Merge "no-diff-to-benchmark" updates into main

This merge brings updates from the "no-diff-to-benchmark" development stream into the main branch, in anticipation of the 14.4.1 release. Signed-off-by: Bob Yantosca <[email protected]>
geoschem · Jun 28, 2024 · 3b28982 · 3b28982
2 parents 1ef3d7f + e0e6e2f
commit 3b28982
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diff --git a/.github/workflows/stale.yml b/.github/workflows/stale.yml
@@ -22,14 +22,7 @@ jobs:
       with:
         repo-token: ${{ secrets.GITHUB_TOKEN }}
         stale-issue-label: 'stale'
-        exempt-issue-labels:
-          - 'category: Discussion'
-          - 'category: Feature Request'
-          - 'deferred'
-          - 'help needed: Open Research Problem'
-          - 'help needed: Request Input from Community'
-          - 'never stale'
-          - 'TODO: Documentation'
+        exempt-issue-labels: 'category: Discussion','category: Feature Request','deferred','help needed: Open Research Problem','help needed: Request Input from Community','never stale','TODO: Documentation'
         days-before-issue-stale: 30
         days-before-issue-close: 7
         stale-issue-message: 'This issue has been automatically marked as stale because it has not had recent activity. If there are no updates within 7 days it will be closed. You can add the "never stale" tag to prevent the issue from closing this issue.'

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,6 +4,29 @@ This file documents all notable changes to the GEOS-Chem repository starting in
 
 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
+### Added
+- Added initialization of PHOTDELTA in `ucx_h2so4phot` to avoid run-time error in CESM
+
+### Changed
+- Alphabetically sort Complex SOA species into `geoschem_config.yml` in run directory creation 
+- Use hard-coded years for met fields and BC files in `HEMCO_Config.rc` so they are not read hourly
+- Updated `run/CESM` with alphabetical sorting of species in `geoschem_config.yml`
+- Added clarifying comments in GCHP configuration files for several settings, particularly related to domain decomposition, mass fluxes, and stretched grid
+- Added pre-run GCHP configuration checks to `setCommonRunSettings.sh` related to domain decomposition, mass fluxes, and stretched grid.
+- Changed search criteria for GCHP auto-update of met-field refresh frequency to not rely on presence of `MetDir` symlink in `ExtData.rc` file path
+
+### Fixed
+- Fixed formatting error in `.github/workflows/stale.yml` that caused the Mark Stale Issues action not to run
+- Fixed typo `$GCAPVERTRESL` -> `$GCAPVERTRES` in `HEMCO_Config.rc.fullchem` template file
+- Fixed GCHP `ExtData.rc` entry for lightning climatology files
+
+### Removed
+- Removed `BudgetWetDep*` entries from simulations with no soluble species in `HISTORY.rc` templates
+- Disabled `run/CESM` ParaNOx extension by default in `HEMCO_Config.rc`
+- Removed MPI broadcasts in CESM-only UCX code; MPI broadcast done at coupler level
+- Remove enabling O-server in GCHP for high core counts
+
 ## [14.4.0] - 2024-05-30
 ### Added
 - Added `SpcConc%Units` for species-specific unit conversion

diff --git a/GeosCore/ucx_mod.F90 b/GeosCore/ucx_mod.F90
@@ -3825,6 +3825,9 @@ SUBROUTINE UCX_H2SO4PHOT( Input_Opt, State_Chm, State_Grid, State_Met )
     ! UCX_H2SO4PHOT begins here!
     !=================================================================
 
+    ! Initialize
+    PHOTDELTA = 0.0_fp
+
     ! Copy fields from species database
     SO2_MW_G = State_Chm%SpcData(id_SO2)%Info%MW_g ! g/mol
     SO4_MW_G = State_Chm%SpcData(id_SO4)%Info%MW_g ! g/mol
@@ -3903,8 +3906,6 @@ SUBROUTINE NOXCOEFF_INIT( Input_Opt, State_Grid, State_Chm )
     USE State_Chm_Mod,      ONLY : ChmState
 #if defined( MODEL_CESM )
     USE UNITS,              ONLY : freeUnit
-    USE CAM_ABORTUTILS,     ONLY : endrun
-    USE SPMD_UTILS,         ONLY : mpicom, masterprocid, mpi_success, mpi_real8
 #endif
 !
 ! !INPUT PARAMETERS:
@@ -3930,10 +3931,6 @@ SUBROUTINE NOXCOEFF_INIT( Input_Opt, State_Grid, State_Chm )
     INTEGER            :: I, AS, IOS
     INTEGER            :: IMON, ITRAC, ILEV
     INTEGER            :: IU_FILE
-#if defined( MODEL_CESM )
-    INTEGER            :: nSize ! Number of elements in State_Chm%NOXCOEFF
-    INTEGER            :: ierr
-#endif
 
     ! Strings
     CHARACTER(LEN=255) :: NOX_FILE
@@ -4057,7 +4054,6 @@ SUBROUTINE NOXCOEFF_INIT( Input_Opt, State_Grid, State_Chm )
     State_Chm%NOXCOEFF = 0.0e+0_fp
 
 #if defined( MODEL_CESM )
-    nSize = State_Chm%JJNOXCOEFF * UCX_NLEVS * 6 * 12
     IF ( Input_Opt%amIRoot ) THEN
 #endif
     ! Fill array
@@ -4138,9 +4134,6 @@ SUBROUTINE NOXCOEFF_INIT( Input_Opt, State_Grid, State_Chm )
     ENDDO !IMON
 #if defined( MODEL_CESM )
     ENDIF
-
-    CALL MPI_BCAST( State_Chm%NOXCOEFF, nSize, mpi_real8, masterprocid, mpicom, ierr )
-    IF ( ierr /= mpi_success ) CALL endrun(subname//': MPI_BCAST ERROR: NOXCOEFF')
 #endif
 
   END SUBROUTINE NOXCOEFF_INIT

diff --git a/run/CESM/HEMCO_Config.rc b/run/CESM/HEMCO_Config.rc
@@ -162,7 +162,7 @@ VerboseOnCores:              root       # Accepted values: root all
 # -----------------------------------------------------------------------------
 100     Custom                 : off   -
 101     SeaFlux                : on    DMS/ACET/ALD2/MENO3/ETNO3/MOH
-102     ParaNOx                : on    NO/NO2/O3/HNO3
+102     ParaNOx                : off   NO/NO2/O3/HNO3
     --> LUT data format        :       nc
     --> LUT source dir         :       $ROOT/PARANOX/v2015-02
 103     LightNOx               : off   NO

diff --git a/run/CESM/geoschem_config.yml b/run/CESM/geoschem_config.yml
@@ -94,16 +94,16 @@ operations:
       - AERI
       - ALD2
       - ALK4
+      - AONITA
+      - AROMP4
+      - AROMP5
       - ASOA1
       - ASOA2
       - ASOA3
       - ASOAN
       - ASOG1
       - ASOG2
       - ASOG3
-      - AONITA
-      - AROMP4
-      - AROMP5
       - ATOOH
       - BALD
       - BCPI

diff --git a/run/GCClassic/HEMCO_Config.rc.templates/HEMCO_Config.rc.CH4 b/run/GCClassic/HEMCO_Config.rc.templates/HEMCO_Config.rc.CH4
@@ -618,7 +618,7 @@ VerboseOnCores:              root       # Accepted values: root all
 # --- GEOS-Chem boundary condition file ---
 #==============================================================================
 (((GC_BCs
-* BC_ $ROOT/SAMPLE_BCs/v2021-07/CH4/GEOSChem.BoundaryConditions.$YYYY$MM$DD_0000z.nc4 SpeciesBC_?ADV?  $YYYY/$MM/$DD/* EFY xyz 1 * - 1 1
+* BC_ $ROOT/SAMPLE_BCs/v2021-07/CH4/GEOSChem.BoundaryConditions.$YYYY$MM$DD_0000z.nc4 SpeciesBC_?ADV?  1900-2100/1-12/1-31/* EFY xyz 1 * - 1 1
 )))GC_BCs
 
 #==============================================================================

diff --git a/run/GCClassic/HEMCO_Config.rc.templates/HEMCO_Config.rc.Hg b/run/GCClassic/HEMCO_Config.rc.templates/HEMCO_Config.rc.Hg
@@ -500,7 +500,7 @@ VerboseOnCores:              root       # Accepted values: root all
 # --- GEOS-Chem boundary condition file ---
 #==============================================================================
 (((GC_BCs
-* BC_  $ROOT/SAMPLE_BCs/v2019-05/tropchem/GEOSChem.BoundaryConditions.$YYYY$MM$DD_$HH$MNz.nc4 SpeciesBC_?ADV?  $YYYY/$MM/$DD/* EFY xyz 1 * - 1 1
+* BC_  $ROOT/SAMPLE_BCs/v2019-05/tropchem/GEOSChem.BoundaryConditions.$YYYY$MM$DD_$HH$MNz.nc4 SpeciesBC_?ADV?  1900-2100/1-12/1-31/* EFY xyz 1 * - 1 1
 )))GC_BCs
 
 (((CHEMISTRY_INPUT

diff --git a/run/GCClassic/HEMCO_Config.rc.templates/HEMCO_Config.rc.aerosol b/run/GCClassic/HEMCO_Config.rc.templates/HEMCO_Config.rc.aerosol
@@ -1967,7 +1967,7 @@ VerboseOnCores:              root       # Accepted values: root all
 # --- GEOS-Chem boundary condition file ---
 #==============================================================================
 (((GC_BCs
-* BC_  $ROOT/SAMPLE_BCs/GC_14.3.0/fullchem/GEOSChem.BoundaryConditions.$YYYY$MM$DD_$HH$MNz.nc4 SpeciesBC_?ADV?  $YYYY/$MM/$DD/* EFY xyz 1 * - 1 1
+* BC_  $ROOT/SAMPLE_BCs/GC_14.3.0/fullchem/GEOSChem.BoundaryConditions.$YYYY$MM$DD_$HH$MNz.nc4 SpeciesBC_?ADV?  1900-2100/1-12/1-31/* EFY xyz 1 * - 1 1
 )))GC_BCs
 
 (((CHEMISTRY_INPUT

diff --git a/run/GCClassic/HEMCO_Config.rc.templates/HEMCO_Config.rc.carbon b/run/GCClassic/HEMCO_Config.rc.templates/HEMCO_Config.rc.carbon
@@ -1067,7 +1067,7 @@ Mask fractions:              false
 # --- GEOS-Chem boundary condition file ---
 #==============================================================================
 (((GC_BCs
-* BC_ $ROOT/SAMPLE_BCs/v2021-07/CH4/GEOSChem.BoundaryConditions.$YYYY$MM$DD_0000z.nc4 SpeciesBC_?ADV? $YYYY/$MM/$DD/* EFY xyz 1 * - 1 1
+* BC_ $ROOT/SAMPLE_BCs/v2021-07/CH4/GEOSChem.BoundaryConditions.$YYYY$MM$DD_0000z.nc4 SpeciesBC_?ADV? 1900-2100/1-12/1-31/* EFY xyz 1 * - 1 1
 )))GC_BCs
 
 #==============================================================================

diff --git a/run/GCClassic/HEMCO_Config.rc.templates/HEMCO_Config.rc.fullchem b/run/GCClassic/HEMCO_Config.rc.templates/HEMCO_Config.rc.fullchem
@@ -1931,10 +1931,10 @@ VerboseOnCores:              root       # Accepted values: root all
 #
 #==============================================================================
 (((CMIP6_AIRCRAFT
-0 CMIP6_AIR_NO     $ROOT/CMIP6/v2021-01/$GCAPSCENARIO/$GCAPSCENARIO_$YYYY_AIR.$GCAP2VERTRESL.nc4    NO_air            1750-2100/1-12/1/0 C xyz kg/m2/s   NO    -        20 1
-0 CMIP6_AIR_CO     $ROOT/CMIP6/v2021-01/$GCAPSCENARIO/$GCAPSCENARIO_$YYYY_AIR.$GCAP2VERTRESL.nc4    CO_air            1750-2100/1-12/1/0 C xyz kg/m2/s   CO    -        20 1
+0 CMIP6_AIR_NO     $ROOT/CMIP6/v2021-01/$GCAPSCENARIO/$GCAPSCENARIO_$YYYY_AIR.$GCAPVERTRES.nc4    NO_air            1750-2100/1-12/1/0 C xyz kg/m2/s   NO    -        20 1
+0 CMIP6_AIR_CO     $ROOT/CMIP6/v2021-01/$GCAPSCENARIO/$GCAPSCENARIO_$YYYY_AIR.$GCAPVERTRES.nc4    CO_air            1750-2100/1-12/1/0 C xyz kg/m2/s   CO    -        20 1
 0 CMIP6_AIR_SOAP   -                                                                                -                 -                  - -   -         SOAP  280      20 1
-0 CMIP6_AIR_SO2    $ROOT/CMIP6/v2021-01/$GCAPSCENARIO/$GCAPSCENARIO_$YYYY_AIR.$GCAP2VERTRESL.nc4    SO2_air           1750-2100/1-12/1/0 C xyz kg/m2/s   SO2   -        20 1
+0 CMIP6_AIR_SO2    $ROOT/CMIP6/v2021-01/$GCAPSCENARIO/$GCAPSCENARIO_$YYYY_AIR.$GCAPVERTRES.nc4    SO2_air           1750-2100/1-12/1/0 C xyz kg/m2/s   SO2   -        20 1
 0 CMIP6_AIR_SO4    -                                                                                -                 -                  - -   -         SO4   63       20 1
 0 CMIP6_AIR_pFe    -                                                                                -                 -                  - -   -         pFe   66       20 1
 0 CMIP6_AIR_ACET   -                                                                                -                 -                  - -   -         ACET  601      20 1
@@ -1946,10 +1946,10 @@ VerboseOnCores:              root       # Accepted values: root all
 0 CMIP6_AIR_PRPE   -                                                                                -                 -                  - -   -         PRPE  607      20 1
 0 CMIP6_AIR_MACR   -                                                                                -                 -                  - -   -         MACR  608      20 1
 0 CMIP6_AIR_RCHO   -                                                                                -                 -                  - -   -         RCHO  609      20 1
-0 CMIP6_AIR_NH3    $ROOT/CMIP6/v2021-01/$GCAPSCENARIO/$GCAPSCENARIO_$YYYY_AIR.$GCAP2VERTRESL.nc4    NH3_air           1750-2100/1-12/1/0 C xyz kg/m2/s   NH3   -        20 1
+0 CMIP6_AIR_NH3    $ROOT/CMIP6/v2021-01/$GCAPSCENARIO/$GCAPSCENARIO_$YYYY_AIR.$GCAPVERTRES.nc4    NH3_air           1750-2100/1-12/1/0 C xyz kg/m2/s   NH3   -        20 1
 # Assume all BC/OC is BCPI/OCPI
-0 CMIP6_AIR_BCPI   $ROOT/CMIP6/v2021-01/$GCAPSCENARIO/$GCAPSCENARIO_$YYYY_AIR.$GCAP2VERTRESL.nc4    BC_air            1750-2100/1-12/1/0 C xyz kg/m2/s   BCPI  -        20 1
-0 CMIP6_AIR_OCPI   $ROOT/CMIP6/v2021-01/$GCAPSCENARIO/$GCAPSCENARIO_$YYYY_AIR.$GCAP2VERTRESL.nc4    OC_air            1750-2100/1-12/1/0 C xyz kg/m2/s   OCPI  -        20 1
+0 CMIP6_AIR_BCPI   $ROOT/CMIP6/v2021-01/$GCAPSCENARIO/$GCAPSCENARIO_$YYYY_AIR.$GCAPVERTRES.nc4    BC_air            1750-2100/1-12/1/0 C xyz kg/m2/s   BCPI  -        20 1
+0 CMIP6_AIR_OCPI   $ROOT/CMIP6/v2021-01/$GCAPSCENARIO/$GCAPSCENARIO_$YYYY_AIR.$GCAPVERTRES.nc4    OC_air            1750-2100/1-12/1/0 C xyz kg/m2/s   OCPI  -        20 1
 0 CMIP6_AIR_POG1   -                                                                                -                 -                  - -  -          POG1  74/76    20 1
 0 CMIP6_AIR_POG2   -                                                                                -                 -                  - -  -          POG2  74/77    20 1
 
@@ -3492,7 +3492,7 @@ VerboseOnCores:              root       # Accepted values: root all
 # --- GEOS-Chem boundary condition file ---
 #==============================================================================
 (((GC_BCs
-* BC_  $ROOT/SAMPLE_BCs/GC_14.3.0/fullchem/GEOSChem.BoundaryConditions.$YYYY$MM$DD_$HH$MNz.nc4 SpeciesBC_?ADV? $YYYY/$MM/$DD/* EFY xyz 1 * - 1 1
+* BC_  $ROOT/SAMPLE_BCs/GC_14.3.0/fullchem/GEOSChem.BoundaryConditions.$YYYY$MM$DD_$HH$MNz.nc4 SpeciesBC_?ADV? 1900-2100/1-12/1-31/* EFY xyz 1 * - 1 1
 )))GC_BCs
 
 (((CHEMISTRY_INPUT