Merge branch 'develop' into bugfix/acollow/#280-cedspathsforg2gdevelop

CHANGELOG.md

@@ -8,35 +8,55 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Removed
 
 - Removed all ExtData.rc files
+
 ### Changed
 - 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.
+
+
+## [Unreleased] - 2024-05-14
+
+### Added
+
+- 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  
+
+
 ## [Unreleased] - 2023-07-24
 
+
 ### Fixed
 
+
+- 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
 
 ### Added
 
 - Additional tuning parameters for the soil moisture and drylimit calculations for application specific tuning.
 
 ### Changed
--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 v11.3.3
-  - ESMA_env v4.20.6 (Baselibs 7.14.0, Updates for SLES15 at NCCS)
-  - ESMA_cmake v3.36.0 (Fixes for NAS, debug flags, Updates for SLES15 at NCCS)
-  - GMAO_Shared v1.9.6 (Bug fix for MITgcm, CI fixes, SLES15 Updates)
-  - MAPL 2.42.0 (Various fixes and features)
+- 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
 
 ### Fixed

CMakeLists.txt

@@ -2,24 +2,42 @@ cmake_minimum_required (VERSION 3.17)
 cmake_policy (SET CMP0053 NEW)
 cmake_policy (SET CMP0054 NEW)
 
-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 ()
+# 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 ()
+
+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 build options
 option (UFS_GOCART "Build GOCART component for UFS" OFF)
@@ -41,11 +59,12 @@ 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
@@ -87,7 +106,9 @@ 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/GOCART2G_GridComp/CA2G_GridComp/CA2G_StateSpecs.rc

@@ -97,10 +97,10 @@ category: EXPORT
  *PSOA        | kg m-2 s-1   | xy    | N     |                                | * Aerosol SOA Production
  *SMASS       | kg m-3       | xy    | N     |                                | * Aerosol Surface Mass Concentration
  *CMASS       | kg m-2       | xy    | N     |                                | * Aerosol Column Mass Density
- *EXTTAU      | 1            | xy    | N     | size(self%wavelengths_vertint) | * Aerosol Extinction AOT
- *STEXTTAU    | 1            | xy    | N     | size(self%wavelengths_vertint) | * Aerosol Extinction AOT Stratosphere
- *SCATAU      | 1            | xy    | N     | size(self%wavelengths_vertint) | * Aerosol Scattering AOT
- *STSCATAU    | 1            | xy    | N     | size(self%wavelengths_vertint) | * Aerosol Scattering AOT Stratosphere
+ *EXTTAU      | 1            | xy    | N     | size(self%wavelengths_vertint) | * Aerosol Optical Depth
+ *STEXTTAU    | 1            | xy    | N     | size(self%wavelengths_vertint) | * Stratospheric Aerosol Optical Thickness
+ *SCATAU      | 1            | xy    | N     | size(self%wavelengths_vertint) | * Aerosol Optical Depth Due to Scattering
+ *STSCATAU    | 1            | xy    | N     | size(self%wavelengths_vertint) | * Stratospheric Aerosol Optical Thickness Due to Scattering
  *ANGSTR      | 1            | xy    | N     |                                | * Aerosol Angstrom parameter [470-870 nm]
  *FLUXU       | kg m-1 s-1   | xy    | N     |                                | * Aerosol column u-wind mass flux
  *FLUXV       | kg m-1 s-1   | xy    | N     |                                | * Aerosol column v-wind mass flux

ESMF/GOCART2G_GridComp/DU2G_GridComp/DU2G_StateSpecs.rc

@@ -71,19 +71,19 @@ category: EXPORT
 #........................................................................................
  DUSMASS       | kg m-3     | xy   | N    |                                | Dust Surface Mass Concentration
  DUCMASS       | kg m-2     | xy   | N    |                                | Dust Column Mass Density
- DUEXTTAU      | 1          | xy   | N    | size(self%wavelengths_vertint) | Dust Extinction AOT
- DUSTEXTTAU    | 1          | xy   | N    | size(self%wavelengths_vertint) | Dust Extinction AOT Stratosphere
- DUSCATAU      | 1          | xy   | N    | size(self%wavelengths_vertint) | Dust Scattering AOT
- DUSTSCATAU    | 1          | xy   | N    | size(self%wavelengths_vertint) | Dust Scattering AOT Stratosphere
- DUSMASS25     | kg m-3     | xy   | N    |                                | Dust Surface Mass Concentration - PM 2.5
- DUCMASS25     | kg m-2     | xy   | N    |                                | Dust Column Mass Density - PM 2.5
- DUEXTT25      | 1          | xy   | N    | size(self%wavelengths_vertint) | Dust Extinction AOT - PM 2.5
- DUSCAT25      | 1          | xy   | N    | size(self%wavelengths_vertint) | Dust Scattering AOT - PM 2.5
+ DUEXTTAU      | 1          | xy   | N    | size(self%wavelengths_vertint) | Dust Aerosol Optical Depth
+ DUSTEXTTAU    | 1          | xy   | N    | size(self%wavelengths_vertint) | Dust Stratospheric Aerosol Optical Thickness
+ DUSCATAU      | 1          | xy   | N    | size(self%wavelengths_vertint) | Dust Aerosol Optical Depth Due to Scattering
+ DUSTSCATAU    | 1          | xy   | N    | size(self%wavelengths_vertint) | Dust Stratospheric Aerosol Optical Thickness Due to Scattering
+ DUSMASS25     | kg m-3     | xy   | N    |                                | Dust Surface Mass Concentration of Particulate Matter < 2.5 microns (PM 2.5)
+ DUCMASS25     | kg m-2     | xy   | N    |                                | Dust Column Mass Density of Particulate Matter < 2.5 microns (PM 2.5)
+ DUEXTT25      | 1          | xy   | N    | size(self%wavelengths_vertint) | Dust Aerosol Optical Depth from Particulate Matter < 2.5 microns (PM2.5)
+ DUSCAT25      | 1          | xy   | N    | size(self%wavelengths_vertint) | Dust Aerosol Optical Depth Due to Scattering from Particulate Matter < 2.5 microns (PM2.5)
  DUAERIDX      | 1          | xy   | N    |                                | Dust TOMS UV Aerosol Index
  DUFLUXU       | kg m-1 s-1 | xy   | N    |                                | Dust column u-wind mass flux
  DUFLUXV       | kg m-1 s-1 | xy   | N    |                                | Dust column v-wind mass flux
- DUEXTTFM      | 1          | xy   | N    | size(self%wavelengths_vertint) | Dust Extinction AOT - PM 1.0 um
- DUSCATFM      | 1          | xy   | N    | size(self%wavelengths_vertint) | Dust Scattering AOT - PM 1.0 um
+ DUEXTTFM      | 1          | xy   | N    | size(self%wavelengths_vertint) | Dust Aerosol Optical Depth from Particulate Matter < 1 micron (PM1.0)
+ DUSCATFM      | 1          | xy   | N    | size(self%wavelengths_vertint) | Dust Aerosol Optical Depth Due to Scattering from Particulate Matter < 1 micron (PM1.0)
  DUANGSTR      | 1          | xy   | N    |                                | Dust Angstrom parameter [470-870 nm]
  DUEM          | kg m-2 s-1 | xy   | N    | self%nbins                     | Dust Emission (Bin %d)
  DUSD          | kg m-2 s-1 | xy   | N    | self%nbins                     | Dust Sedimentation (Bin %d)

ESMF/GOCART2G_GridComp/GOCART2G_StateSpecs.rc

@@ -21,14 +21,14 @@ category: EXPORT
 #----------------------------------------------------------------------------------------
  PSO4TOT        | kg m-2 s-1 | xyz  | C    |                                | Total Sulfate Produced in GOCART
 #........................................................................................
- TOTEXTTAU      | 1          | xy   | N    | size(self%wavelengths_vertint) | Total Aerosol Extinction AOT [550 nm]
- TOTSTEXTTAU    | 1          | xy   | N    | size(self%wavelengths_vertint) | Total Aerosol Extinction AOT [550 nm] Stratosphere
- TOTSCATAU      | 1          | xy   | N    | size(self%wavelengths_vertint) | Total Aerosol Scattering AOT [550 nm]
- TOTSTSCATAU    | 1          | xy   | N    | size(self%wavelengths_vertint) | Total Aerosol Scattering AOT [550 nm] Stratosphere
- TOTEXTT25      | 1          | xy   | N    | size(self%wavelengths_vertint) | Total Aerosol Extinction AOT [550 nm] - PM2.5
- TOTSCAT25      | 1          | xy   | N    | size(self%wavelengths_vertint) | Total Aerosol Extinction AOT [550 nm] - PM2.5
- TOTEXTTFM      | 1          | xy   | N    | size(self%wavelengths_vertint) | Total Aerosol Extinction AOT [550 nm] - PM1.0
- TOTSCATFM      | 1          | xy   | N    | size(self%wavelengths_vertint) | Total Aerosol Extinction AOT [550 nm] - PM1.0
+ TOTEXTTAU      | 1          | xy   | N    | size(self%wavelengths_vertint) | Total Aerosol Optical Depth at 550 nm
+ TOTSTEXTTAU    | 1          | xy   | N    | size(self%wavelengths_vertint) | Total Stratospheric Aerosol Optical Thickness at 550 nm
+ TOTSCATAU      | 1          | xy   | N    | size(self%wavelengths_vertint) | Total Aerosol Optical Depth at 550 nm Due to Scattering
+ TOTSTSCATAU    | 1          | xy   | N    | size(self%wavelengths_vertint) | Total Stratospheric Aerosol Optical Thickness at 550 nm Due to Scattering
+ TOTEXTT25      | 1          | xy   | N    | size(self%wavelengths_vertint) | Total Aerosol Optical Depth at 550 nm from Particluate Matter < 2.5 microns  (PM2.5)
+ TOTSCAT25      | 1          | xy   | N    | size(self%wavelengths_vertint) | Total Aerosol Optical Depth at 550 nm Due to Scattering from Particulate Matter < 2.5 microns (PM2.5)
+ TOTEXTTFM      | 1          | xy   | N    | size(self%wavelengths_vertint) | Total Aerosol Optical Depth at 550 nm from Particluate Matter < 1 micron  (PM1.0)
+ TOTSCATFM      | 1          | xy   | N    | size(self%wavelengths_vertint) | Total Aerosol Optical Depth at 550 nm Due to Scattering from Particulate Matter < 1 micron (PM1.0)
  TOTANGSTR      | 1          | xy   | N    |            | Total Aerosol Angstrom parameter [470-870 nm]
  TOTEXTCOEF     | m-1        | xyz  | C    | size(self%wavelengths_profile) | Total Aerosol Extinction coefficient
  TOTEXTCOEFRH20 | m-1        | xyz  | C    | size(self%wavelengths_profile) | Total Aerosol Extinction coefficient - Fixed RH=20%
@@ -39,12 +39,12 @@ category: EXPORT
  TOTBCKCOEF     | m-1 sr-1   | xyz  | C    | size(self%wavelengths_profile) | Total Aerosol Single Scattering Backscatter coefficient
  TOTABCKTOA     | m-1 sr-1   | xyz  | C    |                                | Total Attenuated Backscatter Coefficient from TOA [532nm]
  TOTABCKSFC     | m-1 sr-1   | xyz  | C    |                                | Total Attenuated Backscatter Coefficient from surface [532nm]
- PM             | kg m-3     | xy   | N    |            | Total reconstructed PM
- PM_RH35        | kg m-3     | xy   | N    |            | Total reconstructed PM(RH=35%)
- PM_RH50        | kg m-3     | xy   | N    |            | Total reconstructed PM(RH=50%)
- PM25           | kg m-3     | xy   | N    |            | Total reconstructed PM2.5
- PM25_RH35      | kg m-3     | xy   | N    |            | Total reconstructed PM2.5(RH=35%)
- PM25_RH50      | kg m-3     | xy   | N    |            | Total reconstructed PM2.5(RH=50%)
+ PM             | kg m-3     | xy   | N    |            | Total Reconstructed Dry Particulate Matter
+ PM_RH35        | kg m-3     | xy   | N    |            | Total Reconstructed Particulate Matter at 35% Relative Humidity
+ PM_RH50        | kg m-3     | xy   | N    |            | Total Reconstructed Particulate Matter at 50% Relative Humidity
+ PM25           | kg m-3     | xy   | N    |            | Total Reconstructed Dry Particulate Matter < 2.5 microns (PM2.5)
+ PM25_RH35      | kg m-3     | xy   | N    |            | Total Reconstructed Particulate Matter < 2.5 microns (PM2.5) at 35% Relative Humidity
+ PM25_RH50      | kg m-3     | xy   | N    |            | Total Reconstructed Particulate Matter < 2.5 microns (PM2.5) at 50% Relative Humidity
 
 category: INTERNAL
 #----------------------------------------------------------------------------------------