Add run directory creation support for processed cubed-sphere GEOS-IT meteorology

CHANGELOG.md

@@ -4,6 +4,10 @@ This file documents all notable changes to the GEOS-Chem repository starting in
 
 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
+- Added createRunDir for processed cubed-sphere GEOS-IT meteorology
+
 ## [14.5.0] - 2024-11-07
 ### Added
 - Added vectors `State_Chm%KPP_AbsTol` and `State_Chm%KPP_RelTol`

run/GCHP/createRunDir.sh

@@ -388,7 +388,7 @@ while [ "${valid_met}" -eq 0 ]; do
 	printf "${thinline}Choose meteorology files:${thinline}"
 	printf "  1. Raw C180 (recommended)\n"
 	printf "  2. Raw 0.5x0.625 \n"
-	printf "  3. Pre-processed C180 (not yet available)\n"
+	printf "  3. Pre-processed C180 \n"
 	printf "  4. Pre-processed 0.5x0.625 \n"
 	valid_response=0
 	while [ "${valid_response}" -eq 0 ]; do
@@ -402,8 +402,7 @@ while [ "${valid_met}" -eq 0 ]; do
 		met_desc="raw_ll"
 	    elif [[ ${response} = "3" ]]; then
 		met_file_type="processed_cs"
-		valid_response=0
-		printf "Pre-processed GEOS-IT data at C180 resolution is not yet available. Try again.\n"
+		met_desc="processed_cs"
 	    elif [[ ${response} = "4" ]]; then
 		met_file_type="processed_ll"
 		met_desc="processed_ll"
@@ -417,7 +416,7 @@ while [ "${valid_met}" -eq 0 ]; do
 	# advection. If using raw lat-lon then always use winds.
 	if [[ ${met_file_type} = "raw_ll" ]]; then
 	    adv_flux_src="wind"
-	elif [[ ${met_file_type} = "raw_cs" ]]; then
+	elif [[ ${met_file_type} = "processed_cs" || ${met_file_type} = "raw_cs" ]]; then
 	    printf "${thinline}Choose meteorology for advection:${thinline}"
 	    printf "  1. C180 1-hourly mass fluxes (recommended)\n"
 	    printf "  2. C180 3-hourly winds\n"
@@ -457,7 +456,15 @@ while [ "${valid_met}" -eq 0 ]; do
 	# Set text files containing settings for met data. Different settings based options aboves.
 	if [[ ${met_file_type} = "processed_ll" ]]; then
 	    RUNDIR_VARS+="$(cat ${metSettingsDir}/geosit/geosit.preprocessed_ll.txt)\n"
-
+
+	elif [[ ${met_file_type} = "processed_cs" ]]; then
+		if [[ ${adv_flux_src} = "mass_flux" ]]; then
+	        RUNDIR_VARS+="$(cat ${metSettingsDir}/geosit/geosit.preprocessed_mass_flux.txt)\n"
+	    elif [[ ${adv_flux_src} == "wind" ]]; then
+			RUNDIR_VARS+="$(cat ${metSettingsDir}/geosit/geosit.preprocessed_wind_cs.txt)\n"
+		fi
+		RUNDIR_VARS+="$(cat ${metSettingsDir}/geosit/geosit.preprocessed_cs.txt)\n"
+
 	else
 	    if [[ ${use_discover} = "y" ]]; then
 
@@ -468,14 +475,14 @@ while [ "${valid_met}" -eq 0 ]; do
 	            RUNDIR_VARS+="$(cat ${metSettingsDir}/geosit/discover/geosit.raw_wind_cs.discover.txt)\n"  
 	        elif [[ ${adv_flux_src} == "wind" && ${met_file_type} == "raw_ll" ]]; then
 	            RUNDIR_VARS+="$(cat ${metSettingsDir}/geosit/discover/geosit.raw_wind_ll.discover.txt)\n"
-		fi
+			fi
 
 		# Settings for all other met vars in ExtData.rc, running on discover
-		if [[ ${met_file_type} = "raw_cs" ]]; then
-	    	    RUNDIR_VARS+="$(cat ${metSettingsDir}/geosit/discover/geosit.raw_cs.discover.txt)\n"
-		elif [[ ${met_file_type} = "raw_ll" ]]; then
-	    	    RUNDIR_VARS+="$(cat ${metSettingsDir}/geosit/discover/geosit.raw_ll.discover.txt)\n"
-		fi
+			if [[ ${met_file_type} = "raw_cs" ]]; then
+	    		    RUNDIR_VARS+="$(cat ${metSettingsDir}/geosit/discover/geosit.raw_cs.discover.txt)\n"
+			elif [[ ${met_file_type} = "raw_ll" ]]; then
+	    		    RUNDIR_VARS+="$(cat ${metSettingsDir}/geosit/discover/geosit.raw_ll.discover.txt)\n"
+			fi
 
 	    elif [[ ${use_discover} = "n" ]]; then
 
@@ -486,14 +493,14 @@ while [ "${valid_met}" -eq 0 ]; do
 	            RUNDIR_VARS+="$(cat ${metSettingsDir}/geosit/geosit.raw_wind_cs.txt)\n"
 	        elif [[ ${adv_flux_src} == "wind" && ${met_file_type} == "raw_ll" ]]; then
 	            RUNDIR_VARS+="$(cat ${metSettingsDir}/geosit/geosit.raw_wind_ll.txt)\n"
-		fi
+			fi
 
 		# Settings for all other met vars in ExtData.rc, NOT running on discover
-		if [[ ${met_file_type} = "raw_cs" ]]; then
+			if [[ ${met_file_type} = "raw_cs" ]]; then
 	    	    RUNDIR_VARS+="$(cat ${metSettingsDir}/geosit/geosit.raw_cs.txt)\n"
-		elif [[ ${met_file_type} = "raw_ll" ]]; then
+			elif [[ ${met_file_type} = "raw_ll" ]]; then
 	    	    RUNDIR_VARS+="$(cat ${metSettingsDir}/geosit/geosit.raw_ll.txt)\n"
-		fi
+			fi
 
 	    fi
 	fi  # end GEOS-IT

run/shared/settings/geosit/geosit.preprocessed_cs.txt

@@ -0,0 +1,123 @@
+RUNDIR_MET='GEOSIT'
+RUNDIR_MET_LOWERCASE='geosit'
+RUNDIR_MET_DIR="${RUNDIR_DATA_ROOT}/GEOS_${RUNDIR_GRID_DIR}/GEOS_IT"
+RUNDIR_MET_DIR_RAW="${RUNDIR_DATA_ROOT}/GEOS_C180/GEOS_IT"
+
+RUNDIR_METEOROLOGY_VERTICAL_INDEX_IS_TOP_DOWN=.false.
+RUNDIR_MET_RES='C180'
+RUNDIR_MET_EXT='nc'
+
+RUNDIR_MET_CN_YR=1998
+RUNDIR_MET_PRES_UNIT='hPa'
+RUNDIR_MET_PRES_SCALE='1.0'
+
+RUNDIR_OFFLINE_EMIS_RES='0.5x0.625'
+RUNDIR_OFFLINE_EMIS_LAT_RES='05'
+
+RUNDIR_METLIGHTNING='MERRA2'
+RUNDIR_METLIGHTNING_DIR="${RUNDIR_DATA_ROOT}/GEOS_0.5x0.625/MERRA2"
+RUNDIR_METLIGHTNING_RES='0.5x0.625'
+RUNDIR_LIGHTNOX_CLIM=true
+RUNDIR_MET_LCLIM='1980-2019'
+
+RUNDIR_PHOT_CLD_NLEV=34
+
+RUNDIR_MET_EXTDATA_PRIMARY_EXPORTS="""
+
+${RUNDIR_MET_EXTDATA_PRIMARY_EXPORTS_FOR_ADVECTION}
+
+#-------------------------------------------------------
+# --- 1-hr time-averaged, 2D ---
+#-------------------------------------------------------
+
+ALBD     1  N Y F0;003000 none none ALBEDO   ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.A1.C180.nc
+CLDFRC   1  N Y F0;003000 none none CLDTOT   ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.A1.C180.nc
+EFLUX    1  N Y F0;003000 none none EFLUX    ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.A1.C180.nc
+EVAP     1  N Y F0;003000 none none EVAP     ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.A1.C180.nc
+FRSEAICE 1  N Y F0;003000 none none FRSEAICE ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.A1.C180.nc
+FRSNO    1  N Y F0;003000 none none FRSNO    ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.A1.C180.nc
+GRN      1  N Y F0;003000 none none GRN      ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.A1.C180.nc
+GWETROOT 1  N Y F0;003000 none none GWETROOT ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.A1.C180.nc
+GWETTOP  1  N Y F0;003000 none none GWETTOP  ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.A1.C180.nc
+HFLUX    1  N Y F0;003000 none none HFLUX    ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.A1.C180.nc
+LAI      1  N Y F0;003000 none none LAI      ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.A1.C180.nc
+PARDF    1  N Y F0;003000 none none PARDF    ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.A1.C180.nc
+PARDR    1  N Y F0;003000 none none PARDR    ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.A1.C180.nc
+PBLH     1  N Y F0;003000 none none PBLH     ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.A1.C180.nc
+PRECANV  1  N Y F0;003000 none none PRECANV  ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.A1.C180.nc
+PRECCON  1  N Y F0;003000 none none PRECCON  ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.A1.C180.nc
+PRECLSC  1  N Y F0;003000 none none PRECLSC  ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.A1.C180.nc
+PRECSNO  1  N Y F0;003000 none none PRECSNO  ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.A1.C180.nc
+PRECTOT  1  N Y F0;003000 none none PRECTOT  ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.A1.C180.nc
+QV2M     1  N Y F0;003000 none none QV2M     ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.A1.C180.nc
+SLP    hPa  N Y F0;003000 none none SLP      ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.A1.C180.nc
+SNODP    1  N Y F0;003000 none none SNODP    ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.A1.C180.nc
+SNOMAS   1  N Y F0;003000 none none SNOMAS   ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.A1.C180.nc
+RADSWG   1  N Y F0;003000 none none SWGDN    ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.A1.C180.nc
+TO3 dobson  N Y F0;003000 none none TO3      ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.A1.C180.nc
+TROPP  hPa  N Y F0;003000 none none TROPPT   ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.A1.C180.nc
+TSKIN    1  N Y F0;003000 none none TS       ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.A1.C180.nc
+TS       1  N Y F0;003000 none none T2M      ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.A1.C180.nc
+USTAR    1  N Y F0;003000 none none USTAR    ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.A1.C180.nc
+U10M m_s-1  N Y F0;003000 none none U10M     ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.A1.C180.nc
+V10M m_s-1  N Y F0;003000 none none V10M     ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.A1.C180.nc
+Z0       1  N Y F0;003000 none none Z0M      ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.A1.C180.nc
+
+# SEAICE[0-9]0 bins not used except in Hg simulation
+
+SEAICE00 1 N Y F0;003000 none none SEAICE00 /dev/null
+SEAICE10 1 N Y F0;003000 none none SEAICE10 /dev/null
+SEAICE20 1 N Y F0;003000 none none SEAICE20 /dev/null
+SEAICE30 1 N Y F0;003000 none none SEAICE30 /dev/null
+SEAICE40 1 N Y F0;003000 none none SEAICE40 /dev/null
+SEAICE50 1 N Y F0;003000 none none SEAICE50 /dev/null
+SEAICE60 1 N Y F0;003000 none none SEAICE60 /dev/null
+SEAICE70 1 N Y F0;003000 none none SEAICE70 /dev/null
+SEAICE80 1 N Y F0;003000 none none SEAICE80 /dev/null
+SEAICE90 1 N Y F0;003000 none none SEAICE90 /dev/null
+
+#-------------------------------------------------------
+# --- 3-hr instantaneous (all 3D) ---
+#-------------------------------------------------------
+
+TMPU1 K N Y 0        none none T ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.I3.C180.nc
+TMPU2 K N Y 0;001000 none none T ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.I3.C180.nc
+
+#-------------------------------------------------------
+# --- 3-hr time-averaged (all 3D) ---
+#-------------------------------------------------------
+
+QI       1      N Y F0;013000 none none QI       ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.A3cld.C180.nc
+QL       1      N Y F0;013000 none none QL       ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.A3cld.C180.nc
+TAUCLI   1      N Y F0;013000 none none TAUCLI   ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.A3cld.C180.nc
+TAUCLW   1      N Y F0;013000 none none TAUCLW   ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.A3cld.C180.nc
+OPTDEP   1      N Y F0;013000 none none OPTDEPTH ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.A3cld.C180.nc
+CLDF     1      N Y F0;013000 none none CLOUD    ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.A3cld.C180.nc
+DTRAIN   1      N Y F0;013000 none none DTRAIN   ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.A3dyn.C180.nc
+OMEGA    Pa_s-1 N Y F0;013000 none none OMEGA    ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.A3dyn.C180.nc
+RH       -      N Y F0;013000 none none RH       ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.A3dyn.C180.nc
+DQRCU    1      N Y F0;013000 none none DQRCU    ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.A3mstC.C180.nc
+DQRLSAN  1      N Y F0;013000 none none DQRLSAN  ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.A3mstC.C180.nc
+REEVAPCN 1      N Y F0;013000 none none REEVAPCN ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.A3mstC.C180.nc
+REEVAPLS 1      N Y F0;013000 none none REEVAPLS ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.A3mstC.C180.nc
+CMFMC    1      N Y F0;013000 none none CMFMC    ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.A3mstE.C180.nc
+PFICU    1      N Y F0;013000 none none PFICU    ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.A3mstE.C180.nc
+PFILSAN  1      N Y F0;013000 none none PFILSAN  ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.A3mstE.C180.nc
+PFLCU    1      N Y F0;013000 none none PFLCU    ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.A3mstE.C180.nc
+PFLLSAN  1      N Y F0;013000 none none PFLLSAN  ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.A3mstE.C180.nc
+
+#-------------------------------------------------------
+# --- Fixed variables, from constants file ---
+#-------------------------------------------------------
+
+FRLAKE     1      N Y - none none FRLAKE   ./MetDir/1998/01/GEOSIT.19980101.CN.C180.nc
+FRLAND     1      N Y - none none FRLAND   ./MetDir/1998/01/GEOSIT.19980101.CN.C180.nc
+FRLANDIC   1      N Y - none none FRLANDIC ./MetDir/1998/01/GEOSIT.19980101.CN.C180.nc
+FROCEAN    1      N Y - none none FROCEAN  ./MetDir/1998/01/GEOSIT.19980101.CN.C180.nc
+PHIS       m2_s-2 N Y - none none PHIS     ./MetDir/1998/01/GEOSIT.19980101.CN.C180.nc
+OCEAN_MASK 1      N Y - none none FROCEAN  ./MetDir/1998/01/GEOSIT.19980101.CN.C180.nc
+
+"""
+
+RUNDIR_MET_EXTDATA_DERIVED_EXPORTS="""
+"""

run/shared/settings/geosit/geosit.preprocessed_ll.txt

@@ -5,11 +5,11 @@ RUNDIR_MET_DIR_RAW="${RUNDIR_DATA_ROOT}/GEOS_0.5x0.625/GEOS_IT"
 
 RUNDIR_METEOROLOGY_VERTICAL_INDEX_IS_TOP_DOWN=.false.
 RUNDIR_MET_RES='05x0625'
-RUNDIR_MET_EXT='nc4'
+RUNDIR_MET_EXT='nc'
 
 RUNDIR_MET_CN_YR=1998
-RUNDIR_MET_PRES_UNIT='Pa '
-RUNDIR_MET_PRES_SCALE='0.01'
+RUNDIR_MET_PRES_UNIT='hPa '
+RUNDIR_MET_PRES_SCALE='1.0'
 
 RUNDIR_OFFLINE_EMIS_RES='0.5x0.625'
 RUNDIR_OFFLINE_EMIS_LAT_RES='05'

run/shared/settings/geosit/geosit.preprocessed_mass_flux.txt

@@ -0,0 +1,19 @@
+RUNDIR_IMPORT_MASS_FLUX_FROM_EXTDATA=.true.
+RUNDIR_USE_TOTAL_AIR_PRESSURE_IN_ADVECTION=0
+
+RUNDIR_MET_EXTDATA_PRIMARY_EXPORTS_FOR_ADVECTION="""
+
+#--------------------------------------
+# --- Meteorology used in advection ---
+#--------------------------------------
+
+# Cubed-sphere 1-hourly mass fluxes
+UA;VA     m_s-1      N Y F0;013000 none  none      U;V       ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.A3dyn.C180.nc
+MFXC;MFYC Pa_m+2_s-1 N H F0;003000 none  0.6666666 MFXC;MFYC ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.CTM_A1.C180.nc
+CXC;CYC   1          N H F0;003000 none  none      CX;CY     ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.CTM_A1.C180.nc
+PS1       hPa        N Y  0        none  none      PS        ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.CTM_I1.C180.nc
+PS2       hPa        N Y  0;001000 none  none      PS        ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.CTM_I1.C180.nc
+SPHU1     kg_kg-1    N Y  0        none  none      QV        ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.CTM_I1.C180.nc
+SPHU2     kg_kg-1    N Y  0;001000 none  none      QV        ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.CTM_I1.C180.nc
+
+"""

run/shared/settings/geosit/geosit.preprocessed_wind_cs.txt

@@ -0,0 +1,17 @@
+RUNDIR_IMPORT_MASS_FLUX_FROM_EXTDATA=.false.
+RUNDIR_USE_TOTAL_AIR_PRESSURE_IN_ADVECTION=0
+
+RUNDIR_MET_EXTDATA_PRIMARY_EXPORTS_FOR_ADVECTION="""
+
+#--------------------------------------
+# --- Meteorology used in advection ---
+#--------------------------------------
+
+# Cubed-sphere 3-hourly winds
+UA;VA   m_s-1   N Y F0;013000 none none U;V ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.A3dyn.05x0625.nc
+PS1     hPa     N Y  0        none none PS  ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.I3.05x0625.nc
+PS2     hPa     N Y  0;001000 none none PS  ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.I3.05x0625.nc
+SPHU1   kg_kg-1 N Y  0        none none QV  ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.I3.05x0625.nc
+SPHU2   kg_kg-1 N Y  0;001000 none none QV  ./MetDir/%y4/%m2/GEOSIT.%y4%m2%d2.I3.05x0625.nc
+
+"""

run/shared/settings/geosit/geosit.raw_cs.txt

@@ -9,8 +9,8 @@ RUNDIR_MET_EXT='nc4'
 
 RUNDIR_MET_CN_YR=Y1998
 RUNDIR_MET_CN_MO=M01
-RUNDIR_MET_PRES_UNIT='hPa'
-RUNDIR_MET_PRES_SCALE='1.0'
+RUNDIR_MET_PRES_UNIT='Pa'
+RUNDIR_MET_PRES_SCALE='0.01'
 
 RUNDIR_OFFLINE_EMIS_RES='0.5x0.625'
 RUNDIR_OFFLINE_EMIS_LAT_RES='05'

run/shared/settings/geosit/geosit.raw_ll.txt

@@ -9,8 +9,8 @@ RUNDIR_MET_EXT='nc4'
 
 RUNDIR_MET_CN_YR=Y1998
 RUNDIR_MET_CN_MO=M01
-RUNDIR_MET_PRES_UNIT='hPa'
-RUNDIR_MET_PRES_SCALE='1.0'
+RUNDIR_MET_PRES_UNIT='Pa'
+RUNDIR_MET_PRES_SCALE='0.01'
 
 RUNDIR_OFFLINE_EMIS_RES='0.5x0.625'
 RUNDIR_OFFLINE_EMIS_LAT_RES='05'