Merge branch 'develop' into feature/pcolarco/carbonChemLossUpd

# Conflicts:
#	CHANGELOG.md
#	ESMF/GOCART2G_GridComp/CA2G_GridComp/AMIP/CA2G_GridComp_ExtData.rc

.circleci/config.yml

@@ -1,11 +1,11 @@
 version: 2.1
 
-# Anchors to prevent forgetting to update a version
-baselibs_version: &baselibs_version v7.7.0
-bcs_version: &bcs_version v11.00.0
+# Anchors in case we need to override the defaults from the orb
+#baselibs_version: &baselibs_version v7.17.0
+#bcs_version: &bcs_version v11.3.0
 
 orbs:
-  ci: geos-esm/circleci-tools@1
+  ci: geos-esm/circleci-tools@2
 
 workflows:
   build-and-test:
@@ -18,7 +18,7 @@ workflows:
           matrix:
             parameters:
               compiler: [gfortran, ifort]
-          baselibs_version: *baselibs_version
+          #baselibs_version: *baselibs_version
           repo: GOCART
           buildtarget: GOCART2G_GridComp
           mepodevelop: true
@@ -32,7 +32,7 @@ workflows:
           matrix:
             parameters:
               compiler: [gfortran, ifort]
-          baselibs_version: *baselibs_version
+          #baselibs_version: *baselibs_version
           repo: GOCART
           buildtarget: GOCART2G_GridComp
           mepodevelop: true
@@ -47,7 +47,7 @@ workflows:
           matrix:
             parameters:
               compiler: [gfortran, ifort]
-          baselibs_version: *baselibs_version
+          #baselibs_version: *baselibs_version
           repo: GEOSgcm
           checkout_fixture: true
           mepodevelop: true

.github/workflows/validate_yaml_files.yml

@@ -24,7 +24,7 @@ jobs:
           format: colored
           config_file: .yamllint.yml
 
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v4
         if: always()
         with:
           name: yamllint-logfile

CHANGELOG.md

@@ -7,40 +7,73 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
-### Fixed
+### Removed
 
-### Added
+- Removed all ExtData.rc files
 
 ### Changed
 
-## [feature/pcolarco/CarbonChemLossUpd] - 2024-03-04
-
-### Changes
+- Modified the file paths in carbon, sulfate, and nitrate ExtData.yaml files to used the revised version of the CEDS anthropogenic emissions. Note the previous version has an incorrect seasonal cycle.
+- Sulfate surface area density calculation in SU_Compute_Diags was incorrectly being passed the effective radius used for settling along with the sigma width of the number distribution. Properly it should be passed the number median radius, also present in the RC file. Added a hook to read that field from the RC file ("particle_radius_number"), store in SU grid comp, and pass to SU_Compute_Diags. This change is zero-diff to the SU internal state. It changes value of export SO4AREA.
+- Changed DMS concentration data holder from ExtData provided (SU_DMSO) to local copy (dmso_conc). This is relevant since if we run source tagged instances where we don't want DMS emissions we would zero out dmso_conc and that is what should be passed to DMSemission subroutine. This is zero diff except in that case.
 - It changes the formulation of the hydrophobic to hydrophilic conversion for carbon species,
-now defined by a time scale specified in the instance RC file. This is now specified by providing 
-an e-folding time in days. This moves the time constant from outside the fortran to the run-time 
-configurable RC file. This is not quite zero-diff with original code because of the precision of 
+now defined by a time scale specified in the instance RC file. This is now specified by providing
+an e-folding time in days. This moves the time constant from outside the fortran to the run-time
+configurable RC file. This is not quite zero-diff with original code because of the precision of
 the specification, but testing shows nearly zero-diff result.
 
-- Also now present in the carbon instance RC files is a run-time configurable optional 
-parameterized loss rate (e-folding time in days) per species and per mode. Default value for all is 
-set to "-1" which means no use of this function. It has been tested separately for hydrophilic 
-brown carbon (-1 6.0) which favorably improves OA:BC ratio for southern African biomass burning. 
-This requires additional rescaling of BB emissions (increase scaling from 0.778->0.9 for BC and 
-0.778->1.25 for BR) to compensate for increased loss (in second case) and to improve simulation of 
-BC (in first case). This requires further testing before recommending configuration changes, but as 
+- Also now present in the carbon instance RC files is a run-time configurable optional
+parameterized loss rate (e-folding time in days) per species and per mode. Default value for all is
+set to "-1" which means no use of this function. It has been tested separately for hydrophilic
+brown carbon (-1 6.0) which favorably improves OA:BC ratio for southern African biomass burning.
+This requires additional rescaling of BB emissions (increase scaling from 0.778->0.9 for BC and
+0.778->1.25 for BR) to compensate for increased loss (in second case) and to improve simulation of
+BC (in first case). This requires further testing before recommending configuration changes, but as
 defined in default it is zero-diff.
 
+### Fixed
 
+- Use 'CA' component name to identify carbonaceous contributions to PM in UFS diagnostic calculations. These contributions were missing due to changes in field names.
+- Add replay import patch for ozone.
+- corrected reading variable 'rhod' from files ( it was mispelled as 'rhop')
+- Silenced unwarranted error messages from wavelength/channel retrieval functions occurring when 470nm and/or 870nm channels are not included in GOCART resource file.
+- Add explicit `find_package()` calls for missing dependencies for MAPL for builds with spack-stack. Will eventually be fixed in MAPL in later versions
+- Corrected the units of the gravimetric soil moisture to percent instead of fractional in the FENGSHA dust scheme.
+- Fix issue of GOCART/GEOSgcm circular CMake dependencies when used as external project
+- Fix UFS/Standalone CMake issue
 
-## [#263] - 2024-02-02
-
-### Changed
--Sulfate surface area density calculation in SU_Compute_Diags was incorrectly being passed the effective radius used for settling along with the sigma width of the number distribution. Properly it should be passed the number median radius, also present in the RC file. Added a hook to read that field from the RC file ("particle_radius_number"), store in SU grid comp, and pass to SU_Compute_Diags. This change is zero-diff to the SU internal state. It changes value of export SO4AREA.
-
--Add some protective logic around reading daily volcanic emission files. If filename does not exist model will write message to standard output and reset volcanic emissions to zero. This is zero difference result unless in a place where the files were not present.
+### Added
 
--Changed DMS concentration data holder from ExtData provided (SU_DMSO) to local copy (dmso_conc). This is relevant since if we run source tagged instances where we don't want DMS emissions we would zero out dmso_conc and that is what should be passed to DMSemission subroutine. This is zero diff except in that case.
+- Additional tuning parameters for the soil moisture and drylimit calculations for application specific tuning.
+- Required attributes for the 2D GOCART export fields in AERO_DP bundle have been set in subroutine append_to_bundle in Chem_AeroGeneric.F90. These export fields are imported by OBIO via Surface GC, and the missing of the attributes was causing the writing of surface import checkpoint to fail. The issue has been explained in detail on https://github.com/GEOS-ESM/GOCART/issues/258
+- Added export line to GOCART2G_GridCompMod to couple allow use of GOCART
+  SU sulfate production tendency elsewhere in Chemistry, specifically for
+  CARMA
+
+- Update ESMF CMake target to `ESMF::ESMF`
+
+- Changed SU2G_instance_SU.rc to now have separate filename inputs for explosive and degassing volcanoes
+- Moved present volcanic emission inventories to one or the other line for these new entries; set other
+  line /dev/null; this is stop gap until next time we update volcanic emission inventories, at which
+  point will provide (for AMIP and AMIP.20C) separate explosive and degassing emissions
+- Made accommodating changes for above in SU2G_GridCompMod.F90 and in the Process Library
+- Verified zero diff in current configuration (this is true of tracers and restarts, but not diagnostics:
+  until an actual split is made in the input emissions then the volcanic emissions are being assigned to
+  one or the other emission diagnostics (explosive or degassing).
+
+- Changed Chem_SettlingSimple in the process library to call Mie Query for radius and rhop inputs to the settling velocity calculation. The calls to Chem_SettlingSimple were then changed accordingly in each of the species' grid comps. Since the RH flag is no longer needed, it was removed from GA_EnvironmentMod.F90 and each of the instance RC files.
+- State Spec RC files for GOCART2G, CA, DU, NI, SU, and SS were updated such that the long names for AOD are more intuitive
+- Modified ExtData.yaml files to persist as climatological anthropogenic emissions after the end of the CEDS dataset in 2019. Analogous rc files removed as this capability is only available with ExtData2G
+- Update `components.yaml` to match that of GEOSgcm v11.6.1
+  - ESMA_env v4.29.0 (Baselibs 7.24.0, Updates for SLES15 at NCCS, various fixes)
+  - ESMA_cmake v3.48.0 (Fixes for NAS, debug flags, Updates for SLES15 at NCCS, MPI detection, ESMF and MPI CMake fixes for Spack)
+  - GMAO_Shared v1.9.8 (Bug fix for MITgcm, CI fixes, SLES15 Updates)
+  - MAPL 2.47.1 (Various fixes and features, support for Spack)
+- Update CI to use Baselibs by default from CircleCI Orb
+- Correct soil moisture parameterization in FENGSHA
+- Add `soil_moisture_factor` to the DU2G_instance_DU.rc (same name used in the K14 scheme) and DU2G_GridCompMod.F90 files for FENGSHA
+- Add `soil_drylimit_factor` to the DU2G_instance_DU.rc and DU2G_GridCompMod.F90 files for FENGSHA
+- Moved process library macros to header file.
 
 ## [v2.2.1] - 2023-05-30
 
@@ -65,8 +98,6 @@ defined in default it is zero-diff.
 - Fix issue with scattering coefficient calculation with oc
 - Fix a long standing issue that one can not start and stop the model in anything less than 3 hour increments to test start/stop regression because of GOCART.
 
-### Added
-
 ### Changed
 
 - Comment out ASSERT to allow `GOCART_DT` to not match the `HEARTBEAT_DT`

CMakeLists.txt

@@ -2,28 +2,51 @@ cmake_minimum_required (VERSION 3.17)
 cmake_policy (SET CMP0053 NEW)
 cmake_policy (SET CMP0054 NEW)
 
-project (
-        GOCART
-        VERSION 2.1.1
-        LANGUAGES Fortran CXX C)  # Note - CXX is required for ESMF
-
-if ("${PROJECT_SOURCE_DIR}" STREQUAL "${PROJECT_BINARY_DIR}")
-    message(SEND_ERROR "In-source builds are disabled. Please
-           issue cmake command in separate build directory.")
-endif ("${PROJECT_SOURCE_DIR}" STREQUAL "${PROJECT_BINARY_DIR}")
-
-# Set the default build type to release
-if (NOT CMAKE_BUILD_TYPE)
-    message (STATUS "Setting build type to 'Release' as none was specified.")
-    set (CMAKE_BUILD_TYPE Release CACHE STRING "Choose the type of build." FORCE)
-    # Set the possible values of build type for cmake-gui
-    set_property (CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS
-            "Debug" "Release" "MinSizeRel" "RelWithDebInfo")
-endif ()
+# Let's look for the ESMA cmake directory in a few places
+# to see if we are building standalone
+set (ESMA_CMAKE_DIRS
+  cmake
+  @cmake
+  cmake@
+  )
+
+foreach (dir IN LISTS ESMA_CMAKE_DIRS)
+  if (EXISTS ${CMAKE_CURRENT_LIST_DIR}/${dir})
+    list (APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_LIST_DIR}/${dir}")
+    set (ESMA_CMAKE_PATH "${CMAKE_CURRENT_LIST_DIR}/${dir}" CACHE PATH "Path to ESMA_cmake code")
+    set(GOCART_STANDALONE TRUE)
+  endif ()
+endforeach ()
 
 # Set build options
 option (UFS_GOCART "Build GOCART component for UFS" OFF)
 
+# Any UFS build of GOCART is by definition a standalone build
+if(UFS_GOCART)
+  set(GOCART_STANDALONE TRUE)
+endif()
+
+if (GOCART_STANDALONE)
+  project (
+          GOCART
+          VERSION 2.2.1
+          LANGUAGES Fortran CXX C)  # Note - CXX is required for ESMF
+
+  if ("${PROJECT_SOURCE_DIR}" STREQUAL "${PROJECT_BINARY_DIR}")
+      message(SEND_ERROR "In-source builds are disabled. Please
+            issue cmake command in separate build directory.")
+  endif ("${PROJECT_SOURCE_DIR}" STREQUAL "${PROJECT_BINARY_DIR}")
+
+  # Set the default build type to release
+  if (NOT CMAKE_BUILD_TYPE)
+      message (STATUS "Setting build type to 'Release' as none was specified.")
+      set (CMAKE_BUILD_TYPE Release CACHE STRING "Choose the type of build." FORCE)
+      # Set the possible values of build type for cmake-gui
+      set_property (CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS
+              "Debug" "Release" "MinSizeRel" "RelWithDebInfo")
+  endif ()
+endif()
+
 set (DOING_GEOS5 YES)
 
 # Should find a better place for this - used in Chem component
@@ -41,11 +64,12 @@ if (UFS_GOCART)
 endif()
 
 if (NOT COMMAND esma)
-    list (APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_LIST_DIR}/cmake@")
     include (esma)
 endif()
 
-ecbuild_declare_project()
+if(GOCART_STANDALONE)
+  ecbuild_declare_project()
+endif()
 
 if (NOT Baselibs_FOUND)
   # Find dependencies
@@ -61,6 +85,12 @@ endif ()
 
 if (UFS_GOCART)
   find_package (GFTL_SHARED REQUIRED)
+  # Dom Heinzeller 2023/08/30 - workaround until https://github.com/GEOS-ESM/MAPL/pull/2320
+  # is merged and finds its way into the ufs-weather-model dependency tree
+  find_package (YAFYAML QUIET)
+  find_package (FARGPARSE QUIET)
+  find_package (PFLOGGER QUIET)
+  #
   find_package (MAPL REQUIRED)
   include(mapl_acg)
 elseif (IS_DIRECTORY "${PROJECT_SOURCE_DIR}/ESMF/Shared/MAPL@")
@@ -81,7 +111,9 @@ include_directories(${MPI_Fortran_INCLUDE_PATH})
 add_subdirectory (ESMF)
 add_subdirectory (Process_Library)
 
-ecbuild_install_project (NAME GOCART)
+if(GOCART_STANDALONE)
+  ecbuild_install_project (NAME GOCART)
+endif()
 
 # https://www.scivision.dev/cmake-auto-gitignore-build-dir/
 # --- auto-ignore build directory

ESMF/Aerosol_GridComp/CMakeLists.txt

@@ -4,7 +4,7 @@ if (EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/Aerosol_GridComp.F90)
 
     esma_add_library (${this}
             SRCS Aerosol_GridComp.F90
-            DEPENDENCIES GOCART2G_GridComp MAPL esmf)
+            DEPENDENCIES GOCART2G_GridComp MAPL ESMF::ESMF)
 
     mapl_acg (${this} Aerosol_StateSpecs.rc
             IMPORT_SPECS EXPORT_SPECS INTERNAL_SPECS

ESMF/Apps/CMakeLists.txt

@@ -1,7 +1,7 @@
 esma_set_this ()
 
 set (srcs
-  GOCART2G_SimpleBundleMod.F90 
+  GOCART2G_SimpleBundleMod.F90
   aop_calculator.F90
   GOCART2G_AopMod.F90
   )
@@ -18,10 +18,10 @@ endforeach ()
 set (resource_files
    aop_calculator.rc
    )
-install( FILES ${resource_files} 
+install( FILES ${resource_files}
    DESTINATION etc
    )
-esma_add_library(${this} 
-  SRCS ${srcs} 
-  DEPENDENCIES MAPL Process_Library esmf NetCDF::NetCDF_Fortran
+esma_add_library(${this}
+  SRCS ${srcs}
+  DEPENDENCIES MAPL Process_Library ESMF::ESMF NetCDF::NetCDF_Fortran
   )