Added fixes to only apply archived PCO_CH4 field for carbon simulatio…

…ns with CO only To make it more clear that the PCO_CH4 fields are read from file, the option in in the CO2 menu of geoschem_config.yml has been renamed from from "use_fullchem_PCO_from_CH4" to "use_archived_PCO_from_CH4 (same for NMVOC source)". The use_archived_PCO_from_CH4 option is now set to false by default for carbon simulations and only set to true in carbon simulations where only CO is advected. Similarly, "3D_chemical_oxidation_source" in the CO2 menu has been renamed to "use_archived_PCO2_from_CO". The carbon mechanism was rebuilt with KPP 3.1.1 here but that is a zero- difference update simply changing the headers of the KPP/carbon/gckpp* files. Signed-off-by: Melissa Sulprizio <[email protected]>
geoschem · Dec 20, 2024 · f408db9 · f408db9
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -49,6 +49,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 - 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/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/geoschem_config.yml.templates/geoschem_config.yml.CO2 b/run/GCClassic/geoschem_config.yml.templates/geoschem_config.yml.CO2
@@ -73,7 +73,7 @@ operations:
 CO2_simulation_options:
 
   sources:
-    3D_chemical_oxidation_source: true
+    use_archived_PCO2_from_CO: true
 
   tagged_species:
     tag_bio_and_ocean_CO2: false

diff --git a/run/GCClassic/geoschem_config.yml.templates/geoschem_config.yml.carbon b/run/GCClassic/geoschem_config.yml.templates/geoschem_config.yml.carbon
@@ -86,8 +86,8 @@ CH4_simulation_options:
 #============================================================================
 
 CO_simulation_options:
-  use_fullchem_PCO_from_CH4: true
-  use_fullchem_PCO_from_NMVOC: true
+  use_archived_PCO_from_CH4: false
+  use_archived_PCO_from_NMVOC: true
 
 #============================================================================
 # Options for CO2
@@ -96,7 +96,7 @@ CO_simulation_options:
 CO2_simulation_options:
 
   sources:
-    3D_chemical_oxidation_source: true
+    use_archived_PCO2_from_CO: false
 
   tagged_species:
     tag_bio_and_ocean_CO2: false

diff --git a/run/GCClassic/geoschem_config.yml.templates/geoschem_config.yml.tagCO b/run/GCClassic/geoschem_config.yml.templates/geoschem_config.yml.tagCO
@@ -84,8 +84,8 @@ operations:
 #============================================================================
 
 CO_simulation_options:
-  use_fullchem_PCO_from_CH4: true
-  use_fullchem_PCO_from_NMVOC: true
+  use_archived_PCO_from_CH4: true
+  use_archived_PCO_from_NMVOC: true
 
 #============================================================================
 # Settings for diagnostics (other than HISTORY and HEMCO)

diff --git a/run/shared/singleCarbonSpecies.sh b/run/shared/singleCarbonSpecies.sh
@@ -31,7 +31,7 @@ function isItemInList() {
     #
     # Arguments:
     # ${1}: The item
-    # ${2}: Thie list
+    # ${2}: The list
     #
     # Returns (via $?)
     # 0 if item is in the list
@@ -110,17 +110,22 @@ function updateGeosChemConfig() {
         sed -i -e "${cmd}" "${file}"
     done
 
-    # NOTE: CH4 options are already deactivated
-    # in the out-of-the-box geoschem_config.yml
-
-    # If CO2 is in the exclude list, turn off CO2 options
+    # If CO2 is in the include list, turn on CO2 production options
     isItemInList "CO2" "${1}"
-    if [[ $? == 0 ]]; then
-        keys=("3D_chemical_oxidation_source"   \
-              "tag_bio_and_ocean_CO2"          \
-              "tag_land_fossil_fuel_CO2"      )
+    if [[ $? == 1 ]]; then
+        keys=("use_archived_PCO2_from_CO" )
+        for key in ${keys[@]}; do
+            keyValueUpdate "${key}" "false" "true" "${file}"
+        done
+    fi
+
+    # If CO is in the include list, turn on CO production options
+    isItemInList "CO" "${1}"
+    if [[ $? == 1 ]]; then
+        keys=("use_archived_PCO_from_CH4"      \
+	      "use_archived_PCO_from_NMVOC"   )
         for key in ${keys[@]}; do
-            keyValueUpdate "${key}" "true" "false" "${file}"
+            keyValueUpdate "${key}" "false" "true" "${file}"
         done
     fi
 }