Merge remote-tracking branch 'origin/main' into dev/14.4.0

Signed-off-by: Melissa Sulprizio <mpayer@seas.harvard.edu>

.gitmodules

@@ -1,36 +1,36 @@
-[submodule "src/MAPL"]
+[submodule "MAPL"]
 	path = src/MAPL
 	url = https://github.com/geoschem/MAPL
-[submodule "src/GMAO_Shared"]
+[submodule "GMAO_Shared"]
 	path = src/GMAO_Shared
 	url = https://github.com/geoschem/GMAO_Shared
 [submodule "ESMA_cmake"]
 	path = ESMA_cmake
 	url = https://github.com/geoschem/ESMA_cmake
-[submodule "src/gFTL-shared"]
+[submodule "gFTL-shared"]
 	path = src/gFTL-shared
 	url = https://github.com/geoschem/gFTL-shared.git
-[submodule "src/FMS"]
+[submodule "FMS"]
 	path = src/FMS
 	url = https://github.com/geoschem/FMS.git
-[submodule "src/GCHP_GridComp/FVdycoreCubed_GridComp"]
+[submodule "FVdycoreCubed_GridComp"]
 	path = src/GCHP_GridComp/FVdycoreCubed_GridComp
 	url = https://github.com/geoschem/FVdycoreCubed_GridComp.git
-[submodule "src/GCHP_GridComp/GEOSChem_GridComp/geos-chem"]
+[submodule "geos-chem"]
 	path = src/GCHP_GridComp/GEOSChem_GridComp/geos-chem
 	url = https://github.com/geoschem/geos-chem.git
-[submodule "src/GCHP_GridComp/HEMCO_GridComp/HEMCO"]
+[submodule "HEMCO"]
 	path = src/GCHP_GridComp/HEMCO_GridComp/HEMCO
 	url = https://github.com/geoschem/HEMCO.git
-[submodule "src/yaFyaml"]
+[submodule "yaFyaml"]
 	path = src/yaFyaml
 	url = https://github.com/geoschem/yaFyaml.git
-[submodule "src/pFlogger"]
+[submodule "pFlogger"]
 	path = src/pFlogger
 	url = https://github.com/geoschem/pFlogger.git
-[submodule "docs/geos-chem-shared-docs"]
+[submodule "geos-chem-shared-docs"]
 	path = docs/source/geos-chem-shared-docs
 	url = https://github.com/geoschem/geos-chem-shared-docs.git
-[submodule "src/GCHP_GridComp/GEOSChem_GridComp/Cloud-J"]
+[submodule "Cloud-J"]
 	path = src/GCHP_GridComp/Cloud-J
 	url = https://github.com/geoschem/Cloud-J

CHANGELOG.md

@@ -7,6 +7,26 @@ This file documents all notable changes to the GCHP wrapper repository starting
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [Unreleased] - TBD
+### Changed
+- Updated GEOS-Chem submodule to 14.4.0
+- Updated HEMCO submodule to 3.9.0
+
+## [14.3.1] - 2024-04-02
+### Added
+- Now print container name being read by ExtData when `CAP.EXTDATA` is set to `DEBUG` in `logging.yml`
+- Added new pre-processer setting GCHP_WRAPPER for use in submodules
+- Added PLEadv export to FV3 submodule for inclusion in GCHP HISTORY.rc files
+
+### Changed
+- Updated GEOS-Chem submodule to 14.3.1
+- Updated HEMCO submodule to 3.8.1
+- Now use short names for submodules (i.e. without the path) in `.gitmodules`
+
+### Fixed
+- Fixed bug where SPHU used to construct PLE for advection was vertically inverted if using raw GMAO meteorology files
+- Fixed bug in UpwardsMassFlux diagnostic that was causing all values to be zero
+
 ## [14.3.0] - 2024-02-07
 ### Added
 - Added capability for TOMAS simulations in GCHP

CMakeLists.txt

@@ -1,6 +1,6 @@
 cmake_minimum_required (VERSION 3.13)
 project (gchp_ctm
-  VERSION 14.3.0
+  VERSION 14.3.1
   LANGUAGES Fortran CXX C
 )
 

docs/source/conf.py

@@ -23,7 +23,7 @@
 author = 'GEOS-Chem Support Team'
 
 # The full version, including alpha/beta/rc tags
-release = '14.3.0'
+release = '14.3.1'
 
 
 # -- General configuration ---------------------------------------------------

src/GCHP_GridComp/CMakeLists.txt

@@ -4,6 +4,7 @@
 # Set cmake logicals needed for subprojects
 #---------------
 set(FV_PRECISION           R8    ) # FV3 precision is R8
+set(GCHP_WRAPPER           TRUE  ) # GCHP model configuration
 set(CLOUDJ_EXTERNAL_CONFIG TRUE  ) # Not Cloud-J standalone
 set(HEMCO_EXTERNAL_CONFIG  TRUE  ) # Not HEMCO standalone
 set(GC_EXTERNAL_CONFIG     TRUE  ) # Not GEOS-Chem Classic

src/GCHP_GridComp/GCHPctmEnv_GridComp/GCHPctmEnv_GridCompMod.F90

@@ -686,11 +686,21 @@ subroutine prepare_ple_exports(IMPORT, EXPORT, PLE, RC)
       ! Also compute dry pressures if using dry pressure in advection
       if ( use_total_air_pressure_in_advection < 1 ) then
 
-         call calculate_ple(PS1_IMPORT, DryPLE0_EXPORT, SPHU1_IMPORT )
+         call calculate_ple(          &
+              PS=PS1_IMPORT,          &
+              PLE=DryPLE0_EXPORT,     &
+              SPHU=SPHU1_IMPORT,      &
+              topDownMet=meteorology_vertical_index_is_top_down )
+
          DryPLE0_EXPORT = 100.0d0 * DryPLE0_EXPORT
          DryPLE0_EXPORT = DryPLE0_EXPORT(:,:,LM:0:-1)
 
-         call calculate_ple(PS2_IMPORT, DryPLE1_EXPORT, SPHU2_IMPORT )
+         call calculate_ple(          &
+              PS=PS2_IMPORT,          &
+              PLE=DryPLE1_EXPORT,     &
+              SPHU=SPHU2_IMPORT,      &
+              topDownMet=meteorology_vertical_index_is_top_down )
+
          DryPLE1_EXPORT = 100.0d0 * DryPLE1_EXPORT
          DryPLE1_EXPORT = DryPLE1_EXPORT(:,:,LM:0:-1)
 
@@ -934,10 +944,10 @@ subroutine prepare_massflux_exports(IMPORT, EXPORT, PLE, dt, RC)
       end if
 
       ! Set vertical motion diagnostic if enabled in HISTORY.rc
+      call MAPL_GetPointer(EXPORT, UpwardsMassFlux, 'UpwardsMassFlux', &
+           NotFoundOK=.TRUE., RC=STATUS)
+      _VERIFY(STATUS)
       if (associated(UpwardsMassFlux)) then
-         call MAPL_GetPointer(EXPORT, UpwardsMassFlux, 'UpwardsMassFlux', &
-                              RC=STATUS)
-         _VERIFY(STATUS)
          call lgr%debug('Calculating diagnostic export UpwardsMassFlux')
 
          ! Get vertical mass flux
@@ -973,12 +983,13 @@ end subroutine prepare_massflux_exports
 !
 ! !INTERFACE:
 !
-   subroutine calculate_ple(PS, PLE, SPHU)
+   subroutine calculate_ple(PS, PLE, SPHU, topDownMet )
 !
 ! !INPUT PARAMETERS:
 !
       real(r4), intent(in)           :: PS(:,:)     ! Surface pressure [hPa]
       real(r4), intent(in), OPTIONAL :: SPHU(:,:,:) ! Specific humidity [kg/kg]
+      logical,  intent(in), OPTIONAL :: topDownMet  ! True if meteorology level 1 is TOA
 !
 ! !INPUT PARAMETERS:
 !
@@ -1070,26 +1081,57 @@ subroutine calculate_ple(PS, PLE, SPHU)
          js = lbound(PS,2)
          je = ubound(PS,2)
          LM = size  (SPHU,3)
-         do J=js,je
-         do I=is,ie
-
-            ! Start with TOA pressure
-            PSDry = AP(LM+1)
-
-            ! Stack up dry delta-P to get surface dry pressure
-            do L=1,LM
-               PEdge_Bot = AP(L  ) + ( BP(L  ) * dble(PS(I,J)) )
-               PEdge_Top = AP(L+1) + ( BP(L+1) * dble(PS(I,J)) )
-               PSDry = PSDry &
-                       + ( ( PEdge_Bot - Pedge_Top ) * ( 1.d0 - SPHU(I,J,L) ) )
-            enddo
 
-            ! Work back up from the surface to get dry level edges
-            do L=1,LM+1
-               PLE(I,J,L) = AP(L) + ( BP(L) * dble(PSDry) )
+         if ( topDownMet ) then
+
+           do J=js,je
+           do I=is,ie
+
+              ! Start with TOA pressure
+              PSDry = AP(LM+1)
+
+              ! Stack up dry delta-P to get surface dry pressure
+              ! Vertically flip humidity if using top-down meteorology (raw GMAO files)
+              do L=1,LM
+                 PEdge_Bot = AP(L  ) + ( BP(L  ) * dble(PS(I,J)) )
+                 PEdge_Top = AP(L+1) + ( BP(L+1) * dble(PS(I,J)) )
+                 PSDry = PSDry &
+                         + ( ( PEdge_Bot - Pedge_Top ) * ( 1.d0 - SPHU(I,J,LM-L+1) ) )
+              enddo
+
+              ! Work back up from the surface to get dry level edges
+              do L=1,LM+1
+                 PLE(I,J,L) = AP(L) + ( BP(L) * dble(PSDry) )
+              enddo
+
+           enddo
+           enddo
+
+         else
+
+            do J=js,je
+            do I=is,ie
+
+               ! Start with TOA pressure
+               PSDry = AP(LM+1)
+
+               ! Stack up dry delta-P to get surface dry pressure
+               do L=1,LM
+                  PEdge_Bot = AP(L  ) + ( BP(L  ) * dble(PS(I,J)) )
+                  PEdge_Top = AP(L+1) + ( BP(L+1) * dble(PS(I,J)) )
+                  PSDry = PSDry &
+                          + ( ( PEdge_Bot - Pedge_Top ) * ( 1.d0 - SPHU(I,J,L) ) )
+               enddo
+
+               ! Work back up from the surface to get dry level edges
+               do L=1,LM+1
+                  PLE(I,J,L) = AP(L) + ( BP(L) * dble(PSDry) )
+               enddo
             enddo
-         enddo
-         enddo
+            enddo
+
+         endif
+
       endif