geoschem/geos-chem: GEOS-Chem 14.5.0

Release date: 08 Nov 2024

From CHANGELOG.md

Added

• Added vectors State_Chm%KPP_AbsTol and State_Chm%KPP_RelTol
• Added setting KPP_AbsTol to 1e5 for dummy species in species_database.yml and species_database_hg.yml
• Implemented PPN photolysis from Horner et al (2024)
• Added four new species ALK4N1, ALK4N2, ALK4O2, and ALK4P to address issues in ALK4 and R4N2 chemistry following Brewer et al. (2023, JGR)
• Added new species ALK4N1 and ALK4N2 to Ox family in KPP
• Added Cloud-J input parameters to geoschem_config.yml in new photolysis sub-menu called cloud-j
• Added computation of water concentration to use in photolysis for application of UV absorption by water in Cloud-J v8
• Added ACO3, ACR, ACRO2, ALK4N{1,2,O}2, ALK4P, ALK6, APAN, APINN, APINO2, APINP, AROCMCHO, AROMCO3, AROMPN, BPINN, BPINO2, BPINON, BPINOO2, BPINOOH, BPINP, BUTN, BUTO2, C4H6, C96N, C96O2, C9602H, EBZ, GCO3, HACTA, LIMAL, LIMKB, LIMKET, LIMKO2, LIMN, LIMNB, LIMO2H, LIMO3, LIMO3H, LIMPAN, MEKCO3, MEKPN, MYRCO, PHAN, PIN, PINAL, PINO3, PINONIC, PINPAN, R7N{1,2}, R7O2, R7P, RNO3, STYR, TLFUO2, TLFUONE, TMB, ZRO2 to species_database.yml following Travis et al. 2024
• Added TSOIL1 field to State_Met for use in HEMCO soil NOx extension. This should only be read in when the UseSoilTemperature option is true in HEMCO config

Changed

• Copied values from State_Chm%KPP_AbsTol to ATOL and State_Chm%KPP_RelTol to RTOL for fullchem and Hg simulations
• Introduced seasalt Ca, K, Mg back to aerosol thermodynamics via HETP.
• Updated HEMCO_Config.rc.fullchem (GCClassic + GCHP) and ExtData.rc to add emissons of new species from Travis et al 2023
• Activated the DryDep collection for GCClassic & GCHP fullchem benchmarks
• Reduced the GCHP DryDep collection to only the necessary species for benchmarks
• Removed unused VDIFFAR routine from vdiff_mod.F90
• Updated MW for CH4 and OH in global_ch4_mod.F90
• Added fix to not convert from kg/kg to mol/mol before passing State_Chm to PBL mixing in vdiff_mod.F90
• Updated GC-Classic and GCHP run scripts and environment files for NASA discover cluster
• Updated GFED4_Climatology entries to point to the climatology file for 2010-2023
• Moved aerosol optical properties files to a new data directory specified in geoschem_config.yml rather than specifying in photolysis input files
• Moved calls to RD_AOD and CALC_AOD from Init_Aerosol rather than Init_Photolysis
• Updated ResME CH4 reservoir emissions to apply seasonality via mask file
• Changed fullchem restart file folder from GC_14.3.0 to GC_14.5.0

Fixed

• Simplified SOA representations and fixed related AOD and TotalOA/OC calculations in benchmark
• Changed mass conservation adjustment in vdiff_mod.F90 to use a mass tendency with units of kg species/kg dry air
• Converted the top pressure edge from hPa to Pa in vdiff_mod.F90
• Updated Jval_ entries in run/GCHP/HISTORY.rc.templates/HISTORY.rc.fullchem
• Updated species database Is_Photolysis entries to remove J-value diagnostics with all zeros in full chemistry simulation
• Removed EDGAR8_CH4_AWB emissions from CH4 and carbon simulations to avoid double counting with GFED
• Fixed formatting error in .github/workflows/stale.yml that caused the Mark Stale Issues action not to run
• Fixed emissions in GCHP carbon ExtData.rc so that data in molecules/cm2/s are converted to kg/m2/s

Removed

• Removed dry-run checks for files that are no longer needed for Cloud-J v8 from cldj_interface_mod.F90

Pull requests included

• Allow per-species definition of KPP absolute and relative solver tolerances; Set absolute tolerances of dummy species to large value by @yantosca in https://github.com/geoschem/geos-chem/pull/2359
• Fix bugs in PDER, OCPISOA and TotalOC in complexSOA by @yuanjianz in https://github.com/geoschem/geos-chem/pull/2315
• Pass non-zero Ca2, Mg, and K cations to HETP by @lizziel in https://github.com/geoschem/geos-chem/pull/2398
• Add fixes for ALK4 and R4N2 chemistry from Brewer et al. (2023, JGR) by @msulprizio in https://github.com/geoschem/geos-chem/pull/2352
• Merge GEOS-Chem 14.4.3 into the 14.5.0 development branch by @yantosca in https://github.com/geoschem/geos-chem/pull/2425
• Restore dry deposition output in GCHP & GCClassic fullchem benchmark simulations by @yantosca in https://github.com/geoschem/geos-chem/pull/2144
• Fix mass non-conservation in VDIFF PBL mixing by @nicholasbalasus in https://github.com/geoschem/geos-chem/pull/2428
• Update GFED4_Climatology entries for period 2010-2023 with new species by @yantosca in https://github.com/geoschem/geos-chem/pull/2436
• Update run scripts and environment files for NASA discover cluster by @lizziel in https://github.com/geoschem/geos-chem/pull/2439
• Support for Cloud-J version 8.0.0 by @lizziel in https://github.com/geoschem/geos-chem/pull/2424
• Store aerosol-specific optics files in new Aerosol_Optics data directory by @lizziel in https://github.com/geoschem/geos-chem/pull/2426
• Bug fix: Reorder photo rxns for PNs and ANs (from PR #2318) by @yantosca in https://github.com/geoschem/geos-chem/pull/2452
• Update Is_Photolysis tags in species_database.yml to be consistent with Cloud-J file FJX_j2j.dat by @yantosca in https://github.com/geoschem/geos-chem/pull/2457
• Updated soil NOx scheme from Yi Wang et al. (2021) as an option by @msulprizio in https://github.com/geoschem/geos-chem/pull/2430
• Bug fix: ALK6 in HEMCO_Config.rc should be ALK7 by @msulprizio in https://github.com/geoschem/geos-chem/pull/2462
• Remove J-value diagnostics which are all zero by @lizziel in https://github.com/geoschem/geos-chem/pull/2464
• Fix dry mass fraction of seasalt in aerosol thermodynamics by @lizziel in https://github.com/geoschem/geos-chem/pull/2467
• Bug fix for double counting CH4 agricultural burning emissions by @msulprizio in https://github.com/geoschem/geos-chem/pull/2477
• Add seasonality to CH4 reservoir emissions by @msulprizio in https://github.com/geoschem/geos-chem/pull/2473
• Bugfix: Restore stale workflow functionality by @msulprizio in https://github.com/geoschem/geos-chem/pull/2472
• Fix a bug in coarse-mode seasalt Ca, Mg, and K by @yc-chan in https://github.com/geoschem/geos-chem/pull/2489
• Clean up CHANGELOG.md for 14.5.0 release by @msulprizio in https://github.com/geoschem/geos-chem/pull/2490
• Use ALK6 species name for >= C6 alkanes instead of ALK7 by @msulprizio in https://github.com/geoschem/geos-chem/pull/2493
• GCHP carbon simulation fixes by @lizziel in https://github.com/geoschem/geos-chem/pull/2492
• Dry run updates for GEOS-Chem Classic 14.5.0 by @yantosca in https://github.com/geoschem/geos-chem/pull/2555
• Update version number to 14.5.0 in CHANGELOG.md by @yantosca in https://github.com/geoschem/geos-chem/pull/2562

New Contributors

• @yuanjianz made their first contribution in https://github.com/geoschem/geos-chem/pull/2315
• @yc-chan made their first contribution in https://github.com/geoschem/geos-chem/pull/2489

Full Changelog: https://github.com/geoschem/geos-chem/compare/14.4.3...14.5.0