Merge GEOS-Chem `develop` into `main` by joewallwork · Pull Request #17 · fetch4/geos-chem

joewallwork · 2025-03-24T11:25:49Z

This PR updates the main branch of the fetch4:geos-chem repository with the code changes from the project.

The changes include upgrading to a more recent version of HEMCO, accounting for MODEL_GISS preprocessor flags, and a bugfix for a case where pressure_mod arrays may be allocated twice.

…ISS-GC. The goal is to try to get GISS-GC to run, so we can go back to before this commit, and imeplement a version that does not break GCClassic. Note, the "GISS_MODEL" mostly robust, it's just edits to where MODEL_CLASSIC lines that are wrong.

Fix typo for MassFlux_Entry

CHANGELOG.md - Added note about fixing typo in setCommonRunSettings.sh Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

@ltmurray

This merge brings PR geoschem#2363 (Update setCommonRunSettings.sh.template, by @ltmurray) into the GEOS-Chem "no-diff-to-benchmark" development stream. This PR fixes a typo that caused GCHP simulations to always think that they were using mass fluxes, regardless of the actual requested met field setting. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

…loud-j Updates include: - Add new Input_Opt setting Nlevs_Phot_Cloud - Set Input_Opt%Nlevs_Phot_Cloud from new setting in geoschem_config.yml photolysis menu - Move a few existing settings in input_opt_mod.F90 to photolysis menu since that is now where they are stored in geoschem_config.yml - Update all geoschem_config.yml templates. All use 34 as number of levels with clouds except CESM which uses 22. Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

@lizziel

This merge brings PR geoschem#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 <yantosca@seas.harvard.edu>

…core

This update goes an update to Cloud-J. Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

@lizziel

This merge brings PR geoschem#2353 (Cloud-J error handling, by @lizziel) into the GEOS-Chem "no-diff-to-benchmark" development stream. This PR implements robust error handling for Cloud-J (i.e. error code passed all the way to the main program, for graceful shutdown). NOTE: Relies on Cloud-J PR geoschem#19, Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

History/history_netcdf_mod.F90 - Moved the zeroing of State_Diag%SatDiagnCount to routine History_Write in history_mod.F90 - Also now test if the container name is either SatDiagn or SatDiagnEdge only once at the top of History_Netcdf_Write. History/history_mod.F90 - Reset State_Diag%SatDiagnCount outside of the loop over containers, after History_Netcdf_Write has been called. This is because we now have separate SatDiagn and SatDiagnEdge collections that both use the same SatDiagnCount array. run/GCClassic/HISTORY.rc.templates/HISTORY.rc.* - Remove `SatDiagnPEDGE` from the `SatDiagn` collection; this needs to be in the separate `SatDiagnEdge` collection - Fix typo "SatDiagnConc_PEDGE" -> "SatDiagnPEDGE" - Remove fields from SatDiagn entries that are not relevant for the given simulation (the user can restore these) CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

@jimmielin

…apability) This merge brings PR geoschem#2366 (Changes for coupling GEOS-Chem to CESM in Spectral-element Dynamical Core (CAM-SE), by @jimmielin) into the GEOS-Chem "no-diff-to-benchmark" development stream. This PR adds the capability of running GEOS-Chem using the spectral-element dynamical core in the latest version of CESM. # Conflicts: # CHANGELOG.md

@yantosca

This merge brings PR # (Fix several issues with the GEOS-Chem Classic satellite diagnostics (SatDiagn and SatDiagnEdge collections) , by @yantosca) into the GEOS-Chem "no-diff-to-benchmark" development stream. This PR resolves several issues in the GEOS-Chem Classic satellite diagnostics, as were reported by users. The satellite diagnostics are now also compatible with the GEOS-Chem carbon simulation. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

This commit addresses the issue raised in geos-chem geoschem#2319. We have now updated the following files so that only the "benchmark" fullchem simulation uses the MEGAN extension, while other "standard" simulations use the offline emissions. run/GCClassic/HEMCO_Config.rc.templates/HEMCO_Config.rc.aerosol run/GCClassic/HEMCO_Config.rc.templates/HEMCO_Config.rc.fullchem run/GCHP/HEMCO_Config.rc.templates/HEMCO_Config.rc.aerosol - Replace "on" with ${RUNDIR_MEGAN_EXT} to toggle the MEGAN extension on or off based on the options given to createRunDir.sh. run/GCClassic/createRunDir.sh run/GCHP/createRunDir.sh - Set RUNDIR_MEGAN_EXT='off' for the aerosol-only simulation - Set RUNDIR_MEGAN_EXT='off' for the fullchem non-benchmark simulations - Set RUNDIR_MEGAN_EXT='on' for the fullchem benchmark simulation CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

run/GCClassic/createRunDir.sh - Add a line to set RUNDIR_MEGAN_EXT env var to "on" for GCAP2 met - Reorder the RUNDIR_*_EXT variables alphabetically Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

@yantosca

This merge brings PR geoschem#2372 (urn off the MEGAN extension for fullchem "non-benchmark" simulations, by @yantosca) into the GEOS-Chem "no-diff-to-benchmark" development stream. This PR edits rundir scripts and HEMCO_Config.rc templates so that the MEGAN emissions are only activated for the fullchem_benchmark simulation. The other fullchem simulations use offline emissions (except when using GCAP2 met, which uses online MEGAN). Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

GeosCore/gc_environment_mod.F90 - Throw an error (right before the call to Init_FJX) if FAST-JX photolysis is activated for fullchem or carbon simulations. FAST-JX is currently only supported for Hg. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

GeosCore/gc_environment_mod.F90 - Now test if it is NOT a Hg simulation rather than testing if it is a fullchem or carbon simulation. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

@yantosca

This merge brings PR geoschem#2379 (Disable support for FAST-JX except for the Hg simulation, by @yantosca) into the GEOS-Chem "no-diff-to-benchmark" simulation. This PR adds a runtime error trap that will halt execution if FAST-JX is selected for any simulation other than Hg. Eventually Hg will use Cloud-J. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

…missions_in_cesm

…_emissions_in_cesm Update standard emissions in CESM to match standard model

@ltmurray

We now run a 2x2.5 ModelE2.1 (aka GCAP 2.0) full-chemistry simulation in the GCClassic integration tests. Only one scenario (SSP2-4.5) is evaluated here simply to ensure these future scenario simulations compile and run for 1 hour successfully. I will defer to @ltmurray for guidance on whether additional simulations are needed. The GCAP 2.0 integration test is passing off of 14.4.1, confirming that the fixes in geoschem#2342 should have resolved the issues of GCAP 2.0 not working in 14.0.0 (as reported by Lee Murray at IGC11). Sample integration test output: ``` ============================================================================== GEOS-Chem Classic: Execution Test Results GCClassic #c49fcec Submod updates: Merge GEOS-Chem PR geoschem#2353 and Cloud-J PR geoschem#19 GEOS-Chem #7e4001658 Merge PR geoschem#2369 (Fix several issues with satellite diagnostics) HEMCO #2192e0e HEMCO 3.9.1 release Using 24 OpenMP threads Number of execution tests: 29 Submitted as SLURM job: 40462513 ============================================================================== Execution tests: ------------------------------------------------------------------------------ gc_05x0625_NA_47L_merra2_CH4........................Execute Simulation....PASS gc_05x0625_NA_47L_merra2_fullchem...................Execute Simulation....PASS gc_2x25_ModelE2.1_fullchem..........................Execute Simulation....PASS ``` Signed-off-by: Melissa Sulprizio <mpayer@seas.harvard.edu>

…racers Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

…ur to 20 minutes To speed up integration tests, we now run the ModelE2.1 (GCAP 2.0) simulation for 20 minutes instead of 1 hour since these simulations run at 2x2.5 resolution. Signed-off-by: Melissa Sulprizio <mpayer@seas.harvard.edu>

@lizziel

… w/ GEOS-IT) This merge brings PR # (Add GC-Classic transport tracer global half-degree run option with GEOS-IT, by @lizziel) into the GEOS-Chem "no-diff-to-benchmark" development stream. This PR updates the GC-Classic create run directory script. It now offers the option of a global 1/2-degree run using the transport tracer simulation with GEOS-IT meteorology fields. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

GeosCore/sulfate_mod.F90 - Remove XNUMOL_H2O2 / CMPERM3 from the equation for DH2O2. This used to convert PH2O2 to molec/cm3/s, but with KPP, PH2O2 is already in molec/cm3/s. - Add !$OMP COLLAPSE( 3 ) for efficiency - Add !$OMP SCHEDULE( DYNAMIC, 8 ) for better load balancing - Change e.g. 0.0e+0_fp to 0.0_fp for clarity Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

GeosCore/sulfate_mod.F90 - Fix typo "SCHEUDLE" -> "SCHEDULE" Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

v14.3.1 build fixes

Previously the run directory was configured to always use online biogenic MOH values for the EmisMOH_Biogenic variable in HEMCO emissions. Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

…ig.rc This update impacts only GCHP emissions for which we have both online and offline sources, namely seasalt, soil NOx, biogenic, and dust emissions. Previously HEMCO_Diagn.rc always specified offline emissions for use in emissions diagnostic unless using the benchmark simulation. Now the file is automatically updated at run-time to use online values instead if the extension is turned on within HEMCO_Config.rc. Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

@yantosca

This merge brings PR geoschem#2413 (Fix incorrect unit conversion for H2O2 in the aerosol-only simulation, by @yantosca) into the GEOS-Chem "no-diff-to-benchmark" development stream. This PR fixes a longstanding unit conversion issue in the aerosol-only simulation. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

@lizziel

This merge brings PR # (Fixes for HEMCO diagnostic config file HEMCO_Diagn.rc, by @lizziel) into the GEOS-Chem "no-diff-to-benchmark" development stream. This PR adds 2 fixes: 1. Use offline biogenic MOH emissions (except for the benchmark simulation, which uses online emissions by default) 2. Auto-set GCHP emissions sources in HEMCO_Diagn.rc based on HEMCO_Config.rc. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

This merge brings the "no-diff-to-benchmark" updates into the main branch in preparation for the GEOS-Chem 14.4.3 release. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

Updated version numbers in: - CHANGELOG.md Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

…d_read_mod

Upgrade `develop` to v14.3.1

Add allocate guards for `PFLT_DRY` and co.

Use `MODEL_GISS` rather than `MODEL_CLASSIC`

Upgrade `develop` to GEOS-Chem v14.4.3

GEOS-Chem only

ltmurray and others added 30 commits May 6, 2024 19:49

Update setCommonRunSettings.sh.template

bbb722e

Fix typo for MassFlux_Entry

Preprocessor fixes for hco_interface_gc_mod

967eab0

Added a changelog entry for PR geoschem#2363

592802f

CHANGELOG.md - Added note about fixing typo in setCommonRunSettings.sh Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

Set # levels with cloud for photolysis based on meteorology used

70d7003

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

Update changelog

e91ce06

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

Fixes to Cloud-J data reading in CESM environment under SE dynamical …

13dc82c

…core

Remove unused CESM-specific variables in UCX_MOD

022c44d

Update CHANGELOG; revert removal of trailing slash

70f30a8

Add Cloud-J status output and error handling for it

c831dbf

This update goes an update to Cloud-J. Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

Rename to CPU_Subdomain_ID and CPU_Subdomain_FirstID for clarity.

da6f6a4

Bug fix: Make sure MEGAN is turned on for GCAP2 simulations

207c9c6

run/GCClassic/createRunDir.sh - Add a line to set RUNDIR_MEGAN_EXT env var to "on" for GCAP2 met - Reorder the RUNDIR_*_EXT variables alphabetically Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

Update CESM HEMCO_Config.rc with standard emissions used in 14.4.0

1c44bdb

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

Change logic in FAST-JX error trap in gc_environment_mod.F90

0118850

GeosCore/gc_environment_mod.F90 - Now test if it is NOT a Hg simulation rather than testing if it is a fullchem or carbon simulation. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

Merge branch 'dev/no-diff-to-benchmark' into feature/standard_model_e…

c6911c2

…missions_in_cesm

Merge pull request geoschem#2375 from geoschem/feature/standard_model…

b9cf981

…_emissions_in_cesm Update standard emissions in CESM to match standard model

Add half-degree global simulation option for GEOS-IT with transport t…

2f52b06

…racers Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

yantosca and others added 25 commits August 5, 2024 18:12

Fix typo in !$OMP PARALLEL loop in Chem_H2O2 routine

6987c2a

GeosCore/sulfate_mod.F90 - Fix typo "SCHEUDLE" -> "SCHEDULE" Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

Apply -fixed compiler flag to a F77 file if compiling with Intel

d2e68d7

Merge pull request #3 from fetch4/jwallwork23/giss-gc-14

fe9a440

v14.3.1 build fixes

Update HEMCO_Diagn.rc templates to use offline MOH biogenic emissions

ce46f08

Previously the run directory was configured to always use online biogenic MOH values for the EmisMOH_Biogenic variable in HEMCO emissions. Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

Update changelog

ee4b30d

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

Merge "no-diff-to-benchmark" updates into main for 14.4.3 release

7b4b808

This merge brings the "no-diff-to-benchmark" updates into the main branch in preparation for the GEOS-Chem 14.4.3 release. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

GEOS-Chem (science codebase) 14.4.3 release

bef56c6

Updated version numbers in: - CHANGELOG.md Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

No need for placeholder program

ffe0758

Add in get_met_mod and set_boundary_conditions_mod; FIXME for flexgri…

a540f1f

…d_read_mod

Merge pull request #5 from fetch4/dev/giss-gc-14

bda4934

Upgrade `develop` to v14.3.1

Add allocate guards for PFLT_DRY and co.

5a53866

Merge pull request #7 from fetch4/allocate-guard

cd91041

Add allocate guards for `PFLT_DRY` and co.

Revert unnecessary GEOS-Chem edits

0cc41a5

Merge branch 'main' into joe/14.4.3

020eede

Merge pull request #10 from fetch4/model_giss

ee5a83f

Use `MODEL_GISS` rather than `MODEL_CLASSIC`

Merge pull request #11 from fetch4/joe/14.4.3

5581b80

Upgrade `develop` to GEOS-Chem v14.4.3

Add MODEL_GISS pre-processing statement to enable GISS-GC

2da0edc

Disable a few GEOS-Chem functions for GISS-GC

232e561

Formatting

f661a2e

Merge pull request #13 from fetch4/12_gc-only

8754737

GEOS-Chem only

joewallwork added bug Something isn't working enhancement New feature or request labels Mar 24, 2025

joewallwork self-assigned this Mar 24, 2025

joewallwork requested a review from ltmurray March 24, 2025 14:54

joewallwork mentioned this pull request Mar 24, 2025

Merge develop into main fetch4/GISS-GC#110

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Merge GEOS-Chem `develop` into `main` - #17

Merge GEOS-Chem `develop` into `main`#17
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joewallwork commented Mar 24, 2025 •

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