geoschem · msulprizio · Jan 8, 2025 · Oct 30, 2024 · Oct 30, 2024 · Nov 1, 2024
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -30,6 +30,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 - Allocated `State_Diag%SatDiagnPEDGE` ffield with vertical dimension `State_Grid%NZ+1`
 - Modified `run/GCClassic/cleanRunDir.sh` to skip removing bpch files, as well as now removing `fort.*` and `OutputDir/*.txt` files
 - Edited `run/shared/kpp_standalone_interface.yml` to include additional entries under `active cells` and `locations`
+- Modified tagCO simulation to use GFED4 biomass burning emissions and GEOS-Chem v5 OH fields for consistency with carbon simulation
 
 ### Fixed
 - Added a fix to skip the call to KPP when only CO2 is defined in the carbon simulation
@@ -43,6 +44,12 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 - Fixed errors in adjoint-only code preventing successful adjoint build
 - Fixed zero convective precipitation and high cloud base in runs using GEOS-FP (>=01Jun2020) or GEOS-IT
 - Updated GEOS-only code for compatibility with GEOS-Chem 14.5
+- Fixed typos in `HEMCO_Config.rc` for CH4 simulations causing mobile combustion emissions to be double counted
+- Fixed handling of FIRST flag in carbon_gases_mod.F to limit log prints to first timestep only
+- Removed extraneous pressure correction in GCHP carbon simulations by adding 'activate: true' to geoschem_config.yml
+- Fixed bug in GC-Classic OCS emissions where unit conversion of km2 to m2 occurred twice
+- Changed dimension of EmisOCS_Total from 2D to 3D since all emissions for all sectors are 2D
+- Added fixes to only apply archived PCO_CH4 field for carbon simulations with CO only
 
 ### Removed
 - Removed duplicate `WD_RetFactor` tag for HgClHO2 in `species_database.yml`

diff --git a/GeosCore/carbon_gases_mod.F90 b/GeosCore/carbon_gases_mod.F90
@@ -238,6 +238,9 @@ SUBROUTINE CO2_Production( Input_Opt,  State_Chm, State_Diag,            &
        Spc => NULL()
     ENDIF
 
+    ! Reset first-time flag
+    FIRST = .FALSE.
+
     ! Free pointers for safety's sake
     Spc   => NULL()
     Ptr2D => NULL()

diff --git a/GeosCore/input_mod.F90 b/GeosCore/input_mod.F90
@@ -2020,7 +2020,7 @@ SUBROUTINE Config_CO( Config, Input_Opt, RC )
     !------------------------------------------------------------------------
     ! Use P(CO) from CH4 (archived from a fullchem simulation)?
     !------------------------------------------------------------------------
-    key    = "CO_simulation_options%use_fullchem_PCO_from_CH4"
+    key    = "CO_simulation_options%use_archived_PCO_from_CH4"
     v_bool = MISSING_BOOL
     CALL QFYAML_Add_Get( Config, key, v_bool, "", RC )
     IF ( RC /= GC_SUCCESS ) THEN
@@ -2033,7 +2033,7 @@ SUBROUTINE Config_CO( Config, Input_Opt, RC )
     !------------------------------------------------------------------------
     ! Use P(CO) from NMVOC (archived from a fullchem simulation)?
     !------------------------------------------------------------------------
-    key    = "CO_simulation_options%use_fullchem_PCO_from_NMVOC"
+    key    = "CO_simulation_options%use_archived_PCO_from_NMVOC"
     v_bool = MISSING_BOOL
     CALL QFYAML_Add_Get( Config, key, v_bool, "", RC )
     IF ( RC /= GC_SUCCESS ) THEN
@@ -2050,8 +2050,8 @@ SUBROUTINE Config_CO( Config, Input_Opt, RC )
        WRITE(6,90 ) 'TAGGED CO SIMULATION SETTINGS'
        WRITE(6,95 ) '(overwrites any other settings related to CO)'
        WRITE(6,95 ) '---------------------------------------------'
-       WRITE(6,100) 'Use full chem. P(CO) from CH4?   :', Input_Opt%LPCO_CH4
-       WRITE(6,100) 'Use full chem. P(CO) from NMVOC? :', Input_Opt%LPCO_NMVOC
+       WRITE(6,100) 'Use archived P(CO) from CH4?   :', Input_Opt%LPCO_CH4
+       WRITE(6,100) 'Use archived P(CO) from NMVOC? :', Input_Opt%LPCO_NMVOC
     ENDIF
 
     ! FORMAT statements
@@ -2113,9 +2113,9 @@ SUBROUTINE Config_CO2( Config, Input_Opt, RC )
     thisLoc = ' -> at Config_CO2 (in module GeosCore/input_mod.F90)'
 
     !------------------------------------------------------------------------
-    ! Turn on CO2 3D chemical source and surface correction?
+    ! Use archived fields of CO2 production from CO oxidation?
     !------------------------------------------------------------------------
-    key    = "CO2_simulation_options%sources%3D_chemical_oxidation_source"
+    key    = "CO2_simulation_options%sources%use_archived_PCO2_from_CO"
     v_bool = MISSING_BOOL
     CALL QFYAML_Add_Get( Config, key, v_bool, "", RC )
     IF ( RC /= GC_SUCCESS ) THEN
@@ -2158,7 +2158,7 @@ SUBROUTINE Config_CO2( Config, Input_Opt, RC )
        WRITE( 6,90  ) 'CO2 SIMULATION SETTINGS'
        WRITE( 6,95  ) '(overwrites any other settings related to CO2)'
        WRITE( 6,95  ) '----------------------------------------------'
-       WRITE( 6,100 ) 'CO2 from oxidation (CO,CH4,..):', Input_Opt%LCHEMCO2
+       WRITE( 6,100 ) 'Use archived P(CO2) from CO?  :', Input_Opt%LCHEMCO2
        WRITE( 6, 95 ) 'Tagged CO2 settings'
        WRITE( 6,100 ) '  Tag Biosphere/Ocean CO2     :', Input_Opt%LBIOSPHTAG
        WRITE( 6,100 ) '  Tag Fossil Fuel CO2         :', Input_Opt%LFOSSILTAG

diff --git a/KPP/carbon/carbon_Funcs.F90 b/KPP/carbon/carbon_Funcs.F90
@@ -193,7 +193,7 @@ SUBROUTINE carbon_ComputeRateConstants(                               &
        C(ind_FixedCl) = ConcClMnd
 
        ! CH4 + offline OH reaction rate [1/s]
-       ! This is a pseudo-2nd order rate appropriate for CH4 + OH
+       ! Use rates saved from full-chemistry run (if CH4 is not advected)
        IF ( PCO_fr_CH4_use ) THEN
           k_Trop(1) = PCO_fr_CH4 * OHdiurnalFac
           k_Trop(1) = SafeDiv( k_Trop(1), C(ind_CH4)*C(ind_FixedOH), 0.0_dp )

diff --git a/KPP/carbon/gckpp_Function.F90 b/KPP/carbon/gckpp_Function.F90
@@ -2,7 +2,7 @@
 ! 
 ! The ODE Function of Chemical Model File
 ! 
-! Generated by KPP-3.0.0 symbolic chemistry Kinetics PreProcessor
+! Generated by KPP-3.1.1 symbolic chemistry Kinetics PreProcessor
 !       (https:/github.com/KineticPreProcessor/KPP
 ! KPP is distributed under GPL, the general public licence
 !       (http://www.gnu.org/copyleft/gpl.html)

diff --git a/KPP/carbon/gckpp_Global.F90 b/KPP/carbon/gckpp_Global.F90
@@ -2,7 +2,7 @@
 ! 
 ! Global Data Module File
 ! 
-! Generated by KPP-3.0.0 symbolic chemistry Kinetics PreProcessor
+! Generated by KPP-3.1.1 symbolic chemistry Kinetics PreProcessor
 !       (https:/github.com/KineticPreProcessor/KPP
 ! KPP is distributed under GPL, the general public licence
 !       (http://www.gnu.org/copyleft/gpl.html)

diff --git a/KPP/carbon/gckpp_Initialize.F90 b/KPP/carbon/gckpp_Initialize.F90
@@ -2,7 +2,7 @@
 ! 
 ! Initialization File
 ! 
-! Generated by KPP-3.0.0 symbolic chemistry Kinetics PreProcessor
+! Generated by KPP-3.1.1 symbolic chemistry Kinetics PreProcessor
 !       (https:/github.com/KineticPreProcessor/KPP
 ! KPP is distributed under GPL, the general public licence
 !       (http://www.gnu.org/copyleft/gpl.html)

diff --git a/KPP/carbon/gckpp_Integrator.F90 b/KPP/carbon/gckpp_Integrator.F90
@@ -2,7 +2,7 @@
 ! 
 ! Numerical Integrator (Time-Stepping) File
 ! 
-! Generated by KPP-3.0.0 symbolic chemistry Kinetics PreProcessor
+! Generated by KPP-3.1.1 symbolic chemistry Kinetics PreProcessor
 !       (https:/github.com/KineticPreProcessor/KPP
 ! KPP is distributed under GPL, the general public licence
 !       (http://www.gnu.org/copyleft/gpl.html)

diff --git a/KPP/carbon/gckpp_Jacobian.F90 b/KPP/carbon/gckpp_Jacobian.F90
@@ -2,7 +2,7 @@
 ! 
 ! The ODE Jacobian of Chemical Model File
 ! 
-! Generated by KPP-3.0.0 symbolic chemistry Kinetics PreProcessor
+! Generated by KPP-3.1.1 symbolic chemistry Kinetics PreProcessor
 !       (https:/github.com/KineticPreProcessor/KPP
 ! KPP is distributed under GPL, the general public licence
 !       (http://www.gnu.org/copyleft/gpl.html)

diff --git a/KPP/carbon/gckpp_LinearAlgebra.F90 b/KPP/carbon/gckpp_LinearAlgebra.F90
@@ -2,7 +2,7 @@
 ! 
 ! Linear Algebra Data and Routines File
 ! 
-! Generated by KPP-3.0.0 symbolic chemistry Kinetics PreProcessor
+! Generated by KPP-3.1.1 symbolic chemistry Kinetics PreProcessor
 !       (https:/github.com/KineticPreProcessor/KPP
 ! KPP is distributed under GPL, the general public licence
 !       (http://www.gnu.org/copyleft/gpl.html)

diff --git a/KPP/carbon/gckpp_Monitor.F90 b/KPP/carbon/gckpp_Monitor.F90
@@ -2,7 +2,7 @@
 ! 
 ! Utility Data Module File
 ! 
-! Generated by KPP-3.0.0 symbolic chemistry Kinetics PreProcessor
+! Generated by KPP-3.1.1 symbolic chemistry Kinetics PreProcessor
 !       (https:/github.com/KineticPreProcessor/KPP
 ! KPP is distributed under GPL, the general public licence
 !       (http://www.gnu.org/copyleft/gpl.html)

diff --git a/KPP/carbon/gckpp_Parameters.F90 b/KPP/carbon/gckpp_Parameters.F90
@@ -2,7 +2,7 @@
 ! 
 ! Parameter Module File
 ! 
-! Generated by KPP-3.0.0 symbolic chemistry Kinetics PreProcessor
+! Generated by KPP-3.1.1 symbolic chemistry Kinetics PreProcessor
 !       (https:/github.com/KineticPreProcessor/KPP
 ! KPP is distributed under GPL, the general public licence
 !       (http://www.gnu.org/copyleft/gpl.html)

diff --git a/KPP/carbon/gckpp_Rates.F90 b/KPP/carbon/gckpp_Rates.F90
@@ -2,7 +2,7 @@
 ! 
 ! The Reaction Rates File
 ! 
-! Generated by KPP-3.0.0 symbolic chemistry Kinetics PreProcessor
+! Generated by KPP-3.1.1 symbolic chemistry Kinetics PreProcessor
 !       (https:/github.com/KineticPreProcessor/KPP
 ! KPP is distributed under GPL, the general public licence
 !       (http://www.gnu.org/copyleft/gpl.html)

diff --git a/KPP/carbon/gckpp_Util.F90 b/KPP/carbon/gckpp_Util.F90
@@ -2,7 +2,7 @@
 !
 ! Auxiliary Routines File
 !
-! Generated by KPP-3.0.0 symbolic chemistry Kinetics PreProcessor
+! Generated by KPP-3.1.1 symbolic chemistry Kinetics PreProcessor
 !       (https:/github.com/KineticPreProcessor/KPP
 ! KPP is distributed under GPL, the general public licence
 !       (http://www.gnu.org/copyleft/gpl.html)

diff --git a/run/GCClassic/HEMCO_Config.rc.templates/HEMCO_Config.rc.CH4 b/run/GCClassic/HEMCO_Config.rc.templates/HEMCO_Config.rc.CH4
@@ -135,6 +135,7 @@ VerboseOnCores:              root       # Accepted values: root all
 )))UseTotalPriorEmis
 
 (((.not.UseTotalPriorEmis
+
 #==============================================================================
 # --- Gridded GHGI v2 (Maasakkers et al., submitted to ES&T, 2023) ---
 #
@@ -251,7 +252,7 @@ VerboseOnCores:              root       # Accepted values: root all
 0 GHGI_EE_COAST_GAS_TRANSMISSION -                                                                                      -                                            -                  - -  -           CH4 1009    2 5
 0 GHGI_EE_GAS_POSTMETER          $ROOT/CH4/v2023-07/Gridded_GHGI_v2/Express_Extension_Gridded_GHGI_Methane_v2_$YYYY.nc  emi_ch4_Supp_1B2b_PostMeter                  2012-2020/1/1/0    C xy molec/cm2/s CH4 1008    2 100
 
-### Coal ###        
+### Coal ###
 0 GHGI_EE_COAL_UNDERGROUND       $ROOT/CH4/v2023-07/Gridded_GHGI_v2/Express_Extension_Gridded_GHGI_Methane_v2_$YYYY.nc  emi_ch4_1B1a_Underground_Coal                2012-2020/1/1/0    C xy molec/cm2/s CH4 1008    3 100
 0 GHGI_EE_COAST_COAL_UNDERGROUND -                                                                                      -                                            -                  - -  -           CH4 1009    3 5
 0 GHGI_EE_COAL_SURFACE           $ROOT/CH4/v2023-07/Gridded_GHGI_v2/Express_Extension_Gridded_GHGI_Methane_v2_$YYYY.nc  emi_ch4_1B1a_Surface_Coal                    2012-2020/1/1/0    C xy molec/cm2/s CH4 1008    3 100
@@ -281,11 +282,11 @@ VerboseOnCores:              root       # Accepted values: root all
 
 ### Rice ###
 0 GHGI_EE_RICE                   $ROOT/CH4/v2023-07/Gridded_GHGI_v2/Express_Extension_Gridded_GHGI_Methane_v2_$YYYY.nc  emi_ch4_3C_Rice_Cultivation                  2012-2020/1-12/1/0 C xy molec/cm2/s CH4 58/1008 7 100
-0 GHGI_EE_COAST_RICE             -                                                                                      -                                            -                  - -y -           CH4 58/1009 7 1
+0 GHGI_EE_COAST_RICE             -                                                                                      -                                            -                  - -  -           CH4 58/1009 7 1
 
 ### Other Anthro ###
 0 GHGI_EE_OTHER_MCOMB            $ROOT/CH4/v2023-07/Gridded_GHGI_v2/Express_Extension_Gridded_GHGI_Methane_v2_$YYYY.nc  emi_ch4_1A_Combustion_Mobile                 2012-2020/1/1/0    C xy molec/cm2/s CH4 1008    8 100
-0 GHGI_EE_COAST_OTHER_MCOMB      -                                                                                      -                                            -                  - -  -           CH4 1008    8 100
+0 GHGI_EE_COAST_OTHER_MCOMB      -                                                                                      -                                            -                  - -  -           CH4 1009    8 1
 0 GHGI_EE_OTHER_SCOMB            $ROOT/CH4/v2023-07/Gridded_GHGI_v2/Express_Extension_Gridded_GHGI_Methane_v2_$YYYY.nc  emi_ch4_1A_Combustion_Stationary             2012-2020/1-12/1/0 C xy molec/cm2/s CH4 50/1008 8 100
 0 GHGI_EE_COAST_OTHER_SCOMB      -                                                                                      -                                            -                  - -  -           CH4 50/1009 8 1
 0 GHGI_EE_OTHER_PIND             $ROOT/CH4/v2023-07/Gridded_GHGI_v2/Express_Extension_Gridded_GHGI_Methane_v2_$YYYY.nc  emi_ch4_2B8_Industry_Petrochemical           2012-2020/1/1/0    C xy molec/cm2/s CH4 1008    8 100
@@ -415,7 +416,7 @@ VerboseOnCores:              root       # Accepted values: root all
 )))EDGARv8
 
 #==============================================================================
-# CEDS (historical) or Shared Socioeconomic Pathways (future)
+# --- CEDS (historical) or Shared Socioeconomic Pathways (future) ---
 #==============================================================================
 (((CMIP6_SFC_LAND_ANTHRO
 0 CMIP6_CH4_AGR   $ROOT/CMIP6/v2021-01/$GCAPSCENARIO/$GCAPSCENARIO_$YYYY.nc4 CH4_agr 1970-2014/1-12/1/0 C xy kg/m2/s CH4 - 4 1
@@ -431,7 +432,7 @@ VerboseOnCores:              root       # Accepted values: root all
 )))CMIP6_SHIP
 
 #==============================================================================
-# BB4MIPs historical / SSP future biomass burning inventories
+# --- BB4MIPs historical / SSP future biomass burning inventories ---
 #==============================================================================
 (((BB4MIPS
 0 CMIP6_BB_CH4    $ROOT/CMIP6/v2021-01/$GCAPSCENARIO/$GCAPSCENARIO_$YYYY.nc4 CH4_bbn 1750-2015/1-12/1/0 C xyL=1:PBL kg/m2/s CH4 75 9 1
@@ -450,7 +451,7 @@ VerboseOnCores:              root       # Accepted values: root all
 #==============================================================================
 # --- CH4: JPL WetCHARTs v1.0 (Bloom et al., https://doi.org/10.3334/ORNLDAAC/1502) ---
 #
-# # Use updated files (v2024-01); these are COARDS-compliant.
+# Use updated files (v2024-01); these are COARDS-compliant.
 #==============================================================================
 (((JPL_WETCHARTS
 0 JPLW_CH4  $ROOT/CH4/v2024-01/JPL_WetCharts/HEensemble/JPL_WetCharts_2010-2019.Ensemble_Mean.0.5x0.5.nc emi_ch4 2010-2019/1-12/1/0 C xy molec/cm2/s CH4 - 10 1
@@ -496,7 +497,7 @@ VerboseOnCores:              root       # Accepted values: root all
 )))FUNG_SOIL_ABSORPTION
 
 #==============================================================================
-# --- # Soil absorption from MeMo model (Murguia-Flores et al. 2018, GMD) ---
+# --- Soil absorption from MeMo model (Murguia-Flores et al. 2018, GMD) ---
 #
 # - Multiply soil absorption by -1 to get a "negative" flux
 #==============================================================================
@@ -623,7 +624,7 @@ VerboseOnCores:              root       # Accepted values: root all
 # --- GEOS-Chem boundary condition file ---
 #==============================================================================
 (((GC_BCs
-* BC_ $ROOT/SAMPLE_BCs/v2021-07/CH4/GEOSChem.BoundaryConditions.$YYYY$MM$DD_0000z.nc4 SpeciesBC_?ADV?  1900-2100/1-12/1-31/* EFY xyz 1 * - 1 1
+* BC_ $ROOT/SAMPLE_BCs/v2021-07/CH4/GEOSChem.BoundaryConditions.$YYYY$MM$DD_0000z.nc4 SpeciesBC_?ADV? 1900-2100/1-12/1-31/* EFY xyz 1 * - 1 1
 )))GC_BCs
 
 #==============================================================================
@@ -945,7 +946,6 @@ ${RUNDIR_GLOBAL_Cl}
 # Country/region masks
 #==============================================================================
 
-# Use updated files (v2024-01); these are COARDS-compliant.
 (((Scarpelli_Mexico
 1001 MEX_MASK          $ROOT/MASKS/v2024-04/Mexico_Mask.01x01.nc        MASK 2000/1/1/0 C xy 1 1 -118/17/-95/33
 1010 MEX_MASK_MIRROR   $ROOT/MASKS/v2024-04/Mexico_Mask_Mirror.01x01.nc MASK 2000/1/1/0 C xy 1 1 -118/17/-95/33