geoschem/geos-chem: GEOS-Chem 14.5.1

Release date 10 Jan 2025

From CHANGELOG.md

Added

• Added allocate guards for arrays in pressure_mod
• Added State_Diag%SatDiagnEdgeCount counter for the SatDiagnEdge collection
• Added State_Diag%Archive_SatDiagnEdgeCount field
• Added State_Diag%Archive_SatDiagnEdge field
• Added routine SatDiagn_or_SatDiagnEdge in History/history_utils_mod.F90
• Added error trap in History/history_mod.F90 to ensure that collection duration is always shorter than frequency
• Added KPP standalone interface (archives model state to selected locations)
• Added https://github/geoschem/KPP-Standalone as a Git submodule
• Added comments in ./run/sharedcleanRunDir.sh describing the --force option (i.e. remove files w/o user confirmation)
• Specified meteorology source in GCHP geoschem_config.yml
• Added Input_Opt logical for whether to reconstruct convective precipitation fluxes rather than use met-fields
• Added to run directory creation a warning about convection discontinuity and bug if GEOS-FP meteorology is chosen
• Added surface precipitation flux fields as inputs to GCHP

Changed

• Renamed Emiss_Carbon_Gases to CO2_Production in carbon_gases_mod.F90
• Updated start date and restart file for CO2 and tagCO simulations for consistency with carbon simulations
• Allocated State_Diag%SatDiagnPEDGE ffield with vertical dimension State_Grid%NZ+1
• Modified run/GCClassic/cleanRunDir.sh to skip removing bpch files, as well as now removing fort.* and OutputDir/*.txt files
• Edited run/shared/kpp_standalone_interface.yml to include additional entries under active cells and locations
• Changed doing Linoz and Linearized chemistry messages to print only if verbose
• Updated HEMCO subroutine calls for error and log handling changes in HEMCO 3.9.1
• Updated configuration files for using GEOS-Chem 14.5 in CESM
• Modified tagCO simulation to use GFED4 biomass burning emissions and GEOS-Chem v5 OH fields for consistency with carbon simulation
• Changed integration tests to use Harvard Cannon GNU 12 environment files by default
• Added Australian Hg emissions for 2000-2019 from MacFarlane et. al. [2022], plus corresponding mask file
• Added comments in GEOS-Chem Classic HISTORY.rc template files advising users not to change the BoundaryConditions.frequency setting

Fixed

• Added a fix to skip the call to KPP when only CO2 is defined in the carbon simulation
• Added fix to turn on ship emissions for CO2 in the carbon simulation
• Updated HEMCO_Config.rc for carbon simulation to read data based on carbon species used
• Fixed entries for CO2 emissions in ExtData.rc.carbon
• Fixed metals simulation name in config file template comments
• Fixed bug in download_data.py which caused script to fail if log filename contained uppercase characters.
• Fixed the satellite diagnostics counters from being inadvertently being reset
• Fixed segmentation fault in qfyaml when running with certain compilers without debug flags on
• Fixed errors in adjoint-only code preventing successful adjoint build
• Fixed zero convective precipitation and high cloud base in runs using GEOS-FP (>=01Jun2020) or GEOS-IT
• Updated GEOS-only code and configuration files for compatibility with GEOS-Chem 14.5
• Fixed missing Is_Advected for TMB in species_database.yml
• Fixed typos in HEMCO_Config.rc for CH4 simulations causing mobile combustion emissions to be double counted
• Fixed handling of FIRST flag in carbon_gases_mod.F to limit log prints to first timestep only
• Removed extraneous pressure correction in GCHP carbon simulations by adding 'activate: true' to geoschem_config.yml
• Fixed bug in GC-Classic OCS emissions where unit conversion of km2 to m2 occurred twice
• Changed dimension of EmisOCS_Total from 3D to 2D since all emissions for all sectors are 2D
• Added fixes to only apply archived PCO_CH4 field for carbon simulations with CO only
• Reverted CH4 livestock emissions to EDGAR v7 to avoid hotspots and to apply seasonality

Removed

• Removed duplicate WD_RetFactor tag for HgClHO2 in species_database.yml
• Removed error messages in HEMCO interface pointing users to HEMCO log

Pull requests merged into GEOS-Chem 14.5.1

• Fix inconsistencies between CO2 simulation and carbon simulation with CO2 only by @msulprizio in https://github.com/geoschem/geos-chem/pull/2510
• Fix trace metals simulation name in config file comments by @ihough in https://github.com/geoschem/geos-chem/pull/2560
• Add allocate guards for arrays in pressure_mod by @jwallwork23 in https://github.com/geoschem/geos-chem/pull/2532
• Fix CEDS TMB emissions by @kelvinhb in https://github.com/geoschem/geos-chem/pull/2507
• Add counter for SatDiagnPedge collection; Prevent satellite diagnostic counters from being inadvertently reset by @yantosca in https://github.com/geoschem/geos-chem/pull/2544
• KPP standalone interface from Obin Sturm by @lizziel in https://github.com/geoschem/geos-chem/pull/2482
• Remove duplicate WD_RetFactor tag for HgClHO2 entry in species-database.yml by @yantosca in https://github.com/geoschem/geos-chem/pull/2580
• Prevent segmentation fault in qfyaml with some compilers by @lizziel in https://github.com/geoschem/geos-chem/pull/2486
• KPP Standalone from Obin Sturm by @lizziel in https://github.com/geoschem/geos-chem/pull/2483
• Fix GEOS-Chem 14.5.0 build in CESM by excluding hard dependencies on HEMCO by @jimmielin in https://github.com/geoschem/geos-chem/pull/2542
• Some fixes required to compile adjoint geos chem by @kaysuselj in https://github.com/geoschem/geos-chem/pull/2578
• Prevent History diagnostic collection duration from being shorter than frequency by @yantosca in https://github.com/geoschem/geos-chem/pull/2593
• Add KPP Standalone into GEOS-Chem 14.5.1 by @yantosca in https://github.com/geoschem/geos-chem/pull/2588
• Fix tagged CO simulation in dev branch by @lizziel in https://github.com/geoschem/geos-chem/pull/2608
• Fix typo in tagco restart date introduced in dev version by @lizziel in https://github.com/geoschem/geos-chem/pull/2612
• Fix convection issues when meteorology is Grell Freitas scheme by @yuanjianz in https://github.com/geoschem/geos-chem/pull/2523
• Updates for GEOS-only code in 14.5 by @lizziel in https://github.com/geoschem/geos-chem/pull/2553
• Fix bug in GCHP integration test creation due to duplicate "Created " entries in log by @lizziel in https://github.com/geoschem/geos-chem/pull/2615
• KPP-Standalone submodule update: Now generate box-model output with 3-digit exponents by @yantosca in https://github.com/geoschem/geos-chem/pull/2617
• Revert CH4 livestock emissions to EDGAR v7 by @msulprizio in https://github.com/geoschem/geos-chem/pull/2626
• Add ozonesonde observation locations to the kpp_standalone_interface.yml file by @yantosca in https://github.com/geoschem/geos-chem/pull/2634
• Update HEMCO interface for changes to HEMCO error and log handling by @lizziel in https://github.com/geoschem/geos-chem/pull/2643
• Updates for 14.5 compatibility in CESM by @lizziel in https://github.com/geoschem/geos-chem/pull/2642
• Fixes for running GEOS-Chem 14.5.1 in GEOS by @lizziel in https://github.com/geoschem/geos-chem/pull/2661
• Implement Australian Hg emissions inventory (2010-2019) from MacFarlane et al. [2022] by @yantosca in https://github.com/geoschem/geos-chem/pull/2669
• Add comments to GCClassic HISTORY.rc template files advising users not to change BoundaryConditions.frequency by @yantosca in https://github.com/geoschem/geos-chem/pull/2670
• Bug fixes for the carbon simulations in GCClassic and GCHP by @msulprizio in https://github.com/geoschem/geos-chem/pull/2554
• Change default environment files for integration tests on Harvard Cannon from gnu10 to gnu12 by @yantosca in https://github.com/geoschem/geos-chem/pull/2674
• Fixed the problem that GCHP cannot read meteorology field from yaml by @yuanjianz in https://github.com/geoschem/geos-chem/pull/2675
• GEOS-Chem (science codebase) 14.5.1 release by @yantosca in https://github.com/geoschem/geos-chem/pull/2678
• Bug fix: allow uppercase log filename in download_data.py by @ihough in https://github.com/geoschem/geos-chem/pull/2508

New Contributors

• @ihough made their first contribution in https://github.com/geoschem/geos-chem/pull/2560
• @jwallwork23 made their first contribution in https://github.com/geoschem/geos-chem/pull/2532
• @kaysuselj made their first contribution in https://github.com/geoschem/geos-chem/pull/2578

Full Changelog: https://github.com/geoschem/geos-chem/compare/14.5.0...14.5.1