Merge branch 'dev/no-diff-to-benchmark' into adjoint

geoschem · Nov 21, 2024 · f2a908f · f2a908f
2 parents 0d115ba + 7507eb5
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,6 +4,32 @@ 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] - TBD
+### Added
+- Added allocate guards for arrays in `pressure_mod`
+- Added `State_Diag%SatDiagnEdgeCount` counter for the `SatDiagnEdge` collection
+- Added `State_Diag%Archive_SatDiagnEdgeCount` field
+- Added `State_Diag%Archive_SatDiagnEdge` field
+- Added routine `SatDiagn_or_SatDiagnEdge` in `History/history_utils_mod.F90`
+
+### Changed
+- Renamed `Emiss_Carbon_Gases` to `CO2_Production` in `carbon_gases_mod.F90`
+- Updated start date and restart file for CO2 and tagCO simulations for consistency with carbon simulations
+- Allocated `State_Diag%SatDiagnPEDGE` ffield with vertical dimension `State_Grid%NZ+1`
+
+### Fixed
+- Added a fix to skip the call to KPP when only CO2 is defined in the carbon simulation
+- Added fix to turn on ship emissions for CO2 in the carbon simulation
+- Updated `HEMCO_Config.rc` for carbon simulation to read data based on carbon species used
+- Fixed entries for CO2 emissions in `ExtData.rc.carbon`
+- Fixed metals simulation name in config file template comments
+- Fixed bug in `download_data.py` which caused script to fail if log filename contained uppercase characters.
+- Fixed the satellite diagnostics counters from being inadvertently being reset
+- Fixed segmentation fault in qfyaml when running with certain compilers without debug flags on
+
+### Removed
+- Removed duplicate `WD_RetFactor` tag for HgClHO2 in `species_database.yml`
+
 ## [14.5.0] - 2024-11-07
 ### Added
 - Added vectors `State_Chm%KPP_AbsTol` and `State_Chm%KPP_RelTol`

diff --git a/GeosCore/carbon_gases_mod.F90 b/GeosCore/carbon_gases_mod.F90
diff --git a/GeosCore/diagnostics_mod.F90 b/GeosCore/diagnostics_mod.F90
@@ -1474,13 +1474,18 @@ SUBROUTINE Do_Archive_SatDiagn( Input_Opt,  State_Chm,  State_Diag,        &
             locTime <= State_Diag%SatDiagn_EndHr   ) good = 1.0_fp
 
        !---------------------------------------------------------------------
-       ! SatDiagnCount: Count number of local times
+       ! SatDiagnCount and SatDiagnEdgeCount: Count number of local times
        !---------------------------------------------------------------------
        IF ( State_Diag%Archive_SatDiagnCount ) THEN
           State_Diag%SatDiagnCount(I,:,:) = &
           State_Diag%SatDiagnCount(I,:,:) + good
        ENDIF
 
+       IF ( State_Diag%Archive_SatDiagnEdgeCount ) THEN
+          State_Diag%SatDiagnEdgeCount(I,:,:) = &
+          State_Diag%SatDiagnEdgeCount(I,:,:) + good
+       ENDIF
+
        !---------------------------------------------------------------------
        ! SatDiagnOH: OH concentration [molec/cm3]:
        !---------------------------------------------------------------------
@@ -1518,8 +1523,7 @@ SUBROUTINE Do_Archive_SatDiagn( Input_Opt,  State_Chm,  State_Diag,        &
        ! Pressure edges [hPa]:
        !---------------------------------------------------------------------
        IF ( State_Diag%Archive_SatDiagnPEdge ) THEN
-          State_Diag%SatDiagnPEdge(I,:,:) = &
-               State_Met%PEDGE(I,:,1:State_Grid%NZ) * good
+          State_Diag%SatDiagnPEdge(I,:,:) = State_Met%PEDGE(I,:,:) * good
        ENDIF
 
        !---------------------------------------------------------------------

diff --git a/GeosCore/emissions_mod.F90 b/GeosCore/emissions_mod.F90
@@ -124,7 +124,7 @@ SUBROUTINE Emissions_Run( Input_Opt, State_Chm, State_Diag, State_Grid,    &
 ! !USES:
 !
     USE CARBON_MOD,            ONLY : EmissCarbon
-    USE Carbon_Gases_Mod,      ONLY : Emiss_Carbon_Gases
+    USE Carbon_Gases_Mod,      ONLY : CO2_Production
     USE CO2_MOD,               ONLY : EmissCO2
     USE ErrCode_Mod
     USE HCO_Interface_GC_Mod,  ONLY : HCOI_GC_Run
@@ -264,8 +264,8 @@ SUBROUTINE Emissions_Run( Input_Opt, State_Chm, State_Diag, State_Grid,    &
     !
     ! Computes CO2 production from CO oxidation
     IF ( Input_Opt%ITS_A_CARBON_SIM ) THEN
-       CALL Emiss_Carbon_Gases( Input_Opt,  State_Chm, State_Diag,            &
-                                State_Grid, State_Met, RC                    )
+       CALL CO2_Production( Input_Opt,  State_Chm, State_Diag,            &
+                            State_Grid, State_Met, RC                    )
 
        ! Trap potential errors
        IF ( RC /= GC_SUCCESS ) THEN

diff --git a/GeosCore/input_mod.F90 b/GeosCore/input_mod.F90
@@ -2015,7 +2015,7 @@ SUBROUTINE Config_CO( Config, Input_Opt, RC )
     ! Initialize
     RC      = GC_SUCCESS
     errMsg  = ''
-    thisLoc = ' -> at Config_CO2 (in module GeosCore/input_mod.F90)'
+    thisLoc = ' -> at Config_CO (in module GeosCore/input_mod.F90)'
 
     !------------------------------------------------------------------------
     ! Use P(CO) from CH4 (archived from a fullchem simulation)?
@@ -2046,7 +2046,7 @@ SUBROUTINE Config_CO( Config, Input_Opt, RC )
     !========================================================================
     ! Print to screen
     !========================================================================
-    IF ( Input_Opt%ITS_A_TAGCO_SIM .and. Input_Opt%amIRoot ) THEN
+    IF ( Input_Opt%amIRoot ) THEN
        WRITE(6,90 ) 'TAGGED CO SIMULATION SETTINGS'
        WRITE(6,95 ) '(overwrites any other settings related to CO)'
        WRITE(6,95 ) '---------------------------------------------'
@@ -2154,7 +2154,7 @@ SUBROUTINE Config_CO2( Config, Input_Opt, RC )
     !=================================================================
     ! Print to screen
     !=================================================================
-    IF ( Input_Opt%ITS_A_CO2_SIM .and. Input_Opt%amIRoot ) THEN
+    IF ( Input_Opt%amIRoot ) THEN
        WRITE( 6,90  ) 'CO2 SIMULATION SETTINGS'
        WRITE( 6,95  ) '(overwrites any other settings related to CO2)'
        WRITE( 6,95  ) '----------------------------------------------'

diff --git a/GeosUtil/pressure_mod.F90 b/GeosUtil/pressure_mod.F90
@@ -517,42 +517,57 @@ SUBROUTINE INIT_PRESSURE( Input_Opt, State_Grid, RC )
     RC      = GC_SUCCESS
     ThisLoc = ' -> at Init_Pressure (in GeosUtil/pressure_mod.F90)'
 
-    ALLOCATE( PFLT_DRY( State_Grid%NX, State_Grid%NY ), STAT=RC )
-    CALL GC_CheckVar( 'vdiff_mod.F90:PFLT_DRY', 2, RC )
-    IF ( RC /= GC_SUCCESS ) RETURN
-    PFLT_DRY = 0e+0_fp
-
-    ALLOCATE( PFLT_WET( State_Grid%NX, State_Grid%NY ), STAT=RC )
-    CALL GC_CheckVar( 'vdiff_mod.F90:PFLT_WET', 2, RC )
-    IF ( RC /= GC_SUCCESS ) RETURN
-    PFLT_WET = 0e+0_fp
-
-    ALLOCATE( AP( State_Grid%NZ+1 ), STAT=RC )
-    CALL GC_CheckVar( 'vdiff_mod.F90:AP', 2, RC )
-    IF ( RC /= GC_SUCCESS ) RETURN
-    AP = 1e+0_fp
-
-    ALLOCATE( BP( State_Grid%NZ+1 ), STAT=RC )
-    CALL GC_CheckVar( 'vdiff_mod.F90:BP', 2, RC )
-    IF ( RC /= GC_SUCCESS ) RETURN
-    BP = 0e+0_fp
-
-    ALLOCATE( AP_FULLGRID( State_Grid%NativeNZ+1 ), STAT=RC )
-    CALL GC_CheckVar( 'vdiff_mod.F90:AP_FULLGRID', 2, RC )
-    IF ( RC /= GC_SUCCESS ) RETURN
-    AP = 1e+0_fp
-
-    ALLOCATE( BP_FULLGRID( State_Grid%NativeNZ+1 ), STAT=RC )
-    CALL GC_CheckVar( 'vdiff_mod.F90:BP_FULLGRID', 2, RC )
-    IF ( RC /= GC_SUCCESS ) RETURN
-    BP = 0e+0_fp
+    IF (.NOT. ALLOCATED( PFLT_DRY )) THEN
+      ALLOCATE( PFLT_DRY( State_Grid%NX, State_Grid%NY ), STAT=RC )
+      CALL GC_CheckVar( 'vdiff_mod.F90:PFLT_DRY', 2, RC )
+      IF ( RC /= GC_SUCCESS ) RETURN
+      PFLT_DRY = 0e+0_fp
+    END IF
+
+    IF (.NOT. ALLOCATED( PFLT_WET )) THEN
+      ALLOCATE( PFLT_WET( State_Grid%NX, State_Grid%NY ), STAT=RC )
+      CALL GC_CheckVar( 'vdiff_mod.F90:PFLT_WET', 2, RC )
+      IF ( RC /= GC_SUCCESS ) RETURN
+      PFLT_WET = 0e+0_fp
+    END IF
+
+    IF (.NOT. ALLOCATED( AP )) THEN
+      ALLOCATE( AP( State_Grid%NZ+1 ), STAT=RC )
+      CALL GC_CheckVar( 'vdiff_mod.F90:AP', 2, RC )
+      IF ( RC /= GC_SUCCESS ) RETURN
+      AP = 1e+0_fp
+    END IF
+
+    IF (.NOT. ALLOCATED( BP )) THEN
+      ALLOCATE( BP( State_Grid%NZ+1 ), STAT=RC )
+      CALL GC_CheckVar( 'vdiff_mod.F90:BP', 2, RC )
+      IF ( RC /= GC_SUCCESS ) RETURN
+      BP = 0e+0_fp
+    END IF
+
+    IF (.NOT. ALLOCATED( AP_FULLGRID )) THEN
+      ALLOCATE( AP_FULLGRID( State_Grid%NativeNZ+1 ), STAT=RC )
+      CALL GC_CheckVar( 'vdiff_mod.F90:AP_FULLGRID', 2, RC )
+      IF ( RC /= GC_SUCCESS ) RETURN
+      AP = 1e+0_fp
+    END IF
+
+    IF (.NOT. ALLOCATED( BP_FULLGRID )) THEN
+      ALLOCATE( BP_FULLGRID( State_Grid%NativeNZ+1 ), STAT=RC )
+      CALL GC_CheckVar( 'vdiff_mod.F90:BP_FULLGRID', 2, RC )
+      IF ( RC /= GC_SUCCESS ) RETURN
+      BP = 0e+0_fp
+    END IF
 
 #if defined( ESMF_ ) || defined( MODEL_ )
-    ALLOCATE( EXTERNAL_PEDGE( State_Grid%NX, State_Grid%NY, State_Grid%NZ+1 ), &
-              STAT=RC )
-    CALL GC_CheckVar( 'vdiff_mod.F90:EXTERNAL_PEDGE', 2, RC )
-    IF ( RC /= GC_SUCCESS ) RETURN
-    EXTERNAL_PEDGE = 0e+0_fp
+    IF (.NOT. ALLOCATED( EXTERNAL_PEDGE )) THEN
+      ALLOCATE( EXTERNAL_PEDGE( State_Grid%NX, State_Grid%NY, &
+                                State_Grid%NZ+1 ), &
+                STAT=RC )
+      CALL GC_CheckVar( 'vdiff_mod.F90:EXTERNAL_PEDGE', 2, RC )
+      IF ( RC /= GC_SUCCESS ) RETURN
+      EXTERNAL_PEDGE = 0e+0_fp
+    END IF
 #endif
 
     IF ( State_Grid%NZ == 47 ) THEN

diff --git a/Headers/qfyaml_mod.F90 b/Headers/qfyaml_mod.F90
@@ -2272,7 +2272,8 @@ SUBROUTINE Partition_Var_List(list, marker)
 
     ! Take the middle element as pivot
     pivot_ix    = SIZE( list ) / 2
-    pivot_value = list(pivot_ix)%var_name
+    temp        = list(pivot_ix)
+    pivot_value = temp%var_name
 
     DO WHILE ( left < right )
 

diff --git a/Headers/state_diag_mod.F90 b/Headers/state_diag_mod.F90
@@ -268,6 +268,7 @@ MODULE State_Diag_Mod
      TYPE(DgnMap),       POINTER :: Map_SatDiagnDryDep
      LOGICAL                     :: Archive_SatDiagnDryDep
      LOGICAL                     :: Archive_SatDiagn
+     LOGICAL                     :: Archive_SatDiagnEdge
 
      REAL(f4),           POINTER :: SatDiagnDryDepVel(:,:,:)
      TYPE(DgnMap),       POINTER :: Map_SatDiagnDryDepVel
@@ -914,6 +915,9 @@ MODULE State_Diag_Mod
 
      REAL(f8),           POINTER :: SatDiagnCount(:,:,:)
      LOGICAL                     :: Archive_SatDiagnCount
+
+     REAL(f8),           POINTER :: SatDiagnEdgeCount(:,:,:)
+     LOGICAL                     :: Archive_SatDiagnEdgeCount
 
      REAL(f8),           POINTER :: SatDiagnConc(:,:,:,:)
      TYPE(DgnMap),       POINTER :: Map_SatDiagnConc
@@ -2381,6 +2385,9 @@ SUBROUTINE Zero_State_Diag( State_Diag, RC )
 
     State_Diag%SatDiagnCount                       => NULL()
     State_Diag%Archive_SatDiagnCount               = .FALSE.
+
+    State_Diag%SatDiagnEdgeCount                   => NULL()
+    State_Diag%Archive_SatDiagnEdgeCount           = .FALSE.
 
     State_Diag%SatDiagnConc                        => NULL()
     State_Diag%Map_SatDiagnConc                    => NULL()
@@ -5208,7 +5215,7 @@ SUBROUTINE Init_State_Diag( Input_Opt, State_Chm,       State_Grid,        &
     ENDIF
 
     !------------------------------------------------------------------------
-    ! Set a single logical for SatDiagn output
+    ! Set logicals for SatDiagn and/or SatDiagnEdge output
     ! For ease of comparison, place fields in alphabetical order
     !------------------------------------------------------------------------
     State_Diag%Archive_SatDiagn = (                                          &
@@ -5218,7 +5225,6 @@ SUBROUTINE Init_State_Diag( Input_Opt, State_Chm,       State_Grid,        &
          State_Diag%Archive_SatDiagnConc                                .or. &
          State_Diag%Archive_SatDiagnDryDep                              .or. &
          State_Diag%Archive_SatDiagnDryDepVel                           .or. &
-         State_Diag%Archive_SatDiagnPEdge                               .or. &
          State_Diag%Archive_SatDiagnTROPP                               .or. &
          State_Diag%Archive_SatDiagnTropLev                             .or. &
          State_Diag%Archive_SatDiagnPBLHeight                           .or. &
@@ -5238,7 +5244,6 @@ SUBROUTINE Init_State_Diag( Input_Opt, State_Chm,       State_Grid,        &
          State_Diag%Archive_SatDiagnPBLHeight                           .or. &
          State_Diag%Archive_SatDiagnPBLTop                              .or. &
          State_Diag%Archive_SatDiagnPBLTopL                             .or. &
-         State_Diag%Archive_SatDiagnPEdge                               .or. &
          State_Diag%Archive_SatDiagnPRECTOT                             .or. &
          State_Diag%Archive_SatDiagnProd                                .or. &
          State_Diag%Archive_SatDiagnRH                                  .or. &
@@ -5252,21 +5257,32 @@ SUBROUTINE Init_State_Diag( Input_Opt, State_Chm,       State_Grid,        &
          State_Diag%Archive_SatDiagnWetLossLS                           .or. &
          State_Diag%Archive_SatDiagnWetLossConv                             )
 
+    State_Diag%Archive_SatDiagnEdge = (                                      &
+         State_Diag%Archive_SatDiagnPEdge                                   )
+
     !------------------------------------------------------------------------
-    ! Satellite diagnostic: Counter
+    ! Satellite diagnostic: Counters
     !------------------------------------------------------------------------
     IF ( State_Diag%Archive_SatDiagn ) THEN 
-
-       ! Array to contain the satellite diagnostic weights
        ALLOCATE( State_Diag%SatDiagnCount( State_Grid%NX,                    &
                                            State_Grid%NY,                    &
                                            State_Grid%NZ ), STAT=RC         )
-       CALL GC_CheckVar( 'State_Diag%DiagnCount', 0, RC )
+       CALL GC_CheckVar( 'State_Diag%SatDiagnCount', 0, RC )
        IF ( RC /= GC_SUCCESS ) RETURN
        State_Diag%SatDiagnCount = 0.0_f4
        State_Diag%Archive_SatDiagnCount = .TRUE.
     ENDIF
 
+    IF ( State_Diag%Archive_SatDiagnEdge ) THEN
+       ALLOCATE( State_Diag%SatDiagnEdgeCount( State_Grid%NX,                &
+                                               State_Grid%NY,                &
+                                               State_Grid%NZ+1 ), STAT=RC   )
+       CALL GC_CheckVar( 'State_Diag%SatDiagnEdgeCount', 0, RC )
+       IF ( RC /= GC_SUCCESS ) RETURN
+       State_Diag%SatDiagnEdgeCount = 0.0_f4
+       State_Diag%Archive_SatDiagnEdgeCount = .TRUE.
+    ENDIF
+
     !=======================================================================
     ! The following diagnostic quantities are only relevant for:
     !
@@ -12985,6 +13001,16 @@ SUBROUTINE Cleanup_State_Diag( State_Diag, RC )
 !       State_Diag%WashFracLS => NULL()
 !    ENDIF
 
+    CALL Finalize( diagId   = 'SatDiagnCount',                               &
+                   Ptr2Data = State_Diag%SatDiagnCount,                      &
+                   RC       = RC                                            )
+    IF ( RC /= GC_SUCCESS ) RETURN
+
+    CALL Finalize( diagId   = 'SatDiagnEdgeCount',                           &
+                   Ptr2Data = State_Diag%SatDiagnEdgeCount,                  &
+                   RC       = RC                                            )
+    IF ( RC /= GC_SUCCESS ) RETURN
+
     CALL Finalize( diagId   = 'SatDiagnConc',                                &
                    Ptr2Data = State_Diag%SatDiagnConc,                       &
                    mapData  = State_Diag%Map_SatDiagnConc,                   &
@@ -15178,7 +15204,7 @@ SUBROUTINE Get_Metadata_State_Diag( am_I_Root,  metadataID, Found,         &
        IF ( isDesc    ) Desc  = 'Pressure edges'
        IF ( isUnits   ) Units = 'hPa'
        IF ( isRank    ) Rank  = 3
-       !IF ( isVLoc    ) VLoc  = VLocationEdge
+       IF ( isVLoc    ) VLoc  = VLocationEdge
 
     ELSE IF ( TRIM( Name_AllCaps ) == 'SATDIAGNTROPP' ) THEN
        IF ( isDesc    ) Desc  = 'Tropopause pressure'
@@ -20104,9 +20130,10 @@ SUBROUTINE Init_and_Register_R8_3D( Input_Opt,   State_Chm,                &
 !
 ! !USES:
 !
-    USE Input_Opt_Mod,  ONLY : OptInput
-    USE State_Chm_Mod,  ONLY : ChmState
-    USE State_Grid_Mod, ONLY : GrdState
+    USE Input_Opt_Mod,       ONLY : OptInput
+    USE State_Chm_Mod,       ONLY : ChmState
+    USE State_Grid_Mod,      ONLY : GrdState
+    USE Registry_Params_Mod, ONLY : VLocationEdge
 !
 ! !INPUT PARAMETERS:
 !
@@ -20142,7 +20169,7 @@ SUBROUTINE Init_and_Register_R8_3D( Input_Opt,   State_Chm,                &
     ! Scalars
     LOGICAL            :: alwaysDefine, found
     INTEGER            :: NX,           NY,       NZ
-    INTEGER            :: NW,           numSlots
+    INTEGER            :: NW,           numSlots, vLoc
 
     ! Strings
     CHARACTER(LEN=1)   :: indFlag
@@ -20159,6 +20186,7 @@ SUBROUTINE Init_and_Register_R8_3D( Input_Opt,   State_Chm,                &
     RC         = GC_SUCCESS
     numSlots   = -1
     found      = .FALSE.
+    vLoc       = .FALSE.
     arrayID    = 'State_Diag%' // TRIM( diagId )
     errMsg     = ''
     thisLoc    = &
@@ -20225,6 +20253,15 @@ SUBROUTINE Init_and_Register_R8_3D( Input_Opt,   State_Chm,                &
     NY = State_Grid%NY
     NZ = State_Grid%NZ
 
+    ! Determine if the array is defined on level edges
+    ! NOTE: This is only needed for the SatDiagnPEDGE field
+    CALL Get_Metadata_State_Diag( am_I_Root  = Input_Opt%amIRoot,          &
+                                  metadataId = diagId,                     &
+                                  found      = found,                      &
+                                  vLoc       = vLoc,                       &
+                                  RC         = RC                         )
+    IF ( vLoc == vLocationEdge ) NZ = NZ + 1
+
     ! Allocate array
     IF ( numSlots > 0 ) THEN
        ALLOCATE( Ptr2Data( NX, NY, numSlots ), STAT=RC )