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Add more netCDF diagnostics and debug the ocean Hg diagnostics
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Corrected various issues with the remaining ocean Hg diagnostics.

Also added the equivalent of ND03 #21 (Hg2 and HgP deposited to snow
and ice).  This involved passing State_Diag to the convection, drydep,
and wetdep modules.  NOTE: This diagnostic does not match the bpch
output, probably due to how the bpch diagnostic was implemented.
Need to think of a better way to handle that.

Also added netCDF diagnostics for particulate bound mercury (PBM)
and reactive gaseous mercury (RGM) in GeosCore/diagnostics_mod.F90.

Added a new routine called Reset_Hg_Diags in GeosCore/mercury_mod.F90,
which zeroes out several relevant fields of State_Diag for the Hg
simulations.

Removed the module fvdas_convect_mod.F; we no longer use GEOS-4
meteorology, so this was orphaned.

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
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yantosca committed Oct 26, 2018
1 parent ac7a651 commit d09a18a
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Showing 12 changed files with 410 additions and 1,546 deletions.
6 changes: 3 additions & 3 deletions GeosCore/Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -509,9 +509,9 @@ co2_mod.o : co2_mod.F \

convection_mod.o : convection_mod.F \
diag_mod.o depo_mercury_mod.o \
fvdas_convect_mod.o wetscav_mod.o \
mercury_mod.o tendencies_mod.o \
hco_interface_mod.o diagnostics_mod.o
wetscav_mod.o mercury_mod.o \
tendencies_mod.o hco_interface_mod.o \
diagnostics_mod.o

dao_mod.o : dao_mod.F

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16 changes: 10 additions & 6 deletions GeosCore/convection_mod.F
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Original file line number Diff line number Diff line change
Expand Up @@ -405,6 +405,7 @@ SUBROUTINE DO_CONVECTION( am_I_Root, Input_Opt, State_Met,
& Input_Opt = Input_Opt,
& State_Met = State_Met,
& State_Chm = State_Chm,
& State_Diag = State_Diag,
& I = I,
& J = J,
& AREA_M2 = AREA_M2,
Expand Down Expand Up @@ -567,6 +568,7 @@ SUBROUTINE DO_CLOUD_CONVECTION( am_I_Root,
& Input_Opt,
& State_Met,
& State_Chm,
& State_Diag,
& I,
& J,
& AREA_M2,
Expand All @@ -590,6 +592,7 @@ SUBROUTINE DO_CLOUD_CONVECTION( am_I_Root,
USE Input_Opt_Mod, ONLY : OptInput
USE PhysConstants
USE State_Chm_Mod, ONLY : ChmState
USE State_Diag_Mod, ONLY : DgnState
USE State_Met_Mod, ONLY : MetState
USE Species_Mod, ONLY : Species
USE WETSCAV_MOD, ONLY : H2O2s_3D => H2O2s ! [v/v]
Expand All @@ -616,6 +619,7 @@ SUBROUTINE DO_CLOUD_CONVECTION( am_I_Root,
! !INPUT/OUTPUT PARAMETERS:
!
TYPE(ChmState), INTENT(INOUT) :: State_Chm ! Chemistry State object
TYPE(DgnState), INTENT(INOUT) :: State_Diag ! Diagnostics State object
!
! !OUTPUT PARAMETERS:
!
Expand Down Expand Up @@ -1537,9 +1541,9 @@ SUBROUTINE DO_CLOUD_CONVECTION( am_I_Root,
Hg_Cat = SpcInfo%Hg_Cat
! Pass to "ocean_mercury_mod.f"
CALL ADD_Hg2_WD ( I, J, Hg_Cat, WET_Hg2 )
CALL ADD_Hg2_SNOWPACK( I, J, Hg_Cat, WET_Hg2,
& State_Met )
CALL ADD_Hg2_WD ( I, J, Hg_Cat, WET_Hg2 )
CALL ADD_Hg2_SNOWPACK( I, J, Hg_Cat, WET_Hg2,
& State_Met, State_Diag )
ENDIF
!--------------------------------------
Expand All @@ -1554,9 +1558,9 @@ SUBROUTINE DO_CLOUD_CONVECTION( am_I_Root,
Hg_Cat = SpcInfo%Hg_Cat
! Pass to "ocean_mercury_mod.f"
CALL ADD_HgP_WD ( I, J, Hg_Cat, WET_HgP )
CALL ADD_Hg2_SNOWPACK( I, J, Hg_Cat, WET_HgP,
& State_Met )
CALL ADD_HgP_WD ( I, J, Hg_Cat, WET_HgP )
CALL ADD_Hg2_SNOWPACK( I, J, Hg_Cat, WET_HgP,
& State_Met, State_Diag )
ENDIF
ENDIF
ENDDO ! End internal timestep loop
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37 changes: 32 additions & 5 deletions GeosCore/depo_mercury_mod.F
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Original file line number Diff line number Diff line change
Expand Up @@ -279,23 +279,30 @@ END SUBROUTINE ADD_HgP_WD
!\\
! !INTERFACE:
!
SUBROUTINE ADD_HG2_SNOWPACK( I, J, Hg_Cat, DEP_Hg2, State_Met )
SUBROUTINE ADD_HG2_SNOWPACK( I, J, Hg_Cat, DEP_Hg2,
& State_Met, State_Diag )
!
! !USES:
!
USE DAO_MOD, ONLY : IS_ICE, IS_LAND
USE State_Diag_Mod, ONLY : DgnState
USE State_Met_Mod, ONLY : MetState
#if defined( BPCH_DIAG )
USE DIAG03_MOD, ONLY : AD03, ND03
#endif
USE Time_Mod, ONLY : Get_Ts_Chem
!
! !INPUT PARAMETERS:
!
! Arguments as input
INTEGER, INTENT(IN) :: I, J ! Grid box lon & lat indices
INTEGER, INTENT(IN) :: Hg_Cat ! Hg category number
REAL(fp), INTENT(IN) :: Dep_Hg2 ! Hg2 (or HgP) deposited
TYPE(MetState), INTENT(IN) :: State_Met ! Meteorology State object
INTEGER, INTENT(IN) :: I, J ! Grid box lon & lat indices
INTEGER, INTENT(IN) :: Hg_Cat ! Hg category number
REAL(fp), INTENT(IN) :: Dep_Hg2 ! Hg2 (or HgP) deposited
TYPE(MetState), INTENT(IN) :: State_Met ! Meteorology State object
!
! !INPUT/OUTPUT PARAMETERS:
!
TYPE(DgnState), INTENT(INOUT) :: State_Diag ! Diagnostics State object
!
! !REVISION HISTORY:
! 02 Sep 2008 - C. Holmes - Initial version
Expand Down Expand Up @@ -327,6 +334,7 @@ SUBROUTINE ADD_HG2_SNOWPACK( I, J, Hg_Cat, DEP_Hg2, State_Met )
LOGICAL :: IS_SNOW_OR_ICE
REAL(fp) :: FRAC_SNOW_OR_ICE
REAL(fp) :: FRAC_O
REAL(fp) :: DT

!=================================================================
! ADD_HG2_SNOWPACK begins here!
Expand All @@ -338,6 +346,9 @@ SUBROUTINE ADD_HG2_SNOWPACK( I, J, Hg_Cat, DEP_Hg2, State_Met )
! Return if snowpack model is disabled
IF ( .NOT. LHGSNOW ) RETURN

! Chemistry timestep [s]
DT = GET_TS_CHEM()

! Don't let fraction be greater than 1
FRAC_SNOW_OR_ICE = MIN( State_Met%FRSNO(I,J) +
& State_Met%FRSEAICE(I,J) +
Expand Down Expand Up @@ -380,6 +391,8 @@ SUBROUTINE ADD_HG2_SNOWPACK( I, J, Hg_Cat, DEP_Hg2, State_Met )
#if defined( BPCH_DIAG )
!----------------------------------------------------------------------------
! %%%%% ND03 (bpch) DIAGNOSTIC %%%%%
!
! NOTE: Archiving to AD03(I,J,21,1) causes the slot #4 of the PL-HG2-$
! diagnostic to yield different results when comparing a GEOS-5 Hg simulation
! done on a single processor to one done with multi-processors. (In other
Expand Down Expand Up @@ -409,6 +422,20 @@ SUBROUTINE ADD_HG2_SNOWPACK( I, J, Hg_Cat, DEP_Hg2, State_Met )
!----------------------------------------------------------------------------
#endif
#if defined( NC_DIAG )
!--------------------------------------------------------------
! %%%%% HISTORY (aka netCDF diagnostics) %%%%%
!
! Store diagnostic of TOTAL HgII/HgP deposition to snow/ice
! NOTE: Units are now kg/s
!--------------------------------------------------------------
IF ( State_Diag%Archive_FluxHg2HgPfromAirToSnow ) THEN
State_Diag%FluxHg2HgPfromAirToSnow(I,J) =
& State_Diag%FluxHg2HgPfromAirToSnow(I,J) +
& ( FRAC_SNOW_OR_ICE * MAX( DEP_HG2, 0e+0_fp ) ) !/ DT
ENDIF
#endif
ENDIF
END SUBROUTINE ADD_HG2_SNOWPACK
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11 changes: 6 additions & 5 deletions GeosCore/diag1.F
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Original file line number Diff line number Diff line change
Expand Up @@ -168,7 +168,6 @@ SUBROUTINE DIAG1( am_I_Root, Input_Opt,
INTEGER :: I, J, K
INTEGER :: L, N, NA
REAL(fp) :: EmMW_g, P0, Spc_VV
REAL(fp) :: EmMW_g_Hg2, EmMW_g_HgP

! SAVEd scalars
LOGICAL, SAVE :: FIRST = .TRUE.
Expand All @@ -184,6 +183,8 @@ SUBROUTINE DIAG1( am_I_Root, Input_Opt,
LOGICAL, SAVE :: Do_ND71 = .FALSE.
INTEGER, SAVE :: id_Hg2 = -1
INTEGER, SAVE :: id_HgP = -1
REAL(fp),SAVE :: EmMW_g_Hg2 = -1.0_fp
REAL(fp),SAVE :: EmMW_g_HgP = -1.0_fp

!=================================================================
! DIAG1 begins here!
Expand Down Expand Up @@ -274,18 +275,18 @@ SUBROUTINE DIAG1( am_I_Root, Input_Opt,
IF ( Do_ND03 .and. NA == 1 ) THEN
!--------------------------------------------------------
! Reactive gaseous mercury (RGM), [pptv]
! Reactive gaseous mercury [pptv]
!--------------------------------------------------------
IF ( N == id_Hg2 ) THEN
IF ( id_Hg2 > 0 ) THEN
AD03_RGM(I,J,L) = AD03_RGM(I,J,L)
& + State_Chm%Species(I,J,L,id_Hg2)
& * ( AIRMW / EmMw_g_Hg2 * 1e+12_fp )
ENDIF
!--------------------------------------------------------
! Reactive particulate mercury (RGM), [pptv]
! Particulate bound mercury [pptv]
!--------------------------------------------------------
IF ( N == id_HgP ) THEN
IF ( id_HgP > 0 ) THEN
AD03_PBM(I,J,L) = AD03_PBM(I,J,L)
& + State_Chm%Species(I,J,L,id_HgP)
& * ( AIRMW / EmMW_g_HgP * 1e+12_fp )
Expand Down
56 changes: 54 additions & 2 deletions GeosCore/diagnostics_mod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -68,8 +68,9 @@ SUBROUTINE Set_Diagnostics_EndofTimestep ( am_I_Root, Input_Opt, &
!
USE Input_Opt_Mod, ONLY : OptInput
USE State_Met_Mod, ONLY : MetState
USE State_Chm_Mod, ONLY : ChmState
USE State_Chm_Mod, ONLY : ChmState, Ind_
USE State_Diag_Mod, ONLY : DgnState
USE PhysConstants, ONLY : AIRMW
!
! !INPUT PARAMETERS:
!
Expand All @@ -95,8 +96,17 @@ SUBROUTINE Set_Diagnostics_EndofTimestep ( am_I_Root, Input_Opt, &
! !LOCAL VARIABLES:
!
#if defined( NC_DIAG )
! Scalars
INTEGER :: I, J, L, N
CHARACTER(LEN=255) :: ErrMsg, thisLoc
REAL(fp) :: ToPptv

! SAVEd scalars
INTEGER, SAVE :: id_Hg2 = -1
INTEGER, SAVE :: id_HgP = -1
LOGICAL, SAVE :: FIRST = .TRUE.

! Strings
CHARACTER(LEN=255) :: ErrMsg, ThisLoc

!=======================================================================
! Set_Diagnostics_EndofTimestep begins here
Expand Down Expand Up @@ -141,6 +151,48 @@ SUBROUTINE Set_Diagnostics_EndofTimestep ( am_I_Root, Input_Opt, &
!$OMP END PARALLEL DO
ENDIF

!-----------------------------------------------------------------------
! Diagnostics for the mercury and tagged mercury simulations
!-----------------------------------------------------------------------
IF ( Input_Opt%ITS_A_MERCURY_SIM ) THEN

! Get species indices for Hg2 and HgP
IF ( FIRST ) THEN
id_Hg2 = Ind_('Hg2')
id_HgP = Ind_('HgP')
FIRST = .FALSE.
ENDIF

!--------------------------------------------
! Ractive gaseous mercury (RGM) [pptv]
!--------------------------------------------
IF ( id_Hg2 > 0 .and. State_Diag%Archive_ReactiveGaseousHg ) THEN

! Conversion factor to pptv
ToPptv = ( AIRMW / &
State_Chm%SpcData(id_Hg2)%Info%EmMW_g * &
1.0e+12_fp )

! Save into State_diag
State_Diag%ReactiveGaseousHg = State_Chm%Species(:,:,:,id_Hg2) &
* ToPptv
ENDIF

!--------------------------------------------
! Ractive particulate mercury (RGM) [pptv]
!--------------------------------------------
IF ( id_HgP > 0 .and. State_Diag%Archive_ParticulateBoundHg ) THEN

! Conversion factor to pptv
ToPptv = ( AIRMW / &
State_Chm%SpcData(id_HgP)%Info%EmMW_g * &
1.0e+12_fp )

! Save into State_Diag
State_Diag%ParticulateBoundHg = State_Chm%Species(:,:,:,id_HgP) &
* ToPptv
ENDIF
ENDIF
#endif

END SUBROUTINE Set_Diagnostics_EndofTimestep
Expand Down

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