Merge branch 'develop' into feature/acollow/persistemissionsafter2019

.circleci/config.yml

@@ -1,11 +1,11 @@
 version: 2.1
 
-# Anchors to prevent forgetting to update a version
-baselibs_version: &baselibs_version v7.7.0
-bcs_version: &bcs_version v10.22.3
+# Anchors in case we need to override the defaults from the orb
+#baselibs_version: &baselibs_version v7.25.0
+#bcs_version: &bcs_version v11.5.0
 
 orbs:
-  ci: geos-esm/circleci-tools@1
+  ci: geos-esm/circleci-tools@2
 
 workflows:
   build-test:
@@ -18,8 +18,38 @@ workflows:
           matrix:
             parameters:
               compiler: [gfortran, ifort]
-          baselibs_version: *baselibs_version
+          #baselibs_version: *baselibs_version
           repo: GEOSgcm
           checkout_fixture: true
           mepodevelop: true
-          persist_workspace: false # Needs to be true to run fv3/gcm experiment, costs extra
+          persist_workspace: true # Needs to be true to run fv3/gcm experiment, costs extra
+
+      # Run AMIP GCM (1 hour, no ExtData)
+      - ci/run_gcm:
+          name: run-GCM-on-<< matrix.compiler >>
+          context:
+            - docker-hub-creds
+          matrix:
+            parameters:
+              compiler: [gfortran, ifort]
+          requires:
+            - build-GEOSgcm-on-<< matrix.compiler >>
+          repo: GEOSgcm
+          #baselibs_version: *baselibs_version
+          #bcs_version: *bcs_version
+
+      # Run Coupled GCM (1 hour, no ExtData)
+      - ci/run_gcm:
+          name: run-coupled-GCM-on-<< matrix.compiler >>
+          context:
+            - docker-hub-creds
+          matrix:
+            parameters:
+              compiler: [gfortran, ifort]
+          requires:
+            - build-GEOSgcm-on-<< matrix.compiler >>
+          repo: GEOSgcm
+          #baselibs_version: *baselibs_version
+          #bcs_version: *bcs_version
+          gcm_ocean_type: MOM6
+          change_layout: false

.github/workflows/enforce-labels.yml

@@ -8,22 +8,25 @@ jobs:
   require-label:
     runs-on: ubuntu-latest
     steps:
-      - uses: mheap/github-action-required-labels@v2
+      - uses: mheap/github-action-required-labels@v5
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         with:
           mode: minimum
           count: 1
           labels: "0 diff,0 diff trivial,Non 0-diff,0 diff structural,0-diff trivial,Not 0-diff,0-diff,automatic,0-diff uncoupled"
           add_comment: true
+          message: "This PR is being prevented from merging because you have not added one of our required labels: {{ provided }}. Please add one so that the PR can be merged."
+
   blocking-label:
     runs-on: ubuntu-latest
     steps:
-      - uses: mheap/github-action-required-labels@v2
+      - uses: mheap/github-action-required-labels@v5
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         with:
           mode: exactly
           count: 0
           labels: "Contingent - DNA,Needs Lead Approval,Contingent -- Do Not Approve"
           add_comment: true
+          message: "This PR is being prevented from merging because you have added one of our blocking labels: {{ provided }}. You'll need to remove it before this PR can be merged."

.github/workflows/validate_yaml_files.yml

@@ -1,14 +1,21 @@
 ---
+
+# Based on code from https://github.com/marketplace/actions/yaml-lint
+
 name: Yaml Lint
 
 on:
   pull_request:
       types: [opened, synchronize, reopened, ready_for_review, labeled, unlabeled]
+
+# This validation is equivalent to running on the command line:
+#   yamllint -d relaxed --no-warnings
+# and is controlled by the .yamllint.yml file
 jobs:
   validate-YAML:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - id: yaml-lint
         name: yaml-lint
         uses: ibiqlik/action-yamllint@v3
@@ -17,7 +24,7 @@ jobs:
           format: colored
           config_file: .yamllint.yml
 
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v4
         if: always()
         with:
           name: yamllint-logfile

CARMAchem_GridComp/CARMA_GridComp.F90

@@ -977,7 +977,7 @@ SUBROUTINE CARMA_GridCompRun ( gcCARMA, qa, impChem, expChem, nymd, nhms, &
 !  Fill the internal state with direct gas species from GMI
 !  Expectation is species are in VMR and needed in MMR for CARMA
 !  -----------
-   if(trim(reg%sulfuric_acid_source) == 'full_field' .and. reg%NGAS > 0) then
+   if(reg%sulfuric_acid_source(1:10) == 'full_field' .and. reg%NGAS > 0) then
     do igas = 1, reg%NGAS
      n  = nCARMAbegin + reg%NBIN*reg%NELEM - 1 + igas
      gasname = ESMF_UtilStringUpperCase(reg%gasname(igas))
@@ -1399,7 +1399,7 @@ SUBROUTINE CARMA_GridCompRun ( gcCARMA, qa, impChem, expChem, nymd, nhms, &
 !  Return the updated gas species to GMI from the internal state
 !  Expectation is species are in MMR and needed in VMR for GMI
 !  -----------
-   if(trim(reg%sulfuric_acid_source) == 'full_field' .and. reg%NGAS > 0) then
+   if(reg%sulfuric_acid_source(1:10) == 'full_field' .and. reg%NGAS > 0) then
     do igas = 1, reg%NGAS
      n  = nCARMAbegin + reg%NBIN*reg%NELEM - 1 + igas
      gasname = ESMF_UtilStringUpperCase(reg%gasname(igas))

CARMAchem_GridComp/CARMA_UtilMod.F90

@@ -685,7 +685,7 @@ SUBROUTINE CARMA_Emissions ( gcCARMA, qa, impChem, expChem, nymd, nhms, cdt, &
      do igas = 1, reg%NGAS
       n = n1 + reg%NELEM*reg%NBIN - 1 + igas
       gasname = ESMF_UtilStringUpperCase(trim(reg%gasname(igas)))
-      if(trim(reg%sulfuric_acid_source) == 'tendency' .and. gasname == 'H2SO4') then
+      if(reg%sulfuric_acid_source(1:8) == 'tendency' .and. gasname == 'H2SO4') then
              qa(n)%data3d = qa(n)%data3d + pso4 * dtime
       endif
       if( gasname == 'HNO3') then  ! go to MMR

CARMAchem_GridComp/CARMAchem_GridCompMod.F90

@@ -748,7 +748,7 @@ SUBROUTINE Initialize_ ( gc, import, export, clock, rc )
         end if
 
         ! attach the aerosol optics method
-        call ESMF_MethodAdd(aero, label='aerosol_optics', userRoutine=aerosol_optics, __RC__)
+        call ESMF_MethodAdd(aero, label='run_aerosol_optics', userRoutine=run_aerosol_optics, __RC__)
 
     end if
 
@@ -1730,7 +1730,7 @@ SUBROUTINE final_(ierr)
    END SUBROUTINE final_
 
 
-subroutine aerosol_optics(state, rc)
+subroutine run_aerosol_optics(state, rc)
 
   implicit none
 
@@ -1774,7 +1774,7 @@ subroutine aerosol_optics(state, rc)
   real    :: x
   integer :: i, j, k
 
-  Iam = 'CARMA::aerosol_optics()'
+  Iam = 'CARMA::run_aerosol_optics()'
 
 
 ! Mie Table instance/index
@@ -1930,7 +1930,7 @@ subroutine mie_(mie_table, aerosol, nb, offset, q, rh, ext, ssa, asy, rc)
 
     end subroutine mie_
 
- end subroutine aerosol_optics
+ end subroutine run_aerosol_optics
 
 
 

CARMAchem_GridComp/CMakeLists.txt

@@ -12,7 +12,7 @@ foreach (dir ${src_directories})
   list (APPEND srcs ${tmpsrcs})
 endforeach()
 
-set (dependencies Chem_Shared Chem_Base GMAO_mpeu esmf)
+set (dependencies Chem_Shared Chem_Base GMAO_mpeu ESMF::ESMF)
 esma_add_library (${this} SRCS ${srcs} DEPENDENCIES ${dependencies})
 target_include_directories (${this} PUBLIC $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/CARMA/source/base>)
 

CHANGELOG.md

@@ -7,19 +7,60 @@ 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]
-
 ### Added
 -Connectivity added between GOCART2G and HEMCO for anthropogenic OC, BC, SO2, SO4, and NH3 in GEOS_ChemGridComp.F90. These species are now added in HEMCOgocart2g* files with diurnal and day of week scaling implemented.
 -ExtData2G is used to persist anthropogenic emissions for the year 2019 after the available emissions data set ends.
 ### Removed
 ### Changed
+
+- The file path was changed for anthropogenic CO emissions that are used by achem. Note that the previous version of the emissions have an incorrect seasonal cycle.
+- Update ESMF CMake target to `ESMF::ESMF`
+- Overhauled the Lopez lightning scheme, and made it the default scheme; note that lightning is used by GMI for computing NOx emissions; PCHEM does not use lightning
+
 ### Fixed
 
-## [1.13.1] - 2023-03-02
+- Updated GAAS_Gridcomp_Extdata.yaml in AMIP/ to avoid the model to crash when GAAS is turned on and AMIP emissions chosen.
+
+### Deprecated
+
+
+## [1.14.0] - 2024-06-21
+
+### Added
+
+- Connectivity from GMI to ACHEM (4 fields), requires GMI v1.2.0 or later to run
+- Slight improvement for lightning flash rate calculation (LOPEZ and MOIST schemes). See the option UsePreconCape in ChemEnv.rc . This involves new imports from MOIST: CAPE, BYNCY and INHB. **NOTE** THIS REQUIRES GEOSgcm_GridComp develop branch (as of 12/12/23).
+- Added a flag for 'strict' child timing, intended to reduce the timing bias against child GC's that employ 'gather' calls. Such calls are occasionally necessary, but can cause timers to attribute excessive time to a child, time that is actually the synchronization lag time that would eventually be spent -somewhere- in the program, but which gets attributed to the child with a 'gather' or barrier call. The new flag is for timing tests only.
+
+### Changed
+
+- Update CI to use v2 orb
+
+### Fixed
+
+- Fixed CARMA to fix radiation callback
+- Fixed code in CARMA to properly check whether GMI or GOCART are providing sulfur inputs
+- Fixed CARMA/GOCART2G sulfate production tendency term
+- Fix a bug in GAAS where it gets the VM (global instead of the correct current)
+- Fix an issue in GAAS where the `aod_?` fields were not declared as `MAPL_RestartSkip` in the Registry file.
+
+## [1.13.1] - 2023-04-24
 
 ### Added
 
 - Added CO2 connectivity in GEOS_ChemGridComp for GOCART-GEOS-Chem coupling
+- Added a wrapper routine for the MAPL Solar Zenith Angle call, in Chem_Shared
+- Added connectivity from GOCART2G aerosols to GMI chem
+
+### Removed
+
+- Removed the GMI routines which computed Solar Zenith Angle, in Chem_Shared; but in a later commit, this was added back temporarily, so that older versions of GMI and TR don't complain.
+
+- Removed parallel read of PChem species file. This parallel read was causing issues at NAS at large node count, so now we just do a read-on-root followed by a broadcast
+
+### Fixed
+
+- Fixed a bug that had prevented GMI running with HEMCO
 
 ## [1.13.0] - 2023-03-01
 
@@ -56,7 +97,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Changed
 
 - Instead of importing a set of QQK diagnostic fields for chemical loss of stOX, TR now imports a single field: stOX_loss
-- For OPS configuration: removal of links, change of QFED paths from vNRT/ to v2.5r1-nrt/ 
+- For OPS configuration: removal of links, change of QFED paths from vNRT/ to v2.5r1-nrt/
 - For AMIP configuration: update of QFED from v2.5r1 to v2.6r1 (most recent collection)
 - Moved to GitHub Actions for label enforcement
 - Update CircleCI to use Baselibs 7.7.0
@@ -104,7 +145,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - Updates to emissions from galactic cosmic rays in GMI
 - Minor improvement to Runtime_Registry module.
-- Broke away the GMI contents from Chem_Registry.rc, into a separate file 
+- Broke away the GMI contents from Chem_Registry.rc, into a separate file
 
 ## [1.10.1] - 2022-08-30
 
@@ -160,7 +201,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - Fix YAML typo in `GEOSachem_GridComp/GEOSachem_ExtData.yaml`
 
-## [1.9.4] - 2022-05-31 
+## [1.9.4] - 2022-05-31
 
 ### Fixed
 

CMakeLists.txt

@@ -25,7 +25,7 @@ set (srcs
 esma_add_library (${this}
   SRCS ${srcs}
   SUBCOMPONENTS ${alldirs}
-  DEPENDENCIES MAPL Chem_Shared Chem_Base GOCART_GridComp GOCART2G_GridComp TR GMI StratChem esmf)
+  DEPENDENCIES MAPL Chem_Shared Chem_Base GOCART_GridComp GOCART2G_GridComp TR GMI StratChem ESMF::ESMF)
 
 install(
    FILES GEOS_ChemGridComp.rc ChemEnv_ExtData.rc  ChemEnv.rc ChemEnv_ExtData.yaml

ChemEnv.rc

@@ -1,7 +1,7 @@
 #-----------------------
 # Settings for Lightning
 #-----------------------
-flashSource: MOIST       # MOIST (default), FIT, HEMCO, LOPEZ
+flashSource: LOPEZ       # MOIST, FIT, HEMCO, LOPEZ (default)
 
 # for FIT only:
 ratioGlobalFile: ExtData/g5chem/x/lightning/RatioGlobal.asc
@@ -20,9 +20,11 @@ MOIST_flashFactor_resvec_REPLAY: 2.0       2.0       2.0       1.84      1.84
   FIT_flashFactor_resvec_REPLAY: 1.0       1.0       1.0       1.0       1.0       1.0 
 
 #  originally called 'alpha'
-LOPEZ_flashFactor_resvec_CTM:    37.5      37.5      37.5      37.5      37.5      37.5
-LOPEZ_flashFactor_resvec_FREE:   37.5      37.5      37.5      37.5      37.5      37.5
-LOPEZ_flashFactor_resvec_REPLAY: 37.5      37.5      37.5      37.5      37.5      37.5
+#  10.29.24 Manyin provided c90 and c180, FREE and REPLAY
+#           Assume CTM is close to REPLAY
+LOPEZ_flashFactor_resvec_CTM:    6705.50   6705.50   6705.50   6941.09   6941.09   6941.09
+LOPEZ_flashFactor_resvec_FREE:   5672.30   5672.30   5672.30   6495.07   6495.07   6495.07
+LOPEZ_flashFactor_resvec_REPLAY: 6705.50   6705.50   6705.50   6941.09   6941.09   6941.09
 
 #  originally called 'otdLisScale'
 #  NOTE: testing (Nov2020) indicated c-90 value of 9.48e-3 might be better
@@ -34,3 +36,5 @@ HEMCO_flashFactor_resvec_REPLAY: 0.6       0.355     0.1       2.095e-2  7.024e-
 lightNOampFactor: 1.07
 numberNOperFlash: 1.50e+26
 minDeepCloudTop: 7.0
+
+usePreconCape: TRUE

DNA_GridComp/CMakeLists.txt

@@ -4,7 +4,7 @@ set (srcs
   DNA_GridCompMod.F90
   )
 
-esma_add_library (${this} SRCS ${srcs} DEPENDENCIES MAPL esmf NetCDF::NetCDF_Fortran)
+esma_add_library (${this} SRCS ${srcs} DEPENDENCIES MAPL ESMF::ESMF NetCDF::NetCDF_Fortran)
 target_compile_definitions (${this} PRIVATE MAPL_MODE GEOS5)
 
 set (resource_files

GAAS_GridComp/AMIP/GAAS_GridComp_ExtData.yaml

@@ -1,29 +1,33 @@
 Collections:
-  GAAS_d5124_m2_jan10.aod_a.sfc.%y4%m2%d2_%h2%n2z.nc4:
-    template: /discover/nobackup/projects/gmao/merra2/data/chem/d5124_m2_jan10/Y%y4/M%m2/d5124_m2_jan10.aod_a.sfc.%y4%m2%d2_%h2%n2z.nc4
+  aod_a.sfc.%y4%m2%d2_%h2%n2z.nc4:
+    template: das.aod_a.sfc.%y4%m2%d2_%h2%n2z.nc4
     freq: PT3H
-  GAAS_d5124_m2_jan10.aod_f.sfc.%y4%m2%d2_%h2%n2z.nc4:
-    template: /discover/nobackup/projects/gmao/merra2/data/chem/d5124_m2_jan10/Y%y4/M%m2/d5124_m2_jan10.aod_f.sfc.%y4%m2%d2_%h2%n2z.nc4
+  aod_f.sfc.%y4%m2%d2_%h2%n2z.nc4:
+    template: das.aod_f.sfc.%y4%m2%d2_%h2%n2z.nc4
     freq: PT3H
-  GAAS_d5124_m2_jan10.aod_k.sfc.%y4%m2%d2_%h2%n2z.nc4:
-    template: /discover/nobackup/projects/gmao/merra2/data/chem/d5124_m2_jan10/Y%y4/M%m2/d5124_m2_jan10.aod_k.sfc.%y4%m2%d2_%h2%n2z.nc4
+  aod_k.sfc.%y4%m2%d2_%h2%n2z.nc4:
+    template: das.aod_k.sfc.%y4%m2%d2_%h2%n2z.nc4
     freq: PT3H
 
 Samplings:
   GAAS_sample_0:
-    time_interpolation: False
+    update_offset: PT450S
+    exact: True
 
 Exports:
   aod_a:
-    collection: GAAS_d5124_m2_jan10.aod_a.sfc.%y4%m2%d2_%h2%n2z.nc4
+    collection: aod_a.sfc.%y4%m2%d2_%h2%n2z.nc4
     sample: GAAS_sample_0
     variable: AOD
+    fail_on_missing_file: false
   aod_f:
-    collection: GAAS_d5124_m2_jan10.aod_f.sfc.%y4%m2%d2_%h2%n2z.nc4
+    collection: aod_f.sfc.%y4%m2%d2_%h2%n2z.nc4
     sample: GAAS_sample_0
     variable: AOD
+    fail_on_missing_file: false
   aod_k:
-    collection: GAAS_d5124_m2_jan10.aod_k.sfc.%y4%m2%d2_%h2%n2z.nc4
+    collection: aod_k.sfc.%y4%m2%d2_%h2%n2z.nc4
     sample: GAAS_sample_0
     variable: AOD
+    fail_on_missing_file: false