Merge 14.3.1 release into dev/14.4.0 (PR #2232)

Resolved conflicts in:
	CHANGELOG.md
	GeosCore/global_ch4_mod.F90
	run/CESM/geoschem_config.yml

Signed-off-by: Melissa Sulprizio <[email protected]>

CHANGELOG.md

@@ -27,6 +27,55 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 - Legacy binary punch diagnostic code contained within `#ifdef BPCH_DIAG` blocks
 - `IU_BPCH` logical file unit (in `GeosUtil/file_mod.F90`)
 
+## [14.3.1] - 2024-04-02
+### Added
+- Added operational run scripts for the Imperial College London (ICL) cluster
+- Added new vertical region option to budget diagnostic for fixed bottom and top levels
+- Added GEOS-IT processed lat-lon fields as a valid option when creating GCHP run directories
+- Functions `charArr2str` and `str2CharArr` in `Headers/charpak_mod.F90`
+- Field `State_Diag%Obspack_CharArray` as a 2-D character array
+- Added util folder in run/CESM to include .cdl file used to generate CESM NetCDF input file for deposition
+- Add GCClassic operational example environment files for Harvard Cannon
+- Added new GCHP history collections for advection diagnostics
+- Added slash in front of names of LUT files read into `photolysis_mod.F90` to avoid needing it in path
+
+### Changed
+- Updated Harvard Cannon operational run scripts to use `huce_cascade` instead of `huce_intel`; also added `sapphire`
+- Changed exponent 'e' to 'd' for one entry in KPP to prevent precision error in external models
+- Changed GCHP sample run scripts to not print script execution commands to log
+- Changed offline emissions grid resolution templates in config files to be more descriptive
+- Read `obspack_id` from netCDF files into a character array, then convert to string
+- Add `#SBATCH -c 1` to GCHP integration test scripts and sample run scripts for Harvard Cannon
+- In GCC/GCHP integration tests, passing `-s none` will run compile-only tests. Query user to proceed or to exit.
+- GCC/GCHP integration tests will exit immediately if `scheduler` is omitted.
+- Now use `raw` instead of `native` in GCHP run directory scripts & templates
+- Rename env var `RUNDIR_METLIGHTNING_DIR_NATIVE` to `RUNDIR_METLIGHTNING_DIR`
+- Rename env var `RUNDIR_METLIGHTNING_NATIVE_RES` to `RUNDIR_METLIGHTNING_RES`
+- Updated config files used in CESM from GEOS-Chem 14.1 to 14.3
+- Don't create run directories for integration/parallel tests if invoked with `-t compile`
+- Refactor integration and parallel test scripts to reduce the number of input arguments
+- Copy utility scripts that allow you to resubmit failed to integration and parallel test root directories
+- Update GCHP operational example environment files for Harvard Cannon
+- Do not run GCClassic integration test compile jobs in the background
+- Updated integration tests to pass quick option to compile scripts
+- Removed emissions handling from `global_ch4_mod.F90` and `carbon_gases_mod.F90` and instead apply scale factors to emissions directly in `HEMCO_Config.rc`
+- Loop over advected species CH4 chemistry routines to allow for multiple CH4 tracers within analytical inversion framework
+- Updated CH4 global anthropogenic emission inventory from EDGARv7 to EDGARv8
+
+### Fixed
+- Fixed unit conversions in GEOS-only code
+- Fixed GEOS-IT native lat-lon filenames used for clusters other than discover
+- Fixed offline emission paths set when using GEOS-IT meteorology
+- Fixed format issue in input_mod RRTMG print statement caught by some compilers
+- Fixed GEOS-IT SLP and TROPP scaling in pre-processed files used in GCHP
+- Fixed reading of NEI emissions through HEMCO
+- Fixed incorrect units metadata for `State_Met%PHIS`
+- Fixed bug in transport tracer ST80 mask criteria which prevented mask from ever being zero
+
+### Removed
+- Removed MPI broadcasts in CESM-only photolysis code; will read on all cores
+- Removed State_Chm%CH4_EMIS
+
 ## [14.3.0] - 2024-02-07
 ### Added
 - Added capability for TOMAS simulations in GCHP

GeosCore/carbon_gases_mod.F90

@@ -32,10 +32,6 @@ MODULE Carbon_Gases_Mod
  PUBLIC :: Init_Carbon_Gases
  PUBLIC :: Cleanup_Carbon_Gases
 !
-! !PUBLIC DATA MEMBERS:
-!
- REAL(fp), ALLOCATABLE, PUBLIC :: CH4_EMIS_J(:,:,:) ! [kg/m2/s]
-!
 ! !REVISION HISTORY:
 ! 04 Apr 2022 - M.S. Long - Initial version, based on work by B. Bukosa
 ! See https://github.com/geoschem/geos-chem for complete history
@@ -116,13 +112,6 @@ SUBROUTINE Emiss_Carbon_Gases( Input_Opt, State_Chm, State_Diag, &
 ! !OUTPUT PARAMETERS:
 !
  INTEGER, INTENT(OUT) :: RC ! Success or failure?
-!
-! !REMARKS:
-! WARNING: Soil absorption has to be the 15th field in CH4_EMIS
-! Also: the ND58 diagnostics have now been removed. We still need to
-! read the HEMCO manual diagnostics into CH4_EMIS for the analytical
-! inversion. Therefore, we will keep EmissCh4 for the time-being
-! but only remove the bpch diagnostic.
 !EOP
 !------------------------------------------------------------------------------
 !BOC
@@ -180,102 +169,6 @@ SUBROUTINE Emiss_Carbon_Gases( Input_Opt, State_Chm, State_Diag, &
  ! Emission timestep
  dtSrce = HcoState%TS_EMIS
 
- !========================================================================
- ! CH4 emissions
- !
- ! --> All emission calculations are now done through HEMCO
- ! HEMCO stores emissions of all species internally in the HEMCO
- ! state object. Here, we pass these emissions into module array
- ! CH4_EMIS in units kg/m2/s. These values are then either added to
- ! the species array (full mixing scheme) or used later on in
- ! vdiff_mod.F90 if the non-local PBL mixing scheme is used.
- !
- ! The CH4_EMIS array is mostly used for backwards compatibility
- ! (especially the diagnostics). It is also used to ensure that
- ! in a multi-species simulation, species 1 (total CH4) is properly
- ! defined.
- ! (ckeller, 9/12/2013)
- !========================================================================
- IF ( id_CH4 > 0 ) THEN
-
- ! Initialize
- CH4_EMIS_J = 0.0_fp
- CH4scale = 1.0_hp
- CH4diag(1) = 'CH4'
- CH4diag(2) = 'CH4_OIL'
- CH4diag(3) = 'CH4_GAS'
- CH4diag(4) = 'CH4_COAL'
- CH4diag(5) = 'CH4_LIVESTOCK'
- CH4diag(6) = 'CH4_LANDFILLS'
- CH4diag(7) = 'CH4_WASTEWATER'
- CH4diag(8) = 'CH4_RICE'
- CH4diag(9) = 'CH4_ANTHROTHER'
- CH4diag(10) = 'CH4_BIOMASS'
- CH4diag(11) = 'CH4_WETLAND'
- CH4diag(12) = 'CH4_SEEPS'
- CH4diag(13) = 'CH4_LAKES'
- CH4diag(14) = 'CH4_TERMITES'
- CH4diag(15) = 'CH4_SOILABSORB' ! CH4 soilabsorb values are negative!
- CH4diag(16) = 'CH4_RESERVOIRS'
- CH4scale(15) = -1.0_hp ! Need to convert to positive
-
- ! Loop over manual CH4 diagnostics
- DO N = 2, N_CH4_DIAGS
-
- ! Get a pointer to the emissions
- CALL HCO_GC_GetDiagn( Input_Opt, State_Grid, CH4diag(N), &
- .FALSE., RC, Ptr2D=Ptr2D )
-
- ! Trap potential errors
- IF ( RC /= HCO_SUCCESS ) THEN
- errMsg = 'Cannot get pointer to HEMCO field ' // TRIM(CH4diag(N))
- CALL GC_Error( errMsg, RC, thisLoc )
- RETURN
- ENDIF
- IF ( .not. ASSOCIATED( Ptr2D ) ) THEN
- errMsg = 'Cannot get pointer to HEMCO field ' // TRIM(CH4diag(N))
- CALL GC_Error( errMsg, RC, thisLoc )
- RETURN
- ENDIF
-
- ! Store emissions in CH4_EMIS_J [kg/m2/s]
- ! CH4scale is either -1 (for soil absorption) or 1 (everything else)
- CH4_EMIS_J(:,:,N) = Ptr2D * CH4scale(N)
-
- ! Free pointer for next iteration
- Ptr2D => NULL()
- ENDDO
-
- !---------------------------------------------------------------------
- ! Total emission: sum of all emissions - (2*soil absorption)
- ! We have to substract soil absorption twice because it is added
- ! to other emissions in the SUM function. (ccc, 7/23/09)
- !---------------------------------------------------------------------
- CH4_EMIS_J(:,:,1) = SUM( CH4_EMIS_J, 3 ) &
- - ( 2.0_fp * CH4_EMIS_J(:,:,15) )
-
- IF ( Input_Opt%Verbose ) THEN
- WRITE(*,*) 'CH4_EMIS (kg/m2/s):'
- WRITE(*,*) 'Total : ', SUM( CH4_EMIS_J(:,:,1 ) )
- WRITE(*,*) 'Oil : ', SUM( CH4_EMIS_J(:,:,2 ) )
- WRITE(*,*) 'Gas : ', SUM( CH4_EMIS_J(:,:,3 ) )
- WRITE(*,*) 'Coal : ', SUM( CH4_EMIS_J(:,:,4 ) )
- WRITE(*,*) 'Livestock : ', SUM( CH4_EMIS_J(:,:,5 ) )
- WRITE(*,*) 'Landfills : ', SUM( CH4_EMIS_J(:,:,6 ) )
- WRITE(*,*) 'Wastewater : ', SUM( CH4_EMIS_J(:,:,7 ) )
- WRITE(*,*) 'Rice : ', SUM( CH4_EMIS_J(:,:,8 ) )
- WRITE(*,*) 'Other anth : ', SUM( CH4_EMIS_J(:,:,9 ) )
- WRITE(*,*) 'Biomass burn : ', SUM( CH4_EMIS_J(:,:,10) )
- WRITE(*,*) 'Wetlands : ', SUM( CH4_EMIS_J(:,:,11) )
- WRITE(*,*) 'Seeps : ', SUM( CH4_EMIS_J(:,:,12) )
- WRITE(*,*) 'Lakes : ', SUM( CH4_EMIS_J(:,:,13) )
- WRITE(*,*) 'Termites : ', SUM( CH4_EMIS_J(:,:,14) )
- WRITE(*,*) 'Soil absorb : ', SUM( CH4_EMIS_J(:,:,15) )
- WRITE(*,*) 'Reservoirs : ', SUM( CH4_EMIS_J(:,:,16) )
- ENDIF
-
- ENDIF
-
  !========================================================================
  ! CO2 production from CO oxidation
  !========================================================================
@@ -1287,27 +1180,6 @@ SUBROUTINE Init_Carbon_Gases( Input_Opt, State_Chm, State_Diag, &
  IF ( RC /= GC_SUCCESS ) RETURN
  sumOfCosSza = 0.0_fp
 
- !========================================================================
- ! Initialize variables for CH4 chemistry
- !========================================================================
- IF ( id_CH4 > 0 ) THEN
- ALLOCATE( CH4_EMIS_J( State_Grid%NX, State_Grid%NY, N_CH4_DIAGS ), &
- STAT=RC )
- CALL GC_CheckVar( 'carbon_gases_mod.F90:CH4_EMIS', 0, RC )
- IF ( RC /= GC_SUCCESS ) RETURN
- CH4_EMIS_J = 0.0_fp
- ENDIF
-
- !========================================================================
- ! Initialize variables for CO2 chemistry
- !========================================================================
- ! none yet
-
- !========================================================================
- ! Initialize variables for OCS chemistry
- !========================================================================
- ! none yet
-
  END SUBROUTINE Init_Carbon_Gases
 !EOC
 !------------------------------------------------------------------------------
@@ -1343,13 +1215,6 @@ SUBROUTINE Cleanup_Carbon_Gases( RC )
  ! Initialize
  RC = GC_SUCCESS
 
- ! Deallocate
- IF ( ALLOCATED( CH4_EMIS_J ) ) THEN
- DEALLOCATE( CH4_EMIS_J, STAT=RC )
- CALL GC_CheckVar( 'carbon_gases_mod.F90:CH4_EMIS', 2, RC )
- RETURN
- ENDIF
-
  IF ( ALLOCATED( sumOfCosSza ) ) THEN
  DEALLOCATE( sumOfCosSza, STAT=RC )
  CALL GC_CheckVar( 'carbon_gases_mod.F90:sumOfCosSza', 2, RC )

GeosCore/chemistry_mod.F90

@@ -168,6 +168,7 @@ SUBROUTINE Do_Chemistry( Input_Opt, State_Chm, State_Diag, &
  CALL Compute_Budget_Diagnostics( &
  Input_Opt = Input_Opt, &
  State_Chm = State_Chm, &
+ State_Diag = State_Diag, &
  State_Grid = State_Grid, &
  State_Met = State_Met, &
  isFull = State_Diag%Archive_BudgetChemistryFull, &
@@ -179,6 +180,9 @@ SUBROUTINE Do_Chemistry( Input_Opt, State_Chm, State_Diag, &
  isPBL = State_Diag%Archive_BudgetChemistryPBL, &
  diagPBL = NULL(), &
  mapDataPBL = State_Diag%Map_BudgetChemistryPBL, &
+ isLevs = State_Diag%Archive_BudgetChemistryLevs, &
+ diagLevs = NULL(), &
+ mapDataLevs = State_Diag%Map_BudgetChemistryLevs, &
  colMass = State_Diag%BudgetColumnMass, &
  before_op = .TRUE., &
  RC = RC )
@@ -1101,6 +1105,7 @@ SUBROUTINE Do_Chemistry( Input_Opt, State_Chm, State_Diag, &
  CALL Compute_Budget_Diagnostics( &
  Input_Opt = Input_Opt, &
  State_Chm = State_Chm, &
+ State_Diag = State_Diag, &
  State_Grid = State_Grid, &
  State_Met = State_Met, &
  isFull = State_Diag%Archive_BudgetChemistryFull, &
@@ -1112,6 +1117,9 @@ SUBROUTINE Do_Chemistry( Input_Opt, State_Chm, State_Diag, &
  isPBL = State_Diag%Archive_BudgetChemistryPBL, &
  diagPBL = State_Diag%BudgetChemistryPBL, &
  mapDataPBL = State_Diag%Map_BudgetChemistryPBL, &
+ isLevs = State_Diag%Archive_BudgetChemistryLevs, &
+ diagLevs = State_Diag%BudgetChemistryLevs, &
+ mapDataLevs = State_Diag%Map_BudgetChemistryLevs, &
  colMass = State_Diag%BudgetColumnMass, &
  timeStep = DT_Chem, &
  RC = RC )

GeosCore/cldj_interface_mod.F90

@@ -160,7 +160,7 @@ SUBROUTINE Run_CloudJ( Input_Opt, State_Chm, State_Diag, &
  USE Cldj_Cmn_Mod, ONLY : L_, L1_, W_, S_, LWEPAR
  USE Cldj_Cmn_Mod, ONLY : JVN_, AN_, NQD_, W_r
  USE Cldj_Cmn_Mod, ONLY : JIND, JFACTA, FL, QAA, RAA, SAA
- USE Cld_Sub_Mod,  ONLY : Cloud_JX
+ USE Cldj_Sub_Mod, ONLY : Cloud_JX
  USE Cmn_Size_Mod, ONLY : NRHAER, NRH, NDUST
  USE ErrCode_Mod
  USE Input_Opt_Mod, ONLY : OptInput

GeosCore/convection_mod.F90

@@ -137,6 +137,7 @@ SUBROUTINE DO_CONVECTION( Input_Opt, State_Chm, State_Diag, &
  CALL Compute_Budget_Diagnostics( &
  Input_Opt = Input_Opt, &
  State_Chm = State_Chm, &
+ State_Diag = State_Diag, &
  State_Grid = State_Grid, &
  State_Met = State_Met, &
  isFull = State_Diag%Archive_BudgetConvectionFull, &
@@ -148,6 +149,9 @@ SUBROUTINE DO_CONVECTION( Input_Opt, State_Chm, State_Diag, &
  isPBL = State_Diag%Archive_BudgetConvectionPBL, &
  diagPBL = NULL(), &
  mapDataPBL = State_Diag%Map_BudgetConvectionPBL, &
+ isLevs = State_Diag%Archive_BudgetConvectionLevs, &
+ diagLevs = NULL(), &
+ mapDataLevs = State_Diag%Map_BudgetConvectionLevs, &
  colMass = State_Diag%BudgetColumnMass, &
  before_op = .TRUE., &
  RC = RC )
@@ -350,6 +354,7 @@ SUBROUTINE DO_CONVECTION( Input_Opt, State_Chm, State_Diag, &
  CALL Compute_Budget_Diagnostics( &
  Input_Opt = Input_Opt, &
  State_Chm = State_Chm, &
+ State_Diag = State_Diag, &
  State_Grid = State_Grid, &
  State_Met = State_Met, &
  isFull = State_Diag%Archive_BudgetConvectionFull, &
@@ -361,6 +366,9 @@ SUBROUTINE DO_CONVECTION( Input_Opt, State_Chm, State_Diag, &
  isPBL = State_Diag%Archive_BudgetConvectionPBL, &
  diagPBL = State_Diag%BudgetConvectionPBL, &
  mapDataPBL = State_Diag%Map_BudgetConvectionPBL, &
+ isLevs = State_Diag%Archive_BudgetConvectionLevs, &
+ diagLevs = State_Diag%BudgetConvectionLevs, &
+ mapDataLevs = State_Diag%Map_BudgetConvectionLevs, &
  colMass = State_Diag%BudgetColumnMass, &
  timeStep = DT_Conv, &
  RC = RC )