Merge PR #2342 (Read number of levels with clouds into Cloud-J)

This merge brings PR #2342 (Read number of levels with clouds used in photolysis from config file used in photolysis from config file, by @lizziel) into the GEOS-Chem "no-diff-to-benchmark" development stream. This PR fixes an issue where hardwiring of the number of levels with clouds (for Cloud-J photolysis) broke GEOS-Chem in CESM. We now specify the number of levels with cloud in geoschem_config.yml. Signed-off-by: Bob Yantosca <[email protected]>
geoschem · Jul 9, 2024 · f78052f · f78052f
2 parents 8554d3a + e91ce06
commit f78052f
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,8 +5,12 @@ 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 number of levels with clouds for photolysis to geoschem_config.yml and Input_Opt to pass to Cloud-J
+
 ### Fixed
 - Typo in `setCommonRunSettings.sh` that made GCHP always choose mass fluxes for meteorology
+- Fixed bug in # levels with cloud used in photolysis when using GCAP met or CESM
 
 ## [14.4.1] - 2024-06-28
 ### Added

diff --git a/GeosCore/cldj_interface_mod.F90 b/GeosCore/cldj_interface_mod.F90
@@ -131,8 +131,9 @@ SUBROUTINE INIT_CLOUDJ( Input_Opt, State_Grid, State_Diag, State_Chm, RC )
     ! Initialize Cloud-J. Includes reading input data files
     ! FJX_spec.dat (RD_XXX), FJX_scat-aer.dat (RD_MIE), and 
     ! FJX_j2j.dat (RD_JS_JX)
-    CALL Init_CldJ(Input_Opt%amIRoot, Input_Opt%CloudJ_Dir, &
-                   State_Grid%NZ, TITLEJXX, JVN_, NJXX)
+    CALL Init_CldJ(Input_Opt%amIRoot, Input_Opt%CloudJ_Dir,   &
+                   State_Grid%NZ, Input_Opt%Nlevs_Phot_Cloud, &
+                   TITLEJXX, JVN_, NJXX)
 
     ! Store # of photolysis reactions in State_Chm object
     State_Chm%Phot%nPhotRxns = NRatJ

diff --git a/GeosCore/input_mod.F90 b/GeosCore/input_mod.F90
@@ -2762,6 +2762,7 @@ SUBROUTINE Config_Photolysis( Config, Input_Opt, RC )
 !
     ! Scalars
     LOGICAL                      :: v_bool
+    INTEGER                      :: v_int
     REAL(yp)                     :: v_real
 
     ! Strings
@@ -2793,6 +2794,19 @@ SUBROUTINE Config_Photolysis( Config, Input_Opt, RC )
     ENDIF
     Input_Opt%Do_Photolysis = v_bool
 
+    !------------------------------------------------------------------------
+    ! Number levels with clouds to use in photolysis
+    !------------------------------------------------------------------------
+    key   = "operations%photolysis%num_levs_with_cloud"
+    v_int = MISSING_INT
+    CALL QFYAML_Add_Get( Config, TRIM( key ), v_int, "", RC )
+    IF ( RC /= GC_SUCCESS ) THEN
+       errMsg = 'Error parsing ' // TRIM( key ) // '!'
+       CALL GC_Error( errMsg, RC, thisLoc )
+       RETURN
+    ENDIF
+    Input_Opt%NLevs_Phot_Cloud = v_int
+
     !------------------------------------------------------------------------
     ! Directories with photolysis input files
     !------------------------------------------------------------------------
@@ -3000,6 +3014,8 @@ SUBROUTINE Config_Photolysis( Config, Input_Opt, RC )
        WRITE( 6,90  ) 'PHOTOLYSIS SETTINGS'
        WRITE( 6,95  ) '-------------------'
        WRITE( 6,100 ) 'Turn on photolysis?         : ', Input_Opt%Do_Photolysis
+       WRITE( 6,130 ) 'Number levels with cloud    : ',                      &
+                       Input_Opt%Nlevs_Phot_Cloud
        WRITE( 6,120 ) 'FAST-JX input directory     : ',                      &
                        TRIM( Input_Opt%FAST_JX_DIR )
        WRITE( 6,120 ) 'Cloud-J input directory     : ',                      &
@@ -3031,7 +3047,8 @@ SUBROUTINE Config_Photolysis( Config, Input_Opt, RC )
 105 FORMAT( A, F8.3 )
 110 FORMAT( A, F4.2 )
 120 FORMAT( A, A    )
-
+130 FORMAT( A, I5   )
+
     END SUBROUTINE Config_Photolysis
 !EOC
 !------------------------------------------------------------------------------

diff --git a/Headers/input_opt_mod.F90 b/Headers/input_opt_mod.F90
@@ -120,12 +120,6 @@ MODULE Input_Opt_Mod
      LOGICAL                     :: LBCAE
      REAL(fp)                    :: BCAE_1
      REAL(fp)                    :: BCAE_2
-     ! for nitrate aerosol photolysis (TMS, 23/08/2018)
-     LOGICAL                     :: hvAerNIT
-     REAL(fp)                    :: hvAerNIT_JNIT
-     REAL(fp)                    :: hvAerNIT_JNITs
-     REAL(fp)                    :: JNITChanA
-     REAL(fp)                    :: JNITChanB
 
      !----------------------------------------
      ! EMISSIONS fields
@@ -171,9 +165,6 @@ MODULE Input_Opt_Mod
      REAL(fp)                    :: GAMMA_HO2
      LOGICAL                     :: LACTIVEH2O
      LOGICAL                     :: LINITSPEC
-     LOGICAL                     :: USE_ONLINE_O3
-     LOGICAL                     :: USE_O3_FROM_MET
-     LOGICAL                     :: USE_TOMS_O3
      LOGICAL                     :: USE_AUTOREDUCE
      LOGICAL                     :: AUTOREDUCE_IS_KEEPACTIVE
      LOGICAL                     :: AUTOREDUCE_IS_KEY_THRESHOLD
@@ -192,6 +183,16 @@ MODULE Input_Opt_Mod
      LOGICAL                     :: Do_Photolysis
      CHARACTER(LEN=255)          :: FAST_JX_DIR
      CHARACTER(LEN=255)          :: CloudJ_Dir
+     INTEGER                     :: Nlevs_Phot_Cloud
+     LOGICAL                     :: USE_ONLINE_O3
+     LOGICAL                     :: USE_O3_FROM_MET
+     LOGICAL                     :: USE_TOMS_O3
+     ! for nitrate aerosol photolysis (TMS, 23/08/2018)
+     LOGICAL                     :: hvAerNIT
+     REAL(fp)                    :: hvAerNIT_JNIT
+     REAL(fp)                    :: hvAerNIT_JNITs
+     REAL(fp)                    :: JNITChanA
+     REAL(fp)                    :: JNITChanB
 
      !----------------------------------------
      ! RADIATION MENU fields
@@ -612,11 +613,6 @@ SUBROUTINE Set_Input_Opt( am_I_Root, Input_Opt, RC )
     Input_Opt%P_ICE_SUPERSAT         = 0.0_fp
     Input_Opt%LPSCCHEM               = .FALSE.
     Input_Opt%LSTRATOD               = .FALSE.
-    Input_Opt%hvAerNIT               = .FALSE.
-    Input_Opt%hvAerNIT_JNIT          = 0.0_fp
-    Input_Opt%hvAerNIT_JNITs         = 0.0_fp
-    Input_Opt%JNITChanA              = 0.0_fp
-    Input_Opt%JNITChanB              = 0.0_fp
 
     !----------------------------------------
     ! EMISSIONS MENU fields
@@ -661,9 +657,6 @@ SUBROUTINE Set_Input_Opt( am_I_Root, Input_Opt, RC )
     Input_Opt%GAMMA_HO2              = 0.0_fp
     Input_Opt%LACTIVEH2O             = .FALSE.
     Input_Opt%LINITSPEC              = .FALSE.
-    Input_Opt%USE_ONLINE_O3          = .FALSE.
-    Input_Opt%USE_O3_FROM_MET        = .FALSE.
-    Input_Opt%USE_TOMS_O3            = .FALSE.
 
     Input_Opt%USE_AUTOREDUCE                = .FALSE.
     Input_Opt%AUTOREDUCE_IS_KEY_THRESHOLD   = .TRUE.
@@ -679,6 +672,15 @@ SUBROUTINE Set_Input_Opt( am_I_Root, Input_Opt, RC )
     Input_Opt%Do_Photolysis         = .FALSE.
     Input_Opt%FAST_JX_DIR           = ''
     Input_Opt%CloudJ_Dir            = ''
+    Input_Opt%Nlevs_Phot_Cloud      = 0
+    Input_Opt%USE_ONLINE_O3         = .FALSE.
+    Input_Opt%USE_O3_FROM_MET       = .FALSE.
+    Input_Opt%USE_TOMS_O3           = .FALSE.
+    Input_Opt%hvAerNIT               = .FALSE.
+    Input_Opt%hvAerNIT_JNIT          = 0.0_fp
+    Input_Opt%hvAerNIT_JNITs         = 0.0_fp
+    Input_Opt%JNITChanA              = 0.0_fp
+    Input_Opt%JNITChanB              = 0.0_fp
 
     !----------------------------------------
     ! RADIATION MENU fields (for RRTMG only)

diff --git a/run/CESM/geoschem_config.yml b/run/CESM/geoschem_config.yml
@@ -46,6 +46,7 @@ operations:
 
   photolysis:
     activate: true
+    num_levs_with_cloud: 22
     input_directories:
       fastjx_input_dir: /see/namelist/file
       cloudj_input_dir: /see/namelist/file

diff --git a/run/GCClassic/geoschem_config.yml.templates/geoschem_config.yml.Hg b/run/GCClassic/geoschem_config.yml.templates/geoschem_config.yml.Hg
@@ -65,6 +65,7 @@ operations:
 
   photolysis:
     activate: true
+    num_levs_with_cloud: ${RUNDIR_PHOT_CLD_NLEV}
     input_directories:
       fastjx_input_dir: ${RUNDIR_DATA_ROOT}/CHEM_INPUTS/FAST_JX/v2024-05-Hg/
       cloudj_input_dir: ${RUNDIR_DATA_ROOT}/CHEM_INPUTS/CLOUD_J/v2024-05/

diff --git a/run/GCClassic/geoschem_config.yml.templates/geoschem_config.yml.aerosol b/run/GCClassic/geoschem_config.yml.templates/geoschem_config.yml.aerosol
@@ -65,6 +65,7 @@ operations:
 
   photolysis:
     activate: true
+    num_levs_with_cloud: ${RUNDIR_PHOT_CLD_NLEV}
     input_directories:
       fastjx_input_dir: ${RUNDIR_DATA_ROOT}/CHEM_INPUTS/FAST_JX/v2024-05/
       cloudj_input_dir: ${RUNDIR_DATA_ROOT}/CHEM_INPUTS/CLOUD_J/v2023-05/

diff --git a/run/GCClassic/geoschem_config.yml.templates/geoschem_config.yml.fullchem b/run/GCClassic/geoschem_config.yml.templates/geoschem_config.yml.fullchem
@@ -88,6 +88,7 @@ operations:
 
   photolysis:
     activate: true
+    num_levs_with_cloud: ${RUNDIR_PHOT_CLD_NLEV}
     input_directories:
       fastjx_input_dir: ${RUNDIR_DATA_ROOT}/CHEM_INPUTS/FAST_JX/v2024-05/
       cloudj_input_dir: ${RUNDIR_DATA_ROOT}/CHEM_INPUTS/CLOUD_J/v2023-05/

diff --git a/run/GCHP/geoschem_config.yml.templates/geoschem_config.yml.fullchem b/run/GCHP/geoschem_config.yml.templates/geoschem_config.yml.fullchem
@@ -71,6 +71,7 @@ operations:
 
   photolysis:
     activate: true
+    num_levs_with_cloud: ${RUNDIR_PHOT_CLD_NLEV}
     input_directories:
       fastjx_input_dir: ${RUNDIR_DATA_ROOT}/CHEM_INPUTS/FAST_JX/v2024-05/
       cloudj_input_dir: ${RUNDIR_DATA_ROOT}/CHEM_INPUTS/CLOUD_J/v2023-05/

diff --git a/run/GEOS/geoschem_config.yml b/run/GEOS/geoschem_config.yml
@@ -59,6 +59,7 @@ operations:
 
   photolysis:
     activate: true
+    num_levs_with_cloud: 34
     input_directories:
       fastjx_input_dir: /discover/nobackup/projects/gmao/share/dasilva/fvInput/ExtData/chemistry/GEOSCHEMchem/v0.0.0/CHEM_INPUTS/FAST_JX/v2023-10/
       cloudj_input_dir: /discover/nobackup/projects/gmao/share/dasilva/fvInput/ExtData/chemistry/GEOSCHEMchem/v0.0.0/CHEM_INPUTS/CLOUD_J/v2023-05/

diff --git a/run/WRF/fullchem/geoschem_config.yml b/run/WRF/fullchem/geoschem_config.yml
@@ -67,6 +67,7 @@ operations:
 
   photolysis:
     input_dir: /n/holyscratch01/external_repos/GEOS-CHEM/gcgrid/data/ExtData/CHEM_INPUTS/FAST_JX/v2021-10/
+    num_levs_with_cloud: 20
     overhead_O3:
       use_online_O3_from_model: true 
       use_column_O3_from_met: true

diff --git a/run/shared/settings/geosfp/geosfp.preprocessed_ll.txt b/run/shared/settings/geosfp/geosfp.preprocessed_ll.txt
@@ -22,6 +22,8 @@ RUNDIR_METLIGHTNING_RES='0.25x0.3125'
 RUNDIR_LIGHTNOX_CLIM=false
 RUNDIR_MET_LCLIM='2014-2019'
 
+RUNDIR_PHOT_CLD_NLEV=34
+
 RUNDIR_MET_EXTDATA_PRIMARY_EXPORTS="""
 ${RUNDIR_MET_EXTDATA_PRIMARY_EXPORTS_FOR_ADVECTION}
 

diff --git a/run/shared/settings/geosfp/geosfp.raw_ll.txt b/run/shared/settings/geosfp/geosfp.raw_ll.txt
@@ -20,6 +20,8 @@ RUNDIR_METLIGHTNING_RES='0.25x0.3125'
 RUNDIR_LIGHTNOX_CLIM=false
 RUNDIR_MET_LCLIM='2014-2019'
 
+RUNDIR_PHOT_CLD_NLEV=34
+
 RUNDIR_MET_EXTDATA_PRIMARY_EXPORTS="""
 
 ${RUNDIR_MET_EXTDATA_PRIMARY_EXPORTS_FOR_ADVECTION}

diff --git a/run/shared/settings/geosit/discover/geosit.raw_cs.discover.txt b/run/shared/settings/geosit/discover/geosit.raw_cs.discover.txt
@@ -21,6 +21,8 @@ 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}

diff --git a/run/shared/settings/geosit/discover/geosit.raw_ll.discover.txt b/run/shared/settings/geosit/discover/geosit.raw_ll.discover.txt
@@ -21,6 +21,8 @@ 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}

diff --git a/run/shared/settings/geosit/geosit.preprocessed_ll.txt b/run/shared/settings/geosit/geosit.preprocessed_ll.txt
@@ -20,6 +20,8 @@ RUNDIR_METLIGHTNING_RES='0.5x0.625'
 RUNDIR_LIGHTNOX_CLIM=true
 RUNDIR_MET_LCLIM='1980-2019'
 
+RUNDIR_PHOT_CLD_NLEV=34
+
 RUNDIR_IMPORT_MASS_FLUX_FROM_EXTDATA=.false.
 RUNDIR_USE_TOTAL_AIR_PRESSURE_IN_ADVECTION=0
 

diff --git a/run/shared/settings/geosit/geosit.raw_cs.txt b/run/shared/settings/geosit/geosit.raw_cs.txt
@@ -21,6 +21,8 @@ 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}

diff --git a/run/shared/settings/geosit/geosit.raw_ll.txt b/run/shared/settings/geosit/geosit.raw_ll.txt
@@ -21,6 +21,8 @@ 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}

diff --git a/run/shared/settings/merra2.txt b/run/shared/settings/merra2.txt
@@ -22,6 +22,8 @@ RUNDIR_METLIGHTNING_RES='0.5x0.625'
 RUNDIR_LIGHTNOX_CLIM=false
 RUNDIR_MET_LCLIM='1980-2019'
 
+RUNDIR_PHOT_CLD_NLEV=34
+
 RUNDIR_OFFLINE_EMIS_RES='0.5x0.625'
 RUNDIR_OFFLINE_EMIS_LAT_RES='05'
 

diff --git a/run/shared/settings/modele2.1.txt b/run/shared/settings/modele2.1.txt
@@ -11,3 +11,5 @@ RUNDIR_MET_EXT='nc4'
 RUNDIR_MET_CN_YR=1950
 RUNDIR_MET_PRES_UNIT='Pa '
 RUNDIR_MET_PRES_SCALE='0.01'
+
+RUNDIR_PHOT_CLD_NLEV=28