Merge updates from GEOS-Chem 14.7.1 into dev/14.8.0

This merge brings updates from GEOS-Chem 14.7.1 (the "main" branch)
into the dev/14.8.0 branch.

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

Author: yantosca

.github/workflows/stale.yml

@@ -18,7 +18,7 @@ jobs:
       pull-requests: write
 
     steps:
-    - uses: actions/stale@v5
+    - uses: actions/stale@v10
       with:
         repo-token: ${{ secrets.GITHUB_TOKEN }}
         stale-issue-label: 'stale'

AUTHORS.txt

@@ -1,8 +1,9 @@
 List of Developers for GEOS-Chem, HEMCO, and Related Software
-(23 May 2024)
+(08 Apr 2026)
 ===============================================================================
 
 ADAMS, Peter
+AKINJOLE, Samuel
 ALEXANDER, Becky
 ALVARADO, Matthew
 AMOS, Helen
@@ -15,6 +16,7 @@ BARKLEY, Michael
 BARRET, Steven
 BARRET, Brice
 BATES, Kelvin
+BERTOLACCI, Michael
 BEY, Isabelle
 BINDLE, Liam
 BOERSMA, Folkert
@@ -43,6 +45,7 @@ CAROUGE, Claire
 CARTER, Therese (Tess)
 CAZORLA, Maria
 CHALIYAKUNNEL, Sreelekha
+CHAN, Yuk Chun
 CHAN MILLER, Christopher
 CHEN, Han
 CHEN, Jing
@@ -52,7 +55,9 @@ CHEN, Qianjie
 CHEN, Xin
 CHEN, Yang
 CHOI, Yunsoo
+CHEN, Zichong
 CHRISTIAN, Kenneth
+CLARIZIO, Tessa
 CLUNE, Tom
 COOPER, Matt
 CORBITT, Bess
@@ -98,13 +103,16 @@ FU, Joshua
 GANTT, Brett
 GE, Cui
 GEDDES, Jeffrey
+GEYMAN, Benjamin
 GIANG, Amanda
 GIANNAKOPOULOS, Christos
 GOUNIA, Harriet
 GRAEF, Edward
 GREENSLADE, Jesse
+GRIFFITHS, Alan
 GU, Xiaoguang
 HAMMER, Melanie
+HANCOCK, Sarah
 HASKINS, Jessica
 HE, Cenlin
 HE, Jourdan
@@ -114,8 +122,10 @@ HENZE, Daven
 HO, Wai-Lo
 HORDIICHUK, Myroslav
 HOLMES, Christopher
+HORNER, Rebekah (Bex)
 HOROWITZ, Hannah
 HOSSENI, Zahra
+HOUGH, Ian
 HU, Lu
 HUANG, Jianping
 HUANG, Jiayue
@@ -157,6 +167,7 @@ LE SAGER, Philippe
 LEE, Chulkyu
 LEE, Colin
 LEE, Meemong
+LEE, Tabitha
 LEHMANN, Ralph
 LEIBENSPERGER, Eric
 LERICHE, Maud
@@ -182,11 +193,13 @@ LIU, Tina
 LIU, Yang
 LIU, Ying
 LOGAN, Jennifer
+LOMAN, Matthew
 LONG, Mike
 LU, Xiao
 LUNDGREN, Lizzie
 LUO, Gan
 MAASAKKERS, J. D. (Bram)
+MACFARLANE, Stephen
 MACINTYRE, Helen
 MACKENZIE, Dave
 MAHIEU, Emmanuel
@@ -196,6 +209,7 @@ MARKS, Marguerite
 MARKUS, Arjen
 MARTIN, Randall
 MARVIN, Maggie
+MAYHEW, Alfred
 MCDUFFIE, Erin
 MCGUFFIN, Dana
 MCLINDEN, Chris
@@ -217,8 +231,10 @@ MURPHY, Killian
 MURRAY, Lee
 NAM, Jun
 NASSAR, Ray
+NASSAU, Racine
 NATHAN, Brian
 NENES, Athanasios
+NESSER, Hannah
 NEVISON, Cynthia
 NIELSEN, Eric
 NOTHOLT, Justus
@@ -269,6 +285,7 @@ SHEN, Lu
 SHERWEN, Tomas
 SHUTTER, Joshua
 SILVA, Sam
+SINGH, Inderjeet
 SMITH-DOWNEY, Nicole
 SOERENSEN, Anne Laerke
 SOFEN, Eric
@@ -281,12 +298,15 @@ STERN, Rebecca
 STEVENS, Robin
 STREETS, David
 STRODE, Sarah
+STURM, Obin
 SU, Flora
 SULPRIZIO, Melissa
+SUN, Jordan
 SUN, Minmin
 SUNDERLAND, Elsie
 SUNTHARALINGAM, Parvada
 SURL, Luke
+SUSELJ, Kay
 SUTHERLAND, Bethany
 SUTO, Kimito
 SZELAG, Monika
@@ -317,11 +337,15 @@ VITT, Francis
 VOHRA, Karn
 WAGSTROM, Kristina
 WALKER, Thomas
+WALLWORK, Joe
+WANG, Daisy
 WANG, James
 WANG, Jun
 WANG, Qiaoqiao
-WANG, Xuan
 WANG, Xiaoli
+WANG, Xiaolin
+WANG, Xuan
+WANG, Yi
 WANG, Yuhang
 WANG, Yuting
 WANG, Yuxuan
@@ -340,6 +364,7 @@ WU, Shiliang
 XIAO, Yaping
 XU, Junwei
 YAN, Yingying
+YANG, Laura
 YANNETTI, Matt
 YANTOSCA, Bob
 YATTEAU, Jack
@@ -362,6 +387,7 @@ ZHANG, Li
 ZHANG, Lin
 ZHANG, Qiang
 ZHANG, Yanxu
+ZHANG, Yuanjian
 ZHU, Haihui
 ZHU, Lei
 ZHU, Liye

CHANGELOG.md

@@ -10,14 +10,68 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 - Added methanediol (MDL) as a transported gas-phase species and to the KPP fullchem and custom mechanisms
 - Added routine `Cloud_CH2O_MDL` in `KPP/fullchem/fullchem_SulfurChemFuncs.F90`
 
+## [14.7.1] - 2026-04-08
+### Added
+- Added `HTAP_SHIP` toggle in `HEMCO_Config.rc.carbon` templates for GC-Classic and GCHP
+- Added routines `Lookup_Grid` and `Register_State_Grid` to `Headers/state_grid_mod.F90`
+- Added `State_Grid` as an argument to History routines `History_Init`, `History_AddItemToCollection`,`History_NetCdf_Define`, `History_Write`, and `IndexVarList_Create`
+- Added routine `History_InitCoordVars` to `history_mod.F90`
+- Added cloud fraction and cloud top pressure to the SatDiagn diagnostic collection
+- Added new field `Input_Opt%CloudJ_Verbose`
+- Added `cloud-j:verbose` YAML tag (with default setting `false`) to  `geoschem_config.yml` templates for GC-Classic, GCHP, GEOS, CESM, and WRF
+- Added routine `Print_Species_Global_Mass_From_VVDry` in `GeosUtil/print_mod.F90`
+- Added build setting `MPI_LOAD_BALANCE` to enable MPI load balancing in chemistry to speed up GCHP runs
+- Added carbon Jacobian tracer simulation using KPP as a build-time option for use with the Integrated Methane Inversion
+- Added script within new folder KPP/carbon/util to expand carbon.eqn to include any number of CH4 Jacobian tracers
+- Added error traps to prevent integration tests and parallel tests from running if a conda environment with netCDF is active
+- Added GCHP run option in setCommonRunSettings.sh to use ExtData2G
+- Added ExtData2G yaml configuration file for GCHP transport tracer simulation
+- Added `${RUNDIR_READ_RESTART_AS_REAL8}` to GEOS-Chem Classic  `geoschem_config.yml` template files
+- Added error trap to routine `Get_GC_Restart` to halt simulations that use `read_restart_as_real8: true` with a reduced vertical grid
+- Added `State_Met%MaxChemLev` and `State_Met%MaxStratLev` integer fields
+- Added `Init_MaxChemLev` routine in `GeosUtil/pressure_mod.F90`, called from routine `Init_Pressure`
+- Added `State_Met` argument to routines `Init_Photolysis`, `Set_Clim_Profiles`, `GC_Init_Extra`, `Init_Pressure`, `Init_Mercury`, `Init_Sulfate`
+
+### Changed
+- Update termite CH4 emissions to the CAMS-GLOB-TERM_v1.1 product
+- Updated routine `SAFETY` (in `GeosCore/wetscav_mod.F90`) to reset small or negative values to zero
+- Moved coordinate variables for GC-Classic History netCDF files from `GeosUtil/grid_registry_mod.F90` to the `State_Grid` object
+- Changed several `State_Grid` fields from `fp` to `f8` precision. (In practice both are `REAL*8` but this makes it more explicit.)
+- Moved the population of coordinate variables for History netCDF  output from `grid_registry_mod.F90` to `history_mod.F90` (in routine `History_InitCoordVars`)
+- Updated `run/GCHP/setCommonRunSettings.template` to disable the HEMCO PARANOx extension for C360 or C720 grids
+- Updated `createRunDir.sh` scripts for GC-Classic and GCHP to turn on offline bulk seasalt emissions and bulk dust emissions in TOMAS simulations
+- Updated `Interfaces/GCClassic/main.F90` to call`Print_Species_Global_Mass_from_VVDry` (instead of`Print_Species_Global_Mass`) in order to avoid numerical differences when verbose printout is on
+- Renamed `Carbon` collection to `ProdLoss` collection in GCClassic and GCHP `HISTORY.rc.carbon` templates
+- Updated GitHub Action `stale@v5` to `stale@v10` in order to avoid deprecation warnings
+- Moved logic to determine whether we read the restart file as `REAL*8` from `run/shared/setupConfigFiles.sh` to `run/GCClassic/createRunDir.sh`
+- Simplified the logic where `isGMAO` and `State_Grid%NativeNZ` are computed in `GeosUtil/gc_grid_mod.F90`
+- Changed definition of `State_Grid%MaxChemLev` and `State_Grid%MaxStratLev` to be the 1 hPa level
+- Moved `MaxChemLev` and `MaxStratLev` fields from `State_Grid` to `State_Met`
+- Removed `State_Grid%MaxTropLev` field
+
+### Fixed
+- Fixed incorrect unit conversion from v/v -> molec/cm3 in `planeflight_mod.F90`
+- Fixed typo in the call to `Finalize` for the `State_Diag%ProdOCPIfromOCPO` diagnostic array
+- Fixed a syntax error in mass flux scaling calculation
+- Fixed an I/O error that caused an infinite loop reading when extra newlines are present at the end of `HISTORY.rc` (GC-Classic only)
+- Fixed timestep mismatch between GCHP C180 and GCC 0.5x0.625
+- Fixed incorrect dust species names in `run/GCClassic/HEMCO_Diagn.rc.templates/HEMCO_Diagn.rc.fullchem.onlineE` 
+- Fixed incorrect extension number for `InvDustL23M` entries in `run/GCHP/HEMCO_Diagn.rc.templates/HEMCO_Diagn.rc.fullchem`
+
+### Removed
+- Removed `ARCTAS_SHIP`, `CORBETT_SHIP`, `ICOADS_SHIP` from `HEMCO_Config.rc` template files
+- Retired Fung termite and soil absorption emission options from carbon simulation
+- Removed `GeosUtil/grid_registry_mod.F90`.
+- Removed `OHconcAfterChem` from GCClassic and GCHP `HISTORY.rc.carbon` templates, as OH is fixed during the simulation
+- Removed `State_Grid` argument from `Set_Prof_FJX` routine
+
 ## [14.7.0] - 2026-02-05
 ### Added
 - Added entries for FINNv25 biomass burning emissions to template HEMCO configuration files
 - Added comments to `HEMCO_Diagn.rc` template files instructing users on which ExtNr/Cat/Hier to use for online vs. offline biomass burning emissions
 - Added subroutine `Print_Species_Global_Mass` to print_mod for use by GC-Classic
 - Added log print of species global mass at start of each timestep if verbose is true
 - Added print of global mass computed from restart file values if delta pressure present in restart file
-- Added the capability for GCHP simulations to use CH4 restarts for Jacobian Tracers
 - Added operational run scripts for WashU Compute2
 - Added the option for LPJ_MERRA2 wetland CH4 emissions in CH4 and carbon simulations
 - Added GC-Classic config file option to read restart file as `REAL*8` via GEOS-Chem rather than HEMCO

GeosCore/aero_drydep.F90

@@ -305,11 +305,11 @@ SUBROUTINE AERO_DRYDEP( Input_Opt,  State_Chm, State_Diag, &
              ENDDO
 
              ! We know the boundary condition at the model top
-             L     = State_Grid%MaxChemLev
+             L     = State_Met%MaxChemLev
              DELZ  = BXHEIGHT(I,J,L)           ![=] meter
              TC(L) = TC(L) / ( 1.d0 + DTCHEM * VTS(L) / DELZ )
 
-             DO L = State_Grid%MaxChemLev-1, 1, -1
+             DO L = State_Met%MaxChemLev-1, 1, -1
                 DELZ  = BXHEIGHT(I,J,L)
                 DELZ1 = BXHEIGHT(I,J,L+1)
                 TC(L) = 1.d0 / &
@@ -364,7 +364,7 @@ SUBROUTINE AERO_DRYDEP( Input_Opt,  State_Chm, State_Diag, &
     !$OMP SCHEDULE( DYNAMIC )
     DO I = 1, State_Grid%NX
     DO J = 1, State_Grid%NY
-    DO L = 1, State_Grid%MaxChemLev
+    DO L = 1, State_Met%MaxChemLev
 
        ! Initialize for safety's sake
        AREA_CM2 = 0d0

GeosCore/aerosol_mod.F90

@@ -1894,7 +1894,7 @@ SUBROUTINE RDAER( Input_Opt, State_Chm, State_Diag, State_Grid, State_Met, &
                 !  Hygroscopic growth of Sea Salt (accum)   [unitless]
                 !  Hygroscopic growth of Sea Salt (coarse)  [unitless]
                 IF ( State_Diag%Archive_AerHygGrowth .AND. &
-                     L <= State_Grid%MaxChemLev      .AND. &
+                     L <= State_Met%MaxChemLev       .AND. &
                      ODSWITCH.EQ.1 ) THEN
                    S = State_Diag%Map_AerHygGrowth%id2slot(NA)
                    IF ( S > 0 ) THEN

GeosCore/calc_met_mod.F90

@@ -579,10 +579,10 @@ SUBROUTINE AIRQNT( Input_Opt, State_Chm, State_Grid, State_Met, &
 
        ! Is this grid box within the stratosphere (but not mesosphere)?
        State_Met%InStratosphere(I,J,L) = &
-            ( L <= State_Grid%MaxStratLev .and. State_Met%InStratMeso(I,J,L) )
+            ( L <= State_Met%MaxStratLev .and. State_Met%InStratMeso(I,J,L) )
 
        ! Is grid box (I,J,L) within the chemistry grid?
-       State_Met%InChemGrid(I,J,L) = ( L <= State_Grid%MaxChemLev )
+       State_Met%InChemGrid(I,J,L) = ( L <= State_Met%MaxChemLev )
 
     ENDDO
     ENDDO

GeosCore/carbon_gases_mod.F90

@@ -491,12 +491,6 @@ SUBROUTINE Chem_Carbon_Gases( Input_Opt,  State_Met,  State_Chm,            &
                I          = I,                                               &
                J          = J,                                               &
                L          = L,                                               &
-               id_CH4     = id_CH4,                                          &
-               id_CO      = id_CO,                                           &
-               id_CO2     = id_CO2,                                          &
-               xnumol_CH4 = xnumol_CH4,                                      &
-               xnumol_CO  = xnumol_CO,                                       &
-               xnumol_CO2 = xnumol_CO2,                                      &
                State_Met  = State_Met,                                       &
                State_Chm  = State_Chm                                       )
 
@@ -569,12 +563,6 @@ SUBROUTINE Chem_Carbon_Gases( Input_Opt,  State_Met,  State_Chm,            &
                I            = I,                                             &
                J            = J,                                             &
                L            = L,                                             &
-               id_CH4       = id_CH4,                                        &
-               id_CO        = id_CO,                                         &
-               id_CO2       = id_CO2,                                        &
-               xnumol_CO    = xnumol_CO,                                     &
-               xnumol_CH4   = xnumol_CH4,                                    &
-               xnumol_CO2   = xnumol_CO2,                                    &
                State_Chm    = State_Chm,                                     &
                State_Met    = State_Met                                     )
 
@@ -870,6 +858,7 @@ SUBROUTINE Init_Carbon_Gases( Input_Opt,  State_Chm, State_Diag,             &
 !
 ! !USES:
 !
+    USE carbon_Funcs,   ONLY : carbon_InitCarbonKPPFuncs
     USE gckpp_Global,   ONLY : SR_MW, HENRY_CR, HENRY_K0
     USE ErrCode_Mod
     USE Input_Opt_Mod,  ONLY : OptInput
@@ -944,6 +933,18 @@ SUBROUTINE Init_Carbon_Gases( Input_Opt,  State_Chm, State_Diag,             &
     IF ( id_OH  > 0 ) &
        xnumol_OH  = AVO / ( State_Chm%SpcData(id_OH )%Info%MW_g * 1.0e-3_fp )
 
+    !========================================================================
+    ! Initialize module variables in carbon_Funcs (in KPP)
+    !========================================================================
+    IF ( (id_CH4 > 0) .OR. (id_CO > 0) ) THEN
+       CALL carbon_InitCarbonKPPFuncs( xnumol_CH4, xnumol_CO, xnumol_CO2, RC )
+       IF ( RC /= GC_SUCCESS ) THEN
+          errMsg = 'Cannot initialize module variables in carbon_InitCarbonChem'
+          CALL GC_Error( errMsg, RC, thisLoc )
+          RETURN
+       ENDIF
+    ENDIF
+
     !========================================================================
     ! Initialize variables for COchemistry
     !========================================================================
@@ -972,6 +973,7 @@ SUBROUTINE Cleanup_Carbon_Gases( RC )
 ! !USES:
 !
     USE ErrCode_Mod
+    USE carbon_Funcs,   ONLY : carbon_CleanupCarbonKPPFuncs
 !
 ! !OUTPUT PARAMETERS:
 !
@@ -990,9 +992,10 @@ SUBROUTINE Cleanup_Carbon_Gases( RC )
     IF ( ALLOCATED( sumOfCosSza ) ) THEN
        DEALLOCATE( sumOfCosSza, STAT=RC )
        CALL GC_CheckVar( 'carbon_gases_mod.F90:sumOfCosSza', 2, RC )
-       RETURN
     ENDIF
 
+    CALL carbon_CleanupCarbonKPPFuncs( RC )
+
   END SUBROUTINE Cleanup_Carbon_Gases
 !EOC
 !------------------------------------------------------------------------------