Bring PR #1992 up to date with the latest dev/no-diff-to-benchmark

This merge brings the dev/no-diff-to-benchmark branch into the branch for PR #1992 (Fix issues in the carbon simulation, branch feature/carbon-sim-fixes). The latest update in the dev/no-diff-to benchmark was the merge of PR #2062 (Updates from GMAO for GEOS, by @lizziel.) Signed-off-by: Bob Yantosca <[email protected]>
geoschem · Jan 9, 2024 · b1bc9ec · b1bc9ec
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diff --git a/.github/ISSUE_TEMPLATE/new-feature-or-discussion.md b/.github/ISSUE_TEMPLATE/new-feature-or-discussion.md
@@ -10,7 +10,7 @@ Institution:
 
 ### Confirm you have reviewed the following documentation
 
-- [ ] [Contributing guidelines](https://geos-chem.readthedocs.io/en/stable/reference/CONTRIBUTING.html)
+- [ ] [Contributing guidelines](https://geos-chem.readthedocs.io/en/stable/help-and-reference/CONTRIBUTING.html)
 
 ### New GEOS-Chem feature or discussion
 

diff --git a/.github/ISSUE_TEMPLATE/question-issue.md b/.github/ISSUE_TEMPLATE/question-issue.md
@@ -10,7 +10,7 @@ Institution:
 
 ### Confirm you have reviewed the following documentation
 
-- [ ] [Support guidelines](https://geos-chem.readthedocs.io/en/stable/reference/SUPPORT.html)
+- [ ] [Support guidelines](https://geos-chem.readthedocs.io/en/stable/help-and-reference/SUPPORT.html)
 - [ ] [User manuals](https://geos-chem.readthedocs.io/en/stable/geos-chem-shared-docs/supplemental-guides/related-docs.html)
 - [ ] [Debugging GEOS-Chem and HEMCO errors](https://geos-chem.readthedocs.io/en/stable/geos-chem-shared-docs/supplemental-guides/debug-guide.html)
 - [ ] [Current and past Github issues](https://github.com/geoschem/geos-chem/issues)

diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -5,7 +5,7 @@ Institution:
 
 ### Confirm you have reviewed the following documentation
 
-- [ ] [Contributing guidelines](https://geos-chem.readthedocs.io/en/stable/reference/CONTRIBUTING.html)
+- [ ] [Contributing guidelines](https://geos-chem.readthedocs.io/en/stable/help-and-reference/CONTRIBUTING.html)
 
 ### Describe the update
 

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,10 +4,48 @@ 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]
+## [Unreleased] - TBD
+### Changed
+- Now read the Hg restart file from `ExtData/GEOSCHEM_RESTARTS/v2023-12`
+- Increse requested time limits in GCHP integration tests (compile 2h30m, run 5h)
+
 ### Fixed
+- Added missing units in comments of `KPP/fullchem/commonIncludeVars.H` 
+- Use run directory (not absolute path) to determine the executable file name in integration & parallel tests.
 - Fix issues that prevented single-species carbon simulations from running
 
+### Removed
+- Reduced timers saved out to essential list used for benchmarking model performance
+
+### Added
+- Added two new diagnostics to track number of negative concentrations after first and last KPP integration
+- Added capability of running GEOS-Chem transport tracer simulation within the GEOS model
+
+## [14.2.3] - 2023-12-01
+### Added
+- GEOS-Chem Classic rundir script `run/GCClassic/setupForRestarts.sh`
+
+### Changed
+- Added the `-n` aka `--no-bootstrap` option to integration tests to disable bootstrapping missing species in restart files
+- Use integer parameters for species units instead of strings (for computational efficiency)
+- Update error message for missing surface CH4 emissions with instructions on how to resolve the problem
+- Change GCHP grid resolution threshold for lowering timesteps from C180 inclusive to C180 exclusive
+- Read GEOS-Chem Classic restart file paths from the relevant `download_data.yml` file
+
+### Fixed
+- Prevent `POAEMISS` from being assigned a value if not allocated (in `carbon_mod.F90`)
+- Changed incorrect comment about static H2O option in `GeosCore/input_mod.F90`
+- Fixed typos (`GCClassic` -> `GCHP`) written to GCHP integration test log files
+- Add fix to properly read GHGI v2 express extension emissions in CH4 and carbon simulations
+- Move OH perturbation scale factor to outside EMISSIONS logical bracket in HEMCO_Config.rc files for CH4 and carbon simulations
+
+### Removed
+- Remove definition of METDIR from primary HEMCO_Config.rc files to ensure use of the definition in the HEMCO_Config.rc.*_metfields files
+
+## [14.2.2] - 2023-10-23
+### Changed
+- Updated sample restart files for fullchem and TransportTracers simulations to files saved out from the 14.2.0 1-year benchmarks
+
 ## [14.2.1] - 2023-10-10
 ### Added
 - Script `test/difference/diffTest.sh`, checks 2 different integration tests for differences
@@ -61,7 +99,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 ### Removed
 - Remove references to the obsolete tagged Hg simulation
 
-## [Unreleased 14.2.0] - TBD
+## [14.2.0] - 2023-10-05
 ### Added
 - Added a printout of GEOS-Chem species and indices
 - Added `NcdfUtil/README.md` file directing users to look for netCDF utility scripts at https://github.com/geoschem/netcdf-scripts
@@ -148,6 +186,14 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 ### Fixed
 - Fixed entries for CH4 emissions in `HEMCO_Config.rc.carbon`
 
+## [14.1.2] - 2023-10-20
+### Added
+- CESM-only update: Added option for correctConvUTLS for correcting buildup of soluble tracers in the UT/LS to match CAM-chem behavior
+
+### Changed
+- CESM-only update: extend existing KppError, KppStop to CESM for model stability
+- CESM-only update: Removed mpi_bcast in ucx_mod NOXCOEFF_INIT to be handled at coupler level to support spectral-element dynamical core
+
 ## [14.1.1] - 2023-03-03
 ### Added
   - New integration test functions in `test/GCClassic/integration` and `test/GCHP/integration`

diff --git a/GeosCore/aero_drydep.F90 b/GeosCore/aero_drydep.F90
@@ -39,6 +39,7 @@ SUBROUTINE AERO_DRYDEP( Input_Opt,  State_Chm, State_Diag, &
     USE CMN_DIAG_MOD
     USE DIAG_MOD,           ONLY : AD44
 #endif
+    USE UnitConv_Mod
 
     IMPLICIT NONE
 !
@@ -119,8 +120,8 @@ SUBROUTINE AERO_DRYDEP( Input_Opt,  State_Chm, State_Diag, &
     nDryDep   = State_Chm%nDryDep
 
     ! Check that species units are in [kg] (ewl, 8/13/15)
-    IF ( TRIM( State_Chm%Spc_Units ) /= 'kg' ) THEN
-       MSG = 'Incorrect species units: ' // TRIM(State_Chm%Spc_Units)
+    IF ( State_Chm%Spc_Units /= KG_SPECIES ) THEN
+       MSG = 'Incorrect species units: ' // TRIM(UNIT_STR(State_Chm%Spc_Units))
        LOC = 'Routine AERO_DRYDEP in aero_drydep.F'
        CALL GC_Error( MSG, RC, LOC )
     ENDIF
@@ -530,9 +531,9 @@ SUBROUTINE AERO_DRYDEP( Input_Opt,  State_Chm, State_Diag, &
     DepFreq  => NULL()
 
     ! Check that species units are still in [kg] (ewl, 8/13/15)
-    IF ( TRIM( State_Chm%Spc_Units ) /= 'kg' ) THEN
+    IF ( State_Chm%Spc_Units /= KG_SPECIES ) THEN
        MSG = 'Incorrect species units at end of routine: ' &
-             // TRIM(State_Chm%Spc_Units)
+             // TRIM(UNIT_STR(State_Chm%Spc_Units))
        LOC = 'Routine AERO_DRYDEP in aero_drydep.F'
        CALL GC_Error( MSG, RC, LOC )
     ENDIF

diff --git a/GeosCore/aerosol_mod.F90 b/GeosCore/aerosol_mod.F90
@@ -185,7 +185,7 @@ SUBROUTINE AEROSOL_CONC( Input_Opt,  State_Chm, State_Diag, &
     USE State_Diag_Mod,    ONLY : DgnState
     USE State_Grid_Mod,    ONLY : GrdState
     USE State_Met_Mod,     ONLY : MetState
-    USE UnitConv_Mod,      ONLY : Convert_Spc_Units
+    USE UnitConv_Mod
     USE TIME_MOD,          ONLY : GET_MONTH
 #ifdef TOMAS
     USE TOMAS_MOD,        ONLY : IBINS
@@ -251,7 +251,8 @@ SUBROUTINE AEROSOL_CONC( Input_Opt,  State_Chm, State_Diag, &
     REAL(fp),      POINTER   :: KG_STRAT_AER(:,:,:,:)
 
     ! Other variables
-    CHARACTER(LEN=63)   :: OrigUnit
+    INTEGER             :: OrigUnit
+
 
     ! For spatially and seasonally varying OM/OC
     CHARACTER(LEN=255)  :: FIELDNAME
@@ -303,8 +304,14 @@ SUBROUTINE AEROSOL_CONC( Input_Opt,  State_Chm, State_Diag, &
     REAA => State_Chm%Phot%REAA
 
     ! Convert species to [kg] for this routine
-    CALL Convert_Spc_Units( Input_Opt, State_Chm, State_Grid, State_Met, &
-                            'kg', RC, OrigUnit=OrigUnit )
+    CALL Convert_Spc_Units(                                                  &
+         Input_Opt  = Input_Opt,                                             &
+         State_Chm  = State_Chm,                                             &
+         State_Grid = State_Grid,                                            &
+         State_Met  = State_Met,                                             &
+         outUnit    = KG_SPECIES,                                            &
+         origUnit   = origUnit,                                              &
+         RC         = RC                                                    )
 
     ! Trap potential errors
     IF ( RC /= GC_SUCCESS ) THEN
@@ -1011,8 +1018,14 @@ SUBROUTINE AEROSOL_CONC( Input_Opt,  State_Chm, State_Diag, &
     !$OMP END PARALLEL DO
 
     ! Convert species back to original unit
-    CALL Convert_Spc_Units( Input_Opt, State_Chm, State_Grid, State_Met, &
-                            OrigUnit, RC )
+    CALL Convert_Spc_Units(                                                  &
+         Input_Opt  = Input_Opt,                                             &
+         State_Chm  = State_Chm,                                             &
+         State_Grid = State_Grid,                                            &
+         State_Met  = State_Met,                                             &
+         outUnit    = origUnit,                                              &
+         RC         = RC                                                    )
+
     IF ( RC /= GC_SUCCESS ) THEN
        CALL GC_Error('Unit conversion error', RC, &
                      'End of AEROSOL_CONC in aerosol_mod.F90')
@@ -2643,7 +2656,7 @@ SUBROUTINE Set_AerMass_Diagnostic( Input_Opt,  State_Chm, State_Diag, &
     USE State_Grid_Mod, ONLY : GrdState
     USE State_Met_Mod,  ONLY : MetState
     USE PhysConstants,  ONLY : MwCarb
-    USE UnitConv_Mod,   ONLY : Convert_Spc_Units
+    USE UnitConv_Mod
 !
 ! !INPUT PARAMETERS:
 !
@@ -2679,7 +2692,7 @@ SUBROUTINE Set_AerMass_Diagnostic( Input_Opt,  State_Chm, State_Diag, &
     INTEGER                  :: I, J, L
 
     ! Strings
-    CHARACTER(LEN=63)        :: OrigUnit
+    INTEGER                  :: origUnit
     CHARACTER(LEN=255)       :: ThisLoc
     CHARACTER(LEN=512)       :: ErrMsg
 
@@ -2711,13 +2724,14 @@ SUBROUTINE Set_AerMass_Diagnostic( Input_Opt,  State_Chm, State_Diag, &
 
     ! Initialize
     RC       = GC_SUCCESS
-    ErrMsg   = ''
-    ThisLoc  = ' -> at Set_AerMass_Diagnostic (in module GeosCore/aerosol_mod.F90)'
+    errMsg   = ''
+    thisLoc  = &
+     ' -> at Set_AerMass_Diagnostic (in module GeosCore/aerosol_mod.F90)'
 
     ! Check that species units are kg/kg dry air
-    IF ( TRIM( State_Chm%Spc_Units ) /= 'kg/kg dry' ) THEN
-       CALL GC_Error( 'Incorrect species units: ' // &
-                      State_Chm%Spc_Units, RC, ThisLoc )
+    IF ( State_Chm%Spc_Units /= KG_SPECIES_PER_KG_DRY_AIR ) THEN
+       errMsg = 'Incorrect species units: ' // UNIT_STR( State_Chm%Spc_Units )
+       CALL GC_Error( errMsg, RC, thisLoc )
        RETURN
     ENDIF
 

diff --git a/GeosCore/airs_ch4_mod.F90 b/GeosCore/airs_ch4_mod.F90
@@ -370,7 +370,7 @@ SUBROUTINE CALC_AIRS_CH4_FORCE( Input_Opt, State_Chm, State_Grid, &
     USE State_Chm_Mod,      ONLY : ChmState, Ind_
     USE State_Grid_Mod,     ONLY : GrdState
     USE State_Met_Mod,      ONLY : MetState
-    USE UnitConv_Mod,       ONLY : Convert_Spc_Units
+    USE UnitConv_Mod
 !
 ! !INPUT PARAMETERS:
 !
@@ -429,7 +429,7 @@ SUBROUTINE CALC_AIRS_CH4_FORCE( Input_Opt, State_Chm, State_Grid, &
     INTEGER            :: IOS
     INTEGER, SAVE      :: TotalObs = 0
     CHARACTER(LEN=255) :: FILENAME
-    CHARACTER(LEN=63)  :: OrigUnit
+    INTEGER            :: origUnit
     CHARACTER(LEN=255) :: ThisLoc
     CHARACTER(LEN=512) :: ErrMsg
     INTEGER            :: RC
@@ -517,8 +517,15 @@ SUBROUTINE CALC_AIRS_CH4_FORCE( Input_Opt, State_Chm, State_Grid, &
     print*, ' found # AIRS observations: ', NOBS
 
     ! Convert species units to [v/v] (mps, 6/12/2020)
-    CALL Convert_Spc_Units( Input_Opt, State_Chm, State_Grid, State_Met, &
-                            'v/v dry', RC,        OrigUnit=OrigUnit )
+    CALL Convert_Spc_Units(                                                  &
+         Input_Opt  = Input_Opt,                                             &
+         State_Chm  = State_Chm,                                             &
+         State_Grid = State_Grid,                                            &
+         State_Met  = State_Met,                                             &
+         outUnit    = MOLES_SPECIES_PER_MOLES_DRY_AIR,                       &
+         origUnit   = origUnit,                                              &
+         RC         = RC                                                    )
+
     IF ( RC /= GC_SUCCESS ) THEN
        ErrMsg = 'Unit conversion error (kg/kg dry -> v/v dry)'
        CALL GC_Error( ErrMsg, RC, ThisLoc )
@@ -687,8 +694,15 @@ SUBROUTINE CALC_AIRS_CH4_FORCE( Input_Opt, State_Chm, State_Grid, &
     !!$OMP END PARALLEL DO
 
     ! Convert species units back to original unit (mps, 6/12/2020)
-    CALL Convert_Spc_Units( Input_Opt, State_Chm, State_Grid, State_Met, &
-                            OrigUnit,  RC ) 
+    CALL Convert_Spc_Units(                                                  &
+         Input_Opt  = Input_Opt,                                             &
+         State_Chm  = State_Chm,                                             &
+         State_Grid = State_Grid,                                            &
+         State_Met  = State_Met,                                             &
+         outUnit    = origUnit,                                              &
+         RC         = RC                                                    )
+
+    ! Trap errors
     IF ( RC /= GC_SUCCESS ) THEN
        ErrMsg = 'Unit conversion error'
        CALL GC_Error( ErrMsg, RC, ThisLoc )

diff --git a/GeosCore/calc_met_mod.F90 b/GeosCore/calc_met_mod.F90
@@ -158,6 +158,7 @@ SUBROUTINE AIRQNT( Input_Opt, State_Chm, State_Grid, State_Met, &
     USE Time_Mod,       ONLY : Get_LocalTime
     USE Time_Mod,       ONLY : Get_LocalTime_In_Sec
     USE Time_Mod,       ONLY : Get_Ts_Dyn
+    USE UnitConv_Mod
 !
 ! !INPUT PARAMETERS:
 !
@@ -673,8 +674,8 @@ SUBROUTINE AIRQNT( Input_Opt, State_Chm, State_Grid, State_Met, &
 
        ! The concentration update formula works only for dry mixing ratios
        ! (kg/kg or v/v) so check if units are correct
-       IF ( State_Chm%Spc_units == 'kg/kg dry' .or. &
-            State_Chm%Spc_units == 'v/v dry' ) THEN
+       IF ( State_Chm%Spc_Units == KG_SPECIES_PER_KG_DRY_AIR        .or.     &
+            State_Chm%Spc_Units == MOLES_SPECIES_PER_MOLES_DRY_AIR ) THEN
 
           !$OMP PARALLEL DO       &
           !$OMP DEFAULT( SHARED ) &
@@ -694,7 +695,8 @@ SUBROUTINE AIRQNT( Input_Opt, State_Chm, State_Grid, State_Met, &
           !$OMP END PARALLEL DO
 
        ELSE
-          ErrMsg = 'Incorrect species units: ' // TRIM( State_Chm%Spc_Units )
+          ErrMsg = 'Incorrect species units: '                            // & 
+                    TRIM( UNIT_STR( State_Chm%Spc_Units ) )
           CALL GC_Error( ErrMsg, RC, ThisLoc )
           RETURN
        ENDIF