diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2a8a64731..09cd81cf2 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -14,6 +14,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 - GCClassic integration tests now display proper commit info in `results.compile.log`
 - Stopped OCEAN_CONC from needlessly being pushed through vertical regridding for Hg simulations
 - Added warning in GCHP HISTORY.rc about outputting area-dependent variables on custom grids
+- Added option to use a single advected species in the carbon simulation
 
 ### Changed
 - Update `DiagnFreq` in GCClassic integration tests to ensure HEMCO diagnostic output
@@ -101,7 +102,9 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 - Change RTOL value from 0.5e-3 back to 0.5e-2 to address model slowdown
 - Allow the use of OFFLINE_SEASALT for seasalt alkalinity, Cl, and Br in GEOS-Chem within CESM
 - Renamed TransportTracer species for consistency with GMAO's TR_GridComp
-- See `KPP/fullchem/CHANGELOG_fullchem.md` for fullchem-mechanism changes
+- See `KPP/fullchem/CHANGELOG_fullchem.md` for fullchem-mechanism
+  changes
+- Update template `HEMCO_Config.rc.carbon` files to allow running the carbon simulation with only a single species.
 
 ### Fixed
 - Fixed typo in `GCClassic/createRunDir.sh` preventing benchmark run script from being copied to the run directory
diff --git a/GeosCore/carbon_gases_mod.F90 b/GeosCore/carbon_gases_mod.F90
index eff5cf1ae..fdf4f4f45 100644
--- a/GeosCore/carbon_gases_mod.F90
+++ b/GeosCore/carbon_gases_mod.F90
@@ -369,7 +369,7 @@ END SUBROUTINE Emiss_Carbon_Gases
 ! !INTERFACE:
 !
   SUBROUTINE Chem_Carbon_Gases( Input_Opt,  State_Met,  State_Chm,            &
-                               State_Grid, State_Diag, RC                   )
+                                State_Grid, State_Diag, RC                   )
 !
 ! !USES:
 !
@@ -684,7 +684,16 @@ SUBROUTINE Chem_Carbon_Gases( Input_Opt,  State_Met,  State_Chm,            &
        ! Update reaction rates
        !===================================================================
 
-       ! Start timer
+       ! Stop KPP timer
+       IF ( Input_Opt%useTimers ) THEN
+          CALL Timer_End(                                                    &
+               timerName = "  -> KPP",                                       &
+               inLoop    = .TRUE.,                                           &
+               threadNum = ThreadNum,                                        &
+               RC        = RC                                               )
+       ENDIF
+
+       ! Start RCONST timer
        IF ( Input_Opt%useTimers ) THEN
           CALL Timer_Start(                                                  &
                timerName = "     RCONST",                                    &
@@ -756,6 +765,15 @@ SUBROUTINE Chem_Carbon_Gases( Input_Opt,  State_Met,  State_Chm,            &
        ! Trap potential errors
        IF ( IERR /= 1 ) failed = .TRUE.
 
+       ! Start KPP timer
+       IF ( Input_Opt%useTimers ) THEN
+          CALL Timer_End(                                                    &
+               timerName = "  -> KPP",                                       &
+               inLoop    = .TRUE.,                                           &
+               threadNum = ThreadNum,                                        &
+               RC        = RC                                               )
+       ENDIF
+
        !=====================================================================
        ! HISTORY: Archive KPP solver diagnostics
        !=====================================================================
diff --git a/GeosCore/chemistry_mod.F90 b/GeosCore/chemistry_mod.F90
index 471d556b4..3ca289bbd 100644
--- a/GeosCore/chemistry_mod.F90
+++ b/GeosCore/chemistry_mod.F90
@@ -988,6 +988,11 @@ SUBROUTINE Do_Chemistry( Input_Opt,  State_Chm, State_Diag,                &
        !=====================================================================
        ELSE IF ( Input_Opt%ITS_A_CARBON_SIM ) THEN
 
+          ! Start "FlexChem" timer
+          IF ( Input_Opt%useTimers ) THEN
+             CALL Timer_Start( "=> FlexChem", RC )
+          ENDIF
+
           ! Do carbon chemistry
           CALL Chem_Carbon_Gases( Input_Opt  = Input_Opt,                    &
                                   State_Met  = State_Met,                    &
@@ -1003,11 +1008,21 @@ SUBROUTINE Do_Chemistry( Input_Opt,  State_Chm, State_Diag,                &
              RETURN
           ENDIF
 
+          ! Stop "FlexChem" timer
+          IF ( Input_Opt%useTimers ) THEN
+             CALL Timer_End( "=> FlexChem", RC )
+          ENDIF
+
        !====================================================================
        ! Mercury (configure with -DMECH=Hg)
        !=====================================================================
        ELSE IF ( Input_Opt%ITS_A_MERCURY_SIM ) THEN
 
+          ! Start "FlexChem" timer
+          IF ( Input_Opt%useTimers ) THEN
+             CALL Timer_Start( "=> FlexChem", RC )
+          ENDIF
+
           ! Do Hg chemistry
           CALL ChemMercury( Input_Opt  = Input_Opt,                          &
                             State_Chm  = State_Chm,                          &
@@ -1023,6 +1038,11 @@ SUBROUTINE Do_Chemistry( Input_Opt,  State_Chm, State_Diag,                &
              RETURN
           ENDIF
 
+          ! Stop "FlexChem" timer
+          IF ( Input_Opt%useTimers ) THEN
+             CALL Timer_End( "=> FlexChem", RC )
+          ENDIF
+
        !=====================================================================
        ! POPs (only used when compiled with BPCH_DIAG=y)
        !=====================================================================
diff --git a/run/GCClassic/HEMCO_Config.rc.templates/HEMCO_Config.rc.carbon b/run/GCClassic/HEMCO_Config.rc.templates/HEMCO_Config.rc.carbon
index 3bf391d0e..75842702d 100644
--- a/run/GCClassic/HEMCO_Config.rc.templates/HEMCO_Config.rc.carbon
+++ b/run/GCClassic/HEMCO_Config.rc.templates/HEMCO_Config.rc.carbon
@@ -1307,7 +1307,6 @@ ${RUNDIR_GLOBAL_OH}
 #------------------------------------------------------------------------------
 # --- Quantities needed for CH4 chemistry ---
 #------------------------------------------------------------------------------
-(((USE_CH4_DATA
 
 # --- Global CH4 loss frequencies [1/s] -----------
 (((CH4_LOSS_FREQ
@@ -1319,12 +1318,9 @@ ${RUNDIR_CH4_LOSS}
 ${RUNDIR_GLOBAL_Cl}
 )))GLOBAL_CL
 
-)))USE_CH4_DATA
-
 #------------------------------------------------------------------------------
 # --- Quantities needed for CO chemistry ---
 #------------------------------------------------------------------------------
-(((USE_CO_DATA
 
 # -- P(CO) from CH4 and NMVOC from the last 10-yr benchmark [molec/cm3/s] ---
 (((PROD_CO_CH4
@@ -1336,13 +1332,21 @@ ${RUNDIR_PCO_NMVOC}
 
 # --- GMI chemistry: prod/loss rates (for strato-/mesosphere) ---
 # --- Units: prod [v/v/s]; loss [1/s]                         ---
+(((USE_CO_DATA
 (((GMI_PROD_LOSS
-${RUNDIR_GMI_LOSS_CO}
-${RUNDIR_GMI_PROD_CO}
+* GMI_LOSS_CO    $ROOT/GMI/v2022-11/gmi.clim.CO.geos5.2x25.nc  loss  2005/1-12/1/0 C xyz s-1     CO - 1 1
+* GMI_PROD_CO    $ROOT/GMI/v2022-11/gmi.clim.CO.geos5.2x25.nc  prod  2005/1-12/1/0 C xyz v/v/s   CO - 1 1
 )))GMI_PROD_LOSS
-
 )))USE_CO_DATA
 
+# If CO is not an advected species, then just read as a chemistry input
+(((.not.USE_CO_DATA
+(((GMI_PROD_LOSS
+* GMI_LOSS_CO    $ROOT/GMI/v2022-11/gmi.clim.CO.geos5.2x25.nc  loss  2005/1-12/1/0 C xyz s-1     *  - 1 1
+* GMI_PROD_CO    $ROOT/GMI/v2022-11/gmi.clim.CO.geos5.2x25.nc  prod  2005/1-12/1/0 C xyz v/v/s   *  - 1 1
+)))GMI_PROD_LOSS
+))).not.USE_CO_DATA
+
 #------------------------------------------------------------------------------
 # --- Quantities needed for CO2 chemistry ---
 #------------------------------------------------------------------------------
@@ -1350,14 +1354,11 @@ ${RUNDIR_GMI_PROD_CO}
 # --- CHEMICAL PRODUCTION FROM CO OXIDATION ------
 # --- Recommended for use in forward modelling ---
 # --- Optional for inversion/assimilation --------
-(((USE_CO2_DATA
 
 (((CO2_COPROD
 ${RUNDIR_CO2_COPROD}
 )))CO2_COPROD
 
-)))USE_CO2_DATA
-
 )))CHEMISTRY_INPUT
 
 ### END SECTION BASE EMISSIONS ###
@@ -1690,12 +1691,15 @@ ${RUNDIR_CO2_COPROD}
 2008 AFRICA_MASK $ROOT/MASKS/v2018-09/AF_LANDMASK.geos.05x0666.global.nc LANDMASK 1985/1/1/0 C xy 1 1 -20/-37/54/40
 )))DICE_Africa
 
+)))USE_CO_DATA.or.USE_CO2_DATA
+
+#==============================================================================
+# --- Masks used for CH4, CO and CO2 simulation emissions ---
+#==============================================================================
 (((CEDSv2.or.CEDS_GBDMAPS.or.CEDS_GBDMAPS_byFuelType
 2009 CHINA_MASK  $ROOT/MASKS/v2018-09/China_mask.generic.1x1.nc          MASK     2000/1/1/0 C xy 1 1  70/10/150/60
 )))CEDSv2.or.CEDS_GBDMAPS.or.CEDS_GBDMAPS_byFuelType
 
-)))USE_CO_DATA.or.USE_CO2_DATA
-
 )))EMISSIONS
 
 ### END SECTION MASKS ###
diff --git a/run/GCClassic/HEMCO_Diagn.rc.templates/HEMCO_Diagn.rc.carbon b/run/GCClassic/HEMCO_Diagn.rc.templates/HEMCO_Diagn.rc.carbon
index fc71f5dba..47504a22c 100644
--- a/run/GCClassic/HEMCO_Diagn.rc.templates/HEMCO_Diagn.rc.carbon
+++ b/run/GCClassic/HEMCO_Diagn.rc.templates/HEMCO_Diagn.rc.carbon
@@ -16,9 +16,8 @@
 # Name               Spec  ExtNr  Cat Hier Dim  OutUnit  LongName
 
 ###############################################################################
-#####  CH4 sources                                                         #####
+#####  CH4 sources                                                        #####
 ###############################################################################
-
 EmisCH4_Total         CH4     -1   -1   -1   2  kg/m2/s  CH4_emissions_from_all_sectors
 EmisCH4_Oil           CH4      0    1   -1   2  kg/m2/s  CH4_emissions_from_oil
 EmisCH4_Gas           CH4      0    2   -1   2  kg/m2/s  CH4_emissions_from_gas
@@ -42,7 +41,7 @@ EmisCH4_Reservoirs    CH4      0   15   -1   2  kg/m2/s  CH4_emissions_from_hydr
 EmisCO_Total          CO      -1   -1   -1   3  kg/m2/s  CO_emission_flux_from_all_sectors
 EmisCO_Aircraft       CO       0   20   -1   3  kg/m2/s  CO_emission_flux_from_aircraft
 EmisCO_Anthro         CO       0    1   -1   3  kg/m2/s  CO_emission_flux_from_anthropogenic
-EmisCO_BioBurn        CO       0    5   -1   2  kg/m2/s  CO_emission_flux_from_biomass_burning
+EmisCO_BiomassBurn    CO     111   -1   -1   2  kg/m2/s  CO_emission_flux_from_biomass_burning
 EmisCO_Ship           CO       0   10   -1   2  kg/m2/s  CO_emission_flux_from_ships
 
 ###############################################################################
@@ -56,13 +55,7 @@ EmisCO2_NetTerrExch   CO2      0    5   -1   2  kg/m2/s  CO2_net_terrestrial_exc
 EmisCO2_Ship          CO2      0    6   -1   2  kg/m2/s  CO2_ship_emissions
 EmisCO2_Aviation      CO2      0    7   -1   3  kg/m2/s  CO2_aviation_emissions
 EmisCO2_CO2SurfCorr   CO2      0    8   -1   2  kg/m2/s  CO2_surface_correction_for_CO_oxidation
-
-#NOTE: Biomass burning doesn't seem to work.  Keep here for now.
-# Uncomment this if GFED is used
-#EmisCO2_Biomass_GFED  CO2    111    1    1   2  kg/m2/s  CO2_biomass_burning_emissions_from_GFED4
-
-# Uncomment this if FINN is used
-#EmisCO2_Biomass_FINN  CO2    114    1    1   2  kg/m2/s  CO2_biomass_burning_emissions_from_FINN
+EmisCO2_BiomassBurn   CO2    111   -1   -1   2  kg/m2/s  CO2_biomass_burning_emissions_from_GFED4
 
 ###############################################################################
 #####  OCS sources                                                        #####
@@ -72,77 +65,3 @@ EmisOCS_Anthro        OCS      0    1   -1   2  kg/m2/s  OCS_emission_flux_from_
 EmisOCS_Bioburn       OCS      0    2   -1   2  kg/m2/s  OCS_emission_flux_from_biomass_burning
 EmisOCS_MissingOcean  OCS      0    3   -1   2  kg/m2/s  OCS_emission_flux_from_missing_ocean
 EmisOCS_Ocean         OCS      0    4   -1   2  kg/m2/s  OCS_emission_flux_from_ocean
-
-# Tagged CO species, uncomment if needed
-#
-################################################################################
-######  COus sources                                                       #####
-################################################################################
-#EmisCOus_Total        COus    -1   -1   -1   3  kg/m2/s  COus_emission_flux_from_all_sectors
-#EmisCOus_Aircraft     COus     0   20   -1   3  kg/m2/s  COus_emission_flux_from_aircraft
-#EmisCOus_Anthro       COus     0    1   -1   3  kg/m2/s  COus_emission_flux_from_anthropogenic
-#EmisCOus_BioBurn      COus     0    5   -1   2  kg/m2/s  COus_emission_flux_from_biomass_burning
-#EmisCOus_Ship         COus     0   10   -1   2  kg/m2/s  COus_emission_flux_from_ships
-#
-################################################################################
-######  COeur sources                                                      #####
-################################################################################
-#EmisCOeur_Total       COeur   -1   -1   -1   3  kg/m2/s  COeur_emission_flux_from_all_sectors
-#EmisCOeur_Aircraft    COeur    0   20   -1   3  kg/m2/s  COeur_emission_flux_from_aircraft
-#EmisCOeur_Anthro      COeur    0    1   -1   3  kg/m2/s  COeur_emission_flux_from_anthropogenic
-#EmisCOeur_BioBurn     COeur    0    5   -1   2  kg/m2/s  COeur_emission_flux_from_biomass_burning
-#EmisCOeur_Ship        COeur    0   10   -1   2  kg/m2/s  COeur_emission_flux_from_ships
-#
-################################################################################
-######  COasia sources                                                     #####
-################################################################################
-#EmisCOasia_Total      COasia  -1   -1   -1   3  kg/m2/s  COasia_emission_flux_from_all_sectors
-#EmisCOasia_Aircraft   COasia   0   20   -1   3  kg/m2/s  COasia_emission_flux_from_aircraft
-#EmisCOasia_Anthro     COasia   0    1   -1   3  kg/m2/s  COasia_emission_flux_from_anthropogenic
-#EmisCOasia_BioBurn    COasia   0    5   -1   2  kg/m2/s  COasia_emission_flux_from_biomass_burning
-#EmisCOasia_Ship       COasia   0   10   -1   2  kg/m2/s  COasia_emission_flux_from_ships
-#
-################################################################################
-######  COoth sources                                                      #####
-################################################################################
-#EmisCOoth_Total       COoth   -1   -1   -1   3  kg/m2/s  COoth_emission_flux_from_all_sectors
-#EmisCOoth_Aircraft    COoth    0   20   -1   3  kg/m2/s  COoth_emission_flux_from_aircraft
-#EmisCOoth_Anthro      COoth    0    1   -1   3  kg/m2/s  COoth_emission_flux_from_anthropogenic
-#EmisCOoth_BioBurn     COoth    0    5   -1   2  kg/m2/s  COoth_emission_flux_from_biomass_burning
-#EmisCOoth_Ship        COoth    0   10   -1   2  kg/m2/s  COoth_emission_flux_from_ships
-#
-################################################################################
-######  COus sources                                                       #####
-################################################################################
-#EmisCOus_Total        COus    -1   -1   -1   3  kg/m2/s  COus_emission_flux_from_all_sectors
-#EmisCOus_Aircraft     COus     0   20   -1   3  kg/m2/s  COus_emission_flux_from_aircraft
-#EmisCOus_Anthro       COus     0    1   -1   3  kg/m2/s  COus_emission_flux_from_anthropogenic
-#EmisCOus_BioBurn      COus     0    5   -1   2  kg/m2/s  COus_emission_flux_from_biomass_burning
-#EmisCOus_Ship         COus     0   10   -1   2  kg/m2/s  COus_emission_flux_from_ships
-#
-################################################################################
-######  COeur sources                                                      #####
-################################################################################
-#EmisCOeur_Total       COeur   -1   -1   -1   3  kg/m2/s  COeur_emission_flux_from_all_sectors
-#EmisCOeur_Aircraft    COeur    0   20   -1   3  kg/m2/s  COeur_emission_flux_from_aircraft
-#EmisCOeur_Anthro      COeur    0    1   -1   3  kg/m2/s  COeur_emission_flux_from_anthropogenic
-#EmisCOeur_BioBurn     COeur    0    5   -1   2  kg/m2/s  COeur_emission_flux_from_biomass_burning
-#EmisCOeur_Ship        COeur    0   10   -1   2  kg/m2/s  COeur_emission_flux_from_ships
-#
-################################################################################
-######  COasia sources                                                     #####
-################################################################################
-#EmisCOasia_Total      COasia  -1   -1   -1   3  kg/m2/s  COasia_emission_flux_from_all_sectors
-#EmisCOasia_Aircraft   COasia   0   20   -1   3  kg/m2/s  COasia_emission_flux_from_aircraft
-#EmisCOasia_Anthro     COasia   0    1   -1   3  kg/m2/s  COasia_emission_flux_from_anthropogenic
-#EmisCOasia_BioBurn    COasia   0    5   -1   2  kg/m2/s  COasia_emission_flux_from_biomass_burning
-#EmisCOasia_Ship       COasia   0   10   -1   2  kg/m2/s  COasia_emission_flux_from_ships
-#
-################################################################################
-######  COoth sources                                                      #####
-################################################################################
-#EmisCOoth_Total       COoth   -1   -1   -1   3  kg/m2/s  COoth_emission_flux_from_all_sectors
-#EmisCOoth_Aircraft    COoth    0   20   -1   3  kg/m2/s  COoth_emission_flux_from_aircraft
-#EmisCOoth_Anthro      COoth    0    1   -1   3  kg/m2/s  COoth_emission_flux_from_anthropogenic
-#EmisCOoth_BioBurn     COoth    0    5   -1   2  kg/m2/s  COoth_emission_flux_from_biomass_burning
-#EmisCOoth_Ship        COoth    0   10   -1   2  kg/m2/s  COoth_emission_flux_from_ships
\ No newline at end of file
diff --git a/run/GCClassic/createRunDir.sh b/run/GCClassic/createRunDir.sh
index cb157d54b..3fc4b6fda 100755
--- a/run/GCClassic/createRunDir.sh
+++ b/run/GCClassic/createRunDir.sh
@@ -43,6 +43,7 @@ cd ${srcrundir}
 # Source common bash functions from scripts in the run/shared folder
 . ${gcdir}/run/shared/setupConfigFiles.sh      # Config file editing
 . ${gcdir}/run/shared/newUserRegistration.sh   # 1st-time user registration
+. ${gcdir}/run/shared/singleCarbonSpecies.sh   # Single carbon species setup
 
 # Initialize run directory variables
 RUNDIR_VARS=""
@@ -247,6 +248,34 @@ elif [[ ${sim_name} = "POPs" ]]; then
 	    printf "Invalid POPs type. Try again.\n"
 	fi
     done
+
+# Ask user to specify carbon simulation options
+elif [[ "x${sim_name}" == "xcarbon" ]]; then
+    printf "${thinline}Do you wish to use a single advected species?${thinline}"
+    printf "  1. Use all species\n"
+    printf "  2. Use CH4 only\n"
+    printf "  3. Use CO2 only\n"
+    printf "  4. Use CO only\n"
+    printf "  5. Use OCS only\n"
+    valid=0
+    while [ "${valid}" -eq 0 ]; do
+	read -p "${USER_PROMPT}" prompt
+	valid=1
+	if [[ "x${prompt}" == "x1" ]]; then
+	    sim_extra_option="none"
+	elif [[ "x${prompt}" == "x2" ]]; then
+	    sim_extra_option="CH4"
+	elif [[ "x${prompt}" == "x3" ]]; then
+	    sim_extra_option="CO2"
+	elif [[ "x${prompt}" == "x4" ]]; then
+	    sim_extra_option="CO"
+	elif [[ "x${prompt}" == "x5" ]]; then
+	    sim_extra_option="OCS"
+	else
+	    valid=0
+	    printf "Invalid selection. Try again.\n"
+	fi
+    done
 fi
 
 RUNDIR_VARS+="RUNDIR_SIM_EXTRA_OPTION=$sim_extra_option\n"
@@ -725,12 +754,11 @@ while [ "$valid_path" -eq 0 ]; do
 	exit 1
     fi
 
-    # Replace ~ with the user's home directory
-    # NOTE: This is a safe algorithm.
-    if [[ "${rundir_path}" =~ '~' ]]; then
-	rundir_path="${rundir_path/#\~/$HOME}"
-	echo "Expanding to: ${rundir_path}"
-    fi
+    # Expand $rundir_path to an absolute path.
+    # Also replace ~ with $HOME.
+    rundir_path="${rundir_path/#\~/$HOME}"
+    rundir_path=$(realpath "${rundir_path}")
+    echo "Expanding to ${rundir_path}"
 
     # If this is just a new directory within an existing one,
     # give the user the option to proceed
@@ -886,6 +914,7 @@ else
     startdate='20190701'
     enddate='20190801'
 fi
+
 if [[ ${met} = "ModelE2.1" ]] || [[ ${met} = "ModelE2.2" ]]; then
     if [[ "$scenario" == "HIST" ]]; then
 	startdate='20050701'
@@ -977,6 +1006,7 @@ echo -e "$RUNDIR_VARS" > ${rundir_config_log}
 #sort -o ${rundir_config_log} ${rundir_config_log}
 
 # Initialize run directory
+# NOTE: This also copies configuration files to the run directory!
 ${srcrundir}/init_rd.sh ${rundir_config_log}
 
 #--------------------------------------------------------------------
@@ -1140,9 +1170,14 @@ fi
 # input_options.yml and modifies diagnostic output based on simulation type.
 if [[ "x${sim_name}" = "xfullchem" ]]; then
     set_common_settings "${sim_extra_option}" "GCClassic"
-fi
+fi 
 
-#
+# If necessary, edit config files for a carbon single species simulation
+if [[ "x${sim_name}" == "xcarbon" ]]; then
+    if [[ "x${sim_extra_option}" != "xnone" ]]; then
+	singleCarbonSpecies "${sim_extra_option}" "${rundir}"
+    fi
+fi
 
 #--------------------------------------------------------------------
 # Navigate back to source code directory
diff --git a/run/GCHP/HEMCO_Config.rc.templates/HEMCO_Config.rc.carbon b/run/GCHP/HEMCO_Config.rc.templates/HEMCO_Config.rc.carbon
index 4ac469a56..5f343eec9 100644
--- a/run/GCHP/HEMCO_Config.rc.templates/HEMCO_Config.rc.carbon
+++ b/run/GCHP/HEMCO_Config.rc.templates/HEMCO_Config.rc.carbon
@@ -1307,7 +1307,6 @@ ${RUNDIR_GLOBAL_OH}
 #------------------------------------------------------------------------------
 # --- Quantities needed for CH4 chemistry ---
 #------------------------------------------------------------------------------
-(((USE_CH4_DATA
 
 # --- Global CH4 loss frequencies [1/s] -----------
 (((CH4_LOSS_FREQ
@@ -1319,8 +1318,6 @@ ${RUNDIR_CH4_LOSS}
 ${RUNDIR_GLOBAL_Cl}
 )))GLOBAL_CL
 
-)))USE_CH4_DATA
-
 #------------------------------------------------------------------------------
 # --- Quantities needed for CO chemistry ---
 #------------------------------------------------------------------------------
@@ -1336,13 +1333,21 @@ ${RUNDIR_PCO_NMVOC}
 
 # --- GMI chemistry: prod/loss rates (for strato-/mesosphere) ---
 # --- Units: prod [v/v/s]; loss [1/s]                         ---
+(((USE_CO_DATA
 (((GMI_PROD_LOSS
-${RUNDIR_GMI_LOSS_CO}
-${RUNDIR_GMI_PROD_CO}
+* GMI_LOSS_CO    $ROOT/GMI/v2022-11/gmi.clim.CO.geos5.2x25.nc  loss  2005/1-12/1/0 C xyz s-1     CO - 1 1
+* GMI_PROD_CO    $ROOT/GMI/v2022-11/gmi.clim.CO.geos5.2x25.nc  prod  2005/1-12/1/0 C xyz v/v/s   CO - 1 1
 )))GMI_PROD_LOSS
-
 )))USE_CO_DATA
 
+# If CO is not an advected species, then just read as a chemistry input
+(((.not.USE_CO_DATA
+(((GMI_PROD_LOSS
+* GMI_LOSS_CO    $ROOT/GMI/v2022-11/gmi.clim.CO.geos5.2x25.nc  loss  2005/1-12/1/0 C xyz s-1     *  - 1 1
+* GMI_PROD_CO    $ROOT/GMI/v2022-11/gmi.clim.CO.geos5.2x25.nc  prod  2005/1-12/1/0 C xyz v/v/s   *  - 1 1
+)))GMI_PROD_LOSS
+))).not.USE_CO_DATA
+
 #------------------------------------------------------------------------------
 # --- Quantities needed for CO2 chemistry ---
 #------------------------------------------------------------------------------
@@ -1350,14 +1355,11 @@ ${RUNDIR_GMI_PROD_CO}
 # --- CHEMICAL PRODUCTION FROM CO OXIDATION ------
 # --- Recommended for use in forward modelling ---
 # --- Optional for inversion/assimilation --------
-(((USE_CO2_DATA
 
 (((CO2_COPROD
 ${RUNDIR_CO2_COPROD}
 )))CO2_COPROD
 
-)))USE_CO2_DATA
-
 )))CHEMISTRY_INPUT
 
 ### END SECTION BASE EMISSIONS ###
@@ -1690,12 +1692,15 @@ ${RUNDIR_CO2_COPROD}
 2008 AFRICA_MASK $ROOT/MASKS/v2018-09/AF_LANDMASK.geos.05x0666.global.nc LANDMASK 1985/1/1/0 C xy 1 1 -20/-37/54/40
 )))DICE_Africa
 
+)))USE_CO_DATA.or.USE_CO2_DATA
+
+#==============================================================================
+# --- Masks used for CH4, CO and CO2 simulation emissions ---
+#==============================================================================
 (((CEDSv2.or.CEDS_GBDMAPS.or.CEDS_GBDMAPS_byFuelType
 2009 CHINA_MASK  $ROOT/MASKS/v2018-09/China_mask.generic.1x1.nc          MASK     2000/1/1/0 C xy 1 1  70/10/150/60
 )))CEDSv2.or.CEDS_GBDMAPS.or.CEDS_GBDMAPS_byFuelType
 
-)))USE_CO_DATA.or.USE_CO2_DATA
-
 )))EMISSIONS
 
 ### END SECTION MASKS ###
diff --git a/run/GCHP/HEMCO_Diagn.rc.templates/HEMCO_Diagn.rc.carbon b/run/GCHP/HEMCO_Diagn.rc.templates/HEMCO_Diagn.rc.carbon
index 43ed75773..73c1d3129 100644
--- a/run/GCHP/HEMCO_Diagn.rc.templates/HEMCO_Diagn.rc.carbon
+++ b/run/GCHP/HEMCO_Diagn.rc.templates/HEMCO_Diagn.rc.carbon
@@ -16,9 +16,8 @@
 # Name               Spec  ExtNr  Cat Hier Dim  OutUnit  LongName
 
 ###############################################################################
-#####  CH4 sources                                                         #####
+#####  CH4 sources                                                        #####
 ###############################################################################
-
 EmisCH4_Total         CH4     -1   -1   -1   2  kg/m2/s  CH4_emissions_from_all_sectors
 EmisCH4_Oil           CH4      0    1   -1   2  kg/m2/s  CH4_emissions_from_oil
 EmisCH4_Gas           CH4      0    2   -1   2  kg/m2/s  CH4_emissions_from_gas
@@ -28,7 +27,7 @@ EmisCH4_Landfills     CH4      0    5   -1   2  kg/m2/s  CH4_emissions_from_land
 EmisCH4_Wastewater    CH4      0    6   -1   2  kg/m2/s  CH4_emissions_from_wastewater
 EmisCH4_Rice          CH4      0    7   -1   2  kg/m2/s  CH4_emissions_from_rice
 EmisCH4_OtherAnth     CH4      0    8   -1   2  kg/m2/s  CH4_emissions_from_other_anthropogenic_sources
-EmisCH4_BiomassBurn   CH4      0    9   -1   2  kg/m2/s  CH4_emissions_from_biomass_burning
+EmisCH4_BiomassBurn   CH4    111   -1   -1   2  kg/m2/s  CH4_emissions_from_biomass_burning
 EmisCH4_Wetlands      CH4      0   10   -1   2  kg/m2/s  CH4_emissions_from_wetlands
 EmisCH4_Seeps         CH4      0   11   -1   2  kg/m2/s  CH4_emissions_from_geological_seeps
 EmisCH4_Lakes         CH4      0   12   -1   2  kg/m2/s  CH4_emissions_from_lakes
@@ -42,7 +41,7 @@ EmisCH4_Reservoirs    CH4      0   15   -1   2  kg/m2/s  CH4_emissions_from_hydr
 EmisCO_Total          CO      -1   -1   -1   3  kg/m2/s  CO_emission_flux_from_all_sectors
 EmisCO_Aircraft       CO       0   20   -1   3  kg/m2/s  CO_emission_flux_from_aircraft
 EmisCO_Anthro         CO       0    1   -1   3  kg/m2/s  CO_emission_flux_from_anthropogenic
-EmisCO_BioBurn        CO       0    5   -1   2  kg/m2/s  CO_emission_flux_from_biomass_burning
+EmisCO_BiomassBurn    CO     111   -1   -1   2  kg/m2/s  CO_emission_flux_from_biomass_burning
 EmisCO_Ship           CO       0   10   -1   2  kg/m2/s  CO_emission_flux_from_ships
 
 ###############################################################################
@@ -56,13 +55,7 @@ EmisCO2_NetTerrExch   CO2      0    5   -1   2  kg/m2/s  CO2_net_terrestrial_exc
 EmisCO2_Ship          CO2      0    6   -1   2  kg/m2/s  CO2_ship_emissions
 EmisCO2_Aviation      CO2      0    7   -1   3  kg/m2/s  CO2_aviation_emissions
 EmisCO2_CO2SurfCorr   CO2      0    8   -1   2  kg/m2/s  CO2_surface_correction_for_CO_oxidation
-
-#NOTE: Biomass burning doesn't seem to work.  Keep here for now.
-# Uncomment this if GFED is used
-#EmisCO2_Biomass_GFED  CO2    111    1    1   2  kg/m2/s  CO2_biomass_burning_emissions_from_GFED4
-
-# Uncomment this if FINN is used
-#EmisCO2_Biomass_FINN  CO2    114    1    1   2  kg/m2/s  CO2_biomass_burning_emissions_from_FINN
+EmisCO2_BiomassBurn   CO2    111   -1   -1   2  kg/m2/s  CO2_biomass_burning_emissions_from_GFED4
 
 ###############################################################################
 #####  OCS sources                                                        #####
@@ -73,76 +66,3 @@ EmisOCS_Bioburn       OCS      0    2   -1   2  kg/m2/s  OCS_emission_flux_from_
 EmisOCS_MissingOcean  OCS      0    3   -1   2  kg/m2/s  OCS_emission_flux_from_missing_ocean
 EmisOCS_Ocean         OCS      0    4   -1   2  kg/m2/s  OCS_emission_flux_from_ocean
 
-# Tagged CO species, uncomment if needed
-#
-################################################################################
-######  COus sources                                                       #####
-################################################################################
-#EmisCOus_Total        COus    -1   -1   -1   3  kg/m2/s  COus_emission_flux_from_all_sectors
-#EmisCOus_Aircraft     COus     0   20   -1   3  kg/m2/s  COus_emission_flux_from_aircraft
-#EmisCOus_Anthro       COus     0    1   -1   3  kg/m2/s  COus_emission_flux_from_anthropogenic
-#EmisCOus_BioBurn      COus     0    5   -1   2  kg/m2/s  COus_emission_flux_from_biomass_burning
-#EmisCOus_Ship         COus     0   10   -1   2  kg/m2/s  COus_emission_flux_from_ships
-#
-################################################################################
-######  COeur sources                                                      #####
-################################################################################
-#EmisCOeur_Total       COeur   -1   -1   -1   3  kg/m2/s  COeur_emission_flux_from_all_sectors
-#EmisCOeur_Aircraft    COeur    0   20   -1   3  kg/m2/s  COeur_emission_flux_from_aircraft
-#EmisCOeur_Anthro      COeur    0    1   -1   3  kg/m2/s  COeur_emission_flux_from_anthropogenic
-#EmisCOeur_BioBurn     COeur    0    5   -1   2  kg/m2/s  COeur_emission_flux_from_biomass_burning
-#EmisCOeur_Ship        COeur    0   10   -1   2  kg/m2/s  COeur_emission_flux_from_ships
-#
-################################################################################
-######  COasia sources                                                     #####
-################################################################################
-#EmisCOasia_Total      COasia  -1   -1   -1   3  kg/m2/s  COasia_emission_flux_from_all_sectors
-#EmisCOasia_Aircraft   COasia   0   20   -1   3  kg/m2/s  COasia_emission_flux_from_aircraft
-#EmisCOasia_Anthro     COasia   0    1   -1   3  kg/m2/s  COasia_emission_flux_from_anthropogenic
-#EmisCOasia_BioBurn    COasia   0    5   -1   2  kg/m2/s  COasia_emission_flux_from_biomass_burning
-#EmisCOasia_Ship       COasia   0   10   -1   2  kg/m2/s  COasia_emission_flux_from_ships
-#
-################################################################################
-######  COoth sources                                                      #####
-################################################################################
-#EmisCOoth_Total       COoth   -1   -1   -1   3  kg/m2/s  COoth_emission_flux_from_all_sectors
-#EmisCOoth_Aircraft    COoth    0   20   -1   3  kg/m2/s  COoth_emission_flux_from_aircraft
-#EmisCOoth_Anthro      COoth    0    1   -1   3  kg/m2/s  COoth_emission_flux_from_anthropogenic
-#EmisCOoth_BioBurn     COoth    0    5   -1   2  kg/m2/s  COoth_emission_flux_from_biomass_burning
-#EmisCOoth_Ship        COoth    0   10   -1   2  kg/m2/s  COoth_emission_flux_from_ships
-#
-################################################################################
-######  COus sources                                                       #####
-################################################################################
-#EmisCOus_Total        COus    -1   -1   -1   3  kg/m2/s  COus_emission_flux_from_all_sectors
-#EmisCOus_Aircraft     COus     0   20   -1   3  kg/m2/s  COus_emission_flux_from_aircraft
-#EmisCOus_Anthro       COus     0    1   -1   3  kg/m2/s  COus_emission_flux_from_anthropogenic
-#EmisCOus_BioBurn      COus     0    5   -1   2  kg/m2/s  COus_emission_flux_from_biomass_burning
-#EmisCOus_Ship         COus     0   10   -1   2  kg/m2/s  COus_emission_flux_from_ships
-#
-################################################################################
-######  COeur sources                                                      #####
-################################################################################
-#EmisCOeur_Total       COeur   -1   -1   -1   3  kg/m2/s  COeur_emission_flux_from_all_sectors
-#EmisCOeur_Aircraft    COeur    0   20   -1   3  kg/m2/s  COeur_emission_flux_from_aircraft
-#EmisCOeur_Anthro      COeur    0    1   -1   3  kg/m2/s  COeur_emission_flux_from_anthropogenic
-#EmisCOeur_BioBurn     COeur    0    5   -1   2  kg/m2/s  COeur_emission_flux_from_biomass_burning
-#EmisCOeur_Ship        COeur    0   10   -1   2  kg/m2/s  COeur_emission_flux_from_ships
-#
-################################################################################
-######  COasia sources                                                     #####
-################################################################################
-#EmisCOasia_Total      COasia  -1   -1   -1   3  kg/m2/s  COasia_emission_flux_from_all_sectors
-#EmisCOasia_Aircraft   COasia   0   20   -1   3  kg/m2/s  COasia_emission_flux_from_aircraft
-#EmisCOasia_Anthro     COasia   0    1   -1   3  kg/m2/s  COasia_emission_flux_from_anthropogenic
-#EmisCOasia_BioBurn    COasia   0    5   -1   2  kg/m2/s  COasia_emission_flux_from_biomass_burning
-#EmisCOasia_Ship       COasia   0   10   -1   2  kg/m2/s  COasia_emission_flux_from_ships
-#
-################################################################################
-######  COoth sources                                                      #####
-################################################################################
-#EmisCOoth_Total       COoth   -1   -1   -1   3  kg/m2/s  COoth_emission_flux_from_all_sectors
-#EmisCOoth_Aircraft    COoth    0   20   -1   3  kg/m2/s  COoth_emission_flux_from_aircraft
-#EmisCOoth_Anthro      COoth    0    1   -1   3  kg/m2/s  COoth_emission_flux_from_anthropogenic
-#EmisCOoth_BioBurn     COoth    0    5   -1   2  kg/m2/s  COoth_emission_flux_from_biomass_burning
-#EmisCOoth_Ship        COoth    0   10   -1   2  kg/m2/s  COoth_emission_flux_from_ships
\ No newline at end of file
diff --git a/run/GCHP/HISTORY.rc.templates/HISTORY.rc.carbon b/run/GCHP/HISTORY.rc.templates/HISTORY.rc.carbon
index fa74116d8..690b02fea 100644
--- a/run/GCHP/HISTORY.rc.templates/HISTORY.rc.carbon
+++ b/run/GCHP/HISTORY.rc.templates/HISTORY.rc.carbon
@@ -130,7 +130,7 @@ COLLECTIONS: 'Emissions',
                               'EmisCO_Total         ', 'GCHPchem',
                               'EmisCO_Aircraft      ', 'GCHPchem',
                               'EmisCO_Anthro        ', 'GCHPchem',
-                              'EmisCO_BioBurn       ', 'GCHPchem',
+                              'EmisCO_BiomassBurn   ', 'GCHPchem',
                               'EmisCO_Ship          ', 'GCHPchem',
                               'EmisCO2_Total        ', 'GCHPchem',
                               'EmisCO2_FossilFuel   ', 'GCHPchem',
@@ -140,7 +140,7 @@ COLLECTIONS: 'Emissions',
                               'EmisCO2_Ship         ', 'GCHPchem',
                               'EmisCO2_Aviation     ', 'GCHPchem',
                               'EmisCO2_CO2SurfCorr  ', 'GCHPchem',
-                             #'EmisCO2_Biomass_GFED ', 'GCHPchem',
+                              'EmisCO2_BiomassBurn  ', 'GCHPchem',
 ::
 #==============================================================================
 # Budget defined as species kg/s in the column (full, troposphere, or PBL)
diff --git a/run/GCHP/createRunDir.sh b/run/GCHP/createRunDir.sh
index 6c353882c..985df82df 100755
--- a/run/GCHP/createRunDir.sh
+++ b/run/GCHP/createRunDir.sh
@@ -42,6 +42,7 @@ cd ${srcrundir}
 # Source common bash functions from scripts in the run/shared folder
 . ${gcdir}/run/shared/setupConfigFiles.sh      # Config file editing
 . ${gcdir}/run/shared/newUserRegistration.sh   # 1st-time user registration
+. ${gcdir}/run/shared/singleCarbonSpecies.sh   # Single carbon species setup
 
 # Initialize run directory variables
 RUNDIR_VARS=""
@@ -204,6 +205,34 @@ if [[ ${sim_name} = "fullchem" ]]; then
 # Currently no transport tracer extra options
 elif [[ ${sim_name} = "TransportTracers" ]]; then
     sim_extra_option=none
+
+# Ask user to specify carbon simulation options
+elif [[ "x${sim_name}" == "xcarbon" ]]; then
+    printf "${thinline}Do you wish to use a single advected species?${thinline}"
+    printf "  1. Use all species\n"
+    printf "  2. Use CH4 only\n"
+    printf "  3. Use CO2 only\n"
+    printf "  4. Use CO only\n"
+    printf "  5. Use OCS only\n"
+    valid=0
+    while [ "${valid}" -eq 0 ]; do
+	read -p "${USER_PROMPT}" prompt
+	valid=1
+        if [[ "x${prompt}" == "x1" ]]; then
+	    sim_extra_option="none"
+	elif [[ "x${prompt}" == "x2" ]]; then
+	    sim_extra_option="CH4"
+	elif [[ "x${prompt}" == "x3" ]]; then
+	    sim_extra_option="CO2"
+	elif [[ "x${prompt}" == "x4" ]]; then
+	    sim_extra_option="CO"
+	elif [[ "x${prompt}" == "x5" ]]; then
+	    sim_extra_option="OCS"
+	else
+	    valid=0
+	    printf "Invalid selection. Try again.\n"
+	fi
+    done
 fi
 
 RUNDIR_VARS+="RUNDIR_SIM_EXTRA_OPTION=$sim_extra_option\n"
@@ -562,6 +591,13 @@ if [[ "x${sim_name}" = "xfullchem" ]]; then
     set_common_settings "${sim_extra_option}" "GCHP"
 fi
 
+# If necessary, edit config files for a carbon single species simulation
+if [[ "x${sim_name}" == "xcarbon" ]]; then
+    if [[ "x${sim_extra_option}" != "xnone" ]]; then
+	singleCarbonSpecies "${sim_extra_option}" "${rundir}"
+    fi
+fi
+
 # Call setCommonRunSettings.sh so that all config files are consistent with its
 # default settings. Suppress informational prints.
 chmod +x setCommonRunSettings.sh
diff --git a/run/shared/singleCarbonSpecies.sh b/run/shared/singleCarbonSpecies.sh
new file mode 100755
index 000000000..775a11574
--- /dev/null
+++ b/run/shared/singleCarbonSpecies.sh
@@ -0,0 +1,343 @@
+#!/bin/bash
+
+#------------------------------------------------------------------------------
+#                  GEOS-Chem Global Chemical Transport Model                  !
+#------------------------------------------------------------------------------
+#BOP
+#
+# !IROUTINE: singleCarbonSpecies.sh
+#
+# !DESCRIPTION: Updates carbon simulation configuration files so that
+#  a simulation with a single species can be performed.
+#
+# !CALLING SEQUENCE:
+#  ./singleCarbonSpecies.sh <species-to-retain> <path-to-rundir>
+#
+# !REVISION HISTORY:
+#  14 Sep 2023 - R. Yantosca - Initial version
+#  See the subsequent Git history with the gitk browser!
+#EOP
+#------------------------------------------------------------------------------
+#BOC
+
+# List of all advected species in the carbon simulation
+ALL_SPECIES=(CO2 CO CH4 OCS)
+
+
+function isItemInList() {
+
+    #=========================================================================
+    # Test if an item is in a list.
+    #
+    # Arguments:
+    # ${1}: The item
+    # ${2}: Thie list
+    #
+    # Returns (via $?)
+    # 0 if item is in the list
+    # 1 if item is not in the list
+    #
+    # See stackoverflow.com/questions/8063228/check-if-a-variable-exists-in-a-list-in-bash
+    #=========================================================================
+    echo "${2}" | tr ' '  '\n' | grep -F -x -q "${1}"
+}
+
+
+function keyValueUpdate() {
+
+    #=========================================================================
+    # Runs an sed command to update a "key: value" pair in a file
+    #
+    # Arguments:
+    # ${1} : Key
+    # ${2} : Value
+    # ${3} : Replacement value
+    # ${4) : File in which the text is found
+    #=========================================================================
+    cmd="s/${1}: ${2}/${1}: ${3}/"
+    sed -i -e "$cmd" "${4}"
+}
+
+
+function speciesToExclude() {
+
+    #========================================================================
+    # Returns the list of species to exclude
+    #
+    # Arguments:
+    # ${1} : Species to retain
+    #
+    # Returns:
+    # List of species to exclude
+    #========================================================================
+
+    # All species
+    list=("${ALL_SPECIES[@]}")
+
+    # Keep all species except for the 1st argument
+    for i in "${!list[@]}"; do
+        if [[ "x${list[i]}" == "x${1}" ]]; then
+            unset 'list[i]'
+        fi
+    done
+
+    # Print the result (that's how we return strings)
+    result=""
+    for spc in "${list[@]}"; do
+        result+="${spc} "
+    done
+    echo $result
+}
+
+
+function updateGeosChemConfig() {
+
+    #========================================================================
+    # Removes advected species from geoschem_config.yml
+    #
+    # Arguments:
+    # ${1} : List of species to exclude
+    # ${2} : Path to the run directory
+    #========================================================================
+
+    # File to modify
+    file="${2}/geoschem_config.yml"
+
+    # Remove advected species (use \< and \> for exact match in order
+    # to prevent inadvertently removing CO2 with when spc is CO.
+    for spc in ${1}; do
+    cmd="/\s*\-\s*\<${spc}\>/d"
+        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
+    isItemInList "CO2" "${1}"
+    if [[ $? == 0 ]]; then
+        keys=("fossil_fuel_emissions"          \
+              "ocean_exchange"                 \
+              "balanced_biosphere_exchange"    \
+              "net_terrestrial_exchange"       \
+              "ship_emissions"                 \
+              "aviation_emissions"             \
+              "3D_chemical_oxidation_source"   \
+              "save_fossil_fuel_in_background" \
+              "tag_bio_and_ocean_CO2"          \
+              "tag_land_fossil_fuel_CO2"       \
+              "tag_global_ship_CO2"            \
+              "tag_global_aircraft_CO2"       )
+        for key in ${keys[@]}; do
+            keyValueUpdate "${key}" "true" "false" "${file}"
+        done
+    fi
+}
+
+
+function updateHemcoConfig() {
+
+    #========================================================================
+    # Removes advected species from geoschem_config.yml
+    #
+    # Arguments:
+    # ${1} : List of species to exclude
+    # ${2} : Path to the run directory
+    #========================================================================
+
+    # File to be modified
+    file="${2}/HEMCO_Config.rc"
+
+    # True/False values in the HEMCO extension switches section
+    true="      true"
+    false="      false"
+
+    # If CO2 is in the exclude list, turn off CO2 options
+    # NOTE: This must precede CO to avoid unintended deletions
+    isItemInList "CO2" "${1}"
+    if [[ $? == 0 ]]; then
+        key="--> USE_CO2_DATA           "
+        keyValueUpdate "${key}" "${true}" "${false}" "${file}"
+    fi
+
+    # If CO is in the exclude list, turn off CO options
+    isItemInList "CO" "${1}"
+    if [[ $? == 0 ]]; then
+        key="--> USE_CO_DATA            "
+        keyValueUpdate "${key}" "${true}" "${false}" "${file}"
+    fi
+
+    # If CH4 is in the exclude list, turn off CH4 options
+    isItemInList "CH4" "${1}"
+    if [[ $? == 0 ]]; then
+        key="--> USE_CH4_DATA           "
+        keyValueUpdate "${key}" "${true}" "${false}" "${file}"
+    fi
+
+    # If OCS is in the exclude list, turn off OCS options
+    isItemInList "OCS" "${1}"
+    if [[ $? == 0 ]]; then
+        key="--> USE_OCS_DATA           "
+        keyValueUpdate "${key}" "${true}" "${false}" "${file}"
+    fi
+}
+
+
+function updateHemcoDiagn() {
+
+    #========================================================================
+    # Comments out lines for unused species in HEMCO_Diagn.rc
+    #
+    # Arguments:
+    # ${1} : List of species to exclude
+    # ${2} : Path to the run directory
+    #========================================================================
+
+    # File to modify
+    file="${2}/HEMCO_Diagn.rc"
+
+    # Remove entries for excluded species
+    exclude=("${1}")
+    for spc in ${exclude[@]}; do
+        sed -i "/Emis${spc}_/d" "${file}"
+    done
+    sed -i "/#####/d" "${file}"
+}
+
+
+function updateHistory() {
+
+    #========================================================================
+    # Removes entries in HISTORY.rc for unused species
+    #
+    # Arguments:
+    # ${1} : List of species to exclude
+    # ${2} : Path to the run directory
+    #========================================================================
+
+    # File to be modified
+    file="${2}/HISTORY.rc"
+
+    # For GCHP: remove entries for species to be excluded
+    for spc in ${ALL_SPECIES[@]}; do
+        isItemInList "${spc}" "${1}"
+        if [[ $? == 0 ]]; then
+            sed -i "/\_${spc}/d"   "${file}"
+            sed -i "/Emis${spc}/d" "${file}"
+        fi
+    done
+}
+
+
+function updateExtData() {
+
+    #========================================================================
+    # Removes entries in ExtData.rc for unused species (GCHP only)
+    #
+    # Arguments:
+    # ${1} : List of species to exclude
+    # ${2} : Path to the run directory
+    #========================================================================
+
+    # File to be modified
+    file="${2}/ExtData.rc"
+
+    # Skip if there is no ExtData.rc file (e.g. for GCClassic)
+    [[ ! -f "${file}" ]] && return 0
+
+    # If CH4 is in the exclude list, remove CH4 entries.
+    isItemInList "CH4" "${1}"
+    if [[ $? == 0 ]]; then
+        sed -i "/^GHGI_/d"              "${file}"
+        sed -i "/^MEX_/d"               "${file}"
+        sed -i "/^CAN_/d"               "${file}"
+        sed -i "/^GFEI_/d"              "${file}"
+        sed -i "/^EDGAR7_CH4_/d"        "${file}"
+        sed -i "/^CAN_/d"               "${file}"
+        sed -i "/^UPDATED_GFED4_CH4/d"  "${file}"
+        sed -i "/^JPLW_CH4/d"           "${file}"
+        sed -i "/^CH4_/d"               "${file}"
+        sed -i "/^\#CH4_/d"             "${file}"
+        sed -i "/CMIP6_CH4_/d"          "${file}"
+        sed -i "/CMIP6_BB_CH4/d"        "${file}"
+        sed -i "/RCP3PD_CH4/d"          "${file}"
+        sed -i "/RCP45_CH4/d"           "${file}"
+        sed -i "/RCP60_CH4/d"           "${file}"
+        sed -i "/RCP85_CH4/d"           "${file}"
+    fi
+
+    # If CO2 is in the exclude list, remove CO2 entries.
+    # NOTE: CO2 deletions must prececde CO deletions.
+    isItemInList "CO2" "${1}"
+    if [[ $? == 0 ]]; then
+        sed -i "/AEIC19_DAILY_CO2 /d"   "${file}"  # trailing space required
+        sed -i "/AEIC19_MONMEAN_CO2 /d" "${file}"  # trailing space required
+        sed -i "/BBIOCO2_/d"            "${file}"
+        sed -i "/^CEDS_CO2_/d"          "${file}"
+        sed -i "/^CO2_/d"               "${file}"
+        sed -i "/COPROD/d"              "${file}"
+        sed -i "/FOSSILCO2_/d"          "${file}"
+        sed -i "/ICOADS_CO2_/d"         "${file}"
+        sed -i "/OCEANCO2_/d"           "${file}"
+        sed -i "/SIB_BBIO_CO2/d"        "${file}"
+    fi
+
+    # If CO is in the exclude list, remove CO entries
+    isItemInList "CO" "${1}"
+    if [[ $? == 0 ]]; then
+        sed -i "/AEIC19_DAILY_CO /d"    "${file}"  # trailing space required
+        sed -i "/AEIC19_MONMEAN_CO /d"  "${file}"  # trailing space required
+        sed -i "/APEI_CO/d"             "${file}"
+        sed -i "/^CEDS_CO/d"            "${file}"
+        sed -i "/CMIP6_CO/d"            "${file}"
+        sed -i "/\#DICE_/d"             "${file}"
+        sed -i "/EDGAR_CO/d"            "${file}"
+        sed -i "/EPA16_CO_/d"           "${file}"
+        sed -i "/HTAP_CO_/d"            "${file}"
+        sed -i "/RCP3PD_CO/d"           "${file}"
+        sed -i "/RCP45_CO/d"            "${file}"
+        sed -i "/RCP60_CO/d"            "${file}"
+        sed -i "/RCP85_CO/d"            "${file}"
+    fi
+
+    # If OSC is in the exclude list, remove OCS entries
+    isItemInList "OCS" "${1}"
+    if [[ $? == 0 ]]; then
+        sed -i "/^OCS_/d"              "${file}"
+    fi
+}
+
+
+function singleCarbonSpecies() {
+
+    #========================================================================
+    # Main function
+    #
+    # Arguments:
+    # ${1} : Species that you wish to retain
+    # ${2} : Path to the run directory
+    #========================================================================
+
+    # Error check arguments
+    if [[ "x${1}" == "x" ]]; then
+        echo "Need to pass the species to retain!"
+        exit 1
+    fi
+
+    # Path to the run directory
+    if [[ "x${2}" == "x" ]]; then
+        rundir="."
+    else
+        rundir="${2}"
+    fi
+
+    # Get species to exclude
+    exclude=$(speciesToExclude "${1}")
+
+    # Update configuration files
+    updateGeosChemConfig "${exclude}" "${rundir}"
+    updateHemcoConfig    "${exclude}" "${rundir}"
+    updateHemcoDiagn     "${exclude}" "${rundir}"
+    updateHistory        "${exclude}" "${rundir}"
+    updateExtData        "${exclude}" "${rundir}"
+}
diff --git a/test/integration/GCClassic/integrationTestCreate.sh b/test/integration/GCClassic/integrationTestCreate.sh
index 350f2d2bd..c7b0dfdc5 100755
--- a/test/integration/GCClassic/integrationTestCreate.sh
+++ b/test/integration/GCClassic/integrationTestCreate.sh
@@ -169,7 +169,11 @@ create_rundir "4\n1\n1\n1\n${rundirsDir}\n\nn\n" "${log}"
 create_rundir "2\n1\n1\n1\n${rundirsDir}\n\nn\n" "${log}"
 
 # 4x5 merra2 carbon
-create_rundir "12\n1\n1\n1\n${rundirsDir}\n\nn\n" "${log}"
+create_rundir "12\n1\n1\n1\n1\n${rundirsDir}\n\nn\n" "${log}"
+
+# 4x5 merra2 carbon CH4 only
+dir="gc_4x5_merra2_carbon_CH4only"
+create_rundir "12\n2\n1\n1\n1\n${rundirsDir}\n${dir}\nn\n" "${log}"
 
 # 4x5 merra2 fullchem
 create_rundir "1\n1\n1\n1\n1\n${rundirsDir}\n\nn\n" "${log}"