GEOS-Chem (science codebase) 14.6.0 release

Updated version numbers in:
- CHANGELOG.md

Please see CHANGELOG.md for updates added to this version.

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

Author: yantosca

CHANGELOG.md

@@ -4,6 +4,76 @@ 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).
 
+## [14.6.0] - 2025-04-18
+### Added
+- Added CEDS 0.1 x 0.1 degree emissions (in `HEMCO/CEDS/v2024-06`)
+- Added met-field dependent dust tuning factors for GCHP C24 resolution in `setCommonRunSettings.sh`.  Others to be added later.
+- Added placeholder values for dust mass tuning factors in `HEMCO_Config.rc.GEOS`
+- Added dust scale factors for MERRA-2, GEOS-IT, and GEOS-FP when using USTAR for Dust DEAD extension
+- Added utility subroutine `Print_Species_Min_Max_Sum` to `print_mod.F90`
+- Added routine `Set_DryDepVel_Diagnostics` to `hco_interface_gc_mod.F90`
+- Added dry-run integration tests for selected simulations
+- Added `State_Diag%SatDiagnPMid` and `State_Diag%Archive_SatDiagnPMid` to save pressure at level midpoints to the `SatDiagn` collection
+- Added option to run GCClassic nested-grid simulations at 0.125x0.15625 resolution using GEOS-FP derived winds fields generated from c720 mass fluxes archived by GMAO
+- Added option for South America (SA), Africa (AF), Middle East (ME), Oceania (OC), and Russia (RU) regions to nested-grid simulations in GCClassic's createRunDir.sh
+- Added updates for compatibility with the Beijing Climate Centre Earth System Model
+
+### Changed
+- Updated default CEDS from CEDSv2 (0.5 deg x 0.5 de) to new CEDS (0.1 deg x 0.1 deg)
+- Added the `KPP_INTEGRATOR_AUTOREDUCE` C-preprocessor switch integrator-specific handling
+- Added code to `KPP/*/CMakeLists.txt` to read the integrator name from the `*.kpp` file
+- Replaced `GOTO` statements with `IF/THEN/ELSE` blocks in `GeosCore/drydep_mod.F90`
+- Changed several diagnostic subroutines to expect species concentrations in mol/mol rather than kg/kg
+- Added precision when registering `State_Met` and `State_Chm` arrays to change output file precision to match precision in the model
+- Changed GEOS-Chem Classic restart file precision of species concentrations (`State_Chm%SpcRestart`) from `REAL*4` to `REAL*8` to match precision in the model
+- Moved GEOS-Chem Classic retrieval of restart variable DELPDRY from HEMCO to `GC_Get_Restart` for consistency with handling of all other restart variables
+- Moved dry dep velocity diagnostic outputs for sea flux and satellite diagnostic species into the `DryDep` collection
+- Moved computation of the `DryDepVelForAlt1` diagnostic into routine `Set_DryDepVel_Diagnostics` 
+- Updated `run/shared/download_data.yml` to use `--no-sign-request` for S3 downloads via anonymous login
+- Changed `KPP/CMakeLists.txt` to not call `add_directory(standalone)` unless we have configured with `-DKPPSA=y`
+- Moved Cloud-J and Fast-JX input directories to Cloud-J and new Fast-JX menus respectively in `geoschem_config.yml`
+- Updated photolysis and aerosol optics input directories to use new mineral dust values in `FJX_scat-aer.dat` and `dust.dat` based on spheroidal shapes
+- Set `State_Diag%Archive_SatDiagn` to true if `State_Diag%Archive_SatDiagnPMID` is true
+- Updated `RxnRates` and `RxnConst` diagnostic fields to use 4-digit reaction numbers.
+- Rebuilt `fullchem`, `Hg`, `carbon` chemical mechanisms with KPP 3.2.0
+- Changed the minimum KPP version to 3.2.0
+- Disabled the `KppTime` diagnostic output in the `fullchem_alldiags` integration tests; this will vary from run to run causing difference tests to fail
+- Updated the `KPP-Standalone` for compatibility with KPP 3.2.0 and to write the proper number of header lines to skip before data begins
+- Set `use_archived_PCO_from_CH4` and `use_archived_PCO2_from_CO2` to true by default for carbon simulations
+- Updated CH4 global oil, gas, and coal emissions from GFEIv2 to GFEIv3
+
+### Fixed
+- Fixed PDOWN definition to lower rather than upper edge
+- Moved where prescribed CH4 is applied in GEOS-Chem Classic to after emissions application so that updated PBL heights are used
+- Moved species concentration unit conversions between mol/mol and kg/kg to start and end of every timestep in GEOS-Chem Classic to remove differences introduced when reading and writing restart files
+- Fixed bug in restart file entry for `ORVCSESQ` in GEOS-Chem Classic fullchem HEMCO_Config.rc that resulted in initializing to all zeros
+- Fixed parallelization issue when computing `State_Chm%DryDepNitrogren` used in HEMCO soil NOx extension
+- Fixed bugs in column mass array affecting budget diagnostics for fixed level and PBL
+- Updated `SatDiagnColEmis` and `SatDiagnSurfFlux` arrays in `hco_interface_gc_mod.F90`, with `(I,J,S)` instead of `(:,:,S)`
+- Fixed incorrect description metadata for `FluxHg0FromAirToOcean` and `FluxHg0FromOceanToAir` diagnostics
+- Placed call to `Convert_Spc_Units` in `main.F90` within an `IF ( notDryrun )` block to avoid executing unit conversions in dryrun simulations
+- Modified CH4 reservoir timestamps in HEMCO_Config.rc to use months 1-12 to ensure HEMCO recalculates those fields monthly and properly applies the seasonal mask
+- Fixed path error `download_data.py` when downloading from `geoschem+http` or `nested+http` portals
+- Retrieve UV flux arrays from Cloud-J used to set UV flux diagnostics
+- Fixed issue in `download_data.py` that was adding an extra `ExtData` to file paths
+- Restored `UVFlux` diagnostic output in the `fullchem_alldiags` integration test
+- Restored convection and ConvertBox unit conversion parallelization to how it was prior to 14.4.0 to fix slowness in TOMAS simulations
+- Modified the carbon mechanism in KPP to separate tropospheric CH4 loss by OH from CO production by CH4 to remove dependency of CH4 and CO on each other and eliminate differences between CH4/tagCO simulations and the carbon simulation
+- Renamed several dummy species in the carbon mechanism for clarity
+- Fixed precision calculations within `co2_mod.F90` and `tagged_co_mod.F90` to eliminate differences with the carbon simulation
+- Fixed simulation date information printed by metrics.py for GCHP
+
+### Removed
+- Removed `CEDSv2`, `CEDS_GBDMAPS`, `CEDS_GBDMAPSbyFuelType` emissions entries from HEMCO and ExtData template files
+- Removed re-evaporation requirement for washout
+- Removed unused level argument passed to `SOIL_DRYDEP` and `SOIL_WETDEP`
+- Removed Fast-JX input directory from geoschem_config.yml files except for Hg simulation
+- Removed `History` attribute from ObsPack output netCDF files; the date info was causing difference tests to fail
+- Removed unused diagnostics: `Tomas_H2SO4`, `Tomas_COAG`, `Tomas_NUCL`, `Tomas_AQOX`, `Tomas_MNFIX`, `Tomas_SOA`
+- Removed diurnal cycle factor applied to OH in `KPP/carbon/carbon_Funcs.F90` to eliminate differences between CH4 and carbon simulations.
+- Removed diurbal cycle factor applied to OH in tagCO simulation for consistency with other carbon species
+- Removed unused functions from `carbon_get_CO2fromOH_flux` and `carbon_get_FixedOH_Flux` from `KPP/carbon/carbon_Funcs.F90`
+
 ## [14.5.3] - 2025-03-04
 ### Changed
 - Changed CESM `HEMCO_Config.rc` to read 3D AEIC emissions every timestep to avoid differences upon restart
@@ -24,18 +94,6 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 - Fixed GCHP refresh time for `CO2_WEEKLY` scale factors so updated daily
 - Fixed bug in GCHP GEOS-IT run directory using raw lat-lon fields on NASA discover cluster
 
-## [14.5.1] - 2025-01-10
-### Added
-- Added Australian Hg emissions for 2000-2019 from MacFarlane et. al. [2022], plus corresponding mask file
-- Added comments in GEOS-Chem Classic `HISTORY.rc` template files advising users not to change the `BoundaryConditions.frequency` setting
-- Added `.zenodo.json` for auto-DOI generation upon version releases
-
-### Fixed
-- Reverted CH4 livestock emissions to EDGAR v7 to avoid hotspots and to apply seasonality
-
-### Removed
-- Removed unused RUNDIR settings for GCHP pressure units and scaling
-
 ## [14.5.1] - 2025-01-10
 ### Added
 - Added allocate guards for arrays in `pressure_mod`
@@ -51,6 +109,9 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 - Added Input_Opt logical for whether to reconstruct convective precipitation fluxes rather than use met-fields
 - Added to run directory creation a warning about convection discontinuity and bug if GEOS-FP meteorology is chosen
 - Added surface precipitation flux fields as inputs to GCHP
+- Added Australian Hg emissions for 2000-2019 from MacFarlane et. al. [2022], plus corresponding mask file
+- Added comments in GEOS-Chem Classic `HISTORY.rc` template files advising users not to change the `BoundaryConditions.frequency` setting
+- Added `.zenodo.json` for auto-DOI generation upon version releases
 
 ### Changed
 - Renamed `Emiss_Carbon_Gases` to `CO2_Production` in `carbon_gases_mod.F90`
@@ -83,10 +144,12 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 - Fixed bug in GC-Classic OCS emissions where unit conversion of km2 to m2 occurred twice
 - Changed dimension of EmisOCS_Total from 3D to 2D since all emissions for all sectors are 2D
 - Added fixes to only apply archived PCO_CH4 field for carbon simulations with CO only
+- Reverted CH4 livestock emissions to EDGAR v7 to avoid hotspots and to apply seasonality
 
 ### Removed
 - Removed duplicate `WD_RetFactor` tag for HgClHO2 in `species_database.yml`
 - Removed error messages in HEMCO interface pointing users to HEMCO log
+- Removed unused RUNDIR settings for GCHP pressure units and scaling
 
 ## [14.5.0] - 2024-11-07
 ### Added
@@ -181,7 +244,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 - Added Cloud-J status output and error handling for it
 
 ### Changed
-- Alphabetically sort Complex SOA species into `geoschem_config.yml` in run directory creation 
+- 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

GeosCore/aerosol_mod.F90

@@ -124,10 +124,12 @@ SUBROUTINE AEROSOL_CONC( Input_Opt,  State_Chm, State_Diag, &
 !
     USE ErrCode_Mod
     USE ERROR_MOD
-#if !defined( MODEL_CESM )
+
+#if !defined( MODEL_CESM ) && !defined( MODEL_BCC )
     USE HCO_State_GC_Mod,     ONLY : HcoState
     USE HCO_Utilities_GC_Mod, ONLY : HCO_GC_EvalFld
 #endif
+
     USE Input_Opt_Mod,     ONLY : OptInput
     USE Species_Mod,       ONLY : SpcConc
     USE State_Chm_Mod,     ONLY : ChmState
@@ -280,13 +282,15 @@ SUBROUTINE AEROSOL_CONC( Input_Opt,  State_Chm, State_Diag, &
     ENDIF
 
     IF ( RC /= GC_SUCCESS ) RETURN
-#if !defined( MODEL_CESM )
+
+#if !defined( MODEL_CESM )  && !defined( MODEL_BCC )
     CALL HCO_GC_EvalFld( Input_Opt, State_Grid, Trim(FieldName), State_Chm%OMOC, RC, FOUND=FND )
 #else
     FND = .True.
     RC  = GC_SUCCESS
 #endif
 
+
     IF ( RC == GC_SUCCESS .AND. FND ) THEN
 
        ! Set OM/OC using spatially and seasonally varying data from

GeosCore/airs_ch4_mod.F90

@@ -371,7 +371,7 @@ SUBROUTINE CALC_AIRS_CH4_FORCE( Input_Opt, State_Chm, State_Grid, &
     USE State_Grid_Mod,     ONLY : GrdState
     USE State_Met_Mod,      ONLY : MetState
     USE Timers_Mod,         ONLY : Timer_End, Timer_Start
-    USE UnitConv_Mod
+    USE UnitConv_Mod,       ONLY : Check_Units, MOLES_SPECIES_PER_MOLES_DRY_AIR
 !
 ! !INPUT PARAMETERS:
 !
@@ -517,33 +517,13 @@ SUBROUTINE CALC_AIRS_CH4_FORCE( Input_Opt, State_Chm, State_Grid, &
     print*, ' for hour range: ', GET_HOUR(), GET_HOUR()+1
     print*, ' found # AIRS observations: ', NOBS
 
-    ! Halt diagnostics timer (so that unit conv can be timed separately)
-    IF ( Input_Opt%useTimers ) THEN
-       CALL Timer_End( "Diagnostics", RC )
-    ENDIF
-
-    ! Convert species units to [v/v] (mps, 6/12/2020)
-    CALL Convert_Spc_Units(                                                  &
-         Input_Opt      = Input_Opt,                                         &
-         State_Chm      = State_Chm,                                         &
-         State_Grid     = State_Grid,                                        &
-         State_Met      = State_Met,                                         &
-         mapping        = State_Chm%Map_Advect,                              &
-         new_units      = MOLES_SPECIES_PER_MOLES_DRY_AIR,                   &
-         previous_units = previous_units,                                    &
-         RC             = RC                                                )
-
-    IF ( RC /= GC_SUCCESS ) THEN
-       ErrMsg = 'Unit conversion error (kg/kg dry -> v/v dry)'
+    ! Verify that incoming State_Chm%Species units are mol/mol dry air.
+    IF ( .not. Check_Units( State_Chm, MOLES_SPECIES_PER_MOLES_DRY_AIR ) ) THEN
+       ErrMsg = 'Not all species are in "mol/mol dry" units!'
        CALL GC_Error( ErrMsg, RC, ThisLoc )
        RETURN
     ENDIF
 
-    ! Start diagnostics timer again
-    IF ( Input_Opt%useTimers ) THEN
-       CALL Timer_Start( "Diagnostics", RC )
-    ENDIF
-
     !! need to update this in order to do i/o with this loop parallel 
     !!      ! Now do a parallel loop for analyzing data 
     !!$OMP PARALLEL DO
@@ -705,33 +685,6 @@ SUBROUTINE CALC_AIRS_CH4_FORCE( Input_Opt, State_Chm, State_Grid, &
     ENDDO  ! NT
     !!$OMP END PARALLEL DO
 
-    ! Halt diagnostics timer (so that unit conv can be timed separately)
-    IF ( Input_Opt%useTimers ) THEN
-       CALL Timer_End( "Diagnostics", RC )
-    ENDIF
-
-    ! Convert species units back to original unit (mps, 6/12/2020)
-    CALL Convert_Spc_Units(                                                  &
-         Input_Opt  = Input_Opt,                                             &
-         State_Chm  = State_Chm,                                             &
-         State_Grid = State_Grid,                                            &
-         State_Met  = State_Met,                                             &
-         mapping    = State_Chm%Map_Advect,                                  &
-         new_units  = previous_units,                                        &
-         RC         = RC                                                    )
-
-    ! Trap errors
-    IF ( RC /= GC_SUCCESS ) THEN
-       ErrMsg = 'Unit conversion error'
-       CALL GC_Error( ErrMsg, RC, ThisLoc )
-       RETURN
-    ENDIF
-
-    ! Start diagnostics timer
-    IF ( Input_Opt%useTimers ) THEN
-       CALL Timer_Start( "Diagnostics", RC )
-    ENDIF
-
 283 FORMAT( I10,2x,I4,2x,I4,2x,F8.3,2x,F8.4,2x,I4,2x,I2,2x,I2,2x,I2, &
             2x,I2,2x,I2,2x,F12.3,2x,E12.6,2x,E12.6,2x,E12.6, &
             2x, E12.6,2x, E12.6,2x,  F12.3, 2x,E12.6, 2x, E12.6, 2x, &

GeosCore/calc_met_mod.F90

@@ -336,12 +336,15 @@ SUBROUTINE AIRQNT( Input_Opt, State_Chm, State_Grid, State_Met, &
        ! Set wet air pressures [hPa]
        ! (lower edge, delta, centroid, and spatially-weighted mean)
        !=============================================================
-
+#ifdef MODEL_BCC
+       PEdge_Top=State_Met%PEDGE(I,J,L+1)
+#else
        ! Pressure at bottom edge of grid box [hPa]
        State_Met%PEDGE(I,J,L) = GET_PEDGE(I,J,L)
 
        ! Pressure at top edge of grid box [hPa]
        PEdge_Top = GET_PEDGE(I,J,L+1)
+#endif
 
        ! Pressure at bottom edge of grid box [hPa](level State_Grid%NZ+1 only)
        IF ( L == State_Grid%NZ ) THEN
@@ -355,7 +358,9 @@ SUBROUTINE AIRQNT( Input_Opt, State_Chm, State_Grid, State_Met, &
        ! ( PEDGE(L) + PEDGE(L+1) ) / 2. This represents the grid box
        ! mass centroid pressure. Use in the ideal gas law yields
        ! a local air density at the centroid.
+#if !defined (MODEL_BCC) 
        State_Met%PMID(I,J,L) = GET_PCENTER( I, J, L )
+#endif
 
        !=============================================================
        ! Calculate water vapor saturation pressure [hPa]
@@ -483,8 +488,9 @@ SUBROUTINE AIRQNT( Input_Opt, State_Chm, State_Grid, State_Met, &
 
        ! Update dry pressure difference as calculated from the
        ! dry surface pressure
+#if !defined (MODEL_BCC) 
        State_Met%DELP_DRY(I,J,L) = GET_DELP_DRY(I,J,L)
-
+#endif
        !==============================================================
        ! Set mass of dry air in grid box [kg]
        !==============================================================