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Bug fixes for Prod/Loss diagnostics for Hg simulation -- Closes #1284, #1285 #1356

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Aug 23, 2022
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Bug fixes for Prod/Loss diagnostics for Hg simulation -- Closes #1284, #1285 #1356

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88cb011
Bug fixes for prod/loss diagnostics in Hg simulation with KPP
yantosca Aug 22, 2022
2b6f32c
Add ProdLoss collection to HISTORY.rc.Hg template file
yantosca Aug 22, 2022
722b7a7
Fix typo in Headers/state_diag_mod.F90
yantosca Aug 22, 2022
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13 changes: 7 additions & 6 deletions GeosCore/mercury_mod.F90
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Expand Up @@ -1236,20 +1236,21 @@ SUBROUTINE ChemMercury( Input_Opt, State_Chm, State_Diag, &

! Chemical loss of species or families [molec/cm3/s]
IF ( State_Diag%Archive_Loss ) THEN
DO F = 1, State_Chm%nLoss
KppID = State_Chm%Map_Loss(F)
State_Diag%Loss(I,J,L,F) = VAR(KppID) / DT
DO S = 1, State_Diag%Map_Loss%nSlots
KppId = State_Diag%Map_Loss%slot2Id(S)
State_Diag%Loss(I,J,L,S) = C(KppID) / DT
ENDDO
ENDIF

! Chemical production of species or families [molec/cm3/s]
IF ( State_Diag%Archive_Prod ) THEN
DO F = 1, State_Chm%nProd
KppID = State_Chm%Map_Prod(F)
State_Diag%Prod(I,J,L,F) = VAR(KppID) / DT
DO S = 1, State_Diag%Map_Prod%nSlots
KppID = State_Diag%Map_Prod%slot2Id(S)
State_Diag%Prod(I,J,L,S) = C(KppID) / DT
ENDDO
ENDIF


!=====================================================================
! HISTORY (aka netCDF diagnostics)
!
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18 changes: 12 additions & 6 deletions Headers/diaglist_mod.F90
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Expand Up @@ -81,11 +81,13 @@ MODULE DiagList_Mod
!=========================================================================
! Configurable Settings Used for Diagnostic Names at Run-time
!=========================================================================
CHARACTER(LEN=5), PUBLIC :: RadWL(3) ! Wavelengths in radiation menu
CHARACTER(LEN=4), PUBLIC :: RadOut(12) ! Names of RRTMG outputs (tags)
INTEGER, PUBLIC :: nRadOut ! # of selected RRTMG outputs
LOGICAL, PUBLIC :: IsFullChem ! Is this a fullchem simulation?
CHARACTER(LEN=10), PUBLIC :: AltAboveSfc ! Alt for O3, HNO3 diagnostics
CHARACTER(LEN=5), PUBLIC :: RadWL(3) ! Wavelengths in radiation menu
CHARACTER(LEN=4), PUBLIC :: RadOut(12) ! Names of RRTMG outputs (tags)
INTEGER, PUBLIC :: nRadOut ! # of selected RRTMG outputs
LOGICAL, PUBLIC :: IsFullChem ! Is it a fullchem simulation?
LOGICAL, PUBLIC :: IsHg ! Is it a Hg simulation?
LOGICAL, PUBLIC :: IsCarbonCycle ! Is it a carboncycle sim?
CHARACTER(LEN=10), PUBLIC :: AltAboveSfc ! Alt for O3, HNO3 diagnostics

!=========================================================================
! Derived type for Collections List
Expand Down Expand Up @@ -226,6 +228,8 @@ SUBROUTINE Init_DiagList ( am_I_Root, historyConfigFile, DiagList, RC )
RadOut = ''
nRadOut = 0
IsFullChem = .FALSE.
IsHg = .FALSE.
IsCarbonCycle = .FALSE.
InDefSection = .FALSE.
InFieldsSection = .FALSE.
Name = ''
Expand Down Expand Up @@ -264,7 +268,9 @@ SUBROUTINE Init_DiagList ( am_I_Root, historyConfigFile, DiagList, RC )
CALL QFYAML_CleanUp( ConfigAnchored )
RETURN
ENDIF
IsFullChem = ( To_UpperCase( v_str ) == "FULLCHEM" )
IsFullChem = ( To_UpperCase( v_str ) == "FULLCHEM" )
IsHg = ( To_UpperCase( v_str ) == "HG" )
IsCarbonCycle = ( To_UpperCase( v_str ) == "CARBONCYCLE" )

! Read the altitude above the surface in meters for drydep diags
key = "operations%dry_deposition%diag_alt_above_sfc_in_m"
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20 changes: 10 additions & 10 deletions Headers/state_diag_mod.F90
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Expand Up @@ -10571,8 +10571,8 @@ SUBROUTINE Get_Metadata_State_Diag( am_I_Root, metadataID, Found, &
!
! !USES:
!
USE Charpak_Mod, ONLY : StrSplit, To_UpperCase
USE DiagList_Mod, ONLY : IsFullChem
USE Charpak_Mod, ONLY : StrSplit, To_UpperCase
USE DiagList_Mod, ONLY : IsFullChem, IsCarbonCycle, IsHg
USE Registry_Params_Mod
!
! !INPUT PARAMETERS:
Expand Down Expand Up @@ -11500,11 +11500,11 @@ SUBROUTINE Get_Metadata_State_Diag( am_I_Root, metadataID, Found, &
IF ( isRank ) Rank = 3
IF ( isTagged ) TagId = 'LOS'

! NOTE: Units are different depending on simulation, due to historical
! baggage. Maybe clean this up at a later point to use the same units
! regardless of simulation type. (bmy, 12/4/17)
! NOTE: Prod/Loss units for simulations with KPP are molec/cm3/s,
! and are currently kg/s for other specialty simulations.
! This will need to be cleaned up later (Bob Yantosca, 22 Aug 2020).
IF ( isUnits ) THEN
IF ( IsFullChem ) THEN
IF ( IsFullChem .or. IsHg .or. IsCarbonCycle ) THEN
Units = 'molec cm-3 s-1'
ELSE
Units = 'kg s-1'
Expand All @@ -11516,11 +11516,11 @@ SUBROUTINE Get_Metadata_State_Diag( am_I_Root, metadataID, Found, &
IF ( isRank ) Rank = 3
IF ( isTagged ) TagId = 'PRD'

! NOTE: Units are different depending on simulation, due to historical
! baggage. Maybe clean this up at a later point to use the same units
! regardless of simulation type. (bmy, 12/4/17)
! NOTE: Prod/Loss units for simulations with KPP are molec/cm3/s,
! and are currently kg/s for other specialty simulations.
! This will need to be cleaned up later (Bob Yantosca, 22 Aug 2020).
IF ( isUnits ) THEN
IF ( IsFullChem ) THEN
IF ( IsFullChem .or. IsHg .or. IsCarbonCycle ) THEN
Units = 'molec cm-3 s-1'
ELSE
Units = 'kg s-1'
Expand Down
7 changes: 7 additions & 0 deletions KPP/Hg/Hg.kpp
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Expand Up @@ -9,6 +9,13 @@

#INCLUDE Hg.eqn { Chemical reactions for Hg mechanism }

#FAMILIES { Chemical families for prod/loss diagnostic }
PHg2 : HgBrNO2 + HgBrHO2 + HgBrClO + HgBrBrO + HgBr2 + HgBrOH + HgBrO + HgOHNO2 + HgOHHO2 + HgOHClO + HgOHBrO + HgOHOH + HgOHO + HgClNO2 + HgClHO2 + HgClClO + HgClBrO + HgClBr + HgClOH + HgClO + HgCl2 + Hg2ClP + Hg2ORGP + HgBr + HgOH + HgCl; {gross GOM production}
PHg0 : Hg0; {gross Hg0 production}
PHg2Br : HgBrNO2 + HgBrHO2 + HgBrClO + HgBrBrO + HgBr2 + HgBrOH + HgBrO + HgBr; {GOM production from Br}
PHg2OH : HgOHNO2 + HgOHHO2 + HgOHClO + HgOHBrO + HgOHOH + HgOHO + HgOH; {GOM production from OH}
PHg2Cl : HgClNO2 + HgClHO2 + HgClClO + HgClBrO + HgClBr + HgClOH + HgClO + HgCl2 + HgCl; {GOM production from Cl}

#INLINE F90_RATES
! All rates are included in Hg_RateLawFuncs.F90, which
! gets referenced directly from subroutine Update_Rconst.
Expand Down
27 changes: 14 additions & 13 deletions KPP/Hg/gckpp.map
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Expand Up @@ -33,9 +33,9 @@ REORDER - ON
### Parameters ----------------------------------------

! NSPEC - Number of chemical species
INTEGER, PARAMETER :: NSPEC = 38
INTEGER, PARAMETER :: NSPEC = 43
! NVAR - Number of Variable species
INTEGER, PARAMETER :: NVAR = 27
INTEGER, PARAMETER :: NVAR = 32
! NVARACT - Number of Active species
INTEGER, PARAMETER :: NVARACT = 26
! NFIX - Number of Fixed species
Expand All @@ -45,21 +45,22 @@ REORDER - ON
! NVARST - Starting of variables in conc. vect.
INTEGER, PARAMETER :: NVARST = 1
! NFIXST - Starting of fixed in conc. vect.
INTEGER, PARAMETER :: NFIXST = 28
INTEGER, PARAMETER :: NFIXST = 33

### Species -------------------------------------------

Variable species
1 = HgCl2 (r) 11 = HgBrNO2 (r) 21 = HgOHHO2 (r)
2 = Hg2ClP (n) 12 = HgBr2 (r) 22 = HgOHOH (r)
3 = HgBrClO (r) 13 = HgOHNO2 (r) 23 = Hg2ORGP (r)
4 = HgBrBrO (r) 14 = HgClO (r) 24 = HgOH (r)
5 = HgClClO (r) 15 = HgClHO2 (r) 25 = Hg0 (r)
6 = HgClBrO (r) 16 = HgClOH (r) 26 = HgBrOH (r)
7 = HgClBr (r) 17 = HgCl (r) 27 = HgBr (r)
8 = HgOHClO (r) 18 = HgBrO (r)
9 = HgOHBrO (r) 19 = HgBrHO2 (r)
10 = HgClNO2 (r) 20 = HgOHO (r)
1 = HgCl2 (r) 12 = HgOHBrO (r) 23 = HgBrHO2 (r)
2 = Hg2ClP (n) 13 = HgBrClO (r) 24 = HgClO (r)
3 = PHg2 (n) 14 = HgBrBrO (r) 25 = HgClHO2 (r)
4 = PHg0 (n) 15 = HgOHNO2 (r) 26 = HgClOH (r)
5 = PHg2Br (n) 16 = HgBrNO2 (r) 27 = HgCl (r)
6 = PHg2OH (n) 17 = HgClNO2 (r) 28 = Hg2ORGP (r)
7 = PHg2Cl (n) 18 = HgBr2 (r) 29 = HgOH (r)
8 = HgClClO (r) 19 = HgOHO (r) 30 = Hg0 (r)
9 = HgClBrO (r) 20 = HgOHOH (r) 31 = HgBrOH (r)
10 = HgClBr (r) 21 = HgOHHO2 (r) 32 = HgBr (r)
11 = HgOHClO (r) 22 = HgBrO (r)

Fixed species
1 = Br (r) 5 = NO (n) 9 = ClO (r)
Expand Down
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