Merge pull request #12 from GEOS-ESM/develop

Preparing for GMI release v1.2.0

.circleci/config.yml

@@ -1,8 +1,8 @@
 version: 2.1
 
-# Anchors to prevent forgetting to update a version
-baselibs_version: &baselibs_version v7.7.0
-bcs_version: &bcs_version v10.23.0
+# Anchors in case we need to override the defaults from the orb
+#baselibs_version: &baselibs_version v7.14.0
+#bcs_version: &bcs_version v11.1.0
 
 orbs:
   ci: geos-esm/circleci-tools@1
@@ -18,7 +18,7 @@ workflows:
           matrix:
             parameters:
               compiler: [gfortran, ifort]
-          baselibs_version: *baselibs_version
+          #baselibs_version: *baselibs_version
           repo: GEOSgcm
           checkout_fixture: true
           mepodevelop: true

CHANGELOG.md

@@ -6,16 +6,36 @@ 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]
-
+### Fixed
 ### Added
-
 ### Changed
+### Removed
+### Deprecated
+
+
+## [1.2.0] - 2023-12-07
 
 ### Fixed
 
-### Removed
+- QQJK diag calc had bug, used time(t+dt) constituents ibstead of time(t) fields, fixed on 2023Jul19
+- Fixed bug in Emissions and Deposition where SZA degrees was used instead of cosine(SZA)
+- Fixed units for degassing volcano point emissions
+- Improved handling of phot_opt cases; allows for phot_opt == 0 again
+- Improved handling of sad_opt cases; allows for sad_opt == 0 again
 
-### Deprecated
+### Added
+
+- Capability for AERO_PROVIDER=GOCART2G data-driven (GOCART.data)
+- Export OCS_JRATE for use by ACHEM
+
+### Changed
+
+- Update CI to use Baselibs default from the CircleCI orb
+- Changed a few SAD reactions to use JPL 2019 approach
+- ExtData now uses Benchmark G configuration
+- Emissions including 2D, 3D and point source (volcano) now are done as in Benchmark G
+- Isoprene scaling changed from 1 to 0.7
+- Boundary condition file now includes HFCs, and no longer includes extra Br (when HFC mech is chosen)
 
 
 ## [1.1.0] - 2023-04-24

GMI_GridComp/GmiChem_GridCompClassMod.F90

@@ -120,6 +120,10 @@ MODULE  GmiChem_GCCMod
    REAL(KIND=DBL), allocatable                 :: rmult(:)  ! vector of multipliers
    CHARACTER(LEN=RXN_LONGNAME_LENGTH), pointer :: rdesc(:)  ! vector of reaction long  names
 
+! for exporting OCS_JRATE
+! -----------------------
+   CHARACTER (LEN=20) :: ocs_jrate_name
+
 ! Extra diagnostics
 ! -----------------
    LOGICAL :: verbose
@@ -325,6 +329,10 @@ SUBROUTINE GmiChemistry_GridCompInitialize( self, bgg, bxx, impChem, expChem, ny
      &           label="do_grav_set:", default=.false., rc=STATUS)
       VERIFY_(STATUS)
 
+      call ESMF_ConfigGetAttribute(gmiConfig, value=self%ocs_jrate_name, &
+     &           label="OCS_JRATE:", default='UNDEFINED_OCS_JRATE', rc=STATUS)
+      VERIFY_(STATUS)
+
       !------------------------------
       ! Emission related variables
       !------------------------------
@@ -722,7 +730,7 @@ SUBROUTINE GmiChemistry_GridCompRun ( self, bgg, bxx, impChem, expChem, nymd, nh
 
 !  Exports not part of internal state
 !  ----------------------------------
-   REAL, POINTER, DIMENSION(:,:,:) :: O3ppmv, O3, stOX_loss
+   REAL, POINTER, DIMENSION(:,:,:) :: O3ppmv, O3, stOX_loss, OCS_jrate
 
 !  Exports for reactions diagnostics
 !  ---------------------------------
@@ -1090,6 +1098,23 @@ SUBROUTINE FillExports(rc)
    IF(ASSOCIATED(O3)) &
         O3(i1:i2,j1:j2,1:km) = bgg%qa(ic)%data3d(i1:i2,j1:j2,1:km)*(MAPL_O3MW/MAPL_AIRMW)
 
+   IF(ASSOCIATED(OCS_jrate)) THEN
+     ! Assume name is QJnnn
+     READ( self%ocs_jrate_name(3:5),*,IOSTAT=rc) rxn_index
+     _ASSERT(rc==0, TRIM(Iam)//': trouble extracting index from '//TRIM(self%ocs_jrate_name))
+
+!    IF(MAPL_AM_I_ROOT( ))PRINT *,TRIM(IAm),': DEFINE OCS_JRATE as '//TRIM(self%ocs_jrate_name)//' index ',rxn_index
+
+     SELECT CASE (self%ocs_jrate_name(1:2))
+
+       CASE("QJ")
+         OCS_jrate(i1:i2,j1:j2,1:km) = gmiQJ(rxn_index)%pArray3D(i1:i2,j1:j2,km:1:-1)
+       CASE DEFAULT
+         _ASSERT(.FALSE., TRIM(Iam)//': reaction must be QJ : '//TRIM(self%ocs_jrate_name))
+
+     END SELECT
+   END IF
+
 ! --------------------------------------------------------------------
 ! Reaction rate constants (q) and rates (qq)
 ! --------------------------------------------------------------------
@@ -1340,6 +1365,8 @@ SUBROUTINE FindPointers(rc)
    VERIFY_(STATUS)
    CALL MAPL_GetPointer(expChem, stOX_loss,  'stOX_loss', RC=STATUS)
    VERIFY_(STATUS)
+   CALL MAPL_GetPointer(expChem, OCS_jrate,  'OCS_JRATE', RC=STATUS)
+   VERIFY_(STATUS)
 
 #include "Reactions_GetPointer___.h"
 

GMI_GridComp/GmiChemistry/GmiUpdateChemistry_mod.F90

@@ -55,7 +55,6 @@ subroutine updateChemistry ( savedVars, rootProc, do_ftiming,            &
 !
       implicit none
 
-#     include "gmi_sad_constants.h"
 #     include "setkin_par.h"
 #     include "gmi_AerDust_const.h"
 !
@@ -119,6 +118,7 @@ subroutine updateChemistry ( savedVars, rootProc, do_ftiming,            &
       integer :: ix
       integer :: num_loops
       real*8  :: chemintv
+      type (t_GmiArrayBundle) :: tm1Conc(num_species)
 !
 ! !REVISION HISTORY:
 !  Initial code.
@@ -135,6 +135,14 @@ subroutine updateChemistry ( savedVars, rootProc, do_ftiming,            &
       else
          num_loops = 1
       end if
+!
+!... save initial concentration for calc of qqj/qqk diags
+      if (pr_qqjk .and. .not. do_qqjk_inchem) then
+        do ix = 1, num_species
+          allocate ( tm1Conc(ix)%pArray3D (i1:i2, ju1:j2, k1:k2) )
+          tm1Conc(ix)%pArray3D(:,:,:) = concentration(ix)%pArray3D(:,:,:)
+        enddo
+      end if
 
       do ix = 1, num_loops
          call Update_Smv2chem (savedVars, chemintv, surfEmissForChem,            &
@@ -149,10 +157,13 @@ subroutine updateChemistry ( savedVars, rootProc, do_ftiming,            &
       end do
 
       if (pr_qqjk .and. .not. do_qqjk_inchem) then
-         call Accum_Qqjk (do_qqjk_reset, imgas_num, concentration,  &
+        call Accum_Qqjk (do_qqjk_reset, imgas_num, tm1Conc,  &
                    qjgmi, qkgmi,  qqjgmi, qqkgmi, num_molefrac,     &
                    num_species, num_qks, num_qjs, num_qjo,          &
                    pr_diag, loc_proc, ilong, i1, i2, ju1, j2, k1, k2)
+        do ix = 1, num_species
+          deallocate ( tm1Conc(ix)%pArray3D )
+        enddo
       end if
 
       return

GMI_GridComp/GmiChemistry/StratTrop_HFC_S/GMI_GridComp.rc

@@ -140,13 +140,22 @@ MEK_biom
 CO_biom
 NO_biom
 NO_air
+ALD2_biof
 ALK4_fosf
+ALK4_biof
 C2H6_fosf
+C2H6_biof
 PRPE_fosf
+PRPE_biof
 C3H8_fosf
+C3H8_biof
+CH2O_biof
 MEK_fosf
+MEK_biof
 CO_fosf
+CO_biof
 NO_fosf
+NO_biof
 SO2_FIRES-FLUX
 SO2_NONENERGY-FLUX
 SO2_ENERGY-FLUX
@@ -176,32 +185,51 @@ emissionSpeciesLayers::
 1
 1
 1
+1
+1
+1
+1
+1
+1
+1
+1
+1
 72
 ::
 
 emissionPointFilenames::
-SO2:volcano:/discover/nobackup/projects/gmao/share/dao_ops/fvInput_nc3/PIESA/sfc/volcanic_v7/so2_volcanic_emissions_Carns.%y4%m2%d2.rc
+SO2:volcano:ExtData/chemistry/CARN/v202106/sfc/so2_volcanic_emissions_Carns.%y4%m2%d2.rc
 ::
-#SO2:volcano:/discover/nobackup/projects/gmao/share/dao_ops/fvInput_nc3/PIESA/sfc/volcanic_v7/so2_volcanic_effusive.v2.rc 
+# NOTE: Units for the volcano point source files: kg(S)/s
+#       Units that GMI wants                    : kg(SO2)/s
+#       GMI does the conversion in Refresh_Daily within the Emission section
+# from GOCART2G SU (AMIP):
+#   ExtData/chemistry/CARN/v202106/sfc/so2_volcanic_emissions_Carns.%y4%m2%d2.rc
+# from GOCART2G SU (OPS):
+#   ExtData/chemistry/CARN/v202106/sfc/so2_volcanic_emissions_CARN_v202106.degassing_only.rc
+# includes eruptions:
+#   /discover/nobackup/projects/gmao/share/dao_ops/fvInput_nc3/PIESA/sfc/volcanic_v7/so2_volcanic_emissions_Carns.%y4%m2%d2.rc
+# does not include eruptions:
+#   /discover/nobackup/projects/gmao/share/dao_ops/fvInput_nc3/PIESA/sfc/volcanic_v7/so2_volcanic_effusive.v2.rc 
 
 # Ship Emissions requires SHIP_NO in ExtData:
 do_ShipEmission: T
 doMEGANemission: T
 doMEGANviaHEMCO: F
 
 isop_scale::
-1.0d0
-1.0d0
-1.0d0
-1.0d0
-1.0d0
-1.0d0
-1.0d0
-1.0d0
-1.0d0
-1.0d0
-1.0d0
-1.0d0
+0.7d0
+0.7d0
+0.7d0
+0.7d0
+0.7d0
+0.7d0
+0.7d0
+0.7d0
+0.7d0
+0.7d0
+0.7d0
+0.7d0
 ::
 
 soil_infile_name:      ExtData/g5chem/x/GMI_SoilType.asc
@@ -262,7 +290,11 @@ forc_bc_kmax: 2
 #forc_bc_infile_name: /discover/nobackup/ldoman/fvInput/RCP6.0_5BrWMO2014_ch4latvar_1950_2100.asc
 #forc_bc_infile_name:              ExtData/g5chem/x/GMI/RCP6.0_5BrWMO2014_ch4latvar_1950_2100.asc
 #forc_bc_infile_name:              ExtData/g5chem/x/GMI/RCP6.0_5BrWMO2018_ch4latvar_1950_2100.asc
-forc_bc_infile_name:               ExtData/g5chem/x/GMI/ccmiRefD1_GMIbc_1950_2018.asc
+#forc_bc_infile_name:              ExtData/g5chem/x/GMI/ccmiRefD1_GMIbc_1950_2018.asc
+#forc_bc_infile_name:  /discover/nobackup/projects/gmao/ccmdev/mmanyin/bench/bench_10-26-0_gmi_free_c360_72lev/INPUT/BC/ccmiRefD1_GMIbc_plusHFC_1950_2018.asc
+forc_bc_infile_name:  /discover/nobackup/projects/gmao/ccmdev/mmanyin/bench/GOLF/INPUT/BC/ccmiRefD1_GMIbc_plusHFC_no5Br_1950_2018.asc
+
+#alternative /discover/nobackup/projects/gmi/gmidata2/users/steenrod/input/source_gas/RCP6.0_WMO2018_QingHFCs_ch4latvarGMDscl_1950_2022Hindcast.asc
 
 forcedBcSpeciesNames:: 
 CFC11
@@ -283,8 +315,19 @@ CH3Br
 CH3Cl
 CH4
 N2O
+HFC23
+HFC32
+HFC125
+HFC134A
+HFC143A
+HFC152A
+xxx
+xxx
 ::
 
+# The xxx entries above are for SF6 and CO2
+
+
 #     ----------------------------------------------------
 #     sad_opt
 #       0:  do not allocate or process SAD array
@@ -371,8 +414,8 @@ do_ozone_inFastJX: F
 
 ## For FastJX 6.5 & JPL10
  fastj_opt: 4
-# cross_section_file: ExtData/g5chem/x/photolysis/FastJX_6.5/xsec_jx65_jpl10update2_JNOx1_0.dat
  cross_section_file: ExtData/g5chem/x/photolysis/FastJX_6.5/xsec_jx65wSO4_jpl10update2_JNOx1_0.dat
+# cross_section_file: ExtData/g5chem/x/photolysis/FastJX_6.5/xsec_jx65_jpl10update2_JNOx1_0.dat
 # rate_file not needed for FastJX6.5; new approach only differs by roundoff
 # rate_file: ExtData/g5chem/x/photolysis/FastJX/ratec_124spc_jx_gmiv2.dat
 # rate_file: ExtData/g5chem/x/photolysis/FastJX/ratec_119spc_jx_gmiv3.dat
@@ -414,7 +457,7 @@ FeedBack_QV: T
 NoPSCZone: 45
 PSC_Max_P_hPa: 175
 # Upper limit for HNO3COND [integer, ppbv]
-Condensed_HNO3_limit: 25
+Condensed_HNO3_limit: 75
 # Upper limit for HCl [real, ppbv]
 HCl_limit: 5.0
 
@@ -447,3 +490,5 @@ stOX_loss_reactions::
   QQK324  1.0   'NO2 =  0.50 HNO2 +  0.50 HNO3'
   QQK331  1.0   'O3 + SO2 = H2SO4'
 ::
+
+OCS_JRATE: QJ075

GMI_GridComp/GmiChemistry/StratTrop_HFC_S/GMI_Registry.rc

@@ -266,6 +266,7 @@
   ICESAD  	    | cm+2 cm-3      | xyz | C |    |	|   |	  | ice_surface_area_density
   LBSSAD  	    | cm+2 cm-3      | xyz | C |    |	|   |	  | LBS_surface_area_density
   AIRMASS           | kg m-2         | xyz | C |    |   |   |     | mass_of_air_in_layer
+  OCS_JRATE         | s-1            | xyz | C |    |   |   |     | Jrate_for_OCS    
 # ------------------|----------------|-----|---|----|---|---|-----|---------------------------------
 </ExportSpec>