDES} namelist.${ARG_CORE} streams.${ARG_CORE})
     add_dependencies(${ARG_TARGET} gen_${ARG_CORE})
 

src/core_atmosphere/CMakeLists.txt

@@ -35,6 +35,7 @@ set(ATMOSPHERE_CORE_PHYSICS_SOURCES
     mpas_atmphys_driver_sfclayer.F
     mpas_atmphys_init.F
     mpas_atmphys_lsm_shared.F
+    mpas_atmphys_driver_lsm_colm2024.F
     mpas_atmphys_packages.F
     mpas_atmphys_todynamics.F
     mpas_atmphys_vars.F
@@ -298,6 +299,146 @@ set(ATMOSPHERE_CORE_PHYSICS_NOAMP_SRC_SOURCES
 )
 list(TRANSFORM ATMOSPHERE_CORE_PHYSICS_NOAMP_SRC_SOURCES PREPEND physics/physics_noahmp/src/)
 
+if(MPAS_COLM2024)
+    set(COLM2024_SOURCE_ROOT ${CMAKE_CURRENT_SOURCE_DIR}/physics/physics_colm2024)
+    set_property(DIRECTORY APPEND PROPERTY CMAKE_CONFIGURE_DEPENDS
+        ${COLM2024_SOURCE_ROOT}/include/define.h)
+    set(COLM2024_SOURCE_SEARCH_DIRS
+        share
+        main
+        main/HYDRO
+        main/BGC
+        main/URBAN
+        main/DA
+        main/ParaOpt
+        drivers/mpas
+    )
+    foreach(_colm2024_dir IN LISTS COLM2024_SOURCE_SEARCH_DIRS)
+        file(GLOB _colm2024_dir_sources CONFIGURE_DEPENDS
+            ${COLM2024_SOURCE_ROOT}/${_colm2024_dir}/*.F90)
+        list(APPEND COLM2024_SOURCE_CANDIDATES ${_colm2024_dir_sources})
+    endforeach()
+    list(REMOVE_DUPLICATES COLM2024_SOURCE_CANDIDATES)
+    list(SORT COLM2024_SOURCE_CANDIDATES)
+    foreach(_colm2024_src IN LISTS COLM2024_SOURCE_CANDIDATES)
+        file(RELATIVE_PATH _colm2024_src_rel ${CMAKE_CURRENT_SOURCE_DIR} ${_colm2024_src})
+        execute_process(
+            COMMAND ${CPP_EXECUTABLE} -traditional-cpp -P -I${COLM2024_SOURCE_ROOT}/include ${_colm2024_src}
+            OUTPUT_VARIABLE _colm2024_preprocessed_src
+            ERROR_VARIABLE _colm2024_preprocess_error
+            RESULT_VARIABLE _colm2024_preprocess_result
+        )
+        if(NOT _colm2024_preprocess_result EQUAL 0)
+            message(FATAL_ERROR "Could not preprocess CoLM2024 source ${_colm2024_src}: ${_colm2024_preprocess_error}")
+        endif()
+        string(TOUPPER "${_colm2024_preprocessed_src}" _colm2024_preprocessed_src_upper)
+        if(NOT "${_colm2024_preprocessed_src_upper}" MATCHES "(^|\n)[ \t]*(MODULE|SUBROUTINE|FUNCTION|PROGRAM)[ \t]+[A-Z0-9_]+")
+            list(APPEND ATMOSPHERE_CORE_PHYSICS_COLM2024_SKIPPED_EMPTY_SOURCES ${_colm2024_src_rel})
+            continue()
+        endif()
+        list(APPEND COLM2024_AVAILABLE_SOURCES ${_colm2024_src_rel})
+        string(REGEX MATCHALL "(^|\n)[ \t]*MODULE[ \t]+[A-Z][A-Z0-9_]*" _colm2024_module_lines
+            "${_colm2024_preprocessed_src_upper}")
+        foreach(_colm2024_module_line IN LISTS _colm2024_module_lines)
+            if(_colm2024_module_line MATCHES "MODULE[ \t]+PROCEDURE")
+                continue()
+            endif()
+            string(REGEX REPLACE ".*MODULE[ \t]+([A-Z][A-Z0-9_]*).*" "\\1" _colm2024_module_name
+                "${_colm2024_module_line}")
+            set(COLM2024_MODULE_SOURCE_${_colm2024_module_name} ${_colm2024_src_rel})
+        endforeach()
+        string(REGEX MATCHALL "(^|\n)[ \t]*USE[^\n]*" _colm2024_use_lines
+            "${_colm2024_preprocessed_src_upper}")
+        set(_colm2024_source_uses)
+        foreach(_colm2024_use_line IN LISTS _colm2024_use_lines)
+            if(_colm2024_use_line MATCHES "INTRINSIC")
+                continue()
+            endif()
+            if(_colm2024_use_line MATCHES "USE[ \t]*(,[^:]*)?(::)?[ \t]*([A-Z][A-Z0-9_]*)")
+                list(APPEND _colm2024_source_uses ${CMAKE_MATCH_3})
+            endif()
+        endforeach()
+        if(_colm2024_source_uses)
+            list(REMOVE_DUPLICATES _colm2024_source_uses)
+        endif()
+        string(MAKE_C_IDENTIFIER "${_colm2024_src_rel}" _colm2024_src_key)
+        set(COLM2024_SOURCE_USES_${_colm2024_src_key} ${_colm2024_source_uses})
+    endforeach()
+    set(ATMOSPHERE_CORE_PHYSICS_COLM2024_SOURCES
+        physics/physics_colm2024/drivers/mpas/MOD_CoLM_MPAS_Interface.F90
+        physics/physics_colm2024/main/CoLMDRIVER.F90
+        physics/physics_colm2024/main/CoLMMAIN.F90
+        physics/physics_colm2024/main/MOD_MonthlyinSituCO2MaunaLoa.F90
+    )
+    foreach(_colm2024_root IN LISTS ATMOSPHERE_CORE_PHYSICS_COLM2024_SOURCES)
+        if(NOT "${_colm2024_root}" IN_LIST COLM2024_AVAILABLE_SOURCES)
+            message(FATAL_ERROR "Required embedded CoLM2024 source is unavailable: ${_colm2024_root}")
+        endif()
+    endforeach()
+
+    set(_colm2024_previous_source_count -1)
+    list(LENGTH ATMOSPHERE_CORE_PHYSICS_COLM2024_SOURCES _colm2024_source_count)
+    while(NOT _colm2024_previous_source_count EQUAL _colm2024_source_count)
+        set(_colm2024_previous_source_count ${_colm2024_source_count})
+        foreach(_colm2024_src IN LISTS ATMOSPHERE_CORE_PHYSICS_COLM2024_SOURCES)
+            string(MAKE_C_IDENTIFIER "${_colm2024_src}" _colm2024_src_key)
+            foreach(_colm2024_use IN LISTS COLM2024_SOURCE_USES_${_colm2024_src_key})
+                if(DEFINED COLM2024_MODULE_SOURCE_${_colm2024_use})
+                    list(APPEND ATMOSPHERE_CORE_PHYSICS_COLM2024_SOURCES
+                        ${COLM2024_MODULE_SOURCE_${_colm2024_use}})
+                endif()
+            endforeach()
+        endforeach()
+        list(REMOVE_DUPLICATES ATMOSPHERE_CORE_PHYSICS_COLM2024_SOURCES)
+        list(LENGTH ATMOSPHERE_CORE_PHYSICS_COLM2024_SOURCES _colm2024_source_count)
+    endwhile()
+    list(SORT ATMOSPHERE_CORE_PHYSICS_COLM2024_SOURCES)
+
+    list(LENGTH ATMOSPHERE_CORE_PHYSICS_COLM2024_SKIPPED_EMPTY_SOURCES _colm2024_skipped_empty_count)
+    list(LENGTH COLM2024_AVAILABLE_SOURCES _colm2024_available_source_count)
+    message(STATUS "CoLM2024 embedded CMake sources: ${_colm2024_source_count} of ${_colm2024_available_source_count}")
+    message(STATUS "CoLM2024 embedded CMake skipped empty sources: ${_colm2024_skipped_empty_count}")
+
+    function(_colm2024_object_path out source)
+        set(${out} "${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/core_atmosphere.dir/${source}.o" PARENT_SCOPE)
+    endfunction()
+
+    function(_colm2024_source_depends source)
+        if(NOT "${source}" IN_LIST ATMOSPHERE_CORE_PHYSICS_COLM2024_SOURCES)
+            return()
+        endif()
+        set(_colm2024_deps)
+        foreach(_colm2024_dep IN LISTS ARGN)
+            if(NOT "${_colm2024_dep}" IN_LIST ATMOSPHERE_CORE_PHYSICS_COLM2024_SOURCES)
+                continue()
+            endif()
+            _colm2024_object_path(_colm2024_dep_obj ${_colm2024_dep})
+            list(APPEND _colm2024_deps ${_colm2024_dep_obj})
+        endforeach()
+        if(_colm2024_deps)
+            set_property(SOURCE ${source} APPEND PROPERTY OBJECT_DEPENDS "${_colm2024_deps}")
+        endif()
+    endfunction()
+
+    foreach(_colm2024_src IN LISTS ATMOSPHERE_CORE_PHYSICS_COLM2024_SOURCES)
+        string(MAKE_C_IDENTIFIER "${_colm2024_src}" _colm2024_src_key)
+        set(_colm2024_dep_sources)
+        set(_colm2024_source_uses ${COLM2024_SOURCE_USES_${_colm2024_src_key}})
+        foreach(_colm2024_use IN LISTS _colm2024_source_uses)
+            if(DEFINED COLM2024_MODULE_SOURCE_${_colm2024_use})
+                set(_colm2024_dep_source ${COLM2024_MODULE_SOURCE_${_colm2024_use}})
+                if(NOT _colm2024_dep_source STREQUAL _colm2024_src)
+                    list(APPEND _colm2024_dep_sources ${_colm2024_dep_source})
+                endif()
+            endif()
+        endforeach()
+        if(_colm2024_dep_sources)
+            list(REMOVE_DUPLICATES _colm2024_dep_sources)
+            _colm2024_source_depends(${_colm2024_src} ${_colm2024_dep_sources})
+        endif()
+    endforeach()
+endif()
+
 # diagnostics/
 set(ATMOSPHERE_CORE_DIAGNOSTIC_SOURCES
     mpas_atm_diagnostic_template.F
@@ -351,6 +492,7 @@ add_library(core_atmosphere ${ATMOSPHERE_CORE_SOURCES}
             ${ATMOSPHERE_CORE_PHYSICS_NOAMP_UTILITY_SOURCES}
             ${ATMOSPHERE_CORE_PHYSICS_NOAMP_MPAS_DRIVER_SOURCES}
             ${ATMOSPHERE_CORE_PHYSICS_NOAMP_SRC_SOURCES}
+            ${ATMOSPHERE_CORE_PHYSICS_COLM2024_SOURCES}
             ${ATMOSPHERE_CORE_PHYSICS_SOURCES}
             ${ATMOSPHERE_CORE_PHYSICS_MMM_SOURCES}
             ${ATMOSPHERE_CORE_PHYSICS_WRF_SOURCES}
@@ -365,9 +507,35 @@ set(CORE_ATMOSPHERE_COMPILE_DEFINITIONS
 if (${DO_PHYSICS})
     list(APPEND CORE_ATMOSPHERE_COMPILE_DEFINITIONS DO_PHYSICS)
 endif ()
+if (MPAS_COLM2024)
+    list(APPEND CORE_ATMOSPHERE_COMPILE_DEFINITIONS MPAS_COLM2024)
+endif ()
 target_compile_definitions(core_atmosphere PRIVATE ${CORE_ATMOSPHERE_COMPILE_DEFINITIONS})
+if (MPAS_COLM2024)
+    target_include_directories(core_atmosphere PRIVATE ${COLM2024_SOURCE_ROOT}/include)
+    target_link_libraries(core_atmosphere PUBLIC NetCDF::NetCDF_Fortran NetCDF::NetCDF_C)
+    set_property(SOURCE ${ATMOSPHERE_CORE_PHYSICS_COLM2024_SOURCES}
+                 PROPERTY Fortran_PREPROCESS ON)
+    if(CMAKE_Fortran_COMPILER_ID MATCHES GNU)
+        set(_colm2024_compile_options -fdefault-real-8 -ffree-line-length-none)
+    elseif(CMAKE_Fortran_COMPILER_ID MATCHES Intel)
+        set(_colm2024_compile_options -real-size 64)
+    elseif(CMAKE_Fortran_COMPILER_ID MATCHES NVHPC)
+        set(_colm2024_compile_options -r8)
+    endif()
+    if(_colm2024_compile_options)
+        set_property(SOURCE ${ATMOSPHERE_CORE_PHYSICS_COLM2024_SOURCES}
+                     APPEND PROPERTY COMPILE_OPTIONS ${_colm2024_compile_options})
+    endif()
+endif ()
 set_MPAS_DEBUG_flag(core_atmosphere)
-mpas_core_target(CORE atmosphere TARGET core_atmosphere INCLUDES ${ATMOSPHERE_CORE_INCLUDES})
+set(ATMOSPHERE_REGISTRY_DEPENDS
+    ${CMAKE_CURRENT_SOURCE_DIR}/diagnostics/Registry_diagnostics.xml
+    ${CMAKE_CURRENT_SOURCE_DIR}/physics/Registry_noahmp.xml
+    ${CMAKE_CURRENT_SOURCE_DIR}/physics/Registry_colm2024.xml)
+mpas_core_target(CORE atmosphere TARGET core_atmosphere
+                 INCLUDES ${ATMOSPHERE_CORE_INCLUDES}
+                 REGISTRY_DEPENDS ${ATMOSPHERE_REGISTRY_DEPENDS})
 
 #Get physics_wrf tables from MPAS-Data
 include(FetchContent)

src/core_atmosphere/Makefile

@@ -48,13 +48,15 @@ post_build:
 
 physcore: mpas_atm_dimensions.o
 	( cd physics; $(MAKE) all )
+	$(RM) -r libphys
 	( mkdir libphys; cd libphys; ar -x ../physics/libphys.a )
 	( cd ../..; ln -sf ./src/core_atmosphere/physics/physics_wrf/files/*TBL .)
 	( cd ../..; ln -sf ./src/core_atmosphere/physics/physics_wrf/files/*DATA* .)
 	( cd ../..; ln -sf ./src/core_atmosphere/physics/physics_noahmp/parameters/*TBL .)
 
 chemcore:
 	( cd chemistry; $(MAKE) all CHEMISTRY="$(CHEMISTRY)" )
+	$(RM) -r libchem
 	( mkdir libchem; cd libchem; ar -x ../chemistry/libchem.a )
 
 dycore: mpas_atm_dimensions.o $(PHYSCORE) $(CHEMCORE)
@@ -67,6 +69,7 @@ utilities: $(PHYSCORE)
 	( cd utils; $(MAKE) all PHYSICS="$(PHYSICS)" )
 
 atmcore: $(PHYSCORE) dycore diagcore $(OBJS)
+	$(RM) libdycore.a
 	ar -ru libdycore.a $(OBJS) dynamics/*.o $(PHYS_OBJS) $(CHEM_OBJS) diagnostics/*.o
 
 mpas_atm_core_interface.o: mpas_atm_core.o