Merge branch 'dev/14.3.0' into feature/updates_from_gmao

CHANGELOG.md

@@ -5,14 +5,24 @@ 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 14.3.0] - TBD
+### Added
+- Added capability for TOMAS simulations in GCHP
+- Added State_Chm%nTomasBins to replace hardcoded bins in TOMAS diagnostics
+
 ### Changed
 - Updated fullchem mechanism following JPL/IUPAC. See `KPP/fullchem/CHANGELOG_fullchem.md` for details.
+- Converted TOMAS bpch diagnostics to netCDF
 
 ### Fixed
 - Fixed bug in stratospheric aerosols optical depths passed to Fast-JX
 - Restored consideration of both isSnow and isIce in dry deposition
 - Fixed calculation of FRLAND_NOSNO_NOICE in `calc_met_mod.F90`
 
+### Added
+- Added interface to Cloud-J package for computing photolysis rates
+- Added compile-time option FASTJX to use legacy Fast-JX photolysis instead of Cloud-J
+- Added new diagnostics OD600 and TCOD600 for 600 nm optical depths (per-level and total column) used for computing J-values in either Fast-JX or Cloud-J
+
 ## [14.2.3] - 2023-12-01
 ### Added
 - GEOS-Chem Classic rundir script `run/GCClassic/setupForRestarts.sh`

GeosCore/CMakeLists.txt

@@ -25,6 +25,7 @@ add_library(GeosCore
   carbon_gases_mod.F90
   chemistry_mod.F90
   cldice_HBrHOBr_rxn.F90
+  cldj_interface_mod.F90
   cleanup.F90
   co2_mod.F90
   convection_mod.F90

GeosCore/aero_drydep.F90

@@ -8,7 +8,7 @@
 !
 ! !DESCRIPTION: Subroutine AERO\_DRYDEP removes size-resolved aerosol number
 !  and mass by dry deposition.  The deposition velocities are calcualted from
-!  drydep_mod.f and only aerosol number NK1-NK30 are really treated as dry
+!  drydep_mod.f and only aerosol number NK01-NK30 are really treated as dry
 !  depositing species while each of the mass species are depositing accordingly
 !  with number.
 !\\
@@ -72,11 +72,11 @@ SUBROUTINE AERO_DRYDEP( Input_Opt,  State_Chm, State_Diag, &
     LOGICAL,  SAVE     :: FIRST      = .TRUE.
     INTEGER,  SAVE     :: H2SO4ID
     INTEGER,  SAVE     :: id_H2SO4
-    INTEGER,  SAVE     :: id_NK1
+    INTEGER,  SAVE     :: id_NK01
 
     ! Scalars
-    INTEGER            :: nDryDep
-    INTEGER            :: I,      J,        L
+    INTEGER            :: nDryDep, IBINS
+    INTEGER            :: I,      J,        L,     AS
     INTEGER            :: N,      JC,       BIN,   ID
     REAL(fp)           :: DTCHEM, AREA_CM2, FLUX,  X,    Y
     REAL(fp)           :: Y0,     RKT,      DEN,   DP,   PDP
@@ -90,20 +90,20 @@ SUBROUTINE AERO_DRYDEP( Input_Opt,  State_Chm, State_Diag, &
     REAL(fp)           :: TC(State_Grid%NZ)
     REAL(fp)           :: TC0(State_Grid%NZ)
     REAL(fp)           :: VTS(State_Grid%NZ) ! Settling V [m/s]
-    REAL(fp)           :: NU0(State_Grid%NX,State_Grid%NY,State_Grid%NZ,IBINS)
-    REAL(fp)           :: DU0(State_Grid%NX,State_Grid%NY,State_Grid%NZ,IBINS)
-    REAL(fp)           :: SIZ_DIA(State_Grid%NX,State_Grid%NY,IBINS)
-    REAL(fp)           :: SIZ_DEN(State_Grid%NX,State_Grid%NY,IBINS)
-    REAL(fp)           :: X0(IBINS,ICOMP-IDIAG+1    )
+    REAL(fp)           :: NU0(State_Grid%NX,State_Grid%NY,State_Grid%NZ,State_Chm%nTomasBins)
+    REAL(fp)           :: DU0(State_Grid%NX,State_Grid%NY,State_Grid%NZ,State_Chm%nTomasBins)
+    REAL(fp)           :: SIZ_DIA(State_Grid%NX,State_Grid%NY,State_Chm%nTomasBins)
+    REAL(fp)           :: SIZ_DEN(State_Grid%NX,State_Grid%NY,State_Chm%nTomasBins)
+    REAL(fp)           :: X0(State_Chm%nTomasBins,ICOMP-IDIAG+1    )
 
     ! Pointers
     TYPE(SpcConc), POINTER  :: Spc     (:      )
     REAL(fp),      POINTER  :: BXHEIGHT(:,:,:  )
     REAL(fp),      POINTER  :: T       (:,:,:  )
-    REAL(fp),      POINTER  :: DepFreq (:,:,:  )                ! IM, JM, nDryDep
+    REAL(fp),      POINTER  :: DepFreq (:,:,:  )  ! IM, JM, nDryDep
 
     ! SAVEd arrays
-    INTEGER,  SAVE     :: DRYD(IBINS)
+    INTEGER, SAVE, ALLOCATABLE :: DRYD(:)
 
     ! Debug
     !integer   :: ii, jj , ix, jx, bb, ll
@@ -119,6 +119,9 @@ SUBROUTINE AERO_DRYDEP( Input_Opt,  State_Chm, State_Diag, &
     ! Number of dry-deposited species
     nDryDep   = State_Chm%nDryDep
 
+    ! Number of bins
+    IBINS     = State_Chm%nTomasBins
+
     ! Check that species units are in [kg] (ewl, 8/13/15)
     IF ( State_Chm%Spc_Units /= KG_SPECIES ) THEN
        MSG = 'Incorrect species units: ' // TRIM(UNIT_STR(State_Chm%Spc_Units))
@@ -140,26 +143,29 @@ SUBROUTINE AERO_DRYDEP( Input_Opt,  State_Chm, State_Diag, &
 
        ! Define species ID flags
        id_H2SO4 = Ind_('H2SO4')
-       id_NK1   = Ind_('NK1'  )
+       id_NK01  = Ind_('NK01'  )
 
        ! Make sure species are defined
        IF ( id_H2SO4 < 0 ) THEN
           MSG = 'H2SO4 is not a defined species!'
           LOC = 'Routine AERO_DRYDEP in aero_drydep.F'
           CALL ERROR_STOP( MSG, LOC )
        ENDIF
-       IF ( id_NK1 < 0 ) THEN
-          MSG = 'NK1 is not a defined species!'
+       IF ( id_NK01 < 0 ) THEN
+          MSG = 'NK01 is not a defined species!'
           LOC = 'Routine AERO_DRYDEP in aero_drydep.F'
           CALL ERROR_STOP( MSG, LOC )
        ENDIF
 
+       ALLOCATE( DRYD( State_Chm%nTomasBins ), STAT=AS )
+       IF ( AS /= 0 ) CALL ALLOC_ERR( 'DRYD (aero_drydep.F90)' )
+       DRYD = 0
+
        ! First identify if the size-resolved aerosol species have their
        ! deposition velocity calculated.
        ! dryd is an array that keeps the drydep species ID.  So if the
        ! aerosol component has dryd = 0, that means it was not included
        ! as a dry depositting species.
-       DRYD = 0
        DO BIN = 1, IBINS
           DO N   = 1, nDryDep
              !just want to match only once (win, 5/24/06)
@@ -169,9 +175,9 @@ SUBROUTINE AERO_DRYDEP( Input_Opt,  State_Chm, State_Diag, &
                 ! Debug
                 !print *, 'DRYDEP Species:',N
              ENDIF
-             IF ( State_Chm%Map_DryDep(N) == ( id_NK1-1+BIN ) )THEN
+             IF ( State_Chm%Map_DryDep(N) == ( id_NK01-1+BIN ) )THEN
                 ! Debug
-                !print *,'Match species:',IDTNK1-1+bin,'Bin',bin
+                !print *,'Match species:',IDTNK01-1+bin,'Bin',bin
                 DRYD( BIN ) = N
                 GOTO 100
              ENDIF
@@ -213,7 +219,7 @@ SUBROUTINE AERO_DRYDEP( Input_Opt,  State_Chm, State_Diag, &
 
        ! SIZ_DIA [=] m  and SIZ_DEN [=] kg/m3
        CALL AERO_DIADEN( 1, Input_Opt, State_Chm, State_Grid, State_Met, &
-                         SIZ_DIA, SIZ_DEN, RC )
+                         State_Diag, SIZ_DIA, SIZ_DEN, RC )
        IF ( RC /= GC_SUCCESS ) THEN
           CALL ERROR_STOP('CALL AERO_DIADEN', 'AERO_DRYDEP in aero_drydep.F')
        ENDIF
@@ -286,7 +292,7 @@ SUBROUTINE AERO_DRYDEP( Input_Opt,  State_Chm, State_Diag, &
           ENDDO  ! L-loop
 
           DO JC = 1, ICOMP-IDIAG+1
-             ID = id_NK1 - 1 + BIN + ( IBINS * (JC-1) )
+             ID = id_NK01 - 1 + BIN + ( IBINS * (JC-1) )
 
              ! Debug
              !IF (i==ix .and. j==jx .and. l==ll) THEN
@@ -408,7 +414,7 @@ SUBROUTINE AERO_DRYDEP( Input_Opt,  State_Chm, State_Diag, &
        ! Save the initial 30-bin number and icomp-1 mass component
        DO JC = 1, ICOMP-IDIAG+1
           DO BIN = 1, IBINS
-             ID = id_NK1 - 1 + BIN + ( IBINS * (JC-1) )
+             ID = id_NK01 - 1 + BIN + ( IBINS * (JC-1) )
              X0(BIN,JC) = Spc(ID)%Conc(I,J,L)
           ENDDO
        ENDDO
@@ -425,7 +431,7 @@ SUBROUTINE AERO_DRYDEP( Input_Opt,  State_Chm, State_Diag, &
        DO JC = 1, ICOMP-IDIAG+1
        DO BIN = 1, IBINS
           X = 0d0
-          ID = id_NK1 - 1 + BIN + (( JC-1 )* IBINS)
+          ID = id_NK01 - 1 + BIN + (( JC-1 )* IBINS)
 
           ! *******************************************************************
           ! NOTE: I'm not sure if this is now covered by dry-deposition in

GeosCore/aerosol_mod.F90

@@ -87,7 +87,7 @@ MODULE AEROSOL_MOD
   INTEGER :: id_POA1,  id_POA2,  id_OPOA1, id_OPOA2
   INTEGER :: id_TSOA1, id_TSOA2, id_TSOA3, id_TSOA0
   INTEGER :: id_ASOAN, id_ASOA1, id_ASOA2, id_ASOA3
-  INTEGER :: id_DUST1, id_SOAS,  id_SALACL, id_HMS   ! (jmm, 06/29/18)
+  INTEGER :: id_DUST01, id_SOAS,  id_SALACL, id_HMS   ! (jmm, 06/29/18)
   INTEGER :: id_SOAGX, id_SOAIE
   INTEGER :: id_INDIOL,id_LVOCOA
 
@@ -133,9 +133,6 @@ SUBROUTINE AEROSOL_CONC( Input_Opt,  State_Chm, State_Diag, &
     USE State_Met_Mod,     ONLY : MetState
     USE UnitConv_Mod
     USE TIME_MOD,          ONLY : GET_MONTH
-#ifdef TOMAS
-    USE TOMAS_MOD,        ONLY : IBINS
-#endif
 !
 ! !INPUT PARAMETERS:
 !
@@ -545,10 +542,10 @@ SUBROUTINE AEROSOL_CONC( Input_Opt,  State_Chm, State_Diag, &
           SOILDUST(I,J,L,:) = 0.e0_fp
 
           ! Loop over the # of TOMAS dust bins
-          DO K = 1, IBINS
+          DO K = 1, State_Chm%nTomasBins
 
              ! Get the overall species index for species K
-             N    = id_DUST1 + K - 1
+             N    = id_DUST01 + K - 1
 
              ! Effective aerosol radius [m]
              REFF = State_Chm%SpcData(N)%Info%Radius
@@ -2268,7 +2265,7 @@ SUBROUTINE Init_Aerosol( Input_Opt, State_Chm, State_Diag, State_Grid, RC )
     id_DST2   = Ind_( 'DST2'   )
     id_DST3   = Ind_( 'DST3'   )
     id_DST4   = Ind_( 'DST4'   )
-    id_DUST1  = Ind_( 'DUST1'  )
+    id_DUST01 = Ind_( 'DUST01' )
     id_NH4    = Ind_( 'NH4'    )
     id_NIT    = Ind_( 'NIT'    )
     id_OCPO   = Ind_( 'OCPO'   )