Merge pull request #1 from geoschem/bugfix/Grell_Friedas_convection

Updates related to Grell Friedas convection fix
geoschem · Nov 15, 2024 · d130988 · d130988
2 parents 9151ed1 + ad3a428
commit d130988
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,21 @@
 This file documents all notable changes to the GEOS-Chem repository starting in version 14.0.0, including all GEOS-Chem Classic and GCHP run directory updates.
 
 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
+- Specified meteorology source in GCHP geoschem_config.yml
+- Added Input_Opt logical for whether to reconstruct convective precipitation fluxes rather than use met-fields
+- Added to run directory creation a warning about convection discontinuity and bug if GEOS-FP meteorology is chosen
+- Added surface precipitation flux fields as inputs to GCHP
+
+### Fixed
+- Fixed zero convective precipitation and high cloud base in runs using GEOS-FP (>=01Jun2020) or GEOS-IT
+- Fixed PDOWN definition to lower rather than upper edge
+
+### Changed
+
+### Removed
+-Removed re-evaporation requirement for washout
 
 ## [14.4.3] - 2024-08-13
 ### Added

diff --git a/GeosCore/convection_mod.F90 b/GeosCore/convection_mod.F90
@@ -502,7 +502,7 @@ SUBROUTINE DO_CLOUD_CONVECTION( Input_Opt,  &
 ! !LOCAL VARIABLES:
 !
     ! Scalars
-    LOGICAL                :: AER,         IS_Hg,     Is_GF_Conv
+    LOGICAL                :: AER,         IS_Hg
     INTEGER                :: IC,          ISTEP,     K
     INTEGER                :: KTOP,        NC,        NDT
     INTEGER                :: NLAY,        NS,        CLDBASE
@@ -592,8 +592,6 @@ SUBROUTINE DO_CLOUD_CONVECTION( Input_Opt,  &
 
     ! Is this a Hg simulation?
     IS_Hg = Input_Opt%ITS_A_MERCURY_SIM
-    ! GF convection scheme?
-    Is_GF_Conv = Input_Opt%Met_Conv_Is_Grell_Freitas
 
     IF ( State_Grid%NZ > 72 .or. &
          Input_Opt%MetField == "MODELE2.1" ) THEN 
@@ -608,7 +606,7 @@ SUBROUTINE DO_CLOUD_CONVECTION( Input_Opt,  &
     DNS      = DBLE( NS )               ! Num internal timesteps (real)
     SDT      = DBLE( NDT ) / DBLE( NS ) ! seconds in internal timestep
 
-    IF ( Is_GF_Conv == .FALSE. ) THEN
+    IF ( .NOT. Input_Opt%Reconstruct_Conv_Precip_Flux ) THEN
        ! RAS scheme
        REEVAPCN(:) = REEVAPCN_MET(:)
        DQRCU(:) = DQRCU_MET(:)
@@ -658,7 +656,7 @@ SUBROUTINE DO_CLOUD_CONVECTION( Input_Opt,  &
     ! PFLCU and PFICU are converted from kg/m2/s to m3/m2/s
     ! using water and ice densities, respectively.
     ! m3/m2/s becomes cm3/cm2/s using a factor of 100.
-    IF ( Is_GF_Conv == .FALSE. ) THEN
+    IF ( .NOT. Input_Opt%Reconstruct_Conv_Precip_Flux ) THEN
        PDOWN(:) = ( ( PFLCU(:) / 1000e+0_fp ) &
                 +   ( PFICU(:) /  917e+0_fp ) ) * 100e+0_fp
     ELSE

diff --git a/GeosCore/input_mod.F90 b/GeosCore/input_mod.F90
@@ -3059,7 +3059,9 @@ END SUBROUTINE Config_Photolysis
 ! !IROUTINE: config_convection_mixing
 !
 ! !DESCRIPTION: Copies convection & PBL mixing information from the Config
-!  object to Input_Opt, and does necessary checks.
+!  object to Input_Opt, and does necessary checks. Also sets whether
+!  to reconstruct convective precipitation flux based on meteorology
+!  source and simulation start date.
 !\\
 !\\
 ! !INTERFACE:
@@ -3143,13 +3145,40 @@ SUBROUTINE Config_Convection_Mixing( Config, Input_Opt, RC )
     ENDIF
     Input_Opt%LNLPBL = v_bool
 
+    !------------------------------------------------------------------------
+    ! Other settings based on inputs
+    !------------------------------------------------------------------------
+
     ! Set the PBL drydep flag. This determines if dry deposition is
     ! applied (and drydep frequencies are calculated) over the entire
     ! PBL or the first model layer only. For now, set this value
     ! automatically based upon the selected PBL scheme: 1st model layer
     ! for the non-local PBL scheme, full PBL for the full-mixing scheme.
     Input_Opt%PBL_DRYDEP = ( .not. Input_Opt%LNLPBL )
 
+    ! Set whether to reconstruct convective precipitation flux based on
+    ! meteorology source and simulation start date. This is important for
+    ! avoiding a bug where convective precipitation met-fields are all zero
+    ! in GEOS-IT for all years and in GEOS-FP following June 1, 2020.
+    !
+    ! IMPORTANT NOTE: The logic for GEOS-FP assumes (1) meteorology year
+    ! is the same as simulation year and (2) the simulation does not
+    ! run across June 1, 2020. Use the following rules to ensure your
+    ! simulation is correct:
+    !   (1) Manually update code below if GEOS-FP data year is
+    !       different than simulation year:
+    !          - Set to .FALSE. if data is prior to June 1, 2020
+    !          - Set to .TRUE. if data is on or after June 1, 2020
+    !   (2) Do not run a GEOS-FP simulation across June 1, 2020. Split
+    !       up the run in time to avoid this.
+    IF ( Input_Opt%MetField == 'GEOSIT' ) THEN
+       Input_Opt%Reconstruct_Conv_Precip_Flux = .TRUE.
+    ELSEIF ( Input_Opt%MetField == 'GEOSFP' .AND. Input_Opt%NYMDb >= 20200601 ) THEN
+       Input_Opt%Reconstruct_Conv_Precip_Flux = .TRUE.
+    ELSE
+       Input_Opt%Reconstruct_Conv_Precip_Flux = .FALSE.
+    ENDIF
+
     ! Return success
     RC = GC_SUCCESS
 
@@ -3160,6 +3189,16 @@ SUBROUTINE Config_Convection_Mixing( Config, Input_Opt, RC )
        WRITE( 6, 90  ) 'CONVECTION SETTINGS'
        WRITE( 6, 95  ) '-------------------'
        WRITE( 6, 100 ) 'Turn on cloud convection?   : ', Input_Opt%LCONV
+       WRITE( 6, 100 ) 'Reconstruct convective precipitation flux?   : ', &
+            Input_Opt%Reconstruct_Conv_Precip_Flux
+
+       IF ( Input_Opt%MetField == 'GEOSFP' ) THEN
+          IF ( Input_Opt%Reconstruct_Conv_Precip_Flux ) THEN
+             WRITE( 6, 90 ) 'WARNING: Convection will assume met data is on or after 01Jun2020!'
+          ELSE
+             WRITE( 6, 90 ) 'WARNING: Convection will assume met data is prior to 01Jun2020!'
+          ENDIF
+       ENDIF
 
        WRITE( 6, 90  ) 'PBL MIXING SETTINGS'
        WRITE( 6, 95  ) '-------------------'

diff --git a/Headers/input_opt_mod.F90 b/Headers/input_opt_mod.F90
@@ -229,6 +229,7 @@ MODULE Input_Opt_Mod
      LOGICAL                     :: LCONV
      LOGICAL                     :: LTURB
      LOGICAL                     :: LNLPBL
+     LOGICAL                     :: Reconstruct_Conv_Precip_Flux
      INTEGER                     :: TS_CONV
 
      !----------------------------------------
@@ -739,6 +740,7 @@ SUBROUTINE Set_Input_Opt( am_I_Root, Input_Opt, RC )
     Input_Opt%LCONV                  = .FALSE.
     Input_Opt%LTURB                  = .FALSE.
     Input_Opt%LNLPBL                 = .FALSE.
+    Input_Opt%Reconstruct_Conv_Precip_Flux = .FALSE.
     Input_Opt%TS_CONV                = 0
 
     !----------------------------------------

diff --git a/run/GCClassic/createRunDir.sh b/run/GCClassic/createRunDir.sh
@@ -353,6 +353,26 @@ while [ "${valid_met}" -eq 0 ]; do
 	met="geosfp"
 	shared_met_settings=${gcdir}/run/shared/settings/geosfp/geosfp.preprocessed_ll.txt
 	RUNDIR_VARS+="RUNDIR_MET_FIELD_CONFIG='HEMCO_Config.rc.gmao_metfields'\n"
+
+	# Print warning about GEOS-FP and require user to acknowledge it.
+	fp_msg="WARNING: The convection scheme used to generate archived GEOS-FP meteorology \nfiles changed from RAS to Grell-Freidas starting June 1 2020 with impact on \nvertical transport. Discussion and analysis of the impact is available at \ngithub.com/geoschem/geos-chem/issues/1409. In addition, there is a bug in \nconvective precipitation flux following the switch where all values are zero \nin the input files. This bug is addressed by computing fluxes online for runs \nstarting on or after June 1 2020. The fix does not extend to the case of running \nacross the time boundary. Due to these issues we recommend splitting up GEOS-FP \nruns in time such that a single simulation does not span the switch. Configure \none run to end on June 1 2020 and then use its output restart to start another \nrun on June 1. Alternatively consider using MERRA2. If you wish to use a \nGEOS-FP meteorology year different from your simulation year please create a \nGEOS-Chem GitHub issue for assistance to avoid accidentally using zero \nconvective precipitation flux.\n"
+	printf "\n${fp_msg}\n"
+	printf "This warning will be printed to run directory file warnings.txt.\n"
+	printf "${thinline}Enter y to acknowledge and proceed, or q to quit:${thinline}"
+	valid_fp_accept=0
+	while [ "${valid_fp_accept}" -eq 0 ]; do
+	    read -p "${USER_PROMPT}" fp_accept
+	    valid_fp_accept=1
+	    if [[ ${fp_accept} = "y" ]]; then
+		x=0
+	    elif [[ ${fp_accept} = "q" ]]; then
+		exit
+	    else
+		valid_fp_accept=0
+		printf "Invalid option. Try again.\n"
+	    fi
+	done
+
     elif [[ ${met_num} = "3" ]]; then
 	met="geosit"
 	shared_met_settings=${gcdir}/run/shared/settings/geosit/geosit.preprocessed_ll.txt
@@ -858,10 +878,6 @@ done
 mkdir -p ${rundir}
 mkdir -p ${rundir}/Restarts
 
-# Define a subdirectory for rundir configuration files
-rundir_config=${rundir}/CreateRunDirLogs
-mkdir -p ${rundir_config}
-
 # Copy run directory files and subdirectories
 cp ${gcdir}/run/shared/cleanRunDir.sh       ${rundir}
 cp ${gcdir}/run/shared/download_data.py     ${rundir}
@@ -1027,8 +1043,13 @@ fi
 # Replace settings in config files with RUNDIR variables
 #--------------------------------------------------------------------
 
+# Define a subdirectory for rundir configuration files
+rundir_config_dirname=CreateRunDirLogs
+mkdir -p ${rundir}/${rundir_config_dirname}
+
 # Save RUNDIR variables to a file in the rundirConfig folder
-rundir_config_log=${rundir_config}/rundir_vars.txt
+rundir_config_logname=rundir_vars.txt
+rundir_config_log=${rundir}/${rundir_config_dirname}/${rundir_config_logname}
 echo -e "$RUNDIR_VARS" > ${rundir_config_log}
 #sort -o ${rundir_config_log} ${rundir_config_log}
 
@@ -1037,10 +1058,10 @@ echo -e "$RUNDIR_VARS" > ${rundir_config_log}
 ${srcrundir}/init_rd.sh ${rundir_config_log}
 
 #--------------------------------------------------------------------
-# Print run direcory setup info to screen
+# Print run directory setup info to screen
 #--------------------------------------------------------------------
 
-printf "\n  -- See rundir_vars.txt for summary of default run directory settings"
+printf "\n  -- See ${rundir_config_dirname}/${rundir_config_logname} for summary of default run directory settings"
 printf "\n  -- This run directory has been set up to start on ${startdate}"
 printf "\n  -- A restart file for this date has been copied to the Restarts subdirectory"
 printf "\n  -- You may add more restart files using format GEOSChem.Restart.YYYYMMDD_HHmmz.nc4"
@@ -1133,7 +1154,7 @@ commit_hash=$(git log -n 1 --pretty=format:"%h")
 cd ${srcrundir}
 
 # Write commit info to a version log
-version_log=${rundir_config}/rundir.version
+version_log=${rundir}/${rundir_config_dirname}/rundir.version
 printf   " This run directory was created with:"        >  ${version_log}
 printf "\n ${srcrundir}/createRunDir.sh.\n"             >> ${version_log}
 printf "\n GEOS-Chem repository version information:\n" >> ${version_log}
@@ -1214,7 +1235,7 @@ unset msg
 printf "\n\n IMPORTANT: ONLY USE THESE RUNDIR SETTINGS WITH THIS COMMIT!\n" >> ${version_log}
 
 # Add a "# " characters to the front of each line so we can use
-# it as a comment heading for rundir_vars.txt
+# it as a comment heading for ${rundir_config_logname}
 sed 's/^/# /' ${version_log} > tmp.txt
 mv tmp.txt ${version_log}
 
@@ -1230,11 +1251,18 @@ if [[ "x${enable_git}" == "xy" ]]; then
     if [[ -f ${rundir_config_log} ]]; then
 	cd ${rundir}
 	git add ${rundir_config_log}
-	git commit -m "Update header of rundirConfig/rundir_vars.txt" > /dev/null
+	git commit -m "Update header of ${rundir_config_dirname}/${rundir_config_logname}" > /dev/null
 	cd ${srcrundir}
     fi
 fi
 
+#-----------------------------------------------------------------
+# Create and populate warnings file
+#-----------------------------------------------------------------
+if [[ $met == "geosfp" ]]; then
+   echo -e ${fp_msg} > ${rundir}/warnings.txt
+fi
+
 #-----------------------------------------------------------------
 # Done!
 #-----------------------------------------------------------------

diff --git a/run/GCHP/createRunDir.sh b/run/GCHP/createRunDir.sh
@@ -317,6 +317,25 @@ while [ "${valid_met}" -eq 0 ]; do
 
        	met="geosfp"
 
+	# Print warning about GEOS-FP and require user to acknowledge it.
+	fp_msg="WARNING: The convection scheme used to generate archived GEOS-FP meteorology \nfiles changed from RAS to Grell-Freidas starting June 1 2020 with impact on \nvertical transport. Discussion and analysis of the impact is available at \ngithub.com/geoschem/geos-chem/issues/1409. In addition, there is a bug in \nconvective precipitation flux following the switch where all values are zero \nin the input files. This bug is addressed by computing fluxes online for runs \nstarting on or after June 1 2020. The fix does not extend to the case of running \nacross the time boundary. Due to these issues we recommend splitting up GEOS-FP \nruns in time such that a single simulation does not span the switch. Configure \none run to end on June 1 2020 and then use its output restart to start another \nrun on June 1. Alternatively consider using MERRA2. If you wish to use a \nGEOS-FP meteorology year different from your simulation year please create a \nGEOS-Chem GitHub issue for assistance to avoid accidentally using zero \nconvective precipitation flux.\n"
+	printf "\n${fp_msg}\n"
+	printf "This warning will be printed to run directory file warnings.txt.\n"
+	printf "${thinline}Enter y to acknowledge and proceed, or q to quit:${thinline}"
+	valid_fp_accept=0
+	while [ "${valid_fp_accept}" -eq 0 ]; do
+	    read -p "${USER_PROMPT}" fp_accept
+	    valid_fp_accept=1
+	    if [[ ${fp_accept} = "y" ]]; then
+		x=0
+	    elif [[ ${fp_accept} = "q" ]]; then
+		exit
+	    else
+		valid_fp_accept=0
+		printf "Invalid option. Try again.\n"
+	    fi
+	done
+
         # Ask user to specify processed or raw files
         printf "${thinline}Choose meteorology file type:${thinline}"
 	printf "  1. 0.25x0.3125 daily files pre-processed for GEOS-Chem\n"
@@ -600,10 +619,6 @@ done
 mkdir -p ${rundir}
 mkdir -p ${rundir}/Restarts
 
-# Define a subdirectory for rundir configuration files
-rundir_config=${rundir}/CreateRunDirLogs
-mkdir -p ${rundir_config}
-
 # Copy run directory files and subdirectories
 cp ${gcdir}/run/shared/cleanRunDir.sh ${rundir}
 cp ./archiveRun.sh                    ${rundir}
@@ -778,8 +793,14 @@ fi
 # Replace settings in config files with RUNDIR variables
 #--------------------------------------------------------------------
 
-# Save RUNDIR variables to file
-rundir_config_log=${rundir_config}/rundir_vars.txt
+# Define a subdirectory for rundir configuration files
+rundir_config_dirname=CreateRunDirLogs
+rundir_config=${rundir}/${rundir_config_dirname}
+mkdir -p ${rundir_config}
+
+# Save RUNDIR variables to a file in the rundirConfig folder
+rundir_config_logname=rundir_vars.txt
+rundir_config_log=${rundir}/${rundir_config_dirname}/${rundir_config_logname}
 echo -e "$RUNDIR_VARS" > ${rundir_config_log}
 
 # Initialize run directory
@@ -812,7 +833,7 @@ cd ${srcrundir}
 #----------------------------------------------------------------------
 # Archive repository version in run directory file rundir.version
 #----------------------------------------------------------------------
-version_log=${rundir_config}/rundir.version
+version_log=${rundir}/${rundir_config_dirname}/rundir.version
 echo "This run directory was created with ${srcrundir}/createRunDir.sh." > ${version_log}
 echo " " >> ${version_log}
 echo "GEOS-Chem repository version information:" >> ${version_log}
@@ -858,11 +879,8 @@ while [ "$valid_response" -eq 0 ]; do
     fi
 done
 
-#-----------------------------------------------------------------
-# Done!
-#-----------------------------------------------------------------
-
 printf "\n${thinline}Created ${rundir}\n"
+printf "\n  -- See ${rundir_config_dirname}/${rundir_config_logname} for summary of default run directory settings"
 printf "\n  -- This run directory is set up for simulation start date $start_date"
 printf "\n  -- Restart files for this date at different grid resolutions are in the"
 printf "\n     Restarts subdirectory"
@@ -909,4 +927,45 @@ msg+="$ make install\n"
 printf "${msg}" > ${rundir}/build/README
 unset msg
 
+#-----------------------------------------------------------------
+# Add the version info to the top of the rundir configuration log
+#-----------------------------------------------------------------
+
+# Add a caveat that these rundir settings only go with this commit
+printf "\n\n IMPORTANT: ONLY USE THESE RUNDIR SETTINGS WITH THIS COMMIT!\n" >> ${version_log}
+
+# Add a "# " characters to the front of each line so we can use
+# it as a comment heading for ${rundir_config_logname}
+sed 's/^/# /' ${version_log} > tmp.txt
+mv tmp.txt ${version_log}
+
+# Add the version log to the top of the rundir config log
+cat ${version_log} ${rundir_config_log} > tmp.txt
+mv tmp.txt ${rundir_config_log}
+
+# Remove the version log
+rm -rf ${version_log}
+
+# Save the updated rundir_vars file to the git repo
+if [[ "x${enable_git}" == "xy" ]]; then
+    if [[ -f ${rundir_config_log} ]]; then
+	cd ${rundir}
+	git add ${rundir_config_log}
+	git commit -m "Update header of ${rundir_config_dirname}/${rundir_config_lognbame}" > /dev/null
+	cd ${srcrundir}
+    fi
+fi
+
+#-----------------------------------------------------------------
+# Create and populate warnings file
+#-----------------------------------------------------------------
+if [[ $met == "geosfp" ]]; then
+   echo -e ${fp_msg} > ${rundir}/warnings.txt
+fi
+
+#-----------------------------------------------------------------
+# Done!
+#-----------------------------------------------------------------
+printf "\nCreated ${rundir}\n"
+
 exit 0
diff --git a/run/GCHP/geoschem_config.yml.templates/geoschem_config.yml.CO2 b/run/GCHP/geoschem_config.yml.templates/geoschem_config.yml.CO2
@@ -10,6 +10,7 @@
 #============================================================================
 simulation:
   name: ${RUNDIR_SIM_NAME}
+  met_field: ${RUNDIR_MET}
   chem_inputs_dir: ./ChemDir/
   species_database_file: ./species_database.yml
   species_metadata_output_file: OutputDir/geoschem_species_metadata.yml

diff --git a/run/GCHP/geoschem_config.yml.templates/geoschem_config.yml.TransportTracers b/run/GCHP/geoschem_config.yml.templates/geoschem_config.yml.TransportTracers
@@ -10,6 +10,7 @@
 #============================================================================
 simulation:
   name: ${RUNDIR_SIM_NAME}
+  met_field: ${RUNDIR_MET}
   chem_inputs_dir: ./ChemDir/
   species_database_file: ./species_database.yml
   species_metadata_output_file: OutputDir/geoschem_species_metadata.yml

diff --git a/run/GCHP/geoschem_config.yml.templates/geoschem_config.yml.carbon b/run/GCHP/geoschem_config.yml.templates/geoschem_config.yml.carbon
@@ -7,6 +7,7 @@
 #============================================================================
 simulation:
   name: ${RUNDIR_SIM_NAME}
+  met_field: ${RUNDIR_MET}
   chem_inputs_dir: ./ChemDir/
   species_database_file: ./species_database.yml
   species_metadata_output_file: OutputDir/geoschem_species_metadata.yml