GEOS-Chem (science codebase) 14.2.3 release

This is the official release of GEOS-Chem (science codebase) 14.2.3. Updates include: - Use integer flags to denote species units instead of strings (PR #1796) - Prevent POAEMISS variable from being assigned if not allocated (PR #1987) - Add an --no-bootstrap option to integration tests (PR #1990) - Fixed incorrect comments on static H2O option (PR #2013) - Improve missing CH4 emissions error message (PR #2039) - Lower GCHP timestep threshold if > C180 rather than >= C180 (PR #2040) - Add fixes to HEMCO_Config.rc for CH4, carbon simulations (PR #2042) - Fix typos written to GCHP integration test log files (PR #2043) - Update GCClassic rundir scripts to read restat file paths from download_data.yml (PR #2050) Signed-off-by: Bob Yantosca <[email protected]>
geoschem · Dec 1, 2023 · 3cd802e · 3cd802e
2 parents 7e00810 + 7d3dea6
commit 3cd802e
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,7 +4,28 @@ 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 14.2.2] - 2023-10-23
+## [14.2.3] - 2023-12-01
+### Added
+- GEOS-Chem Classic rundir script `run/GCClassic/setupForRestarts.sh`
+
+### Changed
+- Added the `-n` aka `--no-bootstrap` option to integration tests to disable bootstrapping missing species in restart files
+- Use integer parameters for species units instead of strings (for computational efficiency)
+- Update error message for missing surface CH4 emissions with instructions on how to resolve the problem
+- Change GCHP grid resolution threshold for lowering timesteps from C180 inclusive to C180 exclusive
+- Read GEOS-Chem Classic restart file paths from the relevant `download_data.yml` file
+
+### Fixed
+- Prevent `POAEMISS` from being assigned a value if not allocated (in `carbon_mod.F90`)
+- Changed incorrect comment about static H2O option in `GeosCore/input_mod.F90`
+- Fixed typos (`GCClassic` -> `GCHP`) written to GCHP integration test log files
+- Add fix to properly read GHGI v2 express extension emissions in CH4 and carbon simulations
+- Move OH perturbation scale factor to outside EMISSIONS logical bracket in HEMCO_Config.rc files for CH4 and carbon simulations
+
+### Removed
+- Remove definition of METDIR from primary HEMCO_Config.rc files to ensure use of the definition in the HEMCO_Config.rc.*_metfields files
+
+## [14.2.2] - 2023-10-23
 ### Changed
 - Updated sample restart files for fullchem and TransportTracers simulations to files saved out from the 14.2.0 1-year benchmarks
 
@@ -61,7 +82,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 ### Removed
 - Remove references to the obsolete tagged Hg simulation
 
-## [Unreleased 14.2.0] - TBD
+## [14.2.0] - 2023-10-05
 ### Added
 - Added a printout of GEOS-Chem species and indices
 - Added `NcdfUtil/README.md` file directing users to look for netCDF utility scripts at https://github.com/geoschem/netcdf-scripts
@@ -148,6 +169,14 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 ### Fixed
 - Fixed entries for CH4 emissions in `HEMCO_Config.rc.carbon`
 
+## [14.1.2] - 2023-10-20
+### Added
+- CESM-only update: Added option for correctConvUTLS for correcting buildup of soluble tracers in the UT/LS to match CAM-chem behavior
+
+### Changed
+- CESM-only update: extend existing KppError, KppStop to CESM for model stability
+- CESM-only update: Removed mpi_bcast in ucx_mod NOXCOEFF_INIT to be handled at coupler level to support spectral-element dynamical core
+
 ## [14.1.1] - 2023-03-03
 ### Added
   - New integration test functions in `test/GCClassic/integration` and `test/GCHP/integration`

diff --git a/GeosCore/aero_drydep.F90 b/GeosCore/aero_drydep.F90
@@ -39,6 +39,7 @@ SUBROUTINE AERO_DRYDEP( Input_Opt,  State_Chm, State_Diag, &
     USE CMN_DIAG_MOD
     USE DIAG_MOD,           ONLY : AD44
 #endif
+    USE UnitConv_Mod
 
     IMPLICIT NONE
 !
@@ -119,8 +120,8 @@ SUBROUTINE AERO_DRYDEP( Input_Opt,  State_Chm, State_Diag, &
     nDryDep   = State_Chm%nDryDep
 
     ! Check that species units are in [kg] (ewl, 8/13/15)
-    IF ( TRIM( State_Chm%Spc_Units ) /= 'kg' ) THEN
-       MSG = 'Incorrect species units: ' // TRIM(State_Chm%Spc_Units)
+    IF ( State_Chm%Spc_Units /= KG_SPECIES ) THEN
+       MSG = 'Incorrect species units: ' // TRIM(UNIT_STR(State_Chm%Spc_Units))
        LOC = 'Routine AERO_DRYDEP in aero_drydep.F'
        CALL GC_Error( MSG, RC, LOC )
     ENDIF
@@ -530,9 +531,9 @@ SUBROUTINE AERO_DRYDEP( Input_Opt,  State_Chm, State_Diag, &
     DepFreq  => NULL()
 
     ! Check that species units are still in [kg] (ewl, 8/13/15)
-    IF ( TRIM( State_Chm%Spc_Units ) /= 'kg' ) THEN
+    IF ( State_Chm%Spc_Units /= KG_SPECIES ) THEN
        MSG = 'Incorrect species units at end of routine: ' &
-             // TRIM(State_Chm%Spc_Units)
+             // TRIM(UNIT_STR(State_Chm%Spc_Units))
        LOC = 'Routine AERO_DRYDEP in aero_drydep.F'
        CALL GC_Error( MSG, RC, LOC )
     ENDIF

diff --git a/GeosCore/aerosol_mod.F90 b/GeosCore/aerosol_mod.F90
@@ -185,7 +185,7 @@ SUBROUTINE AEROSOL_CONC( Input_Opt,  State_Chm, State_Diag, &
     USE State_Diag_Mod,    ONLY : DgnState
     USE State_Grid_Mod,    ONLY : GrdState
     USE State_Met_Mod,     ONLY : MetState
-    USE UnitConv_Mod,      ONLY : Convert_Spc_Units
+    USE UnitConv_Mod
     USE TIME_MOD,          ONLY : GET_MONTH
 #ifdef TOMAS
     USE TOMAS_MOD,        ONLY : IBINS
@@ -251,7 +251,8 @@ SUBROUTINE AEROSOL_CONC( Input_Opt,  State_Chm, State_Diag, &
     REAL(fp),      POINTER   :: KG_STRAT_AER(:,:,:,:)
 
     ! Other variables
-    CHARACTER(LEN=63)   :: OrigUnit
+    INTEGER             :: OrigUnit
+
 
     ! For spatially and seasonally varying OM/OC
     CHARACTER(LEN=255)  :: FIELDNAME
@@ -303,8 +304,14 @@ SUBROUTINE AEROSOL_CONC( Input_Opt,  State_Chm, State_Diag, &
     REAA => State_Chm%Phot%REAA
 
     ! Convert species to [kg] for this routine
-    CALL Convert_Spc_Units( Input_Opt, State_Chm, State_Grid, State_Met, &
-                            'kg', RC, OrigUnit=OrigUnit )
+    CALL Convert_Spc_Units(                                                  &
+         Input_Opt  = Input_Opt,                                             &
+         State_Chm  = State_Chm,                                             &
+         State_Grid = State_Grid,                                            &
+         State_Met  = State_Met,                                             &
+         outUnit    = KG_SPECIES,                                            &
+         origUnit   = origUnit,                                              &
+         RC         = RC                                                    )
 
     ! Trap potential errors
     IF ( RC /= GC_SUCCESS ) THEN
@@ -1011,8 +1018,14 @@ SUBROUTINE AEROSOL_CONC( Input_Opt,  State_Chm, State_Diag, &
     !$OMP END PARALLEL DO
 
     ! Convert species back to original unit
-    CALL Convert_Spc_Units( Input_Opt, State_Chm, State_Grid, State_Met, &
-                            OrigUnit, RC )
+    CALL Convert_Spc_Units(                                                  &
+         Input_Opt  = Input_Opt,                                             &
+         State_Chm  = State_Chm,                                             &
+         State_Grid = State_Grid,                                            &
+         State_Met  = State_Met,                                             &
+         outUnit    = origUnit,                                              &
+         RC         = RC                                                    )
+
     IF ( RC /= GC_SUCCESS ) THEN
        CALL GC_Error('Unit conversion error', RC, &
                      'End of AEROSOL_CONC in aerosol_mod.F90')
@@ -2643,7 +2656,7 @@ SUBROUTINE Set_AerMass_Diagnostic( Input_Opt,  State_Chm, State_Diag, &
     USE State_Grid_Mod, ONLY : GrdState
     USE State_Met_Mod,  ONLY : MetState
     USE PhysConstants,  ONLY : MwCarb
-    USE UnitConv_Mod,   ONLY : Convert_Spc_Units
+    USE UnitConv_Mod
 !
 ! !INPUT PARAMETERS:
 !
@@ -2679,7 +2692,7 @@ SUBROUTINE Set_AerMass_Diagnostic( Input_Opt,  State_Chm, State_Diag, &
     INTEGER                  :: I, J, L
 
     ! Strings
-    CHARACTER(LEN=63)        :: OrigUnit
+    INTEGER                  :: origUnit
     CHARACTER(LEN=255)       :: ThisLoc
     CHARACTER(LEN=512)       :: ErrMsg
 
@@ -2711,13 +2724,14 @@ SUBROUTINE Set_AerMass_Diagnostic( Input_Opt,  State_Chm, State_Diag, &
 
     ! Initialize
     RC       = GC_SUCCESS
-    ErrMsg   = ''
-    ThisLoc  = ' -> at Set_AerMass_Diagnostic (in module GeosCore/aerosol_mod.F90)'
+    errMsg   = ''
+    thisLoc  = &
+     ' -> at Set_AerMass_Diagnostic (in module GeosCore/aerosol_mod.F90)'
 
     ! Check that species units are kg/kg dry air
-    IF ( TRIM( State_Chm%Spc_Units ) /= 'kg/kg dry' ) THEN
-       CALL GC_Error( 'Incorrect species units: ' // &
-                      State_Chm%Spc_Units, RC, ThisLoc )
+    IF ( State_Chm%Spc_Units /= KG_SPECIES_PER_KG_DRY_AIR ) THEN
+       errMsg = 'Incorrect species units: ' // UNIT_STR( State_Chm%Spc_Units )
+       CALL GC_Error( errMsg, RC, thisLoc )
        RETURN
     ENDIF
 

diff --git a/GeosCore/airs_ch4_mod.F90 b/GeosCore/airs_ch4_mod.F90
@@ -370,7 +370,7 @@ SUBROUTINE CALC_AIRS_CH4_FORCE( Input_Opt, State_Chm, State_Grid, &
     USE State_Chm_Mod,      ONLY : ChmState, Ind_
     USE State_Grid_Mod,     ONLY : GrdState
     USE State_Met_Mod,      ONLY : MetState
-    USE UnitConv_Mod,       ONLY : Convert_Spc_Units
+    USE UnitConv_Mod
 !
 ! !INPUT PARAMETERS:
 !
@@ -429,7 +429,7 @@ SUBROUTINE CALC_AIRS_CH4_FORCE( Input_Opt, State_Chm, State_Grid, &
     INTEGER            :: IOS
     INTEGER, SAVE      :: TotalObs = 0
     CHARACTER(LEN=255) :: FILENAME
-    CHARACTER(LEN=63)  :: OrigUnit
+    INTEGER            :: origUnit
     CHARACTER(LEN=255) :: ThisLoc
     CHARACTER(LEN=512) :: ErrMsg
     INTEGER            :: RC
@@ -517,8 +517,15 @@ SUBROUTINE CALC_AIRS_CH4_FORCE( Input_Opt, State_Chm, State_Grid, &
     print*, ' found # AIRS observations: ', NOBS
 
     ! Convert species units to [v/v] (mps, 6/12/2020)
-    CALL Convert_Spc_Units( Input_Opt, State_Chm, State_Grid, State_Met, &
-                            'v/v dry', RC,        OrigUnit=OrigUnit )
+    CALL Convert_Spc_Units(                                                  &
+         Input_Opt  = Input_Opt,                                             &
+         State_Chm  = State_Chm,                                             &
+         State_Grid = State_Grid,                                            &
+         State_Met  = State_Met,                                             &
+         outUnit    = MOLES_SPECIES_PER_MOLES_DRY_AIR,                       &
+         origUnit   = origUnit,                                              &
+         RC         = RC                                                    )
+
     IF ( RC /= GC_SUCCESS ) THEN
        ErrMsg = 'Unit conversion error (kg/kg dry -> v/v dry)'
        CALL GC_Error( ErrMsg, RC, ThisLoc )
@@ -687,8 +694,15 @@ SUBROUTINE CALC_AIRS_CH4_FORCE( Input_Opt, State_Chm, State_Grid, &
     !!$OMP END PARALLEL DO
 
     ! Convert species units back to original unit (mps, 6/12/2020)
-    CALL Convert_Spc_Units( Input_Opt, State_Chm, State_Grid, State_Met, &
-                            OrigUnit,  RC ) 
+    CALL Convert_Spc_Units(                                                  &
+         Input_Opt  = Input_Opt,                                             &
+         State_Chm  = State_Chm,                                             &
+         State_Grid = State_Grid,                                            &
+         State_Met  = State_Met,                                             &
+         outUnit    = origUnit,                                              &
+         RC         = RC                                                    )
+
+    ! Trap errors
     IF ( RC /= GC_SUCCESS ) THEN
        ErrMsg = 'Unit conversion error'
        CALL GC_Error( ErrMsg, RC, ThisLoc )

diff --git a/GeosCore/calc_met_mod.F90 b/GeosCore/calc_met_mod.F90
@@ -158,6 +158,7 @@ SUBROUTINE AIRQNT( Input_Opt, State_Chm, State_Grid, State_Met, &
     USE Time_Mod,       ONLY : Get_LocalTime
     USE Time_Mod,       ONLY : Get_LocalTime_In_Sec
     USE Time_Mod,       ONLY : Get_Ts_Dyn
+    USE UnitConv_Mod
 !
 ! !INPUT PARAMETERS:
 !
@@ -673,8 +674,8 @@ SUBROUTINE AIRQNT( Input_Opt, State_Chm, State_Grid, State_Met, &
 
        ! The concentration update formula works only for dry mixing ratios
        ! (kg/kg or v/v) so check if units are correct
-       IF ( State_Chm%Spc_units == 'kg/kg dry' .or. &
-            State_Chm%Spc_units == 'v/v dry' ) THEN
+       IF ( State_Chm%Spc_Units == KG_SPECIES_PER_KG_DRY_AIR        .or.     &
+            State_Chm%Spc_Units == MOLES_SPECIES_PER_MOLES_DRY_AIR ) THEN
 
           !$OMP PARALLEL DO       &
           !$OMP DEFAULT( SHARED ) &
@@ -694,7 +695,8 @@ SUBROUTINE AIRQNT( Input_Opt, State_Chm, State_Grid, State_Met, &
           !$OMP END PARALLEL DO
 
        ELSE
-          ErrMsg = 'Incorrect species units: ' // TRIM( State_Chm%Spc_Units )
+          ErrMsg = 'Incorrect species units: '                            // & 
+                    TRIM( UNIT_STR( State_Chm%Spc_Units ) )
           CALL GC_Error( ErrMsg, RC, ThisLoc )
           RETURN
        ENDIF

diff --git a/GeosCore/carbon_mod.F90 b/GeosCore/carbon_mod.F90
@@ -4793,9 +4793,6 @@ SUBROUTINE EMISSCARBON( Input_Opt, State_Chm, State_Grid, State_Met, RC )
    ! Assume success
    RC = GC_SUCCESS
 
-   ! Initialize
-   POAEMISS =  0e+0_fp
-
    ! Check if using complex SOA scheme
    IF ( Input_Opt%LSOA ) THEN
 
@@ -4835,6 +4832,9 @@ SUBROUTINE EMISSCARBON( Input_Opt, State_Chm, State_Grid, State_Met, RC )
    ! Nothing to do if none of the species are defined
    IF ( SESQID <= 0 .AND. HCOPOG1 <= 0 .AND. HCOPOG2 <=0 ) RETURN
 
+   ! Initialize
+   POAEMISS =  0.0_fp
+
    ! Maximum extent of PBL [model levels]
    PBL_MAX = State_Met%PBL_MAX_L
 
@@ -4927,7 +4927,7 @@ SUBROUTINE EMISSCARBONTOMAS( Input_Opt, State_Chm, State_Grid, State_Met, RC )
    USE State_Chm_Mod,        ONLY : ChmState
    USE State_Grid_Mod,       ONLY : GrdState
    USE State_Met_Mod,        ONLY : MetState
-   USE UnitConv_Mod,         ONLY : Convert_Spc_Units
+   USE UnitConv_Mod
    USE PRESSURE_MOD,         ONLY : GET_PCENTER
    USE TOMAS_MOD,            ONLY : IBINS,     AVGMASS, SOACOND
    USE TOMAS_MOD,            ONLY : ICOMP,     IDIAG
@@ -4968,7 +4968,7 @@ SUBROUTINE EMISSCARBONTOMAS( Input_Opt, State_Chm, State_Grid, State_Met, RC )
    LOGICAL                  :: SGCOAG = .True.
    INTEGER                  :: L, K, EMTYPE
    INTEGER                  :: ii=53, jj=29
-   CHARACTER(LEN=63)        :: OrigUnit
+   INTEGER                  :: origUnit
    LOGICAL, SAVE            :: FIRST = .TRUE. !(ramnarine 12/27/2018)
    LOGICAL, SAVE            :: USE_FIRE_NUM = .FALSE.
    LOGICAL                  :: FND !(ramnarine 1/2/2019)
@@ -5029,8 +5029,16 @@ SUBROUTINE EMISSCARBONTOMAS( Input_Opt, State_Chm, State_Grid, State_Met, RC )
    ! Convert concentration units to [kg] for TOMAS. This will be
    ! removed once TOMAS uses mixing ratio instead of mass
    ! as species units (ewl, 9/11/15)
-   CALL Convert_Spc_Units( Input_Opt, State_Chm, State_Grid, State_Met, &
-                           'kg', RC, OrigUnit=OrigUnit )
+   CALL Convert_Spc_Units(                                                  &
+         Input_Opt  = Input_Opt,                                             &
+         State_Chm  = State_Chm,                                             &
+         State_Grid = State_Grid,                                            &
+         State_Met  = State_Met,                                             &
+         outUnit    = KG_SPECIES,                                            &
+         origUnit   = origUnit,                                              &
+         RC         = RC                                                    )
+
+   ! Trap errors
    IF ( RC /= GC_SUCCESS ) THEN
       CALL GC_Error( 'Unit conversion error', RC, &
                      'Start of EMISSCARBONTOMAS in carbon_mod.F90' )
@@ -5253,8 +5261,15 @@ SUBROUTINE EMISSCARBONTOMAS( Input_Opt, State_Chm, State_Grid, State_Met, RC )
    IF ( Input_Opt%Verbose ) CALL DEBUG_MSG( '### EMISCARB: after SOACOND (BIOG) ' )
 
    ! Convert concentrations back to original units (ewl, 9/11/15)
-   CALL Convert_Spc_Units( Input_Opt, State_Chm, State_Grid, State_Met, &
-                           OrigUnit, RC )
+   CALL Convert_Spc_Units(                                                   &
+        Input_Opt  = Input_Opt,                                              &
+        State_Chm  = State_Chm,                                              &
+        State_Grid = State_Grid,                                             &
+        State_Met  = State_Met,                                              &
+        outUnit    = origUnit,                                               &
+        RC         = RC                                                     )
+
+   ! Trap errors
    IF ( RC /= GC_SUCCESS ) THEN
       CALL GC_Error('Unit conversion error', RC, &
                     'End of EMISSCARBONTOMAS in carbon_mod.F90')