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

…ns with CO only In KPP/carbon/carbon_Funcs.F90 when using PCO_fr_CH4_use was true there was an extra line taking into account CH4 and OH concentrations. This should not be needed when using the archived PCO_CH4 fields. In addition, PCO_CH4 should only be used when using the carbon simulation with CO only. Otherwise, the CH4 + OH rate function (2.45E-12_dp * EXP( -1775.0E+0_dp /TEMP )) should be used. To make is more clear the PCO_CH4 fields are read from file the option in geoschem_config.yml has been renamed from from "use_fullchem_PCO_from_CH4" to "use_archived_PCO_from_CH4". This is also set to false by default for carbon simulations and only set to true in carbon simulations where only CO is advected. 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 13, 2024 · 8f7746c · 8f7746c
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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

diff --git a/KPP/carbon/carbon_Funcs.F90 b/KPP/carbon/carbon_Funcs.F90
@@ -193,10 +193,9 @@ 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 )
        ELSE
           k_Trop(1) = 2.45E-12_dp * EXP( -1775.0E+0_dp /TEMP )  ! JPL 1997
        ENDIF

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.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: false
 
 #============================================================================
 # Options for CO2

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 $?)
     # 0 if item is in the list
@@ -123,6 +123,16 @@ function updateGeosChemConfig() {
             keyValueUpdate "${key}" "true" "false" "${file}"
         done
     fi
+
+    # If CO is in the include list, turn on CO options
+    isItemInList "CO" "${1}"
+    if [[ $? == 1 ]]; then
+        keys=("use_archived_PCO_from_CH4"      \
+	      "use_archived_PCO_from_NMVOC"   )
+        for key in ${keys[@]}; do
+            keyValueUpdate "${key}" "false" "true" "${file}"
+        done
+    fi
 }