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Fixes for running GEOS-Chem 14.5.1 in GEOS #2661

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merged 7 commits into from
Dec 20, 2024
Merged

Fixes for running GEOS-Chem 14.5.1 in GEOS #2661

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20809a8
Fix bug in HCO_WARNING call within TOMAS code; replace with GC_WARNING
lizziel Dec 20, 2024
80b9296
Update GEOS-only configuration files to versions in geos/develop branch
lizziel Dec 20, 2024
8b7a9bb
Add missing entry in SoilNOx extension of GEOS HEMCO_Config.rc
lizziel Dec 20, 2024
5b4c829
Change SpeciesConc_ to SpeciesConcVV_ in GEOS HISTORY.rc file
lizziel Dec 20, 2024
7af7430
Updated changelog
lizziel Dec 20, 2024
95bc863
HEMCO configuration file updates for GEOS from GMAO
lizziel Dec 20, 2024
492f277
Update chem inputs directory for GEOS
lizziel Dec 20, 2024
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2 changes: 1 addition & 1 deletion CHANGELOG.md
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Expand Up @@ -45,7 +45,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
- Fixed segmentation fault in qfyaml when running with certain compilers without debug flags on
- Fixed errors in adjoint-only code preventing successful adjoint build
- Fixed zero convective precipitation and high cloud base in runs using GEOS-FP (>=01Jun2020) or GEOS-IT
- Updated GEOS-only code for compatibility with GEOS-Chem 14.5
- Updated GEOS-only code and configuration files for compatibility with GEOS-Chem 14.5
- Fixed missing Is_Advected for TMB in species_database.yml

### Removed
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3 changes: 2 additions & 1 deletion GeosCore/sulfate_mod.F90
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Expand Up @@ -996,6 +996,7 @@ SUBROUTINE SRCSF30( Input_Opt, State_Grid, State_Met, State_Chm, TC2, RC )
!
! !USES:
!
USE ErrCode_Mod, ONLY : GC_WARNING
USE ERROR_MOD, ONLY : ERROR_STOP, IT_IS_NAN
USE Input_Opt_Mod, ONLY : OptInput
USE Species_Mod, ONLY : SpcConc
Expand Down Expand Up @@ -1169,7 +1170,7 @@ SUBROUTINE SRCSF30( Input_Opt, State_Grid, State_Met, State_Chm, TC2, RC )
DgnName = 'SO4_ANTH'
CALL HCO_GC_GetDiagn( Input_Opt, State_Grid, DgnName, .FALSE., ERR, Ptr3D=Ptr3D )
IF ( .NOT. ASSOCIATED(Ptr3D) ) THEN
CALL HCO_WARNING('Not found: '//TRIM(DgnName),ERR,THISLOC=LOC)
IF ( Input_Opt%amIRoot ) CALL GC_WARNING('Not found: '//TRIM(DgnName),RC,LOC)
ELSE
SO4_ANTH = Ptr3D(:,:,:)
ENDIF
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128 changes: 64 additions & 64 deletions run/GEOS/GEOSCHEMchem_ExtData.yaml
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34 changes: 22 additions & 12 deletions run/GEOS/GEOSCHEMchem_GridComp.rc
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Expand Up @@ -77,16 +77,16 @@ RUN_PHASES: 2
#
# %%% Stop if KPP integration fails (default: 1) %%%
#
KPP_STOP_IF_FAIL: 0
KPP_STOP_IF_FAIL: 0

# Checks to prevent negative concentrations after KPP integration. These can create
# problems with mass balance. KppCheckNegatives checks for negatives in the N top
# layers. I.e., if set to 5 it will check for negatives in the top 5 model levels.
# If set to 0, it will perform the check in the entire stratosphere and mesosphere.
# If negatives are found, a second integration attempt will be made using HSTART=0
# and by relaxing the KPP tolerances using the scale factor provided in KppTolScale.
KppCheckNegatives: -1
KppTolScale: 1.0
KppCheckNegatives: 0
KppTolScale: 1.0

#
# %%% HEMCO configuration file %%%
Expand Down Expand Up @@ -119,8 +119,8 @@ Online_CLDLIQ: 1
# Use online vertical updraft velocity or use default GEOS-Chem parameterization?
Online_VUD: 1

# Use GAAS on GEOS-Chem aerosols?
Species_friendly_to_GAAS: 0
# make aerosols friendly to GAAS?
Species_friendly_to_GAAS: 1

#
# %%% Tuning parameter to reduce washout efficiency
Expand Down Expand Up @@ -148,6 +148,12 @@ Use_ozonopause: -999.0
#
Prescribe_strat_H2O: 1

# Apply H2O tendency to Q?
# 1 = always do it
# 0 = only do it if GEOSCHEMCHEM is RATS provider
# -1 = never do it
ApplyQtend: -1

# %%% Settings for excluding species from being transported
Reduce_transport_species: 0
Transport_blacklist: CFC115,CFC114,N2O,CFC12,H1301,CFC113,CFC11,CCl4,H2O,H2402,H1211,HCFC142b,HCFC22,HCFC141b,CH3CCl3,CH3Br,CH3Cl,HCFC123
Expand Down Expand Up @@ -180,9 +186,10 @@ Use_GMI_O3_PL: 0

# Analysis options
ANAPHASE: 2
Analysis_nSpecies: 2
Analysis_Settings_Spec001: GEOSCHEMchem_AnaSettings_O3.rc
Analysis_nSpecies: 0
Analysis_Settings_Spec001: GEOSCHEMchem_AnaSettings_O3.CDAS.rc
Analysis_Settings_Spec002: GEOSCHEMchem_AnaSettings_NO2.rc
Analysis_Settings_Spec003: GEOSCHEMchem_AnaSettings_SO2.rc

#
# NOx lightning met inputs
Expand Down Expand Up @@ -222,22 +229,25 @@ TurnOffHetRates: 1
#
Bry_Cly_Family_Transport: 1

#
# Skip GCC during replay predictor step
SkipReplayGCC: 0

#
# CO production from CO2 photolysis
#
CO_production_from_CO2_photolysis: 0
CO2photolysisFile: /discover/nobackup/projects/gmao/share/dasilva/fvInput/ExtData/chemistry/GEOSCHEMchem/v0.0.0/CHEM_INPUTS/StratChem/SC.J_20_12_79_72_200_45.jpl15.nc4

#
#
# CO2 coupling with GOCART
#
#
Import_CO2_from_GOCART: 0
GOCART_CO2_FieldName: GOCART_CO2

#
# Set CO mesosphere upper boundary to external field
# Set CO mesosphere upper boundary to external field
#
Set_CO_Mesosphere: 0
Set_CO_Mesosphere: 1
CO_Mesosphere_FieldName: CO_CMAM

#
Expand Down
77 changes: 32 additions & 45 deletions run/GEOS/HEMCO_Config.rc
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Expand Up @@ -81,8 +81,8 @@ VerboseOnCores: root # Accepted values: root all
--> UCX_PROD_LOSS : false
--> OMOC_RATIO : false
--> GMD_SFC_CH4 : false
--> CMIP6_SFC_CH4 : false
--> GEOS_3HR_CH4 : true
--> CMIP6_SFC_CH4 : false
# OLSON and MODIS read via MAPL not HEMCO in GEOS
--> OLSON_LANDMAP : false
--> YUAN_MODIS_LAI : false
Expand All @@ -99,10 +99,11 @@ VerboseOnCores: root # Accepted values: root all
#C720 --> OTD-LIS scaling : 1.4152E-3
#C180 --> OTD-LIS scaling : 1.527e-2
--> OTD-LIS scaling : 0.12
--> CDF table : /discover/nobackup/cakelle2/data/light_dist.ott2010.dat
--> CDF table : /discover/nobackup/projects/gmao/share/dasilva/fvInput/ExtData/chemistry/HEMCO/v0.0.0/sfc/light_dist.ott2010.dat
--> Use CNV_FRC : false
--> OTD-LIS factors : false
104 SoilNOx : on NO
--> UseSoilTemperature: false
--> Use fertilizer NOx: true
105 DustDead : on DST1/DST2/DST3/DST4
--> Mass tuning factor: 2.454e-4
Expand Down Expand Up @@ -153,11 +154,11 @@ VerboseOnCores: root # Accepted values: root all
--> GFED_subgrid_coag : false
117 Volcano : on SO2
--> Volcano_Source : AeroCom
# use flat degassing file for ops:
# --> Volcano_Table : ./ExtData/AeroCom/sfc/volcanic_CARN_1978-2020_v202005/so2_volcanic_emissions_CARN_v202005.degassing_only.rc
# use flat degassing file for 2022 onwards:
--> Volcano_Table : ./ExtData/AeroCom/sfc/volcanic_CARN_1978-2020_v202005/so2_volcanic_emissions_CARN_v202005.degassing_only.rc
--> Volcano_Climatology : ./ExtData/AeroCom/sfc/volcanic_CARN_1978-2020_v202005/so2_volcanic_emissions_CARN_v202005.degassing_only.rc
# use degassing and eruptive for reanalysis:
--> Volcano_Table : ./ExtData/AeroCom/sfc/volcanic_CARN_1978-2020_v202005/so2_volcanic_emissions_Carns.$YYYY$MM$DD.rc
--> Volcano_Climatology : /discover/nobackup/ewlundgr/data/ExtData/VOLCANO/v2021-09/so2_volcanic_emissions_CARN_v202005.degassing_only.rc
# --> Volcano_Table : ./ExtData/AeroCom/sfc/volcanic_CARN_1978-2020_v202005/so2_volcanic_emissions_Carns.$YYYY$MM$DD.rc
120 Inorg_Iodine : on HOI/I2
--> Emit HOI : true
--> Emit I2 : true
Expand Down Expand Up @@ -193,23 +194,24 @@ VerboseOnCores: root # Accepted values: root all
#205,215 agr DOW,TOD

#97 NOx ems as NO scale factor
#115 NO2toNO scale factor; CEDS emits all as NO2. Convert NO2 to NO here instead of preprocessing.
#0 CEDS_NO_AGR /see/ExtData.rc NOx_agr 2014/1-12/1/0 C xy kg/m2/s NO 97/115/205/215 5 2
0 CEDS_NO_ENE /see/ExtData.rc NOx_ene 2014/1-12/1/0 C xyL=1:11 kg/m2/s NO 97/115/202/212/317 2 2
0 CEDS_NO_IND /see/ExtData.rc NOx_ind 2014/1-12/1/0 C xyL=1:15 kg/m2/s NO 97/115/201/211/318 1 2
0 CEDS_NO_TRA /see/ExtData.rc NOx_tra 2014/1-12/1/0 C xy kg/m2/s NO 97/115/203/213 3 2
0 CEDS_NO_RCO /see/ExtData.rc NOx_rco 2014/1-12/1/0 C xy kg/m2/s NO 97/115/204/214 4 2
0 CEDS_NO_SLV /see/ExtData.rc NOx_slv 2014/1-12/1/0 C xy kg/m2/s NO 97/115/201/211 1 2
0 CEDS_NO_WST /see/ExtData.rc NOx_wst 2014/1-12/1/0 C xy kg/m2/s NO 97/115 9 2
# AGR NOx emissions are not used since soil NOx emissions include those from fertilizers
#0 CEDS_NO_AGR /see/ExtData.rc NO_agr 2014/1-12/1/0 C xy kg/m2/s NO 97/205/215 5 2
0 CEDS_NO_ENE /see/ExtData.rc NO_ene 2014/1-12/1/0 C xyL=1:11 kg/m2/s NO 97/202/212/317 2 2
0 CEDS_NO_IND /see/ExtData.rc NO_ind 2014/1-12/1/0 C xyL=1:15 kg/m2/s NO 97/201/211/318 1 2
0 CEDS_NO_TRA /see/ExtData.rc NO_tra 2014/1-12/1/0 C xy kg/m2/s NO 97/203/213 3 2
0 CEDS_NO_RCO /see/ExtData.rc NO_rco 2014/1-12/1/0 C xy kg/m2/s NO 97/204/214 4 2
0 CEDS_NO_SLV /see/ExtData.rc NO_slv 2014/1-12/1/0 C xy kg/m2/s NO 97/201/211 1 2
0 CEDS_NO_WST /see/ExtData.rc NO_wst 2014/1-12/1/0 C xy kg/m2/s NO 97 9 2

#98 NOx ems as NO2 scale factor
#0 CEDS_NO2_AGR /see/ExtData.rc NOx_agr 2014/1-12/1/0 C xy kg/m2/s NO2 98/205/215 5 2
0 CEDS_NO2_ENE /see/ExtData.rc NOx_ene 2014/1-12/1/0 C xyL=1:11 kg/m2/s NO2 98/202/212/317 2 2
0 CEDS_NO2_IND /see/ExtData.rc NOx_ind 2014/1-12/1/0 C xyL=1:15 kg/m2/s NO2 98/201/211/318 1 2
0 CEDS_NO2_TRA /see/ExtData.rc NOx_tra 2014/1-12/1/0 C xy kg/m2/s NO2 98/203/213 3 2
0 CEDS_NO2_RCO /see/ExtData.rc NOx_rco 2014/1-12/1/0 C xy kg/m2/s NO2 98/204/214 4 2
0 CEDS_NO2_SLV /see/ExtData.rc NOx_slv 2014/1-12/1/0 C xy kg/m2/s NO2 98/201/211 1 2
0 CEDS_NO2_WST /see/ExtData.rc NOx_wst 2014/1-12/1/0 C xy kg/m2/s NO2 98 9 2
#115 NO to NO2 mass conversion
#0 CEDS_NO2_AGR /see/ExtData.rc NO_agr 2014/1-12/1/0 C xy kg/m2/s NO2 98/115/205/215 5 2
0 CEDS_NO2_ENE /see/ExtData.rc NO_ene 2014/1-12/1/0 C xyL=1:11 kg/m2/s NO2 98/115/202/212/317 2 2
0 CEDS_NO2_IND /see/ExtData.rc NO_ind 2014/1-12/1/0 C xyL=1:15 kg/m2/s NO2 98/115/201/211/318 1 2
0 CEDS_NO2_TRA /see/ExtData.rc NO_tra 2014/1-12/1/0 C xy kg/m2/s NO2 98/115/203/213 3 2
0 CEDS_NO2_RCO /see/ExtData.rc NO_rco 2014/1-12/1/0 C xy kg/m2/s NO2 98/115/204/214 4 2
0 CEDS_NO2_SLV /see/ExtData.rc NO_slv 2014/1-12/1/0 C xy kg/m2/s NO2 98/115/201/211 1 2
0 CEDS_NO2_WST /see/ExtData.rc NO_wst 2014/1-12/1/0 C xy kg/m2/s NO2 98/115 9 2

#280 COtoSOAP_anth
#301 ODIAC_ANNUALSCALE_2010 (not applied here but is used in HTAP) **********
Expand Down Expand Up @@ -604,17 +606,16 @@ VerboseOnCores: root # Accepted values: root all
0 CEDS_ACET_SHP /see/MEK_ExtData.rc MEK_shp 2014/1-12/1/0 C xyL=1:3 kg/m2/s ACET 14/51/319 10 5
0 CEDS_HCOOH_SHP /see/HCOOH_ExtData.rc HCOOH_shp 2014/1-12/1/0 C xyL=1:3 kg/m2/s HCOOH 16/319 10 5
#97 NOx ems as NO scale factor
#115 NO2toNO scale factor; CEDS emits all as NO2. Convert NO2 to NO here instead of preprocessing.
#98 NOx ems as NO2 scale factor
0 CEDS_NO_SHP /see/NOx_ExtData.rc NOx_shp 2014/1-12/1/0 C xyL=1:3 kg/m2/s NO 97/115/319 10 5
0 CEDS_NO2_SHP /see/NOx_ExtData.rc NOx_shp 2014/1-12/1/0 C xyL=1:3 kg/m2/s NO2 98/319 10 5
#98 NOx ems as NO2 scale factor and #115 for mass conversion
0 CEDS_NO_SHP /see/NO_ExtData.rc NO_shp 2014/1-12/1/0 C xyL=1:3 kg/m2/s NO 97/319 10 5
0 CEDS_NO2_SHP /see/NO_ExtData.rc NO_shp 2014/1-12/1/0 C xyL=1:3 kg/m2/s NO2 98/115/319 10 5
)))CEDS_SHIP

#=======================================================================================================================================
## --- AEIC aircraft emissions ---
#=======================================================================================================================================
(((AEIC
0 AEIC_NO ~/data/aeic_2005.geos.1x1.72L.nc NO 2005/1-12/1/0 C xyz kg/m2/s NO 110/115 20 1
0 AEIC_NO ~/data/aeic_2005.geos.1x1.72L.nc NO 2005/1-12/1/0 C xyz kg/m2/s NO 110 20 1
0 AEIC_CO ~/data/aeic_2005.geos.1x1.72L.nc CO 2005/1-12/1/0 C xyz kg/m2/s CO 110 20 1
0 AEIC_SOAP - - - - - - SOAP 110/280 20 1
0 AEIC_SO2 ~/data/aeic_2005.geos.1x1.72L.nc FUELBURN 2005/1-12/1/0 C xyz kg/m2/s SO2 111 20 1
Expand Down Expand Up @@ -1360,12 +1361,10 @@ VerboseOnCores: root # Accepted values: root all
* NOAA_GMD_CH4 $ROOT/NOAA_GMD/v2018-01/monthly.gridded.surface.methane.1979-2020.1x1.nc SFC_CH4 1979-2020/1-12/1/0 C xy ppbv * - 1 1
)))GMD_SFC_CH4

#==============================================================================
# --- GEOS 3-hourly CH4 (within PBL) ---
#==============================================================================
(((GEOS_3HR_CH4
* GEOS_CH4 /see/extdata CH4_total_dry 1979-2024/1-12/1-31/0 C xyz v/v * - 1 1
* CH4_OFFSET /see/extdata CH4_offset 2021-2024/1-12/1/0 C xy v/v * - 1 1
* GEOS_CH4 /see/extdata CH4_total_dry 1979-2024/1-12/1-31/0 C xyz ppbv * - 1 1
* CH4_OFFSET /see/extdata CH4_offset 2021-2024/1-12/1/0 C xy v/v * - 1 1
###* CH4_OFFSET 0.0 - - - xy v/v * - 1 1
)))GEOS_3HR_CH4

(((SfcVMR
Expand Down Expand Up @@ -1421,18 +1420,6 @@ VerboseOnCores: root # Accepted values: root all
* surf_iodide $ROOT/OCEAN_O3_DRYDEP/v2020-02/Oi_prj_predicted_iodide_0.125x0.125_No_Skagerrak_Just_Ensemble.nc Ensemble_Monthly_mean 1970/1-12/1/0 C xy 1 * - 1 1
)))OCEAN_O3_DRYDEP


#==============================================================================
# --- Imports for GEOS handled through HEMCO ---
#==============================================================================
# CH4 boundary conditions
(((GEOS_3HR_CH4
* GEOS_CH4 /see/extdata CH4_total_dry 1979-2024/1-12/1-31/0 C xyz ppbv * - 1 1
)))GEOS_3HR_CH4

# GEOS analysis fields
#* GEOSIT_O3 /see/extdata ozone 1979-2099/1-12/1-31/0 C xyz ppmv * - 1 1

### END SECTION BASE EMISSIONS

####################################################################################
Expand Down Expand Up @@ -1571,8 +1558,8 @@ VerboseOnCores: root # Accepted values: root all
97 NOXtoNO 0.9 - - - xy 1 1
98 NOXtoNO2 0.1 - - - xy 1 1

# Conversion factor from NO2 to NO
115 NO2toNO 6.52e-1 - - - xy unitless 1
# Conversion factor from NO to NO2
115 NOtoNO2 1.533 - - - xy unitless 1

# --- AEIC aircraft emissions ---
# See http://geoschemdata.wustl.edu/ExtData/HEMCO/AEIC2019/v2022-03/AEIC_2019_technical_note.pdf
Expand Down
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