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Updates from GMAO for GEOS #2062

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merged 21 commits into from
Jan 5, 2024
Merged

Updates from GMAO for GEOS #2062

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0eb3b7c
Bug fix: get GEOS_CH4 through HEMCO
May 26, 2023
1706b3e
Update ExtData update templates to make sure that the model passes ti…
Sep 7, 2023
dbc588d
This commit (re)adds the ability to turn off 5 heterogeneous reaction…
Sep 29, 2023
2d6db44
add reaction rate updates as suggested by Eric Fleming
Oct 10, 2023
be4b499
revert changes in build_mechanism.sh that got accidentally committed …
Oct 10, 2023
a1d171a
Updates to allow GEOS-Chem to be the RATS/OX provider. Most important…
Oct 18, 2023
b3863d1
make online washout default for GEOS runs
Oct 26, 2023
3f60625
Update photolysis to include updates by Eric Fleming
Oct 26, 2023
d188e58
Added checks for negative concentrations after KPP integration. These…
Oct 26, 2023
35f173f
Update Q directly within GEOS-Chem. This is possible since Q is frien…
Oct 26, 2023
15aeaf7
Merge branch 'feature/cakelle2/fix_kpp_negatives' into geoscf/CFv2/rc1
Oct 26, 2023
31f73d5
Bug fix to properly count number of negatives concentrations after KP…
Oct 27, 2023
0b59550
Merge branch 'feature/cakelle2/fix_kpp_negatives' into geoscf/CFv2/rc1
Oct 27, 2023
6644f25
add option to stop printing # of negative concentrations after applyi…
Dec 5, 2023
bb3ddc8
Revert "revert changes in build_mechanism.sh that got accidentally co…
lizziel Dec 18, 2023
14c090a
Revert "add reaction rate updates as suggested by Eric Fleming"
lizziel Dec 18, 2023
5de637e
Merge branch 'geoscf/CFv2/rc1/t7_revert_KPP_updates_from_EFleming' in…
lizziel Dec 18, 2023
99e092e
Add new KPP diagnostics to HISTORY.rc templates
lizziel Dec 18, 2023
23c9926
Update GEOS-only unit conversions to new method of specifying target …
lizziel Dec 18, 2023
e5be79b
Make new KPP negative diagnostics off by default
lizziel Dec 18, 2023
0c89ca1
Remove duplicate KPP diagnostic when setting archive logical
lizziel Dec 18, 2023
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39 changes: 38 additions & 1 deletion GeosCore/fullchem_mod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -285,6 +285,8 @@ SUBROUTINE Do_FullChem( Input_Opt, State_Chm, State_Diag, &
IF (State_Diag%Archive_KppAutoReducerNVAR) &
State_Diag%KppAutoReducerNVAR = 0.0_f4
IF (State_Diag%Archive_KppcNONZERO) State_Diag%KppcNONZERO = 0.0_f4
IF (State_Diag%Archive_KppNegatives) State_Diag%KppNegatives = 0.0_f4
IF (State_Diag%Archive_KppNegatives0) State_Diag%KppNegatives0 = 0.0_f4
ENDIF

! Also zero satellite diagnostic archival arrays
Expand Down Expand Up @@ -999,20 +1001,42 @@ SUBROUTINE Do_FullChem( Input_Opt, State_Chm, State_Diag, &
ENDIF

#if defined( MODEL_GEOS ) || defined( MODEL_WRF ) || defined( MODEL_CESM )
! Keep track of error boxes
! Keep track of number of error boxes
IF ( State_Diag%Archive_KppError ) THEN
State_Diag%KppError(I,J,L) = State_Diag%KppError(I,J,L) + 1.0
ENDIF
#endif
ENDIF

#if defined( MODEL_GEOS )
! Mark integration as erroneous if negative concentrations so that it will be
! repeated below (cakelle2, 2023/10/26)
IF ( IERR >= 0 .AND. Input_Opt%KppCheckNegatives >= 0 ) THEN
IF ( ( Input_Opt%KppCheckNegatives==0 .AND. State_Met%InStratMeso(I,J,L) ) .OR. &
( L > ( State_Grid%NZ - Input_Opt%KppCheckNegatives) ) ) THEN
IF ( ANY(C < 0.0_dp) ) THEN
IERR = -999
! Include negative concentration boxes within error box diagnostic
IF ( State_Diag%Archive_KppError ) THEN
State_Diag%KppError(I,J,L) = State_Diag%KppError(I,J,L) + 1.0
ENDIF
ENDIF
ENDIF
ENDIF
#endif

!=====================================================================
! HISTORY: Archive KPP solver diagnostics
!
! !TODO: Abstract this into a separate routine
!=====================================================================
IF ( State_Diag%Archive_KppDiags ) THEN

! Check for negative concentrations after first integration
IF ( State_Diag%Archive_KppNegatives0 ) THEN
State_Diag%KppNegatives0(I,J,L) = REAL( COUNT( C < 0.0_dp ), KIND=4 )
ENDIF

! # of integrator calls
IF ( State_Diag%Archive_KppIntCounts ) THEN
State_Diag%KppIntCounts(I,J,L) = ISTATUS(1)
Expand Down Expand Up @@ -1070,6 +1094,12 @@ SUBROUTINE Do_FullChem( Input_Opt, State_Chm, State_Diag, &
RCNTRL(3) = 0.0_dp
C = C_before_integrate

#if defined( MODEL_GEOS )
! In GEOS also inflate the error tolerances (cakelle2, 2023/10/26)
ATOL = 1.0e-2_dp * Input_Opt%KppTolScale
RTOL = 1.0e-2_dp * Input_Opt%KppTolScale
#endif

! Disable auto-reduce solver for the second iteration for safety
IF ( Input_Opt%Use_AutoReduce ) THEN
RCNTRL(12) = -1.0_dp ! without using ICNTRL
Expand Down Expand Up @@ -1235,6 +1265,13 @@ SUBROUTINE Do_FullChem( Input_Opt, State_Chm, State_Diag, &
! Skip if this is not a GEOS-Chem species
IF ( SpcID <= 0 ) CYCLE

! Scan for negatives
IF ( State_Diag%Archive_KppNegatives ) THEN
IF ( C(N) < 0.0_dp ) THEN
State_Diag%KppNegatives(I,J,L) = State_Diag%KppNegatives(I,J,L) + 1.0_f4
ENDIF
ENDIF

! Set negative concentrations to zero
C(N) = MAX( C(N), 0.0_dp )

Expand Down
5 changes: 4 additions & 1 deletion Headers/input_opt_mod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -411,7 +411,10 @@ MODULE Input_Opt_Mod
LOGICAL :: FJX_EXTRAL_ERR = .TRUE.
! Toggle for het rates. If true, turns off three Cl producing het reactions
! in the stratosphere. In MODEL_GEOS, this flag is set in GEOSCHEMchem_GridComp.rc
LOGICAL :: TurnOffHetRates = .FALSE.
LOGICAL :: TurnOffHetRates = .TRUE.
INTEGER :: KppCheckNegatives = -1 ! Check for negatives after KPP integration
REAL(fp) :: KppTolScale = 1.0_fp ! Tolerance scale factor for 2nd KPP integration
LOGICAL :: applyQtend = .FALSE. ! Apply water vapor tendency
#else
LOGICAL :: AlwaysSetH2O
LOGICAL :: TurnOffHetRates
Expand Down
84 changes: 83 additions & 1 deletion Headers/state_diag_mod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -669,6 +669,12 @@ MODULE State_Diag_Mod
REAL(f4), POINTER :: KppSmDecomps(:,:,:)
LOGICAL :: Archive_KppSmDecomps

REAL(f4), POINTER :: KppNegatives(:,:,:)
LOGICAL :: Archive_KppNegatives

REAL(f4), POINTER :: KppNegatives0(:,:,:)
LOGICAL :: Archive_KppNegatives0

!%%%%% KPP auto-reduce solver diagnostics %%%%%
REAL(f4), POINTER :: KppAutoReducerNVAR(:,:,:)
LOGICAL :: Archive_KppAutoReducerNVAR
Expand Down Expand Up @@ -1895,6 +1901,12 @@ SUBROUTINE Zero_State_Diag( State_Diag, RC )
State_Diag%KppSmDecomps => NULL()
State_Diag%Archive_KppSmDecomps = .FALSE.

State_Diag%KppNegatives => NULL()
State_Diag%Archive_KppNegatives = .FALSE.

State_Diag%KppNegatives0 => NULL()
State_Diag%Archive_KppNegatives0 = .FALSE.

State_Diag%KppAutoReducerNVAR => NULL()
State_Diag%Archive_KppAutoReducerNVAR = .FALSE.

Expand Down Expand Up @@ -5996,6 +6008,50 @@ SUBROUTINE Init_State_Diag( Input_Opt, State_Chm, State_Grid, &
RETURN
ENDIF

!-------------------------------------------------------------------
! Number of negative concentrations after KPP integration
!-------------------------------------------------------------------
diagID = 'KppNegatives'
CALL Init_and_Register( &
Input_Opt = Input_Opt, &
State_Chm = State_Chm, &
State_Diag = State_Diag, &
State_Grid = State_Grid, &
DiagList = Diag_List, &
TaggedDiagList = TaggedDiag_List, &
Ptr2Data = State_Diag%KppNegatives, &
archiveData = State_Diag%Archive_KppNegatives, &
diagId = diagId, &
RC = RC )

IF ( RC /= GC_SUCCESS ) THEN
errMsg = TRIM( errMsg_ir ) // TRIM( diagId )
CALL GC_Error( errMsg, RC, thisLoc )
RETURN
ENDIF

!-------------------------------------------------------------------
! Number of negative concentrations after first KPP integration try
!-------------------------------------------------------------------
diagID = 'KppNegatives0'
CALL Init_and_Register( &
Input_Opt = Input_Opt, &
State_Chm = State_Chm, &
State_Diag = State_Diag, &
State_Grid = State_Grid, &
DiagList = Diag_List, &
TaggedDiagList = TaggedDiag_List, &
Ptr2Data = State_Diag%KppNegatives0, &
archiveData = State_Diag%Archive_KppNegatives0, &
diagId = diagId, &
RC = RC )

IF ( RC /= GC_SUCCESS ) THEN
errMsg = TRIM( errMsg_ir ) // TRIM( diagId )
CALL GC_Error( errMsg, RC, thisLoc )
RETURN
ENDIF

!-------------------------------------------------------------------
! AR only -- Number of species in reduced mechanism (NVAR - NRMV)
!-------------------------------------------------------------------
Expand Down Expand Up @@ -6119,7 +6175,7 @@ SUBROUTINE Init_State_Diag( Input_Opt, State_Chm, State_Grid, &
! being requested as diagnostic output when the corresponding
! array has not been allocated.
!-------------------------------------------------------------------
DO N = 1, 35
DO N = 1, 41
! Select the diagnostic ID
SELECT CASE( N )
CASE( 1 )
Expand Down Expand Up @@ -6200,6 +6256,10 @@ SUBROUTINE Init_State_Diag( Input_Opt, State_Chm, State_Grid, &
diagID = 'KppAutoReduceThres'
CASE( 39 )
diagID = 'RxnConst'
CASE( 40 )
diagID = 'KppNegatives'
CASE( 41 )
diagID = 'KppNegatives0'
END SELECT

! Exit if any of the above are in the diagnostic list
Expand Down Expand Up @@ -10460,6 +10520,8 @@ SUBROUTINE Init_State_Diag( Input_Opt, State_Chm, State_Grid, &
State_Diag%Archive_KppLuDecomps .or. &
State_Diag%Archive_KppSubsts .or. &
State_Diag%Archive_KppSmDecomps .or. &
State_Diag%Archive_KppNegatives .or. &
State_Diag%Archive_KppNegatives0 .or. &
State_Diag%Archive_KppAutoReducerNVAR .or. &
State_Diag%Archive_KppAutoReduceThres .or. &
State_Diag%Archive_KppcNONZERO .or. &
Expand Down Expand Up @@ -11893,6 +11955,16 @@ SUBROUTINE Cleanup_State_Diag( State_Diag, RC )
RC = RC )
IF ( RC /= GC_SUCCESS ) RETURN

CALL Finalize( diagId = 'KppNegatives', &
Ptr2Data = State_Diag%KppNegatives, &
RC = RC )
IF ( RC /= GC_SUCCESS ) RETURN

CALL Finalize( diagId = 'KppNegatives0', &
Ptr2Data = State_Diag%KppNegatives0, &
RC = RC )

IF ( RC /= GC_SUCCESS ) RETURN
CALL Finalize( diagId = 'AirMassColumnFull', &
Ptr2Data = State_Diag%AirMassColumnFull, &
RC = RC )
Expand Down Expand Up @@ -13562,6 +13634,16 @@ SUBROUTINE Get_Metadata_State_Diag( am_I_Root, metadataID, Found, &
IF ( isUnits ) Units = 'count'
IF ( isRank ) Rank = 3

ELSE IF ( TRIM( Name_AllCaps ) == 'KPPNEGATIVES' ) THEN
IF ( isDesc ) Desc = 'Number of negative concentrations after KPP integration'
IF ( isUnits ) Units = 'count'
IF ( isRank ) Rank = 3

ELSE IF ( TRIM( Name_AllCaps ) == 'KPPNEGATIVES0' ) THEN
IF ( isDesc ) Desc = 'Number of negative concentrations after first KPP integration attempt'
IF ( isUnits ) Units = 'count'
IF ( isRank ) Rank = 3

ELSE IF ( TRIM( Name_AllCaps ) == 'KPPAUTOREDUCERNVAR' ) THEN
IF ( isDesc ) Desc = 'Number of species in auto-reduced mechanism'
IF ( isUnits ) Units = 'count'
Expand Down
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